Index (Force Field X 1.0.0 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

a - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
a - Variable in class ffx.crystal.Crystal: Length of the cell edge in the direction of the a basis vector.
a - Variable in class ffx.potential.SystemState: Accelerations.
a() - Method in class ffx.potential.SystemState: Get a reference to the internal accelerations array.
a() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the a record component.
A - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
A - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
A - Variable in class ffx.crystal.Crystal: Reciprocal lattice vectors.
A - Variable in class ffx.numerics.math.SSETest: A matrix of double values.
A00 - Variable in class ffx.crystal.Crystal: A* reciprocal lattice vector.
A10 - Variable in class ffx.crystal.Crystal: A* reciprocal lattice vector.
A11 - Variable in class ffx.crystal.Crystal: B* reciprocal lattice vector (A01 is zero).
A20 - Variable in class ffx.crystal.Crystal: A* reciprocal lattice vector.
A21 - Variable in class ffx.crystal.Crystal: B* reciprocal lattice vector (A01 is zero).
A22 - Variable in class ffx.crystal.Crystal: C* reciprocal lattice vector (A02 and A12 are zero).
AA - Enum constant in enum class ffx.potential.bonded.Residue.ResidueType
AA_C - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_C
AA_CA - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_CA
AA_CB - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_CB
AA_HA - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_HA
AA_HN - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_HN
AA_N - Static variable in class ffx.potential.bonded.AminoAcidUtils: Biotype keys for amino acid backbone atom types.
AA_O - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_O
AA1toAA3 - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA1toAA3
AAPATTERN - Static variable in class ffx.potential.bonded.AminoAcidUtils: Repeating atomic numbers of an amino acid chain.
about() - Method in class ffx.ui.MainPanel: about
aboutString - Static variable in class ffx.ui.MainPanel
abs() - Method in class ffx.numerics.math.ComplexNumber: abs
ABSOLUTE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
Ac - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
acceleration - Variable in class ffx.ui.commands.SimulationUpdate
ACCELERATION - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
accept(File) - Method in class ffx.potential.parsers.ARCFileFilter
accept(File) - Method in class ffx.potential.parsers.CoordinateFileFilter
accept(File) - Method in class ffx.potential.parsers.DistanceMatrixFileFilter
accept(File) - Method in class ffx.potential.parsers.DYNFileFilter
accept(File) - Method in class ffx.potential.parsers.ESVFileFilter
accept(File) - Method in class ffx.potential.parsers.FFXFileFilter
accept(File) - Method in class ffx.potential.parsers.ForceFieldFileFilter
accept(File) - Method in class ffx.potential.parsers.InducedFileFilter
accept(File) - Method in class ffx.potential.parsers.INTFileFilter
accept(File) - Method in class ffx.potential.parsers.KeyFileFilter
accept(File) - Method in class ffx.potential.parsers.PDBFileFilter
accept(File) - Method in class ffx.potential.parsers.PDBMLFileFilter
accept(File) - Method in class ffx.potential.parsers.XPHFileFilter
accept(File) - Method in class ffx.potential.parsers.XYZFileFilter
accept(File) - Method in class ffx.xray.parsers.MTZFileFilter
acceptChance(double, double, double) - Static method in class ffx.algorithms.mc.BoltzmannMC: Boltzmann-weighted acceptance probability
acceptDeep(File) - Method in class ffx.potential.parsers.CoordinateFileFilter: acceptDeep
acceptDeep(File) - Method in class ffx.potential.parsers.INTFileFilter: acceptDeep
acceptDeep(File) - Method in class ffx.potential.parsers.PDBFileFilter: acceptDeep Accepts a PDB file if it finds at least one parseable ATOM line.
acceptDeep(File) - Method in class ffx.potential.parsers.XYZFileFilter: acceptDeep
acceptDeep(File) - Method in class ffx.xray.parsers.MTZFileFilter: acceptDeep
ACE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
action(Timer) - Method in interface edu.rit.util.TimerTask: Perform this timer task's timed actions.
actionPerformed(ActionEvent) - Method in class ffx.ui.GraphicsCanvas
actionPerformed(ActionEvent) - Method in class ffx.ui.GraphicsPrefs
actionPerformed(ActionEvent) - Method in class ffx.ui.KeywordComponent
actionPerformed(ActionEvent) - Method in class ffx.ui.KeywordPanel: Handles input from KeywordPanel ToolBar buttons.
actionPerformed(ActionEvent) - Method in class ffx.ui.MainPanel
actionPerformed(ActionEvent) - Method in class ffx.ui.ModelingPanel
actionPerformed(ActionEvent) - Method in class ffx.ui.SimulationLoader
actionPerformed(ActionEvent) - Method in class ffx.ui.Trajectory
activeAssembly - Variable in class ffx.algorithms.cli.AlgorithmsCommand: An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
activeAssembly - Variable in class ffx.potential.cli.PotentialCommand: An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
ACTIVESYSTEM - Enum constant in enum class ffx.ui.GraphicsCanvas.MouseMode
actOnAtoms(MolecularAssembly, String, BiConsumer<Atom, Boolean>, String) - Static method in class ffx.potential.cli.AtomSelectionOptions
actOnResidueAtoms(MolecularAssembly, String, BiConsumer<Atom, Boolean>, String) - Static method in class ffx.potential.cli.AtomSelectionOptions
actualCount - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
actualWork - Variable in class ffx.potential.nonbonded.SpatialDensityRegion: Number of octant work cells with at least one atom (actualWork is less than or equal to nWork).
add(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: sum
add(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: sum
add(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: sum
add(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: sum
add(int) - Method in class ffx.potential.parameters.PolarizeType: Add an atom type to the polarization group.
add(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray: Add a value to the double array at the specified index.
add(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Add a value to the double array at the specified index.
add(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray: Add a value to the double array at the specified index.
add(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray: Add a value to the double array at the specified index.
add(int, int, double) - Method in class ffx.potential.nonbonded.NeighborList.Cell: Add an atom to the cell.
add(int, int, double, double, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Add to the double arrays at the specified index the given values.
add(int, int, Double3) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Add to the double arrays at the specified index the given Double3.
add(ClusterPair) - Method in class ffx.numerics.clustering.DistanceMap: Adds a new ClusterPair if no equivalent pair already exists.
add(Double3) - Method in class ffx.numerics.math.Double3: Finds the sum of this Double3 with b.
add(Float3) - Method in class ffx.numerics.math.Float3: Finds the sum of this Float3 with b.
add(Face) - Method in class ffx.numerics.quickhull.FaceList: Adds a face to the end of this list.
add(Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Adds this vector to v1 and places the result in this vector.
add(Vector3d, Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Adds vector v1 to v2 and places the result in this vector.
addAcceptor(int, int, int, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Add an acceptor to the force.
addAndersenThermostatForce(double) - Method in class ffx.potential.openmm.OpenMMSystem: Add an Andersen thermostat to the system.
addAndersenThermostatForce(double, double) - Method in class ffx.potential.openmm.OpenMMSystem: Add an Andersen thermostat to the system.
addAndGet(byte) - Method in class edu.rit.pj.reduction.SharedByte: Add the given value to this reduction variable and return the new value.
addAndGet(char) - Method in class edu.rit.pj.reduction.SharedCharacter: Add the given value to this reduction variable and return the new value.
addAndGet(double) - Method in class edu.rit.pj.reduction.SharedDouble: Add the given value to this reduction variable and return the new value.
addAndGet(float) - Method in class edu.rit.pj.reduction.SharedFloat: Add the given value to this reduction variable and return the new value.
addAndGet(int) - Method in class edu.rit.pj.reduction.SharedInteger: Add the given value to this reduction variable and return the new value.
addAndGet(int, byte) - Method in class edu.rit.pj.reduction.SharedByteArray: Add the given value to this array reduction variable at the given index and return the new value.
addAndGet(int, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Add the given value to this array reduction variable at the given index and return the new value.
addAndGet(int, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Add the given value to this array reduction variable at the given index and return the new value.
addAndGet(int, float) - Method in class edu.rit.pj.reduction.SharedFloatArray: Add the given value to this array reduction variable at the given index and return the new value.
addAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Add the given value to this array reduction variable at the given index and return the new value.
addAndGet(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Add the given value to this matrix reduction variable at the given row and column and return the new value.
addAndGet(int, int, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Add the given value to this matrix reduction variable at the given row and column and return the new value.
addAndGet(int, long) - Method in class edu.rit.pj.reduction.SharedLongArray: Add the given value to this array reduction variable at the given index and return the new value.
addAndGet(int, short) - Method in class edu.rit.pj.reduction.SharedShortArray: Add the given value to this array reduction variable at the given index and return the new value.
addAndGet(long) - Method in class edu.rit.pj.reduction.SharedLong: Add the given value to this reduction variable and return the new value.
addAndGet(short) - Method in class edu.rit.pj.reduction.SharedShort: Add the given value to this reduction variable and return the new value.
addAndGetEnergy(double) - Method in class ffx.potential.terms.EnergyTerm: Add energy to the total energy for this term and return the new total.
addAndGetRMSD(double) - Method in class ffx.potential.terms.EnergyTerm: Add RMSD to the shared RMSD and return the new total.
addAngle(int, int, int, double, double) - Method in class ffx.openmm.HarmonicAngleForce: Add an angle term to the force field.
addAngle(int, int, int, DoubleArray) - Method in class ffx.openmm.CustomAngleForce: Add an angle term to the force field.
addAngle(Angle) - Method in class ffx.potential.terms.AnglePotentialEnergy: Add an Angle to this term.
addAngles(Angle[]) - Method in class ffx.potential.terms.AnglePotentialEnergy: Add an array of Angles to this term.
addAngles(List<Angle>) - Method in class ffx.potential.terms.AnglePotentialEnergy: Add a list of Angles to this term.
addAngleTorsion(AngleTorsion) - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Add an AngleTorsion to this term.
addAngleTorsions(AngleTorsion[]) - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Add an array of AngleTorsions to this term.
addAngleTorsions(List<AngleTorsion>) - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Add a list of AngleTorsions to this term.
addArgument(String) - Method in class edu.rit.pj.job.Job: Add the given argument string to this job.
addAssembly(MolecularAssembly) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Adds a MolecularAssembly to be tracked by this MolecularDynamics.
addAtoms() - Method in class ffx.potential.openmm.OpenMMSystem: Adds atoms from the molecular assembly to the OpenMM System and reports to the user the number of particles added.
addBond(int, int, double, double) - Method in class ffx.openmm.HarmonicBondForce: Add a bond term to the force field.
addBond(int, int, DoubleArray) - Method in class ffx.openmm.CustomBondForce: Add a bond term to the force field.
addBond(IntArray, DoubleArray) - Method in class ffx.openmm.CustomCentroidBondForce: Add a bond to the force
addBond(IntArray, DoubleArray) - Method in class ffx.openmm.CustomCompoundBondForce: Add a bond to the force.
addBond(Bond) - Method in class ffx.potential.terms.BondPotentialEnergy: Add a Bond to this term.
addBonds(Bond[]) - Method in class ffx.potential.terms.BondPotentialEnergy: Add an array of Bonds to this term.
addBonds(List<Bond>) - Method in class ffx.potential.terms.BondPotentialEnergy: Add a list of Bonds to this term.
addChild(int, int) - Method in class ffx.potential.nonbonded.octree.Octree: Add a child.
addChild(Cluster) - Method in class ffx.numerics.clustering.Cluster: Adds a child cluster to this node.
addCollectiveVariable(Pointer, PointerByReference) - Method in class ffx.openmm.CustomCVForce: Add a collective variable to the force.
addCollectiveVariable(String, PointerByReference) - Method in class ffx.openmm.CustomCVForce: Add a collective variable to the force.
addCOMMRemoverForce() - Method in class ffx.potential.openmm.OpenMMSystem: Adds a force that removes center-of-mass motion.
addComputedValue(String, String) - Method in class ffx.openmm.CustomNonbondedForce: Add a computed value to the force.
addComputedValue(String, String, int) - Method in class ffx.openmm.CustomGBForce: Add a computed value to the force.
addComputeGlobal(String, String) - Method in class ffx.openmm.CustomIntegrator: Add a computation that computes a global value.
addComputePerDof(String, String) - Method in class ffx.openmm.CustomIntegrator: Add a per-DOF computation to this Integrator.
addComputeSum(String, String) - Method in class ffx.openmm.CustomIntegrator: Add a computation that computes a sum over degrees of freedom.
addConstrainPositions() - Method in class ffx.openmm.CustomIntegrator: Add a position constraint to this Integrator.
addConstraint(int, int, double) - Method in class ffx.openmm.System: Add a constraint to the system.
addConstraints(List<Constraint>) - Method in class ffx.algorithms.dynamics.integrators.Integrator: Adds a set of Constraints that this Integrator must respect.
addConstrainVelocities() - Method in class ffx.openmm.CustomIntegrator: Add a velocity constraint to this Integrator.
addCoulombMultiplier(double) - Method in class ffx.numerics.multipole.CombinedTensorGlobal: Add a multiplier to the Coulomb term.
addDonor(int, int, int, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Add a donor to the force.
addEnergyParameterDerivative(Pointer) - Method in class ffx.openmm.ATMForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyParameterDerivative(Pointer) - Method in class ffx.openmm.CustomCVForce: Add an energy parameter derivative to the force.
addEnergyParameterDerivative(Pointer) - Method in class ffx.openmm.CustomTorsionForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.ATMForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomAngleForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomBondForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomCentroidBondForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomCompoundBondForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomCVForce: Add an energy parameter derivative to the force.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomGBForce: Add an energy parameter derivative to the force.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomNonbondedForce: Add an energy parameter derivative to the force.
addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomTorsionForce: Request that this Force compute the derivative of its energy with respect to a global parameter.
addEnergyTerm(EnergyTerm) - Method in class ffx.potential.terms.EnergyTermRegion: Add a EnergyTerm to this bonded region.
addEnergyTerm(String, int) - Method in class ffx.openmm.CustomGBForce: Add an energy term to the force.
ADDER - Enum constant in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl: A java.util.concurrent.atomic.DoubleAdder implementation.
AdderDoubleArray - Class in ffx.numerics.atomic: AdderDoubleArray implements the AtomicDoubleArray interface using an array of java.util.concurrent.atomic.DoubleAdder.
AdderDoubleArray(int) - Constructor for class ffx.numerics.atomic.AdderDoubleArray: Construct an AdderDoubleArray.
addException(int, int, double, double, double, boolean) - Method in class ffx.openmm.NonbondedForce: Add an exception to the force.
addException(int, int, double, double, double, double, double, double, int) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Add an interaction to the list of exceptions that should be calculated differently from other interactions.
addException(int, int, double, double, int) - Method in class ffx.openmm.GayBerneForce: Add an exception to the force.
addExclusion(int, int) - Method in class ffx.openmm.CustomGBForce: Add an exclusion to the force.
addExclusion(int, int) - Method in class ffx.openmm.CustomHbondForce: Add an exclusion to the force.
addExclusion(int, int) - Method in class ffx.openmm.CustomManyParticleForce: Add an exclusion for a pair of particles.
addExclusion(int, int) - Method in class ffx.openmm.CustomNonbondedForce: Add an exclusion to the force.
addForce(Force) - Method in class ffx.openmm.ATMForce: Add a Force whose energy will be computed by the ATMForce.
addForce(Force) - Method in class ffx.openmm.System: Add a force to the system.
addForceFieldType(T) - Method in class ffx.potential.parameters.ForceField: Add an instance of a force field type.
addForces() - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Add forces to the system.
addForces() - Method in class ffx.potential.openmm.OpenMMSystem: Add forces to the system.
addFunction(Pointer, PointerByReference, double, double) - Method in class ffx.openmm.CustomHbondForce: Add a tabulated function that may appear in the energy expression.
addFunction(String, PointerByReference, double, double) - Method in class ffx.openmm.CustomCompoundBondForce: Deprecated.
This method exists only for backward compatibility. Use addTabulatedFunction() instead.
addFunction(String, PointerByReference, double, double) - Method in class ffx.openmm.CustomGBForce: Deprecated.
This method exists only for backward compatibility. Use addTabulatedFunction() instead.
addFunction(String, PointerByReference, double, double) - Method in class ffx.openmm.CustomHbondForce: Add a tabulated function that may appear in the energy expression.
addFunction(String, PointerByReference, double, double) - Method in class ffx.openmm.CustomNonbondedForce: Add a tabulated function that may appear in the energy expression.
addGlobalParameter(Pointer, double) - Method in class ffx.openmm.ATMForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(Pointer, double) - Method in class ffx.openmm.CustomCVForce: Add a global parameter to the force.
addGlobalParameter(Pointer, double) - Method in class ffx.openmm.CustomHbondForce: Add a global parameter to the force.
addGlobalParameter(Pointer, double) - Method in class ffx.openmm.CustomManyParticleForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(Pointer, double) - Method in class ffx.openmm.CustomTorsionForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(Pointer, double) - Method in class ffx.openmm.CustomVolumeForce: Add a new global parameter that the energy may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.ATMForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomAngleForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomBondForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomCentroidBondForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomCompoundBondForce: Add a global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomCVForce: Add a global parameter to the force.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomExternalForce: Add a global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomGBForce: Add a global parameter to the force.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomHbondForce: Add a global parameter to the force.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomManyParticleForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomNonbondedForce: Add a global parameter to the force.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomTorsionForce: Add a new global parameter that the interaction may depend on.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomVolumeForce: Add a new global parameter that the interaction may depend on.
addGlobalVariable(String, double) - Method in class ffx.openmm.CustomIntegrator: Add a global variable to this Integrator.
addGroup(IntArray, DoubleArray) - Method in class ffx.openmm.CustomCentroidBondForce: Add a particle group.
addHeaderLine(String) - Method in class ffx.potential.MolecularAssembly: Adds a header line to this MolecularAssembly (particularly for PDB formats)
addHistogram(HistogramData, LambdaData) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Add an alternate Histogram this OST can use.
addHydrogenConstraints() - Method in class ffx.potential.openmm.OpenMMSystem: Add a constraint to every bond that includes a hydrogen atom.
addI(Double3) - Method in class ffx.numerics.math.Double3: Finds the sum of this Double3 with b in place.
addI(Float3) - Method in class ffx.numerics.math.Float3: Finds the sum of this Float3 with b in place.
addImproperTorsion(ImproperTorsion) - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Add an ImproperTorsion to this term.
addImproperTorsions(ImproperTorsion[]) - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Add an array of ImproperTorsions to this term.
addImproperTorsions(List<ImproperTorsion>) - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Add a list of ImproperTorsions to this term.
addIndElecDeriv(int, double, double) - Method in class ffx.potential.extended.ExtendedSystem: Add Induced Elec deriv to appropriate dU/dL term given the atom index and its contributions.
addIntegrator(Integrator) - Method in class ffx.openmm.CompoundIntegrator: Add an Integrator to this CompoundIntegrator.
addInteractionGroup(IntSet, IntSet) - Method in class ffx.openmm.CustomNonbondedForce: Add an interaction group to the force.
additionalProperties - Variable in class ffx.algorithms.commands.Thermodynamics
addKeyword(Keyword) - Method in class ffx.ui.FFXSystem: addKeyword
addLeafName(String) - Method in class ffx.numerics.clustering.Cluster: Adds a single leaf name contained within this cluster's subtree.
addMap(int, PointerByReference) - Method in class ffx.openmm.CMAPTorsionForce: Create a new map that can be used for torsion pairs.
addMonteCarloBarostatForce(double, double, int) - Method in class ffx.potential.openmm.OpenMMSystem: Add a Monte Carlo Barostat to the system.
addMSNode(MSNode) - Method in class ffx.potential.bonded.Molecule: Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
addMSNode(MSNode) - Method in class ffx.potential.bonded.MSGroup: Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
addMSNode(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
addMSNode(MSNode) - Method in class ffx.potential.bonded.Polymer: Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
addMSNode(MSNode) - Method in class ffx.potential.bonded.Residue: Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
addMSNode(MSNode) - Method in class ffx.potential.MolecularAssembly: Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
addMultipole(double, DoubleArray, DoubleArray, int, int, int, int, double, double, double) - Method in class ffx.openmm.amoeba.MultipoleForce: Add multipole-related info for a particle
addMultiResidue(MultiResidue) - Method in class ffx.potential.bonded.Polymer: addMultiResidue.
addNewFaces(FaceList, Vertex, Vector<HalfEdge>) - Method in class ffx.numerics.quickhull.QuickHull3D: Builds and links the ring of new faces around the horizon using the eye vertex, recording them in the provided newFaces list.
addOutOfPlaneBend(OutOfPlaneBend) - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Add an OutOfPlaneBend to this term.
addOutOfPlaneBends(OutOfPlaneBend[]) - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Add an array of OutOfPlaneBends to this term.
addOutOfPlaneBends(List<OutOfPlaneBend>) - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Add a list of OutOfPlaneBends to this term.
addParticle(double) - Method in class ffx.openmm.System: Add a particle to the System.
addParticle(double, double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Add a particle to the force field.
addParticle(double, double, double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Add the parameters for a particle.
addParticle(double, double, double) - Method in class ffx.openmm.GBSAOBCForce: Add a particle to the force field.
addParticle(double, double, double) - Method in class ffx.openmm.NonbondedForce: Add a particle.
addParticle(double, double, double, double, double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Add the parameters for a particle.
addParticle(double, double, int) - Method in class ffx.openmm.amoeba.GKCavitationForce: Add an atom to the Cavitation force.
addParticle(double, double, int, int, double, double, double, double, double, double) - Method in class ffx.openmm.GayBerneForce: Add a particle to the force.
addParticle(double, PointerByReference, PointerByReference, double, double, double, double, double, double, double, double, double, int, int, int, int) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Add the nonbonded force parameters for a particle.
addParticle(int, double, double, double, int, double) - Method in class ffx.openmm.amoeba.VdwForce: Add the force field parameters for a vdw particle.
addParticle(int, int, double, int, double) - Method in class ffx.openmm.amoeba.VdwForce: Add the force field parameters for a vdw particle.
addParticle(int, int, int, int, int, double, double, double, double) - Method in class ffx.openmm.drude.DrudeForce: Add a Drude particle to which forces should be applied.
addParticle(int, DoubleArray) - Method in class ffx.openmm.CustomExternalForce: Add a particle to the force.
addParticle(PointerByReference, int) - Method in class ffx.openmm.CustomManyParticleForce: Add a particle to the Force.
addParticle(OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.ATMForce: Add a particle to the force.
addParticle(DoubleArray) - Method in class ffx.openmm.CustomGBForce: Add a particle to the force.
addParticle(DoubleArray) - Method in class ffx.openmm.CustomNonbondedForce: Add a particle to the force.
addParticleType(double, double) - Method in class ffx.openmm.amoeba.VdwForce: Add a particle type.
addPerAcceptorParameter(Pointer) - Method in class ffx.openmm.CustomHbondForce: Add a per-acceptor parameter to the force.
addPerAcceptorParameter(String) - Method in class ffx.openmm.CustomHbondForce: Add a per-acceptor parameter to the force.
addPerAngleParameter(String) - Method in class ffx.openmm.CustomAngleForce: Add a new per-angle parameter that the interaction may depend on.
addPerBondParameter(String) - Method in class ffx.openmm.CustomBondForce: Add a new per-bond parameter that the interaction may depend on.
addPerBondParameter(String) - Method in class ffx.openmm.CustomCentroidBondForce: Add a new per-bond parameter that the interaction may depend on.
addPerBondParameter(String) - Method in class ffx.openmm.CustomCompoundBondForce: Add a per-bond parameter that the interaction may depend on.
addPerDofVariable(String, double) - Method in class ffx.openmm.CustomIntegrator: Add a per-DOF variable to this Integrator.
addPerDonorParameter(Pointer) - Method in class ffx.openmm.CustomHbondForce: Add a per-donor parameter to the force.
addPerDonorParameter(String) - Method in class ffx.openmm.CustomHbondForce: Add a per-donor parameter to the force.
addPermElecDeriv(int, double, double) - Method in class ffx.potential.extended.ExtendedSystem: Add Perm Elec deriv to appropriate dU/dL term given the atom index and its contributions.
addPerParticleParameter(Pointer) - Method in class ffx.openmm.CustomManyParticleForce: Add a new per-particle parameter that the interaction may depend on.
addPerParticleParameter(String) - Method in class ffx.openmm.CustomExternalForce: Add a per-particle parameter that the interaction may depend on.
addPerParticleParameter(String) - Method in class ffx.openmm.CustomGBForce: Add a per-particle parameter to the force.
addPerParticleParameter(String) - Method in class ffx.openmm.CustomManyParticleForce: Add a new per-particle parameter that the interaction may depend on.
addPerParticleParameter(String) - Method in class ffx.openmm.CustomNonbondedForce: Add a per-particle parameter to the force.
addPerTorsionParameter(Pointer) - Method in class ffx.openmm.CustomTorsionForce: Add a new per-torsion parameter that the interaction may depend on.
addPerTorsionParameter(String) - Method in class ffx.openmm.CustomTorsionForce: Add a new per-torsion parameter that the interaction may depend on.
addPiOrbitalTorsion(PiOrbitalTorsion) - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Add a PiOrbitalTorsion to this term.
addPiOrbitalTorsions(PiOrbitalTorsion[]) - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Add an array of PiOrbitalTorsions to this term.
addPiOrbitalTorsions(List<PiOrbitalTorsion>) - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Add a list of PiOrbitalTorsions to this term.
addPointToHull(Vertex) - Method in class ffx.numerics.quickhull.QuickHull3D: Incorporates the specified eye vertex into the hull: computes the horizon, creates new faces, merges non-convex adjacencies, and resolves/reassigns outside points.
addProperty(String, String) - Method in class ffx.potential.parameters.ForceField: Add a property from an external parameter file.
addResidue(Residue) - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Add a residue to the box.
addResidue(Residue) - Method in class ffx.potential.bonded.MultiResidue: addResidue.
addRestrainDistance(RestrainDistance) - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Add a RestrainDistance to this term.
addRestrainDistances(RestrainDistance[]) - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Add an array of RestrainDistances to this term.
addRestrainDistances(List<RestrainDistance>) - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Add a list of RestrainDistances to this term.
addRestrainPosition(RestrainPosition) - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Add a RestrainPosition to this term.
addRestrainPositions(RestrainPosition[]) - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Add an array of RestrainPositions to this term.
addRestrainPositions(List<RestrainPosition>) - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Add a list of RestrainPositions to this term.
addRestrainTorsion(Torsion) - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Add a single restrain torsion.
addRestrainTorsions(Torsion[]) - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Add an array of restrain torsions.
addRestrainTorsions(List<Torsion>) - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Add a list of restrain torsions.
addRotation(double[][], double[][], boolean) - Method in class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Accumulate rotations (matrix multiplication)
addRotPatch(String) - Static method in class ffx.potential.bonded.RotamerLibrary: addRotPatch.
addScreenedPair(int, int, double) - Method in class ffx.openmm.drude.DrudeForce: Add an interaction to the list of screened pairs.
addSelections(ArrayList<MSNode>) - Method in class ffx.ui.Hierarchy: addSelections
addStretchBend(StretchBend) - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Add a StretchBend to this term.
addStretchBends(StretchBend[]) - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Add an array of StretchBends to this term.
addStretchBends(List<StretchBend>) - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Add a list of StretchBends to this term.
addStretchTorsion(StretchTorsion) - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Add a StretchTorsion to this term.
addStretchTorsions(StretchTorsion[]) - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Add an array of StretchTorsions to this term.
addStretchTorsions(List<StretchTorsion>) - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Add a list of StretchTorsions to this term.
addSubsystemThermostat(PointerByReference, PointerByReference, double, double, double, double, int, int, int) - Method in class ffx.openmm.NoseHooverIntegrator: Add a subsystem thermostat to the integrator.
addTabulatedFunction(Pointer, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(Pointer, PointerByReference) - Method in class ffx.openmm.CustomManyParticleForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(Pointer, TabulatedFunction) - Method in class ffx.openmm.CustomCVForce: Add a tabulated function to the force.
addTabulatedFunction(String, PointerByReference) - Method in class ffx.openmm.CustomCentroidBondForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(String, PointerByReference) - Method in class ffx.openmm.CustomCompoundBondForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(String, PointerByReference) - Method in class ffx.openmm.CustomGBForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(String, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(String, PointerByReference) - Method in class ffx.openmm.CustomIntegrator: Add a tabulated function that may appear in expressions.
addTabulatedFunction(String, PointerByReference) - Method in class ffx.openmm.CustomManyParticleForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(String, PointerByReference) - Method in class ffx.openmm.CustomNonbondedForce: Add a tabulated function that may appear in the energy expression.
addTabulatedFunction(String, TabulatedFunction) - Method in class ffx.openmm.CustomCVForce: Add a tabulated function to the force.
addTerms(double[]) - Method in class ffx.numerics.multipole.CombinedTensorGlobal: Accumulates onto existing terms.
addTermsSeparate(double[]) - Method in class ffx.numerics.multipole.CombinedTensorGlobal: Accumulates onto existing terms.
addThermostat(double, double, int, int, int) - Method in class ffx.openmm.NoseHooverIntegrator: Add a thermostat to the integrator.
addToAnisouGradient(double[]) - Method in class ffx.potential.bonded.Atom: addToAnisouGradient
addToLambdaXYZGradient(double, double, double) - Method in class ffx.potential.bonded.Atom: addToLambdaXYZGradient
addToMultipole(double[]) - Method in class ffx.potential.nonbonded.octree.OctreeCell
addToOccupancyGradient(double) - Method in class ffx.potential.bonded.Atom: addToOccupancyGradient
addToPhi(double) - Method in class ffx.potential.nonbonded.octree.OctreeParticle
addTors(Atom, int) - Method in class ffx.potential.parsers.PDBFilter.Mutation
addTorsion(int, int, int, int, double, double, double, double, double, double) - Method in class ffx.openmm.RBTorsionForce: Add a torsion to the force.
addTorsion(int, int, int, int, int, double, double) - Method in class ffx.openmm.PeriodicTorsionForce: Add a torsion to the PeriodicTorsionForce.
addTorsion(int, int, int, int, int, int, int, int, int) - Method in class ffx.openmm.CMAPTorsionForce: Add a CMAP torsion term to the force field.
addTorsion(int, int, int, int, PointerByReference) - Method in class ffx.openmm.CustomTorsionForce: Add a torsion to the Force.
addTorsion(Torsion) - Method in class ffx.potential.terms.TorsionPotentialEnergy: Add a Torsion to this term.
addTorsions(Torsion[]) - Method in class ffx.potential.terms.TorsionPotentialEnergy: Add an array of Torsions to this term.
addTorsions(List<Torsion>) - Method in class ffx.potential.terms.TorsionPotentialEnergy: Add a list of Torsions to this term.
addTorsionTorsion(int, int, int, int, int, int, int) - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Add a torsion-torsion term to the force field.
addTorsionTorsion(TorsionTorsion) - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Add a TorsionTorsion to this term.
addTorsionTorsions(TorsionTorsion[]) - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Add an array of TorsionTorsions to this term.
addTorsionTorsions(List<TorsionTorsion>) - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Add a list of TorsionTorsions to this term.
addToTempFactorGradient(double) - Method in class ffx.potential.bonded.Atom: addToTempFactorGradient
addToXYZGradient(double, double, double) - Method in class ffx.potential.bonded.Atom: addToXYZGradient
addToXYZGradient(int, double) - Method in class ffx.potential.bonded.Atom: addToXYZGradient.
addTranslation(double[], double[][], boolean) - Static method in class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Accumulate translations (matrix multiplication)
addTypePair(int, int, double, double) - Method in class ffx.openmm.amoeba.VdwForce: Add a type pair.
addUpBondConstraints() - Method in class ffx.potential.openmm.OpenMMSystem: Add a constraint to every bond.
addUpdateContextState() - Method in class ffx.openmm.CustomIntegrator: Add an update context state to this Integrator.
addUreyBradley(UreyBradley) - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Add a UreyBradley to this term.
addUreyBradleys(UreyBradley[]) - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Add an array of UreyBradleys to this term.
addUreyBradleys(List<UreyBradley>) - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Add a list of UreyBradleys to this term.
addValue(double) - Method in class ffx.numerics.math.RunningStatistics: Add a value and update key variables.
addValue(double, double) - Method in class ffx.numerics.math.RunningStatistics: Add a value and update key variables.
addVdwDeriv(int, double, double[], double) - Method in class ffx.potential.extended.ExtendedSystem: Add van der Waals deriv to appropriate dU/dL term given the atom index and its contributions.
addWork(double) - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Add a work contribution.
addXMLAttributes(Element, ForceField) - Static method in class ffx.potential.parameters.PolarizeType: Add constant attributes to the AmoebaMultipoleForce
ADE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
ADENINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
Adiabatic - Class in ffx.algorithms.dynamics.thermostats: The Adiabatic thermostat is for NVE simulations and does not alter particle velocities.
Adiabatic(SystemState, Potential.VARIABLE_TYPE[]) - Constructor for class ffx.algorithms.dynamics.thermostats.Adiabatic: Constructor for Adiabatic.
Adiabatic(SystemState, Potential.VARIABLE_TYPE[], List<Constraint>) - Constructor for class ffx.algorithms.dynamics.thermostats.Adiabatic
ADIABATIC - Enum constant in enum class ffx.algorithms.dynamics.thermostats.ThermostatEnum
aewald - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
aewald3 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
after() - Method in class ffx.ui.ModelingShell: after
afterClass() - Static method in class ffx.utilities.FFXTest: afterClass.
afterTest() - Method in class ffx.algorithms.misc.AlgorithmsTest
afterTest() - Method in class ffx.potential.utils.PotentialTest
afterTest() - Method in class ffx.utilities.FFXTest: afterTest.
Ag - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
agglomerate(int) - Method in class ffx.numerics.clustering.ClusterPair: Agglomerates left and right clusters under an auto-generated name.
agglomerate(LinkageStrategy) - Method in class ffx.numerics.clustering.HierarchyBuilder: Performs one agglomerative step by merging the two closest clusters and updating linkages.
agglomerate(String) - Method in class ffx.numerics.clustering.ClusterPair: Agglomerates left and right clusters into a new parent with the given name.
Ai - Variable in class ffx.crystal.Crystal: Real space Lattice vectors.
Ai00 - Variable in class ffx.crystal.Crystal: A-axis lattice vector in Cartesian coordinates.
Ai10 - Variable in class ffx.crystal.Crystal: B-axis lattice vector in Cartesian coordinates.
Ai11 - Variable in class ffx.crystal.Crystal: B-axis lattice vector in Cartesian coordinates.
Ai20 - Variable in class ffx.crystal.Crystal: C-axis lattice vector in Cartesian coordinates.
Ai21 - Variable in class ffx.crystal.Crystal: C-axis lattice vector in Cartesian coordinates.
Ai22 - Variable in class ffx.crystal.Crystal: C-axis lattice vector in Cartesian coordinates.
AIB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
Al - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ALA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ALANINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
Alchemical - Class in ffx.realspace.commands.test: The Alchemical Changes script.
Alchemical - Class in ffx.xray.commands.test: The Alchemical Changes script.
Alchemical() - Constructor for class ffx.realspace.commands.test.Alchemical: Alchemical constructor.
Alchemical() - Constructor for class ffx.xray.commands.test.Alchemical: Alchemical constructor.
Alchemical(FFXBinding) - Constructor for class ffx.realspace.commands.test.Alchemical: Alchemical constructor.
Alchemical(FFXBinding) - Constructor for class ffx.xray.commands.test.Alchemical: Alchemical constructor.
Alchemical(String[]) - Constructor for class ffx.realspace.commands.test.Alchemical: Alchemical constructor that sets the command line arguments.
Alchemical(String[]) - Constructor for class ffx.xray.commands.test.Alchemical: Alchemical constructor that sets the command line arguments.
ALCHEMICAL - Enum constant in enum class ffx.potential.ForceFieldEnergy.RestrainMode: Restrain terms are applied with the alchemical restraints (Lambda Bonded Terms).
alchemicalOptions - Variable in class ffx.algorithms.commands.Thermodynamics
AlchemicalOptions - Class in ffx.potential.cli: Represents command line options for scripts that utilize alchemistry on at least one topology.
AlchemicalOptions() - Constructor for class ffx.potential.cli.AlchemicalOptions
AlchemicalParameters - Class in ffx.potential.nonbonded.pme
AlchemicalParameters(ForceField, boolean, boolean, Polarization) - Constructor for class ffx.potential.nonbonded.pme.AlchemicalParameters
AlchemicalParameters.AlchemicalMode - Enum Class in ffx.potential.nonbonded.pme: For OST mode, we are calculating analytic dU/dL, d2U/dL2 and d2U/dL/dX for the permanent and polarization energy terms.
algorithmFunctions - Variable in class ffx.algorithms.cli.AlgorithmsCommand: An instance of AlgorithmFunctions passed into the current context.
AlgorithmFunctions - Interface in ffx.algorithms: AlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional functionality such as molecular dynamics and L-BFGS local optimization.
algorithmListener - Variable in class ffx.algorithms.cli.AlgorithmsCommand: An instance of the AlgorithmListener interface.
algorithmListener - Variable in class ffx.algorithms.dynamics.MolecularDynamics: An Algorithm Listener to send updates to the GUI.
algorithmListener - Variable in class ffx.algorithms.optimize.manybody.DistanceRegion: AlgorithmListener who should receive updates as the optimization runs.
algorithmListener - Variable in class ffx.algorithms.optimize.Minimize: The AlgorithmListener to update the UI.
algorithmListener - Variable in class ffx.algorithms.optimize.PhMinimize: The AlgorithmListener to update the UI.
algorithmListener - Variable in class ffx.algorithms.optimize.RotamerOptimization: AlgorithmListener who should receive updates as the optimization runs.
algorithmListener - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: The AlgorithmListener is called each time a count is added.
AlgorithmListener - Interface in ffx.algorithms: The AlgorithmListener will be notified at regular intervals during an algorithm.
AlgorithmsCommand - Class in ffx.algorithms.cli: Base class for scripts in the Algorithms package, providing some key functions.
AlgorithmsCommand() - Constructor for class ffx.algorithms.cli.AlgorithmsCommand
AlgorithmsCommand(FFXBinding) - Constructor for class ffx.algorithms.cli.AlgorithmsCommand
AlgorithmsCommand(String[]) - Constructor for class ffx.algorithms.cli.AlgorithmsCommand: Create a Script using the supplied command line arguments.
algorithmsScript - Variable in class ffx.algorithms.misc.AlgorithmsTest
AlgorithmsTest - Class in ffx.algorithms.misc: Base class for Algorithm tests.
AlgorithmsTest() - Constructor for class ffx.algorithms.misc.AlgorithmsTest
algorithmUpdate(MolecularAssembly) - Method in interface ffx.algorithms.AlgorithmListener: After a successful step or interval of an algorithm, this method of the listener will be called.
algorithmUpdate(MolecularAssembly) - Method in class ffx.ui.ModelingShell: After a successful step or interval of an algorithm, this method of the listener will be called.
algorithmUpdate(MolecularAssembly) - Method in class ffx.xray.RefinementEnergy: After a successful step or interval of an algorithm, this method of the listener will be called.
AlgorithmUtils - Class in ffx.algorithms: AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional functionality such as molecular dynamics and L-BFGS local optimization.
AlgorithmUtils() - Constructor for class ffx.algorithms.AlgorithmUtils: Constructor for AlgorithmUtils.
ALL - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
ALL - Static variable in interface ffx.xray.parsers.MTZWriter.MTZType: Everything, including fitted/scaled coefficients (e.g. sigmaA, map coefficients).
ALL_NETWORK_INTERFACES - Static variable in class edu.rit.pj.cluster.Constants: Host name referring to all network interfaces ("0.0.0.0").
allGather(int, Buf, Buf[]) - Method in class edu.rit.pj.Comm: All-gather messages from each process to all processes in this communicator using the given message tag.
allGather(Buf, Buf[]) - Method in class edu.rit.pj.Comm: All-gather messages from each process to all processes in this communicator.
alloc(int) - Method in class ffx.numerics.atomic.AdderDoubleArray: Ensure the AtomicDoubleArray instance has at least the specified size.
alloc(int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Ensure the AtomicDoubleArray instance has at least the specified size.
alloc(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Ensure the AtomicDoubleArray3D instance is greater than or equal to size.
alloc(int) - Method in class ffx.numerics.atomic.MultiDoubleArray: Ensure the AtomicDoubleArray instance has at least the specified size.
alloc(int) - Method in class ffx.numerics.atomic.PJDoubleArray: Ensure the AtomicDoubleArray instance has at least the specified size.
allocate(boolean[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given Boolean matrix.
allocate(boolean[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given Boolean matrix.
allocate(byte[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given byte matrix.
allocate(byte[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given byte matrix.
allocate(char[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given character matrix.
allocate(char[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given character matrix.
allocate(double[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given double matrix.
allocate(double[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given double matrix.
allocate(float[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given float matrix.
allocate(float[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given float matrix.
allocate(int[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given integer matrix.
allocate(int[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given integer matrix.
allocate(int, int) - Method in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters
allocate(long[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given long matrix.
allocate(long[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given long matrix.
allocate(short[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given short matrix.
allocate(short[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given short matrix.
allocate(Atom[]) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: Allocate storage given the Atom array.
allocate(Atom[]) - Method in class ffx.potential.nonbonded.implicit.GaussVol
allocate(T[][], int, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given object matrix.
allocate(T[][], Range, int, Range, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row and column index ranges in the given object matrix.
allocate(T[][], Range, int, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given object matrix.
allocate(T[], Range, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given index range in the given object array.
allocate(T[], Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate all elements in the given object array.
allocate2BodyJobMap(Residue[], int, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocate3BodyJobMap(Residue[], int, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocate4BodyJobMap(Residue[], int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocateLists(int, int) - Method in class ffx.potential.nonbonded.pme.PCGSolver: Allocate storage for pre-conditioner neighbor list.
allocateSelfJobMap(Residue[], int, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocateVectors(int) - Method in class ffx.potential.nonbonded.pme.PCGSolver: Allocate PCG vectors.
allowed - Variable in class ffx.crystal.HKL: Allowed is used for centric reflections.
allReduce(int, Buf, Op) - Method in class edu.rit.pj.Comm: Perform an all-reduce on all processes in this communicator using the given message tag.
allReduce(Buf, Op) - Method in class edu.rit.pj.Comm: Perform an all-reduce on all processes in this communicator.
allToAll(int, Buf[], Buf[]) - Method in class edu.rit.pj.Comm: Do an all-to-all among all processes in this communicator using the given message tag.
allToAll(Buf[], Buf[]) - Method in class edu.rit.pj.Comm: Do an all-to-all among all processes in this communicator.
alpha - Variable in class ffx.crystal.Crystal: The interaxial lattice angle between b and c.
Am - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
AMBER_1994 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1996 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1998 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1999 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1999_SB - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMINOACID - Enum constant in enum class ffx.potential.Utilities.PolymerType
aminoAcid1List - Static variable in class ffx.potential.bonded.AminoAcidUtils: List of values from the AminoAcid1 enum.
aminoAcid3 - Variable in class ffx.potential.bonded.Rotamer: The A.A. name of this residue (or null for a N.A.).
aminoAcidList - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant aminoAcidList
AminoAcidUtils - Class in ffx.potential.bonded: Utilities for creating Amino Acid residues.
AminoAcidUtils.AA - Enum Class in ffx.potential.bonded: The 20 standard amino acids.
AminoAcidUtils.AIB - Enum Class in ffx.potential.bonded: Constant AIB
AminoAcidUtils.ALA - Enum Class in ffx.potential.bonded: Constant ALA
AminoAcidUtils.AminoAcid1 - Enum Class in ffx.potential.bonded: Single letter amino acid codes (need to
AminoAcidUtils.AminoAcid3 - Enum Class in ffx.potential.bonded
AminoAcidUtils.AminoAcidBackboneAtoms - Enum Class in ffx.potential.bonded: Constant AminoAcidBackboneAtoms
AminoAcidUtils.ARG - Enum Class in ffx.potential.bonded: Constant ARG
AminoAcidUtils.ASD - Enum Class in ffx.potential.bonded: Constant ASD
AminoAcidUtils.ASH - Enum Class in ffx.potential.bonded: Constant ASH
AminoAcidUtils.ASN - Enum Class in ffx.potential.bonded: Constant ASN
AminoAcidUtils.ASP - Enum Class in ffx.potential.bonded: Constant ASP
AminoAcidUtils.CYD - Enum Class in ffx.potential.bonded: Constant CYD
AminoAcidUtils.CYS - Enum Class in ffx.potential.bonded: Constant CYS
AminoAcidUtils.CYX - Enum Class in ffx.potential.bonded: Constant CYS
AminoAcidUtils.GLD - Enum Class in ffx.potential.bonded: Constant GLD
AminoAcidUtils.GLH - Enum Class in ffx.potential.bonded: Constant GLH
AminoAcidUtils.GLN - Enum Class in ffx.potential.bonded: Constant GlutamineAtomNames
AminoAcidUtils.GLU - Enum Class in ffx.potential.bonded: Constant GLU
AminoAcidUtils.GLY - Enum Class in ffx.potential.bonded: Constant GLY
AminoAcidUtils.GlycineBackboneAtoms - Enum Class in ffx.potential.bonded: Constant GlycineBackboneAtoms
AminoAcidUtils.HID - Enum Class in ffx.potential.bonded: Constant HID
AminoAcidUtils.HIE - Enum Class in ffx.potential.bonded: Constant HIE
AminoAcidUtils.HIS - Enum Class in ffx.potential.bonded: Constant HistidineAtoms
AminoAcidUtils.ILE - Enum Class in ffx.potential.bonded: Constant ILE
AminoAcidUtils.LEU - Enum Class in ffx.potential.bonded: Constant LEU
AminoAcidUtils.LYD - Enum Class in ffx.potential.bonded: Constant LYD
AminoAcidUtils.LYS - Enum Class in ffx.potential.bonded: Constant LYS
AminoAcidUtils.MET - Enum Class in ffx.potential.bonded: Constant MethionineAtomNames
AminoAcidUtils.ORN - Enum Class in ffx.potential.bonded: Constant ORN
AminoAcidUtils.PCA - Enum Class in ffx.potential.bonded: Constant PCA
AminoAcidUtils.PHE - Enum Class in ffx.potential.bonded: Constant PHE
AminoAcidUtils.PRO - Enum Class in ffx.potential.bonded: Constant PRO
AminoAcidUtils.ProlineBackboneAtoms - Enum Class in ffx.potential.bonded: Constant ProlineBackboneAtoms
AminoAcidUtils.ResiduePosition - Enum Class in ffx.potential.bonded: The location of a residue within a chain.
AminoAcidUtils.SER - Enum Class in ffx.potential.bonded: Constant SER
AminoAcidUtils.SideChainType - Interface in ffx.potential.bonded: This interface is used by the "Build" routines.
AminoAcidUtils.THR - Enum Class in ffx.potential.bonded: Constant THR
AminoAcidUtils.TRP - Enum Class in ffx.potential.bonded: Constant TRP
AminoAcidUtils.TYD - Enum Class in ffx.potential.bonded: Constant TYD
AminoAcidUtils.TYR - Enum Class in ffx.potential.bonded: Constant TYR
AminoAcidUtils.VAL - Enum Class in ffx.potential.bonded: Constant VAL
amoeba - Variable in class ffx.ui.commands.SimulationUpdate
AMOEBA - Enum constant in enum class ffx.potential.bonded.Atom.Resolution
AMOEBA_2004 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_2009 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_BIO_2009 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_BIO_2018 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_BIO_2018_CPHMD - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_NUC_2017 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_PLUS_DAMP_FIELD - Enum constant in enum class ffx.numerics.multipole.Operator: Charge-Penetration nucleus-multipole operator.
AMOEBA_PLUS_OVERLAP_FIELD - Enum constant in enum class ffx.numerics.multipole.Operator: Mpole-Mpole Interaction for Amoeba+
AMOEBA_PLUS_SYM_DAMP_FIELD - Enum constant in enum class ffx.numerics.multipole.Operator: Core-Mpole Interaction with 2 identical atoms
AMOEBA_PROTEIN_2004 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_PROTEIN_2013 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_WATER_2003 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_WATER_2014 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
amoebaGeneralizedKirkwoodForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Generalized Kirkwood Force.
AmoebaGeneralizedKirkwoodForce - Class in ffx.potential.openmm
AmoebaGeneralizedKirkwoodForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaGeneralizedKirkwoodForce
amoebaGKCavitationForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM AMOEBA WCA Cavitation Force.
AmoebaGKCavitationForce - Class in ffx.potential.openmm: AmoebaCavitationForce.
AmoebaGKCavitationForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaGKCavitationForce: Constructor.
amoebaMultipoleForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM AMOEBA Multipole Force.
AmoebaMultipoleForce - Class in ffx.potential.openmm: AmoebaMultipoleForce.
AmoebaMultipoleForce(int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.AmoebaMultipoleForce: Construct an AMOEBA Multipole Force.
AmoebaMultipoleForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaMultipoleForce: Construct an AMOEBA Multipole Force.
AmoebaPlusDampTensorGlobal - Class in ffx.numerics.multipole: The AmoebaPlusDampTensorGlobal class computes derivatives of damping via recursion to order <= 2 for Cartesian multipoles defined in AMOEBA+.
AmoebaPlusDampTensorGlobal(int, double, double) - Constructor for class ffx.numerics.multipole.AmoebaPlusDampTensorGlobal: Constructor for CoulombTensorGlobal.
AmoebaPlusDampTensorGlobal(int, double, double, double) - Constructor for class ffx.numerics.multipole.AmoebaPlusDampTensorGlobal: Constructor for CoulombTensorGlobal.
AmoebaPlusOverlapTensorGlobal - Class in ffx.numerics.multipole: The AmoebaPlusDampTensorGlobal class computes derivatives of overlap via recursion to order <= 6 for Cartesian multipoles defined in AMOEBA+.
AmoebaPlusOverlapTensorGlobal(int, double, double) - Constructor for class ffx.numerics.multipole.AmoebaPlusOverlapTensorGlobal: Constructor for CoulombTensorGlobal.
amoebaTorsionTorsionForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Torsion-Torsion Force.
AmoebaTorsionTorsionForce - Class in ffx.potential.openmm: OpenMM TorsionTorsion Force.
AmoebaTorsionTorsionForce(TorsionTorsionPotentialEnergy) - Constructor for class ffx.potential.openmm.AmoebaTorsionTorsionForce: Create an OpenMM TorsionTorsion Force.
AmoebaTorsionTorsionForce(TorsionTorsionPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.AmoebaTorsionTorsionForce: Create a Dual Topology OpenMM TorsionTorsion Force.
amoebaTorsionTorsionForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Torsion-Torsion Force for topology 2.
amoebaVDWForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM AMOEBA van der Waals Force.
AmoebaVdwForce - Class in ffx.potential.openmm: The Amoeba vdW Force.
AmoebaVdwForce(int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.AmoebaVdwForce: The Amoeba vdW Force constructor used for dual-topology simulations.
AmoebaVdwForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaVdwForce: The Amoeba vdW Force constructor.
amoebaWcaDispersionForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM AMOEBA WCA Dispersion Force.
AmoebaWcaDispersionForce - Class in ffx.potential.openmm
AmoebaWcaDispersionForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaWcaDispersionForce: Create a new Amoeba WCA dispersion force.
amplitude - Variable in class ffx.potential.parameters.TorsionType: Amplitudes of the Fourier series.
an0 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
an1 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
an2 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
an3 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
an4 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
an5 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
analyticalEntropies(int) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
analyticalFreeEnergies() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
analyticalIntegral() - Method in class ffx.numerics.integrate.FunctionDataCurve: Evaluates the functions analytical integral over the entire range of points.
analyticalIntegral(double, double) - Method in class ffx.numerics.integrate.FunctionDataCurve: Evaluates the function's analytical integral over a range.
analyticalMeans() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
analyticalObservable(String) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
analyticalStandardDeviations() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
analyzeClusters(List<CentroidCluster<Clustering.Conformation>>, List<Integer>, boolean) - Static method in class ffx.potential.utils.Clustering: Analyze a list of CentroidClusters.
AnalyzeNEQ - Class in ffx.algorithms.commands: Performs analysis of Non-equilibrium work simulations.
AnalyzeNEQ() - Constructor for class ffx.algorithms.commands.AnalyzeNEQ: AnalyzeNEQ Constructor.
AnalyzeNEQ(FFXBinding) - Constructor for class ffx.algorithms.commands.AnalyzeNEQ: AnalyzeNEQ Constructor.
AnalyzeNEQ(String[]) - Constructor for class ffx.algorithms.commands.AnalyzeNEQ: AnalyzeNEQ constructor that sets the command line arguments.
and(Class<? extends Object>, String) - Method in class ffx.ui.Selection: and
AND - Static variable in class edu.rit.pj.reduction.BooleanOp: The Boolean logical "and" binary operation.
AND - Static variable in class edu.rit.pj.reduction.ByteOp: The byte bitwise "and" binary operation.
AND - Static variable in class edu.rit.pj.reduction.CharacterOp: The character bitwise "and" binary operation.
AND - Static variable in class edu.rit.pj.reduction.IntegerOp: The integer bitwise "and" binary operation.
AND - Static variable in class edu.rit.pj.reduction.LongOp: The long bitwise "and" binary operation.
AND - Static variable in class edu.rit.pj.reduction.ShortOp: The short bitwise "and" binary operation.
andersenThermostat - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM thermostat.
AndersenThermostat - Class in ffx.openmm: This class uses the Andersen method to maintain constant temperature.
AndersenThermostat(double, double) - Constructor for class ffx.openmm.AndersenThermostat: Create an AndersenThermostat.
ANG_TO_NM - Static variable in class ffx.utilities.Constants: Constant ANG_TO_NM=0.1
angle - Variable in class ffx.potential.bonded.StretchBend: Angle this Stretch-Bend is based on.
angle - Variable in class ffx.potential.bonded.UreyBradley: The Angle this UreyBradley term is based on.
angle - Variable in class ffx.potential.parameters.AngleType: Equilibrium angle (degrees).
angle(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: angle
angle(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: angle
angle(Double3) - Method in class ffx.numerics.math.Double3: Angle of this Double3 with b.
angle(Float3) - Method in class ffx.numerics.math.Float3: Angle of this Float3 with b.
Angle - Class in ffx.potential.bonded: The Angle class represents an angle formed between three linearly bonded atoms.
Angle(Bond, Bond) - Constructor for class ffx.potential.bonded.Angle: Angle constructor
ANGLE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
angleEq - Variable in class ffx.potential.bonded.StretchBend: Equilibrium angle.
angleForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom Angle Force
AngleForce - Class in ffx.potential.openmm: OpenMM Angle Force.
AngleForce(AnglePotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.AngleForce: Create an OpenMM Angle Force.
AngleForce(AnglePotentialEnergy, OpenMMEnergy) - Constructor for class ffx.potential.openmm.AngleForce: Create an OpenMM Angle Force.
angleForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Angle Force for topology 2.
angleFunction - Variable in class ffx.potential.parameters.AngleType: The angle function in use.
angleMode - Variable in class ffx.potential.parameters.AngleType: The angle mode in use.
ANGLEP - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
AnglePotentialEnergy - Class in ffx.potential.terms: Angle potential energy term using Angle instances.
AnglePotentialEnergy(String) - Constructor for class ffx.potential.terms.AnglePotentialEnergy: Create an AnglePotentialEnergy with the provided name.
AnglePotentialEnergy(String, int) - Constructor for class ffx.potential.terms.AnglePotentialEnergy: Create an AnglePotentialEnergy with the provided name and force group.
AnglePotentialEnergy(String, int, List<Angle>) - Constructor for class ffx.potential.terms.AnglePotentialEnergy: Create an AnglePotentialEnergy initialized with a list of angles and force group.
AnglePotentialEnergy(String, Collection<Angle>) - Constructor for class ffx.potential.terms.AnglePotentialEnergy: Create an AnglePotentialEnergy initialized with a collection of angles.
angles - Variable in class ffx.potential.bonded.Rotamer: An array of chi angles for this rotamer.
angleTime - Static variable in class ffx.potential.bonded.MSGroup: Constant angleTime=0
AngleTorsion - Class in ffx.potential.bonded: The AngleTorsion class represents an angle torsion coupling between four bonded atoms.
AngleTorsion(Angle, Angle) - Constructor for class ffx.potential.bonded.AngleTorsion: AngleTorsion constructor.
AngleTorsion(Bond, Bond, Bond) - Constructor for class ffx.potential.bonded.AngleTorsion: Create a AngleTorsion from 3 connected bonds (no error checking)
AngleTorsion(String) - Constructor for class ffx.potential.bonded.AngleTorsion: AngleTorsion Constructor.
angleTorsionForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Angle-Torsion Force.
AngleTorsionForce - Class in ffx.potential.openmm: OpenMM Angle-Torsion Force.
AngleTorsionForce(AngleTorsionPotentialEnergy) - Constructor for class ffx.potential.openmm.AngleTorsionForce: Create an OpenMM Angle-Torsion Force.
AngleTorsionForce(AngleTorsionPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.AngleTorsionForce: Create a Dual Topology OpenMM Angle-Torsion Force.
angleTorsionForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Angle-Torsion Force for topology 2.
angleTorsionForm() - Static method in class ffx.potential.bonded.AngleTorsion: Returns the mathematical form of an angle-torsion as an OpenMM-parsable String.
AngleTorsionPotentialEnergy - Class in ffx.potential.terms: Angle-Torsion potential energy term using AngleTorsion instances.
AngleTorsionPotentialEnergy(String) - Constructor for class ffx.potential.terms.AngleTorsionPotentialEnergy: Create an AngleTorsionPotentialEnergy with the provided name.
AngleTorsionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.AngleTorsionPotentialEnergy: Create an AngleTorsionPotentialEnergy with the provided name and force group.
AngleTorsionPotentialEnergy(String, int, List<AngleTorsion>) - Constructor for class ffx.potential.terms.AngleTorsionPotentialEnergy: Create an AngleTorsionPotentialEnergy initialized with a list of terms and force group.
AngleTorsionPotentialEnergy(String, Collection<AngleTorsion>) - Constructor for class ffx.potential.terms.AngleTorsionPotentialEnergy: Create an AngleTorsionPotentialEnergy initialized with a collection of terms.
angleTorsionTime - Static variable in class ffx.potential.bonded.MSGroup: Constant angleTorsionTime=0
AngleTorsionType - Class in ffx.potential.parameters: The AngleTorsionType class defines one angle-torsion energy type.
AngleTorsionType(int[], double[]) - Constructor for class ffx.potential.parameters.AngleTorsionType: AngleTorsionType Constructor.
angleType - Variable in class ffx.potential.bonded.Angle: Force field parameters to compute the angle bending energy.
AngleType - Class in ffx.potential.parameters: The AngleType class defines one harmonic angle bend energy term.
AngleType(int[], double, double[]) - Constructor for class ffx.potential.parameters.AngleType: The default AngleType constructor defines use of the Sextic AngleFunction.
AngleType(int[], double, double[], AngleType.AngleMode) - Constructor for class ffx.potential.parameters.AngleType: Constructor for In-Plane AngleType.
AngleType(int[], double, double[], AngleType.AngleMode, AngleType.AngleFunction) - Constructor for class ffx.potential.parameters.AngleType: Constructor for In-Plane AngleType.
AngleType.AngleFunction - Enum Class in ffx.potential.parameters: Angle function types include harmonic or sextic.
AngleType.AngleMode - Enum Class in ffx.potential.parameters: Angle modes include Normal or In-Plane
angleType1 - Variable in class ffx.potential.bonded.AngleTorsion: First angle force field type.
angleType2 - Variable in class ffx.potential.bonded.AngleTorsion: Second angle force field type.
angleUnit - Variable in class ffx.potential.parameters.AngleType: Convert angle bending energy to kcal/mole.
ANGTORS - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
angtorunit - Variable in class ffx.potential.parameters.AngleTorsionType: Convert angle-torsion to kcal/mole.
ANIEnergy - Class in ffx.potential
ANIEnergy(MolecularAssembly) - Constructor for class ffx.potential.ANIEnergy
anmc(int) - Static method in class ffx.numerics.multipole.GKSource: Return coefficients needed when taking derivatives of auxiliary functions.
anneal() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: anneal
Anneal - Class in ffx.algorithms.commands: The Anneal script.
Anneal - Class in ffx.realspace.commands: The Real Space Annealing script.
Anneal - Class in ffx.xray.commands: The X-ray Annealing script.
Anneal() - Constructor for class ffx.algorithms.commands.Anneal: Anneal Constructor.
Anneal() - Constructor for class ffx.realspace.commands.Anneal: Anneal constructor.
Anneal() - Constructor for class ffx.xray.commands.Anneal: Anneal constructor.
Anneal(FFXBinding) - Constructor for class ffx.algorithms.commands.Anneal: Anneal Constructor.
Anneal(FFXBinding) - Constructor for class ffx.realspace.commands.Anneal: Anneal constructor.
Anneal(FFXBinding) - Constructor for class ffx.xray.commands.Anneal: Anneal constructor.
Anneal(String[]) - Constructor for class ffx.algorithms.commands.Anneal: Anneal constructor that sets the command line arguments.
Anneal(String[]) - Constructor for class ffx.realspace.commands.Anneal: Anneal constructor that sets the command line arguments.
Anneal(String[]) - Constructor for class ffx.xray.commands.Anneal: Anneal constructor that sets the command line arguments.
AnnealingSchedule - Interface in ffx.algorithms.optimize.anneal: Temperature schedule for simulated annealing
AnnealOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that utilize simulated annealing.
AnnealOptions() - Constructor for class ffx.algorithms.cli.AnnealOptions
ANY - Enum constant in enum class ffx.potential.Utilities.FileType
anyRotamerInsideCell(Residue, Crystal, SymOp, boolean) - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Checks if any rotamer of a Residue is inside this BoxOptCell.
aperiodic() - Method in class ffx.crystal.Crystal: aperiodic
append(double) - Method in class ffx.openmm.DoubleArray: Append a double value to the array.
append(int) - Method in class ffx.openmm.IntArray: Append a int value to the array.
append(int, int) - Method in class ffx.openmm.BondArray: Append a bond to the bond array.
append(OpenMM_Vec3.ByValue) - Method in class ffx.openmm.Vec3Array: Append a Vec3 to the Vec3Array.
append(SymOp) - Method in class ffx.crystal.SymOp: Return the combined SymOp that is equivalent to first applying this SymOp and then the argument.
append(ForceField) - Method in class ffx.potential.parameters.ForceField: Append a 2nd ForceField "patch" to the current ForceField.
append(File, String) - Static method in class ffx.utilities.FileUtils: Append content to a file.
append(String) - Method in class ffx.openmm.StringArray: Append a String to the String Array.
append(String) - Method in class ffx.utilities.Keyword: append
append(String[]) - Method in class ffx.utilities.Keyword: append
appendLeafNames(List<String>) - Method in class ffx.numerics.clustering.Cluster: Appends a list of leaf names to this cluster's leaf name list.
appendSnapshot(String[]) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Append a snapshot to the trajectory file.
appendSnapshot(String[]) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
applyAllConstraintPositions(double[], double[]) - Method in class ffx.potential.ForceFieldEnergy: Applies constraints to positions
applyAllConstraintPositions(double[], double[], double) - Method in class ffx.potential.ForceFieldEnergy: Applies constraints to positions
applyAllOSTOptions(OrthogonalSpaceTempering, MolecularAssembly, DynamicsOptions, BarostatOptions) - Method in class ffx.algorithms.cli.OSTOptions: Applies relevant options to an OST, and returns either the OST object or something that wraps the OST (such as a Barostat).
applyAndSaveTorsions(String[]) - Method in class ffx.algorithms.misc.GenerateRotamers: Accessory method for more simplistic saving of specific torsion states.
applyAtomProperties() - Method in class ffx.potential.parsers.SystemFilter: Automatically sets atom-specific flags, particularly nouse and inactive, and apply harmonic restraints.
applyCartesianSymOp(double[], double[], SymOp) - Static method in class ffx.crystal.SymOp: Apply a cartesian symmetry operator to an array of coordinates.
applyCartesianSymOp(double[], double[], SymOp, boolean[]) - Static method in class ffx.crystal.SymOp: Apply a cartesian symmetry operator to an array of coordinates.
applyCartesianSymRot(double[], double[], SymOp) - Static method in class ffx.crystal.SymOp: Apply a Cartesian symmetry rotation to an array of Cartesian coordinates.
applyCartesianSymRot(double[], double[], SymOp, boolean[]) - Static method in class ffx.crystal.SymOp: Apply a Cartesian symmetry rotation to an array of Cartesian coordinates.
applyCartSymOp(int, double[], double[], double[], double[], double[], double[], SymOp) - Static method in class ffx.crystal.SymOp: Apply a Cartesian symmetry operator to an array of Cartesian coordinates.
applyChargeConstraintToStep(double[], double[]) - Method in class ffx.potential.constraint.ShakeChargeConstraint: This method follows the SHAKE Charge Constraint laid out in Appendix B of Donnini, Serena, et al.
applyConstraints(double) - Method in class ffx.openmm.Context: Update the positions of particles so that all distance constraints are satisfied.
applyConstraintToStep(double[], double[], double[], double) - Method in interface ffx.numerics.Constraint: Applies this Constraint in the context of a partially calculated MD time-step.
applyConstraintToStep(double[], double[], double[], double) - Method in class ffx.potential.constraint.CcmaConstraint: Applies this Constraint in the context of a partially calculated MD time-step.
applyConstraintToStep(double[], double[], double[], double) - Method in class ffx.potential.constraint.SettleConstraint
applyConstraintToStep(double[], double[], double[], double) - Method in class ffx.potential.constraint.ShakeChargeConstraint
applyConstraintToVelocities(double[], double[], double[], double) - Method in interface ffx.numerics.Constraint: Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions.
applyConstraintToVelocities(double[], double[], double[], double) - Method in class ffx.potential.constraint.CcmaConstraint: Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions.
applyConstraintToVelocities(double[], double[], double[], double) - Method in class ffx.potential.constraint.SettleConstraint
applyConstraintToVelocities(double[], double[], double[], double) - Method in class ffx.potential.constraint.ShakeChargeConstraint
applyFracSymOp(double[], double[], SymOp) - Static method in class ffx.crystal.SymOp: Apply a fractional symmetry operator to one set of coordinates.
applyLambda() - Method in class ffx.potential.bonded.Atom: applyLambda
applyLambda() - Method in class ffx.potential.bonded.BondedTerm: Check if any atom of this BondedTerm has the Lambda flag set.
applyLambda() - Method in class ffx.potential.bonded.RestrainTorsion
applyMask(int, boolean[], double[]...) - Method in interface ffx.potential.nonbonded.MaskingInterface: Interactions with atom i that should not be included in the NeighborList should be set to 0.
applyMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion: Apply permanent field masking rules.
applyMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
applyMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.VanDerWaals: Interactions with atom i that should not be included in the NeighborList should be set to 0.
applyMasks(double, double) - Method in class ffx.numerics.multipole.PolarizableMultipole: Compute the scaled and averaged induced dipole.
applyMasks(DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Compute the scaled and averaged induced dipole.
applyMatrixTranspose(double[], double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath: Multiply coordinates by the transpose of a matrix.
applyProperties(CompositeConfiguration) - Method in class ffx.algorithms.thermodynamics.HistogramData
applyRandomDensity(double) - Method in class ffx.potential.MolecularAssembly: Applies a randomly drawn density to a molecular system's crystal.
applyRandomSymOp(double) - Method in class ffx.potential.MolecularAssembly: Randomizes position in the unit cell of each molecule by applying a Cartesian SymOp with a random translation.
applyRotamer(Residue, Rotamer) - Static method in class ffx.potential.bonded.RotamerLibrary: Applies a Rotamer to a Residue by calling applyAARotamer or applyNARotamer.
applyRotamer(Residue, Rotamer, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: Version of applyRotamer which allows for chain context-independent drawing of nucleic acid Rotamers.
applyRotation(double[], double[][]) - Static method in class ffx.potential.utils.Superpose: Apply a rotation matrix to a set of coordinates.
applySoluteRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Apply solute radii definitions used to calculate Born radii.
applySugarPucker(Residue, RotamerLibrary.NucleicSugarPucker, boolean, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: If place is true, builds C2', C3', and O3' based on delta(i) and returns an empty double[]; if place is false, returns a double[] filled with the coordinates at which O3' would be placed by the specified pucker.
applySymOp(double[], double[], SymOp) - Method in class ffx.crystal.Crystal: Apply a fractional symmetry operator to one set of cartesian coordinates.
applySymOp(int, double[], double[], double[], double[], double[], double[], SymOp) - Method in class ffx.crystal.Crystal: Apply a fractional symmetry operator to an array of Cartesian coordinates.
applySymOp(int, int, int, int[], SymOp, int, int, int) - Static method in class ffx.crystal.SymOp: Apply a symmetry operator to one set of coordinates.
applySymRot(double[], double[], SymOp) - Method in class ffx.crystal.Crystal: Apply a fractional symmetry operator to one set of cartesian coordinates.
applySymRot(HKL, HKL, SymOp) - Static method in class ffx.crystal.SymOp: Apply a symmetry operator to one HKL.
ApplyTorsions - Class in ffx.algorithms.commands.test: The ApplyTorsions script is used to apply a custom set of torsions to a side chain.
ApplyTorsions() - Constructor for class ffx.algorithms.commands.test.ApplyTorsions: ApplyTorsions Constructor.
ApplyTorsions(FFXBinding) - Constructor for class ffx.algorithms.commands.test.ApplyTorsions: ApplyTorsions Constructor.
ApplyTorsions(String[]) - Constructor for class ffx.algorithms.commands.test.ApplyTorsions: ApplyTorsions constructor that sets the command line arguments.
applyTranslation(double[], double[]) - Static method in class ffx.potential.utils.Superpose: Apply a translation matrix [dx,dy,dz] to a molecular system.
applyTransSymRot(int, double[], double[], double[], double[], double[], double[], SymOp, double[][]) - Method in class ffx.crystal.Crystal: Apply the transpose of a symmetry rotation to an array of Cartesian coordinates.
applyTransSymRot(HKL, HKL, SymOp) - Static method in class ffx.crystal.SymOp: Apply a transpose rotation symmetry operator to one HKL.
APPLYUSERCOLOR - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
applyVelocityConstraints(double) - Method in class ffx.openmm.Context: Update the velocities of particles so the net velocity of each constrained distance is zero.
approxEquals(double, double) - Static method in class ffx.numerics.integrate.FunctionDataCurve: Checks for equality to +/- 10 ulp.
approxEquals(double, double, double) - Static method in class ffx.numerics.integrate.FunctionDataCurve: Compare two doubles to machine precision.
aPrevious - Variable in class ffx.potential.SystemState: Previous accelerations.
aPrevious() - Method in class ffx.potential.SystemState: Get a reference to the internal previous accelerations array.
aPrevious() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the aPrevious record component.
Ar - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ARC - Enum constant in enum class ffx.potential.Utilities.FileType
ARCFileFilter - Class in ffx.potential.parsers: The ARCFileFilter class is used to choose a TINKER Archive (*.ARC).
ARCFileFilter() - Constructor for class ffx.potential.parsers.ARCFileFilter: Default Constructor
area - Variable in class ffx.numerics.quickhull.Face
areaSquared(HalfEdge, HalfEdge) - Method in class ffx.numerics.quickhull.Face: Computes the squared area of the triangle defined by hedge0 (tail->head) and the point at the head of hedge1.
ARG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ARGININE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
args - Variable in class ffx.utilities.FFXCommand: The array of args passed into the Script.
ARITHMETIC - Enum constant in enum class ffx.potential.parameters.VDWType.RADIUS_RULE
arm(MSNode, boolean, boolean, RendererCache.ViewModel, boolean, RendererCache.ColorModel) - Method in class ffx.potential.Renderer: arm
arm(ArrayList<MSNode>, boolean, boolean, RendererCache.ViewModel, boolean, RendererCache.ColorModel) - Method in class ffx.potential.Renderer: This node arms UpdateBehavior with a graphics operation to carry out
ArrayIndex_Name - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
Arrays - Class in edu.rit.util: Class Arrays provides static methods for various operations on arrays and matrices of primitive types and object types.
As - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ASD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASH1toASH2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
ASHtoASP - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
askToInterruptScript() - Method in class ffx.ui.ModelingShell: If at exit time, a script is running, the user is given an option to interrupt it first
askToSaveFile() - Method in class ffx.ui.ModelingShell
asMatrix() - Method in class ffx.crystal.SymOp: Return the SymOp as a 4x4 matrix.
asMatrixString(SymOp) - Static method in class ffx.crystal.SymOp: Print a Sym Op matrix as a continued line string.
ASN - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASP - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASPARAGINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
ASPARTATE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
ASPC - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
ASPC - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
aspcPredictor(LambdaMode, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Always-stable predictor-corrector for the mutual induced dipoles.
assembleMolecularDynamics(MolecularAssembly[], CrystalPotential, DynamicsOptions, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions: Assembles a MolecularDynamics wrapped around a Potential.
assemblePotential(MolecularAssembly[], StringBuilder) - Method in class ffx.potential.cli.TopologyOptions: Performs the bulk of the work of setting up a multi-topology system.
AssemblyState - Class in ffx.potential: The AssemblyState class stores the chemical and coordinate state of a Molecular Assembly.
AssemblyState(MolecularAssembly) - Constructor for class ffx.potential.AssemblyState: Construct a snapshot of a MolecularAssembly.
assertXIntegrity() - Method in class ffx.numerics.integrate.FunctionDataCurve: Used to check that x array is composed of equally-spaced points from lb to ub.
assignAminoAcidAtomTypes(Residue, Residue, Residue, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: assignAminoAcidAtomTypes.
assignAminoAcidAtomTypes(List<Residue>, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: Assign atom types to an amino acid polymer.
assignAtomsToCells() - Method in class ffx.potential.nonbonded.SpatialDensityRegion: Assign asymmetric and symmetry mate atoms to cells.
assignAtomTypes(MolecularAssembly, PDBFilter.PDBFileStandard) - Static method in class ffx.potential.bonded.PolymerUtils: Assign force field atoms types to common chemistries using "biotype" records.
assignAxisAtoms(Atom) - Static method in class ffx.potential.parameters.MultipoleType: Assign local multipole frame defining atoms.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.JobFrontend: Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "assign backend" message.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Assign a backend process to the job.
assignBondedTerms(ForceField) - Method in class ffx.potential.bonded.MSGroup: assignBondedTerms
assignBondedTerms(ForceField) - Method in class ffx.potential.bonded.MultiResidue: assignBondedTerms
assigned(int[], boolean, boolean) - Method in class ffx.potential.parameters.ImproperTorsionType: Returns true if the atoms can be assigned this improperTorsionType.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontend: Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "assign job number" message.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Assign a job number to the job.
assignMultipole(ForceField.ELEC_FORM, Atom, ForceField, double[], int, int[][], MultipoleType.MultipoleFrameDefinition[]) - Static method in class ffx.potential.parameters.MultipoleType: Assign the multipole type.
assignNucleicAcidAtomTypes(List<Residue>, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.NucleicAcidUtils: Assign atom types for a nucleic acid polymer.
assignPolarizationGroups() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: AssignPolarizationGroups.
assignPolarizationGroups(Atom[], int[][], int[][], int[][]) - Static method in class ffx.potential.parameters.PolarizeType: Assign polarization groups to atoms based on their connectivity.
ASULimit - Enum Class in ffx.crystal: Enumeration of the different asymmetric unit limit operators.
asuLimitOperators - Variable in class ffx.crystal.SpaceGroup: Real space ASU limit operators.
At - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ATM_TO_BAR - Static variable in class ffx.utilities.Constants: Constant ATM_TO_BAR=1.01325
ATMForce - Class in ffx.openmm: The ATMForce class implements the Alchemical Transfer Method (ATM) for OpenMM.
ATMForce(double, double, double, double, double, double, double, double, double) - Constructor for class ffx.openmm.ATMForce: Create an ATMForce object with the default softplus energy expression.
ATMForce(String) - Constructor for class ffx.openmm.ATMForce: Create an ATMForce object.
atom - Variable in exception class ffx.potential.bonded.BondedUtils.MissingAtomTypeException
Atom - Class in ffx.potential.bonded: The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
Atom(int, Atom, double[], int, char, String) - Constructor for class ffx.potential.bonded.Atom: Creates a new Atom similar to an existing Atom (e.g. for tiling a solvent box over a solute).
Atom(int, String, AtomType, double[]) - Constructor for class ffx.potential.bonded.Atom: Constructor used when parsing XYZ files.
Atom(int, String, Character, double[], String, int, Character, double, double, String) - Constructor for class ffx.potential.bonded.Atom: Constructor used when parsing PDB files.
Atom(int, String, Character, double[], String, int, Character, double, double, String, boolean) - Constructor for class ffx.potential.bonded.Atom: Constructor for Atom.
Atom(String) - Constructor for class ffx.potential.bonded.Atom: Default constructor.
ATOM - Enum constant in enum class ffx.potential.MolecularAssembly.FractionalMode
ATOM - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
ATOM_DISTANCE - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
Atom.Descriptions - Enum Class in ffx.potential.bonded
Atom.ElementSymbol - Enum Class in ffx.potential.bonded: Element symbols for the first 109 elements.
Atom.Resolution - Enum Class in ffx.potential.bonded
atomAttachedToAtom(Atom, Atom) - Static method in class ffx.potential.bonded.BondedUtils: Checks if atom a1 is bonded to atom a2.
atomClass - Variable in class ffx.potential.parameters.AtomType: Atom class.
atomClass - Variable in class ffx.potential.parameters.VDWType: The atom class that uses this van der Waals parameter.
atomClasses - Variable in class ffx.potential.parameters.AngleTorsionType: Atom classes for this stretch-torsion type.
atomClasses - Variable in class ffx.potential.parameters.AngleType: Atom classes that for this Angle type.
atomClasses - Variable in class ffx.potential.parameters.BondType: Atom classes that form this bond stretch.
atomClasses - Variable in class ffx.potential.parameters.ImproperTorsionType: Atom classes that for this Improper Torsion angle.
atomClasses - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Atom classes for this out-of-plane angle bending type.
atomClasses - Variable in class ffx.potential.parameters.PiOrbitalTorsionType: Atom classes that form this Pi-Torsion.
atomClasses - Variable in class ffx.potential.parameters.StretchBendType: Atom class for this stretch-bend type.
atomClasses - Variable in class ffx.potential.parameters.StretchTorsionType: Atom classes for this stretch-torsion type.
atomClasses - Variable in class ffx.potential.parameters.TorsionTorsionType: Atom classes that form this Torsion-Torsion type.
atomClasses - Variable in class ffx.potential.parameters.TorsionType: Atom classes that for this Torsion angle.
atomClasses - Variable in class ffx.potential.parameters.UreyBradleyType: Atom classes that form this Urey-Bradley cross term.
atomClasses - Variable in class ffx.potential.parameters.VDWPairType: Atom classes that form this bond stretch.
AtomColor - Static variable in class ffx.potential.bonded.Atom: Constant AtomColor
atomic - Variable in class ffx.ui.commands.SimulationDefinition
AtomicDoubleArray - Interface in ffx.numerics.atomic: This interface abstracts away the implementation of maintaining a 1D double array that is operated on by multiple threads.
AtomicDoubleArray.AtomicDoubleArrayImpl - Enum Class in ffx.numerics.atomic: AtomicDoubleArray implementations (ADDER, MULTI, PJ).
AtomicDoubleArray3D - Class in ffx.numerics.atomic: Implementation of maintaining a 3D double array that is operated on by multiple threads.
AtomicDoubleArray3D(AtomicDoubleArray.AtomicDoubleArrayImpl, int) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D: Construct an atomic 3D double array of the specified size using the specified implementation.
AtomicDoubleArray3D(AtomicDoubleArray.AtomicDoubleArrayImpl, int, int) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D: Construct an atomic 3D double array of the specified size, using the specified implementation, and the requested number of threads.
AtomicDoubleArray3D(AtomicDoubleArray, AtomicDoubleArray, AtomicDoubleArray) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D: Construct an atomic 3D double array using the specified AtomicDoubleArray instances.
atomicMass - Static variable in class ffx.potential.parameters.AtomType: IUPAC Commission on Isotopic Abundances and Atomic Weights.
atomicNumber - Variable in class ffx.potential.parameters.AtomType: Atomic Number.
atomicWeight - Variable in class ffx.potential.parameters.AtomType: Atomic weight.
AtomIndex(int, int, double) - Constructor for class ffx.potential.nonbonded.NeighborList.AtomIndex
atomInsideCell(Atom, Crystal, SymOp) - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Checks if an Atom would be contained inside this cell.
atomList - Variable in class ffx.potential.parsers.SystemFilter: The atomList is filled by filters that extend SystemFilter.
atomListToSet(List<Integer>, Atom[]) - Static method in class ffx.potential.parsers.SystemFilter: Converts a list of atom indices to an array of atoms.
atomName - Variable in exception class ffx.potential.bonded.BondedUtils.MissingHeavyAtomException
atomName - Variable in class ffx.potential.parameters.BioType: The PDB atom name for this BioType.
atoms - Variable in class ffx.potential.bonded.BondedTerm: Atoms that are used to form this term.
atoms - Variable in class ffx.potential.nonbonded.implicit.BornGradRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.BornRadiiRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.DispersionRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.InducedGKFieldRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.PermanentGKFieldRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.openmm.OpenMMSystem: Array of atoms in the system.
AtomSelectionOptions - Class in ffx.potential.cli: Represents command line options for scripts that support atom selections.
AtomSelectionOptions() - Constructor for class ffx.potential.cli.AtomSelectionOptions
atomType - Variable in exception class ffx.potential.bonded.BondedUtils.MissingHeavyAtomException
atomType - Variable in class ffx.potential.parameters.BioType: The force field atom type to be used for the molecule / atom name combination.
atomType - Variable in class ffx.potential.parameters.ChargeType: The atom type that uses this charge parameter.
AtomType - Class in ffx.potential.parameters: The AtomType class represents one molecular mechanics atom type.
AtomType(int, int, String, String, int, double, int) - Constructor for class ffx.potential.parameters.AtomType: AtomType Constructor.
attachExtendedSystem(ExtendedSystem) - Method in class ffx.potential.ForceFieldEnergy: Overwrites current esvSystem if present.
attachExtendedSystem(ExtendedSystem) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Attach system with extended variable such as titrations.
attachExtendedSystem(ExtendedSystem) - Method in class ffx.potential.nonbonded.VanDerWaals: attachExtendedSystem.
attachExtendedSystem(ExtendedSystem, double) - Method in class ffx.algorithms.dynamics.MolecularDynamics: attachExtendedSystem.
Au - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
AUTO - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
AUTOMATIC_TOLERANCE - Static variable in class ffx.numerics.quickhull.QuickHull3D: Specifies that the distance tolerance should be computed automatically from the input point data.
automaticWriteouts - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Whether MD handles writing restart/trajectory files itself (true), or will be commanded by another class (false) to do it.
average(AngleTorsionType, AngleTorsionType, int[]) - Static method in class ffx.potential.parameters.AngleTorsionType: Average two AngleTorsionType instances.
average(AngleType, AngleType, int[]) - Static method in class ffx.potential.parameters.AngleType: Average two AngleType instances.
average(BondType, BondType, int[]) - Static method in class ffx.potential.parameters.BondType: Average two BondType instances.
average(ChargeType, ChargeType, int) - Static method in class ffx.potential.parameters.ChargeType: Average two ChargeType instances.
average(ImproperTorsionType, ImproperTorsionType, int[]) - Static method in class ffx.potential.parameters.ImproperTorsionType: Average two ImproperTorsionType instances.
average(OutOfPlaneBendType, OutOfPlaneBendType, int[]) - Static method in class ffx.potential.parameters.OutOfPlaneBendType: Average two OutOfPlaneBendType instances.
average(PiOrbitalTorsionType, PiOrbitalTorsionType, int[]) - Static method in class ffx.potential.parameters.PiOrbitalTorsionType: Average two PiTorsionType instances.
average(PolarizeType, PolarizeType, int, int[]) - Static method in class ffx.potential.parameters.PolarizeType: Average two PolarizeType instances.
average(StretchBendType, StretchBendType, int[]) - Static method in class ffx.potential.parameters.StretchBendType: Average two StretchBendType instances.
average(StretchTorsionType, StretchTorsionType, int[]) - Static method in class ffx.potential.parameters.StretchTorsionType: Average two StretchTorsionType objects.
average(TorsionTorsionType, TorsionTorsionType, int[]) - Static method in class ffx.potential.parameters.TorsionTorsionType: Average two TorsionTorsionType instances.
average(TorsionType, TorsionType, int[]) - Static method in class ffx.potential.parameters.TorsionType: Average two TorsionTypes.
average(UreyBradleyType, UreyBradleyType, int[]) - Static method in class ffx.potential.parameters.UreyBradleyType: Average two UreyBradleyType objects.
average(VDWPairType, VDWPairType, int[]) - Static method in class ffx.potential.parameters.VDWPairType: Average.
average(VDWType, VDWType, int) - Static method in class ffx.potential.parameters.VDWType: Average two VDWType objects.
AverageFc(MolecularAssembly[], int) - Method in class ffx.xray.DiffractionData: read in a different assembly to average in structure factors
averageFcs(File, File, ReflectionList, int, CompositeConfiguration) - Method in class ffx.xray.parsers.MTZFilter: Average the computed structure factors for two systems.
averageIntegral(double, double) - Static method in class ffx.numerics.integrate.Integration: averageIntegral.
AverageLinkageStrategy - Class in ffx.numerics.clustering: Linkage strategy that uses the arithmetic mean of pairwise distances between cluster members (UPGMA/average linkage).
AverageLinkageStrategy() - Constructor for class ffx.numerics.clustering.AverageLinkageStrategy
AverageMTZ - Class in ffx.xray.commands: Use AverageMTZ to provide two MTZ files and an iteration for a cumulative moving average.
AverageMTZ() - Constructor for class ffx.xray.commands.AverageMTZ: AverageMTZ constructor.
AverageMTZ(FFXBinding) - Constructor for class ffx.xray.commands.AverageMTZ: AverageMTZ constructor.
AverageMTZ(String[]) - Constructor for class ffx.xray.commands.AverageMTZ: AverageMTZ constructor that sets the command line arguments.
averageTensor(double[][], double[][]) - Method in class ffx.crystal.Crystal: averageTensor
averageTensor(double[], double[][]) - Method in class ffx.crystal.Crystal: averageTensor
averageTypes(MultipoleType, MultipoleType, int[]) - Static method in class ffx.potential.parameters.MultipoleType: Average two MultipoleType instances.
AVOGADRO - Static variable in class ffx.algorithms.commands.test.Freefix
AVOGADRO - Static variable in class ffx.utilities.Constants: Avogadro's number, defining the mol.

B

b - Variable in class ffx.crystal.Crystal: Length of the cell edge in the direction of the b basis vector.
B - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
B - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
B - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
b2u(double) - Static method in class ffx.numerics.math.ScalarMath: b2u
Ba - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
backend - Variable in class edu.rit.pj.cluster.JobInfo: Array of backend nodes for each process assigned to the job in rank order.
backend - Variable in class edu.rit.pj.cluster.ProcessInfo: Reference to the job backend process.
BackendClassLoader - Class in edu.rit.pj.cluster: Class BackendClassLoader provides a class loader for a job backend process in the PJ cluster middleware.
BackendClassLoader(JobBackendRef, JobFrontendRef, ResourceCache) - Constructor for class edu.rit.pj.cluster.BackendClassLoader: Construct a new backend class loader.
BackendClassLoader(ClassLoader, JobBackendRef, JobFrontendRef, ResourceCache) - Constructor for class edu.rit.pj.cluster.BackendClassLoader: Construct a new backend class loader.
backendFailed(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobScheduler: Report that a backend node failed.
backendFailed(JobFrontendRef, String) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "backend failed" message.
backendFailed(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Report that a backend node failed.
backendFailed(JobFrontendRef, String) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Report that a backend node failed.
BackendFileInputStream - Class in edu.rit.pj.cluster: Class BackendFileInputStream provides an object in a job backend process that reads a sequential file in the job frontend process.
BackendFileOutputStream - Class in edu.rit.pj.cluster: Class BackendFileOutputStream provides an object in a job backend process that writes a sequential file in the job frontend process.
BackendFileReader - Class in edu.rit.pj.cluster: Class BackendFileReader provides an object that reads sequential files in the job backend process.
BackendFileReader(JobFrontendRef, JobBackendRef) - Constructor for class edu.rit.pj.cluster.BackendFileReader: Construct a new backend file reader.
BackendFileWriter - Class in edu.rit.pj.cluster: Class BackendFileWriter provides an object that writes sequential files in the job backend process.
BackendFileWriter(JobFrontendRef, JobBackendRef) - Constructor for class edu.rit.pj.cluster.BackendFileWriter: Construct a new backend file writer.
backendFinished(JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontend: Report that a backend process has finished executing the job.
backendFinished(JobBackendRef) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "backend finished" message.
backendFinished(JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Report that a backend process has finished executing the job.
backendFinished(JobBackendRef) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Report that a backend process has finished executing the job.
backendFinished(JobBackendRef) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Report that a backend process has finished executing the job.
BackendInfo - Class in edu.rit.pj.cluster: Class BackendInfo provides a record of information about one backend node in the PJ cluster middleware.
BackendInfo(String, int, BackendInfo.State, long, String, String, String, String[], String) - Constructor for class edu.rit.pj.cluster.BackendInfo: Construct a new backend information record.
BackendInfo.State - Enum Class in edu.rit.pj.cluster: The state of a backend node.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in class edu.rit.pj.cluster.JobFrontend: Report that a backend process is ready to commence executing the job.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "backend ready" message.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Report that a backend process is ready to commence executing the job.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Report that a backend process is ready to commence executing the job.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Report that a backend process is ready to commence executing the job.
BACKWARD - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Direction
BACKWARDS - Enum constant in enum class ffx.numerics.estimator.Zwanzig.Directionality: Backwards perturbation.
BadIntpln - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Bad interpolation result.
BALLANDSTICK - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
BAR - Class in ffx.algorithms.commands: The BAR script finds the free energy difference across a lambda window.
BAR - Enum constant in enum class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType
BAR() - Constructor for class ffx.algorithms.commands.BAR: BAR Constructor.
BAR(FFXBinding) - Constructor for class ffx.algorithms.commands.BAR: BAR Constructor.
BAR(String[]) - Constructor for class ffx.algorithms.commands.BAR: BAR constructor that sets the command line arguments.
BARFilter - Class in ffx.potential.parsers: The BARFilter class parses TINKER bar(*.BAR) files.
BARFilter(File) - Constructor for class ffx.potential.parsers.BARFilter: BARFilter constructor
BARFilter(File, double[], double[], double[], double[], double[], double[], double, double) - Constructor for class ffx.potential.parsers.BARFilter: BARFilter constructor
BARFilter(File, int, int) - Constructor for class ffx.potential.parsers.BARFilter: BARFilter constructor
barostat - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Reference to the Barostat in use; if present this must be turned off during optimization.
Barostat - Class in ffx.algorithms.dynamics: The Barostat class maintains constant pressure using random trial moves in lattice parameters, which are consistent with the space group.
Barostat(MolecularAssembly, CrystalPotential) - Constructor for class ffx.algorithms.dynamics.Barostat: Initialize the Barostat.
Barostat(MolecularAssembly, CrystalPotential, double) - Constructor for class ffx.algorithms.dynamics.Barostat: Initialize the Barostat.
barostatOptions - Variable in class ffx.algorithms.commands.Thermodynamics
BarostatOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that use a barostat/NPT.
BarostatOptions() - Constructor for class ffx.algorithms.cli.BarostatOptions
barrier() - Method in class edu.rit.pj.Comm: Cause all processes in this communicator to wait at a barrier.
barrier() - Method in class edu.rit.pj.ParallelRegion: Perform a barrier.
barrier(int) - Method in class edu.rit.pj.Comm: Cause all processes in this communicator to wait at a barrier, using the given message tag.
barrier(BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Perform a barrier, with a barrier action.
BarrierAction - Class in edu.rit.pj: Class BarrierAction is the abstract base class for an object containing code that is executed as part of a barrier wait.
BarrierAction() - Constructor for class edu.rit.pj.BarrierAction: Construct a new barrier action.
baseDir - Variable in class ffx.algorithms.cli.AlgorithmsCommand: The directory in which to place output files.
baseDir - Variable in class ffx.potential.cli.PotentialCommand: A temporary directory that contains script artifacts.
BaseType - Class in ffx.potential.parameters: All force field types should extend the BaseType class.
BaseType(ForceField.ForceFieldType, int[]) - Constructor for class ffx.potential.parameters.BaseType: Public constructor.
BaseType(ForceField.ForceFieldType, String) - Constructor for class ffx.potential.parameters.BaseType: Public constructor.
Be - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
BEEMAN - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
before() - Method in class ffx.ui.ModelingShell: before
beforeClass() - Static method in class ffx.algorithms.misc.AlgorithmsTest: Initialize the PJ communication layer.
beforeClass() - Static method in class ffx.utilities.FFXTest: beforeClass.
beforeTest() - Method in class ffx.algorithms.misc.AlgorithmsTest
beforeTest() - Method in class ffx.potential.utils.PotentialTest
beforeTest() - Method in class ffx.utilities.FFXTest: beforeTest.
beginIfBlock(String) - Method in class ffx.openmm.CustomIntegrator: Begin a new if block.
beginMCOST(MonteCarloOST, DynamicsOptions, ThermodynamicsOptions) - Method in class ffx.algorithms.cli.OSTOptions: Runs MC-OST.
beginMDOST(OrthogonalSpaceTempering, MolecularAssembly[], CrystalPotential, DynamicsOptions, WriteoutOptions, ThermodynamicsOptions, File, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions: Begins MD-OST sampling from an assembled OST.
beginWhileBlock(String) - Method in class ffx.openmm.CustomIntegrator: Begin a new while block.
BellCurveSwitch - Class in ffx.numerics.switching: Implements a bell-shaped switching function by stitching together a pair of MultiplicativeSwitches. f(midpoint - 0.5*width) = 0, f(midpoint) = 1, f(midpoint + 0.5*width) = 0.
BellCurveSwitch() - Constructor for class ffx.numerics.switching.BellCurveSwitch: Construct a bell curve (spliced 5-'th order Hermite splines) of width 1.0, midpoint 0.5.
BellCurveSwitch(double) - Constructor for class ffx.numerics.switching.BellCurveSwitch: Construct a bell curve (spliced 5-'th order Hermite splines) of width 1.0.
BellCurveSwitch(double, double) - Constructor for class ffx.numerics.switching.BellCurveSwitch: Construct a bell curve (spliced 5-'th order Hermite splines).
BennettAcceptanceRatio - Class in ffx.numerics.estimator: The Bennett Acceptance Ratio class implements the Bennett Acceptance Ratio (BAR) statistical estimator, based on the Tinker implementation.
BennettAcceptanceRatio(double[], double[][], double[][], double[][], double[]) - Constructor for class ffx.numerics.estimator.BennettAcceptanceRatio: Constructs a BAR estimator and obtains an initial free energy estimate.
BennettAcceptanceRatio(double[], double[][], double[][], double[][], double[], double) - Constructor for class ffx.numerics.estimator.BennettAcceptanceRatio: Constructs a BAR estimator and obtains an initial free energy estimate.
BennettAcceptanceRatio(double[], double[][], double[][], double[][], double[], double, int) - Constructor for class ffx.numerics.estimator.BennettAcceptanceRatio: Constructs a BAR estimator and obtains an initial free energy estimate.
Berendsen - Class in ffx.algorithms.dynamics.thermostats: Thermostat a molecular dynamics trajectory to an external bath using the Berendsen weak-coupling thermostat.
Berendsen(SystemState, Potential.VARIABLE_TYPE[], double) - Constructor for class ffx.algorithms.dynamics.thermostats.Berendsen: Constructor for Berendsen.
Berendsen(SystemState, Potential.VARIABLE_TYPE[], double, double) - Constructor for class ffx.algorithms.dynamics.thermostats.Berendsen: Constructor for Berendsen.
Berendsen(SystemState, Potential.VARIABLE_TYPE[], double, double, List<Constraint>) - Constructor for class ffx.algorithms.dynamics.thermostats.Berendsen
BERENDSEN - Enum constant in enum class ffx.algorithms.dynamics.thermostats.ThermostatEnum
beta - Variable in class ffx.crystal.Crystal: The interaxial lattice angle between a and c.
BetterBeeman - Class in ffx.algorithms.dynamics.integrators: Integrate Newton's equations of motion using a Beeman multistep recursion formula; the actual coefficients are Brooks' "Better Beeman" values.
BetterBeeman(SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.BetterBeeman: Constructor for BetterBeeman.
BFACTORS - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine B factors only (if anisotropic, refined as such)
BFACTORS_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine B factors and occupancies
Bh - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Bi - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
bin - Variable in class ffx.crystal.HKL: The bin number of this reflection, which is used for resolution dependent R/Rfree.
BINARY - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: The classic binary (0, 1) model.
binding - Variable in class ffx.algorithms.misc.AlgorithmsTest
binding - Variable in class ffx.potential.utils.PotentialTest
binding - Variable in class ffx.utilities.FFXCommand: The Binding that provides variables to this Command.
binomial(long, long) - Static method in class ffx.numerics.math.ScalarMath: binomial
binWidth() - Method in interface ffx.numerics.integrate.DataSet: Separation between points along x; should be uniform.
binWidth() - Method in class ffx.numerics.integrate.DoublesDataSet: Separation between points along x; should be uniform.
binWidth() - Method in class ffx.numerics.integrate.FunctionDataCurve: Separation between points along x; should be uniform.
biochemistry(MolecularAssembly, List<Atom>) - Static method in class ffx.potential.Utilities: This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.
Biotype - Class in ffx.potential.commands: Print out Biotype records for the atoms in an XYZ file.
Biotype() - Constructor for class ffx.potential.commands.Biotype
Biotype(FFXBinding) - Constructor for class ffx.potential.commands.Biotype
Biotype(String[]) - Constructor for class ffx.potential.commands.Biotype
BioType - Class in ffx.potential.parameters: The BioType class maps PDB identifiers to atom types.
BioType(int, String, String, int, String[]) - Constructor for class ffx.potential.parameters.BioType: BioType Constructor.
BIOTYPE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
BISECTOR - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
Bk - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
BLACK - Static variable in class ffx.potential.bonded.RendererCache: Constant BLACK
BLOCK_LOOP - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
BLOCK_LOOP_128 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
BLOCK_LOOP_256 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
BLOCK_LOOP_512 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
blocked(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor5: Handle factors of 5.
BLOCKED - Enum constant in enum class ffx.numerics.fft.DataLayout1D: Blocked data layout.
BLOCKED_X - Enum constant in enum class ffx.numerics.fft.DataLayout2D: Blocked data layout with im = nX.
BLOCKED_X - Enum constant in enum class ffx.numerics.fft.DataLayout3D: Blocked data layout with im = nX.
BLOCKED_XY - Enum constant in enum class ffx.numerics.fft.DataLayout2D: Blocked data layout with im >= nX*nY.
BLOCKED_XY - Enum constant in enum class ffx.numerics.fft.DataLayout3D: Blocked data layout with im = nX*nY.
BLOCKED_XYZ - Enum constant in enum class ffx.numerics.fft.DataLayout3D: Blocked data layout with im = nX*nY*nZ.
BMP - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
bn - Variable in class ffx.numerics.multipole.GKSource: Chain rule terms from differentiating zeroth order born radii auxiliary functions (bn0) with respect to Ai or Aj.
bn - Variable in class ffx.numerics.multipole.GKSourceSIMD: Chain rule terms from differentiating zeroth order born radii auxiliary functions (bn0) with respect to Ai or Aj.
bn(int) - Method in class ffx.numerics.multipole.GKSource: Compute the function b, which are chain rule terms from differentiating zeroth order auxiliary functions (an0) with respect to Ai or Aj.
bn(int) - Method in class ffx.numerics.multipole.GKSourceSIMD: Compute the function b, which are chain rule terms from differentiating zeroth order auxiliary functions (an0) with respect to Ai or Aj.
BOHR - Static variable in class ffx.utilities.Constants: Conversion from Bohr to Angstroms.
BOHR2 - Static variable in class ffx.utilities.Constants: Conversion from Bohr^2 to Angstroms^2.
BOLTZMANN_SI - Static variable in class ffx.utilities.Constants: Boltzmann's constant in J/K, defining the Kelvin.
BoltzmannMC - Class in ffx.algorithms.mc: The BoltzmannMC abstract class is a skeleton for Boltzmann-weighted Metropolis Monte Carlo simulations.
BoltzmannMC() - Constructor for class ffx.algorithms.mc.BoltzmannMC
Bond - Class in ffx.potential.bonded: The Bond class represents a covalent bond formed between two atoms.
Bond(Atom, Atom) - Constructor for class ffx.potential.bonded.Bond: Bond constructor.
Bond(String) - Constructor for class ffx.potential.bonded.Bond: Simple Bond constructor that is intended to be used with the equals method.
BOND - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
bond0Eq - Variable in class ffx.potential.bonded.StretchBend: First equilibrium bond distance.
bond1Eq - Variable in class ffx.potential.bonded.StretchBend: Second equilibrium bond distance.
bondAngle(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the angle formed by three atoms.
bondAngle(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the angle formed by three atoms
BondArray - Class in ffx.openmm: Bonds are specified by pairs of integers (the atom indices).
BondArray(int) - Constructor for class ffx.openmm.BondArray: Create a new bond array.
bondAtoms(Atom[], double) - Static method in class ffx.potential.parsers.CIFFilter: Add bonds between atoms.
BondedEnergy - Interface in ffx.potential.bonded: The BondedEnergy interface.
BondedTerm - Class in ffx.potential.bonded: The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).
BondedTerm() - Constructor for class ffx.potential.bonded.BondedTerm: Default Constructor
BondedTerm(String) - Constructor for class ffx.potential.bonded.BondedTerm: Constructor which sets the Term's id.
BondedTerm.BondedComparator - Class in ffx.potential.bonded
BondedUtils - Class in ffx.potential.bonded: Utilities for placing atoms.
BondedUtils() - Constructor for class ffx.potential.bonded.BondedUtils
BondedUtils.MissingAtomTypeException - Exception Class in ffx.potential.bonded: This exception is thrown when an atom type could not be assigned.
BondedUtils.MissingHeavyAtomException - Exception Class in ffx.potential.bonded: This exception is thrown when a heavy atom is not found.
bondForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom Bond Force
BondForce - Class in ffx.potential.openmm: Bond Force.
BondForce(BondPotentialEnergy) - Constructor for class ffx.potential.openmm.BondForce: Bond Force constructor.
BondForce(BondPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.BondForce: Bond Force constructor.
bondForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Bond Force for topology 2.
bondFunction - Variable in class ffx.potential.parameters.BondType: The function used by the bond: harmonic or quartic with flat-bottom variants.
bondList - Variable in class ffx.potential.parsers.SystemFilter: The bondList may be filled by the filters that extend SystemFilter.
BondPotentialEnergy - Class in ffx.potential.terms: Bond potential energy term using Bond instances.
BondPotentialEnergy(String) - Constructor for class ffx.potential.terms.BondPotentialEnergy: Create a BondPotentialEnergy with the provided name.
BondPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.BondPotentialEnergy: Create a BondPotentialEnergy with the provided name and force group.
BondPotentialEnergy(String, int, List<Bond>) - Constructor for class ffx.potential.terms.BondPotentialEnergy: Create a BondPotentialEnergy initialized with a list of bonds and force group.
BondPotentialEnergy(String, Collection<Bond>) - Constructor for class ffx.potential.terms.BondPotentialEnergy: Create a BondPotentialEnergy initialized with a collection of bonds.
bonds - Variable in class ffx.potential.bonded.BondedTerm: Bonds that are used to form this term.
bonds - Variable in class ffx.potential.parameters.BioType: Bonds are required to listed atom names.
bondTime - Static variable in class ffx.potential.bonded.MSGroup: Constant bondTime=0
bondType - Variable in class ffx.potential.bonded.Bond: The force field BondType for this bond.
bondType - Variable in class ffx.potential.bonded.RestrainDistance
BondType - Class in ffx.potential.parameters: The BondType class defines one harmonic bond stretch energy term.
BondType(int[], double, double) - Constructor for class ffx.potential.parameters.BondType: The default BondType constructor defines use of the Quartic BondFunction.
BondType(int[], double, double, BondType.BondFunction) - Constructor for class ffx.potential.parameters.BondType: BondType constructor.
BondType(int[], double, double, BondType.BondFunction, double) - Constructor for class ffx.potential.parameters.BondType: BondType constructor.
BondType.BondFunction - Enum Class in ffx.potential.parameters: Describes the function used by the bond.
bondType1 - Variable in class ffx.potential.bonded.StretchTorsion: First bond force field type.
bondType2 - Variable in class ffx.potential.bonded.StretchTorsion: Second bond force field type.
bondType3 - Variable in class ffx.potential.bonded.StretchTorsion: Third bond force field type.
bondUnit - Variable in class ffx.potential.parameters.BondType: Convert bond stretch energy to kcal/mole.
bondwidth - Static variable in class ffx.potential.bonded.RendererCache: Constant bondwidth=3
BOOLE - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType: Boole's Five Point Integration, requiring 5 points.
BooleanArrayBuf - Class in edu.rit.mp.buf: Class BooleanArrayBuf provides a buffer for an array of Boolean items sent or received using the Message Protocol (MP).
BooleanArrayBuf(boolean[], Range) - Constructor for class edu.rit.mp.buf.BooleanArrayBuf: Construct a new Boolean array buffer.
BooleanArrayBuf_1 - Class in edu.rit.mp.buf: Class BooleanArrayBuf_1 provides a buffer for an array of Boolean items sent or received using the Message Protocol (MP).
BooleanArrayBuf_1(boolean[], Range) - Constructor for class edu.rit.mp.buf.BooleanArrayBuf_1: Construct a new Boolean array buffer.
BooleanBuf - Class in edu.rit.mp: Class BooleanBuf is the abstract base class for a buffer of Boolean items sent or received using the Message Protocol (MP).
BooleanBuf(int) - Constructor for class edu.rit.mp.BooleanBuf: Construct a new Boolean buffer.
BooleanItemBuf - Class in edu.rit.mp.buf: Class BooleanItemBuf provides a buffer for a single Boolean item sent or received using the Message Protocol (MP).
BooleanItemBuf() - Constructor for class edu.rit.mp.buf.BooleanItemBuf: Construct a new Boolean item buffer.
BooleanItemBuf(boolean) - Constructor for class edu.rit.mp.buf.BooleanItemBuf: Construct a new Boolean item buffer with the given initial value.
BooleanMatrixBuf - Class in edu.rit.mp.buf: Class BooleanMatrixBuf provides a buffer for a matrix of Boolean items sent or received using the Message Protocol (MP).
BooleanMatrixBuf(boolean[][], Range, Range) - Constructor for class edu.rit.mp.buf.BooleanMatrixBuf: Construct a new Boolean matrix buffer.
BooleanMatrixBuf_1 - Class in edu.rit.mp.buf: Class BooleanMatrixBuf_1 provides a buffer for a matrix of Boolean items sent or received using the Message Protocol (MP).
BooleanMatrixBuf_1(boolean[][], Range, Range) - Constructor for class edu.rit.mp.buf.BooleanMatrixBuf_1: Construct a new Boolean matrix buffer.
BooleanOp - Class in edu.rit.pj.reduction: Class BooleanOp is the abstract base class for a binary operation on Boolean values, used to do reduction in a parallel program.
BooleanOp() - Constructor for class edu.rit.pj.reduction.BooleanOp: Construct a new Boolean binary operation.
booles(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using Boole's rule.
booles(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using Boole's rule.
boolesParallel(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using Boole's rule.
boolesParallel(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using Boole's rule.
bootstrap(long) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Perform bootstrap analysis.
bootstrap(long, long) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Perform bootstrap analysis.
BootstrappableEstimator - Interface in ffx.numerics.estimator: The BootstrappableEstimator interface describes a StatisticalEstimator which can use bootstrap sampling as an additional method of calculating free energy and uncertainty.
BootStrapStatistics - Class in ffx.numerics.math: The BootStrapStatistics class uses bootstrapping to estimate statistics from a given population.
BootStrapStatistics(double[]) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], double[], int, int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int, int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
border - Static variable in class ffx.ui.MainPanel: Constant
BORN - Enum constant in enum class ffx.numerics.multipole.GKTensorMode: The tensor is for the GK Born-chain rule.
BORN_CAV_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
BORN_SOLV - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
BornGradRegion - Class in ffx.potential.nonbonded.implicit: Parallel computation of Born radii chain rule terms via the Grycuk method.
BornGradRegion(int, boolean, boolean, boolean) - Constructor for class ffx.potential.nonbonded.implicit.BornGradRegion: Compute the gradient due to changes in Born radii.
BornRadiiRegion - Class in ffx.potential.nonbonded.implicit: Parallel computation of Born radii via the Grycuk method.
BornRadiiRegion(int, int, ForceField, boolean, boolean, boolean) - Constructor for class ffx.potential.nonbonded.implicit.BornRadiiRegion: BornRadiiRegion Constructor.
bornRadiiTotal - Variable in class ffx.potential.nonbonded.pme.PMETimings
BornTanhRescaling - Class in ffx.potential.nonbonded.implicit: Rescale the Born radius integral to account for interstitial spaces.
BornTanhRescaling() - Constructor for class ffx.potential.nonbonded.implicit.BornTanhRescaling
BOTH - Enum constant in enum class ffx.numerics.Potential.STATE: Include both FAST and SLOW varying energy terms.
BOX - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
Br - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
BR - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
broadcast(int, int, Buf) - Method in class edu.rit.pj.Comm: Broadcast a message to all processes in this communicator using the given message tag.
broadcast(int, Buf) - Method in class edu.rit.pj.Comm: Broadcast a message to all processes in this communicator.
broadcastPattern(int, int, int) - Static method in class edu.rit.pj.cluster.CommPattern: Calculate the communication pattern for a parallel broadcast tree.
BrownianIntegrator - Class in ffx.openmm: This is an Integrator which simulates a System using Brownian dynamics.
BrownianIntegrator(double, double, double) - Constructor for class ffx.openmm.BrownianIntegrator: Create a BrownianIntegrator.
BRUTE_FORCE - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
bSpline(double, int, double[]) - Static method in class ffx.numerics.spline.UniformBSpline: Generate uniform b-Spline coefficients.
bSplineDerivatives(double, int, int, double[][], double[][]) - Static method in class ffx.numerics.spline.UniformBSpline: Generate uniform b-Spline coefficients and their derivatives.
Buf - Class in edu.rit.mp: Class Buf is the abstract base class for a buffer of items sent or received using the Message Protocol (MP).
buff - Variable in class ffx.potential.nonbonded.NonbondedCutoff: A buffer added to the cut-off distance off to define neighbors included when collecting Verlet lists.
buff - Variable in class ffx.potential.nonbonded.RowRegion
buff - Variable in class ffx.potential.nonbonded.SliceRegion
buffer() - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for a Boolean item.
buffer() - Static method in class edu.rit.mp.ByteBuf: Create a buffer for a byte item.
buffer() - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for a character item.
buffer() - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for a double item.
buffer() - Static method in class edu.rit.mp.FloatBuf: Create a buffer for a float item.
buffer() - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.LongBuf: Create a buffer for a long item.
buffer() - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for an object item.
buffer() - Static method in class edu.rit.mp.ShortBuf: Create a buffer for a short item.
buffer() - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for an integer item.
buffer(boolean) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for a Boolean item with the given initial value.
buffer(boolean[]) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for the entire given Boolean array.
buffer(boolean[][]) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for the entire given Boolean matrix.
buffer(byte) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for a byte item with the given initial value.
buffer(byte[]) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for the entire given byte array.
buffer(byte[][]) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for the entire given byte matrix.
buffer(char) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for a character item with the given initial value.
buffer(char[]) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for the entire given character array.
buffer(char[][]) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for the entire given character matrix.
buffer(double) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for a double item with the given initial value.
buffer(double[]) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for the entire given double array.
buffer(double[][]) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for the entire given double matrix.
buffer(float) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for a float item with the given initial value.
buffer(float[]) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for the entire given float array.
buffer(float[][]) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for the entire given float matrix.
buffer(int) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for an integer item with the given initial value.
buffer(int[]) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for the entire given integer array.
buffer(int[][]) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for the entire given integer matrix.
buffer(long) - Static method in class edu.rit.mp.LongBuf: Create a buffer for a long item with the given initial value.
buffer(long[]) - Static method in class edu.rit.mp.LongBuf: Create a buffer for the entire given long array.
buffer(long[][]) - Static method in class edu.rit.mp.LongBuf: Create a buffer for the entire given long matrix.
buffer(short) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for a short item with the given initial value.
buffer(short[]) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for the entire given short array.
buffer(short[][]) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for the entire given short matrix.
buffer(SharedBoolean) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for a shared Boolean item.
buffer(SharedBooleanArray) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for the entire given shared Boolean array.
buffer(SharedByte) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for a shared byte item.
buffer(SharedByteArray) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for the entire given shared byte array.
buffer(SharedCharacter) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for a shared character item.
buffer(SharedCharacterArray) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for the entire given shared character array.
buffer(SharedDouble) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for a shared double item.
buffer(SharedDoubleArray) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for the entire given shared double array.
buffer(SharedFloat) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for a shared float item.
buffer(SharedFloatArray) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for the entire given shared float array.
buffer(SharedInteger) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for a shared integer item.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for the entire given shared integer array.
buffer(SharedLong) - Static method in class edu.rit.mp.LongBuf: Create a buffer for a shared long item.
buffer(SharedLongArray) - Static method in class edu.rit.mp.LongBuf: Create a buffer for the entire given shared long array.
buffer(SharedObject<T>) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for a shared object item.
buffer(SharedObjectArray<T>) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for the entire given shared object array.
buffer(SharedShort) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for a shared short item.
buffer(SharedShortArray) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for the entire given shared short array.
buffer(T) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for an object item with the given initial value.
buffer(T[]) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for the entire given object array.
buffer(T[][]) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for the entire given object matrix.
BUFFERED_14_7 - Enum constant in enum class ffx.potential.parameters.VDWType.VDW_TYPE
build(double[]) - Method in class ffx.numerics.quickhull.QuickHull3D: Constructs the convex hull of a set of points whose coordinates are given by an array of doubles.
build(double[], int) - Method in class ffx.numerics.quickhull.QuickHull3D: Constructs the convex hull of a set of points whose coordinates are given by an array of doubles.
build(Point3d[]) - Method in class ffx.numerics.quickhull.QuickHull3D: Constructs the convex hull of a set of points.
build(Point3d[], int) - Method in class ffx.numerics.quickhull.QuickHull3D: Constructs the convex hull of a set of points.
buildAIB(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildAIB.
buildAlanine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildAlanine.
buildArginine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildArginine.
buildAsparagine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildAsparagine.
buildAspartate(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildAspartate.
buildBond(Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.BondedUtils: Build a bond between two atoms.
buildCysteine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildCysteine.
buildCystine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildCystine.
buildDeprotonatedCysteine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildDeprotonatedCysteine.
buildDeprotonatedLysine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildDeprotonatedLysine.
buildDeprotonatedTyrosine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildDeprotonatedTyrosine.
buildDisulfideBonds(List<Bond>, MolecularAssembly, List<Bond>) - Static method in class ffx.potential.bonded.PolymerUtils: Assign parameters to disulfide bonds.
buildGlutamate(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildGlutamate.
buildGlutamine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildGlutamine.
buildGlycine(Residue, Atom, Atom, Atom, AminoAcidUtils.ResiduePosition, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildGlycine.
buildH(MSGroup, AminoAcidUtils.SideChainType, Atom, double, Atom, double, Atom, double, int, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.BondedUtils: Build a hydrogen atom.
buildH(MSGroup, String, Atom, double, Atom, double, Atom, double, int, int, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.BondedUtils: Build a hydrogen atom.
buildHeavy(MSGroup, AminoAcidUtils.SideChainType, Atom, double, Atom, double, Atom, double, int, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.BondedUtils: Build a heavy atom.
buildHeavy(MSGroup, String, Atom, double, Atom, double, Atom, double, int, int, ForceField) - Static method in class ffx.potential.bonded.BondedUtils: Build a heavy atom.
buildHeavy(MSGroup, String, Atom, double, Atom, double, Atom, double, int, int, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.BondedUtils: Build a heavy atom.
buildHeavy(MSGroup, String, Atom, int, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.BondedUtils: Build a heavy atom.
buildHistidine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildHistidine.
buildHull() - Method in class ffx.numerics.quickhull.QuickHull3D: Builds the full convex hull by repeatedly selecting and adding extreme points until no outside points remain; then reindexes faces and vertices.
buildHydrogenAtom(MSGroup, String, Atom, double, Atom, double, Atom, double, int, AtomType, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.BondedUtils: Build a hydrogen atom.
buildIsoleucine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildIsoleucine.
buildLeucine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildLeucine.
buildList(double[][][], boolean[][], boolean) - Method in class ffx.xray.BulkSolventList: This method can be called as necessary to build/rebuild the neighbor lists.
buildList(double[][], int[][][], boolean[], boolean, boolean) - Method in class ffx.potential.nonbonded.NeighborList: This method can be called as necessary to build/rebuild the neighbor lists.
buildListA - Variable in class ffx.potential.nonbonded.RowLoop
buildListA - Variable in class ffx.potential.nonbonded.SliceLoop
buildListS - Variable in class ffx.potential.nonbonded.RowLoop
buildListS - Variable in class ffx.potential.nonbonded.SliceLoop
buildLysine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildLysine.
buildMethionine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildMethionine.
buildMissingResidues(int, MolecularAssembly, Map<Character, String[]>, Map<Character, int[]>) - Static method in class ffx.potential.bonded.PolymerUtils: Currently builds missing internal loops based on information in DBREF and SEQRES records.
buildNeutralAsparticAcid(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildNeutralAsparticAcid.
buildNeutralGlutamicAcid(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildNeutralGlutamicAcid.
buildNeutralHistidineD(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildNeutralHistidineD.
buildNeutralHistidineE(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildNeutralHistidineE.
buildOrnithine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildOrnithine.
buildPCA(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildPCA.
buildPhenylalanine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildPhenylalanine.
buildProline(Residue, Atom, Atom, Atom, AminoAcidUtils.ResiduePosition, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildProline.
buildSerine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildSerine.
buildThreonine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildThreonine.
buildTree(OctreeCell) - Method in class ffx.potential.nonbonded.octree.Octree: Build the tree.
buildTryptophan(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildTryptophan.
buildTwoProtonAsparticAcid(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildTwoProtonAsparticAcid.
buildTwoProtonGlutamicAcid(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildTwoProtonGlutamicAcid.
buildTyrosine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildTyrosine.
buildValine(Residue, Atom, Atom, Atom, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: buildValine.
buildWorker(int, int) - Method in class ffx.algorithms.optimize.TorsionSearch: Builds the worker assignments for each rank.
BulkSolventDensityRegion - Class in ffx.xray: This class implements a spatial decomposition based on partitioning a grid into octants.
BulkSolventDensityRegion(int, int, int, double[], int, int, int, int, Crystal, Atom[], double[][][], double, ParallelTeam) - Constructor for class ffx.xray.BulkSolventDensityRegion: Constructor for BulkSolventDensityRegion.
BulkSolventList - Class in ffx.xray: The BulkSolventList class builds a list of atoms in symmetry mates that are within a cutoff distance of an atom in the asymmetric unit.
BulkSolventList(Crystal, Atom[], double, ParallelTeam) - Constructor for class ffx.xray.BulkSolventList: Constructor for the NeighborList class.
BulkSolventRowRegion - Class in ffx.xray: BulkSolventRowRegion class.
BulkSolventRowRegion(int, int, int, double[], int, int, Crystal, Atom[], double[][][], double, ParallelTeam) - Constructor for class ffx.xray.BulkSolventRowRegion: Constructor for BulkSolventDensityRegion.
BulkSolventSliceRegion - Class in ffx.xray: This class implements a spatial decomposition based on partitioning a grid into octants.
BulkSolventSliceRegion(int, int, int, double[], int, int, Crystal, Atom[], double[][][], double, ParallelTeam) - Constructor for class ffx.xray.BulkSolventSliceRegion: Constructor for BulkSolventDensityRegion.
Bussi - Class in ffx.algorithms.dynamics.thermostats: Thermostat a molecular dynamics trajectory to an external bath using the Bussi, Donadio, and Parrinello method.
Bussi(SystemState, Potential.VARIABLE_TYPE[], double) - Constructor for class ffx.algorithms.dynamics.thermostats.Bussi: Constructor for Bussi.
Bussi(SystemState, Potential.VARIABLE_TYPE[], double, double) - Constructor for class ffx.algorithms.dynamics.thermostats.Bussi: Constructor for Bussi.
Bussi(SystemState, Potential.VARIABLE_TYPE[], double, double, List<Constraint>) - Constructor for class ffx.algorithms.dynamics.thermostats.Bussi
BUSSI - Enum constant in enum class ffx.algorithms.dynamics.thermostats.ThermostatEnum
buttonPress - Variable in class ffx.ui.behaviors.MouseBehavior
buttonPress - Variable in class ffx.ui.behaviors.PickMouseBehavior
Byte() - Constructor for class edu.rit.util.Searching.Byte
Byte() - Constructor for class edu.rit.util.Sorting.Byte
ByteArrayBuf - Class in edu.rit.mp.buf: Class ByteArrayBuf provides a buffer for an array of byte items sent or received using the Message Protocol (MP).
ByteArrayBuf(byte[], Range) - Constructor for class edu.rit.mp.buf.ByteArrayBuf: Construct a new byte array buffer.
ByteArrayBuf_1 - Class in edu.rit.mp.buf: Class ByteArrayBuf_1 provides a buffer for an array of byte items sent or received using the Message Protocol (MP).
ByteArrayBuf_1(byte[], Range) - Constructor for class edu.rit.mp.buf.ByteArrayBuf_1: Construct a new byte array buffer.
ByteBuf - Class in edu.rit.mp: Class ByteBuf is the abstract base class for a buffer of byte items sent or received using the Message Protocol (MP).
ByteBuf(int) - Constructor for class edu.rit.mp.ByteBuf: Construct a new byte buffer.
ByteItemBuf - Class in edu.rit.mp.buf: Class ByteItemBuf provides a buffer for a single byte item sent or received using the Message Protocol (MP).
ByteItemBuf() - Constructor for class edu.rit.mp.buf.ByteItemBuf: Construct a new byte item buffer.
ByteItemBuf(byte) - Constructor for class edu.rit.mp.buf.ByteItemBuf: Construct a new byte item buffer with the given initial value.
ByteMatrixBuf - Class in edu.rit.mp.buf: Class ByteMatrixBuf provides a buffer for a matrix of byte items sent or received using the Message Protocol (MP).
ByteMatrixBuf(byte[][], Range, Range) - Constructor for class edu.rit.mp.buf.ByteMatrixBuf: Construct a new byte matrix buffer.
ByteMatrixBuf_1 - Class in edu.rit.mp.buf: Class ByteMatrixBuf_1 provides a buffer for a matrix of byte items sent or received using the Message Protocol (MP).
ByteMatrixBuf_1(byte[][], Range, Range) - Constructor for class edu.rit.mp.buf.ByteMatrixBuf_1: Construct a new byte matrix buffer.
ByteOp - Class in edu.rit.pj.reduction: Class ByteOp is the abstract base class for a binary operation on byte values, used to do reduction in a parallel program.
ByteOp() - Constructor for class edu.rit.pj.reduction.ByteOp: Construct a new byte binary operation.
ByteSequence - Class in edu.rit.util: Class ByteSequence provides an abstraction for a sequence of bytes.
ByteSequence(byte[]) - Constructor for class edu.rit.util.ByteSequence: Construct a new byte sequence whose contents are a copy of the given byte array.
ByteSequence(byte[], int, int) - Constructor for class edu.rit.util.ByteSequence: Construct a new byte sequence whose contents are a copy of a portion of the given byte array.
ByteSequence(ByteSequence) - Constructor for class edu.rit.util.ByteSequence: Construct a new byte sequence whose contents are a copy of the given byte sequence.
ByteSequence(InputStream) - Constructor for class edu.rit.util.ByteSequence: Construct a new byte sequence whose contents come from the given input stream.
ByteSwap - Class in ffx.utilities: ByteSwap class.

C

c - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
c - Variable in class ffx.crystal.Crystal: Length of the cell edge in the direction of the c basis vector.
C - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
C - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
C - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
C - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms
C - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
C - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
C2_ENDO - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker
C3_ENDO - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker
C3_EXO - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker
Ca - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
CA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
CA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms
CA - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
CA2 - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
CABANI - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
calcDRMSD(double[], double[], int) - Static method in class ffx.potential.utils.Superpose: Calculates the dRMSD between to sets of coordinates.
calcT1(double, double) - Method in class ffx.potential.utils.LoopClosure: Calculate T1.
calcT2(double) - Method in class ffx.potential.utils.LoopClosure: Calculate T2.
calculateDegreesOfFreedom() - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Calculate the number of degrees of freedom.
calculateDegreesOfFreedom() - Method in class ffx.potential.openmm.OpenMMSystem: Calculate the number of degrees of freedom.
calculateDistance(Collection<Distance>) - Method in class ffx.numerics.clustering.AverageLinkageStrategy: Computes the average of the provided distances.
calculateDistance(Collection<Distance>) - Method in class ffx.numerics.clustering.CompleteLinkageStrategy: Computes the complete-linkage distance, i.e., the maximum of provided distances.
calculateDistance(Collection<Distance>) - Method in interface ffx.numerics.clustering.LinkageStrategy: Computes the linkage distance between two clusters from a collection of pairwise distances between their members (and possibly weights).
calculateDistance(Collection<Distance>) - Method in class ffx.numerics.clustering.SingleLinkageStrategy: Computes the single-linkage distance, i.e., the minimum of provided distances.
calculateDistance(Collection<Distance>) - Method in class ffx.numerics.clustering.WeightedLinkageStrategy: Computes a weighted average of provided distances using their weights.
calculateHorizon(Point3d, HalfEdge, Face, Vector<HalfEdge>) - Method in class ffx.numerics.quickhull.QuickHull3D: Recursively computes the horizon (boundary) edges visible from a given eye point, marking visited faces deleted and collecting the bordering edges.
calculateLikelihoodFree() - Method in class ffx.xray.SigmaAMinimize: calculateLikelihoodFree
calculateRMSDs(int[], boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ffx.potential.utils.Superpose: This method calculates the all versus all RMSD of a multiple model pdb/arc file.
calculateRotation(double[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: Calculate a rotation to minimize RMS distance between two sets of atoms using quaternions, overlapping x2 on x1.
calculateTorsion() - Method in class ffx.potential.parsers.PDBFilter.Mutation
calculateTranslation(double[], double[]) - Static method in class ffx.potential.utils.Superpose: Calculate a translation vector [dx,dy,dz] to move the center of mass to the origin.
cancelJob(JobBackendRef, String) - Method in class edu.rit.pj.cluster.JobFrontend: Cancel the job.
cancelJob(JobBackendRef, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "cancel job" message.
cancelJob(JobBackendRef, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Cancel the job.
cancelJob(JobBackendRef, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Cancel the job.
cancelJob(JobBackendRef, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Cancel the job.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobBackend: Cancel the job.
cancelJob(JobFrontendRef, String) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "cancel job" message.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobBackendProxy: Cancel the job.
cancelJob(JobFrontendRef, String) - Method in interface edu.rit.pj.cluster.JobBackendRef: Cancel the job.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobScheduler: Cancel a job.
cancelJob(JobFrontendRef, String) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "cancel job" message.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Cancel a job.
cancelJob(JobFrontendRef, String) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Cancel a job.
cancelJob(JobSchedulerRef, String) - Method in class edu.rit.pj.cluster.JobFrontend: Cancel the job.
cancelJob(JobSchedulerRef, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "cancel job" message.
cancelJob(JobSchedulerRef, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Cancel the job.
cancelJob(JobSchedulerRef, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Cancel the job.
cancelJob(JobSchedulerRef, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Cancel the job.
Cart2Frac - Class in ffx.potential.commands: Convert from Cartesian to fractional coordinates.
Cart2Frac() - Constructor for class ffx.potential.commands.Cart2Frac
Cart2Frac(FFXBinding) - Constructor for class ffx.potential.commands.Cart2Frac
Cart2Frac(String[]) - Constructor for class ffx.potential.commands.Cart2Frac
cartToFracInducedDipole(double[], double[], double[], double[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: cartToFracInducedDipoles
CAV - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
CAV_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ALA
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYS
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYX
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.SER
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
CB - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
CB - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
CB - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CB1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
CB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
cbmcStep() - Method in class ffx.algorithms.mc.RosenbluthCBMC: cbmcStep.
CcmaConstraint - Class in ffx.potential.constraint
ccmaFactory(List<Bond>, List<Angle>, Atom[], double[], double) - Static method in class ffx.potential.constraint.CcmaConstraint: Constructs a set of bond length Constraints to be satisfied using the Constaint Constraint Matrix Approximation, a parallelizable stable numeric method.
CCP4MapFilter - Class in ffx.realspace.parsers: CCP4MapFilter class.
CCP4MapFilter() - Constructor for class ffx.realspace.parsers.CCP4MapFilter
CCP4MapWriter - Class in ffx.xray.parsers: CCP4MapWriter class.
CCP4MapWriter(int, int, int, int, int, int, int, int, int, Crystal, String) - Constructor for class ffx.xray.parsers.CCP4MapWriter: Constructor for CCP4MapWriter.
CCP4MapWriter(int, int, int, Crystal, String) - Constructor for class ffx.xray.parsers.CCP4MapWriter: construct mapwriter object
Cd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
CD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CD2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
Ce - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
CE - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CE1 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CE3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
Cell(int, int, int) - Constructor for class ffx.potential.nonbonded.NeighborList.Cell
center() - Method in class ffx.potential.MolecularAssembly: center
center() - Method in class ffx.ui.GraphicsAxis: center
centerAt(double[]) - Method in class ffx.potential.MolecularAssembly: centerAt
centerOfMassMotion(boolean, boolean) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Compute the center of mass, linear momentum and angular momentum.
centerView(boolean, boolean) - Method in class ffx.potential.MolecularAssembly: centerView
centerView(boolean, boolean) - Method in class ffx.ui.behaviors.GlobalBehavior: centerView
centric() - Method in class ffx.crystal.HKL: Is this reflection centric?
Cf - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CG - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
CG - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
CG - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CG1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CG1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
CG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
CG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
CH2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CHAIN_IDS - Static variable in class ffx.potential.bonded.Polymer
ChainBreaks - Class in ffx.potential.commands: Fix chain breaks in a PDB file.
ChainBreaks() - Constructor for class ffx.potential.commands.ChainBreaks
ChainBreaks(FFXBinding) - Constructor for class ffx.potential.commands.ChainBreaks
ChainBreaks(String[]) - Constructor for class ffx.potential.commands.ChainBreaks
ChandlerCavitation - Class in ffx.potential.nonbonded.implicit: The ChandlerCavitation class smoothly switches between a volume based dependence for small solutes to a surface area dependence for large solutes.
ChandlerCavitation(Atom[], ConnollyRegion, ForceField) - Constructor for class ffx.potential.nonbonded.implicit.ChandlerCavitation
ChandlerCavitation(Atom[], GaussVol, ForceField) - Constructor for class ffx.potential.nonbonded.implicit.ChandlerCavitation
changedUpdate(DocumentEvent) - Method in class ffx.ui.KeywordComponent
changeUnitCellParameters(double, double, double, double, double, double) - Method in class ffx.crystal.Crystal: This method should be called to update the unit cell parameters of a crystal.
changeUnitCellParameters(double, double, double, double, double, double) - Method in class ffx.crystal.NCSCrystal: Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
changeUnitCellParameters(double, double, double, double, double, double) - Method in class ffx.crystal.ReplicatesCrystal: Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
changeUnitCellParametersAndVolume(double, double, double, double, double, double, double) - Method in class ffx.crystal.Crystal: This method should be called to update the unit cell parameters of a crystal.
changeUnitCellParametersAndVolume(double, double, double, double, double, double, double) - Method in class ffx.crystal.ReplicatesCrystal: Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
channel - Variable in class edu.rit.mp.Status: The channel from which the message was received.
Channel - Class in edu.rit.mp: Class Channel provides a channel for sending and receiving messages in the Message Protocol (MP).
ChannelClosedException - Exception Class in edu.rit.mp: Class ChannelClosedException is thrown to indicate that an I/O operation failed because the channel was closed.
ChannelClosedException() - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with no detail message and no cause.
ChannelClosedException(String) - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with the given detail message and no cause.
ChannelClosedException(String, Throwable) - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with the given detail message and the given cause.
ChannelClosedException(Throwable) - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with no detail message and the given cause.
ChannelGroup - Class in edu.rit.mp: Class ChannelGroup provides a group of Channels for sending and receiving messages in the Message Protocol (MP).
ChannelGroup() - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(Logger) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(InetSocketAddress) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(InetSocketAddress, Logger) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(ServerSocketChannel) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(ServerSocketChannel, Logger) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroupClosedException - Exception Class in edu.rit.mp: Class ChannelGroupClosedException is thrown to indicate that an I/O operation failed because the channel group was closed.
ChannelGroupClosedException() - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with no detail message and no cause.
ChannelGroupClosedException(String) - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with the given detail message and no cause.
ChannelGroupClosedException(String, Throwable) - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with the given detail message and the given cause.
ChannelGroupClosedException(Throwable) - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with no detail message and the given cause.
Character() - Constructor for class edu.rit.util.Searching.Character
Character() - Constructor for class edu.rit.util.Sorting.Character
CharacterArrayBuf - Class in edu.rit.mp.buf: Class CharacterArrayBuf provides a buffer for an array of character items sent or received using the Message Protocol (MP).
CharacterArrayBuf(char[], Range) - Constructor for class edu.rit.mp.buf.CharacterArrayBuf: Construct a new character array buffer.
CharacterArrayBuf_1 - Class in edu.rit.mp.buf: Class CharacterArrayBuf_1 provides a buffer for an array of character items sent or received using the Message Protocol (MP).
CharacterArrayBuf_1(char[], Range) - Constructor for class edu.rit.mp.buf.CharacterArrayBuf_1: Construct a new character array buffer.
CharacterBuf - Class in edu.rit.mp: Class CharacterBuf is the abstract base class for a buffer of character items sent or received using the Message Protocol (MP).
CharacterBuf(int) - Constructor for class edu.rit.mp.CharacterBuf: Construct a new character buffer.
CharacterItemBuf - Class in edu.rit.mp.buf: Class CharacterItemBuf provides a buffer for a single character item sent or received using the Message Protocol (MP).
CharacterItemBuf() - Constructor for class edu.rit.mp.buf.CharacterItemBuf: Construct a new character item buffer.
CharacterItemBuf(char) - Constructor for class edu.rit.mp.buf.CharacterItemBuf: Construct a new character item buffer with the given initial value.
CharacterMatrixBuf - Class in edu.rit.mp.buf: Class CharacterMatrixBuf provides a buffer for a matrix of character items sent or received using the Message Protocol (MP).
CharacterMatrixBuf(char[][], Range, Range) - Constructor for class edu.rit.mp.buf.CharacterMatrixBuf: Construct a new character matrix buffer.
CharacterMatrixBuf_1 - Class in edu.rit.mp.buf: Class CharacterMatrixBuf_1 provides a buffer for a matrix of character items sent or received using the Message Protocol (MP).
CharacterMatrixBuf_1(char[][], Range, Range) - Constructor for class edu.rit.mp.buf.CharacterMatrixBuf_1: Construct a new character matrix buffer.
CharacterOp - Class in edu.rit.pj.reduction: Class CharacterOp is the abstract base class for a binary operation on character values, used to do reduction in a parallel program.
CharacterOp() - Constructor for class edu.rit.pj.reduction.CharacterOp: Construct a new character binary operation.
charge - Variable in class ffx.potential.parameters.ChargeType: Partial atomic charge in units of electrons.
charge - Variable in class ffx.potential.parameters.MultipoleType: Partial atomic charge (e).
charge - Variable in class ffx.ui.commands.SimulationDefinition
CHARGE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
chargeIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to charge I at site K.
chargeIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to charge I at site K.
chargeIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to charge I at site K.
chargeIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the field components due to site I charge at site K.
chargeIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the field components due to site I charge at site K.
chargeIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the field components due to site I charge at site K.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the field components due to site K charge at site I.
chargeKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the field components due to site K charge at site I.
chargeKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the field components due to site K charge at site I.
ChargeType - Class in ffx.potential.parameters: The ChargeType class defines a partial atomic charge type.
ChargeType(int, double) - Constructor for class ffx.potential.parameters.ChargeType: ChargeType constructor.
charLength - Variable in class ffx.numerics.quickhull.QuickHull3D
CHARMM_22 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
CHARMM_27 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
CHARMM_36 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
CHEAP - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
check(double, double) - Method in enum class ffx.crystal.ASULimit: Check the given point is within the asymmetric unit limit.
check(double, double) - Static method in enum class ffx.crystal.LatticeSystem: If the two passed values are the same, within the tolerance, return true.
check(int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for eliminated rotamer; true if eliminated.
check(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for eliminated rotamer pair; true if eliminated.
check(PrintStream) - Method in class ffx.numerics.quickhull.QuickHull3D: Checks the correctness of the hull using the distance tolerance returned by getDistanceTolerance; see check(PrintStream,double) for details.
check(PrintStream, double) - Method in class ffx.numerics.quickhull.QuickHull3D: Checks the correctness of the hull.
checkAlchemicalAtoms - Variable in class ffx.potential.terms.EnergyTermRegion: Alchemical atoms will not be checked for restraints.
checkAtomicNumberAndMass(int, double) - Static method in class ffx.potential.parameters.AtomType: Check if the supplied atomic mass is within 0.1 AMU of the IUPAC value for the given atomic number.
checkAtomicNumberAndMass(int, double, double) - Static method in class ffx.potential.parameters.AtomType: Check if the supplied atomic mass is within the supplied tolerance (in AMU) of the IUPAC value for the given atomic number.
CHECKBOX - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
CHECKBOXES - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
checkDistMatrix(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Gets the raw distance between two rotamers using lazy loading of the distance matrix.
checkFaceConvexity(Face, double, PrintStream) - Method in class ffx.numerics.quickhull.QuickHull3D: Verifies that a face is locally convex by checking distances between opposite face centroids and face planes, and ensuring no redundant vertices exist.
checkFaces(double, PrintStream) - Method in class ffx.numerics.quickhull.QuickHull3D: Performs convexity validation across all visible faces using a specified tolerance.
checkHydrogenAtomNames(Residue, PDBFilter.PDBFileStandard) - Static method in class ffx.potential.bonded.NamingUtils: Ensures proper naming of hydrogen according to latest PDB format.
checkList(int[][][], int) - Method in class ffx.potential.nonbonded.RowLoop: Check if the list is valid for the given zAtListBuild and buff.
checkList(int[][], int) - Method in class ffx.potential.nonbonded.SliceLoop: checkList.
checkMultipoleChirality(MultipoleType.MultipoleFrameDefinition, double[], double[][]) - Static method in class ffx.potential.parameters.MultipoleType: checkMultipoleChirality.
checkNeighboringPair(int, int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Checks if residue i is considered to be interacting with residue j, and thus has non-null elements in the pair energies matrix.
checkNeighboringTriple(int, int, int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Checks if residue i is considered to be interacting with residue j, that residue k is interacting with either i or j, and thus i-j-k has non-null elements in the triple energy matrix.
checkNPT(MolecularAssembly, CrystalPotential) - Method in class ffx.algorithms.cli.BarostatOptions: If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.
checkPairDistThreshold(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks if the i,ri,j,rj pair exceeds the pair distance thresholds.
checkProperties(CompositeConfiguration) - Static method in class ffx.crystal.Crystal: checkProperties
checkProperties(CompositeConfiguration) - Static method in class ffx.crystal.Resolution: checkProperties
checkPrunedPairs(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for pruned rotamer pair; true if eliminated.
checkPrunedSingles(int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for pruned rotamer; true if eliminated.
checkPucker(double, boolean) - Static method in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker: Returns the sugar pucker associated with a delta torsion.
checkQuadDistThreshold(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks if the i,ri,j,rj,k,rk,l,rl quad exceeds the 3-body threshold, or if any component exceeds the pair/triple distance thresholds.
checkRestrictions(int, int, int) - Method in enum class ffx.crystal.LaueSystem: Check the given HKL is valid given the Laue system.
checkThole(double) - Method in class ffx.numerics.multipole.TholeTensorGlobal: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(double) - Method in class ffx.numerics.multipole.TholeTensorQI: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(double, double, double) - Static method in class ffx.numerics.multipole.TholeTensorGlobal: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(DoubleVector) - Method in class ffx.numerics.multipole.TholeTensorGlobalSIMD: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(DoubleVector) - Method in class ffx.numerics.multipole.TholeTensorQISIMD: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(DoubleVector, DoubleVector, DoubleVector) - Static method in class ffx.numerics.multipole.TholeTensorGlobalSIMD: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkToJ(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Checks to see if any eliminations with j,rj have occurred; assumes i,ri self has already been checked.
checkToK(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Checks to see if any eliminations with k,rk have occurred; assumes i,ri,j,rj 2-Body has already been checked.
checkToL(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Checks to see if any eliminations with l,rl have occurred; assumes i,ri,j,rj,k,rk 3-Body has already been checked.
checkTriDistThreshold(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks if the i,ri,j,rj,k,rk triple exceeds the 3-body threshold, or if any component exceeds the pair distance threshold.
checkValidMove(int, int, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Checks the pair elimination array to see if this permutation has been eliminated.
chi1 - Variable in class ffx.potential.bonded.Rotamer: Torsions chi 1-4 are used for amino acids and nucleic acids.
chi2 - Variable in class ffx.potential.bonded.Rotamer
chi3 - Variable in class ffx.potential.bonded.Rotamer
chi4 - Variable in class ffx.potential.bonded.Rotamer
chi5 - Variable in class ffx.potential.bonded.Rotamer: Torsions chi 5-7 are only currently used for nucleic acids.
chunk(int, int) - Method in class edu.rit.util.Range: Slice off a chunk of this range and return the chunk.
chunk(long, long) - Method in class edu.rit.util.LongRange: Slice off a chunk of this range and return the chunk.
CIF - Enum constant in enum class ffx.potential.Utilities.FileType
CIFFilter - Class in ffx.potential.parsers: The CIFFilter class parses CIF coordinate (*.CIF) files.
CIFFilter - Class in ffx.xray.parsers: CIF file reader
CIFFilter() - Constructor for class ffx.xray.parsers.CIFFilter: Constructor.
CIFFilter(File, MolecularAssembly, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter: Constructor for CIFFilter on a single file and a single assembly.
CIFFilter(File, List<MolecularAssembly>, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter: Constructor for CIFFilter on a single file and multiple assemblies.
CIFFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter: Constructor for CIFFilter on a multiple files and a single assembly.
cifForID(String) - Static method in class ffx.utilities.StringUtils: cifForID
CIFtoMTZ - Class in ffx.xray.commands: The CIF2MTZ script saves a CIF file to MTZ format.
CIFtoMTZ() - Constructor for class ffx.xray.commands.CIFtoMTZ: CIF2MTZ constructor.
CIFtoMTZ(FFXBinding) - Constructor for class ffx.xray.commands.CIFtoMTZ: CIF2MTZ constructor.
CIFtoMTZ(String[]) - Constructor for class ffx.xray.commands.CIFtoMTZ: CIF2MTZ constructor that sets the command line arguments.
Cl - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CL - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
classpath - Variable in class edu.rit.pj.cluster.BackendInfo: The Java class path for the Parallel Java Library on the backend.
clazz() - Element in annotation interface ffx.utilities.FFXProperty: The Class used to represent the value of this FFXProperty.
clear() - Method in class ffx.numerics.quickhull.FaceList: Clears this list.
clear() - Method in class ffx.potential.nonbonded.NeighborList.Cell: Clear the list of atoms in the cell.
clear() - Method in class ffx.ui.GraphicsPicking: Clear currently selected nodes
clear() - Method in class ffx.utilities.Keyword: clear
clearContext() - Method in class ffx.ui.ModelingShell
clearContext(EventObject) - Method in class ffx.ui.ModelingShell
clearForceFieldType(ForceField.ForceFieldType) - Method in class ffx.potential.parameters.ForceField: Clear all force field types of a given type.
clearInducedDipoles() - Method in class ffx.numerics.multipole.PolarizableMultipole: Clear the induced dipoles.
clearOutput() - Method in class ffx.ui.ModelingShell
clearOutput(EventObject) - Method in class ffx.ui.ModelingShell
clearProperty(String) - Method in class ffx.potential.parameters.ForceField: Clear a property from the force field instance.
clearSegIDs() - Method in class ffx.potential.parsers.PDBFilter: clearSegIDs
CLOCKWISE - Static variable in class ffx.numerics.quickhull.QuickHull3D: Specifies that (on output) vertex indices for a face should be listed in clockwise order.
clone() - Method in class ffx.numerics.clustering.Distance: Creates a clone of this Distance.
close() - Method in class edu.rit.http.HttpResponse: Close this HTTP response.
close() - Method in class edu.rit.http.HttpServer: Close this HTTP server.
close() - Method in class edu.rit.io.DoubleMatrixFile.Reader: Close the input stream.
close() - Method in class edu.rit.io.DoubleMatrixFile.Writer: Close the output stream.
close() - Method in class edu.rit.io.LineBufferedOutputStream: Close this line buffered output stream.
close() - Method in class edu.rit.mp.Channel: Close this channel.
close() - Method in class edu.rit.mp.ChannelGroup: Close this channel group.
close() - Method in class edu.rit.pj.cluster.BackendFileInputStream: Close this input stream.
close() - Method in class edu.rit.pj.cluster.BackendFileOutputStream: Close this output stream.
close() - Method in class edu.rit.pj.cluster.JobBackend: Close communication with this Job Backend.
close() - Method in interface edu.rit.pj.cluster.JobBackendRef: Close communication with this Job Backend.
close() - Method in class edu.rit.pj.cluster.JobFrontend: Close communication with this Job Frontend.
close() - Method in interface edu.rit.pj.cluster.JobFrontendRef: Close communication with this Job Frontend.
close() - Method in class edu.rit.pj.cluster.JobScheduler: Close communication with this Job Scheduler.
close() - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Close communication with this Job Scheduler.
close() - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Close communication with this Job Frontend.
close() - Method in class edu.rit.pj.cluster.Proxy: Close communication with this proxy's far end process.
close() - Method in class ffx.ui.LogHandler
close() - Method in class ffx.ui.MainPanel: Detach the active FSystem's BranchGroup from the Scene and clear that FSystem's data
close() - Method in class ffx.utilities.StringOutputStream: close.
close(MolecularAssembly) - Method in interface ffx.potential.utils.PotentialsFunctions: Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
close(MolecularAssembly) - Method in class ffx.potential.utils.PotentialsUtils: Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
close(MolecularAssembly) - Method in class ffx.ui.UIUtils
close(FFXSystem) - Method in class ffx.ui.MainPanel: close
closeAll(MolecularAssembly[]) - Method in interface ffx.potential.utils.PotentialsFunctions: Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
closeAll(MolecularAssembly[]) - Method in class ffx.potential.utils.PotentialsUtils: Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
closeAll(MolecularAssembly[]) - Method in class ffx.ui.UIUtils
closeReader() - Method in class ffx.potential.parsers.CIFFilter: Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.INTFilter: Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.MergeFilter: Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.PDBFilter: Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.SystemFilter: Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.XPHFilter: Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.XYZFilter: Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.ui.commands.SimulationFilter
CLOSING - Static variable in class ffx.ui.commands.SimulationMessage: Constant CLOSING=2
Cluster - Class in ffx.algorithms.commands: The Cluster script clusters structures utilizing RMSD.
Cluster - Class in ffx.numerics.clustering: Represents a node in a hierarchical clustering tree (dendrogram).
Cluster() - Constructor for class ffx.algorithms.commands.Cluster: Cluster constructor.
Cluster(FFXBinding) - Constructor for class ffx.algorithms.commands.Cluster: Cluster constructor.
Cluster(String) - Constructor for class ffx.numerics.clustering.Cluster: Creates a new Cluster with the provided name.
Cluster(String[]) - Constructor for class ffx.algorithms.commands.Cluster: Cluster constructor that sets the command line arguments.
ClusterComponent - Class in ffx.numerics.clustering.visualization: Visual component representing a single cluster node within a dendrogram.
ClusterComponent(Cluster, boolean, VCoord) - Constructor for class ffx.numerics.clustering.visualization.ClusterComponent: Constructs a visual node component for a Cluster.
Clustering - Class in ffx.potential.utils: Cluster contains methods used in the Cluster.groovy file.
Clustering() - Constructor for class ffx.potential.utils.Clustering
Clustering.Conformation - Class in ffx.potential.utils: Class for cluster objects.
ClusteringAlgorithm - Interface in ffx.numerics.clustering: Defines algorithms that produce hierarchical clusters from distance data.
ClusterPair - Class in ffx.numerics.clustering: Immutable-like holder describing a pair of clusters and the linkage distance between them; used as entries within the DistanceMap during agglomeration.
ClusterPair() - Constructor for class ffx.numerics.clustering.ClusterPair: Creates an empty ClusterPair.
ClusterPair(Cluster, Cluster, Double) - Constructor for class ffx.numerics.clustering.ClusterPair: Creates a ClusterPair linking two clusters at a given distance.
Cm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CMAPTorsionForce - Class in ffx.openmm: This class implements an interaction between pairs of dihedral angles.
CMAPTorsionForce() - Constructor for class ffx.openmm.CMAPTorsionForce: Create a CMAPTorsionForce.
cmMotionRemover - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM center-of-mass motion remover.
CMMotionRemover - Class in ffx.openmm: This class prevents the center of mass of a System from drifting.
CMMotionRemover(int) - Constructor for class ffx.openmm.CMMotionRemover: Create a CMMotionRemover.
cn(int, double, double) - Static method in class ffx.numerics.multipole.GKSource: Compute the Kirkwood dielectric function for a multipole of order n.
CNSFilter - Class in ffx.xray.parsers: CNSFilter class.
CNSFilter() - Constructor for class ffx.xray.parsers.CNSFilter: Constructor for CNSFilter.
CNSMapWriter - Class in ffx.xray.parsers: The CNSMapWriter class writes an output map that covers the unit cell (not the asymmetric unit).
CNSMapWriter(int, int, int, Crystal, String) - Constructor for class ffx.xray.parsers.CNSMapWriter: Constructor for CNSMapWriter.
Co - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
codePotentialMultipoleI(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor: Collect the potential its partial derivatives at K due to multipole moments at the origin.
codePotentialMultipoleISIMD(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor: Collect the potential its partial derivatives at K due to multipole moments at the origin using SIMD instructions.
codePotentialMultipoleK(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor: Collect the potential its partial derivatives at the origin due to multipole moments at site K.
codePotentialMultipoleKSIMD(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor: Collect the potential its partial derivatives at the origin due to multipole moments at site K using SIMD instructions.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: This function is a driver to collect elements of the Cartesian multipole tensor.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This function is a driver to collect elements of the Cartesian multipole tensor.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: This function is a driver to collect elements of the Cartesian multipole tensor.
codeVectorTensorRecursion() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Emit code to calculate the Cartesian multipole tensor using SIMD vectorization.
codeVectorTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This function is a driver to collect elements of the Cartesian multipole tensor.
codeVectorTensorRecursion(int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Emit code to calculate the Cartesian multipole tensor using SIMD vectorization.
CoformerBindingSearch - Class in ffx.algorithms.commands.test: CoformerBindingSearch is a Groovy script that generates a set of molecular orientations in vacuum and calculates the energy of each conformation.
CoformerBindingSearch() - Constructor for class ffx.algorithms.commands.test.CoformerBindingSearch: Constructor.
CoformerBindingSearch(FFXBinding) - Constructor for class ffx.algorithms.commands.test.CoformerBindingSearch: Constructor.
CoformerBindingSearch(String[]) - Constructor for class ffx.algorithms.commands.test.CoformerBindingSearch: Constructor that sets the command line arguments.
COH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
collectAtoms(Atom, ArrayList<Atom>) - Static method in class ffx.potential.parsers.CIFFilter: Finds all atoms that are bonded to one another.
collectResidues(MolecularAssembly) - Method in class ffx.algorithms.cli.ManyBodyOptions: Collect residues based on residue selection flags.
colLength(boolean[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given Boolean matrix.
colLength(byte[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given byte matrix.
colLength(char[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given character matrix.
colLength(double[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given double matrix.
colLength(float[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given float matrix.
colLength(int[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given integer matrix.
colLength(long[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given long matrix.
colLength(short[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given short matrix.
colLength(T[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given object matrix.
color - Variable in class ffx.utilities.FFXCommand: Unix shells are able to evaluate PicoCLI ANSI color codes, but right now the FFX GUI Shell does not.
colorModelHash - Static variable in class ffx.potential.bonded.RendererCache: Constant colorModelHash
colorWait(String) - Method in class ffx.ui.GraphicsCanvas: colorWait
cols() - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Returns the number of columns in this matrix reduction variable.
cols() - Method in class edu.rit.pj.reduction.SharedLongMatrix: Returns the number of columns in this matrix reduction variable.
colSliceBuffer(boolean[][], Range) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for one column slice of the given Boolean matrix.
colSliceBuffer(byte[][], Range) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for one column slice of the given byte matrix.
colSliceBuffer(char[][], Range) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for one column slice of the given character matrix.
colSliceBuffer(double[][], Range) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for one column slice of the given double matrix.
colSliceBuffer(float[][], Range) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for one column slice of the given float matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(long[][], Range) - Static method in class edu.rit.mp.LongBuf: Create a buffer for one column slice of the given long matrix.
colSliceBuffer(short[][], Range) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for one column slice of the given short matrix.
colSliceBuffer(T[][], Range) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for one column slice of the given object matrix.
colSliceBuffers(boolean[][], Range[]) - Static method in class edu.rit.mp.BooleanBuf: Create an array of buffers for multiple column slices of the given Boolean matrix.
colSliceBuffers(byte[][], Range[]) - Static method in class edu.rit.mp.ByteBuf: Create an array of buffers for multiple column slices of the given byte matrix.
colSliceBuffers(char[][], Range[]) - Static method in class edu.rit.mp.CharacterBuf: Create an array of buffers for multiple column slices of the given character matrix.
colSliceBuffers(double[][], Range[]) - Static method in class edu.rit.mp.DoubleBuf: Create an array of buffers for multiple column slices of the given double matrix.
colSliceBuffers(float[][], Range[]) - Static method in class edu.rit.mp.FloatBuf: Create an array of buffers for multiple column slices of the given float matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.IntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(long[][], Range[]) - Static method in class edu.rit.mp.LongBuf: Create an array of buffers for multiple column slices of the given long matrix.
colSliceBuffers(short[][], Range[]) - Static method in class edu.rit.mp.ShortBuf: Create an array of buffers for multiple column slices of the given short matrix.
colSliceBuffers(T[][], Range[]) - Static method in class edu.rit.mp.ObjectBuf: Create an array of buffers for multiple column slices of the given object matrix.
COM_DISTANCE - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
CombinedTensorGlobal - Class in ffx.numerics.multipole: This class allows for the source terms of tensors to be combined, and therefore multiple interaction tensors can be computed simultaneously (as a sum).
CombinedTensorGlobal(int) - Constructor for class ffx.numerics.multipole.CombinedTensorGlobal: Constructor for CoulombTensorGlobal.
combineSymOps(SymOp, SymOp) - Static method in class ffx.crystal.SymOp: Return the combined SymOp that is equivalent to first applying symOp1 and then SymOp2.
COMBOBOX - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
comesBefore(byte[], int, int) - Method in class edu.rit.util.Sorting.Byte: Compare two elements in the given array.
comesBefore(char[], int, int) - Method in class edu.rit.util.Sorting.Character: Compare two elements in the given array.
comesBefore(double[], int, int) - Method in class edu.rit.util.Sorting.Double: Compare two elements in the given array.
comesBefore(float[], int, int) - Method in class edu.rit.util.Sorting.Float: Compare two elements in the given array.
comesBefore(int[], int, int) - Method in class edu.rit.util.Sorting.Integer: Compare two elements in the given array.
comesBefore(long[], int, int) - Method in class edu.rit.util.Sorting.Long: Compare two elements in the given array.
comesBefore(short[], int, int) - Method in class edu.rit.util.Sorting.Short: Compare two elements in the given array.
comesBefore(T[], int, int) - Method in class edu.rit.util.Sorting.Object: Compare two elements in the given array.
Comm - Class in edu.rit.pj: Class Comm provides a communicator for a PJ cluster parallel program.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Method in class edu.rit.pj.cluster.JobBackend: Commence the job.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "commence job" message.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Method in class edu.rit.pj.cluster.JobBackendProxy: Commence the job.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Method in interface edu.rit.pj.cluster.JobBackendRef: Commence the job.
comment - Variable in class edu.rit.pj.cluster.JobInfo: Comment for each process in the job in rank order.
CommPattern - Class in edu.rit.pj.cluster: Class CommPattern provides static methods for calculating communication patterns for collective communication operations.
CommRequest - Class in edu.rit.pj: Class CommRequest provides an object for doing a non-blocking message passing operation in a PJ cluster parallel program.
CommRequest() - Constructor for class edu.rit.pj.CommRequest: Construct a new CommRequest object.
CommStatus - Class in edu.rit.pj: Class CommStatus provides the result of receiving a message from a communicator (class Comm).
compare(byte, byte) - Method in class edu.rit.util.Searching.Byte: Compare two elements according to the desired ordering criterion.
compare(char, char) - Method in class edu.rit.util.Searching.Character: Compare two elements according to the desired ordering criterion.
compare(double, double) - Method in class edu.rit.util.Searching.Double: Compare two elements according to the desired ordering criterion.
compare(float, float) - Method in class edu.rit.util.Searching.Float: Compare two elements according to the desired ordering criterion.
compare(int, int) - Method in class edu.rit.util.Searching.Integer: Compare two elements according to the desired ordering criterion.
compare(long, long) - Method in class edu.rit.util.Searching.Long: Compare two elements according to the desired ordering criterion.
compare(short, short) - Method in class edu.rit.util.Searching.Short: Compare two elements according to the desired ordering criterion.
compare(Atom, Atom, Atom, Atom) - Method in class ffx.potential.bonded.AngleTorsion: compare
compare(Atom, Atom, Atom, Atom) - Method in class ffx.potential.bonded.StretchTorsion: compare
compare(Atom, Atom, Atom, Atom) - Method in class ffx.potential.bonded.Torsion: compare
compare(BondedTerm, BondedTerm) - Method in class ffx.potential.bonded.BondedTerm.BondedComparator: Sort using position in the naturalOrder list; fallback to alphabetical.
compare(String, String) - Method in class ffx.potential.parameters.AngleTorsionType
compare(String, String) - Method in class ffx.potential.parameters.AngleType
compare(String, String) - Method in class ffx.potential.parameters.AtomType
compare(String, String) - Method in class ffx.potential.parameters.BioType
compare(String, String) - Method in class ffx.potential.parameters.BondType
compare(String, String) - Method in class ffx.potential.parameters.ChargeType
compare(String, String) - Method in class ffx.potential.parameters.ImproperTorsionType
compare(String, String) - Method in class ffx.potential.parameters.MultipoleType
compare(String, String) - Method in class ffx.potential.parameters.OutOfPlaneBendType
compare(String, String) - Method in class ffx.potential.parameters.PiOrbitalTorsionType
compare(String, String) - Method in class ffx.potential.parameters.PolarizeType
compare(String, String) - Method in class ffx.potential.parameters.RelativeSolvationType
compare(String, String) - Method in class ffx.potential.parameters.SoluteType
compare(String, String) - Method in class ffx.potential.parameters.StretchBendType
compare(String, String) - Method in class ffx.potential.parameters.StretchTorsionType
compare(String, String) - Method in class ffx.potential.parameters.TorsionTorsionType
compare(String, String) - Method in class ffx.potential.parameters.TorsionType
compare(String, String) - Method in class ffx.potential.parameters.UreyBradleyType
compare(String, String) - Method in class ffx.potential.parameters.VDWPairType
compare(String, String) - Method in class ffx.potential.parameters.VDWType
compare(T, T) - Method in class edu.rit.util.Searching.Object: Compare two elements according to the desired ordering criterion.
compareAndSet(boolean, boolean) - Method in class edu.rit.pj.reduction.SharedBoolean: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(byte, byte) - Method in class edu.rit.pj.reduction.SharedByte: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(char, char) - Method in class edu.rit.pj.reduction.SharedCharacter: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(double, double) - Method in class edu.rit.pj.reduction.SharedDouble: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(float, float) - Method in class edu.rit.pj.reduction.SharedFloat: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(int, boolean, boolean) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, byte, byte) - Method in class edu.rit.pj.reduction.SharedByteArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, char, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, double, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, float, float) - Method in class edu.rit.pj.reduction.SharedFloatArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, int) - Method in class edu.rit.pj.reduction.SharedInteger: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Atomically set this matrix reduction variable at the given row and column to the given updated value if the current value equals the expected value.
compareAndSet(int, int, long, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Atomically set this matrix reduction variable at the given row and column to the given updated value if the current value equals the expected value.
compareAndSet(int, long, long) - Method in class edu.rit.pj.reduction.SharedLongArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, short, short) - Method in class edu.rit.pj.reduction.SharedShortArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, T, T) - Method in class edu.rit.pj.reduction.SharedObjectArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(long, long) - Method in class edu.rit.pj.reduction.SharedLong: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(short, short) - Method in class edu.rit.pj.reduction.SharedShort: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(T, T) - Method in class edu.rit.pj.reduction.SharedObject: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareTo(ClusterPair) - Method in class ffx.numerics.clustering.ClusterPair
compareTo(Distance) - Method in class ffx.numerics.clustering.Distance: Compares by distance value, with null other treated as greater (this < other).
compareTo(Atom) - Method in class ffx.potential.bonded.Atom
compareTo(BondedTerm) - Method in class ffx.potential.bonded.Angle
compareTo(BondedTerm) - Method in class ffx.potential.bonded.Bond
compareTo(BondedTerm) - Method in class ffx.potential.bonded.BondedTerm
compareTo(BondedTerm) - Method in class ffx.potential.bonded.ImproperTorsion
compareTo(BondedTerm) - Method in class ffx.potential.bonded.OutOfPlaneBend
compareTo(BondedTerm) - Method in class ffx.potential.bonded.StretchBend
compareTo(BondedTerm) - Method in class ffx.potential.bonded.UreyBradley
compareTo(Residue) - Method in class ffx.potential.bonded.Residue
compareTo(ResidueState) - Method in class ffx.potential.bonded.ResidueState
compareTo(NeighborList.AtomIndex) - Method in class ffx.potential.nonbonded.NeighborList.AtomIndex
compareTo(DoubleIndexPair) - Method in record class ffx.utilities.DoubleIndexPair
compareTo(ObjectPair<T, S>) - Method in record class ffx.utilities.ObjectPair
compareTo(Object) - Method in record class ffx.utilities.IndexIndexPair
comparisons(int, double, double, double, int, int, String, String, boolean, boolean, boolean, int, boolean, int, double, boolean, boolean, boolean, boolean, boolean, int, double, boolean, boolean, boolean, String, StringBuilder, StringBuilder) - Method in class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Compare the crystals within the SystemFilters that were inputted into the constructor of this class.
CompleteLinkageStrategy - Class in ffx.numerics.clustering: Linkage strategy that uses the maximum of pairwise distances between cluster members (complete-linkage / farthest-neighbor).
CompleteLinkageStrategy() - Constructor for class ffx.numerics.clustering.CompleteLinkageStrategy
Complex - Class in ffx.numerics.fft: Compute the FFT of complex, double precision data of arbitrary length n.
Complex(int) - Constructor for class ffx.numerics.fft.Complex: Construct a Complex instance for interleaved data of length n.
Complex(int, DataLayout1D, int) - Constructor for class ffx.numerics.fft.Complex: Construct a Complex instance for data of length n.
Complex(int, DataLayout1D, int, int) - Constructor for class ffx.numerics.fft.Complex: Construct a Complex instance for data of length n.
Complex2D - Class in ffx.numerics.fft: Compute the 2D FFT of complex, double precision input of arbitrary dimensions via 1D Mixed Radix FFTs.
Complex2D(int, int) - Constructor for class ffx.numerics.fft.Complex2D: Create a new 2D Complex FFT for interleaved data.
Complex2D(int, int, DataLayout2D, int) - Constructor for class ffx.numerics.fft.Complex2D: Create a new 2D Complex FFT.
Complex3D - Class in ffx.numerics.fft: Compute the 3D FFT of complex, double precision input of arbitrary dimensions via 1D Mixed Radix FFTs.
Complex3D(int, int, int) - Constructor for class ffx.numerics.fft.Complex3D: Initialize the 3D FFT for complex 3D matrix using interleaved data layout.
Complex3D(int, int, int, DataLayout3D) - Constructor for class ffx.numerics.fft.Complex3D: Initialize the 3D FFT for complex 3D matrix.
Complex3DParallel - Class in ffx.numerics.fft: Compute the 3D FFT of complex, double precision input of arbitrary dimensions via 1D Mixed Radix FFTs in parallel.
Complex3DParallel(int, int, int, ParallelTeam) - Constructor for class ffx.numerics.fft.Complex3DParallel: Initialize the 3D FFT for complex 3D matrix.
Complex3DParallel(int, int, int, ParallelTeam, IntegerSchedule) - Constructor for class ffx.numerics.fft.Complex3DParallel: Initialize the 3D FFT for complex 3D matrix.
Complex3DParallel(int, int, int, ParallelTeam, IntegerSchedule, DataLayout3D) - Constructor for class ffx.numerics.fft.Complex3DParallel: Initialize the 3D FFT for complex 3D matrix.
Complex3DParallel(int, int, int, ParallelTeam, DataLayout3D) - Constructor for class ffx.numerics.fft.Complex3DParallel: Initialize the 3D FFT for complex 3D matrix.
ComplexNumber - Class in ffx.numerics.math: ComplexNumber class.
ComplexNumber() - Constructor for class ffx.numerics.math.ComplexNumber: Constructor for ComplexNumber.
ComplexNumber(double, double) - Constructor for class ffx.numerics.math.ComplexNumber: Constructor for ComplexNumber.
CompositeCurve - Class in ffx.numerics.integrate: A CompositeCurve represents points along a sum of functions which also extend FunctionDataCurve.
CompositeCurve(List<FunctionDataCurve>, List<Double>) - Constructor for class ffx.numerics.integrate.CompositeCurve: Constructs a CompositeCurve that aggregates multiple FunctionDataCurves with variable weights to each component FunctionDataCurve.
CompositeSwitch - Class in ffx.numerics.switching: The CompositeSwitch uses a primary switch in the middle, and then two secondary switches at the ends of the path to smoothly switch to the primary switch.
CompositeSwitch() - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a switch that uses MultiplicativeSwitches at the ends (0-0.1, 0.9-1.0) to smoothly interpolate a linear switch between 0 and 1 with smooth 2'nd and 3'rd derivatives.
CompositeSwitch(UnivariateSwitchingFunction) - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a switch that uses MultiplicativeSwitches at the ends (0-0.1, 0.9-1.0) to smoothly interpolate a provided switch between 0 and 1 with smooth 2'nd and 3'rd derivatives.
CompositeSwitch(UnivariateSwitchingFunction, UnivariateSwitchingFunction, UnivariateSwitchingFunction, double, double) - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a composite switch in .
CompositeSwitch(UnivariateSwitchingFunction, UnivariateSwitchingFunction, UnivariateSwitchingFunction, double, double, double, double) - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a composite switch in .
CompoundIntegrator - Class in ffx.openmm: This class allows you to use multiple integration algorithms within a single simulation, switching back and forth between them.
CompoundIntegrator() - Constructor for class ffx.openmm.CompoundIntegrator: Create a CompoundIntegrator.
compute2BodyEnergy(Residue[], int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a pair energy, defined as energy with all side-chains but two turned off, minus the sum of backbone and component self energies.
compute3BodyEnergy(Residue[], int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a 3-body energy, defined as the energy with all sidechains but three turned off, minus the sum of backbone and component self/2-Body energies.
compute4BodyEnergy(Residue[], int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a 4-body energy, defined as the energy with all sidechains but four turned off, minus the sum of backbone and component self/2-Body/3-body energies.
computeAtomicDensity() - Method in class ffx.xray.DiffractionData: Parallelized call to compute atomic density on a grid, followed by FFT to compute structure factors.
computeAtomicGradients(double[][], int[], int, RefinementMinimize.RefinementMode) - Method in class ffx.xray.CrystalReciprocalSpace: compute inverse FFT to determine atomic gradients
computeBackboneEnergy(Residue[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Computes the environment/backbone energy, defined as energy with all sidechains under consideration turned off in their 0th rotamer.
computeBornRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: computeBornRadii
computeBSplines() - Method in class ffx.potential.nonbonded.ReciprocalSpace: computeBSplines
computeCentroid(Point3d) - Method in class ffx.numerics.quickhull.Face: Computes the centroid (arithmetic mean of vertices) of this face into the provided point.
computeCurrentPressure(Context) - Method in class ffx.openmm.MonteCarloBarostat: Compute the instantaneous pressure of a system to which this barostat is applied.
computeCurrentPressure(Context, PointerByReference) - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Compute the current pressure in the system.
computedEdL(Potential, LambdaInterface, ForceField) - Static method in class ffx.potential.FiniteDifferenceUtils: Compute dE/dL using finite differences.
computeDft(float[], float[], float[], float[]) - Static method in class ffx.numerics.fft.TornadoDFT: Compute the Discrete Fourier Transform.
computeDrudeKineticEnergy() - Method in class ffx.openmm.drude.DrudeNoseHooverIntegrator: Compute the kinetic energy of the Drude particles.
computeDrudeTemperature() - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Compute the instantaneous temperature of the Drude system, measured in Kelvin.
computeDrudeTemperature() - Method in class ffx.openmm.drude.DrudeNoseHooverIntegrator: Compute the instantaneous temperature of the Drude particles.
computeElasticityTensor(boolean) - Method in class ffx.algorithms.optimize.CrystalMinimize: computeStressTensor.
computeEnergy(Residue[], int[], boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Uses existing backbone, self, 2-Body, and 3-body energies from rotamerEnergies() to calculate an approximate energy for a rotamer permutation.
ComputeFc - Class in ffx.xray.commands: The X-ray ComputeFc script.
ComputeFc() - Constructor for class ffx.xray.commands.ComputeFc: ComputeFc constructor.
ComputeFc(FFXBinding) - Constructor for class ffx.xray.commands.ComputeFc: ComputeFc constructor.
ComputeFc(String[]) - Constructor for class ffx.xray.commands.ComputeFc: ComputeFc constructor that sets the command line arguments.
computeFractionalCoordinates() - Method in class ffx.potential.MolecularAssembly: Compute fractional coordinates.
computeHeatBathEnergy() - Method in class ffx.openmm.NoseHooverIntegrator: Compute the total energy of all heat baths.
computeInducedGKField() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: computeInducedGKField
computeInduceDipoleField() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
computeInducedPhi(double[][], double[][], double[][], double[][]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: computeInducedPhi
computeKineticEnergy() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Compute the current temperature and kinetic energy of the system.
computeMaxAndMin() - Method in class ffx.numerics.quickhull.QuickHull3D: Computes per-axis min/max vertices and sets characteristic length and tolerance.
computeMoments(Atom[], boolean) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Compute multipole moments for an array of atoms.
computeNormal(Vector3d) - Method in class ffx.numerics.quickhull.Face: Computes a unit-length normal vector for this face using the vertex winding and writes it into the provided vector.
computeNormal(Vector3d, double) - Method in class ffx.numerics.quickhull.Face: Computes a unit-length normal for this face, and if the preliminary area is below the specified minArea, adjusts the normal to be more orthogonal to the longest edge to improve robustness.
computePermanentGKField() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: computePermanentGKField
computePermanentPhi(double[][], double[][]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: Compute the potential Phi and its derivatives for all atoms.
computeSelfEnergy(Residue[], int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a self energy, defined as energy with all side-chains but one turned off, minus the backbone energy.
computeSolventDensity(double[][]) - Method in class ffx.xray.CrystalReciprocalSpace: parallelized computation of bulk solvent structure factors
computeSystemTemperature() - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Compute the instantaneous temperature of the System, measured in Kelvin.
computeSystemTemperature() - Method in class ffx.openmm.drude.DrudeNoseHooverIntegrator: Compute the instantaneous temperature of the real atoms.
computeTotalKineticEnergy() - Method in class ffx.openmm.drude.DrudeNoseHooverIntegrator: Compute the total kinetic energy of the system.
computeVirtualSites() - Method in class ffx.openmm.Context: Recompute the locations of all virtual sites.
computeVolumeAndSA(double[][]) - Method in class ffx.potential.nonbonded.implicit.GaussVol: Compute molecular volume and surface area.
computeVolumeIntegrals(double, double, double, double, double) - Static method in class ffx.algorithms.commands.test.Freefix: Compute volume integrals and their temperature derivatives for restraint thermodynamics.
COMRestraint - Class in ffx.potential.nonbonded: Restrain molecules to their center of mass.
COMRestraint(MolecularAssembly) - Constructor for class ffx.potential.nonbonded.COMRestraint: This COMRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
CONDENSED - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
CONDENSED_NO_LIGAND - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
conditions - Variable in class ffx.ui.behaviors.PickMouseBehavior
coneFactory(Appearance, int) - Static method in class ffx.potential.bonded.RendererCache: coneFactory
confidenceInterval() - Method in class ffx.numerics.math.BootStrapStatistics: Computes a 95% confidence interval based on a Student's T-distribution.
confidenceInterval() - Method in class ffx.numerics.math.SummaryStatistics: Computes a 95% confidence interval based on a Student's T-distribution.
confidenceInterval(double) - Method in class ffx.numerics.math.BootStrapStatistics: Computes a confidence interval based on a Student's T-distribution.
confidenceInterval(double) - Method in class ffx.numerics.math.SummaryStatistics: Computes a confidence interval based on a Student's T-distribution.
Configuration - Class in edu.rit.pj.cluster: Class Configuration provides configuration information about a parallel computer running Parallel Java.
Configuration(String) - Constructor for class edu.rit.pj.cluster.Configuration: Construct a new configuration.
ConformationScan - Class in ffx.algorithms.optimize: This class is for a configuration optimization of two small systems.
ConformationScan(MolecularAssembly, Molecule[], Molecule[], double, int, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.ConformationScan
conjugate() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the conjugate of this.
conjugateIP() - Method in class ffx.numerics.math.ComplexNumber: conjugateIP
connect() - Method in class ffx.ui.commands.FFXClient: Attempts to connect to a Tinker FServer.
connect(InetSocketAddress) - Method in class edu.rit.mp.ChannelGroup: Create a new channel connected to the given far end host and port.
connectivity - Variable in class ffx.ui.commands.SimulationDefinition
ConnectListener - Interface in edu.rit.mp: Interface ConnectListener specifies the interface for an object that is notified whenever a Channel is connected in a ChannelGroup.
ConnollyRegion - Class in ffx.potential.nonbonded.implicit: ConnollyRegion uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the analytical molecular surface area and volume of a collection of spherical atoms; thus it implements Fred Richards' molecular surface definition as a set of analytically defined spherical and toroidal polygons.
ConnollyRegion(Atom[], double[], int) - Constructor for class ffx.potential.nonbonded.implicit.ConnollyRegion: ConnollyRegion constructor.
consecutiveInts(int[]) - Static method in class ffx.utilities.StringUtils: Finds consecutive subranges in an array of ints, and returns their mins and maxes.
CONSENSUS - Enum constant in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE
constantOutsideBounds() - Method in class ffx.numerics.switching.BellCurveSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e. a multiplicative switch).
constantOutsideBounds() - Method in class ffx.numerics.switching.CompositeSwitch
constantOutsideBounds() - Method in class ffx.numerics.switching.ConstantSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e. a multiplicative switch).
constantOutsideBounds() - Method in class ffx.numerics.switching.LinearDerivativeSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e. a multiplicative switch).
constantOutsideBounds() - Method in class ffx.numerics.switching.MultiplicativeSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e. a multiplicative switch).
constantOutsideBounds() - Method in class ffx.numerics.switching.PowerSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e. a multiplicative switch).
constantOutsideBounds() - Method in class ffx.numerics.switching.SquaredTrigSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e. a multiplicative switch).
constantOutsideBounds() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: Remains 0 below the lower bound, and 1 above the upper bound (i.e. a multiplicative switch).
ConstantPhMolecularDynamics - Enum constant in enum class ffx.utilities.PropertyGroup: Constant pH molecular dynamics parameters.
Constants - Class in edu.rit.pj.cluster: Class Constants contains various constants used in the PJ cluster middleware.
Constants - Class in ffx.utilities: Library class containing constants such as Avogadro's number.
ConstantSwitch - Class in ffx.numerics.switching: The ConstantSwitch returns a constant value for all input values x.
ConstantSwitch() - Constructor for class ffx.numerics.switching.ConstantSwitch: Default constructor: constant 1.0 value.
ConstantSwitch(double) - Constructor for class ffx.numerics.switching.ConstantSwitch: Permits specification of a value.
constrain - Variable in class ffx.potential.cli.SaveOptions: -c or --constrain Apply geometric constraints before saving.
constrainedAtomIndices() - Method in interface ffx.numerics.Constraint: Returns the atomic XYZ indices of all Atoms constrained.
constrainedAtomIndices() - Method in class ffx.potential.constraint.CcmaConstraint: Returns the atomic XYZ indices of all Atoms constrained.
constrainedAtomIndices() - Method in class ffx.potential.constraint.SettleConstraint
constrainedAtomIndices() - Method in class ffx.potential.constraint.ShakeChargeConstraint
Constraint - Interface in ffx.numerics: Defines a set of geometric constraints that must be applied self-consistently.
constraints - Variable in class ffx.algorithms.dynamics.integrators.Integrator: Any geometric constraints to apply during integration.
constraints - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat: Any geometric constraints to apply during integration.
constraintSatisfied(double[], double) - Method in interface ffx.numerics.Constraint: Checks if this Constraint is satisfied.
constraintSatisfied(double[], double) - Method in class ffx.potential.constraint.CcmaConstraint: Checks if this Constraint is satisfied.
constraintSatisfied(double[], double) - Method in class ffx.potential.constraint.SettleConstraint
constraintSatisfied(double[], double) - Method in class ffx.potential.constraint.ShakeChargeConstraint
constraintSatisfied(double[], double[], double, double) - Method in interface ffx.numerics.Constraint: Checks if this Constraint is satisfied.
constraintSatisfied(double[], double[], double, double) - Method in class ffx.potential.constraint.CcmaConstraint: Checks if this Constraint is satisfied.
constraintSatisfied(double[], double[], double, double) - Method in class ffx.potential.constraint.SettleConstraint
constraintSatisfied(double[], double[], double, double) - Method in class ffx.potential.constraint.ShakeChargeConstraint
constraintTolerance - Variable in class ffx.algorithms.dynamics.integrators.Integrator: Numerical tolerance (as a fraction of bond length) permitted for numerical solutions to constraints.
construct() - Method in class ffx.ui.SwingWorker: Compute the value to be returned by the get method.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.AmoebaMultipoleForce: Convenience method to construct an AMOEBA Multipole Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.AmoebaTorsionTorsionForce: Convenience method to construct a Dual Topology OpenMM Torsion-Torsion Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.AmoebaVdwForce: Convenience method to construct an AMOEBA vdW force for a dual-topology simulation.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.AngleForce: Add a bond force to the OpenMM System
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.AngleTorsionForce: Convenience method to construct a Dual Topology OpenMM Angle-Torsion Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.BondForce: Add a bond force to the OpenMM System.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.ImproperTorsionForce: Convenience method to construct a Dual Topology OpenMM Improper Torsion Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.InPlaneAngleForce: Convenience method to construct a Dual Topology OpenMM In-Plane Angle Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.OutOfPlaneBendForce: Convenience method to construct a Dual-Topology OpenMM Out-of-Plane Bend Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.PiOrbitalTorsionForce: Convenience method to construct a Dual-Topology OpenMM Pi-Orbital Torsion Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.RestrainTorsionsForce: Convenience method to construct a Dual-Topology OpenMM Torsion Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.StretchBendForce: Convenience method to construct a Dual-Topology OpenMM Stretch-Bend Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.StretchTorsionForce: Convenience method to construct a Dual Topology OpenMM Stretch-Torsion Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.TorsionForce: Convenience method to construct a Dual-Topology OpenMM Torsion Force.
constructForce(int, OpenMMDualTopologyEnergy) - Static method in class ffx.potential.openmm.UreyBradleyForce: Convenience method to construct an OpenMM Urey-Bradley Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AmoebaGeneralizedKirkwoodForce: Convenience method to construct an AMOEBA Generalized Kirkwood Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AmoebaGKCavitationForce: Convenience method to construct an AMOEBA Cavitation Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AmoebaMultipoleForce: Convenience method to construct an AMOEBA Multipole Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AmoebaTorsionTorsionForce: Convenience method to construct an OpenMM Torsion-Torsion Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AmoebaVdwForce: Convenience method to construct an AMOEBA vdW force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AmoebaWcaDispersionForce: Convenience method to construct an AMOEBA WCA Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AngleForce: Convenience method to construct an OpenMM Angle Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.AngleTorsionForce: Convenience method to construct an OpenMM Angle-Torsion Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.BondForce: Creat a bond force for the OpenMM System.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.FixedChargeGBForce: Construct a GB force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.FixedChargeNonbondedForce: Convenience method to construct an OpenMM Non-Bonded Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.ImproperTorsionForce: Convenience method to construct an OpenMM Improper Torsion Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.InPlaneAngleForce: Convenience method to construct an OpenMM In-Plane Angle Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.OutOfPlaneBendForce: Convenience method to construct an OpenMM Out-of-Plane Bend Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.PiOrbitalTorsionForce: Convenience method to construct an OpenMM Pi-Orbital Torsion Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.RestrainGroupsForce: Add a Restrain-Groups force to the OpenMM System.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.RestrainPositionsForce: Add a Restrain-Position force to the OpenMM System.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.RestrainTorsionsForce: Convenience method to construct an OpenMM Torsion Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.StretchBendForce: Convenience method to construct an OpenMM Stretch-Bend Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.StretchTorsionForce: Convenience method to construct an OpenMM Stretch-Torsion Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.TorsionForce: Convenience method to construct an OpenMM Torsion Force.
constructForce(OpenMMEnergy) - Static method in class ffx.potential.openmm.UreyBradleyForce: Convenience method to construct an OpenMM Urey-Bradley Force.
constructForce(BondType.BondFunction, OpenMMEnergy) - Static method in class ffx.potential.openmm.RestrainDistanceForce: Add a Restrain-Bond force to the OpenMM System.
constructHull(Atom[]) - Static method in class ffx.potential.utils.ConvexHullOps: Constructs a convex hull from a set of atoms.
constructOST(CrystalPotential, File, File, MolecularAssembly, Configuration, DynamicsOptions, ThermodynamicsOptions, LambdaParticleOptions, AlgorithmListener, boolean) - Method in class ffx.algorithms.cli.OSTOptions: constructOST.
contains(int) - Method in class edu.rit.util.Range: Determine if this range contains the given value.
contains(long) - Method in class edu.rit.util.LongRange: Determine if this range contains the given value.
contains(LongRange) - Method in class edu.rit.util.LongRange: Determine if this range contains the given range.
contains(Range) - Method in class edu.rit.util.Range: Determine if this range contains the given range.
contains(Cluster) - Method in class ffx.numerics.clustering.Cluster: Tests whether this cluster has the specified child.
contains(MSNode) - Method in class ffx.potential.bonded.MSNode: If this MSNode or any MSNode below it equals the argument, that MSNode is returned.
contains(String) - Method in class edu.rit.pj.cluster.ResourceCache: Determine if this resource cache contains resource information for the given resource name.
containsContent(String) - Method in class edu.rit.pj.cluster.ResourceCache: Determine if this resource cache contains the resource content for the given resource name.
containsHydrogen() - Method in class ffx.potential.bonded.BondedTerm: containsHydrogen
containsResolution(Atom.Resolution) - Method in class ffx.potential.bonded.BondedTerm: Checks if at least one atom in this BondedTerm is of the given resolution.
Context - Class in ffx.openmm: A Context stores the complete state of a simulation.
Context() - Constructor for class ffx.openmm.Context: Constructor.
Context(System, Integrator, Platform) - Constructor for class ffx.openmm.Context: Construct a new Context in which to run a simulation, explicitly specifying what Platform should be used to perform calculations.
Continuous1DFunction - Class in ffx.openmm: This is a TabulatedFunction that computes a continuous one dimensional function.
Continuous1DFunction(PointerByReference, double, double, boolean) - Constructor for class ffx.openmm.Continuous1DFunction: Create a Continuous1DFunction f(x) based on a set of tabulated values.
Continuous2DFunction - Class in ffx.openmm: This is a TabulatedFunction that computes a continuous two dimensional function.
Continuous2DFunction(PointerByReference, int, int, double, double, double, double, boolean) - Constructor for class ffx.openmm.Continuous2DFunction: Create a Continuous2DFunction f(x,y) based on a set of tabulated values.
Continuous3DFunction - Class in ffx.openmm: This is a TabulatedFunction that computes a continuous three dimensional function.
Continuous3DFunction(PointerByReference, int, int, int, double, double, double, double, double, double, boolean) - Constructor for class ffx.openmm.Continuous3DFunction: Create a Continuous3DFunction f(x,y,z) based on a set of tabulated values.
contractMultipoleI(PolarizableMultipole, double[], int, int, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Contract multipole moments with their respective electrostatic potential derivatives.
controlButton - Variable in class ffx.ui.behaviors.PickMouseBehavior
controlStep() - Method in class ffx.algorithms.mc.RosenbluthCBMC: controlStep.
ConvexHullOps - Class in ffx.potential.utils: This ConvexHullOps class uses the QuickHull3D package by John E.
ConvexHullOps() - Constructor for class ffx.potential.utils.ConvexHullOps
convolution(double[]) - Method in class ffx.numerics.fft.Complex3D: Perform a convolution.
convolution(double[]) - Method in class ffx.numerics.fft.Complex3DParallel: Compute the 3D FFT, perform a multiplication in reciprocal space, and the inverse 3D FFT in parallel.
convolution(double[]) - Method in class ffx.numerics.fft.Real3D: convolution
convolution(double[]) - Method in class ffx.numerics.fft.Real3DParallel: Compute a convolution in parallel.
CoordinateFileFilter - Class in ffx.potential.parsers: The CoordinateFileFilter class globally determines if a file is a valid coordinate file (PDB, XYZ, INT, or ARC formats).
CoordinateFileFilter() - Constructor for class ffx.potential.parsers.CoordinateFileFilter: Public Constructor.
coordinates - Variable in class ffx.numerics.multipole.MultipoleTensor: The coordinate system in use (global or QI).
coordinates - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: The coordinate system in use (global or QI).
coordinates - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Dimensions of [nsymm][xyz][nAtoms].
coordinates - Variable in class ffx.potential.nonbonded.RowRegion
coordinates - Variable in class ffx.potential.nonbonded.SliceRegion
coordinates - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
coordinates - Variable in class ffx.ui.commands.SimulationDefinition
coordinates - Variable in class ffx.ui.commands.SimulationUpdate
COORDINATES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine coordinates only
COORDINATES_AND_BFACTORS - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine coordinates and B factors (if anisotropic, refined as such)
COORDINATES_AND_BFACTORS_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine all
COORDINATES_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine coordinates and occupancies
CoordinateSystem - Enum Class in ffx.numerics.multipole: Global and Quasi-Internal (QI) coordinate systems are supported.
copy() - Method in class ffx.numerics.math.Double3: Returns a new copy of this Double3.
copy() - Method in class ffx.numerics.math.Float3: Returns a new copy of this Float3.
copy(boolean[][], Range, Range, boolean[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one Boolean matrix to a range of elements in another Boolean matrix.
copy(boolean[], Range, boolean[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one Boolean array to a range of elements in another Boolean array.
copy(byte[]) - Method in class edu.rit.util.ByteSequence: Copy this byte sequence's contents into the given byte array.
copy(byte[][], Range, Range, byte[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one byte matrix to a range of elements in another byte matrix.
copy(byte[], int, int) - Method in class edu.rit.util.ByteSequence: Copy this byte sequence's contents into a portion of the given byte array.
copy(byte[], Range, byte[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one byte array to a range of elements in another byte array.
copy(char[][], Range, Range, char[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one character matrix to a range of elements in another character matrix.
copy(char[], Range, char[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one character array to a range of elements in another character array.
copy(double[][], Range, Range, double[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one double matrix to a range of elements in another double matrix.
copy(double[], Range, double[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one double array to a range of elements in another double array.
copy(float[][], Range, Range, float[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one float matrix to a range of elements in another float matrix.
copy(float[], Range, float[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one float array to a range of elements in another float array.
copy(int[][], Range, Range, int[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one integer matrix to a range of elements in another integer matrix.
copy(int[], Range, int[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one integer array to a range of elements in another integer array.
copy(long[][], Range, Range, long[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one long matrix to a range of elements in another long matrix.
copy(long[], Range, long[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one long array to a range of elements in another long array.
copy(short[][], Range, Range, short[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one short matrix to a range of elements in another short matrix.
copy(short[], Range, short[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one short array to a range of elements in another short array.
copy(Buf) - Method in class edu.rit.mp.BooleanBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.BooleanArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.BooleanMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ByteArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ByteMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.CharacterArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.CharacterMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Buf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.DoubleArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.DoubleMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyBooleanBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyByteBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyCharacterBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyDoubleBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyFloatBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyLongBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyObjectBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyShortBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.FloatArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.FloatMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.IntegerArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.IntegerMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.LongArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.LongMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ObjectArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ObjectMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ShortArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ShortMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.ByteBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.CharacterBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.DoubleBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.FloatBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.IntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.LongBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.ObjectBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.ShortBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Signed16BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Signed8BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf: Copy items from the given buffer to this buffer.
copy(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: copy
copy(ST[][], Range, Range, DT[][], Range, Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one object matrix to a range of elements in another object matrix.
copy(ST[], Range, DT[], Range) - Static method in class edu.rit.util.Arrays: Copy a range of elements from one object array to a range of elements in another object array.
copyAccelerationsToPrevious() - Method in class ffx.potential.SystemState: Copy the current accelerations to the previous accelerations.
copyAccelerationToPrevious() - Method in class ffx.algorithms.dynamics.integrators.Integrator: Copy acceleration to previous acceleration.
copyEstimator() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Return a copy of this Estimator.
copyEstimator() - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Return a copy of this Estimator.
copyEstimator() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
copyEstimator() - Method in class ffx.numerics.estimator.Zwanzig: Return a copy of this Estimator.
copyESVHistogramTo(int[][]) - Method in class ffx.potential.extended.ExtendedSystem: Changes this ESV's histogram to equal the one passed
copyInputStreamToTmpFile(InputStream, String, String, String) - Static method in class ffx.utilities.FileUtils: Returns the file name of a temporary copy of input content.
copyResidue(Residue, Residue) - Static method in class ffx.potential.bonded.AminoAcidUtils: copyResidue.
copyState(AssemblyState) - Static method in class ffx.potential.AssemblyState: Copies an AssemblyState.
coreInteraction(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.AmoebaPlusDampTensorGlobal: Terms 1, 2, 3 in Eq. 5 of AMOEBA+ paper.
coreInteractionAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[]) - Method in class ffx.numerics.multipole.AmoebaPlusDampTensorGlobal: Compute the core interaction and gradient between two sites.
cos - Variable in class ffx.potential.parameters.ImproperTorsionType: Value of cos(toRadians(phase)).
cos() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the complex cosine of this.
cosDiameter - Variable in class ffx.potential.parameters.SoluteType: Solute atomic diameter for ddCOSMO.
cosine - Variable in class ffx.potential.parameters.TorsionType: Cosine of the phase angle.
CosineWave - Class in ffx.numerics.integrate: A CosineWave describes points along a sine wave of f(x) = a*sin(jx).
CosineWave(double[], boolean, double, double) - Constructor for class ffx.numerics.integrate.CosineWave: Constructs f(x) = a*cos(nx).
CosineWave(double[], double, double) - Constructor for class ffx.numerics.integrate.CosineWave: Constructs f(x) = a*cos(nx).
COULOMB - Enum constant in enum class ffx.numerics.multipole.Operator: Coulomb operator.
coulombSource - Variable in class ffx.numerics.multipole.MultipoleTensor: These are the "source" terms for the recursion for the Coulomb operator (1/R).
coulombSource - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: These are the "source" terms for the recursion for the Coulomb operator (1/R).
CoulombTensorGlobal - Class in ffx.numerics.multipole: The CoulombTensorGlobal class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame.
CoulombTensorGlobal(int) - Constructor for class ffx.numerics.multipole.CoulombTensorGlobal: Constructor for CoulombTensorGlobal.
CoulombTensorGlobalSIMD - Class in ffx.numerics.multipole: The CoulombTensorGlobal class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame using SIMD instructions.
CoulombTensorGlobalSIMD(int) - Constructor for class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Constructor for CoulombTensorGlobalSIMD.
CoulombTensorQI - Class in ffx.numerics.multipole: The CoulombTensorQI class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
CoulombTensorQI(int) - Constructor for class ffx.numerics.multipole.CoulombTensorQI: Create a new CoulombTensorQI object.
CoulombTensorQISIMD - Class in ffx.numerics.multipole: The CoulombTensorQISIMD class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame using SIMD instructions.
CoulombTensorQISIMD(int) - Constructor for class ffx.numerics.multipole.CoulombTensorQISIMD: Create a new CoulombTensorQI object.
count - Variable in class edu.rit.pj.cluster.JobInfo: The number of processes that have been assigned to the job so far.
count - Variable in class ffx.numerics.math.BootStrapStatistics: The number of entries.
count - Variable in class ffx.numerics.math.SummaryStatistics: Count of observations.
countLeafs() - Method in class ffx.numerics.clustering.Cluster: Counts the number of leaf descendants beneath this cluster.
countLeafs(Cluster, int) - Method in class ffx.numerics.clustering.Cluster: Recursive helper to count leaves under the specified node.
countNumModels() - Method in class ffx.potential.parsers.PDBFilter
countNumModels() - Method in class ffx.potential.parsers.SystemFilter
countNumModels() - Method in class ffx.potential.parsers.XPHFilter
countNumModels() - Method in class ffx.potential.parsers.XYZFilter
counts - Variable in class ffx.algorithms.thermodynamics.HistogramData: The number of hills added to the recursion kernel.
CPK - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
cpus - Variable in class edu.rit.pj.cluster.JobInfo: Number of CPUs assigned to each process in the job in rank order.
Cr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
create(Vertex[], int[]) - Static method in class ffx.numerics.quickhull.Face: Creates a Face by linking the specified indices of a vertex array into a closed counter-clockwise half-edge loop and computing its normal and centroid.
createAnnealer(DynamicsOptions, MolecularAssembly, Potential, AlgorithmListener) - Method in class ffx.algorithms.cli.AnnealOptions: Creates a SimulatedAnnealing object.
createAnnealer(DynamicsOptions, MolecularAssembly, Potential, AlgorithmListener, File) - Method in class ffx.algorithms.cli.AnnealOptions: Creates a SimulatedAnnealing object.
createBarostat(MolecularAssembly, CrystalPotential) - Method in class ffx.algorithms.cli.BarostatOptions: Creates a Barostat around a CrystalPotential.
createBox() - Method in class ffx.potential.MolecularAssembly: createBox
createComm(boolean) - Method in class edu.rit.pj.Comm: Create a new communicator.
createComm(boolean, int) - Method in class edu.rit.pj.Comm: Create a new communicator.
createCustomMTSIntegrator(double, OpenMMSystem) - Static method in class ffx.potential.openmm.OpenMMIntegrator: Create a Custom MTS Integrator.
createCustomMTSLangevinIntegrator(double, double, OpenMMSystem) - Static method in class ffx.potential.openmm.OpenMMIntegrator: Create a Custom MTS Langevin integrator.
createdFiles - Variable in class ffx.potential.commands.ImportCIF: Array of strings containing files created.
createExceptionsFromBonds(BondArray, double, double) - Method in class ffx.openmm.NonbondedForce: Create exceptions from bonds.
createExclusionsFromBonds(PointerByReference, int) - Method in class ffx.openmm.CustomManyParticleForce: Identify exclusions based on the molecular topology.
createExclusionsFromBonds(BondArray, int) - Method in class ffx.openmm.CustomNonbondedForce: Create exclusions based on the molecular topology.
createGzipReader(File) - Static method in class ffx.utilities.StringUtils: Creates a reader from a Gzip file to text.
createGzipReader(File, Charset) - Static method in class ffx.utilities.StringUtils: Creates a reader from a Gzip file to text.
createGzipWriter(File) - Static method in class ffx.utilities.StringUtils: Creates a writer for text to a Gzip file.
createGzipWriter(File, Charset) - Static method in class ffx.utilities.StringUtils: Creates a writer for text to a Gzip file.
createInitialSimplex() - Method in class ffx.numerics.quickhull.QuickHull3D: Creates the initial tetrahedral simplex from extremal points, throwing if points are coincident/colinear/coplanar within the current tolerance.
createInstance(int, int) - Method in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl: Factory method to create an AtomicDoubleArray instance.
createIntegrator(String, double, double, OpenMMSystem) - Static method in class ffx.potential.openmm.OpenMMIntegrator: Create a integrator.
createJob(int) - Method in class edu.rit.pj.job.JobGenerator: Create the job with the given job number.
createJoint(Bond, MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MSGroup: Create a joint between two chemical groups.
createJoint(Bond, MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MultiResidue: Create a joint between two chemical groups.
createJoint(MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MSGroup: Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
createJoint(MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MultiResidue: Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
createJoint(Residue, Residue, ForceField) - Method in class ffx.potential.bonded.Polymer: Form a Joint between two residues.
createLangevinIntegrator(double, double, ForceField) - Static method in class ffx.potential.openmm.OpenMMIntegrator: Create a Langevin integrator.
createMTSLangevinSubStep(int, int[], int[], StringBuilder) - Method in class ffx.potential.openmm.CustomMTSLangevinIntegrator: Create substeps for the MTS Langevin CustomIntegrator.
createMTSSubStep(int, int[], int[]) - Method in class ffx.potential.openmm.CustomMTSIntegrator: Create substeps for the MTS CustomIntegrator.
CreateRotamers - Class in ffx.algorithms.commands.test: The CreateRotamers script creates a set of conformation dependent rotamers.
CreateRotamers() - Constructor for class ffx.algorithms.commands.test.CreateRotamers: CreateRotamers Constructor.
CreateRotamers(FFXBinding) - Constructor for class ffx.algorithms.commands.test.CreateRotamers: CreateRotamers Constructor.
CreateRotamers(String[]) - Constructor for class ffx.algorithms.commands.test.CreateRotamers: CreateRotamers constructor that sets the command line arguments.
createTimer(TimerTask) - Method in class edu.rit.util.TimerThread: Create a new timer associated with the given timer task and under the control of this timer thread.
createTriangle(Vertex, Vertex, Vertex) - Static method in class ffx.numerics.quickhull.Face: Convenience method to create a triangular Face from three vertices.
createTriangle(Vertex, Vertex, Vertex, double) - Static method in class ffx.numerics.quickhull.Face: Constructs a triangular Face from vertices v0, v1, and v2 and computes its normal and centroid.
createVerletIntegrator(double) - Static method in class ffx.potential.openmm.OpenMMIntegrator: Create a Verlet integrator.
critical(Lock, ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Perform a section of code in a critical region with exclusive locking using the given lock.
critical(ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Perform a section of code in a critical region with exclusive locking.
criticalNonexclusive(Lock, ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Perform a section of code in a critical region with nonexclusive locking using the given lock.
criticalNonexclusive(ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Perform a section of code in a critical region with nonexclusive locking.
cross(Vector3d, Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Computes the cross product of v1 and v2 and places the result in this vector.
crystal - Variable in class ffx.crystal.ReflectionList: The Crystal instance.
crystal - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
Crystal - Class in ffx.crystal: The Crystal class encapsulates the lattice parameters and space group that describe the geometry and symmetry of a crystal.
Crystal(double, double, double, double, double, double, int) - Constructor for class ffx.crystal.Crystal: The Crystal class encapsulates the lattice parameters and space group.
Crystal(double, double, double, double, double, double, String) - Constructor for class ffx.crystal.Crystal: The Crystal class encapsulates the lattice parameters and space group.
CrystalMinimize - Class in ffx.algorithms.optimize: Minimize the energy of a system to an RMS gradient per atom convergence criteria.
CrystalMinimize(MolecularAssembly, XtalEnergy, AlgorithmListener) - Constructor for class ffx.algorithms.optimize.CrystalMinimize: Constructor for CrystalMinimize.
CrystalPotential - Interface in ffx.crystal: The CrystalPotential interface extends Potential to provide methods that change the periodic boundary conditions and symmetry via a Crystal instance.
CrystalReciprocalSpace - Class in ffx.xray: Structure factor calculation (including bulk solvent structure factors)
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam) - Constructor for class ffx.xray.CrystalReciprocalSpace: Crystal Reciprocal Space constructor, assumes this is not a bulk solvent mask and is not a neutron data set
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam, boolean) - Constructor for class ffx.xray.CrystalReciprocalSpace: Crystal Reciprocal Space constructor, assumes this is not a neutron data set and implements a polynomial bulk solvent mask if needed
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam, boolean, boolean) - Constructor for class ffx.xray.CrystalReciprocalSpace: Crystal Reciprocal Space constructor, assumes a polynomial bulk solvent mask if needed
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam, boolean, boolean, CrystalReciprocalSpace.SolventModel, CrystalReciprocalSpace.GridMethod) - Constructor for class ffx.xray.CrystalReciprocalSpace: Crystal Reciprocal Space constructor, all parameters provided
CrystalReciprocalSpace.GridMethod - Enum Class in ffx.xray
CrystalReciprocalSpace.SolventModel - Enum Class in ffx.xray: The possible solvent model methods
CrystalSearch - Class in ffx.algorithms.commands.test: The CrystalSearch script searches for minimum energy polymorphs for a given space group.
CrystalSearch() - Constructor for class ffx.algorithms.commands.test.CrystalSearch: CrystalSearch Constructor.
CrystalSearch(FFXBinding) - Constructor for class ffx.algorithms.commands.test.CrystalSearch: CrystalSearch Constructor.
CrystalSearch(String[]) - Constructor for class ffx.algorithms.commands.test.CrystalSearch: CrystalSearch constructor that sets the command line arguments.
CrystalStats - Class in ffx.xray: Crystal statistics output/logger
crystalSystem - Variable in class ffx.crystal.SpaceGroup: Crystal system.
CrystalSystem - Enum Class in ffx.crystal: Enumeration of the 7 crystal systems.
Cs - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
csdPercent - Static variable in class ffx.crystal.SpaceGroupInfo: Space group frequency ranking for the 1,231,510 CSD structures for which the space group is fully defined.
CTRL_ALL - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
Cu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
cubic - Variable in class ffx.potential.parameters.AngleType: Cubic coefficient in angle bending potential.
cubic - Variable in class ffx.potential.parameters.BondType: Cubic coefficient in bond stretch potential.
cubic - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Cubic coefficient in out-of-plane angle bending potential.
cubic - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
cubic - Variable in class ffx.potential.parameters.UreyBradleyType: Cubic coefficient in bond stretch potential.
CUBIC - Enum constant in enum class ffx.crystal.CrystalSystem: Cubic crystal system.
CUBIC_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem: Cubic lattice system.
CUBIC_MEAN - Enum constant in enum class ffx.potential.parameters.VDWType.RADIUS_RULE
currentEnergy() - Method in class ffx.algorithms.mc.BoltzmannMC: Must return the current energy of the system.
currentEnergy() - Method in class ffx.algorithms.mc.MolecularMC: Must return the current energy of the system.
currentEnergy() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMC: If useFullAMOEBAEnergy is set to true, explicitly evaluates energy, else computes energy from the rotamer energy matrices.
currentEnergy() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Must return the current energy of the system.
currentEnergy(Residue[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Calculates the energy at the current state.
currentEnergyWrapper(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization: Wrapper intended for use with RotamerMatrixMC.
currentFFXPE() - Method in class ffx.algorithms.optimize.RotamerOptimization: Forces the use of a ForceFieldEnergyOpenMM's underlying ForceFieldEnergy.
currGrp - Variable in class ffx.ui.behaviors.PickMouseBehavior
currXform - Variable in class ffx.ui.behaviors.MouseBehavior
CustomAngleForce - Class in ffx.openmm: This class implements interactions between sets of three particles that depend on the angle between them.
CustomAngleForce(String) - Constructor for class ffx.openmm.CustomAngleForce: Create a CustomAngleForce.
CustomBondForce - Class in ffx.openmm: This class implements bonded interactions between pairs of particles.
CustomBondForce(String) - Constructor for class ffx.openmm.CustomBondForce: Create a CustomBondForce.
CustomCentroidBondForce - Class in ffx.openmm: This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles, it applies them between the centers of groups of particles.
CustomCentroidBondForce(int, String) - Constructor for class ffx.openmm.CustomCentroidBondForce: Create a CustomCentroidBondForce.
CustomCompoundBondForce - Class in ffx.openmm: This class supports a wide variety of bonded interactions.
CustomCompoundBondForce(int, String) - Constructor for class ffx.openmm.CustomCompoundBondForce: Create a CustomCompoundBondForce.
CustomCVForce - Class in ffx.openmm: This class supports energy functions that depend on collective variables.
CustomCVForce(String) - Constructor for class ffx.openmm.CustomCVForce: Create a new CustomCVForce.
CustomExternalForce - Class in ffx.openmm: This class implements an "external" force on particles.
CustomExternalForce(String) - Constructor for class ffx.openmm.CustomExternalForce: Create a CustomExternalForce.
CustomGBForce - Class in ffx.openmm: This class implements complex, multiple stage nonbonded interactions between particles.
CustomGBForce() - Constructor for class ffx.openmm.CustomGBForce: Create a CustomGBForce.
CustomHbondForce - Class in ffx.openmm: This class supports a wide variety of energy functions used to represent hydrogen bonding.
CustomHbondForce(String) - Constructor for class ffx.openmm.CustomHbondForce: Create a new CustomHbondForce.
CustomIntegrator - Class in ffx.openmm: This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms.
CustomIntegrator(double) - Constructor for class ffx.openmm.CustomIntegrator: Constructor.
CustomManyParticleForce - Class in ffx.openmm: This class supports a wide variety of nonbonded N-particle interactions, where N is user specified.
CustomManyParticleForce(int, String) - Constructor for class ffx.openmm.CustomManyParticleForce: Create a CustomManyParticleForce.
CustomMTSIntegrator - Class in ffx.potential.openmm: OpenMM Custom MTS Integrator.
CustomMTSIntegrator(double, double, boolean) - Constructor for class ffx.potential.openmm.CustomMTSIntegrator
CustomMTSLangevinIntegrator - Class in ffx.potential.openmm: OpenMM Custom MTS Langevin Integrator.
CustomMTSLangevinIntegrator(double, double, double, boolean) - Constructor for class ffx.potential.openmm.CustomMTSLangevinIntegrator: Constructor.
CustomNonbondedForce - Class in ffx.openmm: This class implements nonbonded interactions between particles.
CustomNonbondedForce(String) - Constructor for class ffx.openmm.CustomNonbondedForce: Constructor.
CustomTorsionForce - Class in ffx.openmm: This class implements interactions between sets of four particles that depend on the torsion angle between them.
CustomTorsionForce(String) - Constructor for class ffx.openmm.CustomTorsionForce: Create a CustomTorsionForce.
CustomVolumeForce - Class in ffx.openmm: This class computes an energy that depends only on the volume of the periodic box, or more generally on the box shape as specified by the elements of the box vectors.
CustomVolumeForce(String) - Constructor for class ffx.openmm.CustomVolumeForce: Create a CustomVolumeForce.
cut - Variable in class ffx.potential.nonbonded.NonbondedCutoff: At the distance "cut", a multiplicative switch begins to be applied.
cut2 - Variable in class ffx.potential.nonbonded.NonbondedCutoff: The distance cut squared.
CYD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
CYD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysStates
CYS - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
CYS - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysStates
CYSTEINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
CYStoCYD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
CYT - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
CYTOSINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
CYX - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
CZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
CZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CZ2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CZ3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP

D

d - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
D - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
D - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
d11scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: DIRECT-11-SCALE factor.
d12scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The DIRECT_12_SCALE factor is assumed to be 1.0.
d13scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The DIRECT_13_SCALE factor is assumed to be 1.0.
d14scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The DIRECT_14_SCALE factor is assumed to be 1.0.
d2lAlpha - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
d2lfAlpha - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Second lambda derivative of buffer distance.
d2lfPowPerm - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Second lambda derivative of lPowPerm.
d2lfPowPol - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Second lambda derivative of lPowPol.
d2lPowPerm - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
d2lPowPol - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
DAD - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
dampSource(double, double, double[]) - Static method in class ffx.numerics.multipole.AmoebaPlusDampTensorGlobal: Generate source terms for the Challacombe et al. recursion.
DataContainer - Interface in ffx.xray: DataContainer interface.
DataInputStream - Class in edu.rit.io: Class DataInputStream provides an input stream that reads primitive data types and strings in binary form.
DataInputStream(InputStream) - Constructor for class edu.rit.io.DataInputStream: Construct a new data input stream.
DataLayout1D - Enum Class in ffx.numerics.fft: The Complex FFT supports interleaved or blocked data.
DataLayout2D - Enum Class in ffx.numerics.fft: The Complex FFT supports interleaved or blocked data.
DataLayout3D - Enum Class in ffx.numerics.fft: The Complex FFT supports interleaved or blocked data.
DATAONLY - Static variable in interface ffx.xray.parsers.MTZWriter.MTZType: Output unscaled data only.
DataOutputStream - Class in edu.rit.io: Class DataOutputStream provides an output stream that writes primitive data types and strings in binary form.
DataOutputStream(OutputStream) - Constructor for class edu.rit.io.DataOutputStream: Construct a new data output stream.
DataRefinementOptions - Class in ffx.xray.cli: Represents command line options for scripts that utilize some form of crystallographic data.
DataRefinementOptions() - Constructor for class ffx.xray.cli.DataRefinementOptions
DataSet - Interface in ffx.numerics.integrate: A DataSet represents a set of points along a single dimension, and is able to be numerically integrated.
date - Static variable in class ffx.ui.MainPanel: Constant date="January 2025"
Db - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
DCY - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
ddgunToNPChange(List<String>) - Method in class ffx.potential.utils.GetProteinFeatures: Use the ddgun output file to get the amino acid changes
ddp - Variable in class ffx.potential.parameters.PolarizeType: Direct polarization damping.
deallocate(boolean[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given Boolean matrix.
deallocate(boolean[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given Boolean matrix.
deallocate(byte[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given byte matrix.
deallocate(byte[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given byte matrix.
deallocate(char[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given character matrix.
deallocate(char[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given character matrix.
deallocate(double[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given double matrix.
deallocate(double[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given double matrix.
deallocate(float[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given float matrix.
deallocate(float[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given float matrix.
deallocate(int[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given integer matrix.
deallocate(int[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given integer matrix.
deallocate(long[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given long matrix.
deallocate(long[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given long matrix.
deallocate(short[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given short matrix.
deallocate(short[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given short matrix.
deallocate(T[]) - Static method in class edu.rit.util.Arrays: Deallocate all elements in the given object array.
deallocate(T[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given object matrix.
deallocate(T[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given object matrix.
deallocate(T[][], Range, Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row and column index ranges in the given object matrix.
deallocate(T[], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given index range in the given object array.
decode(int, String) - Static method in class ffx.utilities.Hybrid36: Hybrid-36 decoder: converts string s to integer result.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedByte: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedCharacter: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedDouble: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedFloat: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedInteger: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedLong: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedShort: Subtract one from this reduction variable and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedByteArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedFloatArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedLongArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedShortArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Subtract one from this matrix reduction variable at the given row and column and return the new value.
decrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Subtract one from this matrix reduction variable at the given row and column and return the new value.
dEdLSign - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dEdLZeroAtEnds() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in interface ffx.potential.bonded.LambdaInterface: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.DualTopologyEnergy: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.ForceFieldEnergy: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.QuadTopologyEnergy: Returns true if dUdL is guaranteed to be zero at 0 and 1.
Default - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
DEFAULT_ANGLE_CUBIC - Static variable in class ffx.potential.parameters.AngleType: Default cubic coefficient in angle bending potential.
DEFAULT_ANGLE_PENTIC - Static variable in class ffx.potential.parameters.AngleType: Default pentic coefficient in angle bending potential.
DEFAULT_ANGLE_QUARTIC - Static variable in class ffx.potential.parameters.AngleType: Default quartic coefficient in angle bending potential.
DEFAULT_ANGLE_SEXTIC - Static variable in class ffx.potential.parameters.AngleType: Default quintic coefficient in angle bending potential.
DEFAULT_ANGLE_UNIT - Static variable in class ffx.potential.parameters.AngleType: Default convert angle bending energy to kcal/mole.
DEFAULT_ANGLEMAX - Static variable in class ffx.numerics.optimization.LBFGS: The default maximum angle between search direction and gradient.
DEFAULT_ANGTOR_UNIT - Static variable in class ffx.potential.parameters.AngleTorsionType
DEFAULT_BAROSTAT_INTERVAL - Static variable in class ffx.algorithms.cli.BarostatOptions: Default mean number of MD steps (Poisson distribution) between barostat move proposals.
DEFAULT_BAROSTAT_PRINT_INTERVAL - Static variable in class ffx.algorithms.cli.BarostatOptions: Default number of Barostat moves between print statements.
DEFAULT_BOND_CUBIC - Static variable in class ffx.potential.parameters.BondType: Default cubic coefficient in bond stretch potential.
DEFAULT_BOND_QUARTIC - Static variable in class ffx.potential.parameters.BondType: Default quartic coefficient in bond stretch potential.
DEFAULT_BOND_UNIT - Static variable in class ffx.potential.parameters.BondType
DEFAULT_CAPPA - Static variable in class ffx.numerics.optimization.LBFGS: Controls the accuracy of the line search.
DEFAULT_CAVDISP_SURFACE_TENSION - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default surface tension for apolar models with an explicit dispersion term.
DEFAULT_CCMA_NONZERO_CUTOFF - Static variable in class ffx.potential.constraint.CcmaConstraint
DEFAULT_CG_PRECONDITIONER_CUTOFF - Static variable in class ffx.potential.nonbonded.pme.PCGSolver: A preconditioner cut-off of 3 to 4 Angstroms generally works well.
DEFAULT_CG_PRECONDITIONER_EWALD - Static variable in class ffx.potential.nonbonded.pme.PCGSolver: An Ewald coefficient of 0 indicates use of Coulomb's law with no damping.
DEFAULT_CG_PRECONDITIONER_SCALE - Static variable in class ffx.potential.nonbonded.pme.PCGSolver: The scale factor is applied to the diagonal terms of the preconditioner.
DEFAULT_CHG_12_SCALE - Static variable in class ffx.potential.parameters.ChargeType
DEFAULT_CHG_13_SCALE - Static variable in class ffx.potential.parameters.ChargeType
DEFAULT_CHG_14_SCALE - Static variable in class ffx.potential.parameters.ChargeType
DEFAULT_CHG_15_SCALE - Static variable in class ffx.potential.parameters.ChargeType
DEFAULT_CONSTRAINT_TOLERANCE - Static variable in class ffx.potential.ForceFieldEnergy: Default tolerance for numerical methods of solving constraints.
DEFAULT_CROSSOVER - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Using a S.P. of 0.0334 kcal/mol/A^3, and a limiting surface tension of 0.103 kcal/mol/A^2, the cross-over point is 9.2515 A.
DEFAULT_DELTA - Static variable in class ffx.potential.parameters.VDWType: The default delta parameter in Halgren’s buffered 14-7 vdw potential energy functional form.
DEFAULT_DIELECTRIC_OFFSET - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default dielectric offset
DEFAULT_DIRECT_11_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_DIRECT_12_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_DIRECT_13_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_DIRECT_14_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_DISPERSION_OFFSET - Static variable in class ffx.potential.nonbonded.implicit.DispersionRegion: The dispersion integral begins for each atom at: Rmin_ij + DISPERSION_OFFSET
DEFAULT_ELECTRIC - Static variable in class ffx.utilities.Constants: Coulomb constant in units of kcal*Ang/(mol*electron^2)
DEFAULT_EPSILON_RULE - Static variable in class ffx.potential.parameters.VDWType: The default epsilon combining rule.
DEFAULT_EWALD_COEFFICIENT - Static variable in class ffx.potential.nonbonded.pme.EwaldParameters: The default Ewald coefficient.
DEFAULT_EWALD_CUTOFF - Static variable in class ffx.potential.nonbonded.pme.EwaldParameters: Default cutoff values for PME under periodic boundary conditions.
DEFAULT_GAMMA - Static variable in class ffx.potential.parameters.VDWType: The default gamma parameter in Halgren’s buffered 14-7 vdw potential energy functional form.
DEFAULT_GAUSSVOL_RADII_OFFSET - Static variable in class ffx.potential.nonbonded.implicit.GaussVol: Default offset applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms.
DEFAULT_GAUSSVOL_RADII_SCALE - Static variable in class ffx.potential.nonbonded.implicit.GaussVol: Default scaling applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms and general underestimation of molecular volume
DEFAULT_GKC - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default constant for the Generalized Kirkwood cross-term.
DEFAULT_IMPTOR_UNIT - Static variable in class ffx.potential.parameters.ImproperTorsionType
DEFAULT_INTMAX - Static variable in class ffx.numerics.optimization.LBFGS: The default maximum number of interpolations during line search.
DEFAULT_LBFGS_VECTORS - Static variable in class ffx.algorithms.optimize.Minimize: The default number of correction vectors used by the limited-memory L-BFGS optimization routine.
DEFAULT_MAX_ANGLE_MOVE - Static variable in class ffx.algorithms.cli.BarostatOptions: Default width of proposed crystal angle moves (uniformly distributed) in degrees.
DEFAULT_MAX_DENSITY - Static variable in class ffx.algorithms.cli.BarostatOptions: Default maximum density constraint on the barostat that prevents reduction in unit cell (particularly at or near vapor states).
DEFAULT_MAX_VOLUME_MOVE - Static variable in class ffx.algorithms.cli.BarostatOptions: Default size of proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
DEFAULT_MIN_DENSITY - Static variable in class ffx.algorithms.cli.BarostatOptions: Default "tin box" constraint on the barostat that prevents expansion of the unit cell (particularly at or near vapor states).
DEFAULT_MPOLE_12_SCALE - Static variable in class ffx.potential.parameters.MultipoleType
DEFAULT_MPOLE_13_SCALE - Static variable in class ffx.potential.parameters.MultipoleType
DEFAULT_MPOLE_14_SCALE - Static variable in class ffx.potential.parameters.MultipoleType
DEFAULT_MPOLE_15_SCALE - Static variable in class ffx.potential.parameters.MultipoleType
DEFAULT_OPBEND_CUBIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default cubic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_PENTIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default pentic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_QUARTIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default quartic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_SEXTIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default quintic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_UNIT - Static variable in class ffx.potential.parameters.OutOfPlaneBendType
DEFAULT_PITORS_UNIT - Static variable in class ffx.potential.parameters.PiOrbitalTorsionType
DEFAULT_POLAR_12_INTRA - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_POLAR_12_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_POLAR_13_INTRA - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_POLAR_13_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_POLAR_14_INTRA - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_POLAR_14_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_POLAR_15_INTRA - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_POLAR_15_SCALE - Static variable in class ffx.potential.parameters.PolarizeType
DEFAULT_RADIUS_RULE - Static variable in class ffx.potential.parameters.VDWType: The default radius combining rule.
DEFAULT_RADIUS_SIZE - Static variable in class ffx.potential.parameters.VDWType: The default radius size.
DEFAULT_RADIUS_TYPE - Static variable in class ffx.potential.parameters.VDWType: The default radius type.
DEFAULT_RB_LAM_END - Static variable in class ffx.potential.bonded.RestrainDistance
DEFAULT_RB_LAM_START - Static variable in class ffx.potential.bonded.RestrainDistance
DEFAULT_SLOPEMAX - Static variable in class ffx.numerics.optimization.LBFGS: The default projected gradient above which step size is reduced.
DEFAULT_SNECK - Variable in class ffx.potential.parameters.SoluteType
DEFAULT_SOLUTE_OFFSET - Static variable in class ffx.potential.nonbonded.implicit.DispersionRegion: Each solute atom blocks dispersion interactions with solvent: Rmin + SOLUTE_OFFSET
DEFAULT_SOLVENT_PRESSURE - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default solvent pressure for apolar models with an explicit volume term.
DEFAULT_STEPMAX - Static variable in class ffx.numerics.optimization.LBFGS: This specifies the default upper bound for the step in the line search.
DEFAULT_STEPMIN - Static variable in class ffx.numerics.optimization.LBFGS: This specifies the default lower bound for the step in the line search.
DEFAULT_STRBND_UNIT - Static variable in class ffx.potential.parameters.StretchBendType: Constant units=PI / 180.0
DEFAULT_STRTOR_UNIT - Static variable in class ffx.potential.parameters.StretchTorsionType
DEFAULT_TANH_BETA0 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default value of beta0 for tanh scaling
DEFAULT_TANH_BETA1 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default value of beta1 for tanh scaling
DEFAULT_TANH_BETA2 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default value of beta2 for tanh scaling
DEFAULT_TORSION_UNIT - Static variable in class ffx.potential.parameters.TorsionType
DEFAULT_TORTOR_UNIT - Static variable in class ffx.potential.parameters.TorsionTorsionType: Default units to convert Torsion-Torsion energy to kcal/mole.
DEFAULT_UREY_CUBIC - Static variable in class ffx.potential.parameters.UreyBradleyType: Default cubic coefficient in Urey-Bradley stretch potential.
DEFAULT_UREY_QUARTIC - Static variable in class ffx.potential.parameters.UreyBradleyType: Default quartic coefficient in Urey-Bradley stretch potential.
DEFAULT_UREY_UNIT - Static variable in class ffx.potential.parameters.UreyBradleyType: Default conversion Urey-Bradley stretch energy to kcal/mole.
DEFAULT_VDW_12_SCALE - Static variable in class ffx.potential.parameters.VDWType: The default van der Waals scale factor for 1-2 (bonded) interactions.
DEFAULT_VDW_13_SCALE - Static variable in class ffx.potential.parameters.VDWType: The default van der Waals scale factor for 1-3 (angle) interactions.
DEFAULT_VDW_14_SCALE - Static variable in class ffx.potential.parameters.VDWType: The default van der Waals scale factor for 1-4 (torisonal) interactions.
DEFAULT_VDW_CUTOFF - Static variable in class ffx.potential.nonbonded.VanDerWaalsForm: The default van der Waals cut-off radius is 12.0 Angstroms.
DEFAULT_VDW_TAPER - Static variable in class ffx.potential.nonbonded.VanDerWaalsForm: The default van der Waals taper location is at 90% of the cut-off distance.
DEFAULT_VDW_TYPE - Static variable in class ffx.potential.parameters.VDWType: The default van der Waals functional form type.
DEFAULT_WIGGLE - Static variable in class ffx.potential.nonbonded.implicit.ConnollyRegion: Default size of a vector to randomly perturb coordinates.
DefaultClusteringAlgorithm - Class in ffx.numerics.clustering: Clustering algorithm that operates on a full N x N distance matrix to produce hierarchical agglomerative clusters (dendrogram), with optional support for per-element weights and flat clustering by threshold.
DefaultClusteringAlgorithm() - Constructor for class ffx.numerics.clustering.DefaultClusteringAlgorithm
defaultCopy(BooleanBuf, BooleanBuf) - Static method in class edu.rit.mp.BooleanBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(ByteBuf, ByteBuf) - Static method in class edu.rit.mp.ByteBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(CharacterBuf, CharacterBuf) - Static method in class edu.rit.mp.CharacterBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(DoubleBuf, DoubleBuf) - Static method in class edu.rit.mp.DoubleBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(FloatBuf, FloatBuf) - Static method in class edu.rit.mp.FloatBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(IntegerBuf, IntegerBuf) - Static method in class edu.rit.mp.IntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(LongBuf, LongBuf) - Static method in class edu.rit.mp.LongBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(ObjectBuf<T>, ObjectBuf<T>) - Static method in class edu.rit.mp.ObjectBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(ShortBuf, ShortBuf) - Static method in class edu.rit.mp.ShortBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Signed16BitIntegerBuf, Signed16BitIntegerBuf) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Signed8BitIntegerBuf, Signed8BitIntegerBuf) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Unsigned16BitIntegerBuf, Unsigned16BitIntegerBuf) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Unsigned8BitIntegerBuf, Unsigned8BitIntegerBuf) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultEngine(MolecularAssembly, Potential) - Static method in class ffx.algorithms.optimize.Minimize
DefaultRandom - Class in edu.rit.util: Class DefaultRandom provides a default pseudorandom number generator (PRNG) designed for use in parallel scientific programming.
DefaultRandom(long) - Constructor for class edu.rit.util.DefaultRandom: Construct a new PRNG with the given seed.
defaultRotamerFactory(Residue) - Static method in class ffx.potential.bonded.Rotamer: Factory method to construct an original-coordinates Rotamer from a residue.
defaultRotamerFactory(Residue, TitrationUtils) - Static method in class ffx.potential.bonded.Rotamer: Factory method to construct an original-coordinates Rotamer from a residue.
defaultValue() - Element in annotation interface ffx.utilities.FFXProperty: The default value for this FFXProperty.
DEGREES_PER_RADIAN - Static variable in class ffx.utilities.Constants: Degrees per radian.
degreesOfFreedom - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat: Number of degrees of freedom, which can be less than the number of variables.
DEL_V_Cs_SI - Static variable in class ffx.utilities.Constants: Hyperfine transition frequency of cesium in Hertz, defining the second.
DELETED - Static variable in class ffx.numerics.quickhull.Face
deleteDirectoryTree(Path) - Static method in class ffx.utilities.DirectoryUtils: Recursively delete the contents of a directory.
deleteFacePoints(Face, Face) - Method in class ffx.numerics.quickhull.QuickHull3D: Removes all outside vertices from a face and either discards them as unclaimed or reassigns them to an absorbing face if they lie above it.
deleteMolecule(Molecule) - Method in class ffx.potential.MolecularAssembly: deleteMolecule
delta - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Second constant suggested by Halgren for the Buffered-14-7 potential.
DendrogramFrame - Class in ffx.numerics.clustering.visualization: Simple Swing JFrame that hosts a DendrogramPanel to visualize a clustering result.
DendrogramFrame(Cluster) - Constructor for class ffx.numerics.clustering.visualization.DendrogramFrame: Creates a frame displaying a dendrogram for the provided clustering result.
DendrogramPanel - Class in ffx.numerics.clustering.visualization: Swing panel responsible for laying out and drawing a dendrogram for a hierarchical Cluster model, including optional scale and distance labels.
DendrogramPanel() - Constructor for class ffx.numerics.clustering.visualization.DendrogramPanel
density - Variable in class ffx.ui.commands.SimulationUpdate
density() - Method in class ffx.algorithms.dynamics.Barostat: density.
Density - Class in ffx.potential.commands: Calculate the mean system density for single topology systems.
Density() - Constructor for class ffx.potential.commands.Density
Density(FFXBinding) - Constructor for class ffx.potential.commands.Density
Density(String[]) - Constructor for class ffx.potential.commands.Density
densityNorm(double[], double[], boolean) - Method in class ffx.xray.CrystalReciprocalSpace: densityNorm
DEOXYADENINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
DEOXYCYTOSINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
DEOXYGUANINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
deprotForm - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
describe() - Method in class ffx.numerics.math.BootStrapStatistics: Describe the Summary Statistics.
describe() - Method in class ffx.numerics.math.RunningStatistics: Describe the Summary Statistics.
describe() - Method in class ffx.numerics.math.SummaryStatistics: Describe the Summary Statistics.
describe(Atom.Descriptions) - Method in class ffx.potential.bonded.Atom: describe.
description - Variable in class ffx.potential.parameters.SoluteType: Optional SMARTS description.
description() - Element in annotation interface ffx.utilities.FFXProperty: A description of this FFXProperty.
destroy() - Method in class ffx.algorithms.dynamics.Barostat: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in interface ffx.numerics.OptimizationInterface: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.openmm.amoeba.DoubleArray3D: Destroy the array.
destroy() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Destroy the force.
destroy() - Method in class ffx.openmm.amoeba.GKCavitationForce: Destroy the force.
destroy() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Destroy the force.
destroy() - Method in class ffx.openmm.amoeba.MultipoleForce: Destroy the force.
destroy() - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Destroy the Amoeba Torsion-Torsion Force.
destroy() - Method in class ffx.openmm.amoeba.VdwForce: Destroy the force.
destroy() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Destroy the force.
destroy() - Method in class ffx.openmm.AndersenThermostat: Destroy the force.
destroy() - Method in class ffx.openmm.ATMForce: Destroy the force.
destroy() - Method in class ffx.openmm.BondArray: Destroy the bond array.
destroy() - Method in class ffx.openmm.BrownianIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.CMAPTorsionForce: Destroy the force.
destroy() - Method in class ffx.openmm.CMMotionRemover: Destroy the OpenMM CMMotionRemover.
destroy() - Method in class ffx.openmm.CompoundIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.Context: Destroy the context.
destroy() - Method in class ffx.openmm.Continuous1DFunction: Destroy the continuous 1D function.
destroy() - Method in class ffx.openmm.Continuous2DFunction: Destroy the continuous 2D function.
destroy() - Method in class ffx.openmm.Continuous3DFunction: Destroy the continuous 3D function.
destroy() - Method in class ffx.openmm.CustomAngleForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomBondForce: Destroy the OpenMM CustomBondForce.
destroy() - Method in class ffx.openmm.CustomCentroidBondForce: Destroy the OpenMM CustomCentroidBondForce.
destroy() - Method in class ffx.openmm.CustomCompoundBondForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomCVForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomExternalForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomGBForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomHbondForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.CustomManyParticleForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomNonbondedForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomTorsionForce: Destroy the force.
destroy() - Method in class ffx.openmm.CustomVolumeForce: Destroy the force.
destroy() - Method in class ffx.openmm.Discrete1DFunction: Destroy the discrete 1D function.
destroy() - Method in class ffx.openmm.Discrete2DFunction: Destroy the discrete 2D function.
destroy() - Method in class ffx.openmm.Discrete3DFunction: Destroy the discrete 3D function.
destroy() - Method in class ffx.openmm.DoubleArray: Destroy the array.
destroy() - Method in class ffx.openmm.drude.DrudeForce: Destroy the force.
destroy() - Method in class ffx.openmm.drude.DrudeIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.drude.DrudeNoseHooverIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.drude.DrudeSCFIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.Force: Destroy the force.
destroy() - Method in class ffx.openmm.GayBerneForce: Destroy the force.
destroy() - Method in class ffx.openmm.GBSAOBCForce: Destroy the force.
destroy() - Method in class ffx.openmm.HarmonicAngleForce: Destroy the force.
destroy() - Method in class ffx.openmm.HarmonicBondForce: Destroy the force.
destroy() - Method in class ffx.openmm.IntArray: Destroy the array.
destroy() - Method in class ffx.openmm.Integrator: This method will be called by subclasses when the integrator is destroyed.
destroy() - Method in class ffx.openmm.IntSet: Destroy the set.
destroy() - Method in class ffx.openmm.LangevinMiddleIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.LocalCoordinatesSite: Destroy the virtual site.
destroy() - Method in class ffx.openmm.MinimizationReporter: Destroy the reporter.
destroy() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Destroy the force.
destroy() - Method in class ffx.openmm.MonteCarloBarostat: Destroy the force.
destroy() - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Destroy the force.
destroy() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Destroy the force.
destroy() - Method in class ffx.openmm.NonbondedForce: Destroy the force.
destroy() - Method in class ffx.openmm.NoseHooverIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.OutOfPlaneSite: Destroy the virtual site.
destroy() - Method in class ffx.openmm.PeriodicTorsionForce: Destroy the force.
destroy() - Method in class ffx.openmm.Platform: Destroy the OpenMM Platform instance.
destroy() - Method in class ffx.openmm.RBTorsionForce: Destroy the force.
destroy() - Method in class ffx.openmm.RMSDForce: Destroy the force.
destroy() - Method in class ffx.openmm.State: Destroy the state.
destroy() - Method in class ffx.openmm.StringArray: Destroy the String Array.
destroy() - Method in class ffx.openmm.System: Destroy the system.
destroy() - Method in class ffx.openmm.TabulatedFunction: Destroy the tabulated function.
destroy() - Method in class ffx.openmm.ThreeParticleAverageSite: Destroy the virtual site.
destroy() - Method in class ffx.openmm.TwoParticleAverageSite: Destroy the virtual site.
destroy() - Method in class ffx.openmm.VariableLangevinIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.VariableVerletIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.Vec3Array: Destroy the Vec3Array.
destroy() - Method in class ffx.openmm.VerletIntegrator: Destroy the integrator.
destroy() - Method in class ffx.openmm.VirtualSite: Destroy the virtual site.
destroy() - Method in class ffx.potential.bonded.BondedTerm: destroy
destroy() - Method in class ffx.potential.bonded.MSNode: destroy
destroy() - Method in class ffx.potential.DualTopologyEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.potential.ForceFieldEnergy: Frees up assets associated with this ForceFieldEnergy, such as worker Threads.
destroy() - Method in class ffx.potential.MolecularAssembly: destroy
destroy() - Method in class ffx.potential.nonbonded.NeighborList: destroy.
destroy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
destroy() - Method in class ffx.potential.nonbonded.VanDerWaals: destroy.
destroy() - Method in class ffx.potential.openmm.OpenMMEnergy: Frees up assets associated with this ForceFieldEnergy, such as worker Threads.
destroy() - Method in class ffx.potential.QuadTopologyEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.potential.XtalEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.realspace.RealSpaceData: Similar to Potential.destroy(), frees up resources associated with this RealSpaceData.
destroy() - Method in class ffx.realspace.RealSpaceEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.ui.FFXSystem: destroy
destroy() - Method in class ffx.xray.DiffractionData: Similar to Potential.destroy(), frees up resources associated with this RealSpaceData.
destroy() - Method in class ffx.xray.RefinementEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.ScaleBulkEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.SigmaAEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.SplineEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.XRayEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
DESTROY - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
destroyPotentials() - Method in class ffx.algorithms.cli.AlgorithmsCommand: Reclaims resources associated with all Potential objects associated with this script.
destroyPotentials() - Method in class ffx.algorithms.commands.Anneal: Reclaims resources associated with all Potential objects associated with this script.
destroyPotentials() - Method in class ffx.algorithms.commands.Thermodynamics
destroyPotentials() - Method in class ffx.potential.cli.PotentialCommand: Reclaims resources associated with all Potential objects associated with this script.
destroyPotentials() - Method in class ffx.realspace.commands.Minimize
destroyPotentials() - Method in class ffx.xray.commands.ComputeFc
destroyPotentials() - Method in class ffx.xray.commands.Minimize
destroyPotentials() - Method in class ffx.xray.commands.ModelvsData
detach() - Method in class ffx.potential.MolecularAssembly: detach
detail - Static variable in class ffx.potential.bonded.RendererCache: Constant detail=3
DETAIL - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
determinant3(double[]) - Static method in class ffx.numerics.math.MatrixMath: determinant3
determinant3(double[][]) - Static method in class ffx.numerics.math.MatrixMath: Returns the determinant for a 3x3 matrix.
determineIntxyz(double[], double, double[], double, double[], double, int) - Static method in class ffx.potential.bonded.BondedUtils: This routine was derived from a similar routine in TINKER.
deterministic - Variable in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
Deuterate - Class in ffx.xray.commands: Deuterate changes exchangeable hydrogen atoms to deuterium atoms for a PDB file.
Deuterate() - Constructor for class ffx.xray.commands.Deuterate: Deuterate constructor.
Deuterate(FFXBinding) - Constructor for class ffx.xray.commands.Deuterate: Deuterate constructor.
Deuterate(String[]) - Constructor for class ffx.xray.commands.Deuterate: Deuterate constructor that sets the command line arguments.
dfi0() - Method in class ffx.crystal.ReflectionSpline: dfi0
dfi1() - Method in class ffx.crystal.ReflectionSpline: dfi1
dfi2() - Method in class ffx.crystal.ReflectionSpline: dfi2
dft(double[], double[]) - Static method in class ffx.numerics.fft.Complex: Static DFT method used to test the FFT.
dftBlocked(double[], double[]) - Static method in class ffx.numerics.fft.Complex: Static DFT method used to test the FFT.
DGU - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
di - Variable in class ffx.numerics.fft.MixedRadixFactor: Equal to 2 * nextInput for interleaved complex data.
DIAMETER - Enum constant in enum class ffx.potential.parameters.VDWType.RADIUS_SIZE
dieOnMissingAtom - Variable in class ffx.potential.parsers.SystemFilter: Constant dieOnMissingAtom=
DiffractionData - Class in ffx.xray: DiffractionData class.
DiffractionData(MolecularAssembly[], CompositeConfiguration) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
DiffractionData(MolecularAssembly[], CompositeConfiguration, CrystalReciprocalSpace.SolventModel, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionData(MolecularAssembly[], CompositeConfiguration, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionData(MolecularAssembly, CompositeConfiguration) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
DiffractionData(MolecularAssembly, CompositeConfiguration, CrystalReciprocalSpace.SolventModel) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
DiffractionData(MolecularAssembly, CompositeConfiguration, CrystalReciprocalSpace.SolventModel, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionData(MolecularAssembly, CompositeConfiguration, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionFile - Class in ffx.xray.parsers: DiffractionFile class.
DiffractionFile(MolecularAssembly) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
DiffractionFile(MolecularAssembly[]) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
DiffractionFile(MolecularAssembly[], double) - Constructor for class ffx.xray.parsers.DiffractionFile: Constructor for DiffractionFile.
DiffractionFile(MolecularAssembly[], double, boolean) - Constructor for class ffx.xray.parsers.DiffractionFile: Constructor for DiffractionFile.
DiffractionFile(MolecularAssembly, double) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a neutron value of false
DiffractionFile(MolecularAssembly, double, boolean) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
DiffractionFile(String) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file, weight set to 1.0 and neutron value of false
DiffractionFile(String, double) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file, neutron value set to false
DiffractionFile(String, double, boolean) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file
DiffractionFileFilter - Interface in ffx.xray.parsers: DiffractionFileFilter interface.
DiffractionRefinementData - Class in ffx.xray: DiffractionRefinementData class.
DiffractionRefinementData(CompositeConfiguration, ReflectionList) - Constructor for class ffx.xray.DiffractionRefinementData: allocate data given a ReflectionList
dihedralAngle(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the dihedral angle formed between 4 atoms, a, b, c, d, via position vectors AB, BC, and CD.
dihedralAngle(double[], double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the dihedral angle formed between 4 atoms.
dihedralAngle(float[], float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the dihedral angle formed between 4 atoms
DIPHOSPHATE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
dipole - Variable in class ffx.potential.parameters.MultipoleType: Atomic dipole. 1 x 3 (e Angstroms).
DIPOLE - Enum constant in enum class ffx.numerics.multipole.GKMultipoleOrder: Dipole potential.
dipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Permanent multipole energy and gradient using the GK dipole tensor.
dipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Permanent multipole energy and gradient using the GK dipole tensor.
dipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Permanent multipole energy and gradient using the GK dipole tensor.
dipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Permanent multipole energy and gradient using the GK dipole tensor.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the induced dipole field components due to site I at site K.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the induced dipole field components due to site K at site I.
dipolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Dipole Polarization Energy and Gradient.
dipolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Dipole Polarization Energy and Gradient.
dipolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Dipole Polarization Energy and Gradient.
dipolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Dipole Polarization Energy and Gradient.
dipoleTorque(PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the torque on a permanent dipole.
dipoleTorque(PolarizableMultipoleSIMD, DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the torque on a permanent dipole.
DIRECT - Enum constant in enum class ffx.potential.nonbonded.pme.Polarization
directDipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Direct induced dipoles.
directDipole - Variable in class ffx.potential.nonbonded.pme.DirectRegion: Direct induced dipoles.
directDipole - Variable in class ffx.potential.nonbonded.pme.SORRegion: Direct induced dipoles.
directDipoleCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
directDipoleCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
directDipoleCR - Variable in class ffx.potential.nonbonded.pme.SORRegion
directField - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
directField - Variable in class ffx.potential.nonbonded.pme.DirectRegion
directFieldCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
directFieldCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
direction - Variable in class ffx.algorithms.optimize.RotamerOptimization: The sliding window direction.
directionality - Variable in class ffx.numerics.estimator.Zwanzig: Directionality of the Zwanzig estimation (forwards perturbation or backwards perturbation).
DirectoryUtils - Class in ffx.utilities: DirectoryUtils class.
DirectRegion - Class in ffx.potential.nonbonded.pme: Parallel computation of induced dipoles due to the direct field.
DirectRegion(int) - Constructor for class ffx.potential.nonbonded.pme.DirectRegion
directSum() - Method in class ffx.potential.nonbonded.octree.Octree: Direct summation.
disableResetStatistics() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
Discrete1DFunction - Class in ffx.openmm: This is a TabulatedFunction that computes a discrete one dimensional function f(x).
Discrete1DFunction(PointerByReference) - Constructor for class ffx.openmm.Discrete1DFunction: Create a Discrete1DFunction f(x) based on a set of tabulated values.
Discrete2DFunction - Class in ffx.openmm: This is a TabulatedFunction that computes a discrete two dimensional function f(x,y).
Discrete2DFunction(int, int, PointerByReference) - Constructor for class ffx.openmm.Discrete2DFunction: Create a Discrete2DFunction f(x,y) based on a set of tabulated values.
Discrete3DFunction - Class in ffx.openmm: This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z).
Discrete3DFunction(int, int, int, PointerByReference) - Constructor for class ffx.openmm.Discrete3DFunction: Create a Discrete3DFunction f(x,y,z) based on a set of tabulated values.
DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
DispersionRegion - Class in ffx.potential.nonbonded.implicit: Parallel calculation of continuum dispersion energy via pairwise descreening.
DispersionRegion(int, Atom[], ForceField) - Constructor for class ffx.potential.nonbonded.implicit.DispersionRegion: DispersionRegion constructor.
dist(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the distance between two vectors.
dist(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the distance between two vectors.
dist(Double3) - Method in class ffx.numerics.math.Double3: Finds the Euclidean distance between two positions.
dist(Float3) - Method in class ffx.numerics.math.Float3: Finds the distance between two vectors.
dist2(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the squared distance between two vectors
dist2(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the squared distance between two vectors.
dist2(Double3) - Method in class ffx.numerics.math.Double3: Finds the square of the Euclidean distance between two positions.
dist2(Float3) - Method in class ffx.numerics.math.Float3: Finds the squared distance between two vectors
distance - Variable in class ffx.potential.parameters.BondType: Equilibrium separation (Angstroms).
distance - Variable in class ffx.potential.parameters.UreyBradleyType: Equilibrium 1-3 separation (Angstroms).
distance(double[], OctreePoint) - Method in class ffx.potential.nonbonded.octree.Octree: Compute a distance between a position and the OctreePoint.
distance(Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Returns the Euclidean distance between this vector and vector v.
distance(OctreeCell) - Method in class ffx.potential.nonbonded.octree.OctreePoint
distance(OctreePoint) - Method in class ffx.potential.nonbonded.octree.OctreePoint
Distance - Class in ffx.numerics.clustering: Simple value object storing a distance and an optional weight used during linkage computations; comparable by distance and cloneable.
Distance() - Constructor for class ffx.numerics.clustering.Distance: Creates a Distance with value 0 and weight 1.
Distance(Double) - Constructor for class ffx.numerics.clustering.Distance: Creates a Distance with the given value and unit weight.
Distance(Double, Double) - Constructor for class ffx.numerics.clustering.Distance: Creates a Distance with the given value and weight.
DistanceMap - Class in ffx.numerics.clustering: Container for linkages with the minimal methods needed in the package Created by Alexandre Masselot on 7/18/14.
DistanceMap() - Constructor for class ffx.numerics.clustering.DistanceMap
DistanceMatrix - Class in ffx.algorithms.optimize.manybody: Calculates a residue-residue distance matrix.
DistanceMatrix(MolecularAssembly, AlgorithmListener, Residue[], List<Residue>, RotamerOptimization.DistanceMethod, double, double, double) - Constructor for class ffx.algorithms.optimize.manybody.DistanceMatrix
DistanceMatrix.NeighborDistances - Class in ffx.algorithms.optimize.manybody: Store all neighbors of a residue / rotamer pair.
DistanceMatrixFileFilter - Class in ffx.potential.parsers: The DistanceMatrixFileFilter class is used to choose a Distance Matrix (*.DST) file.
DistanceMatrixFileFilter() - Constructor for class ffx.potential.parsers.DistanceMatrixFileFilter: Default Constructor.
DistanceMatrixFilter - Class in ffx.potential.parsers: The DistanceMatrixFilter class parses a Distance Matrix (*.DST) files.
DistanceMatrixFilter() - Constructor for class ffx.potential.parsers.DistanceMatrixFilter: No public constructor for DistanceMatrixFilter.
DistanceRegion - Class in ffx.algorithms.optimize.manybody: Compute the minimum distance between each pair of residues for all rotamer permutations.
DistanceRegion(int, int, Crystal, int[][][], IntegerSchedule) - Constructor for class ffx.algorithms.optimize.manybody.DistanceRegion
distanceSquared(Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Returns the squared of the Euclidean distance between this vector and vector v.
distanceToPlane(Point3d) - Method in class ffx.numerics.quickhull.Face: Computes the distance from a point p to the plane of this face.
distribute(MolecularAssembly[], CrystalPotential, AlgorithmFunctions, int, int) - Method in class ffx.algorithms.cli.MultiDynamicsOptions: If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
distribute(MolecularAssembly[], Potential[], CrystalPotential, AlgorithmFunctions, int, int) - Method in class ffx.algorithms.cli.MultiDynamicsOptions: If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
distRow - Variable in class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Row of RMSD values (length = targetSize).
divides(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: Return a / b.
dj - Variable in class ffx.numerics.fft.MixedRadixFactor: Equal to 2 * innerLoopLimit for interleaved complex data.
dlAlpha - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dlfAlpha - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: First lambda derivative of buffer distance.
dlfPowPerm - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: First lambda derivative of lPowPerm.
dlfPowPol - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: First lambda derivative of lPowPol.
dLpdL - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Derivative of lambdaProduct w.r.t. lambda.
dLpdLi - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Derivative of lambdaProduct w.r.t. esvLambda[i].
dLpdLk - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Derivative of lambdaProduct w.r.t. esvLambda[k].
dlPowPerm - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dlPowPol - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
doCauseSevere() - Method in exception class ffx.potential.utils.EnergyException: doCauseSevere.
dof - Variable in class ffx.numerics.math.BootStrapStatistics: The number of degrees of freedom.
dof - Variable in class ffx.numerics.math.SummaryStatistics: Degrees of freedom.
dOffset - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion: Dielectric offset from:
doLigandGKElec - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Intramolecular electrostatics for the ligand in done in GK implicit solvent.
doLigandVaporElec - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Intramolecular electrostatics for the ligand in vapor is included by default.
done - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Flag to indicate a run has finished.
done - Variable in class ffx.algorithms.optimize.Minimize: A flag to indicate the algorithm is done.
done - Variable in class ffx.algorithms.optimize.PhMinimize: A flag to indicate the algorithm is done.
doNoLigandCondensedSCF - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Condensed phase SCF without the ligand present is included by default.
doPermanentRealSpace - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
doPolarization - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dot(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the dot product between two vectors.
dot(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the dot product between two vectors.
dot(Double3) - Method in class ffx.numerics.math.Double3: Finds the dot product between two vectors.
dot(Float3) - Method in class ffx.numerics.math.Float3: Finds the dot product between two vectors.
dot(Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Returns the dot product of this vector and v1.
dotVec(DoubleVector[], DoubleVector[]) - Static method in class ffx.numerics.multipole.QIFrameSIMD: Compute the dot product of two vectors.
Double() - Constructor for class edu.rit.util.Searching.Double
Double() - Constructor for class edu.rit.util.Sorting.Double
DOUBLE_SPECIES - Static variable in class ffx.numerics.fft.MixedRadixFactor: The preferred vector species for double precision.
Double3 - Class in ffx.numerics.math: Convenience class for working with 3D double vectors.
Double3() - Constructor for class ffx.numerics.math.Double3: Construct a Double3 at (0.0, 0.0, 0.0).
Double3(double[]) - Constructor for class ffx.numerics.math.Double3: Construct a Double3 at a.
Double3(double, double, double) - Constructor for class ffx.numerics.math.Double3: Construct a Double3 at (x, y, z).
DoubleArray - Class in ffx.openmm: DoubleArray wrapper.
DoubleArray(int) - Constructor for class ffx.openmm.DoubleArray: Constructor.
DoubleArray3D - Class in ffx.openmm.amoeba: DoubleArray3D.
DoubleArray3D(int, int, int) - Constructor for class ffx.openmm.amoeba.DoubleArray3D: Constructor.
DoubleArrayBuf - Class in edu.rit.mp.buf: Class DoubleArrayBuf provides a buffer for an array of double items sent or received using the Message Protocol (MP).
DoubleArrayBuf(double[], Range) - Constructor for class edu.rit.mp.buf.DoubleArrayBuf: Construct a new double array buffer.
DoubleArrayBuf_1 - Class in edu.rit.mp.buf: Class DoubleArrayBuf_1 provides a buffer for an array of double items sent or received using the Message Protocol (MP).
DoubleArrayBuf_1(double[], Range) - Constructor for class edu.rit.mp.buf.DoubleArrayBuf_1: Construct a new double array buffer.
DoubleBuf - Class in edu.rit.mp: Class DoubleBuf is the abstract base class for a buffer of double items sent or received using the Message Protocol (MP).
DoubleBuf(int) - Constructor for class edu.rit.mp.DoubleBuf: Construct a new double buffer.
doubleFactorial(long) - Static method in class ffx.numerics.math.ScalarMath: Returns n!!
DoubleIndexPair - Record Class in ffx.utilities: DoubleIndexPair record.
DoubleIndexPair(int, double) - Constructor for record class ffx.utilities.DoubleIndexPair: Creates an instance of a DoubleIndexPair record class.
DoubleItemBuf - Class in edu.rit.mp.buf: Class DoubleItemBuf provides a buffer for a single double item sent or received using the Message Protocol (MP).
DoubleItemBuf() - Constructor for class edu.rit.mp.buf.DoubleItemBuf: Construct a new double item buffer.
DoubleItemBuf(double) - Constructor for class edu.rit.mp.buf.DoubleItemBuf: Construct a new double item buffer with the given initial value.
DoubleMath - Class in ffx.numerics.math: The DoubleMath class is a simple math library that operates on 3-coordinate double arrays.
DoubleMatrixBuf - Class in edu.rit.mp.buf: Class DoubleMatrixBuf provides a buffer for a matrix of double items sent or received using the Message Protocol (MP).
DoubleMatrixBuf(double[][], Range, Range) - Constructor for class edu.rit.mp.buf.DoubleMatrixBuf: Construct a new double matrix buffer.
DoubleMatrixBuf_1 - Class in edu.rit.mp.buf: Class DoubleMatrixBuf_1 provides a buffer for a matrix of double items sent or received using the Message Protocol (MP).
DoubleMatrixBuf_1(double[][], Range, Range) - Constructor for class edu.rit.mp.buf.DoubleMatrixBuf_1: Construct a new double matrix buffer.
DoubleMatrixFile - Class in edu.rit.io: Class DoubleMatrixFile provides an object for reading or writing a double matrix from or to a file.
DoubleMatrixFile() - Constructor for class edu.rit.io.DoubleMatrixFile: Construct a new double matrix file object.
DoubleMatrixFile(int, int, double[][]) - Constructor for class edu.rit.io.DoubleMatrixFile: Construct a new double matrix file object with the given number of rows, number of columns, and underlying matrix.
DoubleMatrixFile.Reader - Class in edu.rit.io: Class DoubleMatrixFile.Reader provides an object with which to read a DoubleMatrixFile from an input stream.
DoubleMatrixFile.Writer - Class in edu.rit.io: Class DoubleMatrixFile.Writer provides an object with which to write a DoubleMatrixFile to an output stream.
DoubleOp - Class in edu.rit.pj.reduction: Class DoubleOp is the abstract base class for a binary operation on double values, used to do reduction in a parallel program.
DoubleOp() - Constructor for class edu.rit.pj.reduction.DoubleOp: Construct a new double binary operation.
DoublesDataSet - Class in ffx.numerics.integrate: Describes a set of x, f(x) obtained by some mechanism; intended for numerical integration.
DoublesDataSet(double[], double[]) - Constructor for class ffx.numerics.integrate.DoublesDataSet: Constructs a DataSet from actual data, with no known underlying function (or at least none with an analytically solved integral).
DoublesDataSet(double[], double[], boolean) - Constructor for class ffx.numerics.integrate.DoublesDataSet: Constructs a DataSet from actual data, with no known underlying function (or at least none with an analytically solved integral).
DoublesDataSet(DataSet) - Constructor for class ffx.numerics.integrate.DoublesDataSet: Constructs a DataSet from another DataSet, effectively masquerading a test set such as a sine wave as data from an "unknown" function.
doubleValue() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in record class ffx.utilities.DoubleIndexPair: Returns the value of the doubleValue record component.
DoubleXMLAdapter - Class in ffx.utilities: Convert a Double to a String and vice versa for use with JAXB.
DoubleXMLAdapter() - Constructor for class ffx.utilities.DoubleXMLAdapter: Default constructor.
downloadPDB(String) - Static method in class ffx.utilities.DownloadUtils: Download a PDB file.
DownloadUtils - Class in ffx.utilities: Download utilities.
DP2 - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
drag - Variable in class ffx.ui.behaviors.PickRotateBehavior
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in class ffx.potential.bonded.Atom: drawLabel
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in class ffx.potential.bonded.MSNode: drawLabel
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in class ffx.potential.bonded.Residue: drawLabel
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in interface ffx.potential.bonded.ROLS: drawLabel
DrudeForce - Class in ffx.openmm.drude: This class implements forces that are specific to Drude oscillators.
DrudeForce() - Constructor for class ffx.openmm.drude.DrudeForce: Create a DrudeForce.
DrudeIntegrator - Class in ffx.openmm.drude: A base class to encapsulate features common to Drude integrators.
DrudeIntegrator(double) - Constructor for class ffx.openmm.drude.DrudeIntegrator: Create a DrudeIntegrator.
DrudeIntegrator(PointerByReference) - Constructor for class ffx.openmm.drude.DrudeIntegrator: Create a DrudeIntegrator.
DrudeLangevinIntegrator - Class in ffx.openmm.drude: This Integrator simulates systems that include Drude particles.
DrudeLangevinIntegrator(double, double, double, double, double) - Constructor for class ffx.openmm.drude.DrudeLangevinIntegrator: Create a DrudeLangevinIntegrator.
DrudeNoseHooverIntegrator - Class in ffx.openmm.drude: This Integrator simulates systems that include Drude particles.
DrudeNoseHooverIntegrator(double, double, double, double, double, int, int, int) - Constructor for class ffx.openmm.drude.DrudeNoseHooverIntegrator: Create a DrudeNoseHooverIntegrator.
DrudeSCFIntegrator - Class in ffx.openmm.drude: This is a leap-frog Verlet Integrator that simulates systems with Drude particles.
DrudeSCFIntegrator(double) - Constructor for class ffx.openmm.drude.DrudeSCFIntegrator: Create a DrudeSCFIntegrator.
dt - Variable in class ffx.algorithms.dynamics.integrators.Integrator: Time step (psec).
dt - Variable in class ffx.algorithms.dynamics.MolecularDynamics: The time step (picoseconds).
dtaper(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: First derivative of the switching function at r.
dtaper(double, double, double, double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: First derivative of the switching function at r.
DTDResolver - Class in ffx.ui.commands: The DTDResolver class just points the DOM DocumentBuilder to the XML Document Type Definition (DTD) files.
DTDResolver() - Constructor for class ffx.ui.commands.DTDResolver
DTY - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
DualTopologyEnergy - Class in ffx.potential: Compute the potential energy and derivatives for a dual-topology system.
DualTopologyEnergy(MolecularAssembly, MolecularAssembly, UnivariateSwitchingFunction) - Constructor for class ffx.potential.DualTopologyEnergy: Constructor for DualTopologyEnergy.
dUdLBins - Variable in class ffx.algorithms.thermodynamics.HistogramData: It is useful to have an odd number of bins, so that there is a bin from FL=-dFL/2 to dFL/2 so that as FL approaches zero its contribution to thermodynamic integration goes to zero.
dUdLBinWidth_2 - Variable in class ffx.algorithms.thermodynamics.HistogramData: Half the width of the F_lambda bin.
dUdLError - Variable in class ffx.algorithms.commands.test.OSTGradient
dUdLMaximum - Variable in class ffx.algorithms.thermodynamics.HistogramData: The maximum value of the last dUdL bin.
dUdLVariance - Variable in class ffx.algorithms.thermodynamics.HistogramData: The variance for the Gaussian bias in the dU/dL dimension.
dump(PrintStream, String) - Method in class edu.rit.mp.Channel: Dump the state of this channel on the given print stream.
dump(PrintStream, String) - Method in class edu.rit.mp.ChannelGroup: Dump the state of this channel group on the given print stream.
dump(PrintStream, String) - Method in class edu.rit.pj.Comm: Dump the state of this communicator on the given print stream.
dVdA - Variable in class ffx.crystal.Crystal: Change in the volume with respect to a.
dVdAlpha - Variable in class ffx.crystal.Crystal: Change in the volume with respect to alpha (in Radians).
dVdB - Variable in class ffx.crystal.Crystal: Change in the volume with respect to b.
dVdBeta - Variable in class ffx.crystal.Crystal: Change in the volume with respect to beta (in Radians).
dVdC - Variable in class ffx.crystal.Crystal: Change in the volume with respect to c.
dVdGamma - Variable in class ffx.crystal.Crystal: Change in the volume with respect to gamma (in Radians).
dWater - Static variable in class ffx.utilities.Constants: Permittivity of water at STP.
dx - Variable in class ffx.numerics.multipole.PolarizableMultipole: Dipole x-component.
dx - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Dipole x-component.
dx - Variable in class ffx.potential.parameters.TorsionTorsionType: First derivative along x.
dxy - Variable in class ffx.potential.parameters.TorsionTorsionType: Second derivatives.
dy - Variable in class ffx.numerics.multipole.PolarizableMultipole: Dipole y-component.
dy - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Dipole y-component.
dy - Variable in class ffx.potential.parameters.TorsionTorsionType: First derivative along y.
Dy - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
dynamic() - Static method in class edu.rit.pj.IntegerSchedule: Returns a dynamic schedule object with a chunk size of 1.
dynamic() - Static method in class edu.rit.pj.LongSchedule: Returns a dynamic schedule object with a chunk size of 1.
dynamic(int) - Static method in class edu.rit.pj.IntegerSchedule: Returns a dynamic schedule object with the given chunk size.
dynamic(long) - Static method in class edu.rit.pj.LongSchedule: Returns a dynamic schedule object with the given chunk size.
dynamic(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Blocking molecular dynamics.
dynamic(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: Blocking molecular dynamics.
dynamic(long, double, double, double, double, boolean, String, double, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Blocking molecular dynamics.
Dynamics - Class in ffx.algorithms.commands: The Dynamics script implements molecular and stochastic dynamics algorithms.
Dynamics - Class in ffx.realspace.commands: The Real Space Dynamics script.
Dynamics - Class in ffx.xray.commands: The X-ray Dynamics script.
Dynamics() - Constructor for class ffx.algorithms.commands.Dynamics: Dynamics Constructor.
Dynamics() - Constructor for class ffx.realspace.commands.Dynamics: Dynamics constructor.
Dynamics() - Constructor for class ffx.xray.commands.Dynamics: Dynamics constructor.
Dynamics(FFXBinding) - Constructor for class ffx.algorithms.commands.Dynamics: Dynamics Constructor.
Dynamics(FFXBinding) - Constructor for class ffx.realspace.commands.Dynamics: Dynamics constructor.
Dynamics(FFXBinding) - Constructor for class ffx.xray.commands.Dynamics: Dynamics constructor.
Dynamics(String[]) - Constructor for class ffx.algorithms.commands.Dynamics: Dynamics constructor that sets the command line arguments.
Dynamics(String[]) - Constructor for class ffx.realspace.commands.Dynamics: Dynamics constructor that sets the command line arguments.
Dynamics(String[]) - Constructor for class ffx.xray.commands.Dynamics: Dynamics constructor that sets the command line arguments.
dynamicsFactory(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum) - Static method in class ffx.algorithms.dynamics.MolecularDynamics: Method that determines whether a dynamics is done by the java implementation native to ffx or the OpenMM implementation
dynamicsFactory(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum, MDEngine) - Static method in class ffx.algorithms.dynamics.MolecularDynamics: dynamicsFactory.
dynamicsOptions - Variable in class ffx.algorithms.commands.Thermodynamics
DynamicsOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that run molecular dynamics.
DynamicsOptions() - Constructor for class ffx.algorithms.cli.DynamicsOptions
DYNFileFilter - Class in ffx.potential.parsers: The DYNFileFilter class is used to choose a TINKER Restart (*.DYN) file.
DYNFileFilter() - Constructor for class ffx.potential.parsers.DYNFileFilter: Default Constructor.
DYNFilter - Class in ffx.potential.parsers: The DYNFilter class parses TINKER Restart (*.DYN) files.
DYNFilter(String) - Constructor for class ffx.potential.parsers.DYNFilter: Constructor for DYNFilter.
dz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Dipole z-component.
dz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Dipole z-component.

E

e - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
E - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
e0 - Variable in class ffx.potential.commands.test.LambdaGradient
E000 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E001 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E002 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E003 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E010 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E011 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E012 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E020 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E021 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E030 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
e1 - Variable in class ffx.potential.commands.test.LambdaGradient
E100 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E101 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E102 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E110 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E111 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E120 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E200 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E201 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E210 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
E300 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
eAll - Variable in class ffx.numerics.estimator.SequentialEstimator: The potential energies of the snapshots at all other lambda values.
eAllFlat - Variable in class ffx.numerics.estimator.SequentialEstimator: The potential energies of the snapshots at all other lambda values.
EDITCOMBOBOX - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
edu.rit.http - package edu.rit.http: The HTTP package provides a lightweight HTTP/1.0 server.
edu.rit.io - package edu.rit.io: The IO package provides the DataOutputStream and DataInputStream classes to read/write primitive data types and strings in binary form.
edu.rit.mp - package edu.rit.mp: The MP package provides low-level support for Message Passing.
edu.rit.mp.buf - package edu.rit.mp.buf: The BUF package provides data buffers for Message Passing.
edu.rit.pj - package edu.rit.pj: The PJ package (Parallel Java) support shared memory, message passing and hybrid shared memory/message passing parallelization in pure Java.
edu.rit.pj.cluster - package edu.rit.pj.cluster: The Cluster package contains the Parallel Java cluster middleware and the main program for the PJ Job Scheduler Daemon process for a parallel computer.
edu.rit.pj.io - package edu.rit.pj.io: The IO package represents a file that resides in the user's account in the job frontend process of a PJ cluster parallel program.
edu.rit.pj.job - package edu.rit.pj.job: The Job package encapsulates a job and its attributes.
edu.rit.pj.reduction - package edu.rit.pj.reduction: The Reduction package provides a variety of reduction variables.
edu.rit.pj.replica - package edu.rit.pj.replica: The Replica package provides replicated, shared reduction variables.
edu.rit.util - package edu.rit.util: The Util package contains utilities that support the PJ API.
eLambda - Variable in class ffx.numerics.estimator.SequentialEstimator: The potential energy of each snapshot at lambda.
eLambdaMinusdL - Variable in class ffx.numerics.estimator.SequentialEstimator: The potential energy of each snapshot at lambda - dL.
eLambdaPlusdL - Variable in class ffx.numerics.estimator.SequentialEstimator: The potential energy of each snapshot at lambda + dL.
ELEC_ANG_TO_DEBYE - Static variable in class ffx.utilities.Constants: Conversion from electron-Angstroms to Debye.
ELEC_ANG2_TO_BUCKINGHAMS - Static variable in class ffx.utilities.Constants: Conversion from electron-Angstroms^2 to Buckinghams.
electric - Variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Conversion from electron**2/Ang to kcal/mole.
electric - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion: Conversion from electron**2/Ang to kcal/mole.
electric - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Coulomb constant in units of kcal*Ang/(mol*electron^2)
ELECTRIC_CODATA_2018 - Static variable in class ffx.utilities.Constants: Coulomb constant in units of kcal*Ang/(mol*electron^2), as derived from CODATA 2018 permittivity of free space measured at 8.8541878128*10^-12 F/m ELECTRIC_CODATA_2018=332.063713299
ElectrostaticsFunctionalForm - Enum constant in enum class ffx.utilities.PropertyGroup: Electrostatics functional form.
ELEMENTARY_CHARGE_SI - Static variable in class ffx.utilities.Constants: Elementary charge in Coulombs, defining the Coulomb.
eliminatedPairs - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Eliminated rotamer pairs.
EliminatedRotamers - Class in ffx.algorithms.optimize.manybody
EliminatedRotamers(RotamerOptimization, DistanceMatrix, List<Residue>, int, double, double, double, double, double, double, boolean, boolean, boolean, Residue[]) - Constructor for class ffx.algorithms.optimize.manybody.EliminatedRotamers
eliminatedSingles - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Eliminated rotamers.
eliminateRotamer(Residue[], int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Safe method to eliminate a rotamer: will not eliminate if there are no alternate rotamers for residue i, or if i-ri is already eliminated.
eliminateRotamerPair(Residue[], int, int, int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
eliminateRotamerPairs(Residue[], int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
EmptyBooleanBuf - Class in edu.rit.mp.buf: Class EmptyBooleanBuf provides a Boolean buffer that contains no items for messages using the Message Protocol (MP).
EmptyBooleanBuf() - Constructor for class edu.rit.mp.buf.EmptyBooleanBuf: Construct a new empty Boolean buffer.
emptyBuffer() - Static method in class edu.rit.mp.BooleanBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ByteBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.CharacterBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.DoubleBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.FloatBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.IntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.LongBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ObjectBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ShortBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an empty buffer.
EmptyByteBuf - Class in edu.rit.mp.buf: Class EmptyByteBuf provides a byte buffer that contains no items for messages using the Message Protocol (MP).
EmptyByteBuf() - Constructor for class edu.rit.mp.buf.EmptyByteBuf: Construct a new empty byte buffer.
EmptyCharacterBuf - Class in edu.rit.mp.buf: Class EmptyCharacterBuf provides a character buffer that contains no items for messages using the Message Protocol (MP).
EmptyCharacterBuf() - Constructor for class edu.rit.mp.buf.EmptyCharacterBuf: Construct a new empty character buffer.
EmptyDoubleBuf - Class in edu.rit.mp.buf: Class EmptyDoubleBuf provides a double buffer that contains no items for messages using the Message Protocol (MP).
EmptyDoubleBuf() - Constructor for class edu.rit.mp.buf.EmptyDoubleBuf: Construct a new empty double buffer.
EmptyFloatBuf - Class in edu.rit.mp.buf: Class EmptyFloatBuf provides a float buffer that contains no items for messages using the Message Protocol (MP).
EmptyFloatBuf() - Constructor for class edu.rit.mp.buf.EmptyFloatBuf: Construct a new empty float buffer.
EmptyIntegerBuf - Class in edu.rit.mp.buf: Class EmptyIntegerBuf provides an integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyIntegerBuf: Construct a new empty integer buffer.
EmptyLongBuf - Class in edu.rit.mp.buf: Class EmptyLongBuf provides a long buffer that contains no items for messages using the Message Protocol (MP).
EmptyLongBuf() - Constructor for class edu.rit.mp.buf.EmptyLongBuf: Construct a new empty long buffer.
EmptyObjectBuf - Class in edu.rit.mp.buf: Class EmptyObjectBuf provides an object buffer that contains no items for messages using the Message Protocol (MP).
EmptyObjectBuf() - Constructor for class edu.rit.mp.buf.EmptyObjectBuf: Construct a new empty object buffer.
EmptyShortBuf - Class in edu.rit.mp.buf: Class EmptyShortBuf provides a short buffer that contains no items for messages using the Message Protocol (MP).
EmptyShortBuf() - Constructor for class edu.rit.mp.buf.EmptyShortBuf: Construct a new empty short buffer.
EmptySigned16BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptySigned16BitIntegerBuf provides a signed 16-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptySigned16BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Construct a new empty signed 16-bit integer buffer.
EmptySigned8BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptySigned8BitIntegerBuf provides a signed 8-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptySigned8BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Construct a new empty signed 8-bit integer buffer.
EmptyUnsigned16BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptyUnsigned16BitIntegerBuf provides an unsigned 16-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyUnsigned16BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Construct a new empty unsigned 16-bit integer buffer.
EmptyUnsigned8BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptyUnsigned8BitIntegerBuf provides an unsigned 8-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyUnsigned8BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Construct a new empty unsigned 8-bit integer buffer.
encode(int, int) - Static method in class ffx.utilities.Hybrid36: Hybrid-36 encoder: converts integer value to string result.
endBlock() - Method in class ffx.openmm.CustomIntegrator: End the most recently begun if or while block.
endstateEnergyMap - Variable in class ffx.potential.commands.test.PhGradient
energy - Variable in class ffx.algorithms.optimize.Minimize: The final potential energy.
energy - Variable in class ffx.algorithms.optimize.PhMinimize: The final potential energy.
energy - Variable in class ffx.potential.bonded.BondedTerm: Energy of the term (kcal/mol).
energy - Variable in class ffx.potential.commands.Energy
energy - Variable in class ffx.potential.commands.PhEnergy
energy - Variable in class ffx.potential.parameters.TorsionTorsionType: Energy values.
energy - Variable in class ffx.potential.terms.EnergyTerm: Total potential energy for this term.
energy - Variable in class ffx.ui.commands.SimulationUpdate
energy() - Method in class ffx.potential.ForceFieldEnergy: energy.
energy() - Method in class ffx.ui.ModelingShell: energy
energy(boolean) - Method in interface ffx.potential.bonded.BondedEnergy: energy.
energy(boolean) - Method in class ffx.potential.nonbonded.RestrainGroups: Compute energy and derivatives for group distance restraint terms.
energy(boolean, boolean) - Method in class ffx.potential.ANIEnergy: Compute the ANI energy and gradint.
energy(boolean, boolean) - Method in class ffx.potential.ForceFieldEnergy: Compute the potential energy of the system.
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Calculate the PME electrostatic energy.
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.VanDerWaals: The energy routine may be called repeatedly.
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.VanDerWaalsTornado: The energy routine may be called repeatedly.
energy(boolean, int, AtomicDoubleArray3D) - Method in interface ffx.potential.bonded.BondedEnergy: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Angle: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.AngleTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Bond: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in interface ffx.potential.bonded.BondedEnergy: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.ImproperTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.OutOfPlaneBend: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.PiOrbitalTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.RestrainDistance: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.RestrainPosition: Calculates energy and gradients for this coordinate restraint.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.RestrainTorsion
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.StretchBend: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.StretchTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Torsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.TorsionTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.UreyBradley: energy.
energy(double[]) - Method in class ffx.algorithms.dynamics.Barostat: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Compute the force field + bias energy.
energy(double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: MBAR objective function evaluation at a given free energy estimate for L-BFGS optimization.
energy(double[]) - Method in interface ffx.numerics.OptimizationInterface: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.ANIEnergy
energy(double[]) - Method in class ffx.potential.DualTopologyEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.extended.ExtendedSystem
energy(double[]) - Method in class ffx.potential.ForceFieldEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.QuadTopologyEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.XtalEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.realspace.RealSpaceEnergy: The parameters passed in are only for "active" atoms.
energy(double[]) - Method in class ffx.xray.RefinementEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.ScaleBulkEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.SigmaAEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.SplineEnergy: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.XRayEnergy: This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in interface ffx.numerics.OptimizationInterface: This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.DualTopologyEnergy: This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.ForceFieldEnergy: This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy: This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.QuadTopologyEnergy: This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.xray.RefinementEnergy: This method is called repeatedly to compute the function energy.
energy(MolecularAssembly) - Method in interface ffx.potential.utils.PotentialsFunctions: Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.
energy(MolecularAssembly) - Method in class ffx.potential.utils.PotentialsUtils: Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.
energy(MolecularAssembly) - Method in class ffx.ui.UIUtils
energy(MolecularAssembly[]) - Method in interface ffx.potential.utils.PotentialsFunctions: Evaluates the energy of each MolecularAssembly and returns their ForceFieldEnergy instances.
energy(MolecularAssembly[]) - Method in class ffx.potential.utils.PotentialsUtils: Evaluates the energy of each MolecularAssembly and returns their ForceFieldEnergy instances.
Energy - Class in ffx.potential.commands: Compute the force field potential energy.
Energy() - Constructor for class ffx.potential.commands.Energy
Energy(FFXBinding) - Constructor for class ffx.potential.commands.Energy
Energy(String[]) - Constructor for class ffx.potential.commands.Energy
ENERGY - Enum constant in enum class ffx.potential.ForceFieldEnergy.RestrainMode: Restrain terms are applied with the energy.
energyAndGradient(double[][], AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation: Compute molecular volume and surface area.
energyAndGradient(double[], double[]) - Method in class ffx.algorithms.dynamics.Barostat: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: MBAR objective function evaluation and gradient at a given free energy estimate for L-BFGS optimization.
energyAndGradient(double[], double[]) - Method in interface ffx.numerics.OptimizationInterface: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.ANIEnergy
energyAndGradient(double[], double[]) - Method in class ffx.potential.DualTopologyEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.extended.ExtendedSystem
energyAndGradient(double[], double[]) - Method in class ffx.potential.ForceFieldEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.QuadTopologyEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.XtalEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.realspace.RealSpaceEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.RefinementEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.ScaleBulkEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.SigmaAEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.SplineEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.XRayEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in interface ffx.numerics.OptimizationInterface: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.DualTopologyEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.ForceFieldEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.QuadTopologyEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.xray.RefinementEnergy: This method is called repeatedly to compute the function energy and gradient.
energyAndGradientConnolly(AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation: Compute the cavitation energy.
energyAndGradientFFX(double[], double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: Compute the energy and gradient using the pure Java code path.
energyAndGradientFFX(double[], double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy: Compute the energy and gradient using the pure Java code path.
energyAndGradientGausVol(double[][], AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation: Compute molecular volume and surface area.
EnergyException - Exception Class in ffx.potential.utils: This Exception class indicates an error in calculating energy or gradients.
EnergyException() - Constructor for exception class ffx.potential.utils.EnergyException: Constructor for EnergyException.
EnergyException(String) - Constructor for exception class ffx.potential.utils.EnergyException: Constructor for EnergyException.
EnergyException(String, boolean) - Constructor for exception class ffx.potential.utils.EnergyException: Constructor for EnergyException.
EnergyException(String, boolean, double) - Constructor for exception class ffx.potential.utils.EnergyException: Constructor for EnergyException.
EnergyExpansion - Class in ffx.algorithms.optimize.manybody
EnergyExpansion(RotamerOptimization, DistanceMatrix, EliminatedRotamers, MolecularAssembly, Potential, AlgorithmListener, List<Residue>, int[][], boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.manybody.EnergyExpansion
energyFactory(MolecularAssembly) - Static method in class ffx.potential.ForceFieldEnergy: Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.
energyFactory(MolecularAssembly, int) - Static method in class ffx.potential.ForceFieldEnergy: Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.
energyFactory(MolecularAssembly, MolecularAssembly, UnivariateSwitchingFunction) - Static method in class ffx.potential.DualTopologyEnergy: Static factory method to create a DualTopologyEnergy, possibly via FFX or OpenMM implementations.
energyFFX(double[]) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Compute the energy using the pure Java code path.
energyFFX(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: Compute the energy using the pure Java code path.
energyFFX(double[], boolean) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Compute the energy using the pure Java code path.
energyFFX(double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy: Compute the energy using the pure Java code path.
energyList - Variable in class ffx.algorithms.optimize.Minimize: The energy of each step in the minimization.
EnergyRegion - Class in ffx.algorithms.optimize.manybody
EnergyRegion(int) - Constructor for class ffx.algorithms.optimize.manybody.EnergyRegion
EnergyTerm - Class in ffx.potential.terms: Base class for potential energy terms used by ForceFieldEnergy.
EnergyTerm() - Constructor for class ffx.potential.terms.EnergyTerm: Create an unnamed EnergyTerm with default force group 0.
EnergyTerm(String) - Constructor for class ffx.potential.terms.EnergyTerm: Create a named EnergyTerm with default force group 0.
EnergyTerm(String, int) - Constructor for class ffx.potential.terms.EnergyTerm: Create a named EnergyTerm with a specified force group.
EnergyTermRegion - Class in ffx.potential.terms
EnergyTermRegion(ParallelTeam, MolecularAssembly, boolean) - Constructor for class ffx.potential.terms.EnergyTermRegion: Constructor for BondedRegion.
EnergyUnitConversion - Enum constant in enum class ffx.utilities.PropertyGroup: Energy unit conversion factors.
energyWriter - Variable in class ffx.algorithms.optimize.RotamerOptimization: Writes energies to restart file.
environment - Variable in class ffx.potential.parameters.AtomType: Description of the atom's bonding environment.
epsilon - Variable in class ffx.crystal.HKL: The epsilon value of the reflection, which is used for systematic absences.
epsilonc() - Method in class ffx.crystal.HKL: epsilonc
epsilonRule - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Epsilon combining rule.
EPT - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
equals(Object) - Method in class edu.rit.pj.io.StreamFile: Determine if this stream file is equal to the given object.
equals(Object) - Method in class edu.rit.util.LongRange: Determine if this range is equal to the given object.
equals(Object) - Method in class edu.rit.util.Range: Determine if this range is equal to the given object.
equals(Object) - Method in class ffx.crystal.Crystal: Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.HKL
equals(Object) - Method in class ffx.crystal.NCSCrystal: Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.ReplicatesCrystal: Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.numerics.clustering.Cluster
equals(Object) - Method in record class ffx.numerics.clustering.visualization.VCoord: Compares this coordinate to another object for equality.
equals(Object) - Method in record class ffx.numerics.fft.PassConstants: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ffx.potential.bonded.Atom
equals(Object) - Method in class ffx.potential.bonded.BondedTerm
equals(Object) - Method in class ffx.potential.bonded.Molecule
equals(Object) - Method in class ffx.potential.bonded.MSNode
equals(Object) - Method in class ffx.potential.bonded.MSRoot
equals(Object) - Method in class ffx.potential.bonded.MultiResidue
equals(Object) - Method in class ffx.potential.bonded.Polymer
equals(Object) - Method in class ffx.potential.bonded.Residue
equals(Object) - Method in class ffx.potential.bonded.ROLSP
equals(Object) - Method in class ffx.potential.parameters.AngleTorsionType
equals(Object) - Method in class ffx.potential.parameters.AngleType
equals(Object) - Method in class ffx.potential.parameters.AtomType
equals(Object) - Method in class ffx.potential.parameters.BioType
equals(Object) - Method in class ffx.potential.parameters.BondType
equals(Object) - Method in class ffx.potential.parameters.ImproperTorsionType
equals(Object) - Method in class ffx.potential.parameters.MultipoleType
equals(Object) - Method in class ffx.potential.parameters.OutOfPlaneBendType
equals(Object) - Method in class ffx.potential.parameters.PiOrbitalTorsionType
equals(Object) - Method in class ffx.potential.parameters.PolarizeType
equals(Object) - Method in class ffx.potential.parameters.RelativeSolvationType
equals(Object) - Method in class ffx.potential.parameters.SoluteType
equals(Object) - Method in class ffx.potential.parameters.StretchBendType
equals(Object) - Method in class ffx.potential.parameters.StretchTorsionType
equals(Object) - Method in class ffx.potential.parameters.TorsionTorsionType
equals(Object) - Method in class ffx.potential.parameters.TorsionType
equals(Object) - Method in class ffx.potential.parameters.UreyBradleyType
equals(Object) - Method in class ffx.potential.parameters.VDWPairType
equals(Object) - Method in class ffx.potential.parameters.VDWType
equals(Object) - Method in record class ffx.potential.UnmodifiableState: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ffx.ui.KeywordComponent
equals(Object) - Method in record class ffx.utilities.DoubleIndexPair: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ffx.utilities.IndexIndexPair: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ffx.utilities.ObjectPair: Indicates whether some other object is "equal to" this one.
Er - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
erf(double) - Static method in class ffx.numerics.special.Erf: Evaluates erf(x) for a real argument x.
Erf - Class in ffx.numerics.special: Static methods to evaluate erf(x) and erfc(x) for a real argument x.
erfc(double) - Static method in class ffx.numerics.special.Erf: Evaluate erfc(x) for a real argument x.
err - Variable in class edu.rit.pj.cluster.BackendFileWriter: Print stream for printing on the job frontend's standard error.
err() - Static method in class edu.rit.io.Stdio: Get the standard error stream for the calling thread.
err(PrintStream) - Static method in class edu.rit.io.Stdio: Set the standard error stream for the calling thread.
error(SAXParseException) - Method in class ffx.potential.parsers.PDBMLFilter
Es - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
EstimateBootstrapper - Class in ffx.numerics.estimator: Bootstrap Free Energy Estimate.
EstimateBootstrapper(BootstrappableEstimator) - Constructor for class ffx.numerics.estimator.EstimateBootstrapper: Constructor.
estimateDG() - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Re-calculates free energy and enthalpy without bootstrapping.
estimateDG() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: Get the MBAR free-energy estimates at each lambda value.
estimateDG() - Method in class ffx.numerics.estimator.Zwanzig: Re-calculates free energy and enthalpy without bootstrapping.
estimateDG(boolean) - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Main driver for estimation of BAR free energy differences.
estimateDG(boolean) - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Re-calculates free energy and enthalpy.
estimateDG(boolean) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: MBAR solved with self-consistent iteration and Newton/L-BFGS optimization.
estimateDG(boolean) - Method in class ffx.numerics.estimator.Zwanzig: Re-calculates free energy and enthalpy.
ESVFileFilter - Class in ffx.potential.parsers: The ESVFileFilter class is used to choose a Extended System Restart (*.ESV) file.
ESVFileFilter() - Constructor for class ffx.potential.parsers.ESVFileFilter: Default Constructor.
ESVFilter - Class in ffx.potential.parsers: The ESVFilter class parses Extended System Restart (*.ESV) files.
ESVFilter(String) - Constructor for class ffx.potential.parsers.ESVFilter: Constructor for ESVFilter.
esvSystem - Variable in class ffx.algorithms.optimize.PhMinimize: The extended system that contains the fictitious particle
Eu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
evalPotnetial() - Method in class ffx.potential.nonbonded.octree.Octree: Evaluate potential at all target points
evaluate2DOSTBias(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: evaluate2DOSTBias.
evaluateMove(double, double) - Method in class ffx.algorithms.mc.BoltzmannMC: Returns true if the move from e1 to e2 is accepted.
evaluateMove(double, double) - Method in interface ffx.algorithms.mc.MetropolisMC: Returns true if the move from e1 to e2 is accepted.
evaluateMove(Random, double, double, double) - Static method in class ffx.algorithms.mc.BoltzmannMC: Boltzmann-weighted acceptance probability
evaluateStates(double[][], double[][], double[][], double[][]) - Method in class ffx.algorithms.ParallelStateEnergy: Evaluate the energies for each state.
evaluateTotalOSTBias(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: evaluateTotalBias.
ewaldCutoff(double, double, double) - Static method in class ffx.potential.nonbonded.pme.EwaldParameters: Determine the Ewald real space cutoff given the Ewald coefficient and a target precision.
EwaldParameters - Class in ffx.potential.nonbonded.pme: Mutable Particle Mesh Ewald constants.
EwaldParameters(double, double) - Constructor for class ffx.potential.nonbonded.pme.EwaldParameters
EwaldTensorGlobal - Class in ffx.numerics.multipole: The EwaldMultipoleTensorGlobal class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame.
EwaldTensorGlobal(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorGlobal: Constructor for EwaldMultipoleTensorGlobal.
EwaldTensorGlobalSIMD - Class in ffx.numerics.multipole: The EwaldMultipoleTensorGlobal class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame.
EwaldTensorGlobalSIMD(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorGlobalSIMD: Constructor for EwaldMultipoleTensorGlobal.
EwaldTensorQI - Class in ffx.numerics.multipole: The EwaldTensorQI class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
EwaldTensorQI(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorQI: Constructor for EwaldTensorQI.
EwaldTensorQISIMD - Class in ffx.numerics.multipole: The EwaldTensorQI class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
EwaldTensorQISIMD(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorQISIMD: Constructor for EwaldTensorQI.
excludeExcessAtoms(Set<Atom>, int[], MolecularAssembly, List<Residue>) - Method in class ffx.algorithms.optimize.TitrationManyBody
excludeExcessAtoms(Set<Atom>, int[], List<Residue>) - Method in class ffx.algorithms.optimize.TitrationManyBody
exclusiveScan(int, Buf, Op, Object) - Method in class edu.rit.pj.Comm: Perform an exclusive scan on all processes in this communicator using the given message tag.
exclusiveScan(Buf, Op, Object) - Method in class edu.rit.pj.Comm: Perform an exclusive scan on all processes in this communicator.
execute() - Method in class ffx.numerics.fft.TornadoDFT: Execute the Discrete Fourier Transform on the default TornadoDevice.
execute(int, int, int, IntegerStrideForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, int, IntegerStrideForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, int, WorkerIntegerStrideForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(int, int, IntegerForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, IntegerForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, WorkerIntegerForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(long, long, long, LongStrideForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, long, LongStrideForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, long, WorkerLongStrideForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(long, long, LongForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, LongForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, WorkerLongForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(ParallelRegion) - Method in class edu.rit.pj.ParallelTeam: Execute the given parallel region.
execute(ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel section within this parallel region.
execute(ParallelSection[]) - Method in class edu.rit.pj.ParallelRegion: Execute a group of parallel sections concurrently within this parallel region.
execute(ParallelSection[], BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a group of parallel sections concurrently within this parallel region.
execute(ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel section within this parallel region.
execute(ParallelSection, ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Execute a group of two parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a group of two parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Execute a group of three parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a group of three parallel sections concurrently within this parallel region.
execute(WorkerRegion) - Method in class edu.rit.pj.WorkerTeam: Execute the given worker region.
execute(Iterable<T>, ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterable<T>, ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterable<T>, WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion: Execute a worker iteration within this worker region.
execute(Iterator<T>, ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterator<T>, ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterator<T>, WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion: Execute a worker iteration within this worker region.
execute(T[], ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(T[], ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(T[], WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion: Execute a worker iteration within this worker region.
execute(TornadoDevice) - Method in class ffx.numerics.fft.TornadoDFT: Execute the Discrete Fourier Transform on a TornadoDevice.
executeCommand() - Method in class ffx.ui.ModelingPanel: Launch the TINKER command specified by the ModelingPanel
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.implicit.BornGradRegion: Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.implicit.InitializationRegion: Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.DirectRegion: Execute the DirectRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion: Execute the ExpandInducedDipolesRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion: Execute the InducedDipoleFieldReduceRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion: Execute the InducedDipoleFieldRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InitializationRegion: Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion: Execute the RealSpaceEnergyRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion: Execute the ReciprocalEnergyRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ReduceRegion: Execute the ReduceRegion with the passed ParallelTeam.
exit() - Method in class ffx.ui.MainPanel: exit with current exit code (default: 0 (ExitStatus.NORMAL))
exp() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the complex exponential of this.
EXP - Enum constant in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules
expandInducedDipoles() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
ExpandInducedDipolesRegion - Class in ffx.potential.nonbonded.pme: Parallel expansion of the asymmetric unit induced dipoles to symmetry mates by applying symmetry operator rotation matrices.
ExpandInducedDipolesRegion(int) - Constructor for class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
ExpAnnealSchedule - Class in ffx.algorithms.optimize.anneal: Exponential temperature schedule for simulated annealing
ExpAnnealSchedule(int, double, double) - Constructor for class ffx.algorithms.optimize.anneal.ExpAnnealSchedule: Creates an exponential annealing schedule that decays as tHigh*((tLow/tHigh)^(1/(nWindows-1)))^(n-1).
EXPENSIVE - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
expireTimer - Variable in class edu.rit.pj.cluster.JobInfo: Lease expiration timer.
expireTimer - Variable in class edu.rit.pj.cluster.ProcessInfo: Lease expiration timer.
EXPLICIT - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
explicitTolerance - Variable in class ffx.numerics.quickhull.QuickHull3D
ExportQE - Class in ffx.potential.commands: Generate Quantum Espresso (QE) input from an XYZ file.
ExportQE() - Constructor for class ffx.potential.commands.ExportQE
ExportQE(FFXBinding) - Constructor for class ffx.potential.commands.ExportQE
ExportQE(String[]) - Constructor for class ffx.potential.commands.ExportQE
ExtendedSystem - Class in ffx.potential.extended: ExtendedSystem class.
ExtendedSystem(MolecularAssembly, double, File) - Constructor for class ffx.potential.extended.ExtendedSystem: Construct extended system with the provided configuration.
extractCoordinates(int[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: Extract used coordinate subset from the entire system.

F

f - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
f() - Method in class ffx.crystal.ReflectionSpline: f
f(double, double[]) - Method in class ffx.crystal.ReflectionSpline: Evaluate basis function and derivative at a given resolution
f(HKL) - Method in class ffx.xray.NeutronFormFactor: f
f(HKL) - Method in class ffx.xray.XRayFormFactor: f
F - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
F - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
F1F2 - Static variable in interface ffx.xray.SplineEnergy.Type
face - Variable in class ffx.numerics.quickhull.HalfEdge: Triangular face associated with this half-edge.
Face - Class in ffx.numerics.quickhull: Basic triangular face used to form the hull.
Face() - Constructor for class ffx.numerics.quickhull.Face
FaceList - Class in ffx.numerics.quickhull: Maintains a single-linked list of faces for use by QuickHull3D.
FaceList() - Constructor for class ffx.numerics.quickhull.FaceList
faces - Variable in class ffx.numerics.quickhull.QuickHull3D
factor - Variable in class ffx.numerics.fft.MixedRadixFactor: The mixed radix factor.
factor() - Method in record class ffx.numerics.fft.PassConstants: Returns the value of the factor record component.
factorial(long) - Static method in class ffx.numerics.math.ScalarMath: Returns n!
FAILED - Enum constant in enum class edu.rit.pj.cluster.BackendInfo.State: The backend has failed.
FAILED - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State: The job backend process has failed.
farEndAddress() - Method in class edu.rit.mp.Channel: Obtain this channel's far end address.
farEndChannelGroupId() - Method in class edu.rit.mp.Channel: Obtain the channel group ID of this channel's far end channel group.
farEndConnected(ChannelGroup, Channel) - Method in interface edu.rit.mp.ConnectListener: Report that a channel was connected in the given channel group, initiated by the far end.
FAST - Enum constant in enum class ffx.numerics.Potential.STATE: Include FAST varying energy terms.
Fasta - Class in ffx.potential.commands: Fasta outputs a sub-sequence from a FASTA file.
Fasta() - Constructor for class ffx.potential.commands.Fasta
Fasta(FFXBinding) - Constructor for class ffx.potential.commands.Fasta
Fasta(String[]) - Constructor for class ffx.potential.commands.Fasta
fatalError(SAXParseException) - Method in class ffx.potential.parsers.PDBMLFilter
fc - Variable in class ffx.xray.DiffractionRefinementData: Calculated atomic structure factors.
fcF(int) - Method in class ffx.xray.DiffractionRefinementData: get the amplitude of a complex Fc
FCONLY - Static variable in interface ffx.xray.parsers.MTZWriter.MTZType: Output unscaled Fcs only (still requires data to be read in).
fcPhi(int) - Method in class ffx.xray.DiffractionRefinementData: get the phase of a complex Fc
FCTOESQ - Static variable in interface ffx.xray.SplineEnergy.Type
fcTotF(int) - Method in class ffx.xray.DiffractionRefinementData: fcTotF
fcTotPhi(int) - Method in class ffx.xray.DiffractionRefinementData: fcTotPhi
Fe - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
FeatureMap - Class in ffx.potential.commands: Create a Feature Map for a given protein structure.
FeatureMap() - Constructor for class ffx.potential.commands.FeatureMap
FeatureMap(FFXBinding) - Constructor for class ffx.potential.commands.FeatureMap
FeatureMap(String[]) - Constructor for class ffx.potential.commands.FeatureMap
fermiFunction(double) - Static method in class ffx.numerics.math.ScalarMath: Compute 1.0 / (1.0 + exp(x)).
fft(double[]) - Method in class ffx.numerics.fft.Complex3D: Compute the 3D FFT.
fft(double[]) - Method in class ffx.numerics.fft.Complex3DParallel: Compute the 3D FFT in parallel.
fft(double[]) - Method in class ffx.numerics.fft.Real3D: Compute the 3D FFT.
fft(double[]) - Method in class ffx.numerics.fft.Real3DParallel: Compute the 3D FFT.
fft(double[], int) - Method in class ffx.numerics.fft.Complex2D: Compute the 2D FFT.
fft(double[], int) - Method in class ffx.numerics.fft.Real: fft
fft(double[], int, int) - Method in class ffx.numerics.fft.Complex: Compute the Fast Fourier Transform of data leaving the result in data.
fft(double[], int, int, int) - Method in class ffx.numerics.fft.Complex: Compute the Fast Fourier Transform of data leaving the result in data.
FFtoXML - Class in ffx.potential.commands: The FFtoXML command saves a force field as an XML file usable by OpenMM.
FFtoXML() - Constructor for class ffx.potential.commands.FFtoXML
FFtoXML(FFXBinding) - Constructor for class ffx.potential.commands.FFtoXML
FFtoXML(String[]) - Constructor for class ffx.potential.commands.FFtoXML
ffx - package ffx: Force Field X implements fixed charge and polarizable atomic multipole molecular mechanics potentials, local and global optimization, molecular dynamics, free energy differences, etc, with special support for crystal space groups.
FFX - Enum constant in enum class ffx.algorithms.dynamics.MDEngine
FFX - Enum constant in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine
FFX - Enum constant in enum class ffx.potential.Platform: Reference FFX implementation.
ffx.algorithms - package ffx.algorithms: The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.cli - package ffx.algorithms.cli: The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.commands - package ffx.algorithms.commands
ffx.algorithms.commands.test - package ffx.algorithms.commands.test
ffx.algorithms.dynamics - package ffx.algorithms.dynamics: The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.dynamics.integrators - package ffx.algorithms.dynamics.integrators: The Integrators package implements integrators for molecular dynamics simulations.
ffx.algorithms.dynamics.thermostats - package ffx.algorithms.dynamics.thermostats: The Thermostats package implements thermostats for molecular dynamics simulations.
ffx.algorithms.mc - package ffx.algorithms.mc: The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc - package ffx.algorithms.misc: The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize - package ffx.algorithms.optimize: The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.anneal - package ffx.algorithms.optimize.anneal: The anneal package implements simulated annealing-based optimization, including an interface for annealing schedules and several concrete schedule implementations (linear, exponential, and flat-end) used to control temperature during optimization runs.
ffx.algorithms.optimize.manybody - package ffx.algorithms.optimize.manybody: The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
ffx.algorithms.thermodynamics - package ffx.algorithms.thermodynamics: The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
ffx.crystal - package ffx.crystal: The Crystal package implements space group symmetry and periodic boundary condition support.
ffx.numerics - package ffx.numerics: The Numerics package has support for atomic double arrays, FFTs (1D and 3D), numerical integration (1D), complex numbers, vector operations, multipole tensors, multi-dimensional optimization, special functions, splines and switching functions.
ffx.numerics.atomic - package ffx.numerics.atomic: The Atomic package has implementations of a double array that can be safely operated on by multiple threads.
ffx.numerics.clustering - package ffx.numerics.clustering: The clustering package provides hierarchical agglomerative clustering utilities, including linkage strategies (single, complete, average, weighted), distance map management, and supporting data structures and algorithms.
ffx.numerics.clustering.visualization - package ffx.numerics.clustering.visualization: Visualization components for clustering results, including Swing-based classes to render dendrograms and related views of hierarchical clusters.
ffx.numerics.estimator - package ffx.numerics.estimator: The Estimator package implements free energy estimators (e.g., Zwanzig, BAR/MBAR) and related bootstrapping and reporting utilities.
ffx.numerics.fft - package ffx.numerics.fft: The FFT package implements 1D and 3D FFTs of real or complex valued data, including SMP parallelization of 3D transforms and convolution using the Parallel Java library.
ffx.numerics.func1d - package ffx.numerics.func1d: The func1d package defines one-dimensional differentiable functions and utilities, including an interface for univariate functions and specific mappings (e.g., QuasiLinearThetaMap) used in lambda/theta transformations.
ffx.numerics.integrate - package ffx.numerics.integrate: The Integrate package implements 1D numerical integration.
ffx.numerics.math - package ffx.numerics.math: The Math package implements complex numbers, a software square root, and vector operations.
ffx.numerics.multipole - package ffx.numerics.multipole: The Multipole package computes derivatives of 1/|r| via recursion to arbitrary order using Cartesian multipoles in either a global frame or a quasi-internal frame.
ffx.numerics.optimization - package ffx.numerics.optimization: The Optimization package implements the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm for large-scale multidimensional unconstrained optimization problems.
ffx.numerics.quickhull - package ffx.numerics.quickhull: The Quickhull package provides a 3D convex hull implementation and supporting data structures (faces, half-edges, vertices, points and vectors).
ffx.numerics.special - package ffx.numerics.special: The Special package implements special functions including the complex error function (Erf) and the modified Bessel functions.
ffx.numerics.spline - package ffx.numerics.spline: The Spline package implements implements B-splines and Tricubic splines.
ffx.numerics.switching - package ffx.numerics.switching: The Switching package implements univariate switching functions.
ffx.numerics.tornado - package ffx.numerics.tornado
ffx.openmm - package ffx.openmm: The OpenMM package includes Java classes that are analogues of the OpenMM C++ API.
ffx.openmm.amoeba - package ffx.openmm.amoeba: The AMOEBA package includes Java classes that are analogues of the OpenMM C++ API for the AMOEBA model.
ffx.openmm.drude - package ffx.openmm.drude: The Drude package includes Java classes that are analogues of the OpenMM C++ API for the Charmm Drude model.
ffx.potential - package ffx.potential: The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded - package ffx.potential.bonded: The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.cli - package ffx.potential.cli: The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands - package ffx.potential.commands
ffx.potential.commands.test - package ffx.potential.commands.test
ffx.potential.constraint - package ffx.potential.constraint: The constraint package implements holonomic constraint algorithms used during molecular dynamics and minimization, including CCMA, SETTLE, and SHAKE-style constraints (as well as charge constraints).
ffx.potential.extended - package ffx.potential.extended: The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).
ffx.potential.nonbonded - package ffx.potential.nonbonded: The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.implicit - package ffx.potential.nonbonded.implicit: The implicit package implements implicit solvent models and related terms, including Generalized Kirkwood (GK) electrostatics, surface area terms, dispersion/cavitation contributions, and supporting parallel regions for Born radii and field evaluation.
ffx.potential.nonbonded.octree - package ffx.potential.nonbonded.octree: The octree package provides spatial data structures used to accelerate nonbonded interactions, neighbor list construction, and related queries.
ffx.potential.nonbonded.pme - package ffx.potential.nonbonded.pme: The pme package implements polarization and permanent electrostatics using Particle Mesh Ewald (PME).
ffx.potential.openmm - package ffx.potential.openmm: The openmm package contains utilities to construct and run Force Field X potentials on the OpenMM platform, including system builders, custom forces, alchemical fixed-charge forces, and integrators tailored to FFX simulations.
ffx.potential.parameters - package ffx.potential.parameters: The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.potential.parsers - package ffx.potential.parsers: The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.terms - package ffx.potential.terms: The terms package contains analytical potential energy terms and their gradients for bonded interactions (bond, angle, stretch-bend, torsions, impropers, Urey-Bradley) and restraint terms used by Force Field X.
ffx.potential.utils - package ffx.potential.utils: The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.realspace - package ffx.realspace: The Real Space package implements real space structure refinement.
ffx.realspace.cli - package ffx.realspace.cli: The Real Space CLI package defines options for PicoCLI command line scripts.
ffx.realspace.commands - package ffx.realspace.commands
ffx.realspace.commands.test - package ffx.realspace.commands.test
ffx.realspace.parsers - package ffx.realspace.parsers: The Parsers package reads and writes CCP4 map files.
ffx.ui - package ffx.ui: The UI package provides views and controllers for manipulating molecular systems.
ffx.ui.behaviors - package ffx.ui.behaviors: The Behaviors package contains Java3D Behaviors that turn user actions into scenegraph changes.
ffx.ui.commands - package ffx.ui.commands: The Commands package implements a Client/Server interface between Force Field X and simulations.
ffx.ui.properties - package ffx.ui.properties: The Properties package will eventually encapsulate internationalization features.
ffx.utilities - package ffx.utilities: The Utilities package implements a variety of useful Directory, File, Port, String, etc functionality.
ffx.xray - package ffx.xray: The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.cli - package ffx.xray.cli: The X-ray CLI package defines options for PicoCLI command line scripts.
ffx.xray.commands - package ffx.xray.commands
ffx.xray.commands.test - package ffx.xray.commands.test
ffx.xray.parsers - package ffx.xray.parsers: The Parsers package reads CNS files and reads/writes MTZ files.
FFXBinding - Class in ffx.utilities: The FFXBinding binds variable names to their instances for an FFX Command.
FFXBinding() - Constructor for class ffx.utilities.FFXBinding: Constructor for FFXContext.
FFXBinding(String[]) - Constructor for class ffx.utilities.FFXBinding: A helper constructor used in main(String[]) method calls
FFXBinding(Map<String, Object>) - Constructor for class ffx.utilities.FFXBinding: Constructor for FFXContext.
ffxCI - Static variable in class ffx.utilities.FFXTest: Constant ffxCI=System.getProperty("ffx.ci", "false").equalsIgnoreCase("true")
FFXClient - Class in ffx.ui.commands: The FFXClient class encapsulates a socket connection to an FFXServer started by an executing FFX instance.
FFXClient() - Constructor for class ffx.ui.commands.FFXClient: Constructor for FFXClient.
FFXClient(int) - Constructor for class ffx.ui.commands.FFXClient: Constructor for FFXClient.
FFXClient(InetSocketAddress) - Constructor for class ffx.ui.commands.FFXClient: Constructor for FFXClient.
FFXCommand - Class in ffx.utilities: Base FFX Command class.
FFXCommand() - Constructor for class ffx.utilities.FFXCommand: Default constructor for an FFX Command.
FFXCommand(FFXBinding) - Constructor for class ffx.utilities.FFXCommand: Default constructor for an FFX Command.
FFXCommand(String[]) - Constructor for class ffx.utilities.FFXCommand: Create an FFX Command using the supplied command line arguments.
FFXExec - Class in ffx.ui: FFXExec encapsulates a native replacement for the JDK System.exec() method.
FFXExec(FFXSystem, String, String, String, MainPanel, File, boolean) - Constructor for class ffx.ui.FFXExec: Constructor
FFXFileFilter - Class in ffx.potential.parsers: The FFXFileFilter class is used to choose Force Field X script (*.FFX) files.
FFXFileFilter() - Constructor for class ffx.potential.parsers.FFXFileFilter: Default Constructor.
FFXLocale - Class in ffx.ui.properties: The FFXLocale class will encapsulate internationalization features.
FFXLocale() - Constructor for class ffx.ui.properties.FFXLocale: Constructor for FFXLocale.
FFXLocale(String, String) - Constructor for class ffx.ui.properties.FFXLocale: Constructor for FFXLocale.
ffxOpenMM - Static variable in class ffx.utilities.FFXTest: Constant ffxOpenMM=System.getProperty("ffx.openMM", "false").equalsIgnoreCase("true")
FFXProperties - Annotation Interface in ffx.utilities: The FFXProperty Annotation can be applied multiple times to some classes.
FFXProperty - Annotation Interface in ffx.utilities: The FFXProperty Annotation should be used to document fields that are set using property files, keyword files, force field parameter files and the Java property system.
ffxScript(String[]) - Static method in class ffx.Main: A main entry point that runs a script and return a refernce to the result.
FFXServer - Class in ffx.ui.commands: The FFXServer is launched by an FFX instance to allow Force Field X Clients to connect.
FFXServer(SimulationDefinition) - Constructor for class ffx.ui.commands.FFXServer: Constructor for FFXServer.
FFXSystem - Class in ffx.ui: The FFXSystem class contains extensions to the generic MolecularAssembly class.
FFXSystem(File, String, CompositeConfiguration) - Constructor for class ffx.ui.FFXSystem: Constructor.
FFXTest - Class in ffx.utilities: The FFXTest configures the context for FFX tests.
FFXTest() - Constructor for class ffx.utilities.FFXTest: FFXTest constructor.
FFXTornado - Class in ffx.numerics.tornado: Utility Routines to use the TornadoVM
file - Variable in class ffx.ui.commands.SimulationDefinition
FILE_READ_DATA - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message containing data read from a file.
FILE_WRITE_DATA - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message containing data to write to a file.
fileAppend(File, String) - Static method in class edu.rit.io.Files: Append the given suffix to the given file.
fileForRank(File, int) - Static method in class edu.rit.io.Files: Append the given rank to the given file.
fileNameAppend(String, String) - Static method in class edu.rit.io.Files: Append the given suffix to the given file name.
fileNameForRank(String, int) - Static method in class edu.rit.io.Files: Append the given rank to the given file name.
fileNamePrepend(String, String) - Static method in class edu.rit.io.Files: Prepend the given prefix to the given file name.
filenames - Variable in class ffx.algorithms.commands.Thermodynamics: The final argument(s) should be one or more filenames.
fileNewWindow() - Method in class ffx.ui.ModelingShell
fileNewWindow(EventObject) - Method in class ffx.ui.ModelingShell
FileOpener - Interface in ffx.potential.parsers: The FileOpener interface specifies Runnable objects which can return one or more MolecularAssemblies.
filePrepend(File, String) - Static method in class edu.rit.io.Files: Prepend the given prefix to the given file.
fileRead - Variable in class ffx.potential.parsers.SystemFilter: True after the file has been read successfully.
fileRead() - Method in class ffx.potential.parsers.SystemFilter: Returns true if the read was successful
files - Variable in class ffx.potential.parsers.SystemFilter: Append multiple files into one MolecularAssembly.
Files - Class in edu.rit.io: Class Files provides static methods for various file related operations.
fileType - Variable in class ffx.algorithms.dynamics.MolecularDynamics: File type to use when saving files.
fileType - Variable in class ffx.potential.cli.WriteoutOptions: -F or --fileFormat Choose the file type to write [PDB/XYZ].
fileType - Variable in class ffx.potential.parsers.SystemFilter: The file format being handled.
FileUtils - Class in ffx.utilities: FileUtils class.
fill(Object) - Method in class edu.rit.mp.BooleanBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Buf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ByteBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.CharacterBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.DoubleBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.FloatBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.IntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.LongBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ObjectBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ShortBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Signed16BitIntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Signed8BitIntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf: Fill this buffer with the given item.
FILL - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
fillEwaldSource(int, double, double[], double, double[]) - Static method in class ffx.numerics.multipole.EwaldTensorGlobal: Fill the Ewald source terms.
fillEwaldSource(int, double, double[], DoubleVector, DoubleVector[], double[]) - Static method in class ffx.numerics.multipole.EwaldTensorGlobalSIMD: Fill the Ewald source terms.
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Molecule: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MSGroup: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MultiResidue: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Polymer: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Residue: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.MolecularAssembly: Abstract method that should specify how to finalize a MSGroup
findAtom(Atom) - Method in class ffx.potential.MolecularAssembly: findAtom
findAtomsOfElement(Residue, int) - Static method in class ffx.potential.bonded.BondedUtils: Finds all Atoms belonging to a Residue of a given atomic number.
findAtomType(int, ForceField) - Static method in class ffx.potential.bonded.BondedUtils: findAtomType.
findBondedAtoms(Atom, int) - Static method in class ffx.potential.bonded.BondedUtils: Finds Atoms bonded to a given Atom that match a certain atomic number.
findBondedAtoms(Atom, Atom, int) - Static method in class ffx.potential.bonded.BondedUtils: Finds Atoms bonded to a given Atom that match a certain atomic number that do not match an excluded atom.
findByCodePair(Cluster, Cluster) - Method in class ffx.numerics.clustering.DistanceMap: Finds the ClusterPair for the two provided clusters.
findChainBreaks(List<Residue>, double) - Static method in class ffx.potential.bonded.PolymerUtils
findClass(String) - Method in class edu.rit.pj.cluster.BackendClassLoader: Find the class with the given name.
findDangelingAtoms() - Method in class ffx.potential.bonded.MSGroup: This method constructs a List of atoms which are under-constrained.
findDangelingAtoms() - Method in class ffx.potential.bonded.MultiResidue: This method constructs a List of atoms which are under-constrained.
findEdge(Vertex, Vertex) - Method in class ffx.numerics.quickhull.Face: Finds the half-edge within this face which has tail vt and head vh.
findIndex - Variable in class ffx.numerics.quickhull.QuickHull3D
findNitrogenAtom(Residue) - Static method in class ffx.potential.bonded.BondedUtils: Finds the backbone nitrogen of a residue.
findNucleotideO4s(Residue) - Static method in class ffx.potential.bonded.BondedUtils: Find the O4' of a nucleic acid Residue.
findPlatform(StringArray) - Static method in class ffx.openmm.Platform: Find a platform that supports a specified set of kernels.
findResource(String) - Method in class edu.rit.pj.cluster.BackendClassLoader: Find the resource with the given name.
FindRestraints - Class in ffx.algorithms.commands.test: The FindRestraints script identifies guest molecule atoms that should be restrained based on their proximity to specific atoms in a host molecule.
FindRestraints() - Constructor for class ffx.algorithms.commands.test.FindRestraints: FindRestraints Constructor.
FindRestraints(FFXBinding) - Constructor for class ffx.algorithms.commands.test.FindRestraints: FindRestraints Constructor.
FindRestraints(String[]) - Constructor for class ffx.algorithms.commands.test.FindRestraints: FindRestraints constructor that sets the command line arguments.
findSeed(Atom, Atom) - Static method in class ffx.potential.Utilities: Returns an atom bonded to the "end" atom, which is not equal to "other".
findSymHKL(int, int, int, HKL) - Method in class ffx.crystal.ReflectionList: findSymHKL
findSymHKL(int, int, int, HKL, boolean) - Method in class ffx.crystal.ReflectionList: findSymHKL
findSymHKL(HKL, HKL) - Method in class ffx.crystal.ReflectionList: findSymHKL
finish() - Method in class edu.rit.pj.IntegerForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.IntegerStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.LongForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.LongStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.ParallelIteration: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.ParallelRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class edu.rit.pj.WorkerIntegerForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerIteration: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerLongForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerLongStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
finish() - Method in class ffx.algorithms.optimize.manybody.SelfEnergyRegion
finish() - Method in class ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
finish() - Method in class ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
finish() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
finish() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
finish() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
finish() - Method in class ffx.potential.nonbonded.NeighborList: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
finish() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
finish() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
finish() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
finish() - Method in class ffx.potential.nonbonded.RowRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.potential.nonbonded.SliceRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.xray.BulkSolventList: Perform finalization actions after parallel execution ends.
finished() - Method in class ffx.ui.SwingWorker: Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
FINISHED - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State: The job backend process has finished.
FiniteDifferenceUtils - Class in ffx.potential: FiniteDifference
FiniteDifferenceUtils() - Constructor for class ffx.potential.FiniteDifferenceUtils
first() - Method in class ffx.numerics.quickhull.FaceList: Returns the first face in this list (head), or null if empty.
FIRST_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
firstDerivative(double) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
firstDerivative(double) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.BellCurveSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.CompositeSwitch
firstDerivative(double) - Method in class ffx.numerics.switching.ConstantSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.LinearDerivativeSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.PowerSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.SquaredTrigSwitch: First derivative at a point.
fixed() - Static method in class edu.rit.pj.IntegerSchedule: Returns a fixed schedule object.
fixed() - Static method in class edu.rit.pj.LongSchedule: Returns a fixed schedule object.
FIXED - Enum constant in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm
FIXED_CHARGE - Enum constant in enum class ffx.potential.parameters.ForceField.ELEC_FORM
FIXEDCHARGE - Enum constant in enum class ffx.potential.bonded.Atom.Resolution
fixedChargeAlchemicalForces - Variable in class ffx.potential.openmm.OpenMMSystem: Custom forces to handle alchemical transformations for fixed charge systems.
FixedChargeAlchemicalForces - Class in ffx.potential.openmm: Fixed Charge Alchemical Forces.
FixedChargeAlchemicalForces(OpenMMEnergy, FixedChargeNonbondedForce) - Constructor for class ffx.potential.openmm.FixedChargeAlchemicalForces
fixedChargeGBForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom GB Force.
FixedChargeGBForce - Class in ffx.potential.openmm: FixedChargeGBForce.
FixedChargeGBForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.FixedChargeGBForce: FixedChargeGBForce constructor.
fixedChargeNonBondedForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Fixed Charge Non-Bonded Force.
FixedChargeNonbondedForce - Class in ffx.potential.openmm: Define a fixed charge non-bonded force.
FixedChargeNonbondedForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.FixedChargeNonbondedForce
fixParameters(double, double, double, double, double, double) - Method in enum class ffx.crystal.LatticeSystem: Change the lattice parameters to satisfy the restrictions of the lattice system.
flags - Variable in class ffx.ui.behaviors.MouseBehavior
FLAT_BOTTOM_HARMONIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
FLAT_BOTTOM_QUARTIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
flatAgg(LinkageStrategy, Double) - Method in class ffx.numerics.clustering.HierarchyBuilder: Performs agglomeration until the minimal inter-cluster distance exceeds the threshold, and returns the remaining clusters (flat clustering at that cut).
flatBottomRadius - Variable in class ffx.potential.parameters.BondType: Radius of a flat bottom where energy and force is 0; typically used for restraints.
FlatEndAnnealSchedule - Class in ffx.algorithms.optimize.anneal: Composite annealing schedule with flat ends (i.e. spends extra time at the low and high temperatures).
FlatEndAnnealSchedule(AnnealingSchedule, double, double, double, double) - Constructor for class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule: Creates a flat-ended annealing schedule based on a provided schedule for the middle, which is flat for some number of steps at the ends.
Float() - Constructor for class edu.rit.util.Searching.Float
Float() - Constructor for class edu.rit.util.Sorting.Float
Float3 - Class in ffx.numerics.math: Convenience class for working with 3D float vectors.
Float3() - Constructor for class ffx.numerics.math.Float3: Construct a Float3 at (0.0, 0.0, 0.0).
Float3(float[]) - Constructor for class ffx.numerics.math.Float3: Construct a Float3 at a.
Float3(float, float, float) - Constructor for class ffx.numerics.math.Float3: Construct a Float3 at (x, y, z).
FloatArrayBuf - Class in edu.rit.mp.buf: Class FloatArrayBuf provides a buffer for an array of float items sent or received using the Message Protocol (MP).
FloatArrayBuf(float[], Range) - Constructor for class edu.rit.mp.buf.FloatArrayBuf: Construct a new float array buffer.
FloatArrayBuf_1 - Class in edu.rit.mp.buf: Class FloatArrayBuf_1 provides a buffer for an array of float items sent or received using the Message Protocol (MP).
FloatArrayBuf_1(float[], Range) - Constructor for class edu.rit.mp.buf.FloatArrayBuf_1: Construct a new float array buffer.
FloatBuf - Class in edu.rit.mp: Class FloatBuf is the abstract base class for a buffer of float items sent or received using the Message Protocol (MP).
FloatBuf(int) - Constructor for class edu.rit.mp.FloatBuf: Construct a new float buffer.
FloatItemBuf - Class in edu.rit.mp.buf: Class FloatItemBuf provides a buffer for a single float item sent or received using the Message Protocol (MP).
FloatItemBuf() - Constructor for class edu.rit.mp.buf.FloatItemBuf: Construct a new float item buffer.
FloatItemBuf(float) - Constructor for class edu.rit.mp.buf.FloatItemBuf: Construct a new float item buffer with the given initial value.
FloatMath - Class in ffx.numerics.math: The FloatMath class is a simple math library that operates on 3-coordinate float arrays.
FloatMatrixBuf - Class in edu.rit.mp.buf: Class FloatMatrixBuf provides a buffer for a matrix of float items sent or received using the Message Protocol (MP).
FloatMatrixBuf(float[][], Range, Range) - Constructor for class edu.rit.mp.buf.FloatMatrixBuf: Construct a new float matrix buffer.
FloatMatrixBuf_1 - Class in edu.rit.mp.buf: Class FloatMatrixBuf_1 provides a buffer for a matrix of float items sent or received using the Message Protocol (MP).
FloatMatrixBuf_1(float[][], Range, Range) - Constructor for class edu.rit.mp.buf.FloatMatrixBuf_1: Construct a new float matrix buffer.
FloatOp - Class in edu.rit.pj.reduction: Class FloatOp is the abstract base class for a binary operation on float values, used to do reduction in a parallel program.
FloatOp() - Constructor for class edu.rit.pj.reduction.FloatOp: Construct a new float binary operation.
floatValue() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns this reduction variable's current value converted to type float.
floodReceive(Buf) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator.
floodReceive(Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator (non-blocking).
floodReceive(Integer, Buf) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator with the given message tag.
floodReceive(Integer, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator with the given message tag (non-blocking).
floodSend(int, Buf) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator with the given message tag.
floodSend(int, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator with the given message tag (non-blocking).
floodSend(Buf) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator.
floodSend(Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator (non-blocking).
flush() - Method in class edu.rit.io.LineBufferedOutputStream: Flush this line buffered output stream.
flush() - Method in class edu.rit.pj.cluster.BackendFileOutputStream: Flush this output stream.
flush() - Method in class ffx.ui.LogHandler
Fm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
fma(double[], double, double[]) - Static method in class ffx.numerics.math.DoubleMath: Compute a * b + c and return the result in a new array.
fma(double[], double, double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Compute a * b + c.
fma(double, Double3) - Method in class ffx.numerics.math.Double3: Compute this * b + c and return the result in a new Double3.
fma(float[], float, float[]) - Static method in class ffx.numerics.math.FloatMath: Compute a * b + c and return the result in a new array.
fma(float[], float, float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Compute a * b + c.
fma(float, Float3) - Method in class ffx.numerics.math.Float3: Compute a * b + c and return the result in a new Float3.
fmaI(double, Double3) - Method in class ffx.numerics.math.Double3: Compute this * b + c and return the result in a new Double3.
fmaI(float, Float3) - Method in class ffx.numerics.math.Float3: Compute a * b + c and return the result in a new Float3.
fN(HKL, int) - Method in class ffx.xray.XRayFormFactor: f_n
FOFC - Static variable in interface ffx.xray.SplineEnergy.Type
foFc1 - Variable in class ffx.xray.DiffractionRefinementData: mFo - DFc coefficients.
foFc1F(int) - Method in class ffx.xray.DiffractionRefinementData: foFc1F
foFc1Phi(int) - Method in class ffx.xray.DiffractionRefinementData: foFc1Phi
FoFc2F(int) - Method in class ffx.xray.DiffractionRefinementData: FoFc2F
FoFc2Phi(int) - Method in class ffx.xray.DiffractionRefinementData: FoFc2Phi
fomPhi - Variable in class ffx.xray.DiffractionRefinementData: Figure of merit and phase.
FOR - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
Force - Class in ffx.openmm: Force objects apply forces to the particles in a System, or alter their behavior in other ways.
Force(PointerByReference) - Constructor for class ffx.openmm.Force: Create a new Force object with the specified pointer.
FORCE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
FORCE_ZEROS_SEED - Static variable in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
force0 - Variable in class ffx.potential.bonded.StretchBend: Force constant.
force1 - Variable in class ffx.potential.bonded.StretchBend: Force constant.
forceConstant - Variable in class ffx.potential.parameters.AngleType: Force constant (Kcal/mole/radian^2).
forceConstant - Variable in class ffx.potential.parameters.BondType: Force constant (Kcal/mol/A^2).
forceConstant - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Force constant (Kcal/mol/Angstrom).
forceConstant - Variable in class ffx.potential.parameters.PiOrbitalTorsionType: Force constant.
forceConstant - Variable in class ffx.potential.parameters.UreyBradleyType: Force constant (Kcal/mole/angstroms^2).
forceConstants - Variable in class ffx.potential.parameters.AngleTorsionType: Force constants.
forceConstants - Variable in class ffx.potential.parameters.StretchBendType: Force constants (Kcal/mole/Angstrom-Degrees).
forceConstants - Variable in class ffx.potential.parameters.StretchTorsionType: Force constants.
forcefield - Variable in class ffx.ui.commands.SimulationDefinition
forceField - Variable in class ffx.potential.MolecularAssembly
forceField - Variable in class ffx.potential.openmm.OpenMMSystem: The Force Field in use.
forceField - Variable in class ffx.potential.parsers.SystemFilter: The molecular mechanics force field being used.
ForceField - Class in ffx.potential.parameters: The ForceField class organizes parameters for a molecular mechanics force field.
ForceField(CompositeConfiguration) - Constructor for class ffx.potential.parameters.ForceField: ForceField Constructor.
ForceField.ELEC_FORM - Enum Class in ffx.potential.parameters
ForceField.ForceFieldName - Enum Class in ffx.potential.parameters: Available force fields.
ForceField.ForceFieldType - Enum Class in ffx.potential.parameters
forceFieldEnergy - Variable in class ffx.algorithms.commands.test.CreateRotamers
forceFieldEnergy - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Force Field Potential Energy (i.e. with no bias terms added).
forceFieldEnergy - Variable in class ffx.potential.commands.Energy
forceFieldEnergy - Variable in class ffx.potential.commands.PhEnergy
forceFieldEnergy - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: The ForceFieldEnergy instance for the first topology.
ForceFieldEnergy - Class in ffx.potential: Compute the potential energy and derivatives of a molecular system described by a force field.
ForceFieldEnergy(MolecularAssembly) - Constructor for class ffx.potential.ForceFieldEnergy: Constructor for ForceFieldEnergy.
ForceFieldEnergy(MolecularAssembly, int) - Constructor for class ffx.potential.ForceFieldEnergy: Constructor for ForceFieldEnergy.
ForceFieldEnergy.RestrainMode - Enum Class in ffx.potential: RestrainMode specifies how restrain terms are applied for dual topology calculations.
forceFieldEnergy2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: The ForceFieldEnergy instance for the second topology.
ForceFieldFileFilter - Class in ffx.potential.parsers: The ForceFieldFileFilter class is used to choose a TINKER Parameter file (*.PRM).
ForceFieldFileFilter() - Constructor for class ffx.potential.parsers.ForceFieldFileFilter: Default Constructor
ForceFieldFilter - Class in ffx.potential.parsers: The ForceFieldFilter Class is used to parse and store molecular mechanics data from keyword/property and parameter (*.PRM) files.
ForceFieldFilter(CompositeConfiguration) - Constructor for class ffx.potential.parsers.ForceFieldFilter: Constructor for ForceFieldFilter.
forceFieldURL - Variable in class ffx.potential.parameters.ForceField: URL to the force field parameter file.
forceGroup - Variable in class ffx.potential.terms.EnergyTerm: Integer force group this term belongs to.
ForEachFile - Class in ffx.algorithms.commands: Run an FFX command on a series of files.
ForEachFile() - Constructor for class ffx.algorithms.commands.ForEachFile: ForEachFile Constructor.
ForEachFile(FFXBinding) - Constructor for class ffx.algorithms.commands.ForEachFile: ForEachFile Constructor.
ForEachFile(String[]) - Constructor for class ffx.algorithms.commands.ForEachFile: ForEachFile constructor that sets the command line arguments.
format(LogRecord) - Method in class ffx.ui.LogFormatter
formatEnergy(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Utility method for formatting energies, using 16 spaces with 8 digits of precision.
FormFactor - Interface in ffx.xray: FormFactor interface.
FORWARD - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Direction
FORWARDS - Enum constant in enum class ffx.numerics.estimator.Zwanzig.Directionality: Forwards perturbation.
FOTOESQ - Static variable in interface ffx.xray.SplineEnergy.Type
FourBodyEnergyRegion - Class in ffx.algorithms.optimize.manybody: Compute 4-Body energies.
FourBodyEnergyRegion(RotamerOptimization, DistanceMatrix, EnergyExpansion, EliminatedRotamers, Residue[], List<Residue>, double) - Constructor for class ffx.algorithms.optimize.manybody.FourBodyEnergyRegion
Fr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Frac2Cart - Class in ffx.potential.commands: Convert from fractional to Cartesian coordinates.
Frac2Cart() - Constructor for class ffx.potential.commands.Frac2Cart
Frac2Cart(FFXBinding) - Constructor for class ffx.potential.commands.Frac2Cart
Frac2Cart(String[]) - Constructor for class ffx.potential.commands.Frac2Cart
fractionalCount() - Method in class ffx.potential.MolecularAssembly: Count the number of fractional coordinate entities in the system.
fractionalMultipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Fractional multipoles in the global frame with dimensions of [nsymm][nAtoms][10]
frame() - Method in class ffx.ui.MainPanel: frame
frameAtomTypes - Variable in class ffx.potential.parameters.MultipoleType: Atom types that define the local frame of this multipole.
frameDefinition - Variable in class ffx.potential.parameters.MultipoleType: Local frame definition method.
free() - Method in class ffx.potential.openmm.OpenMMContext: Free OpenMM memory for the current Context and Integrator.
free() - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Destroy the dual-topology system.
free() - Method in class ffx.potential.openmm.OpenMMSystem: Destroy the system.
freeEnergyDiff - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
freeEnergyDiff2 - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
FreeEnergyDifferenceReporter - Class in ffx.numerics.estimator: The FreeEnergyDifferenceReporter class reports free energy differences using the Bennett Acceptance Ratio (BAR) method.
FreeEnergyDifferenceReporter(int, double[], double[], double, int, double[][], double[][], double[][], double[][]) - Constructor for class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Report Free Energy Differences based on a series of states.
freeEnergyDiffGK - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
freeEnergyDiffGK2 - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
Freefix - Class in ffx.algorithms.commands.test: The Freefix script calculates analytical free energy, entropy, and enthalpy corrections for flat-bottom harmonic restraints with inner and outer radii.
Freefix() - Constructor for class ffx.algorithms.commands.test.Freefix: Freefix Constructor.
Freefix(FFXBinding) - Constructor for class ffx.algorithms.commands.test.Freefix: Freefix Constructor.
Freefix(String[]) - Constructor for class ffx.algorithms.commands.test.Freefix: Freefix constructor that sets the command line arguments.
freeR - Variable in class ffx.xray.DiffractionRefinementData: Array of R free flags;
FROM_JOB_BACKEND - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job backend process.
FROM_JOB_FRONTEND - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job frontend process.
FROM_JOB_LAUNCHER - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job launcher process.
FROM_JOB_SCHEDULER - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job scheduler process.
fromRank - Variable in class edu.rit.pj.CommStatus: The rank of the source process that sent the message.
frontend - Variable in class edu.rit.pj.cluster.JobInfo: Reference to the job frontend process.
frontendAddress - Variable in class edu.rit.pj.cluster.ProcessInfo: Host/port to which the job backend process is listening for the frontend communicator, or null if the frontend communicator does not exist.
FrontendFileReader - Class in edu.rit.pj.cluster: Class FrontendFileReader provides an object that reads sequential files in the job frontend process.
FrontendFileReader(JobFrontend) - Constructor for class edu.rit.pj.cluster.FrontendFileReader: Construct a new frontend file reader.
FrontendFileWriter - Class in edu.rit.pj.cluster: Class FrontendFileWriter provides an object that writes sequential files in the job frontend process.
FrontendFileWriter(JobFrontend) - Constructor for class edu.rit.pj.cluster.FrontendFileWriter: Construct a new frontend file writer.
fs - Variable in class ffx.xray.DiffractionRefinementData: Calculated bulk solvent structure factors.
FSEC_TO_PSEC - Static variable in class ffx.utilities.Constants: Constant FSEC_TO_PSEC=0.001
fsF(int) - Method in class ffx.xray.DiffractionRefinementData: fsF
fSigFCutoff - Variable in class ffx.xray.DiffractionRefinementData
fsPhi(int) - Method in class ffx.xray.DiffractionRefinementData: fsPhi
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic: The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Berendsen: The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Bussi: The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: The full-step temperature correction.
FunctionDataCurve - Class in ffx.numerics.integrate: A FunctionDataCurve represents a set of points along a 1-dimensional, analytically integrable function.
FunctionDataCurve() - Constructor for class ffx.numerics.integrate.FunctionDataCurve: Constructor.
fwDec(double, int, int) - Static method in class ffx.utilities.StringUtils: Prints a fixed-width decimal, similar to String.format(%width.precf, val), but ensuring the resulting string is never longer than width.
fwFpDec(double, int, int) - Static method in class ffx.utilities.StringUtils: Prints a fixed-width decimal using String.format conventions, throwing an error if the value cannot be formatted within that space.
fwFpTrunc(double, int, int) - Static method in class ffx.utilities.StringUtils: Prints a fixed-width decimal using String.format conventions, reducing the value if necessary to fit within the width.
fX(double) - Method in class ffx.numerics.integrate.CompositeCurve: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.CosineWave: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.FunctionDataCurve: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.PolynomialCurve: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.SinWave: Evaluates the function at x.

G

G - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
G - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
G - Variable in class ffx.crystal.Crystal: The direct space metric matrix.
Ga - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
gamma - Variable in class ffx.crystal.Crystal: The interaxial lattice angle between a and b.
gamma - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: First constant suggested by Halgren for the Buffered-14-7 potential.
gather(int, int, Buf, Buf[]) - Method in class edu.rit.pj.Comm: Gather messages from all processes in this communicator using the given message tag.
gather(int, Buf, Buf[]) - Method in class edu.rit.pj.Comm: Gather messages from all processes in this communicator.
GAUSS_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
GAUSSIAN - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: Smooth the boundary of the classic model using Gaussians.
GaussVol - Class in ffx.potential.nonbonded.implicit: GaussVol implements a description molecular volume and surface area described by overlapping Gaussian spheres.
GaussVol(Atom[], ForceField, ParallelTeam) - Constructor for class ffx.potential.nonbonded.implicit.GaussVol: Creates/Initializes a GaussVol instance.
GayBerneForce - Class in ffx.openmm: This class implements the Gay-Berne anisotropic potential.
GayBerneForce() - Constructor for class ffx.openmm.GayBerneForce: Create a new GayBerneForce.
GBSAOBCForce - Class in ffx.openmm: This class implements an implicit solvation force using the GBSA-OBC model.
GBSAOBCForce() - Constructor for class ffx.openmm.GBSAOBCForce: Create a new GBSAOBCForce.
Gd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Ge - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
GeneralizedKirkwood - Class in ffx.potential.nonbonded: This Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a NeighborList.
GeneralizedKirkwood(ForceField, Atom[], ParticleMeshEwald, Crystal, ParallelTeam, double) - Constructor for class ffx.potential.nonbonded.GeneralizedKirkwood: Constructor for GeneralizedKirkwood.
GeneralizedKirkwood.NonPolarModel - Enum Class in ffx.potential.nonbonded
GeneralizedKirkwoodForce - Class in ffx.openmm.amoeba: This class implements an implicit solvation force using the Amoeba Generalized Kirkwood model.
GeneralizedKirkwoodForce() - Constructor for class ffx.openmm.amoeba.GeneralizedKirkwoodForce
generate(int, double, double) - Method in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules: Creates an AnnealingSchedule corresponding to this enum and provided values.
generateFsigFfromAnomalousFsigF(double[][]) - Method in class ffx.xray.DiffractionRefinementData: Generate average F/sigF from anomalous F/sigF.
generateLoops(int, int) - Method in class ffx.potential.utils.Loop: The generateLoops method generates loop closure solutions for a specified range of residues.
generateLoops(int, int, double[]) - Method in class ffx.potential.utils.Loop: The generateLoops method generates loop closure solutions for a specified range of residues.
generateRFree() - Method in class ffx.xray.DiffractionRefinementData: Mark 5% of reflections for cross validation (R free flags).
GenerateRotamers - Class in ffx.algorithms.misc: The GenerateRotamers class helps generate a rotamer library (particularly for nonstandard amino acids) for a Residue.
GenerateRotamers(MolecularAssembly, Potential, Residue, File, int, AlgorithmListener) - Constructor for class ffx.algorithms.misc.GenerateRotamers: Intended to create rotamer sets for nonstandard amino acids.
GenerateRotamers(MolecularAssembly, Potential, Residue, File, int, AlgorithmListener, RotamerLibrary) - Constructor for class ffx.algorithms.misc.GenerateRotamers: Intended to create rotamer sets for nonstandard amino acids.
generateSource(GKTensorMode, GKMultipoleOrder, double, double, double) - Method in class ffx.numerics.multipole.GKSource: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
generateSource(GKTensorMode, GKMultipoleOrder, DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.GKSourceSIMD: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
generateTensor() - Method in class ffx.numerics.multipole.MultipoleTensor: Generate the tensor using hard-coded methods or via recursion.
generateTensor() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Generate the tensor using hard-coded methods.
generateTensor(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: For the MultipoleTensorTest class and testing.
generateTestData_v1() - Static method in class ffx.numerics.integrate.Integration: generateTestData_v1.
generateXPoints(double, double, int, boolean) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Generates a set of points along x.
GenZ - Class in ffx.algorithms.commands: The ReductionPartition script performs a discrete optimization using a many-body expansion and elimination expressions.
GenZ - Class in ffx.realspace.commands: Run GenZ for ensemble generation.
GenZ - Class in ffx.xray.commands: The GenZ script for calculating free energy changes.
GenZ() - Constructor for class ffx.algorithms.commands.GenZ: ManyBody Constructor.
GenZ() - Constructor for class ffx.realspace.commands.GenZ: GenZ Constructor.
GenZ() - Constructor for class ffx.xray.commands.GenZ: GenZ Constructor.
GenZ(FFXBinding) - Constructor for class ffx.algorithms.commands.GenZ: ManyBody Constructor.
GenZ(FFXBinding) - Constructor for class ffx.realspace.commands.GenZ: GenZ Constructor.
GenZ(FFXBinding) - Constructor for class ffx.xray.commands.GenZ: GenZ Constructor.
GenZ(String[]) - Constructor for class ffx.algorithms.commands.GenZ: GenZ constructor that sets the command line arguments.
GenZ(String[]) - Constructor for class ffx.realspace.commands.GenZ: GenZ constructor that sets the command line arguments.
GenZ(String[]) - Constructor for class ffx.xray.commands.GenZ: GenZ constructor that sets the command line arguments.
GEOMETRIC - Enum constant in enum class ffx.potential.parameters.VDWType.EPSILON_RULE
GEOMETRIC - Enum constant in enum class ffx.potential.parameters.VDWType.RADIUS_RULE
get() - Method in class edu.rit.pj.reduction.SharedBoolean: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedObject: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedBoolean: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedObject: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns this replicated, shared reduction variable's current value.
get() - Method in class ffx.numerics.math.Double3: Returns a reference to the internal double array that stores this Double3.
get() - Method in class ffx.numerics.math.Float3: Returns a reference to the internal float array that stores this Float3.
get() - Method in class ffx.ui.SwingWorker: Return the value created by the construct method.
get(int) - Method in class edu.rit.mp.BooleanBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyBooleanBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyByteBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyCharacterBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyDoubleBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyFloatBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyLongBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyObjectBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyShortBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedBooleanBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedByteArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedByteBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedCharacterBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedDoubleBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedFloatBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedLongArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedLongBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedObjectBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedShortArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedShortBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.ByteBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.CharacterBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.DoubleBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.FloatBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.IntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.LongBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.ObjectBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.ShortBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Signed16BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Signed8BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf: Obtain the given item from this buffer.
get(int) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedByteArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedFloatArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedLongArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedObjectArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedShortArray: Returns this array reduction variable's current value at the given index.
get(int) - Method in class ffx.numerics.atomic.AdderDoubleArray: Get the value of the array at the specified index.
get(int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Get the value of the array at the specified index.
get(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Get the Double3 at the specified index.
get(int) - Method in class ffx.numerics.atomic.MultiDoubleArray: Get the value of the array at the specified index.
get(int) - Method in class ffx.numerics.atomic.PJDoubleArray: Get the value of the array at the specified index.
get(int) - Method in class ffx.numerics.math.Double3: Returns the coordinate at position i.
get(int) - Method in class ffx.numerics.math.Float3: Returns the coordinate at position i.
get(int) - Method in class ffx.numerics.quickhull.Vector3d: Gets a single element of this vector.
get(int) - Method in class ffx.openmm.DoubleArray: Get a value from the array.
get(int) - Method in class ffx.openmm.IntArray: Get a value from the array.
get(int) - Method in class ffx.openmm.StringArray: Return the String at index i.
get(int) - Method in class ffx.openmm.Vec3Array: Get a Vec3 from the Vec3Array.
get(int) - Method in class ffx.potential.nonbonded.NeighborList.Cell
get(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Returns this matrix reduction variable's current value at the given row and column.
get(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Returns this matrix reduction variable's current value at the given row and column.
get(int, int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Get the value of the array at the specified index after calling the reduce method.
get(int, IntByReference, IntByReference) - Method in class ffx.openmm.BondArray: Get the bond at index.
get(int, IntBuffer, IntBuffer) - Method in class ffx.openmm.BondArray: Get the bond at index.
get(String) - Method in class edu.rit.pj.cluster.ResourceCache: Obtain the resource content for the given resource name from this resource cache (blocking).
GET_METHOD - Static variable in class edu.rit.http.HttpRequest: The GET method string, "GET".
get1_2(Atom) - Method in class ffx.potential.bonded.Bond: Find the other Atom in this Bond.
get1_2(Atom) - Method in class ffx.potential.bonded.RestrainDistance: Find the other Atom in this Bond.
get1_3(Atom) - Method in class ffx.potential.bonded.Angle: If the specified atom is not the central atom of this angle, the atom of the opposite leg is returned.
get1_4(Atom) - Method in class ffx.potential.bonded.AngleTorsion: If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
get1_4(Atom) - Method in class ffx.potential.bonded.StretchTorsion: If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
get1_4(Atom) - Method in class ffx.potential.bonded.Torsion: If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
get12List() - Method in class ffx.potential.bonded.Atom: Get the list of 1-2 atoms ordered by XYZ index.
get13List() - Method in class ffx.potential.bonded.Atom: Get the list of 1-3 atoms ordered by XYZ index.
get14List() - Method in class ffx.potential.bonded.Atom: Get the list of 1-4 atoms ordered by XYZ index.
get15List() - Method in class ffx.potential.bonded.Atom: Get the list of 1-5 atoms ordered by XYZ index.
get2Body(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Return a previously computed 2-body energy.
get2BodyDistance(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks the distance matrix, finding the shortest distance between two residues' rotamers or any rotamers from two residues under any symmetry operator; will evaluate this if distance matrix not already filled.
get3Body(Residue[], int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Return a previously computed 3-body energy.
get3BodyResidueDistance(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Returns the RMS separation distance for the closest rotamers of three residues' 2-body distances.
get4BodyResidueDistance(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Returns the RMS separation distance for the closest rotamers of 6 2-body distances from four residues.
getABCIndices() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Returns the a, b, and c axis indices of this cell.
getAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat: getAcceleration.
getAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: getAcceleration.
getAcceleration(double[]) - Method in interface ffx.numerics.Potential: getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
getAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field acceleration.
getAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy: getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
getAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy: getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy: getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.XtalEnergy: getAcceleration.
getAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy: getAcceleration.
getAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy: getAcceleration.
getAcceleration(double[]) - Method in class ffx.xray.XRayEnergy: getAcceleration.
getAccelerations(double[], Atom[]) - Method in class ffx.potential.openmm.OpenMMState: The acceleration array will contain the acceleration information for all atoms.
getAccept() - Method in class ffx.algorithms.mc.BoltzmannMC: If last step taken was a success.
getAccept() - Method in interface ffx.algorithms.mc.MetropolisMC: If last step taken was a success.
getAcceptanceRate() - Method in class ffx.algorithms.mc.MCLoop: Get the current MC acceptance rate.
getAcceptorParameters(int, IntByReference, IntByReference, IntByReference, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Get the parameters for an acceptor.
getAcceptorParameters(int, IntBuffer, IntBuffer, IntBuffer, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Get the parameters for an acceptor.
getActive() - Method in class ffx.potential.bonded.MultiResidue: getActive.
getActive() - Method in class ffx.ui.Hierarchy: Returns the active FSystem.
getActiveAccelerations(double[], Atom[]) - Method in class ffx.potential.openmm.OpenMMState: The acceleration array will contain the acceleration information for all atoms.
getActiveAssemblies(String) - Method in class ffx.algorithms.cli.AlgorithmsCommand: If a filename is supplied, open it and return the MolecularAssemblies.
getActiveAssemblies(String) - Method in class ffx.potential.cli.PotentialCommand: If a filename is supplied, open it and return the MolecularAssemblies.
getActiveAssembly() - Method in interface ffx.potential.utils.PotentialsFunctions: Returns either the active assembly from the overlying UI, or the "active" molecular assembly from the last used SystemFilter.
getActiveAssembly() - Method in class ffx.ui.UIUtils
getActiveAssembly(String) - Method in class ffx.algorithms.cli.AlgorithmsCommand: If a filename is supplied, open it and return the MolecularAssembly.
getActiveAssembly(String) - Method in class ffx.potential.cli.PotentialCommand: If a filename is supplied, open it and return the MolecularAssembly.
getActiveAtomArray() - Method in class ffx.potential.MolecularAssembly: getActiveAtomArray
getActiveAtomArray() - Method in class ffx.realspace.RealSpaceData: getActiveAtomArray
getActiveAtomArray() - Method in interface ffx.xray.DataContainer: getActiveAtomArray
getActiveAtomArray() - Method in class ffx.xray.DiffractionData: getActiveAtomArray.
getActiveAtomArray() - Method in class ffx.xray.RefinementModel: Getter for the field activeAtomArray.
getActiveAtomList() - Method in class ffx.xray.RefinementModel: Getter for the field activeAtomList.
getActiveAtoms() - Method in class ffx.potential.cli.AtomSelectionOptions: --aa or --activeAtoms Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].
getActiveAtoms() - Method in class ffx.xray.RefinementEnergy: getActiveAtoms.
getActiveGradient(double[], Atom[]) - Method in class ffx.potential.openmm.OpenMMState: The force array contains the OpenMM force information for active atoms.
getActiveMolecularSystem() - Method in class ffx.potential.parsers.SystemFilter: Return the MolecularSystem that has been read in
getActiveNode() - Method in class ffx.ui.Hierarchy: Getter for the field activeNode.
getActivePositions(double[], Atom[]) - Method in class ffx.potential.openmm.OpenMMState: The position array contains the OpenMM atomic position information for active atoms.
getActiveVelocities(double[], Atom[]) - Method in class ffx.potential.openmm.OpenMMState: The velocity array contains the OpenMM atomic position information for active atoms.
getAddress() - Method in class edu.rit.http.HttpServer: Obtain the host and port to which this HTTP server is listening for connections.
getAEwald() - Method in class ffx.openmm.amoeba.MultipoleForce: Deprecated.
This method exists only for backward compatibility. Use getPMEParameters() instead.
getAlchemicalAlchemicalStericsForce() - Method in class ffx.potential.openmm.FixedChargeAlchemicalForces
getAlchemicalAtoms() - Method in class ffx.potential.cli.AlchemicalOptions: --ac or --alchemicalAtoms Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N]."
getAlchemicalAtoms(boolean) - Method in class ffx.potential.parsers.PDBFilter.Mutation: Determines what atoms should be alchemical for a purine to purine or pyrimidine to pyrimidine mutation.
getAlchemicalAtoms2() - Method in class ffx.potential.cli.TopologyOptions: --ac2 or --alchemicalAtoms2 Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N].
getAlchemicalMethod() - Method in class ffx.openmm.amoeba.VdwForce: Get the alchemical method.
getAlchemicalParameters() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Return the PME AlchemicalParameters.
getAlchemicalResidues() - Method in class ffx.potential.cli.AlchemicalOptions: --acRes or --alchemicalResidues Specify alchemical residues by chain and residue number [A4,B21].
getAlchemicalResidues2() - Method in class ffx.potential.cli.TopologyOptions: --acRes2 or --alchemicalResidues2 Specify alchemical residues by chain and residue number [e.g.
getAlgorithm() - Method in class ffx.algorithms.cli.ThermodynamicsOptions: Return the selected Thermodynamics algorithm as an enumerated type.
getAlgorithm(int) - Method in class ffx.algorithms.cli.ManyBodyOptions: Returns the user selected algorithm or one chosen based on number of residues.
getAlgorithm(int) - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
getAllAssemblies() - Method in interface ffx.potential.parsers.FileOpener: getAllAssemblies.
getAllAssemblies() - Method in class ffx.potential.utils.PotentialsFileOpener: getAllAssemblies.
getAllAssemblies() - Method in class ffx.ui.UIFileOpener: Returns all MolecularAssemblys in the user interface hierarchy.
getAllBondedEntities() - Method in class ffx.potential.MolecularAssembly: Gets all bonded entities in this MolecularAssembly, where an entity can be a polymer, molecule, monoatomic ion, or monoatomic gas (i.e. noble gas atoms).
getAllFxPoints() - Method in interface ffx.numerics.integrate.DataSet: Returns copy of the array of points f(x) to integrate (y-axis).
getAllFxPoints() - Method in class ffx.numerics.integrate.DoublesDataSet: Returns copy of the array of points f(x) to integrate (y-axis).
getAllFxPoints() - Method in class ffx.numerics.integrate.FunctionDataCurve: Returns copy of the array of points f(x) to integrate (y-axis).
getAllHistograms() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
getAllowed() - Method in class ffx.crystal.HKL: getAllowed
getAllProperties() - Method in interface ffx.potential.parsers.FileOpener: getAllProperties.
getAllProperties() - Method in class ffx.potential.utils.PotentialsFileOpener: getAllProperties.
getAllProperties() - Method in class ffx.ui.UIFileOpener: Returns the properties of all FFXSystems in the hierarchy.
getAlpha() - Method in class ffx.potential.nonbonded.VanDerWaals: getAlpha.
getAlphaCarbon(Residue, Atom) - Static method in class ffx.potential.bonded.BondedUtils: Finds the alpha carbon of a residue, and handles any C-terminal ACE caps while at it.
getAlternateLocation() - Method in class ffx.potential.MolecularAssembly: Get the alternate location.
getAltLoc() - Method in class ffx.potential.bonded.Atom: Getter for the field altLoc.
getAltLocs() - Method in class ffx.potential.parsers.PDBFilter: Get the list of alternate locations encountered.
getAltMolecules() - Method in class ffx.realspace.RealSpaceData: getAltMolecules
getAltMolecules() - Method in interface ffx.xray.DataContainer: getAltMolecules
getAltMolecules() - Method in class ffx.xray.DiffractionData: getAltMolecules
getAltMolecules() - Method in class ffx.xray.RefinementModel: Getter for the field altMolecules.
getAltResidues() - Method in class ffx.realspace.RealSpaceData: getAltResidues
getAltResidues() - Method in interface ffx.xray.DataContainer: getAltResidues
getAltResidues() - Method in class ffx.xray.DiffractionData: getAltResidues
getAltResidues() - Method in class ffx.xray.RefinementModel: Getter for the field altResidues.
getAminoAcid(String) - Static method in class ffx.potential.bonded.AminoAcidUtils: getAminoAcid.
getAminoAcid3() - Method in class ffx.potential.bonded.MultiResidue: getAminoAcid3.
getAminoAcid3() - Method in class ffx.potential.bonded.Residue: getAminoAcid3.
getAminoAcid3From1(String) - Static method in class ffx.potential.bonded.AminoAcidUtils: This method takes a one letter amino acid code and converts it to a three letter amino acid code.
getAminoAcidNumber(String) - Static method in class ffx.potential.bonded.AminoAcidUtils: getAminoAcidNumber.
getAndAdd(byte) - Method in class edu.rit.pj.reduction.SharedByte: Add the given value to this reduction variable and return the previous value.
getAndAdd(char) - Method in class edu.rit.pj.reduction.SharedCharacter: Add the given value to this reduction variable and return the previous value.
getAndAdd(double) - Method in class edu.rit.pj.reduction.SharedDouble: Add the given value to this reduction variable and return the previous value.
getAndAdd(float) - Method in class edu.rit.pj.reduction.SharedFloat: Add the given value to this reduction variable and return the previous value.
getAndAdd(int) - Method in class edu.rit.pj.reduction.SharedInteger: Add the given value to this reduction variable and return the previous value.
getAndAdd(int, byte) - Method in class edu.rit.pj.reduction.SharedByteArray: Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, float) - Method in class edu.rit.pj.reduction.SharedFloatArray: Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Add the given value to this matrix reduction variable at the given row and column and return the previous value.
getAndAdd(int, int, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Add the given value to this matrix reduction variable at the given row and column and return the previous value.
getAndAdd(int, long) - Method in class edu.rit.pj.reduction.SharedLongArray: Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, short) - Method in class edu.rit.pj.reduction.SharedShortArray: Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(long) - Method in class edu.rit.pj.reduction.SharedLong: Add the given value to this reduction variable and return the previous value.
getAndAdd(short) - Method in class edu.rit.pj.reduction.SharedShort: Add the given value to this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedByte: Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedCharacter: Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedDouble: Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedFloat: Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedInteger: Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedLong: Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedShort: Subtract one from this reduction variable and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedByteArray: Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedFloatArray: Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedLongArray: Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedShortArray: Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Subtract one from this matrix reduction variable at the given row and column and return the previous value.
getAndDecrement(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Subtract one from this matrix reduction variable at the given row and column and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedByte: Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedCharacter: Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedDouble: Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedFloat: Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedInteger: Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedLong: Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedShort: Add one to this reduction variable and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedByteArray: Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedFloatArray: Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedLongArray: Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedShortArray: Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Add one to this matrix reduction variable at the given row and column and return the previous value.
getAndIncrement(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Add one to this matrix reduction variable at the given row and column and return the previous value.
getAndSet(boolean) - Method in class edu.rit.pj.reduction.SharedBoolean: Set this reduction variable to the given value and return the previous value.
getAndSet(byte) - Method in class edu.rit.pj.reduction.SharedByte: Set this reduction variable to the given value and return the previous value.
getAndSet(char) - Method in class edu.rit.pj.reduction.SharedCharacter: Set this reduction variable to the given value and return the previous value.
getAndSet(double) - Method in class edu.rit.pj.reduction.SharedDouble: Set this reduction variable to the given value and return the previous value.
getAndSet(float) - Method in class edu.rit.pj.reduction.SharedFloat: Set this reduction variable to the given value and return the previous value.
getAndSet(int) - Method in class edu.rit.pj.reduction.SharedInteger: Set this reduction variable to the given value and return the previous value.
getAndSet(int, boolean) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, byte) - Method in class edu.rit.pj.reduction.SharedByteArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, float) - Method in class edu.rit.pj.reduction.SharedFloatArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Set this matrix reduction variable at the given row and column to the given value and return the previous value.
getAndSet(int, int, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Set this matrix reduction variable at the given row and column to the given value and return the previous value.
getAndSet(int, long) - Method in class edu.rit.pj.reduction.SharedLongArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, short) - Method in class edu.rit.pj.reduction.SharedShortArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, T) - Method in class edu.rit.pj.reduction.SharedObjectArray: Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(long) - Method in class edu.rit.pj.reduction.SharedLong: Set this reduction variable to the given value and return the previous value.
getAndSet(short) - Method in class edu.rit.pj.reduction.SharedShort: Set this reduction variable to the given value and return the previous value.
getAndSet(T) - Method in class edu.rit.pj.reduction.SharedObject: Set this reduction variable to the given value and return the previous value.
getAngle(int) - Method in class ffx.potential.terms.AnglePotentialEnergy: Get the Angle at a given index.
getAngle(Atom, Atom) - Method in class ffx.potential.bonded.Atom: getAngle.
getAngleArray() - Method in class ffx.potential.terms.AnglePotentialEnergy: Get an array of Angles in this term.
getAngleEnergyString() - Method in class ffx.potential.terms.AnglePotentialEnergy: Get the String used for OpenMM angle energy expressions.
getAngleList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Angles below the present MSNode.
getAngleMode() - Method in class ffx.potential.bonded.Angle: Getter for the field angleMode.
getAngleParameters(int, IntByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.HarmonicAngleForce: Get the force field parameters for an angle term.
getAngleParameters(int, IntByReference, IntByReference, IntByReference, DoubleArray) - Method in class ffx.openmm.CustomAngleForce: Get the force field parameters for an angle term.
getAngleParameters(int, IntBuffer, IntBuffer, IntBuffer, DoubleArray) - Method in class ffx.openmm.CustomAngleForce: Get the force field parameters for an angle term.
getAngleParameters(int, IntBuffer, IntBuffer, IntBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.HarmonicAngleForce: Get the force field parameters for an angle term.
getAnglePotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the AnglePotentialEnergy.
getAnglepTypes() - Method in class ffx.potential.parameters.ForceField
getAngles() - Method in class ffx.potential.bonded.Atom: Getter for the field angles.
getAngles() - Method in class ffx.potential.bonded.MSGroup: Returns the MultiScaleGroup's angles FNode.
getAngles() - Method in class ffx.potential.bonded.MultiResidue: Returns the MultiScaleGroup's angles FNode.
getAngles() - Method in class ffx.potential.bonded.Rotamer
getAngles() - Method in class ffx.potential.terms.AnglePotentialEnergy: Get an unmodifiable view of the Angles in this term.
getAngles(AngleType.AngleMode) - Method in class ffx.potential.ForceFieldEnergy: Getter for the field angles with only AngleMode angles.
getAngleTorsion(int) - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Get the AngleTorsion at a given index.
getAngleTorsionArray() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Get an array of AngleTorsions in this term.
getAngleTorsionList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all AngleTorsions below the present MSNode.
getAngleTorsionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the AngleTorsionPotentialEnergy.
getAngleTorsions() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Get an unmodifiable view of the AngleTorsions in this term.
getAngleTorsionType(String) - Method in class ffx.potential.parameters.ForceField: getAngleTorsionType
getAngleTorsionTypes() - Method in class ffx.potential.parameters.ForceField: Get AngleTorsionTypes.
getAngleType() - Method in class ffx.potential.bonded.Angle: Get the AngleType for this angle.
getAngleType(AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField: getAngleType
getAngleType(String) - Method in class ffx.potential.parameters.ForceField: getAngleType
getAngleTypes() - Method in class ffx.potential.parameters.ForceField: Get AngleTypes.
getAnisou(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field anisou.
getAnisouAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field anisouAcceleration.
getAnisouGradient(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field anisouGradient.
getAnisouPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field anisouPreviousAcceleration.
getAnisouVelocity(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field anisouVelocity.
getAnnealing() - Method in class ffx.algorithms.commands.Anneal: Get the SimulatedAnnealing object.
getApproxBoxLength() - Method in class ffx.algorithms.cli.ManyBodyOptions: Approximate side lengths of boxes to be constructed (over-rides numXYZBoxes).
getApproximate() - Method in class ffx.algorithms.cli.ManyBodyOptions
getApproximate() - Method in class ffx.algorithms.optimize.RotamerOptimization
getaRadBuff() - Method in class ffx.xray.DiffractionData: Getter for the field aRadBuff.
getArchiveFile() - Method in class ffx.potential.MolecularAssembly: Getter for the field archiveFile.
getArea() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
getArgs() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's command line arguments.
getArguments() - Method in interface ffx.potential.utils.PotentialsFunctions: If available, returns CLI arguments; the default implementation does not have access to CLI arguments and throws UnsupportedOperationException.
getArguments() - Method in class ffx.ui.UIUtils
getArray() - Method in class ffx.openmm.Vec3Array: Convert the Vec3Array to a double array.
getArrayIndex() - Method in class ffx.potential.bonded.Atom: getArrayIndex.
getAssembly() - Method in interface ffx.potential.parsers.FileOpener: getAssembly.
getAssembly() - Method in class ffx.potential.utils.PotentialsFileOpener: getAssembly.
getAssembly() - Method in class ffx.ui.UIFileOpener: Returns the active MolecularAssembly from the user interface hierarchy.
getAssembly() - Method in class ffx.xray.DiffractionData: Getter for the field assembly.
getAssemblyArray() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Returns the MolecularAssembly array.
getAtom(int) - Method in class ffx.potential.bonded.BondedTerm: Get the constituent Atom specified by index.
getAtom(int) - Method in class ffx.potential.bonded.RestrainTorsion
getAtom(String) - Method in class ffx.potential.bonded.Molecule: getAtom
getAtom4() - Method in class ffx.potential.bonded.Angle: Getter for the field atom4.
getAtomArray() - Method in class ffx.potential.bonded.BondedTerm: Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
getAtomArray() - Method in class ffx.potential.ForceFieldEnergy: Get all atoms that make up this ForceFieldEnergy.
getAtomArray() - Method in class ffx.potential.MolecularAssembly: Return an Array of all atoms in the System.
getAtomArray() - Method in class ffx.realspace.RealSpaceData: getAtomArray
getAtomArray() - Method in interface ffx.xray.DataContainer: getAtomArray
getAtomArray() - Method in class ffx.xray.DiffractionData: getAtomArray
getAtomArray(boolean) - Method in class ffx.potential.bonded.BondedTerm: Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
getAtomByName(String, boolean) - Method in class ffx.potential.bonded.MSGroup: getAtomByName.
getAtomElement(Atom) - Static method in class ffx.potential.parsers.CIFFilter: Parse atom name to determine atomic element.
getAtomFromWireVertex(int) - Method in class ffx.potential.MolecularAssembly: getAtomFromWireVertex
getAtomicNumber() - Method in class ffx.potential.bonded.Atom: Gets the Atomic Number
getAtomInitial() - Method in class ffx.potential.bonded.Residue
getAtomList() - Method in class ffx.potential.bonded.Atom: Returns a List of all Atoms below the present MSNode.
getAtomList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Atoms below the present MSNode.
getAtomList() - Method in class ffx.potential.parsers.SystemFilter: Getter for the field atomList.
getAtomList(boolean) - Method in class ffx.potential.bonded.MSNode: getAtomList.
getAtomNode() - Method in class ffx.potential.bonded.MSGroup: Returns the AtomNode.
getAtomNode() - Method in class ffx.potential.bonded.MultiResidue: Returns the AtomNode.
getAtomNode(int) - Method in class ffx.potential.bonded.MSGroup: Returns the MSNode at the given index.
getAtomNode(int) - Method in class ffx.potential.bonded.MultiResidue: Returns the MSNode at the given index.
getAtomNode(String) - Method in class ffx.potential.bonded.MSGroup: Returns the AtomNode specified by the String n.
getAtomNode(String) - Method in class ffx.potential.bonded.MultiResidue: Returns the AtomNode specified by the String n.
getAtomNodeList() - Method in class ffx.potential.bonded.MSGroup: Returns a List of the AtomNode's children.
getAtomNodeList() - Method in class ffx.potential.bonded.MultiResidue: Returns a List of the AtomNode's children.
getAtoms() - Method in class ffx.potential.bonded.BondedTerm: Returns a reference to the Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
getAtoms() - Method in class ffx.potential.bonded.ResidueState: Getter for the field atoms.
getAtoms() - Method in class ffx.potential.bonded.RestrainPosition: Returns a copy of the atoms array.
getAtoms() - Method in class ffx.potential.bonded.RestrainTorsion
getAtoms() - Method in class ffx.potential.openmm.OpenMMSystem: Get the atoms in the system.
getAtomType() - Method in class ffx.potential.bonded.Atom: Getter for the field atomType.
getAtomType(String) - Method in class ffx.potential.parameters.ForceField: getAtomType
getAtomType(String, String) - Method in class ffx.potential.parameters.ForceField: getAtomType
getAtomTypes() - Method in class ffx.potential.parameters.ForceField: Get AtomTypes.
getAtomTypes(String) - Method in class ffx.potential.parameters.ForceField: Getter for the field atomTypes.
getAvailableCommands() - Method in class ffx.ui.ModelingPanel: getAvailableCommands
getAverageEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
getAverageEnergyNoOutlier() - Method in class ffx.algorithms.optimize.ConformationScan
getAwater() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the water density parameter.
getAxisAtomIndices() - Method in class ffx.potential.bonded.Atom: Getter for the field axisAtomIndices.
getAxisAtoms() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getBackboneAtoms() - Method in class ffx.potential.bonded.Residue: Returns a list of backbone atoms; for our purposes, nucleic acid backbone atoms are those of the nucleobase.
getBackBoneAtoms() - Method in class ffx.potential.MolecularAssembly: getBackBoneAtoms
getBackboneEnergy() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
getBackboneEnergy() - Method in class ffx.algorithms.optimize.RotamerOptimization
getBackendCount() - Method in class edu.rit.pj.cluster.Configuration: Returns the number of backend processors.
getBackendHost() - Method in class edu.rit.pj.cluster.JobBackend: Obtain the backend host name on which this job is running.
getBackendInfo(int) - Method in class edu.rit.pj.cluster.Configuration: Returns information about the given backend processor.
getBackendInfoList() - Method in class edu.rit.pj.cluster.Configuration: Returns information about all backend processors.
getBackendNames() - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Obtain a list of the backend names assigned to this Non-PJ Job Frontend.
getBackwardTotalEnthalpyChange() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Enthalpy difference from backward FEP.
getBackwardTotalEntropyChange() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Entropy difference from backward FEP.
getBackwardTotalFEDifference() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Free energy difference from backward FEP.
getBAR() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getBarBSTotalEnthalpyChange() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Enthalpy difference from BAR.
getBarBSTotalEntropyChange() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Entropy difference from BAR.
getBarBSTotalFEDiff() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Free energy difference from BAR using boot-strapping.
getBarInt() - Method in class ffx.algorithms.cli.BarostatOptions: The mean number of MD steps (Poisson distribution) between barostat move proposals.
getBarIterTotalFEDiff() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Free energy difference from BAR.
getBaseDirString(String) - Method in class ffx.potential.cli.PotentialCommand: Check that we can write into the current base directory.
getBaseRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the base radii used for the GK calculation.
getBeta() - Method in class ffx.potential.nonbonded.VanDerWaals: getBeta.
getBeta0() - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
getBeta1() - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
getBeta2() - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
getBiasDecomposition() - Method in class ffx.potential.extended.ExtendedSystem: getBiasDecomposition.
getBiasEnergy() - Method in class ffx.potential.extended.ExtendedSystem: Sum up total bias (Ubias = UpH + Udiscr - Umod)
getBiasMag() - Method in class ffx.algorithms.cli.OSTOptions: Sets the initial Gaussian bias magnitude in kcal/mol.
getBiasMag() - Method in class ffx.algorithms.thermodynamics.HistogramData: Gets the Gaussian bias magnitude in kcal/mol.
getBin() - Method in class ffx.crystal.HKL: The bin number of this reflection, which is used for resolution dependent R/Rfree.
getBinEntropies() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getBioType(String) - Method in class ffx.potential.parameters.ForceField: getBioType
getBioType(String, String) - Method in class ffx.potential.parameters.ForceField: getBioType.
getBioTypeMap() - Method in class ffx.potential.parameters.ForceField: getBioTypeMap.
getBioTypes() - Method in class ffx.potential.commands.Biotype: Get the list of created Biotype records.
getBond(int) - Method in class ffx.potential.bonded.BondedTerm: Get the constituent Bond specified by index.
getBond(int) - Method in class ffx.potential.bonded.MSGroup: Returns the Bond at the supplied index.
getBond(int) - Method in class ffx.potential.bonded.MultiResidue: Returns the Bond at the supplied index.
getBond(int) - Method in class ffx.potential.terms.BondPotentialEnergy: Get the Bond at a given index.
getBond(Atom) - Method in class ffx.potential.bonded.Atom: getBond
getBond(String) - Method in class ffx.potential.bonded.MSGroup: Returns the Bond with the given id.
getBond(String) - Method in class ffx.potential.bonded.MultiResidue: Returns the Bond with the given id.
getBondArray() - Method in class ffx.potential.terms.BondPotentialEnergy: Get an array of Bonds in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.AnglePotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.BondPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.EnergyTerm: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get an array of BondedTerms in this term.
getBondedTermsArray() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Get an array of BondedTerms in this term.
getBondEnergyString() - Method in class ffx.potential.terms.BondPotentialEnergy
getBondList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Bonds below the present MSNode.
getBondParameters(int, IntByReference, IntByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.HarmonicBondForce: Get the force field parameters for a bond term.
getBondParameters(int, IntByReference, IntByReference, DoubleArray) - Method in class ffx.openmm.CustomBondForce: Get the force field parameters for a bond term.
getBondParameters(int, IntArray, DoubleArray) - Method in class ffx.openmm.CustomCentroidBondForce: Get the properties of a bond.
getBondParameters(int, IntArray, DoubleArray) - Method in class ffx.openmm.CustomCompoundBondForce: Get the parameters for a bond.
getBondParameters(int, IntBuffer, IntBuffer, DoubleArray) - Method in class ffx.openmm.CustomBondForce: Get the force field parameters for a bond term.
getBondParameters(int, IntBuffer, IntBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.HarmonicBondForce: Get the force field parameters for a bond term.
getBondPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the BondPotentialEnergy.
getBonds() - Method in class ffx.potential.bonded.Atom: Gets the list of the Bonds this Atom helps to form
getBonds() - Method in class ffx.potential.bonded.MSGroup: Returns the MultiScaleGroup's bonds FNode.
getBonds() - Method in class ffx.potential.bonded.MultiResidue: Returns the MultiScaleGroup's bonds FNode.
getBonds() - Method in class ffx.potential.terms.BondPotentialEnergy: Get an unmodifiable view of the Bonds in this term.
getBonds(String, String) - Method in class ffx.potential.parameters.ForceField: getBonds
getBondType() - Method in class ffx.potential.bonded.Bond: Return the BondType for this Bond.
getBondType() - Method in class ffx.potential.bonded.RestrainDistance: Getter for the field bondType.
getBondType(AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField: getBondType
getBondType(String) - Method in class ffx.potential.parameters.ForceField: getBondType
getBondTypes() - Method in class ffx.potential.parameters.ForceField: Get BondTypes.
getBoolean(String) - Method in class ffx.potential.parameters.ForceField: getBoolean
getBoolean(String, boolean) - Method in class ffx.potential.parameters.ForceField: getBoolean
getBootstrapIndices(int) - Static method in class ffx.numerics.estimator.EstimateBootstrapper: Gets randomized bootstrap indices; ensures there are at least two distinct indices.
getBootstrapIndices(int, Random) - Static method in class ffx.numerics.estimator.EstimateBootstrapper: Gets randomized bootstrap indices; ensures there are at least two distinct indices.
getBootstrapIndices(int, Random, int) - Static method in class ffx.numerics.estimator.EstimateBootstrapper: Gets randomized bootstrap indices; ensures there are at least a few distinct indices.
getBorderBottom() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getBorderLeft() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getBorderRight() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getBorderTop() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getBorn() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getBorn() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
getBoxBorderSize() - Method in class ffx.algorithms.cli.ManyBodyOptions: Extent of overlap between optimization boxes (default: 0.0 A).
getBoxInclusionCriterion() - Method in class ffx.algorithms.cli.ManyBodyOptions: Criterion to use for adding residues to boxes. (1) uses C alpha only (N1/9 for nucleic acids) (2) uses any atom. (3) uses any rotamer.
getBoxTitration() - Method in class ffx.algorithms.cli.ManyBodyOptions
getBranchGroup() - Method in class ffx.potential.MolecularAssembly: Getter for the field branchGroup.
getBuffer() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the buffer size.
getBuilt() - Method in class ffx.potential.bonded.Atom: If true, this atom was built during PDB file parsing.
getCart() - Method in class ffx.potential.commands.Cart2Frac: Return Cartesian Coordinate input.
getCart() - Method in class ffx.potential.commands.Frac2Cart: Return Cartesian Coordinate output.
getCavitationEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the cavitation component of the solvation energy.
getCavitationEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getCCDCPercent(int) - Static method in class ffx.crystal.SpaceGroupInfo: Return the given space group representation in the CCDC.
getCellIndex() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Returns the linear index of this Box.
getCellParametersFromVectors(double[][]) - Method in class ffx.crystal.Crystal: Set the unit cell parameters from unit cell vectors.
getCensusSoluteType(int) - Static method in class ffx.potential.parameters.SoluteType
getCenter() - Method in class ffx.potential.bonded.MSGroup: Returns the MultiScaleGroup's center as a double[3].
getCenter() - Method in class ffx.potential.bonded.MultiResidue: Returns the MultiScaleGroup's center as a double[3].
getCenter(boolean) - Method in class ffx.potential.bonded.MSNode: getCenter
getCenter(boolean) - Method in interface ffx.potential.bonded.ROLS: getCenter
getCentralAtom() - Method in class ffx.potential.bonded.Angle: getCentralAtom.
getCentroid() - Method in class ffx.numerics.quickhull.Face: Returns the centroid previously computed for this face.
getChain() - Method in class ffx.algorithms.cli.ManyBodyOptions: Single character chain ID of the residues to optimize.
getChain(String) - Method in class ffx.potential.MolecularAssembly: getChain
getChainID() - Method in class ffx.potential.bonded.Atom: Get the chain name
getChainID() - Method in class ffx.potential.bonded.Molecule: Getter for the field chainID.
getChainID() - Method in class ffx.potential.bonded.Polymer: Getter for the field chainID.
getChainID() - Method in class ffx.potential.bonded.Residue: Returns this Residues Parent Polymer name.
getChainID(int) - Static method in class ffx.potential.Utilities: Determine chainID for a given polymer number.
getChainNames() - Method in class ffx.potential.MolecularAssembly: getChainNames
getChains() - Method in class ffx.potential.MolecularAssembly: getChains
getChandlerCavitation() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Return the Chandler Cavitation instance.
getChannelGroup() - Method in class edu.rit.mp.Channel: Obtain the channel group that created this channel.
getChannelGroupId() - Method in class edu.rit.mp.ChannelGroup: Obtain this channel group's channel group ID.
getCharge() - Method in class ffx.potential.bonded.Atom: Gets the partial atomic charge
getCharge() - Method in class ffx.potential.nonbonded.octree.OctreeParticle
getCharge() - Method in class ffx.potential.parameters.MultipoleType: Getter for the field charge.
getCharge(boolean) - Method in class ffx.potential.MolecularAssembly: Sums up charge of the system, checking nonstandard residues for non-unitary charges.
getCharge(ForceField) - Method in class ffx.potential.bonded.Atom: Gets the partial atomic charge.
getCheckAlchemicalAtoms() - Method in class ffx.potential.terms.EnergyTermRegion
getCheckpoint() - Method in class ffx.algorithms.cli.DynamicsOptions: The restart save frequency in picoseconds (1.0 psec default).
getCheckpointFrequency(int) - Method in class ffx.algorithms.cli.DynamicsOptions: The checkpoint frequency in steps.
getCheckRestrictions() - Method in class ffx.crystal.Crystal: Are space group restrictions being checked.
getCheckRestrictions() - Method in class ffx.crystal.ReplicatesCrystal: Are space group restrictions being checked.
getChildAtIndex(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
getChildList() - Method in class ffx.potential.bonded.MSNode: Returns a List of the MSNode's Children (instead of using an Enumeration).
getChildren() - Method in class ffx.numerics.clustering.Cluster: Returns the list of child clusters, creating it lazily if needed.
getChildren() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Returns the child visual components corresponding to child clusters.
getChiralAtom() - Method in class ffx.potential.bonded.TorsionTorsion: getChiralAtom.
getClashThreshold() - Method in class ffx.algorithms.cli.ManyBodyOptions: The threshold for pruning clashes.
getClassLoader() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's backend class loader.
getCluster() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Gets the Cluster model represented by this component.
getClusterList() - Method in class ffx.algorithms.commands.Cluster: Return the Clusters.
getClusterName() - Method in class edu.rit.pj.cluster.Configuration: Returns the cluster name.
getClusters() - Method in class ffx.numerics.clustering.HierarchyBuilder: Returns the current working list of clusters (not necessarily a single root).
getColCount() - Method in class edu.rit.io.DoubleMatrixFile: Returns the number of columns in this matrix file.
getCollectiveVariable(int) - Method in class ffx.openmm.CustomCVForce: Get a collective variable by index.
getCollectiveVariableName(int) - Method in class ffx.openmm.CustomCVForce: Get the name of a collective variable.
getCollectiveVariableValues(Context, PointerByReference) - Method in class ffx.openmm.CustomCVForce: Get the values of all collective variables in a given context.
getCollisionFrequency(int) - Method in class ffx.openmm.NoseHooverIntegrator: Get the collision frequency for a thermostat.
getColRange() - Method in class edu.rit.io.DoubleMatrixFile.Reader: Obtain the column range of the next matrix element segment in the input stream.
getCombinedEps(double, double, double, double, VDWType.EPSILON_RULE) - Static method in class ffx.potential.nonbonded.VanDerWaalsForm: Get the combined EPS value.
getCombinedEps(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm: Return the combined well depth (kcal/mol)
getCombinedEps14(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm: Return the combined well depth (kcal/mol) for special 1-4 interactions
getCombinedInverseRmin(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm: Return the combined inverse Rmin value (1/Rmin).
getCombinedInverseRmin14(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm: Return the combined inverse Rmin value (1/Rmin) for special 1-4 interactions.
getCombinedRadius(double, double, VDWType.RADIUS_RULE) - Static method in class ffx.potential.nonbonded.VanDerWaalsForm: Get the combined radius value.
getCommand() - Method in class ffx.ui.ModelingPanel
getCommand(String) - Static method in class ffx.utilities.FFXCommand: Use the System ClassLoader to find the requested Command.
getComputationStep(int, IntByReference, PointerByReference, PointerByReference) - Method in class ffx.openmm.CustomIntegrator: Get information about a computation in the integrator.
getComputationStep(int, IntBuffer, PointerByReference, PointerByReference) - Method in class ffx.openmm.CustomIntegrator: Get information about a computation in the integrator.
getComputedValueParameters(int, PointerByReference, PointerByReference) - Method in class ffx.openmm.CustomNonbondedForce: Get the parameters for a computed value.
getComputedValueParameters(int, PointerByReference, PointerByReference, IntByReference) - Method in class ffx.openmm.CustomGBForce: Get the parameters for a computed value.
getComputedValueParameters(int, PointerByReference, PointerByReference, IntBuffer) - Method in class ffx.openmm.CustomGBForce: Get the parameters for a computed value.
getConfidenceScore(Residue) - Method in class ffx.potential.utils.GetProteinFeatures: Get the alphafold confidence score or b-factor from an X-ray model.
getConformers() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return the rotamer index for each conformer (A,B,C) in xray and realspace genZ
getConnollyRegion() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
getConsideredResidues() - Method in class ffx.potential.bonded.MultiResidue: Returns a copy of this MultiResidue's consideredResidues array.
getConstantPh() - Method in class ffx.potential.extended.ExtendedSystem: getConstantPh.
getConstants() - Method in class ffx.potential.bonded.AngleTorsion: Returns the array of stretch-torsion constants, in units of kcal/mol/degree.
getConstants() - Method in class ffx.potential.bonded.StretchTorsion: Returns the array of stretch-torsion constants, in units of kcal/mol/A.
getConstraintParameters(int, IntByReference, IntByReference, DoubleByReference) - Method in class ffx.openmm.System: Get the parameters defining a constraint.
getConstraintParameters(int, IntBuffer, IntBuffer, DoubleBuffer) - Method in class ffx.openmm.System: Get the parameters defining a constraint.
getConstraints() - Method in class ffx.algorithms.dynamics.integrators.Integrator: Returns a copy of the list of Constraints.
getConstraints() - Method in interface ffx.numerics.Potential: Returns the list of Constraints associated with this Potential.
getConstraints() - Method in class ffx.potential.extended.ExtendedSystem
getConstraints() - Method in class ffx.potential.ForceFieldEnergy: Returns a copy of the list of constraints this ForceFieldEnergy has.
getConstraintTolerance() - Method in class ffx.openmm.CompoundIntegrator: Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
getConstraintTolerance() - Method in class ffx.openmm.Integrator: Get the tolerance within which constraints must be satisfied during the simulation.
getContext() - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Returns the Context instance.
getContext() - Method in class ffx.potential.openmm.OpenMMEnergy: Returns the Context instance.
getContext() - Method in interface ffx.potential.openmm.OpenMMPotential: Returns the Context instance.
getCoordinates() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Get the coordinates.
getCoordinates() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getCoordinates(double[]) - Method in class ffx.algorithms.dynamics.Barostat: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getCoordinates(double[]) - Method in interface ffx.numerics.OptimizationInterface: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.ANIEnergy
getCoordinates(double[]) - Method in class ffx.potential.DualTopologyEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.extended.ExtendedSystem
getCoordinates(double[]) - Method in class ffx.potential.ForceFieldEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.QuadTopologyEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.XtalEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.realspace.RealSpaceEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.RefinementEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.ScaleBulkEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.ScaleBulkMinimize: getCoordinates.
getCoordinates(double[]) - Method in class ffx.xray.SigmaAEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.SigmaAMinimize: getCoordinates.
getCoordinates(double[]) - Method in class ffx.xray.SplineEnergy: Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.SplineMinimize: getCoordinates.
getCoordinates(double[]) - Method in class ffx.xray.XRayEnergy: Load the current value of the parameters.
getCoordinatesCopy() - Method in class ffx.potential.SystemState: Get a copy of the internal coordinate array.
getCount() - Method in class ffx.numerics.math.RunningStatistics: Get the count.
getCount() - Method in class ffx.potential.nonbonded.NeighborList.Cell
getCount(int) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
getCountInterval() - Method in class ffx.algorithms.cli.OSTOptions: Sets the number of time steps between OST counts.
getCovalentMap(int, int) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the covalent map for a given atom index and covalent type.
getCovalentMaps(int) - Method in class ffx.openmm.amoeba.MultipoleForce: Get all covalent maps for a given atom index.
getCreatedFileNames() - Method in class ffx.potential.parsers.CIFFilter: Obtain a list of output files written from the conversion.
getCrossOver() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
getCrystal() - Method in class ffx.algorithms.dynamics.Barostat: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in interface ffx.crystal.CrystalPotential: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in class ffx.potential.DualTopologyEnergy: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in class ffx.potential.ForceFieldEnergy: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in class ffx.potential.MolecularAssembly: getCrystal
getCrystal() - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Get the Crystal instance.
getCrystal() - Method in class ffx.potential.openmm.OpenMMSystem: Get the Crystal instance.
getCrystal() - Method in class ffx.potential.QuadTopologyEnergy: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in class ffx.realspace.RealSpaceData: Getter for the field crystal.
getCrystal() - Method in class ffx.realspace.RealSpaceEnergy: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in class ffx.xray.DiffractionData: Getter for the field crystal.
getCrystal() - Method in class ffx.xray.RefinementEnergy: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal() - Method in class ffx.xray.XRayEnergy: Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
getCrystal(String, CompositeConfiguration) - Method in class ffx.realspace.parsers.CCP4MapFilter: getCrystal
getCrystal(String, CompositeConfiguration) - Method in interface ffx.realspace.parsers.RealSpaceFileFilter: getCrystal
getCrystalPotential() - Method in class ffx.algorithms.dynamics.Barostat: Get the CrystalPotential that this Barostat is applying to.
getCrystalReciprocalSpacesFc() - Method in class ffx.xray.DiffractionData: Getter for the field crs_fc.
getCrystalReciprocalSpacesFs() - Method in class ffx.xray.DiffractionData: Getter for the field crs_fs.
getCrystalStats() - Method in class ffx.xray.DiffractionData: Getter for the field crystalStats.
getCurrentCycle() - Method in class ffx.potential.MolecularAssembly: Getter for the field currentCycle.
getCurrentDistance() - Method in class ffx.potential.bonded.Bond: Gets the current distance between the two Atoms in this Bond.
getCurrentIntegrator() - Method in class ffx.openmm.CompoundIntegrator: Get the index of the current Integrator.
getCurrentLambdaBin(long) - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Get the current lambda bin for a given MD step.
getCurrentTemperature() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Get the current temperature.
getCutoff() - Method in class ffx.algorithms.cli.ManyBodyOptions: The sliding window and box cutoff radius (Angstroms).
getCutoff() - Method in class ffx.openmm.amoeba.VdwForce: Deprecated.
This method exists only for backward compatibility. Use getCutoffDistance() instead.
getCutoff() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Getter for the field cutoff.
getCutoff() - Method in class ffx.potential.nonbonded.NeighborList: Returns the cutoff distance used internally by NeighborList.
getCutoffDistance() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the cutoff distance.
getCutoffDistance() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the cutoff distance (in nm) being used for nonbonded interactions.
getCutoffDistance() - Method in class ffx.openmm.amoeba.VdwForce: Get the cutoff distance (in nm) being used for nonbonded interactions.
getCutoffDistance() - Method in class ffx.openmm.CustomGBForce: Get the cutoff distance.
getCutoffDistance() - Method in class ffx.openmm.CustomHbondForce: Get the cutoff distance.
getCutoffDistance() - Method in class ffx.openmm.CustomManyParticleForce: Get the cutoff distance (in nm) being used for interactions.
getCutoffDistance() - Method in class ffx.openmm.CustomNonbondedForce: Get the cutoff distance.
getCutoffDistance() - Method in class ffx.openmm.GayBerneForce: Get the cutoff distance.
getCutoffDistance() - Method in class ffx.openmm.GBSAOBCForce: Get the cutoff distance (in nm) being used for nonbonded interactions.
getCutoffDistance() - Method in class ffx.openmm.NonbondedForce: Get the cutoff distance.
getCutoffPlusBuffer() - Method in class ffx.potential.ForceFieldEnergy: Getter for the field cutoffPlusBuffer.
getCycles() - Method in class ffx.potential.MolecularAssembly: Getter for the field cycles.
getd2EdL2() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.ANIEnergy
getd2EdL2() - Method in class ffx.potential.bonded.AngleTorsion: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in interface ffx.potential.bonded.LambdaInterface: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.PiOrbitalTorsion: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.RestrainDistance: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.RestrainPosition: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.RestrainTorsion
getd2EdL2() - Method in class ffx.potential.bonded.StretchTorsion: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.Torsion: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.TorsionTorsion: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.DualTopologyEnergy: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.ForceFieldEnergy: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.COMRestraint: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.NCSRestraint: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.openmm.OpenMMEnergy: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.QuadTopologyEnergy: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get the energy contribution from all Torsions in this term.
getd2EdL2() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get the energy contribution from all Torsions in this term.
getd2EdL2() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get the energy contribution from all Torsion-Torsions in this term.
getd2EdL2() - Method in class ffx.realspace.RealSpaceEnergy: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.xray.RefinementEnergy: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.xray.XRayEnergy: Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdZ2() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: getd2EdZ2.
getd2EdZ2() - Method in class ffx.numerics.multipole.MultipoleTensor: getd2EdZ2.
getDanglingAtoms() - Method in class ffx.potential.bonded.MSGroup: Returns the MultiScaleGroup's dangling Atoms list.
getDanglingAtoms() - Method in class ffx.potential.bonded.MultiResidue: Returns the MultiScaleGroup's dangling Atoms list.
getData() - Method in class ffx.realspace.RealSpaceRefinementData: Getter for the field data.
getDataEnergy() - Method in class ffx.xray.RefinementEnergy: Getter for the field dataEnergy.
getDataFiles() - Method in class ffx.xray.DiffractionData: Getter for the field dataFiles.
getDataTypes() - Method in class ffx.openmm.State: Get the data types.
getDataTypes() - Method in class ffx.potential.openmm.OpenMMState: Get the mask of information contained in the state.
getDDGunValues(List<String>) - Method in class ffx.potential.utils.GetProteinFeatures: Get ddgun values from ddgun file
getdEdL() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.ANIEnergy
getdEdL() - Method in class ffx.potential.bonded.AngleTorsion: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in interface ffx.potential.bonded.LambdaInterface: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.PiOrbitalTorsion: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.RestrainDistance: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.RestrainPosition: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.RestrainTorsion
getdEdL() - Method in class ffx.potential.bonded.StretchTorsion: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.Torsion: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.TorsionTorsion: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.DualTopologyEnergy: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.ForceFieldEnergy: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.COMRestraint: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.NCSRestraint: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.openmm.OpenMMEnergy: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.QuadTopologyEnergy: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get the energy contribution from all Pi-Orbital Torsions in this term.
getdEdL() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get the energy contribution from all Torsions in this term.
getdEdL() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get the energy contribution from all Torsion-Torsions in this term.
getdEdL() - Method in class ffx.realspace.RealSpaceEnergy: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.xray.RefinementEnergy: Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.xray.XRayEnergy: Get the partial derivative of the energy with respect to lambda.
getdEdXdL(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.ANIEnergy
getdEdXdL(double[]) - Method in class ffx.potential.bonded.AngleTorsion: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in interface ffx.potential.bonded.LambdaInterface: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.PiOrbitalTorsion: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.RestrainDistance: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.RestrainPosition: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.RestrainTorsion
getdEdXdL(double[]) - Method in class ffx.potential.bonded.StretchTorsion: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.Torsion: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.TorsionTorsion: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.DualTopologyEnergy: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.ForceFieldEnergy: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.COMRestraint: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.NCSRestraint: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.VanDerWaals: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.QuadTopologyEnergy: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.realspace.RealSpaceEnergy: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.xray.RefinementEnergy: Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.xray.XRayEnergy: Get the gradient of dEdL with respect to each parameter.
getdEdZ() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: getdEdZ.
getdEdZ() - Method in class ffx.numerics.multipole.MultipoleTensor: getdEdZ.
getDefault() - Static method in class edu.rit.util.TimerThread: Get the default timer thread, a single shared instance of class TimerThread.
getDefaultAlpha() - Method in enum class ffx.crystal.LatticeSystem: Returns the default alpha for the lattice system.
getDefaultBAxis(double) - Method in enum class ffx.crystal.LatticeSystem: Returns the default b-axis for the lattice system.
getDefaultBeta() - Method in enum class ffx.crystal.LatticeSystem: Returns the default beta for the lattice system.
getDefaultCAxis(double, double) - Method in enum class ffx.crystal.LatticeSystem: Returns the default c-axis for the lattice system.
getDefaultCollisionFrequency() - Method in class ffx.openmm.AndersenThermostat: Get the default collision frequency (in 1/ps).
getDefaultDevice(CompositeConfiguration) - Static method in class ffx.potential.openmm.OpenMMEnergy: Gets the default coprocessor device, ignoring any CUDA_DEVICE over-ride.
getDefaultGamma() - Method in enum class ffx.crystal.LatticeSystem: Returns the default gamma for the lattice system.
getDefaultLibrary() - Static method in class ffx.potential.bonded.RotamerLibrary: getDefaultLibrary.
getDefaultListener() - Method in interface ffx.algorithms.AlgorithmFunctions: Returns a default Listener if available (null by default).
getDefaultListener() - Method in class ffx.ui.UIUtils
getDefaultPeriodicBoxVectors(OpenMM_Vec3, OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.System: Get the default periodic box vectors.
getDefaultPluginsDirectory() - Static method in class ffx.openmm.Platform: Get the default directory from which to load plugins.
getDefaultPressure() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Get the default pressure (in bar).
getDefaultPressure() - Method in class ffx.openmm.MonteCarloBarostat: Get the default pressure acting on the system (in bar).
getDefaultPressure() - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Get the default pressure (in bar).
getDefaultPressure() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Get the default pressure (in bar).
getDefaultSurfaceTension() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Get the default surface tension (in bar*nm).
getDefaultTemperature() - Method in class ffx.openmm.AndersenThermostat: Get the default temperature of the heat bath (in Kelvin).
getDefaultTemperature() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Get the default temperature at which the system is being maintained (in Kelvin).
getDefaultTemperature() - Method in class ffx.openmm.MonteCarloBarostat: Get the default temperature at which the system is being maintained, measured in Kelvin.
getDefaultTemperature() - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Get the default temperature at which the system is being maintained (in Kelvin).
getDefaultTemperature() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Get the default temperature at which the system is being maintained (in Kelvin).
getDefaultThreadCount() - Static method in class edu.rit.pj.HybridTeam: Determine the default number of threads per process for a hybrid team.
getDefaultThreadCount() - Static method in class edu.rit.pj.ParallelTeam: Determine the default number of threads for a parallel team.
getDegreesOfFreedom() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Return the number of degrees of freedom.
getDensity(double) - Method in class ffx.crystal.Crystal: Compute the density of the system.
getDensity(double) - Method in class ffx.crystal.ReplicatesCrystal: Return the density of the ReplicatesCrystal.
getDensityGrid() - Method in class ffx.xray.CrystalReciprocalSpace: Getter for the field densityGrid.
getDerivatives() - Method in class ffx.potential.extended.ExtendedSystem: get array of dU/dL for each titrating residue
getDescreenOffset() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the descreen offset.
getDescreenOffset() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Return the descreening dielectric offset.
getDescreenRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the descreening radii used for the GK calculation.
getDescription() - Method in class edu.rit.pj.job.Job: Returns this job's description.
getDescription() - Method in class ffx.potential.parsers.ARCFileFilter
getDescription() - Method in class ffx.potential.parsers.CoordinateFileFilter
getDescription() - Method in class ffx.potential.parsers.DistanceMatrixFileFilter
getDescription() - Method in class ffx.potential.parsers.DYNFileFilter
getDescription() - Method in class ffx.potential.parsers.ESVFileFilter
getDescription() - Method in class ffx.potential.parsers.FFXFileFilter
getDescription() - Method in class ffx.potential.parsers.ForceFieldFileFilter
getDescription() - Method in class ffx.potential.parsers.InducedFileFilter
getDescription() - Method in class ffx.potential.parsers.INTFileFilter
getDescription() - Method in class ffx.potential.parsers.KeyFileFilter
getDescription() - Method in class ffx.potential.parsers.PDBFileFilter
getDescription() - Method in class ffx.potential.parsers.PDBMLFileFilter
getDescription() - Method in class ffx.potential.parsers.XPHFileFilter
getDescription() - Method in class ffx.potential.parsers.XYZFileFilter
getDescription() - Method in class ffx.xray.parsers.MTZFileFilter
getDevice() - Static method in class ffx.numerics.tornado.FFXTornado: Get the default Tornado Device.
getDevice(int) - Static method in class ffx.numerics.tornado.FFXTornado: Get the specified Tornado Device.
getDevice(int, int) - Static method in class ffx.numerics.tornado.FFXTornado: Get the Tornado Device using specified driver and device index.
getDielecOffset() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the dielectric offset (in Angstroms).
getDielectricOffset() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the dielectric offset.
getDiffractionData(List<String>, MolecularAssembly[], CompositeConfiguration) - Method in class ffx.xray.cli.XrayOptions: Process input from opened molecular assemblies to a DiffractionData.
getDiffractionfilter() - Method in class ffx.xray.parsers.DiffractionFile: getDiffractionfilter.
getDipole() - Method in class ffx.potential.parameters.MultipoleType: Getter for the field dipole.
getDispersionEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the dispersion component of the solvation energy.
getDispersionEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getDispersionOffset() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: The dispersion integral begins offset from the vdW radius.
getDispersionOverlapFactor() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
getDispersionRegion() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getDispoff() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the dispersion offset.
getDistance() - Method in class ffx.numerics.clustering.Cluster: Gets the Distance metadata for this cluster (linkage distance and weight).
getDistance() - Method in class ffx.numerics.clustering.Distance: Gets the distance value.
getDistance(int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix.NeighborDistances: Get a distance.
getDistances() - Method in class ffx.numerics.clustering.HierarchyBuilder: Gets the DistanceMap used to track inter-cluster distances during agglomeration.
getDistanceTolerance() - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the distance tolerance that was used for the most recently computed hull.
getDistanceValue() - Method in class ffx.numerics.clustering.Cluster: Convenience accessor for this cluster's linkage distance value.
getDistributeWalkersString() - Method in class ffx.algorithms.cli.MultiDynamicsOptions: Allows walkers to start from multiple conformations; AUTO picks up per-walker conformations as filename.pdb_(walker number), and specifying a residue starts a rotamer optimization to generate side-chain configurations to start from.
getDOF() - Method in class ffx.numerics.math.RunningStatistics: Get the DOF.
getDoLongRangeCorrection() - Method in class ffx.potential.nonbonded.VanDerWaals: Return use of the long-range vdW correction.
getDonorParameters(int, IntByReference, IntByReference, IntByReference, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Get the parameters for a donor.
getDonorParameters(int, IntBuffer, IntBuffer, IntBuffer, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Get the parameters for a donor.
getDotRadius() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Gets the radius of node dots in pixels.
getDouble(String) - Method in class ffx.potential.parameters.ForceField: getDouble
getDouble(String, Double) - Method in class ffx.potential.parameters.ForceField: getDouble
getDPMEParameters(DoubleByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the DPME parameters.
getDPMEParameters(DoubleBuffer, IntBuffer, IntBuffer, IntBuffer) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the DPME parameters.
getDPMEParametersInContext(Context, DoubleByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the DPME parameters in context.
getDPMEParametersInContext(Context, DoubleBuffer, IntBuffer, IntBuffer, IntBuffer) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the DPME parameters in context.
getDrudeFriction() - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Get the friction coefficient which determines how strongly the internal coordinates of Drude particles are coupled to the heat bath (in inverse ps).
getDrudeTemperature() - Method in class ffx.openmm.drude.DrudeIntegrator: Get the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).
getDt() - Method in class ffx.algorithms.cli.DynamicsOptions: The time step in femtoseconds (default of 1.0).
getDtPsec() - Method in class ffx.algorithms.cli.DynamicsOptions
getDualTopA() - Method in class ffx.potential.QuadTopologyEnergy: Returns the first component DualTopologyEnergy.
getDualTopB() - Method in class ffx.potential.QuadTopologyEnergy: Returns the second component DualTopologyEnergy.
getDualTopologyAtom(int, int) - Method in class ffx.potential.DualTopologyEnergy: Get the atom from the dual-topology atom array corresponding to the specified topology and index.
getDualTopologyAtoms(int) - Method in class ffx.potential.DualTopologyEnergy: Get the dual topology atoms for the specified topology.
getDualTopologyIndex1() - Method in class ffx.potential.DualTopologyEnergy: Get the atom index for topology 1 into the overall dual-topology atom array.
getDualTopologyIndex2() - Method in class ffx.potential.DualTopologyEnergy: Get the atom index for topology 2 into the overall dual-topology atom array.
getDUDLBins() - Method in class ffx.algorithms.thermodynamics.HistogramData
getDx() - Method in class ffx.potential.cli.GradientOptions: -d or --dx Finite-difference step size.
getDynamics(WriteoutOptions, Potential, MolecularAssembly, AlgorithmListener) - Method in class ffx.algorithms.cli.DynamicsOptions: Initialize a MolecularDynamics from the parsed options.
getDynamics(WriteoutOptions, Potential, MolecularAssembly, AlgorithmListener, MDEngine) - Method in class ffx.algorithms.cli.DynamicsOptions: Initialize a MolecularDynamics from the parsed options.
getDynFile() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Returns the associated dynamics file.
getE1() - Method in class ffx.algorithms.mc.BoltzmannMC: Return starting energy from last attempted step.
getE1() - Method in interface ffx.algorithms.mc.MetropolisMC: Return starting energy from last attempted step.
getE1l1() - Method in class ffx.potential.parsers.BARFilter: Return the potential energy for each snapshot of ensemble 1 at lambda 1.
getE1l2() - Method in class ffx.potential.parsers.BARFilter: Return the potential energy for each snapshot of ensemble 1 at lambda 2.
getE2() - Method in class ffx.algorithms.mc.BoltzmannMC: Return trial energy from last attempted step.
getE2() - Method in interface ffx.algorithms.mc.MetropolisMC: Return trial energy from last attempted step.
getE2l1() - Method in class ffx.potential.parsers.BARFilter: Return the potential energy for each snapshot of ensemble 2 at lambda 1.
getE2l2() - Method in class ffx.potential.parsers.BARFilter: Return the potential energy for each snapshot of ensemble 2 at lambda 2.
getEdge(int) - Method in class ffx.numerics.quickhull.Face: Gets the i-th half-edge associated with the face.
getEffectiveRadius() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
getElecForm() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Returns the ELEC_FORM.
getElectrostaticPotential(Context, DoubleArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the electrostatic potential at specified points.
getElectrostatics() - Method in class ffx.potential.bonded.Atom: Getter for the field electrostatics.
getEliminatedRotamers() - Method in class ffx.algorithms.optimize.RotamerOptimization
getEnd() - Method in class ffx.algorithms.optimize.TorsionSearch
getEnergies() - Method in class ffx.algorithms.optimize.ConformationScan
getEnergies() - Method in class ffx.algorithms.optimize.TorsionSearch: List of energies for each state in order of lowest to highest energy.
getEnergiesWithinEnergy(double) - Method in class ffx.algorithms.optimize.ConformationScan
getEnergy() - Method in class ffx.algorithms.commands.Minimize: Get the final energy after minimization.
getEnergy() - Method in class ffx.algorithms.optimize.Minimize: Getter for the field energy.
getEnergy() - Method in class ffx.algorithms.optimize.PhMinimize: Getter for the field energy.
getEnergy() - Method in class ffx.potential.commands.Energy
getEnergy() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
getEnergy() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
getEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
getEnergy() - Method in class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
getEnergy() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
getEnergy() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the total Van der Waals potential energy.
getEnergy() - Method in class ffx.potential.nonbonded.VanDerWaalsTornado: Get the total Van der Waals potential energy.
getEnergy() - Method in class ffx.potential.terms.EnergyTerm: Get the total potential energy of this term.
getEnergy() - Method in class ffx.potential.terms.EnergyTermRegion: Get the total energy of all EnergyTerms.
getEnergy() - Method in exception class ffx.potential.utils.EnergyException: Return the reported Energy.
getEnergyChange() - Method in class ffx.algorithms.mc.MDMove: Get the total energy change for the current move.
getEnergyCount() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Returns the number of energy evaluations performed by this OST, including those picked up in the lambda file.
getEnergyExpansion() - Method in class ffx.algorithms.optimize.RotamerOptimization
getEnergyFunction() - Method in class ffx.openmm.ATMForce: Get the energy function.
getEnergyFunction() - Method in class ffx.openmm.CustomAngleForce: Get the algebraic expression that gives the interaction energy for each angle
getEnergyFunction() - Method in class ffx.openmm.CustomBondForce: Get the algebraic expression that gives the interaction energy for each bond
getEnergyFunction() - Method in class ffx.openmm.CustomCentroidBondForce: Get the algebraic expression that gives the interaction energy of each bond
getEnergyFunction() - Method in class ffx.openmm.CustomCompoundBondForce: Get the energy expression for the force.
getEnergyFunction() - Method in class ffx.openmm.CustomCVForce: Get the energy function.
getEnergyFunction() - Method in class ffx.openmm.CustomExternalForce: Get the energy expression for the force.
getEnergyFunction() - Method in class ffx.openmm.CustomHbondForce: Get the energy expression for the force.
getEnergyFunction() - Method in class ffx.openmm.CustomManyParticleForce: Get the algebraic expression that gives the interaction energy for each set of particles.
getEnergyFunction() - Method in class ffx.openmm.CustomNonbondedForce: Get the energy expression for the force.
getEnergyFunction() - Method in class ffx.openmm.CustomTorsionForce: Get the algebraic expression that gives the interaction energy of each torsion.
getEnergyFunction() - Method in class ffx.openmm.CustomVolumeForce: Get the algebraic expression that defines the energy.
getEnergyList() - Method in class ffx.algorithms.commands.Minimize: Get the list of energies recorded during minimization.
getEnergyList() - Method in class ffx.algorithms.optimize.Minimize: Get the energy for each step in the minimization.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.ATMForce: Get the name of an energy parameter derivative.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomAngleForce: Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomBondForce: Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomCentroidBondForce: Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomCompoundBondForce: Get the name of a parameter with respect to which the derivative of the energy should be computed.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomCVForce: Get the name of an energy parameter derivative.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomGBForce: Get the name of a parameter with respect to which the derivative of the energy should be computed.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomNonbondedForce: Get the name of a parameter with respect to which the derivative of the energy should be computed.
getEnergyParameterDerivativeName(int) - Method in class ffx.openmm.CustomTorsionForce: Get the name of a parameter with respect to which the derivative of the energy should be computed.
getEnergyParameterDerivatives() - Method in class ffx.openmm.State: Get the energy parameter derivatives.
getEnergyRestart() - Method in class ffx.algorithms.cli.ManyBodyOptions: Energy restart file from a previous run (requires that all parameters are the same).
getEnergyTerm(int) - Method in class ffx.potential.terms.EnergyTermRegion: Get the BondedEnergyTerm at a specific index.
getEnergyTermParameters(int, PointerByReference, IntByReference) - Method in class ffx.openmm.CustomGBForce: Get the parameters for an energy term.
getEnergyTermParameters(int, PointerByReference, IntBuffer) - Method in class ffx.openmm.CustomGBForce: Get the parameters for an energy term.
getEnergyTerms() - Method in class ffx.potential.terms.EnergyTermRegion: Get an unmodifiable view of the energy terms.
getEnergyTermState() - Method in class ffx.algorithms.dynamics.Barostat: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in interface ffx.numerics.Potential: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.ANIEnergy
getEnergyTermState() - Method in class ffx.potential.DualTopologyEnergy: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.extended.ExtendedSystem
getEnergyTermState() - Method in class ffx.potential.ForceFieldEnergy: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.QuadTopologyEnergy: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.XtalEnergy: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.realspace.RealSpaceEnergy: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.xray.RefinementEnergy: Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.xray.XRayEnergy: Get the Potential Energy terms that is active.
getEngineString() - Method in class ffx.algorithms.cli.DynamicsOptions: The default engine choice for integrating the equations of motion
getEnsemble() - Method in class ffx.algorithms.optimize.RotamerOptimization: getEnsemble.
getEnthalpyChanges() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get bootstrap enthalpy estimate for each window.
getEnthalpyDifferences() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Gets the enthalpy change between each pair of states.
getEnthalpyDifferences() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getEnthalpyDifferences() - Method in interface ffx.numerics.estimator.StatisticalEstimator: Gets the enthalpy change between each pair of states.
getEnthalpyDifferences() - Method in class ffx.numerics.estimator.Zwanzig: Gets the enthalpy change between each pair of states.
getEnthalpyResults() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get bootstrap Enthalpy results for each window.
getEnthalpyStdDevs() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the enthalpy standard deviation estimate from bootstrap analysis for each window.
getEnthalpyVariances() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the enthalpy variance estimate from bootstrap analysis for each window.
getEntries() - Method in class ffx.utilities.Keyword: getEntries
getEntropyChanges() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get bootstrap entropy estimate for each window (-TdS).
getEntropyStdDevs() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the entropy standard deviation estimate from bootstrap analysis for each window.
getEntry(int) - Method in class ffx.utilities.Keyword: getEntry
getEps() - Method in class ffx.algorithms.cli.MinimizeOptions: Convergence criteria.
getEps() - Method in class ffx.potential.nonbonded.pme.SORRegion
getEps() - Method in class ffx.potential.nonbonded.VanDerWaalsForm: Return the eps value for each class.
getEps() - Method in class ffx.xray.RefinementMinimize: Getter for the field eps.
getEpsh() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the water hydrogen epsilon parameter.
getEpsilon() - Method in class ffx.crystal.HKL: getEpsilon
getEpsilon() - Method in class ffx.potential.bonded.Atom: Gets the Epsilon value
getEpsilonCombiningRule() - Method in class ffx.openmm.amoeba.VdwForce: Get the epsilon combining rule.
getEpso() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the water oxygen epsilon parameter.
getEquilibrationSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions: The number of equilibration steps prior to production OST counts begin.
getEquilibriumCoordinates() - Method in class ffx.potential.bonded.RestrainPosition: Returns the original coordinates of this restraint, indexed by atoms then x,y,z.
getEquilSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions: getEquilSteps.
getErrorTolerance() - Method in class ffx.openmm.VariableLangevinIntegrator: Get the error tolerance for adaptive step sizing.
getErrorTolerance() - Method in class ffx.openmm.VariableVerletIntegrator: Get the error tolerance for adaptive step sizing.
getEsvBiasEnergy() - Method in class ffx.potential.ForceFieldEnergy: getEsvBiasEnergy.
getESVHistogram(int[][]) - Method in class ffx.potential.extended.ExtendedSystem: Overwrites the histogram passed into it and returns the new one out ~output never used?
getEwaldCoefficient() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getEwaldCutoff() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getEwaldErrorTolerance() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the Ewald error tolerance.
getEwaldErrorTolerance() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the error tolerance for Ewald summation.
getExceptionMap() - Method in exception class edu.rit.pj.MultipleParallelException: Obtain this multiple parallel exception's exception map.
getExceptionParameters(int, IntByReference, IntByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.GayBerneForce: Get the parameters for an exception.
getExceptionParameters(int, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.NonbondedForce: Get the exception parameters.
getExceptionParameters(int, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the scale factors for an interaction that should be calculated differently from others.
getExceptionParameters(int, IntBuffer, IntBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.GayBerneForce: Get the parameters for an exception.
getExceptionParameters(int, IntBuffer, IntBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the scale factors for an interaction that should be calculated differently from others.
getExclude() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
getExcludeAtoms() - Method in class ffx.algorithms.optimize.TitrationManyBody
getExclusionParticles(int, IntByReference, IntByReference) - Method in class ffx.openmm.CustomGBForce: Get the particles in an exclusion.
getExclusionParticles(int, IntByReference, IntByReference) - Method in class ffx.openmm.CustomHbondForce: Get the particles in an exclusion.
getExclusionParticles(int, IntByReference, IntByReference) - Method in class ffx.openmm.CustomManyParticleForce: Get the particles in an exclusion.
getExclusionParticles(int, IntByReference, IntByReference) - Method in class ffx.openmm.CustomNonbondedForce: Get the particles in an exclusion.
getExclusionParticles(int, IntBuffer, IntBuffer) - Method in class ffx.openmm.CustomGBForce: Get the particles in an exclusion.
getExclusionParticles(int, IntBuffer, IntBuffer) - Method in class ffx.openmm.CustomHbondForce: Get the particles in an exclusion.
getExclusionParticles(int, IntBuffer, IntBuffer) - Method in class ffx.openmm.CustomManyParticleForce: Get the particles in an exclusion.
getExclusionParticles(int, IntBuffer, IntBuffer) - Method in class ffx.openmm.CustomNonbondedForce: Get the particles in an exclusion.
getExplicitDistanceTolerance() - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the explicit distance tolerance.
getExponent() - Method in class ffx.algorithms.cli.RepExOptions
getExponent() - Method in class ffx.numerics.switching.PowerSwitch: Gets the value of beta in f(x) = (a*x)^beta
getExtendedAtoms() - Method in class ffx.potential.extended.ExtendedSystem: All atoms of the fully-protonated system (not just those affected by this system).
getExtendedLambdas() - Method in class ffx.potential.extended.ExtendedSystem: Gets a copy of the array of doubles that matches the nESVs correspoding to each titration and tautomer lambda
getExtendedMolecule() - Method in class ffx.potential.extended.ExtendedSystem: Companion to getExtendedAtoms() for vdw::setAtoms and pme::setAtoms.
getExtendedResidueList() - Method in class ffx.potential.extended.ExtendedSystem: Return the List of Extended Residues which = TitratingResidueList + TautomerizingResidueList
getExtendedSystem() - Method in class ffx.potential.ForceFieldEnergy: getExtendedSystem.
getExtendedSystem() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the ExtendedSystem instance.
getExtendedSystem() - Method in class ffx.potential.parsers.XPHFilter
getExtent() - Method in class ffx.potential.bonded.MSNode: getExtent
getExtent() - Method in class ffx.potential.MolecularAssembly: getExtent
getExtrapolationCoefficients() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the extrapolation coefficients.
getExtrapolationCoefficients() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the extrapolation coefficients.
getF(int) - Method in class ffx.xray.DiffractionRefinementData: getF
getFace() - Method in class ffx.numerics.quickhull.HalfEdge: Returns the triangular face located to the left of this half-edge.
getFaces() - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the faces associated with this hull.
getFaces(int) - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the faces associated with this hull.
getFactor() - Method in class ffx.ui.behaviors.MouseZoom: Return the y-axis movement multipler.
getFactors() - Method in class ffx.numerics.fft.Complex: Getter for the field factors.
getFcTot(int) - Method in class ffx.xray.DiffractionRefinementData: getFcTot
getFEDifferenceStdDevs() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the free energy difference uncertainties (standard deviations) from bootstrap analysis for each window.
getFEDifferenceUncertainties() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Gets the uncertainty in free energy difference between each pair of states.
getFEDifferenceUncertainties() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getFEDifferenceUncertainties() - Method in interface ffx.numerics.estimator.StatisticalEstimator: Gets the uncertainty in free energy difference between each pair of states.
getFEDifferenceUncertainties() - Method in class ffx.numerics.estimator.Zwanzig: Gets the uncertainty in free energy difference between each pair of states.
getFEDifferenceVariances() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the free energy difference variance estimate from bootstrap analysis for each window.
getFieldGK() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getFieldGKCR() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getFile() - Method in class edu.rit.pj.io.StreamFile: Obtain the file in the frontend processor to which this stream file refers.
getFile() - Method in class ffx.potential.MolecularAssembly: Getter for the field file.
getFile() - Method in class ffx.potential.parsers.BARFilter: Return the number of snapshots in the BAR file.
getFile() - Method in class ffx.potential.parsers.SystemFilter: getFile
getFilename() - Method in class ffx.realspace.parsers.RealSpaceFile: Getter for the field filename.
getFilename() - Method in class ffx.xray.parsers.DiffractionFile: getFilename.
getFileReader() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's backend file reader.
getFiles() - Method in class ffx.potential.parsers.SystemFilter: Getter for the field files.
getFileType() - Method in class ffx.potential.cli.WriteoutOptions: Getter for the field fileType.
getFileWriter() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's backend file writer.
getFilter() - Method in class ffx.potential.utils.PotentialsFileOpener: Getter for the field filter.
getFilter() - Method in interface ffx.potential.utils.PotentialsFunctions: Returns the last SystemFilter created by this (can be null).
getFilter() - Method in class ffx.potential.utils.PotentialsUtils: Returns the last SystemFilter created by this (can be null).
getFilter() - Method in class ffx.ui.MainPanel: Return the active SystemFilter.
getFilter() - Method in class ffx.ui.UIUtils
getFinish() - Method in class ffx.algorithms.cli.ManyBodyOptions: Final residue to perform the optimization on (-1 exits).
getFirstAngleAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend: Get the first atom of the Angle.
getFirstDir() - Method in class ffx.algorithms.cli.MultiDynamicsOptions
getFirstEdge() - Method in class ffx.numerics.quickhull.Face: Returns the first half-edge of this face (the start of the circular list).
getFirstResidue() - Method in class ffx.potential.bonded.Polymer: getFirstResidue
getFitSoluteType(ForceField, int) - Static method in class ffx.potential.parameters.SoluteType
getFixedChargeSoftcoreForce() - Method in class ffx.potential.openmm.FixedChargeAlchemicalForces
getFoFc1(int) - Method in class ffx.xray.DiffractionRefinementData: getFoFc1
getFoFc1IP(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData: getFoFc1IP
getFoFc2(int) - Method in class ffx.xray.DiffractionRefinementData: getFoFc2
getFoFc2IP(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData: getFoFc2IP
getForce(int) - Method in class ffx.openmm.ATMForce: Get a force by index.
getForce(int) - Method in class ffx.openmm.System: Get a force in the system.
getForceConstant() - Method in class ffx.potential.bonded.RestrainPosition: Returns the force constant in kcal/mol/Angstrom^2.
getForceConstants() - Method in class ffx.potential.nonbonded.RestrainGroups: Force constant for each restraint.
getForceField() - Method in class ffx.potential.MolecularAssembly: Getter for the field forceField.
getForceField() - Method in class ffx.potential.openmm.OpenMMSystem: Get the ForceField in use.
getForceFieldEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Getter for the field forceFieldEnergy.
getForceFieldEnergy() - Method in class ffx.potential.commands.Energy
getForceFieldEnergy(int) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Get the OpenMMEnergy for the specified topology.
getForceFieldEnergy1() - Method in class ffx.potential.DualTopologyEnergy: Get the ForceFieldEnergy for topology 1.
getForceFieldEnergy2() - Method in class ffx.potential.DualTopologyEnergy: Get the ForceFieldEnergy for topology 2.
getForceFieldTypeCount(ForceField.ForceFieldType) - Method in class ffx.potential.parameters.ForceField: getForceFieldTypeCount
getForceFieldURL(ForceField.ForceFieldName) - Static method in class ffx.potential.parameters.ForceField: Get for the URL for the named force field.
getForceGroup() - Method in class ffx.openmm.Force: Get the force group.
getForceGroup() - Method in class ffx.potential.terms.EnergyTerm: Get the current force group identifier.
getForceIndex() - Method in class ffx.openmm.Force: Get the force index.
getForces() - Method in class ffx.openmm.State: Get the forces.
getFormFactorA(String) - Static method in class ffx.xray.NeutronFormFactor: getFormFactorA
getFormFactorA(String) - Static method in class ffx.xray.XRayFormFactor: getFormFactorA
getFormFactorB(String) - Static method in class ffx.xray.XRayFormFactor: getFormFactorB
getFormFactorIndex() - Method in class ffx.potential.bonded.Atom: Getter for the field formFactorIndex.
getFormFactorIndex(String) - Static method in class ffx.xray.NeutronFormFactor: getFormFactorIndex
getFormFactorIndex(String) - Static method in class ffx.xray.XRayFormFactor: getFormFactorIndex
getFormFactorWidth() - Method in class ffx.potential.bonded.Atom: Getter for the field formFactorWidth.
getFormFactorWidth2() - Method in class ffx.potential.bonded.Atom: Getter for the field formFactorWidth.
getForwardTotalEnthalpyChange() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Enthalpy difference from forward FEP.
getForwardTotalEntropyChange() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Entropy difference from forward FEP.
getForwardTotalFEDifference() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Free energy difference from forward FEP.
getFourBodyEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
getFourthAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend: The atom of this out-of-plane bend that was not part of the Angle.
getFourthAtomOfTrigonalCenter() - Method in class ffx.potential.bonded.Angle: If the central atom of the angle is trigonal, the 4th member of the trigonal center (that is not a part of the angle) will be returned.
getFrac() - Method in class ffx.potential.commands.Cart2Frac: Return Fractional Coordinate output.
getFrac() - Method in class ffx.potential.commands.Frac2Cart: Return Fractional Coordinate input.
getFraction() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return the ensemble average of protonated rotamers for all titratable sites
getFractionalMode() - Method in class ffx.potential.MolecularAssembly: Getter for the field fractionalMode.
getFractions(Residue[], int, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Calculate population of each rotamer for residues in the system
getFractions(Residue[], int, int[], boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Return population of each rotamer for residues in the system
getFrame() - Method in class ffx.ui.MainPanel: Getter for the field frame.
getFrame() - Method in class ffx.ui.Trajectory: getFrame
getFreeEnergyDifferences() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Gets the free energy difference between each pair of states.
getFreeEnergyDifferences() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get bootstrap free energy estimate for each window.
getFreeEnergyDifferences() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getFreeEnergyDifferences() - Method in interface ffx.numerics.estimator.StatisticalEstimator: Gets the free energy difference between each pair of states.
getFreeEnergyDifferences() - Method in class ffx.numerics.estimator.Zwanzig: Gets the free energy difference between each pair of states.
getFreeR(int) - Method in class ffx.xray.DiffractionRefinementData: getFreeR
getFrequency() - Method in class ffx.openmm.CMMotionRemover: Get the frequency (in time steps) at which center of mass motion should be removed.
getFrequency() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
getFrequency() - Method in class ffx.openmm.MonteCarloBarostat: Get the frequency.
getFrequency() - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
getFrequency() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
getFriction() - Method in class ffx.openmm.BrownianIntegrator: Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps).
getFriction() - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Get the friction coefficient which determines how strongly the system is coupled to the main heat bath (in inverse ps).
getFriction() - Method in class ffx.openmm.LangevinMiddleIntegrator: Get the friction coefficient.
getFriction() - Method in class ffx.openmm.VariableLangevinIntegrator: Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in 1/ps).
getFrontendAddress() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's array of hosts/ports for the frontend communicator.
getFrontendChannelGroup() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's frontend communicator channel group.
getFrontendHost() - Method in class edu.rit.pj.cluster.Configuration: Returns the host name of the cluster's frontend processor.
getFs(int) - Method in class ffx.xray.DiffractionRefinementData: getFs
getFSigF(int) - Method in class ffx.xray.DiffractionRefinementData: getFSigF
getFsigfCutoff() - Method in class ffx.xray.DiffractionData: Getter for the field fsigfCutoff.
getFSystem() - Method in class ffx.ui.Trajectory: getFSystem
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.CustomCompoundBondForce: Get the parameters for a tabulated function.
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.CustomGBForce: Get the parameters for a tabulated function.
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.CustomHbondForce: Get the parameters for a tabulated function.
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.CustomNonbondedForce: Get the parameters for a tabulated function.
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.CustomCompoundBondForce: Get the parameters for a tabulated function.
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.CustomGBForce: Get the parameters for a tabulated function.
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.CustomHbondForce: Get the parameters for a tabulated function.
getFunctionParameters(int, PointerByReference, PointerByReference, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.CustomNonbondedForce: Get the parameters for a tabulated function.
getFunctionParameters(IntByReference, IntByReference, IntByReference, PointerByReference) - Method in class ffx.openmm.Discrete3DFunction: Get the parameters for the tabulated function.
getFunctionParameters(IntByReference, IntByReference, PointerByReference) - Method in class ffx.openmm.Discrete2DFunction: Get the parameters for the tabulated function.
getFunctionParameters(PointerByReference) - Method in class ffx.openmm.Discrete1DFunction: Get the parameters for the tabulated function.
getFunctionParameters(PointerByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.Continuous1DFunction: Get the parameters for the tabulated function.
getFunctionParameters(PointerByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.Continuous2DFunction: Get the parameters for the tabulated function.
getFunctionParameters(PointerByReference, IntByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.Continuous3DFunction: Get the parameters for the tabulated function.
getFunctionParameters(IntBuffer, IntBuffer, PointerByReference) - Method in class ffx.openmm.Discrete2DFunction: Get the parameters for the tabulated function.
getFunctionParameters(IntBuffer, IntBuffer, IntBuffer, PointerByReference) - Method in class ffx.openmm.Discrete3DFunction: Get the parameters for the tabulated function.
getFxPoint(int) - Method in interface ffx.numerics.integrate.DataSet: Point f(x) at index.
getFxPoint(int) - Method in class ffx.numerics.integrate.DoublesDataSet: Point f(x) at index.
getFxPoint(int) - Method in class ffx.numerics.integrate.FunctionDataCurve: Point f(x) at index.
getGaussVol() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
getGeneralizedKirkwoordEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the GK component of the solvation energy.
getGeneralizedKirkwoordPermanentEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the GK component of the solvation energy.
getGeneralizedKirkwoordPolariztionEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the GK component of the solvation energy.
getGK() - Method in class ffx.potential.ForceFieldEnergy: getGK.
getGK() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getGKEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: getGeneralizedKirkwoodEnergy.
getGKInteractions() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: getGKInteractions
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.ATMForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomAngleForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomBondForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomCentroidBondForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomCompoundBondForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomCVForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomExternalForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomGBForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomHbondForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomManyParticleForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomNonbondedForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomTorsionForce: Get the default value of a global parameter.
getGlobalParameterDefaultValue(int) - Method in class ffx.openmm.CustomVolumeForce: Get the default value of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.ATMForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomAngleForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomBondForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomCentroidBondForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomCompoundBondForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomCVForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomExternalForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomGBForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomHbondForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomManyParticleForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomNonbondedForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomTorsionForce: Get the name of a global parameter.
getGlobalParameterName(int) - Method in class ffx.openmm.CustomVolumeForce: Get the name of a global parameter.
getGlobalVariable(int) - Method in class ffx.openmm.CustomIntegrator: Get the value of a global variable.
getGlobalVariableByName(String) - Method in class ffx.openmm.CustomIntegrator: Get the value of a global variable, specified by name.
getGlobalVariableName(int) - Method in class ffx.openmm.CustomIntegrator: Get the name of a global variable.
getGrad() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getGradient() - Method in class ffx.potential.terms.EnergyTermRegion: Get whether the gradient will be computed.
getGradient(double[]) - Method in class ffx.potential.ForceFieldEnergy: Returns the gradient array for this ForceFieldEnergy.
getGradient(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: Re-compute the gradient using OpenMM and return it.
getGradient(double[]) - Method in class ffx.potential.openmm.OpenMMState: The force array contains the OpenMM force information for all atoms.
getGradientAtoms() - Method in class ffx.potential.cli.GradientOptions: --ga or --gradientAtoms Ranges of atoms to test [ALL, NONE, Range(s): 1-3,6-N].
getGrid() - Method in class ffx.potential.nonbonded.RowRegion: Getter for the field grid.
getGrid() - Method in class ffx.potential.nonbonded.SliceRegion: Getter for the field grid.
getGrid() - Method in class ffx.potential.nonbonded.SpatialDensityRegion: Getter for the field grid.
getGroup1() - Method in class ffx.potential.nonbonded.RestrainGroups: Group 1 for each restraint.
getGroup2() - Method in class ffx.potential.nonbonded.RestrainGroups: Group 2 for each restraint.
getGroupCount() - Method in class ffx.potential.nonbonded.NeighborList.Cell
getGroupMembers(int) - Method in class ffx.potential.nonbonded.RestrainGroups: Get group members.
getGroupParameters(int, IntArray, DoubleArray) - Method in class ffx.openmm.CustomCentroidBondForce: Get the properties of a group.
getH() - Method in class ffx.crystal.HKL: The h-index of the reflection.
getHalfStepEnergy() - Method in class ffx.algorithms.dynamics.integrators.Respa: Get the potential energy of the fast degrees of freedom.
getHeader(String) - Method in class edu.rit.http.HttpRequest: Obtain the value of the given header in this HTTP request.
getHeaderLines() - Method in class ffx.potential.MolecularAssembly: Gets the header lines associated with this MolecularAssembly (particularly for PDB)
getHeaders() - Method in class edu.rit.http.HttpRequest: Obtain a collection of all the headers in this HTTP request.
getHierarchy() - Method in class ffx.ui.MainPanel: Getter for the field hierarchy.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.BellCurveSwitch: The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.CompositeSwitch
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.ConstantSwitch: The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.LinearDerivativeSwitch: The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.MultiplicativeSwitch: The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.PowerSwitch: The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.SquaredTrigSwitch: The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: The highest-order derivative that is zero at the bounds.
getHighlighting() - Method in class ffx.ui.MainMenu: getHighlighting
getHighTemp() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Gets the starting temperature.
getHighTemp() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
getHighTemp() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
getHighTemp() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
getHilbertIndices() - Method in class ffx.algorithms.optimize.TorsionSearch: List of hilbert indices for each state in order of lowest to highest energy.
getHistogram() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Return the current 2D Histogram of counts.
getHistogramFile() - Method in class ffx.algorithms.thermodynamics.HistogramData
getHistogramFileName() - Method in class ffx.algorithms.thermodynamics.HistogramData
getHistogramIndex() - Method in class ffx.algorithms.thermodynamics.SendSynchronous
getHKL(int, int, int) - Method in class ffx.crystal.ReflectionList: getHKL
getHKL(HKL) - Method in class ffx.crystal.ReflectionList: getHKL
getHttpVersion() - Method in class edu.rit.http.HttpRequest: Obtain this HTTP request's version.
getHybridization() - Method in class ffx.potential.bonded.Atom: Gets the Atomic Hybridization
getID() - Method in class ffx.potential.bonded.BondedTerm: Get the Term's id.
getIdent() - Method in class ffx.potential.bonded.Atom: Gets the atom ID
getImproperTorsion(int) - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Get the ImproperTorsion at a given index.
getImproperTorsionArray() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Get an array of ImproperTorsions in this term.
getImproperTorsionList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all ImproperTorsions below the present MSNode.
getImproperTorsionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the ImproperTorsionPotentialEnergy.
getImproperTorsions() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Get an unmodifiable view of the ImproperTorsions in this term.
getImproperType(String) - Method in class ffx.potential.parameters.ForceField: getImproperType
getImproperTypes() - Method in class ffx.potential.parameters.ForceField: getImproperType
getInactive() - Method in class ffx.potential.bonded.MultiResidue: Returns a list of this MultiResidue's inactive residues.
getInactiveAtoms() - Method in class ffx.potential.cli.AtomSelectionOptions: --ia or --inactiveAtoms Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].
getIncludeCavityTerm() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the include cavity term.
getInclusionCutoff() - Method in class ffx.algorithms.cli.ManyBodyOptions
getIncrement() - Method in class ffx.algorithms.cli.ManyBodyOptions: Sliding window increment (default = 3).
getIndependentWalkers() - Method in class ffx.algorithms.cli.OSTOptions: Checks if independent walkers has been specified.
getIndependentWalkers() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: For MPI parallel jobs, returns true if the walkers are independent (i.e. contribute to only their own histogram).
getIndex() - Method in class ffx.crystal.HKL: Get the index of this reflection.
getIndex() - Method in class ffx.potential.bonded.Atom: Getter for the field index.
getIndRealEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: getIndRealEnergy.
getIndRecipEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: getIndRecipEnergy.
getIndSelfEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: getIndSelfEnergy.
getInducedDipoleReciprocalEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
getInducedDipoles(Context, PointerByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the induced dipoles.
getInducedDipoles(Context, DoubleArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the induced dipoles.
getInducedDipoleSelfEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
getInitAtomGradients() - Method in class ffx.potential.terms.EnergyTermRegion
getInitialBackwardsGuess() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Returns the backwards Zwanzig estimator used to seed BAR.
getInitialForwardsGuess() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Returns the forwards Zwanzig estimator used to seed BAR.
getInitialKinetic() - Method in class ffx.algorithms.mc.MDMove
getInitialKineticEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Gets the kinetic energy at the start of the last dynamics run.
getInitialLambda() - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Get the initial lambda value.
getInitialLambda() - Method in class ffx.potential.cli.AlchemicalOptions: -l or --lambda sets the initial lambda value.
getInitialLambda(boolean) - Method in class ffx.potential.cli.AlchemicalOptions: Gets the initial value of lambda.
getInitialLambda(int, int) - Method in class ffx.potential.cli.AlchemicalOptions: Gets the initial value of lambda.
getInitialLambda(int, int, boolean) - Method in class ffx.potential.cli.AlchemicalOptions: Gets the initial value of lambda.
getInitialPotential() - Method in class ffx.algorithms.mc.MDMove
getInitialPotentialEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Gets the potential energy at the start of the last dynamics run.
getInitialTemperature() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Gets the temperature at the start of the last dynamics run.
getInitialTotal() - Method in class ffx.algorithms.mc.MDMove
getInitialTotalEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Gets the total energy at the start of the last dynamics run.
getInitPoint() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Gets the virtual coordinate at which this node is drawn.
getInitTime(int) - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
getInnerContext(Context) - Method in class ffx.openmm.CustomCVForce: Get the inner context used for evaluating collective variables.
getInPlaneAngleEnergyString() - Method in class ffx.potential.terms.AnglePotentialEnergy
getInputAngles(double[], double[], double[], double[]) - Method in class ffx.potential.utils.LoopClosure: Get the input angles.
getInputStream() - Method in class edu.rit.pj.io.StreamFile: Open an input stream for reading this stream file.
getInstance(long) - Static method in class edu.rit.util.Random: Construct a new PRNG with the given seed using the default algorithm.
getInstance(long, String) - Static method in class edu.rit.util.Random: Construct a new PRNG with the given seed using the given algorithm.
getInteger(String) - Method in class ffx.potential.parameters.ForceField: getInteger
getInteger(String, Integer) - Method in class ffx.potential.parameters.ForceField: getInteger
getIntegrationForceGroups() - Method in class ffx.openmm.CompoundIntegrator: Get which force groups to use for integration.
getIntegrationForceGroups() - Method in class ffx.openmm.Integrator: Get the set of force groups this integrator acts on.
getIntegrator() - Method in class ffx.openmm.Context: Get Integrator being used by this context.
getIntegrator(int) - Method in class ffx.openmm.CompoundIntegrator: Get a reference to one of the Integrators that have been added to this CompoundIntegrator.
getIntegratorString() - Method in class ffx.algorithms.cli.DynamicsOptions: The integrator: current choices are Beeman, RESPA, Stochastic (Langevin) or Verlet.
getInteractionGroupParameters(int, PointerByReference, PointerByReference) - Method in class ffx.openmm.CustomNonbondedForce: Get the parameters for an interaction group.
getInteractions() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: getInteractions
getInteractions() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
getInteractions() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Getter for the field interactions.
getInteractions() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
getInteractions() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the number of interacting pairs.
getInteractions() - Method in class ffx.potential.nonbonded.VanDerWaalsTornado: Get the number of interacting pairs.
getInterestedResidue() - Method in class ffx.algorithms.cli.ManyBodyOptions
getIntervalSteps() - Method in class ffx.algorithms.dynamics.MolecularDynamics: getIntervalSteps.
getIntervalSteps() - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: getIntervalSteps.
getIntramolecularSoftcore() - Method in class ffx.potential.nonbonded.VanDerWaals: If true, intra-molecular interactions are annihilated by the lambda state variable.
getIonNames() - Static method in class ffx.utilities.StringUtils: Returns a Map from recognized ion names to standard ion names.
getIons() - Method in class ffx.potential.MolecularAssembly: Getter for the field ions.
getIterations() - Method in class ffx.algorithms.cli.MinimizeOptions: Number of minimization steps.
getIterations() - Method in class ffx.algorithms.optimize.Minimize: Getter for the number of iterations completed this minimization.
getIterations() - Method in class ffx.potential.cli.TimerOptions: Getter for the field iterations.
getJobBackend() - Static method in class edu.rit.pj.cluster.JobBackend: Obtain the Job Backend object.
getJobNumber() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's job number.
getJobNumber() - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Obtain the job number assigned to this Non-PJ Job Frontend.
getJobNumber() - Method in class edu.rit.pj.job.Job: Returns this job's number.
getJobTime() - Method in class edu.rit.pj.cluster.Configuration: Returns the maximum job time.
getK() - Method in class edu.rit.pj.cluster.JobBackend: Obtain the number of backend processes in this job.
getK() - Method in class ffx.crystal.HKL: Get the k-index of the reflection.
getKey() - Method in class ffx.potential.bonded.Atom: Gets the atom Key
getKey() - Method in class ffx.potential.bonded.Molecule
getKey() - Method in class ffx.potential.parameters.BaseType: Get the key for this Type.
getKey(String) - Method in class ffx.ui.properties.FFXLocale: getKey
getKeyFile() - Method in class ffx.ui.FFXSystem: Getter for the field keyFile.
getKeyword() - Method in class ffx.ui.KeywordComponent: Getter for the field keyword.
getKeyword() - Method in class ffx.utilities.Keyword: Getter for the field keyword.
getKeyword(String) - Method in class ffx.ui.FFXSystem: getKeyword
getKeyword(String) - Method in class ffx.ui.KeywordPanel: getKeyword
getKeywordDescription(String) - Method in class ffx.ui.KeywordPanel: getKeywordDescription
getKeywords() - Method in class ffx.ui.FFXSystem: Getter for the field keywords.
getKeywordValue(String) - Method in class ffx.ui.KeywordPanel: getKeywordValue
getKineticEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Get the system kinetic energy.
getKineticEnergy() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Get the current kinetic energy.
getKineticEnergy() - Method in class ffx.algorithms.mc.MDMove: getKineticEnergy.
getKineticEnergy() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: getKineticEnergy.
getKineticEnergy() - Method in class ffx.openmm.State: Get the kinetic energy.
getKineticEnergy() - Method in class ffx.potential.openmm.OpenMMState: Get the kinetic energy.
getKineticEnergy() - Method in class ffx.potential.SystemState: Get the kinetic energy.
getKineticEnergyExpression() - Method in class ffx.openmm.CustomIntegrator: Get the expression used to compute the kinetic energy.
getKineticEnergyFromVelocities() - Method in class ffx.potential.SystemState: Compute the kinetic energy from the current velocities and masses.
getKTScale() - Method in class ffx.xray.RefinementEnergy: get the current kT scaling weight
getL() - Method in class ffx.crystal.HKL: Get the l-index of the reflection.
getL() - Method in class ffx.crystal.ReplicatesCrystal: The number of replicates along the a-axis.
getLabFramePermanentDipoles(Context, PointerByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the lab frame permanent dipoles.
getLabFramePermanentDipoles(Context, DoubleArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the lab frame permanent dipoles.
getLambda() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Returns the current value of lambda
getLambda() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Getter for the field lambda.
getLambda() - Method in class ffx.openmm.amoeba.VdwForce: Get the lambda parameter.
getLambda() - Method in class ffx.potential.ANIEnergy
getLambda() - Method in class ffx.potential.bonded.AngleTorsion: Get the current value of the state variable.
getLambda() - Method in interface ffx.potential.bonded.LambdaInterface: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.PiOrbitalTorsion: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.RestrainDistance: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.RestrainPosition: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.RestrainTorsion
getLambda() - Method in class ffx.potential.bonded.StretchTorsion: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.Torsion: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.TorsionTorsion: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.DualTopologyEnergy: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.ForceFieldEnergy: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.COMRestraint: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.NCSRestraint: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the current value of the state variable.
getLambda() - Method in class ffx.potential.QuadTopologyEnergy: Get the current value of the state variable.
getLambda() - Method in class ffx.realspace.RealSpaceData: Getter for the field lambda.
getLambda() - Method in class ffx.realspace.RealSpaceEnergy: Get the current value of the state variable.
getLambda() - Method in class ffx.xray.RefinementEnergy: Get the current value of the state variable.
getLambda() - Method in class ffx.xray.XRayEnergy: Get the current value of the state variable.
getLambdaAllBondedTerms() - Method in class ffx.potential.terms.EnergyTermRegion
getLambdaBins() - Method in class ffx.algorithms.thermodynamics.HistogramData
getLambdaBinWidth() - Method in class ffx.algorithms.thermodynamics.HistogramData
getLambdaBondedTerms() - Method in class ffx.potential.terms.EnergyTermRegion
getLambdaFile() - Method in class ffx.algorithms.thermodynamics.LambdaData
getLambdaFileName() - Method in class ffx.algorithms.thermodynamics.LambdaData
getLambdaFriction() - Method in class ffx.algorithms.cli.LambdaParticleOptions: Friction on the lambda particle.
getLambdaFunction() - Method in class ffx.potential.cli.TopologyOptions: -sf or --switchingFunction
getLambdaHistogram(List<Residue>, int[][][], double) - Method in class ffx.potential.parsers.ESVFilter
getLambdaList() - Method in class ffx.potential.extended.ExtendedSystem: getLambdaList.
getLambdaMass() - Method in class ffx.algorithms.cli.LambdaParticleOptions: The mass of the lambda particle.
getLambdaResetValue() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
getLambdaTerm() - Method in class ffx.potential.ForceFieldEnergy: Get the lambdaTerm flag.
getLambdaTerm() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: If true, there are alchemical atoms impacted by the lambda state variable.
getLambdaTerm() - Method in class ffx.potential.nonbonded.VanDerWaals: If true, there are alchemical atoms impacted by the lambda state variable.
getLambdaWriteOut() - Method in class ffx.algorithms.cli.OSTOptions: Only write out snapshots if lambda is greater than the value specified.
getLambdaXYZGradient(double[]) - Method in class ffx.potential.bonded.Atom: getLambdaXYZGradient
getLargerDistance() - Method in class ffx.potential.nonbonded.RestrainGroups: Larger distance for each restraint.
getLastAngleAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend: Get the first atom of the Angle.
getLastReadLambda() - Method in class ffx.potential.parsers.PDBFilter: Gets the last read lambda value read by the filter, if any.
getLastReadLambda() - Method in class ffx.potential.parsers.SystemFilter: Gets the last read lambda value read by the filter, if any.
getLastReadLambda() - Method in class ffx.potential.parsers.XPHFilter: Gets the last read lambda value read by the filter, if any.
getLastReadLambda() - Method in class ffx.potential.parsers.XYZFilter: Gets the last read lambda value read by the filter, if any.
getLayout() - Method in class ffx.numerics.fft.Complex2D: Get the Data Layout.
getlCluster() - Method in class ffx.numerics.clustering.ClusterPair: Gets the left cluster.
getLeafNames() - Method in class ffx.numerics.clustering.Cluster: Returns the list of leaf names beneath this cluster.
getLeavesValueAtIndex(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
getLibrary() - Method in class ffx.algorithms.cli.ManyBodyOptions: Ponder and Richards (1) or Richardson (2) rotamer library.
getLibrary() - Method in class ffx.potential.bonded.RotamerLibrary: Get the protein rotamer library.
getLineColor() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getLink() - Method in class ffx.potential.bonded.Polymer: Getter for the field link.
getLinkageDistance() - Method in class ffx.numerics.clustering.ClusterPair: Gets the linkage distance.
getLinkPoint() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Gets the virtual coordinate where this node connects to its parent.
getList(Class<T>) - Method in class ffx.potential.bonded.MSNode: Returns a List of all MSNodes below the present MSNode.
getList(Class<T>, List<T>) - Method in class ffx.potential.bonded.MSNode: getList
getList(Class<T>, List<T>) - Method in interface ffx.potential.bonded.ROLS: getList
getListResidues() - Method in class ffx.algorithms.cli.ManyBodyOptions: Choose a list of individual residues to optimize (eg.
getLocalPosition() - Method in class ffx.openmm.LocalCoordinatesSite: Get the position of the virtual site in the local coordinate system.
getLogFile() - Method in class edu.rit.pj.cluster.Configuration: Returns the Job Scheduler's log file name.
getLogFile() - Method in class ffx.ui.FFXSystem: Getter for the field logFile.
getLow() - Method in class ffx.algorithms.cli.AnnealOptions: Low temperature limit in degrees Kelvin.
getLowerBounds() - Method in class ffx.xray.GradientSchedule: Getter for the field lowerBounds.
getLowTemp() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Gets the final temperature.
getLowTemp() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
getLowTemp() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
getLowTemp() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
getM() - Method in class ffx.crystal.ReplicatesCrystal: The number of replicates along the b-axis.
getM1MinEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
getM2MinEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
getMainClassName() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's main class name.
getMainMenu() - Method in class ffx.ui.MainPanel: Getter for the field mainMenu.
getManyBodyOptions() - Method in class ffx.algorithms.commands.ManyBody: Get ManyBodyOptions to access script parameters.
getManyBodyOptions() - Method in class ffx.realspace.commands.ManyBody: Get ManyBodyOptions.
getManyBodyOptions() - Method in class ffx.xray.commands.ManyBody: Get the ManyBodyOptions.
getMapParameters(int, IntByReference, PointerByReference) - Method in class ffx.openmm.CMAPTorsionForce: Get the energy values of a map.
getMapParameters(int, IntBuffer, PointerByReference) - Method in class ffx.openmm.CMAPTorsionForce: Get the energy values of a map.
getMask12() - Method in class ffx.potential.nonbonded.VanDerWaals: Getter for the field bondMask.
getMask13() - Method in class ffx.potential.nonbonded.VanDerWaals: Getter for the field angleMask.
getMask14() - Method in class ffx.potential.nonbonded.VanDerWaals: Getter for the field torsionMask.
getMass() - Method in class ffx.algorithms.dynamics.Barostat: Get the mass of each degree of freedom.
getMass() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the mass of each degree of freedom.
getMass() - Method in interface ffx.numerics.Potential: Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.ANIEnergy
getMass() - Method in class ffx.potential.bonded.Atom: Gets the Atomic Mass.
getMass() - Method in class ffx.potential.DualTopologyEnergy: Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.extended.ExtendedSystem
getMass() - Method in class ffx.potential.ForceFieldEnergy: Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.MolecularAssembly: getMass.
getMass() - Method in class ffx.potential.QuadTopologyEnergy: Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.SystemState: Get a reference to the internal mass array.
getMass() - Method in class ffx.potential.XtalEnergy: Get the mass of each degree of freedom.
getMass() - Method in class ffx.realspace.RealSpaceEnergy: Get the mass of each degree of freedom.
getMass() - Method in class ffx.xray.RefinementEnergy: Get the mass of each degree of freedom.
getMass() - Method in class ffx.xray.XRayEnergy: Get the mass of each degree of freedom.
getMatrix() - Method in class edu.rit.io.DoubleMatrixFile: Obtain this matrix file's underlying matrix.
getMax() - Method in class ffx.numerics.math.RunningStatistics: Get the max.
getMaxAM() - Method in class ffx.algorithms.cli.BarostatOptions: The width of proposed crystal angle moves (uniformly distributed) in degrees.
getMaxD() - Method in class ffx.algorithms.cli.BarostatOptions: The maximum density accepted by the MC Barostat (g/cc).
getMaxDrudeDistance() - Method in class ffx.openmm.drude.DrudeIntegrator: Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm.
getMaxDrudeDistance() - Method in class ffx.openmm.drude.DrudeNoseHooverIntegrator: Get the maximum allowed distance between Drude particles and their parent atoms.
getMaximumDepth() - Method in class ffx.potential.nonbonded.implicit.GaussVol: Returns the maximum depth of the overlap tree
getMaximumPairDistance() - Method in class ffx.openmm.NoseHooverIntegrator: Get the maximum pair distance for neighbor list updates.
getMaximumStepSize() - Method in class ffx.openmm.VariableLangevinIntegrator: Get the maximum step size the integrator is allowed to use (in ps).
getMaximumStepSize() - Method in class ffx.openmm.VariableVerletIntegrator: Get the maximum step size the integrator is allowed to use (in ps).
getMaxNameWidth(Graphics2D, boolean) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Recursively computes the maximal name width across this node and its children.
getMaxResolution() - Method in class ffx.crystal.ReflectionList: Get the maximum resolution.
getMaxV() - Method in class ffx.algorithms.cli.BarostatOptions: The volume of a proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
getMBAR(MultistateBennettAcceptanceRatio.SeedType) - Method in class ffx.numerics.estimator.MBARFilter: Create an MBAR instance with the given seed type.
getMBAR(MultistateBennettAcceptanceRatio.SeedType, double) - Method in class ffx.numerics.estimator.MBARFilter: Create an MBAR instance with the given seed type and tolerance.
getMBARFreeEnergies() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getMcLambdaStdDev() - Method in class ffx.algorithms.cli.OSTOptions: The standard deviation for lambda moves.
getMcMDSteps() - Method in class ffx.algorithms.cli.OSTOptions: The number of steps to take for each MD trajectory for MC-OST.
getMD() - Method in class ffx.algorithms.mc.MDMove
getMD() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
getMean() - Method in class ffx.numerics.math.BootStrapStatistics: The mean.
getMean() - Method in class ffx.numerics.math.RunningStatistics: Gets the mean as of the last value added.
getMean() - Method in class ffx.numerics.math.SummaryStatistics: The mean.
getMeanBarostatInterval() - Method in class ffx.algorithms.dynamics.Barostat: Returns the mean number of steps between barostat applications.
getMessage() - Method in class ffx.ui.commands.SimulationMessage: Getter for the field message.
getMethod() - Method in class edu.rit.http.HttpRequest: Obtain this HTTP request's method.
getMiddleBond() - Method in class ffx.potential.bonded.PiOrbitalTorsion: Get the middle bond that the Pi-Orbital Torsion is formed around.
getMin() - Method in class ffx.numerics.math.RunningStatistics: Get the min.
getMinD() - Method in class ffx.algorithms.cli.BarostatOptions: The minimum density accepted by the MC Barostat (g/cc).
getMinimizationErrorTolerance() - Method in class ffx.openmm.drude.DrudeSCFIntegrator: Get the error tolerance to use when minimizing the potential energy.
getMinimumEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
getMinResolution() - Method in class ffx.crystal.ReflectionList: Get the minimum resolution.
getMissedResidues() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
getMode() - Method in class ffx.algorithms.mc.RosenbluthChiAllMove: Getter for the field mode.
getModel() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getModelingJobs() - Method in class ffx.ui.ModelingPanel: Get an ArrayList of executing jobs
getModelingShell() - Method in class ffx.ui.MainPanel: Getter for the field modelingShell.
getModelName() - Method in class ffx.xray.DiffractionData: Getter for the field modelName.
getMolecularAssemblies() - Method in class ffx.realspace.RealSpaceData: getMolecularAssemblies
getMolecularAssemblies() - Method in interface ffx.xray.DataContainer: getMolecularAssemblies
getMolecularAssemblies() - Method in class ffx.xray.DiffractionData: getMolecularAssemblies
getMolecularAssembly() - Method in class ffx.algorithms.mc.MolecularMC: Returns the associated MolecularAssembly.
getMolecularAssembly() - Method in class ffx.potential.AssemblyState: Returns the MolecularAssembly associated with this AssemblyState.
getMolecularAssembly() - Method in class ffx.potential.ForceFieldEnergy: Get the MolecularAssembly associated with this ForceFieldEnergy.
getMolecularAssembly() - Method in class ffx.potential.openmm.OpenMMEnergy: Returns the MolecularAssembly instance.
getMolecularAssembly(int) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Get the MolecularAssembly.
getMolecularAssemblyArray() - Method in class ffx.potential.parsers.SystemFilter: Get the MolecularAssembly array.
getMolecularDynamics() - Method in class ffx.algorithms.commands.Dynamics
getMolecularDynamics() - Method in class ffx.algorithms.commands.test.PhDynamics
getMoleculeArray() - Method in class ffx.potential.MolecularAssembly
getMoleculeNumber() - Method in class ffx.potential.bonded.Atom: Getter for the field moleculeNumber.
getMoleculeNumbers() - Method in class ffx.potential.MolecularAssembly: This method assigns a unique integer to every molecule in the MolecularAssembly beginning at 0.
getMolecules() - Method in class ffx.potential.MolecularAssembly: Getter for the field molecules.
getMonteCarlo() - Method in class ffx.algorithms.cli.ManyBodyOptions: Follow elimination criteria with 'n' Monte Carlo steps, or enumerate all remaining conformations, whichever is smaller.
getMonteCarlo() - Method in class ffx.algorithms.cli.RepExOptions
getMouseMode() - Method in class ffx.ui.MainMenu: getMouseMode
getMoveSize() - Method in class ffx.algorithms.mc.LambdaMove: Get the Lambda move size, which is a standard deviation for continuous moves or step size for discrete moves.
getMSCount(Class<T>, long) - Method in class ffx.potential.bonded.MSNode: getMSCount
getMSCount(Class<T>, long) - Method in interface ffx.potential.bonded.ROLS: getMSCount
getMSNode(Class<T>) - Method in class ffx.potential.bonded.MSNode: getMSNode
getMSNode(Class<T>) - Method in interface ffx.potential.bonded.ROLS: getMSNode
getMultiplier() - Method in class ffx.numerics.switching.PowerSwitch: Gets the value of a in f(x) = (a*x)^beta.
getMultipole() - Method in class ffx.potential.nonbonded.octree.OctreeCell
getMultipole() - Method in class ffx.potential.parameters.MultipoleType: Getter for the field multipole.
getMultipole(Atom, double, double, double[]) - Method in class ffx.potential.parameters.TitrationUtils
getMultipoleParameters(int, DoubleByReference, PointerByReference, PointerByReference, IntByReference, IntByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the multipole parameters for a particle.
getMultipoleTautomerDeriv(Atom, double, double, double[]) - Method in class ffx.potential.parameters.TitrationUtils
getMultipoleTitrationDeriv(Atom, double, double, double[]) - Method in class ffx.potential.parameters.TitrationUtils
getMultipoleType() - Method in class ffx.potential.bonded.Atom: Getter for the field multipoleType.
getMultipoleType(int) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Get the MultipoleType for Atom i.
getMultipoleType(String) - Method in class ffx.potential.parameters.ForceField: getMultipoleType
getMultipoleTypeBeginsWith(String) - Method in class ffx.potential.parameters.ForceField: Find the MultipoleType whose key begins with the supplied String.
getMultipoleTypes() - Method in class ffx.potential.parameters.ForceField: Get MultipoleTypes.
getMultipoleTypes(String) - Method in class ffx.potential.parameters.ForceField: Find each MultipoleType whose key begins with the supplied String.
getMultiScaleCenter(boolean) - Method in class ffx.potential.bonded.MSGroup: This method finds the Geometrical center of this MultiScaleGroup, or the atomicWeight-weighted center if w is set to true, and returns it as a double[3].
getMultiScaleCenter(boolean) - Method in class ffx.potential.bonded.MultiResidue: This method finds the Geometrical center of this MultiScaleGroup, or the atomicWeight-weighted center if w is set to true, and returns it as a double[3].
getMutualInducedMaxIterations() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the mutual induced max iterations.
getMutualInducedTargetEpsilon() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the mutual induced target epsilon.
getMW() - Method in class ffx.potential.bonded.MSNode: getMW
getMW() - Method in interface ffx.potential.bonded.ROLS: getMW
getN() - Method in class ffx.crystal.ReplicatesCrystal: The number of replicates along the c-axis.
getN() - Method in class ffx.xray.DiffractionData: Getter for the field n.
getNaLibraryName() - Method in class ffx.algorithms.cli.ManyBodyOptions: Nucleic acid library: currently only Richardson available.
getName() - Method in class ffx.numerics.clustering.Cluster: Gets the name of this cluster.
getName() - Method in class ffx.openmm.Force: Get the name of the force.
getName() - Method in class ffx.openmm.Platform: Get the name of the OpenMM Platform.
getName() - Method in class ffx.potential.bonded.MSNode: Returns the name of this MSNode.
getName() - Method in class ffx.potential.bonded.MultiResidue: Returns the name of this MSNode.
getName() - Method in class ffx.potential.bonded.Rotamer
getName() - Method in class ffx.potential.terms.EnergyTerm: Get the name of this energy term.
getNamePadding() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Gets the pixel padding between a leaf node and its name text.
getNames(Class<? extends Enum<?>>) - Static method in class ffx.potential.bonded.AminoAcidUtils: Turn an Enum into String array.
getNameWidth(Graphics2D, boolean) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Computes the width in pixels of this node's name label.
getNativeEnvironmentApproximation() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Checks whether GK uses the Native Environment Approximation.
getNatoms() - Method in class ffx.potential.nonbonded.RowRegion: getNatoms.
getNatoms() - Method in class ffx.potential.nonbonded.SliceRegion: getNatoms.
getNavigation() - Method in class ffx.ui.GraphicsCanvas: getNavigation
getNB() - Method in class ffx.xray.RefinementMinimize: get the number of B factor parameters being fit
getNB() - Method in class ffx.xray.XRayEnergy: get the number of B factor parameters being fit
getNBFGS() - Method in class ffx.algorithms.cli.MinimizeOptions: The number of corrections used in the BFGS update.
getnChild() - Method in class ffx.potential.nonbonded.octree.OctreeCell
getNeckConstants(double, double) - Static method in class ffx.potential.nonbonded.implicit.NeckIntegral
getNeckScale() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the neck scale factors used for the GK calculation.
getNeighborList() - Method in class ffx.potential.nonbonded.NeighborList: Return the Verlet list.
getNeighborList() - Method in class ffx.potential.nonbonded.VanDerWaals: Allow sharing the of the VanDerWaals NeighborList with ParticleMeshEwald.
getNeighborLists() - Method in class ffx.potential.nonbonded.VanDerWaals: Getter for the field neighborLists.
getNeuralNetworkIdentity() - Method in class ffx.potential.MolecularAssembly: Construct a boolean orray of flags to indicate atoms treated by a neural network.
getNext() - Method in class ffx.numerics.quickhull.HalfEdge: Gets the value of the next edge adjacent (counter-clockwise) to this one within the triangle.
getNextLambda(long, double) - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Get the non-equilibrium lambda value for a given MD step.
getNextResidue() - Method in class ffx.potential.bonded.Residue: Returns the Residue bonded to this Residue at this Residue's 3' or C-terminal end.
getNi() - Method in class ffx.realspace.RealSpaceRefinementData: Getter for the field ni.
getNOcc() - Method in class ffx.xray.RefinementMinimize: get the number of occupancy parameters being fit
getNOcc() - Method in class ffx.xray.XRayEnergy: get the number of occupancy parameters being fit
getNodeList() - Method in class ffx.potential.MolecularAssembly: getNodeList
getNoGradient() - Method in class ffx.potential.cli.TimerOptions: Getter for the field noGradient.
getNonAlchemicalAlchemicalStericsForce() - Method in class ffx.potential.openmm.FixedChargeAlchemicalForces
getNonbondedCutoff() - Method in class ffx.potential.nonbonded.VanDerWaals: Get details of the non-bonded cutoff.
getNonbondedMethod() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the nonbonded method.
getNonbondedMethod() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the nonbonded method for the multipole force.
getNonbondedMethod() - Method in class ffx.openmm.amoeba.VdwForce: Get the nonbonded method.
getNonbondedMethod() - Method in class ffx.openmm.CustomGBForce: Get the nonbonded method.
getNonbondedMethod() - Method in class ffx.openmm.CustomHbondForce: Get the nonbonded method.
getNonbondedMethod() - Method in class ffx.openmm.CustomManyParticleForce: Get the method used for handling long range nonbonded interactions.
getNonbondedMethod() - Method in class ffx.openmm.CustomNonbondedForce: Get the nonbonded method.
getNonbondedMethod() - Method in class ffx.openmm.GayBerneForce: Get the nonbonded method.
getNonbondedMethod() - Method in class ffx.openmm.GBSAOBCForce: Get the method used for handling long range nonbonded interactions.
getNonEquilibriumLambdaSteps() - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Get the number of non-equilibrium lambda steps.
getNonPolarModel() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: getNonPolarModel.
getNonPolarModel(String) - Static method in class ffx.potential.nonbonded.GeneralizedKirkwood: getNonPolarModel.
getNormal() - Method in class ffx.numerics.quickhull.Face: Returns the normal of the plane associated with this face.
getNoWait(String) - Method in class edu.rit.pj.cluster.ResourceCache: Obtain the resource content for the given resource name from this resource cache (non-blocking).
getNsymm() - Method in class ffx.potential.nonbonded.RowRegion: getNsymm.
getNsymm() - Method in class ffx.potential.nonbonded.SliceRegion: getNsymm.
getNsymm() - Method in class ffx.potential.nonbonded.SpatialDensityRegion: getNsymm
getNucleicAcid3() - Method in class ffx.potential.bonded.Residue: getNucleicAcid3.
getNucleicAcid3(boolean) - Method in class ffx.potential.bonded.Residue: Returns the NucleicAcid3 corresponding to this Residue, with additional robust checking for 1- or 2-letter names.
getNucleicAcidNumber(String) - Static method in class ffx.potential.bonded.NucleicAcidUtils: getNucleicAcidNumber.
getNumAcceptors() - Method in class ffx.openmm.CustomHbondForce: Get the number of acceptors.
getNumAngles() - Method in class ffx.openmm.CustomAngleForce: Get the number of angles.
getNumAngles() - Method in class ffx.openmm.HarmonicAngleForce: Get the number of angles in the force.
getNumAngles() - Method in class ffx.potential.bonded.Atom: getNumAngles
getNumAtoms() - Method in class ffx.potential.bonded.RestrainPosition: getNumAtoms.
getNumberOfAngles() - Method in class ffx.potential.terms.AnglePotentialEnergy: Get the number of Angles in this term.
getNumberOfAngleTorsions() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Get the number of AngleTorsions in this term.
getNumberOfAtoms() - Method in class ffx.potential.DualTopologyEnergy: Get the number of dual topology atoms.
getNumberOfBins() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute the total free energy difference.
getNumberOfBins() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getNumberOfBins() - Method in interface ffx.numerics.estimator.StatisticalEstimator: Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute the total free energy difference.
getNumberOfBins() - Method in class ffx.numerics.estimator.Zwanzig: Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute the total free energy difference.
getNumberOfBondedHydrogen() - Method in class ffx.potential.bonded.Atom: Count the number of bonded hydrogen.
getNumberOfBonds() - Method in class ffx.potential.terms.BondPotentialEnergy: Get the number of Bonds in this term.
getNumberOfDevices() - Static method in class ffx.numerics.tornado.FFXTornado: Get all TornadoDevice instances.
getNumberOfGroups() - Method in class ffx.potential.nonbonded.RestrainGroups: Get the number of groups.
getNumberOfImproperTorsions() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Get the number of ImproperTorsions in this term.
getNumberOfOutOfPlaneBends() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Get the number of OutOfPlaneBends in this term.
getNumberOfPiOrbitalTorsions() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get the number of PiOrbitalTorsions in this term.
getNumberOfRestrainDistances() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Get the number of RestrainDistances in this term.
getNumberOfRestrainPositions() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Get the number of RestrainPositions in this term.
getNumberOfRestrainTorsions() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Get the number of restrain torsions.
getNumberOfRestraints() - Method in class ffx.potential.nonbonded.RestrainGroups: Get the number of group restraints.
getNumberOfSnapshots() - Method in class ffx.potential.parsers.BARFilter: Return the number of snapshots in the BAR file.
getNumberOfStretchBends() - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Get the number of StretchBends in this term.
getNumberOfStretchTorsions() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Get the number of StretchTorsions in this term.
getNumberOfSymOps() - Method in class ffx.crystal.SpaceGroup: Return the number of symmetry operators.
getNumberOfTerms() - Method in class ffx.potential.terms.AnglePotentialEnergy: Get the number of terms in this potential energy term.
getNumberOfTerms() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.BondPotentialEnergy: Get the number of terms in this potential energy term.
getNumberOfTerms() - Method in class ffx.potential.terms.EnergyTerm: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Get the number of terms in this potential energy term.
getNumberOfTerms() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get the number of BondedTerms in this term.
getNumberOfTerms() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Get the number of terms in this potential energy term.
getNumberOfTopologies(List<String>) - Method in class ffx.potential.cli.TopologyOptions: Validate the number of topologies.
getNumberOfTorsions() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get the number of Torsions in this term.
getNumberOfTorsionTorsions() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get the number of TorsionTorsions in this term.
getNumberOfUreyBradleys() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Get the number of UreyBradleys in this term.
getNumberOfVariables() - Method in class ffx.algorithms.dynamics.Barostat: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getNumberOfVariables() - Method in interface ffx.numerics.OptimizationInterface: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.ANIEnergy
getNumberOfVariables() - Method in class ffx.potential.DualTopologyEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.extended.ExtendedSystem
getNumberOfVariables() - Method in class ffx.potential.ForceFieldEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Get the number of variables.
getNumberOfVariables() - Method in class ffx.potential.openmm.OpenMMSystem: Get the number of variables.
getNumberOfVariables() - Method in class ffx.potential.QuadTopologyEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.SystemState: Get the number of variables.
getNumberOfVariables() - Method in class ffx.potential.XtalEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.realspace.RealSpaceEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.RefinementEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.ScaleBulkEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.ScaleBulkMinimize: getNumberOfVariables.
getNumberOfVariables() - Method in class ffx.xray.SigmaAEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.SigmaAMinimize: getNumberOfVariables.
getNumberOfVariables() - Method in class ffx.xray.SplineEnergy: Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.SplineMinimize: getNumberOfVariables.
getNumberOfVariables() - Method in class ffx.xray.XRayEnergy: Get the number of variables being operated on.
getNumBonds() - Method in class ffx.openmm.CustomBondForce: Get the number of bonds for which force field parameters have been defined.
getNumBonds() - Method in class ffx.openmm.CustomCentroidBondForce: Get the number of bonds for which force field parameters have been defined.
getNumBonds() - Method in class ffx.openmm.CustomCompoundBondForce: Get the number of bonds.
getNumBonds() - Method in class ffx.openmm.HarmonicBondForce: Get the number of bonds.
getNumBonds() - Method in class ffx.potential.bonded.Atom: Gets the number of atoms bonded to this Atom
getNumBoxes() - Method in class ffx.algorithms.cli.ManyBodyOptions: The number of boxes along X, Y, and Z (default: '3,3,3').
getNumCollectiveVariables() - Method in class ffx.openmm.CustomCVForce: Get the number of collective variables.
getNumComputations() - Method in class ffx.openmm.CustomIntegrator: Get the number of computation steps defined for this integrator.
getNumComputedValues() - Method in class ffx.openmm.CustomGBForce: Get the number of computed values.
getNumComputedValues() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of computed values.
getNumConstraints() - Method in class ffx.openmm.System: Get the number of constraints in the system.
getNumDegreesFrozen() - Method in interface ffx.numerics.Constraint: Returns the number of degrees of freedom this Constraint constrains.
getNumDegreesFrozen() - Method in class ffx.potential.constraint.CcmaConstraint: Returns the number of degrees of freedom this Constraint constrains.
getNumDegreesFrozen() - Method in class ffx.potential.constraint.SettleConstraint
getNumDegreesFrozen() - Method in class ffx.potential.constraint.ShakeChargeConstraint
getNumDihedrals() - Method in class ffx.potential.bonded.Atom: getNumDihedrals
getNumDonors() - Method in class ffx.openmm.CustomHbondForce: Get the number of donors.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.ATMForce: Get the number of energy parameter derivatives.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomAngleForce: Get the number of parameters with respect to which the derivative of the energy should be computed.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomBondForce: Get the number of parameters with respect to which the derivative of the energy should be computed.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomCentroidBondForce: Get the number of global parameters with respect to which the derivative of the energy should be computed.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomCompoundBondForce: Get the number of parameters with respect to which the derivative of the energy should be computed.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomCVForce: Get the number of energy parameter derivatives.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomGBForce: Get the number of parameters with respect to which the derivative of the energy should be computed.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of parameters with respect to which the derivative of the energy should be computed.
getNumEnergyParameterDerivatives() - Method in class ffx.openmm.CustomTorsionForce: Get the number of parameters with respect to which the derivative of the energy should be computed.
getNumEnergyTerms() - Method in class ffx.openmm.CustomGBForce: Get the number of energy terms.
getNumExceptions() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the number of exceptions.
getNumExceptions() - Method in class ffx.openmm.GayBerneForce: Get the number of exceptions.
getNumExceptions() - Method in class ffx.openmm.NonbondedForce: Get the number of exceptions.
getNumExclusions() - Method in class ffx.openmm.CustomGBForce: Get the number of exclusions.
getNumExclusions() - Method in class ffx.openmm.CustomHbondForce: Get the number of exclusions.
getNumExclusions() - Method in class ffx.openmm.CustomManyParticleForce: Get the number of exclusions.
getNumExclusions() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of exclusions.
getNumFaces() - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the number of faces in this hull.
getNumForces() - Method in class ffx.openmm.ATMForce: Get the number of forces.
getNumForces() - Method in class ffx.openmm.System: Get the number of forces in the system.
getNumFunctions() - Method in class ffx.openmm.CustomCentroidBondForce: Deprecated.
This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
getNumFunctions() - Method in class ffx.openmm.CustomCompoundBondForce: Deprecated.
This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
getNumFunctions() - Method in class ffx.openmm.CustomGBForce: Deprecated.
This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
getNumFunctions() - Method in class ffx.openmm.CustomHbondForce: Deprecated.
This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
getNumFunctions() - Method in class ffx.openmm.CustomNonbondedForce: Deprecated.
This method exists only for backward compatibility. Use getNumTabulatedFunctions() instead.
getNumGlobalParameters() - Method in class ffx.openmm.ATMForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomAngleForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomBondForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomCentroidBondForce: Get the number of global parameters that the interaction depends on.
getNumGlobalParameters() - Method in class ffx.openmm.CustomCompoundBondForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomCVForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomExternalForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomGBForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomHbondForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomManyParticleForce: Get the number of global parameters that the interaction depends on.
getNumGlobalParameters() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of global parameters.
getNumGlobalParameters() - Method in class ffx.openmm.CustomTorsionForce: Get the number of global parameters that the interaction depends on.
getNumGlobalParameters() - Method in class ffx.openmm.CustomVolumeForce: Get the number of global parameters that the energy depends on.
getNumGlobalVariables() - Method in class ffx.openmm.CustomIntegrator: Get the number of global variables that have been defined.
getNumGroups() - Method in class ffx.openmm.CustomCentroidBondForce: Get the number of particle groups that have been defined.
getNumGroupsPerBond() - Method in class ffx.openmm.CustomCentroidBondForce: Get the number of groups used to define each bond.
getNumIntegrators() - Method in class ffx.openmm.CompoundIntegrator: Get the number of Integrators that have been added to this CompoundIntegrator.
getNumInteractionGroups() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of interaction groups.
getNumLeaves() - Method in class ffx.potential.nonbonded.octree.OctreeCell
getNumMaps() - Method in class ffx.openmm.CMAPTorsionForce: Get the number of maps that have been defined.
getNumMultipoles() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the number of multipoles.
getNumParticles() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the number of particles in the force.
getNumParticles() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.amoeba.VdwForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the number of particles
getNumParticles() - Method in class ffx.openmm.ATMForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.CustomExternalForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.CustomGBForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.CustomManyParticleForce: Get the number of particles for which force field parameters have been defined.
getNumParticles() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.drude.DrudeForce: Get the number of particles for which force field parameters have been defined.
getNumParticles() - Method in class ffx.openmm.GayBerneForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.GBSAOBCForce: Get the number of particles in the force field.
getNumParticles() - Method in class ffx.openmm.NonbondedForce: Get the number of particles.
getNumParticles() - Method in class ffx.openmm.System: Get the number of particles in the system.
getNumParticles() - Method in class ffx.openmm.VirtualSite: Get the number of particles this virtual site depends on.
getNumParticlesPerBond() - Method in class ffx.openmm.CustomCompoundBondForce: Get the number of particles per bond.
getNumParticlesPerSet() - Method in class ffx.openmm.CustomManyParticleForce: Get the number of particles involved in each interaction.
getNumParticleTypes() - Method in class ffx.openmm.amoeba.VdwForce: Get the number of particle types.
getNumPerAcceptorParameters() - Method in class ffx.openmm.CustomHbondForce: Get the number of per-acceptor parameters.
getNumPerAngleParameters() - Method in class ffx.openmm.CustomAngleForce: Get the number of per-angle parameters.
getNumPerBondParameters() - Method in class ffx.openmm.CustomBondForce: Get the number of per-bond parameters.
getNumPerBondParameters() - Method in class ffx.openmm.CustomCentroidBondForce: Get the number of per-bond parameters that the interaction depends on.
getNumPerBondParameters() - Method in class ffx.openmm.CustomCompoundBondForce: Get the number of per-bond parameters.
getNumPerDofVariables() - Method in class ffx.openmm.CustomIntegrator: Get the number of per-DOF variables that have been defined.
getNumPerDonorParameters() - Method in class ffx.openmm.CustomHbondForce: Get the number of per-donor parameters.
getNumPerParticleParameters() - Method in class ffx.openmm.CustomExternalForce: Get the number of per-particle parameters.
getNumPerParticleParameters() - Method in class ffx.openmm.CustomGBForce: Get the number of per-particle parameters.
getNumPerParticleParameters() - Method in class ffx.openmm.CustomManyParticleForce: Get the number of per-particle parameters that the interaction depends on.
getNumPerParticleParameters() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of per-particle parameters.
getNumPerTorsionParameters() - Method in class ffx.openmm.CustomTorsionForce: Get the number of per-torsion parameters that the interaction depends on.
getNumPlatforms() - Static method in class ffx.openmm.Platform: Get the number of OpenMM Platforms.
getNumScreenedPairs() - Method in class ffx.openmm.drude.DrudeForce: Get the number of special interactions that should be calculated differently from other interactions.
getNumSharedVariables() - Method in class ffx.potential.DualTopologyEnergy: Returns the number of shared variables (3 * number of shared atoms).
getNumSharedVariables() - Method in class ffx.potential.QuadTopologyEnergy: Returns number of shared variables.
getNumSteps() - Method in class ffx.algorithms.cli.DynamicsOptions
getNumSymOps() - Method in class ffx.crystal.Crystal: Return the number of symmetry operators for this crystal.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomCentroidBondForce: Get the number of tabulated functions that have been defined.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomCompoundBondForce: Get the number of tabulated functions.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomCVForce: Get the number of tabulated functions.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomGBForce: Get the number of tabulated functions.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomHbondForce: Get the number of tabulated functions.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomIntegrator: Get the number of tabulated functions that have been defined.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomManyParticleForce: Get the number of tabulated functions that have been defined.
getNumTabulatedFunctions() - Method in class ffx.openmm.CustomNonbondedForce: Get the number of tabulated functions.
getNumThermostats() - Method in class ffx.openmm.NoseHooverIntegrator: Get the number of thermostats.
getNumTorsions() - Method in class ffx.openmm.CMAPTorsionForce: Get the number of CMAP torsion terms in the potential function
getNumTorsions() - Method in class ffx.openmm.CustomTorsionForce: Get the number of torsions for which force field parameters have been defined.
getNumTorsions() - Method in class ffx.openmm.PeriodicTorsionForce: Get the number of torsions in the force.
getNumTorsions() - Method in class ffx.openmm.RBTorsionForce: Get the number of torsions in the force.
getNumTorsionTorsionGrids() - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Get the number of torsion-torsion grids
getNumTorsionTorsions() - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Get the number of torsion-torsion terms in the potential function
getNumTypePairs() - Method in class ffx.openmm.amoeba.VdwForce: Get the number of type pairs.
getNumVertices() - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the number of vertices in this hull.
getNumWindows() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Gets the number of annealing windows (including repeat windows).
getNumWindows() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
getNumWindows() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
getNumWindows() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
getNXYZ() - Method in class ffx.xray.RefinementMinimize: get the number of xyz parameters being fit
getNXYZ() - Method in class ffx.xray.XRayEnergy: Get the number of xyz parameters being fit.
getObservationEnsembleAverages() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getObservationEnsembleUncertainties() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getOccupancy() - Method in class ffx.potential.bonded.Atom: Getter for the field occupancy.
getOccupancyAcceleration() - Method in class ffx.potential.bonded.Atom: Getter for the field occupancyAccelerationy.
getOccupancyGradient() - Method in class ffx.potential.bonded.Atom: Getter for the field occupancyGradient.
getOccupancyPreviousAcceleration() - Method in class ffx.potential.bonded.Atom: Getter for the field occupancyPreviousAccelerationy.
getOccupancyVelocity() - Method in class ffx.potential.bonded.Atom: Getter for the field occupancyVelocity.
getOffset() - Method in class ffx.potential.MolecularAssembly: Getter for the field offset.
getOffsetCYS(TitrationUtils.CysStates) - Method in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
getOffsetHIS(TitrationUtils.HisStates) - Method in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
getOffsetLYS(TitrationUtils.LysStates) - Method in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
getOmega(Residue) - Method in class ffx.potential.utils.GetProteinFeatures: Get the omega angle of a residue
getOneBound() - Method in class ffx.numerics.switching.BellCurveSwitch: Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.CompositeSwitch
getOneBound() - Method in class ffx.numerics.switching.ConstantSwitch: Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.LinearDerivativeSwitch: Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.MultiplicativeSwitch: Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.PowerSwitch: Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.SquaredTrigSwitch: Gets the one bound, where f(x) becomes one.
getOneBound() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: Gets the one bound, where f(x) becomes one.
getOnlyTitration() - Method in class ffx.algorithms.cli.ManyBodyOptions
getOpenMMState(int) - Method in class ffx.potential.openmm.OpenMMContext: Get an OpenMM State from the Context.
getOpenMMState(int) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Create an immutable OpenMM State.
getOpenMMState(int) - Method in class ffx.potential.openmm.OpenMMEnergy: Create an immutable OpenMM State.
getOpenMMState(int) - Method in interface ffx.potential.openmm.OpenMMPotential: Create an immutable OpenMM State.
getOpenMMVersion() - Static method in class ffx.openmm.Platform: Get the OpenMM version.
getOpposite() - Method in class ffx.numerics.quickhull.HalfEdge: Returns the half-edge opposite to this half-edge.
getOptimizationParameters() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Return the OST optimization information.
getOptimize() - Method in class ffx.algorithms.cli.DynamicsOptions: Getter for the field optimize.
getOptimumCoordinates() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters: The coordinates of the lowest energy structure found during optimization.
getOptimumEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters: getOptimumEnergy.
getOptimumRotamers() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return an integer array of optimized rotamers following rotamer optimization.
getOrder() - Method in enum class ffx.numerics.multipole.GKMultipoleOrder: Return the multipole order.
getOrigin() - Method in class ffx.realspace.RealSpaceRefinementData: Getter for the field origin.
getOriginToRot() - Method in class ffx.potential.MolecularAssembly: Getter for the field originToRot.
getOriginWeights(PointerByReference) - Method in class ffx.openmm.LocalCoordinatesSite: Get the weights used for computing the origin of the local coordinate system.
getOscillate() - Method in class ffx.ui.Trajectory: Getter for the field oscillate.
getOST() - Method in class ffx.algorithms.commands.test.RepexThermo
getOST() - Method in class ffx.algorithms.commands.Thermodynamics
getOST() - Method in class ffx.algorithms.thermodynamics.RepExOST
getOtherCluster(Cluster) - Method in class ffx.numerics.clustering.ClusterPair: Returns the opposite cluster of the provided one in this pair.
getOutOfPlaneBend(int) - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Get the OutOfPlaneBend at a given index.
getOutOfPlaneBendArray() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Get an array of OutOfPlaneBends in this term.
getOutOfPlaneBendList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Out-of-Plane Bends below the present MSNode.
getOutOfPlaneBendPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the OutOfPlaneBendPotentialEnergy.
getOutOfPlaneBends() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Get an unmodifiable view of the OutOfPlaneBends in this term.
getOutOfPlaneBendType(AtomType, AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField: getOutOfPlaneBendType
getOutOfPlaneBendType(String) - Method in class ffx.potential.parameters.ForceField: getOutOfPlaneBendType
getOutOfPlaneBendTypes() - Method in class ffx.potential.parameters.ForceField: Get OutOfPlaneBendTypes.
getOutOfPlaneEnergyString() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Get a string representation of the Out-of-Plane Bend energy expression.
getOutputStream() - Method in class edu.rit.pj.io.StreamFile: Open an output stream for writing this stream file.
getOutputStream(boolean) - Method in class edu.rit.pj.io.StreamFile: Open an output stream for writing this stream file.
getOverlapScale() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the overlap scale factors used for the GK calculation.
getPairClashThreshold() - Method in class ffx.algorithms.cli.ManyBodyOptions: The threshold for pruning clashes.
getPairwiseSchedule() - Method in class ffx.potential.nonbonded.NeighborList: Getter for the field pairwiseSchedule.
getParallelTeam() - Method in class ffx.potential.ForceFieldEnergy: Getter for the field parallelTeam.
getParallelTeam() - Method in class ffx.potential.MolecularAssembly: getParallelTeam.
getParallelTeam() - Method in class ffx.xray.DiffractionData: Getter for the field parallelTeam.
getParameter(Pointer) - Method in class ffx.openmm.Context: Get the value of an adjustable parameter defined by a Force object in the System.
getParameter(String) - Method in class ffx.openmm.Context: Get the value of an adjustable parameter defined by a Force object in the System.
getParameters() - Method in class ffx.openmm.Context: Get all adjustable parameters that have been defined by Force objects in the System, along with their current values.
getParameters() - Method in class ffx.openmm.State: Get the parameters.
getParamPath(String) - Method in class ffx.ui.KeywordPanel: getParamPath
getParent() - Method in class ffx.numerics.clustering.Cluster: Gets the parent cluster of this node, or null if this is the root.
getParent() - Method in class ffx.potential.bonded.ResidueState: Getter for the field parent.
getParentIndex() - Method in class ffx.potential.nonbonded.octree.OctreeCell
getParticle(int) - Method in class ffx.openmm.VirtualSite: Get the index of a particle this virtual site depends on.
getParticleExclusions(int) - Method in class ffx.openmm.amoeba.VdwForce: Get the particle exclusions.
getParticleMass(int) - Method in class ffx.openmm.System: Get the mass (in atomic mass units) of a particle.
getParticleParameters(int, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the force field parameters for a WCA dispersion particle.
getParticleParameters(int, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.GBSAOBCForce: Get the force field parameters for a particle.
getParticleParameters(int, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.NonbondedForce: Get the particle parameters.
getParticleParameters(int, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the force field parameters for a particle.
getParticleParameters(int, DoubleByReference, DoubleByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.GayBerneForce: Get the parameters for a particle.
getParticleParameters(int, DoubleByReference, PointerByReference, PointerByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, IntByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the nonbonded force parameters for a particle.
getParticleParameters(int, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference, IntByReference, IntByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.VdwForce: Get the particle parameters.
getParticleParameters(int, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.drude.DrudeForce: Get the parameters for a Drude particle.
getParticleParameters(int, IntByReference, DoubleArray) - Method in class ffx.openmm.CustomExternalForce: Get the parameters for a particle.
getParticleParameters(int, PointerByReference) - Method in class ffx.openmm.CustomNonbondedForce: Get the parameters for a particle.
getParticleParameters(int, PointerByReference, IntByReference) - Method in class ffx.openmm.CustomManyParticleForce: Get the parameters for a particle.
getParticleParameters(int, PointerByReference, IntBuffer) - Method in class ffx.openmm.CustomManyParticleForce: Get the parameters for a particle.
getParticleParameters(int, OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.ATMForce: Get the parameters for a particle
getParticleParameters(int, DoubleArray) - Method in class ffx.openmm.CustomGBForce: Get the parameters for a particle.
getParticleParameters(int, DoubleBuffer, PointerByReference, PointerByReference, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, IntBuffer, IntBuffer, IntBuffer, IntBuffer) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the nonbonded force parameters for a particle.
getParticleParameters(int, DoubleBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.GBSAOBCForce: Get the force field parameters for a particle.
getParticleParameters(int, DoubleBuffer, DoubleBuffer, IntBuffer, IntBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.GayBerneForce: Get the parameters for a particle.
getParticleParameters(int, IntBuffer, DoubleArray) - Method in class ffx.openmm.CustomExternalForce: Get the parameters for a particle.
getParticles() - Method in class ffx.openmm.RMSDForce: Get the indices of the particles to use when computing the RMSD.
getParticleTypeParameters(int, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.VdwForce: Get the particle type parameters.
getPDBHeaderString() - Method in class ffx.potential.ForceFieldEnergy: Create a PDB REMARK 3 string containing the potential energy terms.
getPDBRank(SpaceGroup) - Static method in class ffx.crystal.SpaceGroupInfo: PDB space group ranking (as of Feb. 2017).
getPerAcceptorParameterName(int) - Method in class ffx.openmm.CustomHbondForce: Get the name of a per-acceptor parameter.
getPerAngleParameterName(int) - Method in class ffx.openmm.CustomAngleForce: Get the name of a per-angle parameter.
getPerBondParameterName(int) - Method in class ffx.openmm.CustomBondForce: Get the name of a per-bond parameter.
getPerBondParameterName(int) - Method in class ffx.openmm.CustomCentroidBondForce: Get the name of a per-bond parameter.
getPerBondParameterName(int) - Method in class ffx.openmm.CustomCompoundBondForce: Get the name of a per-bond parameter.
getPerDofVariable(int, PointerByReference) - Method in class ffx.openmm.CustomIntegrator: Get the values of a per-DOF variable.
getPerDofVariableByName(String, PointerByReference) - Method in class ffx.openmm.CustomIntegrator: Get the values of a per-DOF variable, specified by name.
getPerDofVariableName(int) - Method in class ffx.openmm.CustomIntegrator: Get the name of a per-DOF variable.
getPerDonorParameterName(int) - Method in class ffx.openmm.CustomHbondForce: Get the name of a per-donor parameter.
getPerfectRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Return perfect Born radii read in as keywords, or base radii if perfect radii are not available.
getPerfectRadii() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion: Return perfect Born radii read in as keywords, or base radii if perfect radii are not available.
getPeriod() - Method in class ffx.numerics.switching.SquaredTrigSwitch: Get the repeating period of this switch.
getPeriodComparisonMBAR(MultistateBennettAcceptanceRatio.SeedType, double) - Method in class ffx.numerics.estimator.MBARFilter: 10% of the total samples at different time points.
getPeriodic() - Method in class ffx.openmm.TabulatedFunction: Get the periodicity status of the tabulated function.
getPeriodicBoxVectors() - Method in class ffx.openmm.State: Get the periodic box vectors.
getPeriodicBoxVectors() - Method in class ffx.potential.openmm.OpenMMState: Read the periodic lattice vectors from a state.
getPeriodicBoxVolume() - Method in class ffx.openmm.State: Get the periodic box volume.
getPeriodicBoxVolume() - Method in class ffx.potential.openmm.OpenMMState: Get the periodic box volume.
getPermanentChargeCorrectionEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPermanentChargeCorrectionEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
getPermanentEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
getPermanentEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPermanentEnergy() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
getPermanentInteractions() - Method in class ffx.potential.ForceFieldEnergy: getPermanentInteractions.
getPermanentMultipoleEnergy() - Method in class ffx.potential.ForceFieldEnergy: Getter for the field permanentMultipoleEnergy.
getPermanentReciprocalEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
getPermanentSelfEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
getPermRealEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPermRecipEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPermSelfEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: getPermSelfEnergy.
getPermTime(int) - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
getPermutationMode() - Method in class ffx.openmm.CustomManyParticleForce: Get the permutation mode.
getPerParticleParameterName(int) - Method in class ffx.openmm.CustomExternalForce: Get the name of a per-particle parameter.
getPerParticleParameterName(int) - Method in class ffx.openmm.CustomGBForce: Get the name of a per-particle parameter.
getPerParticleParameterName(int) - Method in class ffx.openmm.CustomManyParticleForce: Get the name of a per-particle parameter.
getPerParticleParameterName(int) - Method in class ffx.openmm.CustomNonbondedForce: Get the name of a per-particle parameter.
getPerTorsionParameterName(int) - Method in class ffx.openmm.CustomTorsionForce: Get the name of a per-torsion parameter.
getPerturbationEnergy(Context, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.ATMForce: Returns the current perturbation energy.
getPerturbationEnergy(Context, DoubleBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.ATMForce: Returns the current perturbation energy.
getPH() - Method in class ffx.algorithms.optimize.RotamerOptimization: Get the enviroment pH
getPhi(Residue) - Method in class ffx.potential.utils.GetProteinFeatures: Get the phi angle of a residue
getPhiPsiList() - Method in class ffx.potential.bonded.Polymer: Get lists of the phi and psi torsions.
getPHRestraint() - Method in class ffx.algorithms.cli.ManyBodyOptions
getPHRestraint() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return the K in the harmonic pH restraint
getPhScale() - Method in class ffx.algorithms.dynamics.PhReplicaExchange: Get the pH scale array.
getPicking() - Method in class ffx.ui.GraphicsPicking: Getter for the field picking.
getPicking() - Method in class ffx.ui.MainMenu: getPicking
getPickMode() - Method in class ffx.ui.behaviors.PickOrbitBehavior: Return the pickMode component of this PickTranslateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickPropertiesBehavior: getPickMode
getPickMode() - Method in class ffx.ui.behaviors.PickRotateBehavior: Return the pickMode component of this PickRotateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickSelectionBehavior: Return the pickMode component of this PickRotateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickTranslateBehavior: Return the pickMode component of this PickTranslateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickZoomBehavior: Return the pickMode component of this PickTranslateBehavior.
getPiOrbitalTorsion(int) - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get the PiOrbitalTorsion at a given index.
getPiOrbitalTorsionArray() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get an array of PiOrbitalTorsions in this term.
getPiOrbitalTorsionEnergyString() - Static method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy
getPiOrbitalTorsionList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Pi-Orbital Torsions below the present MSNode.
getPiOrbitalTorsionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the PiOrbitalTorsionPotentialEnergy.
getPiOrbitalTorsions() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Get an unmodifiable view of the PiOrbitalTorsions in this term.
getPiOrbitalTorsionType(AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField: getPiOrbitalTorsionType
getPiOrbitalTorsionType(String) - Method in class ffx.potential.parameters.ForceField: getPiOrbitalTorsionType
getPiOrbitalTorsionTypes() - Method in class ffx.potential.parameters.ForceField: Get PiOrbitalTorsions.
getPjHost() - Static method in class edu.rit.pj.PJProperties: Determine the host name of the Job Scheduler Daemon to use when running a cluster parallel program.
getPjJobTime() - Static method in class edu.rit.pj.PJProperties: Determine the maximum amount of time (seconds) the job is allowed to run when running a cluster parallel program.
getPjJvmFlags() - Static method in class edu.rit.pj.PJProperties: Determine the JVM flags to include on the Java command line when running a backend process in a cluster parallel program.
getPjNn() - Static method in class edu.rit.pj.PJProperties: Determine the number of backend nodes in a parallel program.
getPjNp() - Static method in class edu.rit.pj.PJProperties: Determine the number of processes in a parallel program.
getPjNt() - Static method in class edu.rit.pj.PJProperties: Determine the number of CPUs per process in a parallel program.
getPjPort() - Static method in class edu.rit.pj.PJProperties: Determine the port number of the Job Scheduler Daemon to use when running a cluster parallel program.
getPjPrng() - Static method in class edu.rit.pj.PJProperties: Determine the fully-qualified class name of the default pseudorandom number generator (PRNG) class.
getPjSchedule() - Static method in class edu.rit.pj.PJProperties: Determine the schedule for a parallel loop in an SMP parallel program.
getPjVt() - Static method in class edu.rit.pj.PJProperties: Determine whether a ParallelTeam should use virtual threads.
getPlatform() - Method in class ffx.openmm.Context: Get the Platform being used for calculations.
getPlatform() - Method in class ffx.potential.ForceFieldEnergy: Gets the Platform associated with this force field energy.
getPlatform() - Method in class ffx.potential.openmm.OpenMMEnergy: Gets the Platform associated with this force field energy.
getPlatform(int) - Static method in class ffx.openmm.Platform: Get a registered platform by index.
getPlatform_1(String) - Static method in class ffx.openmm.Platform: Get a registered platform by name.
getPluginLoadFailures() - Static method in class ffx.openmm.Platform: Get the plugin load failures.
getPmeBSplineOrder() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the PME B-spline order.
getPmeGridDimensions() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the PME grid dimensions.
getPmeNode() - Method in class ffx.potential.ForceFieldEnergy: getPmeNode.
getPMEParameters(DoubleByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the PME parameters.
getPMEParameters(DoubleByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the parameters to use for PME calculations.
getPMEParameters(DoubleBuffer, IntBuffer, IntBuffer, IntBuffer) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the PME parameters.
getPMEParametersInContext(Context, DoubleByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the PME parameters in context.
getPMEParametersInContext(Context, DoubleByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the PME parameters in the context.
getPMEParametersInContext(Context, DoubleBuffer, IntBuffer, IntBuffer, IntBuffer) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the PME parameters in context.
getPoint() - Method in class ffx.potential.utils.Clustering.Conformation
getPointer() - Method in class ffx.openmm.amoeba.DoubleArray3D: Get the pointer to the array.
getPointer() - Method in class ffx.openmm.BondArray: Get the pointer to the bond array.
getPointer() - Method in class ffx.openmm.Context: Get the pointer to the context.
getPointer() - Method in class ffx.openmm.DoubleArray: Get the pointer to the array.
getPointer() - Method in class ffx.openmm.Force: Get the pointer to the OpenMM Force.
getPointer() - Method in class ffx.openmm.IntArray: Get the pointer to the array.
getPointer() - Method in class ffx.openmm.Integrator: Get the OpenMM Integrator pointer.
getPointer() - Method in class ffx.openmm.IntSet: Get the pointer to the set.
getPointer() - Method in class ffx.openmm.MinimizationReporter: Pointer to the reporter.
getPointer() - Method in class ffx.openmm.Platform: Get the OpenMM Platform pointer.
getPointer() - Method in class ffx.openmm.State: Get the pointer to the state.
getPointer() - Method in class ffx.openmm.StringArray: Get the pointer to the String Array.
getPointer() - Method in class ffx.openmm.System: Get the pointer to the system.
getPointer() - Method in class ffx.openmm.TabulatedFunction: Get the pointer to the OpenMM TabulatedFunction.
getPointer() - Method in class ffx.openmm.Vec3Array: Get the pointer to the vec3 array pointer.
getPointer() - Method in class ffx.openmm.VirtualSite: Get the pointer to the OpenMM VirtualSite.
getPolarEps() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPolarGeom(int) - Static method in class ffx.potential.bonded.RendererCache: getPolarGeom
getPolarityAndAcidityChange(List<String>, boolean, boolean) - Method in class ffx.potential.utils.GetProteinFeatures: Get the polarity and acidity changes
getPolarizability(Atom, double, double, double) - Method in class ffx.potential.parameters.TitrationUtils
getPolarizabilityTautomerDeriv(Atom, double, double) - Method in class ffx.potential.parameters.TitrationUtils
getPolarizabilityTitrationDeriv(Atom, double, double) - Method in class ffx.potential.parameters.TitrationUtils
getPolarization11() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPolarization12() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPolarization13() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPolarizationEnergy() - Method in class ffx.potential.ForceFieldEnergy: Getter for the field polarizationEnergy.
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Getter for the field polarizationEnergy.
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion: Return the final polarization energy.
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
getPolarizationType() - Method in class ffx.openmm.amoeba.MultipoleForce: Get the polarization type.
getPolarizationType() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPolarizeType() - Method in class ffx.potential.bonded.Atom: Getter for the field polarizeType.
getPolarizeType(int) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Get the PolarizeType for Atom i.
getPolarizeType(String) - Method in class ffx.potential.parameters.ForceField: getPolarizeType
getPolarizeTypes() - Method in class ffx.potential.parameters.ForceField: Get PolarizeTypes.
getPolyCoeff(double[]) - Method in class ffx.potential.utils.LoopClosure: Get Polynomial Coefficient.
getPolymer(Character, String, boolean) - Method in class ffx.potential.MolecularAssembly: getPolymer
getPopulationArray() - Method in class ffx.algorithms.commands.GenZ
getPopulationBoltzmann() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return the Protonated Boltzmann for all sites
getPopulationStandardDeviation() - Method in class ffx.numerics.math.RunningStatistics: Get the population standard deviations.
getPopulationVariance() - Method in class ffx.numerics.math.RunningStatistics: Get the population variance.
getPositions() - Method in class ffx.openmm.State: Get the positions.
getPositions(double[]) - Method in class ffx.potential.openmm.OpenMMState: The position array contains the OpenMM atomic position information for all atoms.
getPotential() - Method in class ffx.algorithms.commands.GenZ: Returns the potential energy of the active assembly.
getPotential() - Method in class ffx.algorithms.commands.ManyBody: Returns the potential energy of the active assembly.
getPotential() - Method in class ffx.algorithms.commands.test.RepexThermo
getPotential() - Method in class ffx.algorithms.commands.Thermodynamics
getPotential() - Method in class ffx.algorithms.mc.MolecularMC: Returns the associated Potential.
getPotential() - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Get the Potential in use.
getPotential() - Method in class ffx.potential.openmm.OpenMMSystem: Get the Potential in use.
getPotentialEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Get the system potential energy.
getPotentialEnergy() - Method in class ffx.algorithms.mc.MDMove: getPotentialEnergy.
getPotentialEnergy() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: getPotentialEnergy.
getPotentialEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: getPotentialEnergy.
getPotentialEnergy() - Method in class ffx.openmm.State: Get the potential energy.
getPotentialEnergy() - Method in class ffx.potential.MolecularAssembly: Getter for the field potentialEnergy.
getPotentialEnergy() - Method in class ffx.potential.openmm.OpenMMState: Get the potential energy.
getPotentialEnergy() - Method in class ffx.potential.SystemState: Get the potential energy.
getPotentialFunction() - Method in class ffx.openmm.amoeba.VdwForce: Get the potential function.
getPotentialObject() - Method in class ffx.algorithms.commands.Dynamics
getPotentialObject() - Method in class ffx.algorithms.commands.test.FindRestraints: Get the potential object.
getPotentialObject() - Method in class ffx.algorithms.commands.test.PhDynamics
getPotentials() - Method in class ffx.algorithms.cli.AlgorithmsCommand: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.AnalyzeNEQ: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.Anneal: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.BAR: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.Cluster: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.Dynamics: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.ForEachFile
getPotentials() - Method in class ffx.algorithms.commands.Histogram: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.ManyBody: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.MBAR: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.Minimize: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.MinimizeCrystals: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.MinimizeOpenMM: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.MutatePDB: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.SaveRotamers
getPotentials() - Method in class ffx.algorithms.commands.SortArc
getPotentials() - Method in class ffx.algorithms.commands.Superpose
getPotentials() - Method in class ffx.algorithms.commands.SuperposeCrystals
getPotentials() - Method in class ffx.algorithms.commands.test.OSTGradient: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.test.PhDynamics: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.algorithms.commands.test.RepexThermo
getPotentials() - Method in class ffx.algorithms.commands.Thermodynamics
getPotentials() - Method in class ffx.algorithms.commands.TorsionScan
getPotentials() - Method in class ffx.potential.cli.PotentialCommand: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.potential.commands.Cart2Frac
getPotentials() - Method in class ffx.potential.commands.Energy
getPotentials() - Method in class ffx.potential.commands.Frac2Cart
getPotentials() - Method in class ffx.potential.commands.ImportCIF
getPotentials() - Method in class ffx.potential.commands.MoveIntoUnitCell
getPotentials() - Method in class ffx.potential.commands.PhEnergy
getPotentials() - Method in class ffx.potential.commands.PrepareSpaceGroups
getPotentials() - Method in class ffx.potential.commands.Solvator
getPotentials() - Method in class ffx.potential.commands.test.Gradient
getPotentials() - Method in class ffx.potential.commands.test.LambdaGradient
getPotentials() - Method in class ffx.potential.commands.test.PhGradient
getPotentials() - Method in class ffx.potential.commands.Timer
getPotentials() - Method in class ffx.realspace.commands.Anneal
getPotentials() - Method in class ffx.realspace.commands.Dynamics
getPotentials() - Method in class ffx.realspace.commands.ManyBody
getPotentials() - Method in class ffx.realspace.commands.test.Alchemical
getPotentials() - Method in class ffx.realspace.commands.test.LambdaGradient
getPotentials() - Method in class ffx.xray.commands.Anneal
getPotentials() - Method in class ffx.xray.commands.AverageMTZ
getPotentials() - Method in class ffx.xray.commands.CIFtoMTZ
getPotentials() - Method in class ffx.xray.commands.ComputeFc
getPotentials() - Method in class ffx.xray.commands.Deuterate
getPotentials() - Method in class ffx.xray.commands.Dynamics
getPotentials() - Method in class ffx.xray.commands.GenZ
getPotentials() - Method in class ffx.xray.commands.ManyBody
getPotentials() - Method in class ffx.xray.commands.Minimize
getPotentials() - Method in class ffx.xray.commands.ModelvsData
getPotentials() - Method in class ffx.xray.commands.MTZInfo
getPotentials() - Method in class ffx.xray.commands.test.Alchemical
getPotentials() - Method in class ffx.xray.commands.test.LambdaGradient: Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.xray.commands.Timer: Returns a List of all Potential objects associated with this script.
getPPI(Residue) - Method in class ffx.potential.utils.GetProteinFeatures
getPreconditionerCounts() - Method in class ffx.potential.nonbonded.pme.PCGSolver: Number of neighbors when applying the preconditioner.
getPreconditionerCutoff() - Method in class ffx.potential.nonbonded.pme.PCGSolver: Get the preconditioner cutoff.
getPreconditionerEwald() - Method in class ffx.potential.nonbonded.pme.PCGSolver: Get the preconditioner Ewald coefficient.
getPreconditionerLists() - Method in class ffx.potential.nonbonded.pme.PCGSolver: Neighbor lists when applying the preconditioner.
getPreconditionerMode() - Method in class ffx.potential.nonbonded.pme.PCGSolver: Get the preconditioner mode.
getPreconditionerScale() - Method in class ffx.potential.nonbonded.pme.PCGSolver: Get the preconditioner matrix diagonal scale factor.
getPressure() - Method in class ffx.algorithms.cli.BarostatOptions: -p or --npt Specify use of a Monte Carlo Barostat at the given pressure (default 0 = constant volume).
getPressure() - Method in class ffx.algorithms.dynamics.Barostat: Gets the pressure of this Barostat in atm.
getPrev() - Method in class ffx.numerics.quickhull.HalfEdge: Gets the value of the previous edge adjacent (clockwise) to this one within the triangle.
getPreviousAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in interface ffx.numerics.Potential: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
getPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field previousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
getPreviousAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.XtalEnergy: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy: getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.xray.XRayEnergy: getPreviousAcceleration.
getPreviousResidue() - Method in class ffx.potential.bonded.Residue: Returns the Residue bonded to this Residue at this Residue's 5' or N-terminal end.
getPrintInt() - Method in class ffx.algorithms.cli.BarostatOptions: --bpi or --barostatPrintInterval Sets the number of Barostat MC cycles between print statements.
getPrintOnFailure() - Method in class ffx.xray.RefinementEnergy: Getter for the field printOnFailure.
getPrintWriter() - Method in class edu.rit.http.HttpResponse: Obtain the print writer for writing the entity body to this HTTP response.
getProbe() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
getProbeRadius() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the probe radius.
getProbeRadius() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the probe radius (typically 1.4 Angstroms).
getPropagateLambda() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: If true, the Lambda extended system particle is propagated using Langevin dynamics.
getProperties() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's Java system properties.
getProperties() - Method in class ffx.potential.MolecularAssembly: Getter for the field properties.
getProperties() - Method in class ffx.potential.parameters.ForceField: Getter for the field properties.
getProperties() - Method in interface ffx.potential.parsers.FileOpener: getProperties.
getProperties() - Method in class ffx.potential.utils.PotentialsFileOpener: getProperties.
getProperties() - Method in class ffx.ui.FFXSystem: Getter for the field properties.
getProperties() - Method in class ffx.ui.UIFileOpener: Returns the properties of the hierarchy's active FFXSystem.
getPropertyDefaultValue(String) - Method in class ffx.openmm.Platform: Get the default value of a platform property.
getPropertyNames() - Method in class ffx.openmm.Platform: Get the names of all platform properties.
getPropertyValue(Context, String) - Method in class ffx.openmm.Platform: Get the value of a context-specific platform property.
GetProteinFeatures - Class in ffx.potential.utils
GetProteinFeatures(MolecularAssembly) - Constructor for class ffx.potential.utils.GetProteinFeatures
getProteinLibrary(String) - Static method in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary: Parses a String input to a ProteinLibrary.
getProtonatedAssemblies() - Method in class ffx.algorithms.optimize.TitrationManyBody
getProtonatedAssembly() - Method in class ffx.algorithms.optimize.TitrationManyBody
getProtonationPopulations(Residue[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Return the populations of the titratable residue states and print
getPrune() - Method in class ffx.algorithms.cli.ManyBodyOptions: Prune no clashes (0), only single clashes (1), or all clashes (2).
getPsi(Residue) - Method in class ffx.potential.utils.GetProteinFeatures: Get the psi angle of a residue
getQuadrupole() - Method in class ffx.potential.parameters.MultipoleType: Getter for the field quadrupole.
getR() - Method in class ffx.potential.nonbonded.octree.OctreeCell: Returns cell radius
getR() - Method in class ffx.xray.CrystalStats: Simply return the current R value.
getr_o() - Method in class ffx.potential.bonded.SturmMethod: Used only in JUnit testing.
getRA() - Method in class ffx.potential.utils.Loop: Get the rA coordinates.
getRadii() - Method in class ffx.potential.nonbonded.implicit.GaussVol: Get the radii.
getRandomCartTranslation() - Method in class ffx.crystal.Crystal: Create a random Cartesian translation vector.
getRandomNumberSeed() - Method in class ffx.openmm.AndersenThermostat: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.BrownianIntegrator: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.CustomIntegrator: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.drude.DrudeIntegrator: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.LangevinMiddleIntegrator: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.MonteCarloBarostat: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Get the random number seed.
getRandomNumberSeed() - Method in class ffx.openmm.VariableLangevinIntegrator: Get the random number seed.
getRandomSymOp() - Method in class ffx.algorithms.cli.RandomUnitCellOptions: A random SymOp with translation range -X/2 ..
getRandomUnitCell() - Method in class ffx.algorithms.cli.RandomUnitCellOptions: Random unit cell parameters will be used achieve the specified density (g/cc) (no default density).
getRank() - Method in class edu.rit.pj.cluster.JobBackend: Obtain the rank of this backend process in this job.
getRank() - Method in class ffx.algorithms.ParallelStateEnergy: Get the rank of this process.
getRank() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: For MPI parallel jobs, return the rank of this process.
getRate() - Method in class ffx.ui.Trajectory: getRate
getRawNBodyDistance(int...) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Returns the RMS distance between an arbitrary set of rotamers.
getRC() - Method in class ffx.potential.utils.Loop: Get the rC coordinates.
getrCluster() - Method in class ffx.numerics.clustering.ClusterPair: Gets the right cluster.
getRCrystalStat() - Method in class ffx.xray.DiffractionData: Return R value for OST x-ray minimization.
getRealSpaceFileFilter() - Method in class ffx.realspace.parsers.RealSpaceFile: Getter for the field realSpaceFileFilter.
getRealSpaceGradient(double[]) - Method in class ffx.realspace.RealSpaceData: Getter for the field realSpaceGradient.
getRealSpacePermTime() - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
getReciprocalSpace() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getRectMaxX() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Computes the maximal X value of this component and its children in model space.
getRectMaxY() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Computes the maximal Y value of this component and its children in model space.
getRectMinX() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Computes the minimal X value of this component and its children in model space.
getRectMinY() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Computes the minimal Y value of this component and its children in model space.
getReducedPotentials() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyBooleanBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyByteBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyCharacterBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyDoubleBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyFloatBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyLongBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyObjectBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyShortBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.Buf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedBooleanBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedByteArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedByteBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedCharacterBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedDoubleBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedFloatBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedLongArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedLongBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedObjectBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedShortArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedShortBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1: Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf: Create a buffer for performing parallel reduction using the given binary operation.
getReductionIndex() - Method in class ffx.potential.nonbonded.VanDerWaals: Get the reduction index.
getRedX() - Method in class ffx.potential.bonded.Atom: Gets the reduced x coordinate (van der Waals center).
getRedXYZ() - Method in class ffx.potential.bonded.Atom: getRedXYZ
getRedXYZ(double[]) - Method in class ffx.potential.bonded.Atom: getRedXYZ
getRedY() - Method in class ffx.potential.bonded.Atom: Gets the reduced y coordinate (van der Waals center).
getRedZ() - Method in class ffx.potential.bonded.Atom: Gets the reduced z coordinate (van der Waals center).
getRefEnergy() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return reference energy for partition function boltzmann weights
getReferenceAtom() - Method in class ffx.potential.bonded.Residue: Returns a reference Atom for a Residue, primarily intended for rough distance calculations.
getReferencePositions() - Method in class ffx.openmm.RMSDForce: Get the reference positions to compute the deviation from.
getRefinementData() - Method in class ffx.realspace.RealSpaceData: Getter for the field refinementData.
getRefinementData() - Method in class ffx.xray.DiffractionData: Getter for the field refinementData.
getRefinementMode() - Method in class ffx.realspace.RealSpaceEnergy: Getter for the field refinementMode.
getRefinementMode() - Method in class ffx.xray.XRayEnergy: Getter for the field refinementMode.
getRefinementModel() - Method in class ffx.realspace.RealSpaceData: getRefinementModel
getRefinementModel() - Method in interface ffx.xray.DataContainer: getRefinementModel
getRefinementModel() - Method in class ffx.xray.DiffractionData: getRefinementModel
getReflectionList() - Method in class ffx.xray.DiffractionData: Getter for the field reflectionList.
getReflectionList(File) - Method in class ffx.xray.parsers.CIFFilter: Get reflection information from a reflection file.
getReflectionList(File) - Method in class ffx.xray.parsers.CNSFilter: Get reflection information from a reflection file.
getReflectionList(File) - Method in interface ffx.xray.parsers.DiffractionFileFilter: Get reflection information from a reflection file.
getReflectionList(File) - Method in class ffx.xray.parsers.MTZFilter: Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in class ffx.xray.parsers.CIFFilter: Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in class ffx.xray.parsers.CNSFilter: Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in interface ffx.xray.parsers.DiffractionFileFilter: Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in class ffx.xray.parsers.MTZFilter: Get reflection information from a reflection file.
getRelativeCollisionFrequency(int) - Method in class ffx.openmm.NoseHooverIntegrator: Get the relative collision frequency for a thermostat.
getRelativeSolvationTypes() - Method in class ffx.potential.parameters.ForceField: Getter for the field relativeSolvationTypes.
getRelativeTemperature(int) - Method in class ffx.openmm.NoseHooverIntegrator: Get the relative temperature for a thermostat.
getRemarkLines() - Method in class ffx.potential.parsers.PDBFilter: Returns all the remark lines found by the last readFile call.
getRemarkLines() - Method in class ffx.potential.parsers.SystemFilter: Gets all remark lines read by the last readFile or readNext call.
getRemarkLines() - Method in class ffx.potential.parsers.XPHFilter
getRemarkLines() - Method in class ffx.potential.parsers.XYZFilter
getRemoveCenterOfMassMotion() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Getter for the field removeCenterOfMassMotion.
getRepEx() - Method in class ffx.algorithms.cli.RepExOptions
getRepexFrequency() - Method in class ffx.algorithms.cli.RepexOSTOptions: The interval (in psec) between replica exchange attempts.
getReplicaSteps() - Method in class ffx.algorithms.cli.RepExOptions
getReport() - Method in class ffx.algorithms.cli.DynamicsOptions: The thermodynamics reporting frequency in picoseconds (0.1 psec default).
getReporter() - Method in class ffx.algorithms.commands.BAR: Obtain the Free Energy Difference reporter for this class.
getReportFrequency(int) - Method in class ffx.algorithms.cli.DynamicsOptions: The molecular dynamics reporting frequency in steps.
getResetNumSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions: Getter for the field resetNumSteps.
getResetStatistics() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
getResidue() - Method in class ffx.potential.bonded.RotamerLibrary.RotamerGuess
getResidue(int) - Method in class ffx.potential.bonded.Polymer: getResidue
getResidue(String, int, boolean) - Method in class ffx.potential.bonded.Polymer: getResidue
getResidue(String, int, boolean, Residue.ResidueType) - Method in class ffx.potential.bonded.Polymer: getResidue
getResidueCount() - Method in class ffx.potential.bonded.MultiResidue: getResidueCount.
getResidueDistance(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks the distance matrix, finding the shortest distance between the closest rotamers of two residues.
getResidueList() - Method in class ffx.potential.MolecularAssembly: getResidueList
getResidueName() - Method in class ffx.potential.bonded.Atom: Get the residue name
getResidueName() - Method in class ffx.potential.bonded.Molecule: Getter for the field residueName.
getResidueNumber() - Method in class ffx.potential.bonded.Atom: getResidueNumber
getResidueNumber() - Method in class ffx.potential.bonded.Molecule: getResidueNumber
getResidueNumber() - Method in class ffx.potential.bonded.Residue: Returns this Residue's sequence number.
getResidues() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return the residue list.
getResidues() - Method in class ffx.potential.bonded.Polymer: getResidues
getResiduesAsList() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Returns a copy of the ArrayList of residues.
getResidueSurfaceArea(Residue) - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
getResidueType() - Method in class ffx.potential.bonded.Residue: Getter for the field residueType.
getResName() - Method in class ffx.potential.parameters.RelativeSolvationType: Getter for the field resName.
getResolution() - Method in class ffx.potential.bonded.Atom: Getter for the field resolution.
getResolution() - Method in class ffx.xray.DiffractionData: Getter for the field resolution.
getResolution(File, Crystal) - Method in class ffx.xray.parsers.CIFFilter: Attempt to determine resolution of reflection file.
getResolution(File, Crystal) - Method in class ffx.xray.parsers.CNSFilter: Attempt to determine resolution of reflection file.
getResolution(File, Crystal) - Method in interface ffx.xray.parsers.DiffractionFileFilter: Attempt to determine resolution of reflection file.
getResolution(File, Crystal) - Method in class ffx.xray.parsers.MTZFilter: Attempt to determine resolution of reflection file.
getResourceFile(String) - Method in class ffx.algorithms.misc.AlgorithmsTest: Get a resource file from the classpath.
getResourceFile(String) - Method in class ffx.potential.utils.PotentialTest: Get a resource file from the classpath.
getResourcePath(String) - Method in class ffx.algorithms.misc.AlgorithmsTest: Get a resource file from the classpath.
getResourcePath(String) - Method in class ffx.potential.utils.PotentialTest: Get a resource file from the classpath.
getRestartColumn() - Method in class ffx.potential.parsers.DistanceMatrixFilter: Get the number of columns in the last row that was read in.
getRestartFile() - Method in class ffx.algorithms.cli.ManyBodyOptions: Gets the restart file created during rotamer optimization.
getRestartFile() - Method in class ffx.algorithms.optimize.RotamerOptimization: Returns the restart file.
getRestartRow() - Method in class ffx.potential.parsers.DistanceMatrixFilter: Get the number of rows read in.
getRestrainDistance(int) - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Get the RestrainDistance at a given index.
getRestrainDistanceArray() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Get an array of RestrainDistances in this term.
getRestrainDistancePotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the RestrainDistancePotentialEnergy.
getRestrainDistances() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Get an unmodifiable view of the RestrainDistances in this term.
getRestrainDistances(BondType.BondFunction) - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Returns a list of restraint distances filtered by the specified bond function.
getRestrainGroups() - Method in class ffx.potential.ForceFieldEnergy: Getter for the RestrainGroup field.
getRestrainMode() - Method in class ffx.potential.ForceFieldEnergy
getRestrainPosition(int) - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Get the RestrainPosition at a given index.
getRestrainPositionArray() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Get an array of RestrainPositions in this term.
getRestrainPositionEnergyString() - Static method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Get the mathematical form of the Restrain Position interaction.
getRestrainPositionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the RestrainPositionPotentialEnergy.
getRestrainPositions() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Get an unmodifiable view of the RestrainPositions in this term.
getRestrainTorsion(int) - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Get a restrain torsion at an index.
getRestrainTorsionArray() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Get an array of restrain torsions.
getRestrainTorsionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the RestrainTorsionPotentialEnergy.
getRestrainTorsions() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Get an unmodifiable view of restrain torsions.
getReturnValue() - Method in class ffx.ui.FFXExec: Getter for the field returnValue.
getRmin() - Method in class ffx.potential.nonbonded.VanDerWaalsForm: Return the Rmin value for each class.
getRminh() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the water hydrogen radius parameter.
getRmino() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the water oxygen radius parameter.
getRMSD() - Method in class ffx.potential.bonded.RotamerLibrary.RotamerGuess
getRMSD() - Method in class ffx.potential.terms.EnergyTerm: Get the RMSD for this term.
getRMSGradient() - Method in class ffx.algorithms.commands.Minimize: Get the final RMS gradient after minimization.
getRMSGradient() - Method in class ffx.algorithms.optimize.Minimize: getRMSGradient.
getRMSGradient() - Method in class ffx.algorithms.optimize.PhMinimize: getRMSGradient.
getRN() - Method in class ffx.potential.utils.Loop: Get the rN coordinates.
getRootCluster() - Method in class ffx.numerics.clustering.HierarchyBuilder: Returns the root cluster if the hierarchy is complete.
getRotamer() - Method in class ffx.potential.bonded.Residue: Get the current rotamer.
getRotamer() - Method in class ffx.potential.bonded.RotamerLibrary.RotamerGuess
getRotamerLibrary(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
getRotamerPhBias() - Method in class ffx.potential.bonded.Rotamer
getRotamerPhBias(AminoAcidUtils.AminoAcid3) - Method in class ffx.potential.parameters.TitrationUtils
getRotamers() - Method in class ffx.potential.bonded.MultiResidue: Return all currently set rotamers.
getRotamers() - Method in class ffx.potential.bonded.Residue: Return all currently set rotamers.
getRotamers(AminoAcidUtils.AminoAcid3) - Method in class ffx.potential.bonded.RotamerLibrary: Return an array of Rotamers for the given amino acid.
getRotamers(AminoAcidUtils.AminoAcid3, TitrationUtils) - Method in class ffx.potential.bonded.RotamerLibrary: Return an array of Rotamers for the given amino acid.
getRotamers(NucleicAcidUtils.NucleicAcid3) - Method in class ffx.potential.bonded.RotamerLibrary: Return an array of Rotamers for the given nucleic acid.
getRotationMatrix(MultipoleType.MultipoleFrameDefinition, double[], double[][]) - Static method in class ffx.potential.parameters.MultipoleType: Return the rotation matrix for the local to lab frame.
getRotationMatrix(MultipoleType.MultipoleFrameDefinition, double[], double[][], double[][]) - Static method in class ffx.potential.parameters.MultipoleType: Return the rotation matrix for the local to lab frame.
getRowCount() - Method in class edu.rit.io.DoubleMatrixFile: Returns the number of rows in this matrix file.
getRowRange() - Method in class edu.rit.io.DoubleMatrixFile.Reader: Obtain the row range of the next matrix element segment in the input stream.
getScale14() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getScale14() - Method in class ffx.potential.nonbonded.VanDerWaalsForm: Getter for the field scale14.
getScaleBulkMinimize() - Method in class ffx.xray.DiffractionData: Getter for the field scaleBulkMinimize.
getScaled() - Method in class ffx.xray.DiffractionData: Getter for the field scaled.
getScaleMoleculesAsRigid() - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Get whether molecules are scaled as rigid bodies.
getScalePadding() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel: Gets the padding (pixels) between the dendrogram and the scale axis.
getScaleTickLength() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getScaleValueDecimals() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getScaleValueInterval() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
getScaleX() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Get whether to scale the X dimension of the periodic box.
getScaleY() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Get whether to scale the Y dimension of the periodic box.
getScaleZ() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Get whether to scale the Z dimension of the periodic box.
getScaling() - Method in class ffx.algorithms.dynamics.Barostat: Get the problem scaling.
getScaling() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the problem scaling.
getScaling() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getScaling() - Method in interface ffx.numerics.OptimizationInterface: Get the problem scaling.
getScaling() - Method in class ffx.potential.ANIEnergy
getScaling() - Method in class ffx.potential.DualTopologyEnergy: Get the problem scaling.
getScaling() - Method in class ffx.potential.extended.ExtendedSystem
getScaling() - Method in class ffx.potential.ForceFieldEnergy: Get the problem scaling.
getScaling() - Method in class ffx.potential.QuadTopologyEnergy: Get the problem scaling.
getScaling() - Method in class ffx.potential.XtalEnergy: Get the problem scaling.
getScaling() - Method in class ffx.realspace.RealSpaceEnergy: Get the problem scaling.
getScaling() - Method in class ffx.xray.RefinementEnergy: Get the problem scaling.
getScaling() - Method in class ffx.xray.ScaleBulkEnergy: Get the problem scaling.
getScaling() - Method in class ffx.xray.SigmaAEnergy: Get the problem scaling.
getScaling() - Method in class ffx.xray.SplineEnergy: Get the problem scaling.
getScaling() - Method in class ffx.xray.XRayEnergy: Get the problem scaling.
getSchedule() - Method in class ffx.algorithms.cli.AnnealOptions: Constructs an AnnealingSchedule.
getSchedulerHost() - Method in class edu.rit.pj.cluster.Configuration: Returns the Job Scheduler's channel group host name.
getSchedulerPort() - Method in class edu.rit.pj.cluster.Configuration: Returns the Job Scheduler's channel group port number.
getScreenedPairParameters(int, IntByReference, IntByReference, DoubleByReference) - Method in class ffx.openmm.drude.DrudeForce: Get the force field parameters for a screened pair.
getScreenedPairParameters(int, IntBuffer, IntBuffer, DoubleBuffer) - Method in class ffx.openmm.drude.DrudeForce: Get the force field parameters for a screened pair.
getSd() - Method in class ffx.numerics.math.BootStrapStatistics: The standard deviation.
getSd() - Method in class ffx.numerics.math.SummaryStatistics: The standard deviation.
getSecondaryStructure() - Method in class ffx.potential.utils.GetProteinFeatures: Get the secondary structure annotation from the ramachandran angle map
getSegID() - Method in class ffx.potential.bonded.Atom: Getter for the field segID.
getSegID() - Method in class ffx.potential.bonded.Molecule: Getter for the field segID.
getSegID() - Method in class ffx.potential.bonded.Residue: Getter for the field segID.
getSelf() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
getSelf(int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Return a previously computed self-energy.
getSelf(int, int, Rotamer, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Return a previously computed self-energy.
getSelfEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getSelfEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
getSelfEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
getSelfVolumeFractions() - Method in class ffx.potential.nonbonded.implicit.GaussVol: Return the self volume fraction for each atom.
getShctd() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the overlap factor.
getSideChainAtoms() - Method in class ffx.potential.bonded.MultiResidue: Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
getSideChainAtoms() - Method in class ffx.potential.bonded.Residue: Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
getSigF(int) - Method in class ffx.xray.DiffractionRefinementData: getSigF
getSigma() - Method in class ffx.potential.bonded.Atom: Gets the Sigma value
getSigmaA() - Method in class ffx.xray.CrystalStats: Simply return the current sigmaA value.
getSigmaAMinimize() - Method in class ffx.xray.DiffractionData: Getter for the field sigmaAMinimize.
getSigmaATol() - Method in class ffx.xray.DiffractionData: Getter for the field sigmaATol.
getSigmaCombiningRule() - Method in class ffx.openmm.amoeba.VdwForce: Get the sigma combining rule.
getSimilarAtomTypes(AtomType) - Method in class ffx.potential.parameters.ForceField: Getter for the field atomTypes.
getSize() - Method in class ffx.openmm.BondArray: Get the size of the bond array.
getSize() - Method in class ffx.openmm.DoubleArray: Get the size of the array.
getSize() - Method in class ffx.openmm.IntArray: Get the size of the array.
getSize() - Method in class ffx.openmm.IntSet: Get the size of the set.
getSize() - Method in class ffx.openmm.StringArray: Get the number of strings in the String Array.
getSize() - Method in class ffx.openmm.Vec3Array: Get the size of the Vec3Array.
getSlevy() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Get the Levy parameter.
getSmallerDistance() - Method in class ffx.potential.nonbonded.RestrainGroups: Smaller distance for each restraint.
getSnaps() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getSnapshot() - Method in class ffx.potential.parsers.PDBFilter
getSnapshot() - Method in class ffx.potential.parsers.SystemFilter: Return snapshot number.
getSnapshot() - Method in class ffx.potential.parsers.XPHFilter
getSnapshot() - Method in class ffx.potential.parsers.XYZFilter
getSnapshotInterval() - Method in class ffx.algorithms.cli.DynamicsOptions: Write/snapshot appending interval.
getSoftcoreAlpha() - Method in class ffx.openmm.amoeba.VdwForce: Get the softcore alpha.
getSoftcorePower() - Method in class ffx.openmm.amoeba.VdwForce: Get the softcore power.
getSoluteDielectric() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the solute dielectric constant.
getSoluteDielectric() - Method in class ffx.openmm.GBSAOBCForce: Get the dielectric constant for the solute.
getSoluteOffset() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
getSolutePermittivity() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the solvent relative permittivity (typically 1.0).
getSoluteType() - Method in class ffx.potential.bonded.Atom: getSoluteType
getSoluteType(Atom, ForceField, SoluteType.SOLUTE_RADII_TYPE) - Static method in class ffx.potential.parameters.SoluteType
getSoluteType(String) - Method in class ffx.potential.parameters.ForceField: Get a SoluteType.
getSoluteTypes() - Method in class ffx.potential.parameters.ForceField
getSolvationEnergy() - Method in class ffx.potential.ForceFieldEnergy: Getter for the field solvationEnergy.
getSolvationEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: getGKEnergy
getSolvationEnergy(Residue, boolean) - Method in class ffx.potential.bonded.RelativeSolvation: Gets the solvation energy (de-solvation penalty) for a given residue, allowing for sequence optimization to include an estimate of energy relative to the unfolded state.
getSolvationInteractions() - Method in class ffx.potential.ForceFieldEnergy: getSolvationInteractions.
getSolvEnergy() - Method in class ffx.potential.parameters.RelativeSolvationType: Getter for the field solvEnergy.
getSolventDielectric() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the solvent dielectric constant.
getSolventDielectric() - Method in class ffx.openmm.GBSAOBCForce: Get the dielectric constant for the solvent.
getSolventModel() - Method in class ffx.xray.DiffractionData: Getter for the field solventModel.
getSolventPermittivity() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the solvent relative permittivity (typically 78.3).
getSolventPressure() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
getSOR() - Method in class ffx.potential.nonbonded.pme.SORRegion
getSource() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Return the source terms.
getSpecialPositionCutoff() - Method in class ffx.crystal.Crystal: Getter for the field specialPositionCutoff.
getSpecialPositionCutoff2() - Method in class ffx.crystal.Crystal: Getter for the field specialPositionCutoff2.
getSpecialResidueList() - Method in class ffx.potential.extended.ExtendedSystem
getSpeed() - Method in class ffx.openmm.Platform: Get an estimate of how fast this Platform class is.
getSplineMinimize() - Method in class ffx.xray.DiffractionData: Getter for the field splineMinimize.
getStandardDeviation() - Method in class ffx.numerics.math.RunningStatistics: Get the standard deviation.
getStart() - Method in class ffx.algorithms.cli.ManyBodyOptions: Starting residue to perform the optimization on (-1 exits).
getState() - Method in class ffx.potential.extended.ExtendedSystem
getState(int, int) - Method in class ffx.openmm.Context: Get a State object recording the current state information stored in this context.
getState(int, int, int) - Method in class ffx.openmm.Context: Get a State object recording the current state information stored in this context.
getStates() - Method in class ffx.algorithms.optimize.ConformationScan
getStates() - Method in class ffx.algorithms.optimize.TorsionSearch: List of states in order of lowest to highest energy.
getStatesAroundAverage(double, double) - Method in class ffx.algorithms.optimize.ConformationScan
getStatesFilteredByRMSD(double) - Method in class ffx.algorithms.optimize.ConformationScan
getStatesWithinEnergy(double) - Method in class ffx.algorithms.optimize.ConformationScan
getStatus() - Method in class ffx.algorithms.optimize.Minimize: Getter for the field status.
getStatus() - Method in class ffx.algorithms.optimize.PhMinimize: Getter for the field status.
getStdOfEnergies() - Method in class ffx.algorithms.optimize.ConformationScan
getStdOfEnergiesNoOutlier() - Method in class ffx.algorithms.optimize.ConformationScan
getStep() - Method in class ffx.ui.commands.SimulationMessage: Getter for the field step.
getStepCount() - Method in class ffx.openmm.Context: Get the current step count.
getStepCount() - Method in class ffx.openmm.State: Get the step count.
getSteps() - Method in class ffx.algorithms.cli.DynamicsOptions: The number of molecular dynamics steps (default is 1,000,000).
getStepSize() - Method in class ffx.openmm.CompoundIntegrator: Get the size of each time step, in picoseconds.
getStepSize() - Method in class ffx.openmm.Integrator: Get the size of each time step, in picoseconds.
getStretchBend(int) - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Get the StretchBend at a given index.
getStretchBendArray() - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Get an array of StretchBends in this term.
getStretchBendEnergyString() - Static method in class ffx.potential.terms.StretchBendPotentialEnergy: Get a formatted string representing the energy expression for Stretch-Bend interactions.
getStretchBendList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Stretch-Bends below the present MSNode.
getStretchBendPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the StretchBendPotentialEnergy.
getStretchBends() - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Get an unmodifiable view of the StretchBends in this term.
getStretchBendType(AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField: getStretchBendType
getStretchBendType(String) - Method in class ffx.potential.parameters.ForceField: getStretchBendType
getStretchBendTypes() - Method in class ffx.potential.parameters.ForceField: Get StretchBendTypes.
getStretchTorsion(int) - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Get the StretchTorsion at a given index.
getStretchTorsionArray() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Get an array of StretchTorsions in this term.
getStretchTorsionList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all StretchTorsions below the present MSNode.
getStretchTorsionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the StretchTorsionPotentialEnergy.
getStretchTorsions() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Get an unmodifiable view of the StretchTorsions in this term.
getStretchTorsionType(String) - Method in class ffx.potential.parameters.ForceField: getStretchTorsionType
getStretchTorsionTypes() - Method in class ffx.potential.parameters.ForceField: Get StretchTorsionTypes.
getString(String) - Method in class ffx.potential.parameters.ForceField: getBoolean
getString(String, String) - Method in class ffx.potential.parameters.ForceField: getBoolean
getSubCurves() - Method in class ffx.numerics.integrate.CompositeCurve: Gets the component FunctionDataCurves of this CompositeCurve.
getSum() - Method in class ffx.numerics.math.RunningStatistics: Get the sum.
getSumOverK() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
getSupportedPlatforms() - Method in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine: Gets the set of Platforms supported by this DynamicsEngine
getSurfaceArea() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation: Return Surface Area (A^2).
getSurfaceArea() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
getSurfaceArea() - Method in class ffx.potential.nonbonded.implicit.GaussVol: Return Surface Area (A^2).
getSurfaceAreaEnergy() - Method in class ffx.openmm.GBSAOBCForce: Get the energy scale for the surface area term, measured in kJ/mol/nmˆ2.
getSurfaceAreaEnergy() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation: Return Surface Area based cavitation energy.
getSurfaceAreaFactor() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the surface area factor.
getSurfaceAreaGradient() - Method in class ffx.potential.nonbonded.implicit.GaussVol
getSurfaceAreaRegion() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getSurfaceTension() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Getter for the field surfaceTension.
getSurfaceTension() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
getSwitch() - Method in class ffx.potential.DualTopologyEnergy: Returns the switching function used by this DualTopologyEnergy; presently, switching functions are immutable, and cannot be changed once a DualTopologyEnergy is constructed.
getSwitchEnd() - Method in class ffx.numerics.switching.MultiplicativeSwitch: Get the value where the switch starts.
getSwitchingDistance() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Get the switching distance.
getSwitchingDistance() - Method in class ffx.openmm.CustomNonbondedForce: Get the switching distance.
getSwitchingDistance() - Method in class ffx.openmm.GayBerneForce: Get the switching distance.
getSwitchingFunction() - Method in class ffx.potential.cli.TopologyOptions: Return the switching function between topology energies.
getSwitchStart() - Method in class ffx.numerics.switching.MultiplicativeSwitch: Get the value where the switch starts.
getSymOp(int) - Method in class ffx.crystal.SpaceGroup: Return the ith symmetry operator.
getSymOpAtoms(int, int[]) - Method in class ffx.potential.nonbonded.NeighborList.Cell: Return the number of atoms in the cell for a given symmetry operator.
getSynchronousSend() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: Return the SynchronousSend associated with this Histogram, if any.
getSystem() - Method in class ffx.openmm.Context: Get System being simulated in this context.
getSystem() - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Get a reference to the System instance.
getSystem() - Method in class ffx.potential.openmm.OpenMMEnergy: Get a reference to the System instance.
getSystem() - Method in interface ffx.potential.openmm.OpenMMPotential: Get a reference to the System instance.
getSystem() - Method in class ffx.ui.commands.FFXClient: Getter for the field system.
getSystemMultipoleMoments(Context, DoubleArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the system multipole moments.
getSystems() - Method in class ffx.ui.Hierarchy: getSystems
getTabulatedFunction(int) - Method in class ffx.openmm.CustomCentroidBondForce: Get a reference to a tabulated function that may appear in the energy expression.
getTabulatedFunction(int) - Method in class ffx.openmm.CustomCompoundBondForce: Get a reference to a tabulated function.
getTabulatedFunction(int) - Method in class ffx.openmm.CustomCVForce: Get a tabulated function by index.
getTabulatedFunction(int) - Method in class ffx.openmm.CustomGBForce: Get a reference to a tabulated function.
getTabulatedFunction(int) - Method in class ffx.openmm.CustomHbondForce: Get a reference to a tabulated function that may appear in the energy expression.
getTabulatedFunction(int) - Method in class ffx.openmm.CustomIntegrator: Get a reference to a tabulated function that may appear in expressions.
getTabulatedFunction(int) - Method in class ffx.openmm.CustomManyParticleForce: Get a reference to a tabulated function that may appear in the energy expression.
getTabulatedFunction(int) - Method in class ffx.openmm.CustomNonbondedForce: Get a reference to a tabulated function that may appear in the energy expression.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomCentroidBondForce: Get the name of a tabulated function that may appear in the energy expression.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomCompoundBondForce: Get the name of a tabulated function.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomCVForce: Get the name of a tabulated function.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomGBForce: Get the name of a tabulated function.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomHbondForce: Get the name of a tabulated function that may appear in the energy expression.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomIntegrator: Get the name of a tabulated function that may appear in expressions.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomManyParticleForce: Get the name of a tabulated function that may appear in the energy expression.
getTabulatedFunctionName(int) - Method in class ffx.openmm.CustomNonbondedForce: Get the name of a tabulated function that may appear in the energy expression.
getTag() - Method in class edu.rit.pj.cluster.Message: Get the message tag to use when sending this message.
getTanhBetas() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getTanhCorrection() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Returns the tanh correction factor.
getTanhParameters(DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get Tanh function parameters b0, b1 and b2.
getTanhRescaling() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Get the tanh rescaling.
getTargetTemperature() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Get the target temperature.
getTau() - Method in class ffx.algorithms.dynamics.thermostats.Berendsen: Getter for the field tau.
getTau() - Method in class ffx.algorithms.dynamics.thermostats.Bussi: Getter for the field tau.
getTautomerESVIndex(int) - Method in class ffx.potential.extended.ExtendedSystem
getTautomerizingResidueList() - Method in class ffx.potential.extended.ExtendedSystem: Return the List of Tautomerizing Residues
getTautomerLambda(int) - Method in class ffx.potential.extended.ExtendedSystem: get Tautomer Lambda for an extended atom
getTautomerLambda(Residue) - Method in class ffx.potential.extended.ExtendedSystem: Gets the tautomer lambda for the input residue if the residue is tautomerizing
getTemperAfter() - Method in class ffx.algorithms.cli.AnnealOptions: Sets the number of annealing windows to hold flat at the low temperature (in addition to normal windows).
getTemperature() - Method in class ffx.algorithms.cli.DynamicsOptions: The simulation temperature (Kelvin).
getTemperature() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Get the current temperature of the system
getTemperature() - Method in class ffx.algorithms.mc.BoltzmannMC: Returns temperature of the Monte Carlo criterion.
getTemperature() - Method in interface ffx.algorithms.mc.MetropolisMC: Returns temperature of the Monte Carlo criterion.
getTemperature() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: getTemperature.
getTemperature() - Method in class ffx.openmm.BrownianIntegrator: Get the temperature of the heat bath (in Kelvin).
getTemperature() - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Get the temperature of the main heat bath (in Kelvin).
getTemperature() - Method in class ffx.openmm.LangevinMiddleIntegrator: Get the temperature.
getTemperature() - Method in class ffx.openmm.VariableLangevinIntegrator: Get the temperature of the heat bath (in Kelvin).
getTemperature() - Method in class ffx.potential.SystemState: Get the temperature.
getTemperature(double) - Method in class ffx.potential.openmm.OpenMMSystem
getTemperature(int) - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Get the temperature for annealing step i.
getTemperature(int) - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
getTemperature(int) - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
getTemperature(int) - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
getTemperature(int) - Method in class ffx.openmm.NoseHooverIntegrator: Get the temperature for a thermostat.
getTemperature1() - Method in class ffx.potential.parsers.BARFilter: Returns the temperature for ensemble 1.
getTemperature2() - Method in class ffx.potential.parsers.BARFilter: Returns the temperature for ensemble 2.
getTemperatures() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Get all temperatures this schedule specifies.
getTemperatures() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
getTemperatures() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
getTemperatures() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
getTemperBefore() - Method in class ffx.algorithms.cli.AnnealOptions: Sets the number of annealing windows to hold flat at the high temperature (in addition to normal windows).
getTemperingOffset() - Method in class ffx.algorithms.thermodynamics.HistogramData: Gets the tempering offset.
getTemperingRate() - Method in class ffx.algorithms.cli.OSTOptions: The Dama et al. tempering rate parameter, in multiples of kBT.
getTemperingThreshold() - Method in class ffx.algorithms.cli.OSTOptions: The tempering threshold/offset in kcal/mol.
getTemperString() - Method in class ffx.algorithms.cli.AnnealOptions: Sets the schedule to be used.
getTempFactor() - Method in class ffx.potential.bonded.Atom: Getter for the field tempFactor.
getTempFactorAcceleration() - Method in class ffx.potential.bonded.Atom: Getter for the field tempFactorAcceleration.
getTempFactorGradient() - Method in class ffx.potential.bonded.Atom: Getter for the field tempFactorGradient.
getTempFactorPreviousAcceleration() - Method in class ffx.potential.bonded.Atom: Getter for the field tempFactorPreviousAcceleration.
getTempFactorVelocity() - Method in class ffx.potential.bonded.Atom: Getter for the field tempFactorVelocity.
getTemporaryBuf() - Method in class edu.rit.mp.BooleanBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Buf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.ByteBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.CharacterBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.DoubleBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.FloatBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.IntegerBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.LongBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.ObjectBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.ShortBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Signed16BitIntegerBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Signed8BitIntegerBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a temporary buffer with the same type of items and the same length as this buffer.
getTensor(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Load the tensor components.
getTermNode() - Method in class ffx.potential.bonded.MSGroup: Returns the MultiScaleGroup's terms FNode.
getTermNode() - Method in class ffx.potential.bonded.MultiResidue: Returns the MultiScaleGroup's terms FNode.
getThermoAlgoString() - Method in class ffx.algorithms.cli.ThermodynamicsOptions: The algorithm to be used (e.g.
getThermostat() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Getter for the field thermostat.
getThermostat() - Method in class ffx.xray.RefinementEnergy: Getter for the field thermostat.
getThermostat(int) - Method in class ffx.openmm.NoseHooverIntegrator: Get a reference to a thermostat.
getThermostatString() - Method in class ffx.algorithms.cli.DynamicsOptions: The desired thermostat: current choices are Adiabatic, Berendsen, or Bussi.
getThetaAccel() - Method in class ffx.potential.extended.ExtendedSystem
getThetaFriction() - Method in class ffx.potential.extended.ExtendedSystem
getThetaMass() - Method in class ffx.potential.extended.ExtendedSystem
getThetaMassArray() - Method in class ffx.potential.extended.ExtendedSystem
getThetaPosition() - Method in class ffx.potential.extended.ExtendedSystem
getThetaVelocity() - Method in class ffx.potential.extended.ExtendedSystem
getThreadCount() - Method in class edu.rit.pj.ParallelConstruct: Determine the number of threads in the parallel team executing this parallel construct.
getThreadCount() - Method in class edu.rit.pj.ParallelTeam: Determine the number of threads in this parallel team.
getThreadCount() - Method in class edu.rit.pj.WorkerConstruct: Determine the number of worker threads in the current process in the worker team executing this worker construct.
getThreadCount() - Method in class edu.rit.pj.WorkerTeam: Determine the number of worker threads in this worker team in this process.
getThreadIndex() - Method in class edu.rit.pj.ParallelConstruct: Determine the index of the calling thread in the parallel team executing this parallel construct.
getThreadIndex() - Method in class edu.rit.pj.WorkerConstruct: Determine the index of the calling thread in the worker team executing this worker construct.
getThreads() - Method in class ffx.potential.cli.TimerOptions: Getter for the field threads.
getThreadsPerTopology(int) - Method in class ffx.potential.cli.TopologyOptions: The number of threads per topology.
getThreadWeights() - Method in class ffx.xray.GradientSchedule: getThreadWeights.
getThreeBody() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
getThreeBodyCutoff() - Method in class ffx.algorithms.cli.ManyBodyOptions: Cutoff distance for three-body interactions.
getThreeBodyEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
getTIIntegral() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getTime() - Method in class ffx.openmm.Context: Get the current time of the simulation (in picoseconds).
getTime() - Method in class ffx.openmm.State: Get the time.
getTime() - Method in class ffx.potential.terms.EnergyTerm: Get the time taken to compute the energy for this term in seconds.
getTime() - Method in class ffx.ui.commands.SimulationMessage: Getter for the field time.
getTimeout() - Method in class edu.rit.util.Timer: Determine the time when this timer is or was scheduled to time out.
getTimerTask() - Method in class edu.rit.util.Timer: Returns this timer's timer task.
getTimeStep() - Method in class ffx.algorithms.dynamics.integrators.Integrator: Get the time step.
getTimeStep() - Method in class ffx.algorithms.dynamics.MolecularDynamics: getTimeStep.
getTimeStep() - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: getTimeStep.
getTiming() - Method in class ffx.numerics.fft.Complex3DParallel: Get the timings for each thread.
getTitratingHydrogenDirection(AminoAcidUtils.AminoAcid3, Atom) - Static method in class ffx.potential.parameters.TitrationUtils
getTitratingResidueList() - Method in class ffx.potential.extended.ExtendedSystem: Return the List of Titrating Residues
getTitration() - Method in class ffx.algorithms.cli.ManyBodyOptions
getTitrationESVIndex(int) - Method in class ffx.potential.extended.ExtendedSystem: get the index of the extended residue list that corresponds to this atom
getTitrationLambda(int) - Method in class ffx.potential.extended.ExtendedSystem: get Titration Lambda for an extended atom
getTitrationLambda(Residue) - Method in class ffx.potential.extended.ExtendedSystem: Gets the titration lambda for the input residue if the residue is titrating
getTitrationPH() - Method in class ffx.algorithms.cli.ManyBodyOptions
getTitrationUtils() - Method in class ffx.potential.bonded.Residue
getTitrationUtils() - Method in class ffx.potential.extended.ExtendedSystem
getTolerance() - Method in class ffx.potential.cli.GradientOptions: --tol or --tolerance Gradient error tolerance (kcal/mol/Å).
getTopologiesInParallel() - Method in class ffx.potential.cli.TopologyOptions: --np or --nParallel sets the number of topologies to evaluate in parallel; currently 1, 2, or 4.
getTopologiesInParallel(int) - Method in class ffx.potential.cli.TopologyOptions: The number of topologies to run in parallel.
getTopology(MolecularAssembly[], UnivariateSwitchingFunction, List<Integer>, List<Integer>, int, StringBuilder) - Method in class ffx.potential.cli.TopologyOptions: Configure a Dual-, Quad- or Oct- Topology.
getTopologyAtomIndex() - Method in class ffx.potential.bonded.Atom: Dual-topology atom index.
getTopologyIndex() - Method in class ffx.potential.bonded.Atom: Get the topology index of this atom.
getTopologyScale(int) - Method in class ffx.potential.DualTopologyEnergy: The scale factor for the specified topology.
getTorque() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getTorsion(int) - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get the Torsion at a given index.
getTorsion(Atom, Atom, Atom) - Method in class ffx.potential.bonded.Atom: Finds a Torsion which contains this atom, and atoms 2, 3, and 4.
getTorsionArray() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get an array of Torsions in this term.
getTorsionList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Torsions below the present MSNode.
getTorsionParameters(int, IntByReference, IntByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.RBTorsionForce: Get the parameters for a torsion.
getTorsionParameters(int, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.PeriodicTorsionForce: Get the parameters for a torsion.
getTorsionParameters(int, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.CMAPTorsionForce: Get the force field parameters for a CMAP torsion term.
getTorsionParameters(int, IntByReference, IntByReference, IntByReference, IntByReference, PointerByReference) - Method in class ffx.openmm.CustomTorsionForce: Get the force field parameters for a torsion.
getTorsionParameters(int, IntBuffer, IntBuffer, IntBuffer, IntBuffer, PointerByReference) - Method in class ffx.openmm.CustomTorsionForce: Get the force field parameters for a torsion.
getTorsionParameters(int, IntBuffer, IntBuffer, IntBuffer, IntBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.RBTorsionForce: Get the parameters for a torsion.
getTorsionParameters(int, IntBuffer, IntBuffer, IntBuffer, IntBuffer, IntBuffer, DoubleBuffer, DoubleBuffer) - Method in class ffx.openmm.PeriodicTorsionForce: Get the parameters for a torsion.
getTorsionParameters(int, IntBuffer, IntBuffer, IntBuffer, IntBuffer, IntBuffer, IntBuffer, IntBuffer, IntBuffer, IntBuffer) - Method in class ffx.openmm.CMAPTorsionForce: Get the force field parameters for a CMAP torsion term.
getTorsionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the TorsionPotentialEnergy.
getTorsions() - Method in class ffx.potential.bonded.Atom: Getter for the field torsions.
getTorsions() - Method in class ffx.potential.bonded.MSGroup: Returns the MultiScaleGroup's Torsion MSNode.
getTorsions() - Method in class ffx.potential.bonded.MultiResidue: Returns the MultiScaleGroup's Torsion MSNode.
getTorsions() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Get an unmodifiable view of the Torsions in this term.
getTorsionScale() - Method in class ffx.potential.bonded.Torsion: Get the torsion scale up factor.
getTorsionTorsion(int) - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get the TorsionTorsion at a given index.
getTorsionTorsionArray() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get an array of TorsionTorsions in this term.
getTorsionTorsionGrid(int) - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Get the torsion-torsion grid at the specified index
getTorsionTorsionList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Torsion-Torsions below the present MSNode.
getTorsionTorsionParameters(int, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference, IntByReference) - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Get the force field parameters for a torsion-torsion term.
getTorsionTorsionPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the TorsionTorsionPotentialEnergy.
getTorsionTorsions() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Get an unmodifiable view of the TorsionTorsions in this term.
getTorsionTorsionType(String) - Method in class ffx.potential.parameters.ForceField: getTorsionTorsionType
getTorsionTorsionTypes() - Method in class ffx.potential.parameters.ForceField: Get TorsionTorsionTypes.
getTorsionType(AtomType, AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField: getTorsionType
getTorsionType(String) - Method in class ffx.potential.parameters.ForceField: getTorsionType
getTorsionTypes() - Method in class ffx.potential.parameters.ForceField: Get TorsionTypes.
getTotalAtomArray() - Method in class ffx.xray.RefinementModel: Getter for the field totalAtomArray.
getTotalBoltzmann() - Method in class ffx.algorithms.optimize.RotamerOptimization: Return the total boltzmann weight for an ensemble
getTotaldEdLambda() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: getTotaldEdLambda.
getTotalDipoles(Context, DoubleArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Get the total dipoles.
getTotalDistance() - Method in class ffx.numerics.clustering.Cluster: Computes the cumulative distance down the leftmost branch of this cluster.
getTotalEnergy() - Method in class ffx.algorithms.dynamics.Barostat: Get the total energy of the system
getTotalEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Get the total system energy (kinetic plus potential).
getTotalEnergy() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: getTotalEnergy.
getTotalEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the total energy of the system
getTotalEnergy() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getTotalEnergy() - Method in interface ffx.numerics.OptimizationInterface: Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.ANIEnergy
getTotalEnergy() - Method in class ffx.potential.DualTopologyEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.extended.ExtendedSystem
getTotalEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.openmm.OpenMMState: Get the total energy.
getTotalEnergy() - Method in class ffx.potential.QuadTopologyEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.SystemState: Get the total energy as the sum of the kinetic and potential energies.
getTotalEnergy() - Method in record class ffx.potential.UnmodifiableState
getTotalEnergy() - Method in class ffx.potential.XtalEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.realspace.RealSpaceEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.RefinementEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.ScaleBulkEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.SigmaAEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.SplineEnergy: Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.XRayEnergy: Get the total energy of the system
getTotalEnthalpyChange() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total enthalpy estimate from bootstrap analysis.
getTotalEnthalpyChange(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total enthalpy estimate from per window bootstrap analysis.
getTotalEnthalpyDifference() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Gets the total enthalpy difference between the first and last state.
getTotalEnthalpyDifference() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: Gets the total enthalpy difference between the first and last state.
getTotalEnthalpyDifference() - Method in interface ffx.numerics.estimator.StatisticalEstimator: Gets the total enthalpy difference between the first and last state.
getTotalEnthalpyDifference() - Method in class ffx.numerics.estimator.Zwanzig: Gets the total enthalpy difference between the first and last state.
getTotalEnthalpyDifference(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Obtains bootstrap total enthalpy change.
getTotalEnthalpyUncertainty() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total enthalpy uncertainty estimate from bootstrap analysis.
getTotalEnthalpyUncertainty(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Obtains bootstrap enthalpy uncertainty.
getTotalEnthalpyUncertainty(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total enthalpy uncertainty estimate from per window bootstrap analysis.
getTotalEntropyChange() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total entropy change (-TdS) from bootstrap analysis.
getTotalEntropyUncertainty() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total entropy uncertainty estimate from bootstrap analysis.
getTotalFEDifferenceUncertainty() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Returns the total uncertainty in the computed free energy difference between the first and last state.
getTotalFEDifferenceUncertainty() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total free energy difference uncertainty estimate from bootstrap analysis.
getTotalFEDifferenceUncertainty() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getTotalFEDifferenceUncertainty() - Method in interface ffx.numerics.estimator.StatisticalEstimator: Returns the total uncertainty in the computed free energy difference between the first and last state.
getTotalFEDifferenceUncertainty() - Method in class ffx.numerics.estimator.Zwanzig: Returns the total uncertainty in the computed free energy difference between the first and last state.
getTotalFEDifferenceUncertainty(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Obtains bootstrap free energy difference uncertainty.
getTotalFEDifferenceUncertainty(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total free energy difference uncertainty estimate from per window bootstrap analysis.
getTotalFreeEnergyDifference() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Returns the total free energy difference between the first and last state.
getTotalFreeEnergyDifference() - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total free energy difference estimate from bootstrap analysis.
getTotalFreeEnergyDifference() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getTotalFreeEnergyDifference() - Method in interface ffx.numerics.estimator.StatisticalEstimator: Returns the total free energy difference between the first and last state.
getTotalFreeEnergyDifference() - Method in class ffx.numerics.estimator.Zwanzig: Returns the total free energy difference between the first and last state.
getTotalFreeEnergyDifference(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Obtains bootstrap total free energy difference.
getTotalFreeEnergyDifference(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Get the total free energy difference estimate from per window bootstrap analysis.
getTotalMass() - Method in class ffx.potential.bonded.MSNode: Returns the total mass of all atoms in the MolecularAssembly, calculating the mass if it has not already been done, defaulting to simple addition.
getTotalMonomerMinimizedEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
getTotalMultipoleEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Getter for the field totalMultipoleEnergy.
getTotalNumberOfOverlaps() - Method in class ffx.potential.nonbonded.implicit.GaussVol: Return the total number of overlaps in the tree
getTotalRotamerPhBias(Rotamer[]) - Method in class ffx.potential.parameters.TitrationUtils
getTotalRotamerPhBias(List<Residue>, int[], double, double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Compute the total rotamer Ph bias for an array of residues.
getTotalSurfaceArea() - Method in class ffx.potential.utils.GetProteinFeatures: Get the total surface area for the protein
getTotalThreadCount() - Method in class edu.rit.pj.WorkerConstruct: Determine the total number of worker threads in all processes in the worker team executing this worker construct.
getTotalThreadCount() - Method in class edu.rit.pj.WorkerTeam: Determine the total number of worker threads in this worker team in all processes.
getTrajectory() - Method in class ffx.ui.FFXSystem: Getter for the field trajectory.
getTrajectoryCoords(int) - Method in class ffx.potential.bonded.Atom: getTrajectoryCoords
getTrajectoryLength() - Method in class ffx.potential.bonded.Atom: getTrajectoryLength
getTrajSteps() - Method in class ffx.algorithms.cli.DynamicsOptions: Number of steps for each OpenMM MD cycle.
getTransformationOperator(SymOp, double[][]) - Method in class ffx.crystal.Crystal: Compute the total transformation operator R = ToCart * Rot * ToFrac.
getTransformGroup() - Method in class ffx.potential.MolecularAssembly: getTransformGroup
getTrigonalAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend: Get the trigonal atom of this out-of-plane bend (central atom of the Angle).
getTwoBody() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
getTwoBodyCutoff() - Method in class ffx.algorithms.cli.ManyBodyOptions: Cutoff distance for two-body interactions.
getTwoBodyEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.AIB: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ALA: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ARG: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASD: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASH: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASN: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASP: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.CYD: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.CYS: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.CYX: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLD: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLH: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLN: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLU: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.HID: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.HIE: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.HIS: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ILE: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.LEU: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.LYD: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.LYS: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.MET: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ORN: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.PCA: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.PHE: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.PRO: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.SER: Returns Biotype of this atom.
getType() - Method in interface ffx.potential.bonded.AminoAcidUtils.SideChainType: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.THR: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.TRP: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.TYD: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.TYR: Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.VAL: Returns Biotype of this atom.
getType() - Method in class ffx.potential.bonded.Atom: getType
getType() - Method in class ffx.potential.parsers.SystemFilter: getType
getType() - Method in class ffx.ui.commands.SimulationMessage: Getter for the field type.
getTypeFilter(int, PointerByReference) - Method in class ffx.openmm.CustomManyParticleForce: Get the type filter for the specified type.
getTypePairParameters(int, IntByReference, IntByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.amoeba.VdwForce: Get the type pair parameters.
getTypes(ForceField.ForceFieldType) - Method in class ffx.potential.parameters.ForceField: Return all force field types of a given type.
getUIAlgorithmUtils() - Method in class ffx.ui.ModelingShell
getUIPotentialsUtils() - Method in class ffx.ui.ModelingShell
getUncertaintyMatrix() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
getUnchargedAtoms() - Method in class ffx.potential.cli.AlchemicalOptions: --uc or --unchargedAtoms Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].
getUnchargedAtoms2() - Method in class ffx.potential.cli.TopologyOptions: --uc2 or --unchargedAtoms2 Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].
getUnderlyingPotentials() - Method in class ffx.algorithms.dynamics.Barostat
getUnderlyingPotentials() - Method in interface ffx.numerics.OptimizationInterface: Returns a List of Potentials this Potential depends on with a recursive search, excluding the top level of this call.
getUnderlyingPotentials() - Method in class ffx.potential.DualTopologyEnergy
getUnderlyingPotentials() - Method in class ffx.potential.QuadTopologyEnergy
getUnderlyingPotentials() - Method in class ffx.xray.RefinementEnergy
getUniqueAtoms(MolecularAssembly, String, String) - Static method in class ffx.potential.cli.TopologyOptions: Collect unique atoms for a dual-topology.
getUniqueAtomsA(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions: Collect unique atoms for the A dual-topology.
getUniqueAtomsB(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions: Collect unique atoms for the B dual-topology.
getUnitCell() - Method in class ffx.crystal.Crystal: The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
getUnitCell() - Method in class ffx.crystal.NCSCrystal: The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
getUnitCell() - Method in class ffx.crystal.ReplicatesCrystal: The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
getUnmodifiableState() - Method in class ffx.potential.SystemState: Get an unmodifiable view of the current state.
getUnscaledBornIntegral() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
getUnsharedA() - Method in class ffx.potential.cli.TopologyOptions: --uaA or --unsharedA sets atoms unique to the A dual-topology, as period-separated hyphenated ranges or singletons.
getUnsharedB() - Method in class ffx.potential.cli.TopologyOptions: --uaB or --unsharedB sets atoms unique to the A dual-topology, as period-separated hyphenated ranges or singletons.
getUpdate() - Method in class ffx.ui.commands.FFXClient: Getter for the field update.
getUpdateCount() - Method in class ffx.openmm.TabulatedFunction: Get the value of a counter that is updated every time setFunctionParameters() is called.
getUpper() - Method in class ffx.algorithms.cli.AnnealOptions: Upper temperature limit in degrees Kelvin.
getUreyBradley(int) - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Get the UreyBradley at a given index.
getUreyBradleyArray() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Get an array of UreyBradleys in this term.
getUreyBradleyList() - Method in class ffx.potential.bonded.MSNode: Returns a List of all Urey-Bradleys below the present MSNode.
getUreyBradleyPotentialEnergy() - Method in class ffx.potential.ForceFieldEnergy: Get the UreyBradleyPotentialEnergy.
getUreyBradleys() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Get an unmodifiable view of the UreyBradleys in this term.
getUreyBradleyType(String) - Method in class ffx.potential.parameters.ForceField: getUreyBradleyType
getUreyBradleyTypes() - Method in class ffx.potential.parameters.ForceField: Get UreyBradleyTypes.
getUri() - Method in class edu.rit.http.HttpRequest: Obtain this HTTP request's URI.
getUse() - Method in class ffx.potential.bonded.Atom: If true, this atom should be used in potential energy functions.
getUse() - Method in class ffx.potential.bonded.BondedTerm: This method returns true if any atom is being used.
getUseDispersionCorrection() - Method in class ffx.openmm.amoeba.VdwForce: Get whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.
getUseLongRangeCorrection() - Method in class ffx.openmm.CustomNonbondedForce: Get whether to use the long range correction.
getUseParticleTypes() - Method in class ffx.openmm.amoeba.VdwForce: Get whether to use particle types.
getUsePerfectRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: GK is using perfect radii where available.
getUserName() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's user name.
getUseSwitchingFunction() - Method in class ffx.openmm.CustomNonbondedForce: Get whether to use a switching function.
getUseSwitchingFunction() - Method in class ffx.openmm.GayBerneForce: Get whether a switching function is used.
getUsingOrigCoordsRotamer() - Method in class ffx.potential.bonded.RotamerLibrary: getUsingOrigCoordsRotamer.
getUsingOriginalCoordinates() - Method in class ffx.algorithms.cli.ManyBodyOptions
getV3D(Vector3d) - Method in class ffx.potential.bonded.Atom: Gets the Atom's Cartesian Coordinates return The Cartesian Coordinates
getValue() - Method in class ffx.potential.bonded.BondedTerm: Get the Term's value.
getValue() - Method in class ffx.ui.SwingWorker: Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValue(String) - Method in class ffx.ui.properties.FFXLocale: getValue
getVanDerWaalsEnergy() - Method in class ffx.potential.ForceFieldEnergy: Getter for the field vanDerWaalsEnergy.
getVanDerWaalsInteractions() - Method in class ffx.potential.ForceFieldEnergy: getVanDerWaalsInteractions.
getVar() - Method in class ffx.numerics.math.BootStrapStatistics: The variance.
getVar() - Method in class ffx.numerics.math.SummaryStatistics: The variance.
getVariable(String) - Method in class ffx.utilities.FFXBinding: getVariable.
getVariableAtoms() - Method in class ffx.potential.bonded.MultiResidue: Returns a list of atoms liable to change during dead-end elimination repacking.
getVariableAtoms() - Method in class ffx.potential.bonded.Residue: Returns a list of atoms liable to change during dead-end elimination repacking.
getVariables() - Method in class ffx.utilities.FFXBinding: Get the Map of all variables.
getVariableTypes() - Method in class ffx.algorithms.dynamics.Barostat: Get the type of all variables.
getVariableTypes() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Get the type of all variables.
getVariableTypes() - Method in interface ffx.numerics.Potential: Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.ANIEnergy
getVariableTypes() - Method in class ffx.potential.DualTopologyEnergy: Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.extended.ExtendedSystem
getVariableTypes() - Method in class ffx.potential.ForceFieldEnergy: Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.QuadTopologyEnergy: Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.XtalEnergy: Get the type of all variables.
getVariableTypes() - Method in class ffx.realspace.RealSpaceEnergy: Get the type of all variables.
getVariableTypes() - Method in class ffx.xray.RefinementEnergy: Get the type of all variables.
getVariableTypes() - Method in class ffx.xray.XRayEnergy: Get the type of all variables.
getVariance() - Method in class ffx.numerics.math.RunningStatistics: Get the variance.
getVDW14Type(String) - Method in class ffx.potential.parameters.ForceField: getVDW14Type
getVDW14Types() - Method in class ffx.potential.parameters.ForceField: getVDW14Types
getVDWForm() - Method in class ffx.potential.nonbonded.VanDerWaals: getVDWForm.
getVdwNode() - Method in class ffx.potential.ForceFieldEnergy: getVdwNode.
getVDWPairType(String) - Method in class ffx.potential.parameters.ForceField: getVDWPairType
getVDWPairTypes() - Method in class ffx.potential.parameters.ForceField: getVDWPairTypes
getVdwPrefactor(int, double[]) - Method in class ffx.potential.extended.ExtendedSystem: Calculate prefactor for scaling the van der Waals based on titration/tautomer state if titrating proton
getVDWR() - Method in class ffx.potential.bonded.Atom: Gets the van der Waals radius.
getVDWSoluteType(VDWType) - Static method in class ffx.potential.parameters.SoluteType
getVDWType() - Method in class ffx.potential.bonded.Atom: getVDWType
getVDWType(String) - Method in class ffx.potential.parameters.ForceField: getVDWType
getVDWTypes() - Method in class ffx.potential.parameters.ForceField: getVDWTypes
getVelocities() - Method in class ffx.openmm.State: Get the velocities.
getVelocities(double[]) - Method in class ffx.potential.openmm.OpenMMState: The velocity array contains the OpenMM atomic position information for all atoms.
getVelocity(double[]) - Method in class ffx.algorithms.dynamics.Barostat: getVelocity.
getVelocity(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: getVelocity.
getVelocity(double[]) - Method in interface ffx.numerics.Potential: getVelocity.
getVelocity(double[]) - Method in class ffx.potential.ANIEnergy
getVelocity(double[]) - Method in class ffx.potential.bonded.Atom: Getter for the field velocity.
getVelocity(double[]) - Method in class ffx.potential.DualTopologyEnergy: getVelocity.
getVelocity(double[]) - Method in class ffx.potential.extended.ExtendedSystem
getVelocity(double[]) - Method in class ffx.potential.ForceFieldEnergy: getVelocity.
getVelocity(double[]) - Method in class ffx.potential.QuadTopologyEnergy: getVelocity.
getVelocity(double[]) - Method in class ffx.potential.XtalEnergy: getVelocity.
getVelocity(double[]) - Method in class ffx.realspace.RealSpaceEnergy: getVelocity.
getVelocity(double[]) - Method in class ffx.xray.RefinementEnergy: getVelocity.
getVelocity(double[]) - Method in class ffx.xray.XRayEnergy: getVelocity.
getVerbose() - Method in class ffx.potential.cli.GradientOptions: -v or --verbose is a flag to print out energy at each step.
getVerbose() - Method in class ffx.potential.cli.TimerOptions: Getter for the field verbose.
getVerbosityLevel() - Method in class ffx.algorithms.dynamics.MolecularDynamics
getVertexIndices(int[]) - Method in class ffx.numerics.quickhull.Face: Writes the vertex indices of this face into the provided array in CCW order.
getVertexPointIndices() - Method in class ffx.numerics.quickhull.QuickHull3D: Returns an array specifing the index of each hull vertex with respect to the original input points.
getVertexString() - Method in class ffx.numerics.quickhull.Face: Returns a space-separated string of the vertex indices defining this face in counter-clockwise order.
getVertexString() - Method in class ffx.numerics.quickhull.HalfEdge: Produces a string identifying this half-edge by the point index values of its tail and head vertices.
getVertices() - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the vertex points in this hull.
getVertices(double[]) - Method in class ffx.numerics.quickhull.QuickHull3D: Returns the coordinates of the vertex points of this hull.
getVirtualSite(int) - Method in class ffx.openmm.System: Get the virtual site for a particle.
getVolume() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation: Return Volume (A^3).
getVolume() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
getVolume() - Method in class ffx.potential.nonbonded.implicit.GaussVol: Return Volume (A^3).
getVolume1() - Method in class ffx.potential.parsers.BARFilter: Return the volume for each snapshot of ensemble 1.
getVolume2() - Method in class ffx.potential.parsers.BARFilter: Return the volume for each snapshot of ensemble 2.
getVolumeEnergy() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation: Return Volume based cavitation energy.
getVolumeGradient() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
getVolumeGradient() - Method in class ffx.potential.nonbonded.implicit.GaussVol
getwA() - Method in class ffx.xray.cli.DataRefinementOptions: Getter for the field wA.
getWater() - Method in class ffx.potential.MolecularAssembly: getWater
getWaterNames() - Static method in class ffx.utilities.StringUtils: Returns a List of recognized water names (defensive copy).
getWebHost() - Method in class edu.rit.pj.cluster.Configuration: Returns the Job Scheduler's web interface host name.
getWebPort() - Method in class edu.rit.pj.cluster.Configuration: Returns the Job Scheduler's web interface port number.
getWeight() - Method in class ffx.numerics.clustering.Distance: Gets the weight.
getWeight() - Method in class ffx.numerics.math.RunningStatistics: Get the weight.
getWeight() - Method in class ffx.realspace.parsers.RealSpaceFile: Return the weight of this dataset.
getWeight() - Method in class ffx.realspace.RealSpaceData: getWeight
getWeight() - Method in class ffx.xray.CrystalReciprocalSpace: return dataset weight
getWeight() - Method in interface ffx.xray.DataContainer: getWeight
getWeight() - Method in class ffx.xray.DiffractionData: getWeight
getWeight() - Method in class ffx.xray.parsers.DiffractionFile: return the weight of this dataset
getWeight(int) - Method in class ffx.openmm.ThreeParticleAverageSite: Get the weight factor used for a particle this virtual site depends on.
getWeight(int) - Method in class ffx.openmm.TwoParticleAverageSite: Get the weight factor used for a particle this virtual site depends on.
getWeight12() - Method in class ffx.openmm.OutOfPlaneSite: Get the weight for the vector from particle1 to particle2.
getWeight13() - Method in class ffx.openmm.OutOfPlaneSite: Get the weight for the vector from particle1 to particle3.
getWeightCross() - Method in class ffx.openmm.OutOfPlaneSite: Get the weight for the cross product of the two vectors.
getWeights() - Method in class ffx.numerics.integrate.CompositeCurve: Gets the weights to the corresponding component curves.
getWeightValue() - Method in class ffx.numerics.clustering.Cluster: Convenience accessor for this cluster's aggregate weight.
getWindow() - Method in class ffx.algorithms.cli.ManyBodyOptions: Size of the sliding window with respect to adjacent residues (default = 7).
getWindows() - Method in class ffx.algorithms.cli.AnnealOptions: Number of annealing windows.
getWireFrame() - Method in class ffx.potential.MolecularAssembly: getWireFrame
getWn() - Method in class ffx.algorithms.mc.RosenbluthChiAllMove: getWn.
getWork() - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Get the total work for a given range of lambda bins.
getWorldAddress() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's array of hosts/ports for the world communicator.
getWorldChannelGroup() - Method in class edu.rit.pj.cluster.JobBackend: Obtain this job's world communicator channel group.
getWrite() - Method in class ffx.algorithms.cli.DynamicsOptions: Snapshot save frequency in picoseconds (1.0 psec default).
getWrittenFile() - Method in class ffx.potential.commands.Solvator
getX() - Method in interface ffx.numerics.integrate.DataSet: Returns copy of the array of points x (x-axis).
getX() - Method in class ffx.numerics.integrate.DoublesDataSet: Returns copy of the array of points x (x-axis).
getX() - Method in class ffx.numerics.integrate.FunctionDataCurve: Returns copy of the array of points x (x-axis).
getX() - Method in class ffx.potential.bonded.Atom: Gets the x coordinate
getX() - Method in class ffx.potential.nonbonded.octree.OctreeCell: Gets x coordinate of center of cell
getX() - Method in class ffx.potential.nonbonded.octree.OctreePoint
getX(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Get the X-value of the array at the specified index after calling the reduce method.
getXDim() - Method in class ffx.potential.nonbonded.ReciprocalSpace: getXDim
getXDim() - Method in class ffx.xray.CrystalReciprocalSpace: getXDim
getXFactor() - Method in class ffx.ui.behaviors.MouseOrbit: Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseProperties: Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseRotate: Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseSelection: Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseTranslate: Return the x-axis movement multipler.
getXMLAtomTypes(Document, ForceField) - Static method in class ffx.potential.parameters.AtomType: Create an AtomType Element.
getXMLElement(Document, ForceField) - Static method in class ffx.potential.parameters.PiOrbitalTorsionType: Create an AmoebaPiTorsionForce Element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.AngleTorsionType: Create an AmoebaAngleTorsionForce Element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.AngleType: Create an AmoebaAngleForce
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.BondType
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.MultipoleType: Create an AmoebaMultipoleForce Element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.OutOfPlaneBendType: Create an AmoebaOutOfPlaneBendForce instance.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.StretchBendType: Create an AmoebaStretchBendForce element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.StretchTorsionType: Create an AmoebaStretchTorsionForce Element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.TorsionTorsionType: Create an AmoebaTorsionTorsionForce Element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.TorsionType: Create a PeriodicTorsionForce Element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.UreyBradleyType: Create an AmoebaUreyBradleyForce element.
getXMLForce(Document, ForceField) - Static method in class ffx.potential.parameters.VDWType: Create an AmoebaVdwForce force node.
getXrayScaleTol() - Method in class ffx.xray.DiffractionData: Getter for the field xrayScaleTol.
getxWeight() - Method in class ffx.xray.DiffractionData: Getter for the field xWeight.
getXWeight() - Method in class ffx.xray.RefinementEnergy: Get the current data weight (wA).
getXWeights(PointerByReference) - Method in class ffx.openmm.LocalCoordinatesSite: Get the weights used for computing the x direction of the local coordinate system.
getXYMode() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Get the mode for scaling the XY dimensions.
getXYZ() - Method in class ffx.potential.bonded.Atom: getXYZ
getXYZ(double[]) - Method in class ffx.potential.bonded.Atom: getXYZ
getXYZGradient(double[]) - Method in class ffx.potential.bonded.Atom: getXYZGradient
getXyzIndex() - Method in class ffx.potential.bonded.Atom: Getter for the field xyzIndex.
getY() - Method in class ffx.potential.bonded.Atom: Gets the y coordinate
getY() - Method in class ffx.potential.nonbonded.octree.OctreeCell: Gets y coordinate of center of cell
getY() - Method in class ffx.potential.nonbonded.octree.OctreePoint
getY(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Get the Y-value of the array at the specified index after calling the reduce method.
getYDim() - Method in class ffx.potential.nonbonded.ReciprocalSpace: getYDim
getYDim() - Method in class ffx.xray.CrystalReciprocalSpace: getYDim
getYFactor() - Method in class ffx.ui.behaviors.MouseOrbit: Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseProperties: Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseRotate: Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseSelection: Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseTranslate: Return the y-axis movement multipler.
getYWeights(PointerByReference) - Method in class ffx.openmm.LocalCoordinatesSite: Get the weights used for computing the y direction of the local coordinate system.
getZ() - Method in class ffx.potential.bonded.Atom: Gets the z coordinate
getZ() - Method in class ffx.potential.nonbonded.octree.OctreeCell: Gets z coordinate of center of cell
getZ() - Method in class ffx.potential.nonbonded.octree.OctreePoint
getZ(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Get the Z-value of the array at the specified index after calling the reduce method.
getZDim() - Method in class ffx.potential.nonbonded.ReciprocalSpace: getZDim
getZDim() - Method in class ffx.xray.CrystalReciprocalSpace: getZDim
getZeroBound() - Method in class ffx.numerics.switching.BellCurveSwitch: Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.CompositeSwitch
getZeroBound() - Method in class ffx.numerics.switching.ConstantSwitch: Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.LinearDerivativeSwitch: Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.MultiplicativeSwitch: Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.PowerSwitch: Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.SquaredTrigSwitch: Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: Gets the zero bound, where f(x) becomes zero.
getZMode() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Get the mode for scaling the Z dimension.
GIF - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
GK - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
gkc - Variable in class ffx.potential.nonbonded.GeneralizedKirkwood: The Generalized Kirkwood cross-term parameter.
gkc - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion: Empirical constant that controls the GK cross-term.
GKCavitationForce - Class in ffx.openmm.amoeba: Implicit Solvent Cavitation Force.
GKCavitationForce() - Constructor for class ffx.openmm.amoeba.GKCavitationForce: Constructor.
gkDiameter - Variable in class ffx.potential.parameters.SoluteType: Solute atomic diameter for GK.
GKEnergyGlobal - Class in ffx.numerics.multipole: GKEnergyGlobal computes the generalized Kirkwood energy and forces in a global frame.
GKEnergyGlobal(double, double, boolean) - Constructor for class ffx.numerics.multipole.GKEnergyGlobal: Constructor for GKEnergyGlobal.
GKEnergyGlobalSIMD - Class in ffx.numerics.multipole: GKEnergyGlobal computes the generalized Kirkwood energy and forces in a global frame.
GKEnergyGlobalSIMD(double, double, boolean) - Constructor for class ffx.numerics.multipole.GKEnergyGlobalSIMD: Constructor for GKEnergyGlobal.
GKEnergyQI - Class in ffx.numerics.multipole: The GKEnergyQI class computes the Generalized Kirkwood energy and forces using a QI frame.
GKEnergyQI(double, double, double, boolean) - Constructor for class ffx.numerics.multipole.GKEnergyQI: Compute the GK Energy using a QI frame.
GKEnergyQISIMD - Class in ffx.numerics.multipole: The GKEnergyQI class computes the Generalized Kirkwood energy and forces using a QI frame.
GKEnergyQISIMD(double, double, double, boolean) - Constructor for class ffx.numerics.multipole.GKEnergyQISIMD: Compute the GK Energy using a QI frame.
GKEnergyRegion - Class in ffx.potential.nonbonded.implicit: Parallel calculation of the Generalized Kirkwood reaction field energy.
GKEnergyRegion(int, Polarization, GeneralizedKirkwood.NonPolarModel, double, double, double, double, double, double, boolean) - Constructor for class ffx.potential.nonbonded.implicit.GKEnergyRegion
gkEnergyTotal - Variable in class ffx.potential.nonbonded.pme.PMETimings
GKMultipoleOrder - Enum Class in ffx.numerics.multipole: The GK tensor can be constructed for a monopole potential (GB), a dipole potential or a quadrupole potential.
GKSource - Class in ffx.numerics.multipole: The GKSource class generates the source terms for the Generalized Kirkwood version of the tensor recursion.
GKSource(int, double) - Constructor for class ffx.numerics.multipole.GKSource: Construct a new GKSource object.
GKSourceSIMD - Class in ffx.numerics.multipole: The GKSource class generates the source terms for the Generalized Kirkwood version of the tensor recursion.
GKSourceSIMD(int, double) - Constructor for class ffx.numerics.multipole.GKSourceSIMD: Construct a new GKSource object.
GKTensorGlobal - Class in ffx.numerics.multipole: The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood interaction tensors.
GKTensorGlobal(GKMultipoleOrder, int, GKSource, double, double) - Constructor for class ffx.numerics.multipole.GKTensorGlobal: Construct a new GKTensorGlobal object.
GKTensorGlobalSIMD - Class in ffx.numerics.multipole: The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood interaction tensors.
GKTensorGlobalSIMD(GKMultipoleOrder, int, GKSourceSIMD, double, double) - Constructor for class ffx.numerics.multipole.GKTensorGlobalSIMD: Construct a new GKTensorGlobal object.
GKTensorMode - Enum Class in ffx.numerics.multipole: The "mode" for the tensor (either POTENTIAL or BORN).
GKTensorQI - Class in ffx.numerics.multipole: The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood interaction tensors.
GKTensorQI(GKMultipoleOrder, int, GKSource, double, double) - Constructor for class ffx.numerics.multipole.GKTensorQI: Create a new GKTensorQI object.
GKTensorQISIMD - Class in ffx.numerics.multipole: The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood interaction tensors.
GKTensorQISIMD(GKMultipoleOrder, int, GKSourceSIMD, double, double) - Constructor for class ffx.numerics.multipole.GKTensorQISIMD: Create a new GKTensorQI object.
GLD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
GLH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
GLH1toGLH2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
GLHtoGLU - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
GLN - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
GLOBAL - Enum constant in enum class ffx.numerics.multipole.CoordinateSystem: Global coordinate system.
GlobalBehavior - Class in ffx.ui.behaviors: The GlobalBehavior class allows mouse control over camera position, adding a few functions to the OrbitBehavior class.
GlobalBehavior() - Constructor for class ffx.ui.behaviors.GlobalBehavior: Constructor for GlobalBehavior.
GlobalBehavior(Canvas3D) - Constructor for class ffx.ui.behaviors.GlobalBehavior: Constructor for GlobalBehavior.
globalMultipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Cartesian multipoles in the global frame with dimensions of [nsymm][nAtoms][10]
globalOptimization(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization: The main driver for optimizing a block of residues using DEE.
GLU - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
GLUTAMATE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
GLUTAMINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
GLY - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
GLYCINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
GO_PARALLEL - Static variable in class ffx.potential.bonded.ROLSP: Constant GO_PARALLEL=false
GoldsteinPairRegion - Class in ffx.algorithms.optimize.manybody
GoldsteinPairRegion(int) - Constructor for class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
goldsteinPairSumOverK(Residue[], int, int, int, int, int, int, int, int, List<Residue>, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization
grad - Variable in class ffx.algorithms.optimize.Minimize: The gradient.
grad - Variable in class ffx.algorithms.optimize.PhMinimize: The gradient.
gradESV - Variable in class ffx.algorithms.optimize.PhMinimize: The gradient.
gradient - Variable in class ffx.potential.SystemState: The gradient.
gradient() - Method in class ffx.potential.SystemState: Get a reference to the internal gradient array.
gradient() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the gradient record component.
Gradient - Class in ffx.potential.commands.test: The Gradient script evaluates the consistency of the energy and gradient.
Gradient() - Constructor for class ffx.potential.commands.test.Gradient: Gradient constructor.
Gradient(FFXBinding) - Constructor for class ffx.potential.commands.test.Gradient: Gradient constructor.
Gradient(String[]) - Constructor for class ffx.potential.commands.test.Gradient: Gradient constructor that sets the command line arguments.
GradientOptions - Class in ffx.potential.cli: Represents command line options for scripts that test gradients.
GradientOptions() - Constructor for class ffx.potential.cli.GradientOptions
gradients - Variable in class ffx.ui.commands.SimulationUpdate
GradientSchedule - Class in ffx.xray: GradientSchedule class.
GradientSchedule(int, int) - Constructor for class ffx.xray.GradientSchedule: Constructor for GradientSchedule.
GradientUtils - Class in ffx.potential.utils: GradientUtils is a utility class for testing the gradient of a potential.
GradientUtils(Potential) - Constructor for class ffx.potential.utils.GradientUtils: Constructor.
GraphicsAxis - Class in ffx.ui: The GraphicsAxis class encapsulates the 3D Axis that is used to display and control rotation/translation in the global frame.
GraphicsCanvas - Class in ffx.ui: The GraphicsCanvas class provides a Canvas on which to render 3D Graphics.
GraphicsCanvas(MainPanel) - Constructor for class ffx.ui.GraphicsCanvas: Constructor for GraphicsCanvas.
GraphicsCanvas.ImageFormat - Enum Class in ffx.ui: The ImageFormat enum lists supported image formats.
GraphicsCanvas.LeftButtonMode - Enum Class in ffx.ui: The LeftButtonMode enum describes what the left mouse button does.
GraphicsCanvas.MouseMode - Enum Class in ffx.ui: The MouseMode enum describes what system is affected by mouse drags.
GraphicsEvents - Class in ffx.ui: The GraphicsEvents class listens for mouse events over the Java3D GraphicsCanvas, dispatching work to more specialized System Rotation and Translation Behaviors or to the GlobalOrbitBehavior.
GraphicsEvents(MainPanel, GraphicsCanvas, GraphicsAxis, SimpleUniverse, Bounds, BranchGroup, TransformGroup) - Constructor for class ffx.ui.GraphicsEvents: Constructor for GraphicsEvents.
GraphicsFullScreen - Class in ffx.ui: The FullScreenWindow class controls full screen graphics.
GraphicsFullScreen(Frame, GraphicsCanvas) - Constructor for class ffx.ui.GraphicsFullScreen: Constructor for GraphicsFullScreen.
GraphicsPanel - Class in ffx.ui: The GraphicsPanel class contains the 3D Canvas and its status box.
GraphicsPanel(GraphicsCanvas, JPanel) - Constructor for class ffx.ui.GraphicsPanel: Constructor for GraphicsPanel.
GraphicsPicking - Class in ffx.ui: The GraphicsPicking class is used to make selections and measurements.
GraphicsPicking(BranchGroup, Bounds, GraphicsCanvas, MainPanel) - Constructor for class ffx.ui.GraphicsPicking: Constructor
GraphicsPicking.PickLevel - Enum Class in ffx.ui
GraphicsPrefs - Class in ffx.ui: The GraphicsPrefs class allows users to select graphics preferences.
GraphicsSplitPane - Class in ffx.ui: The GraphicsSplitPane is an early attempt at working around issues caused by the heavyweight Canvas3D inside a lightweight Swing SplitPane.
GraphicsSplitPane() - Constructor for class ffx.ui.GraphicsSplitPane: Constructor for GraphicsSplitPane.
GraphicsSplitPane(int, boolean, Component, Component) - Constructor for class ffx.ui.GraphicsSplitPane: Constructor for GraphicsSplitPane.
gridDensity(int, int) - Method in class ffx.potential.nonbonded.SpatialDensityLoop: gridDensity
gridDensity(int, int, int, int) - Method in class ffx.potential.nonbonded.RowLoop: Apply electron density "as normal" for an atom, but check that the y and z indeces are within the supplied bounds (inclusive).
gridDensity(int, int, int, int) - Method in class ffx.potential.nonbonded.SliceLoop: Apply electron density "as normal" for an atom, but check that the z index is within the supplied bounds (inclusive).
GROUP - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
groupAdd(int) - Method in class ffx.potential.nonbonded.NeighborList.Cell
groupSelection(MSNode, MSNode) - Method in class ffx.ui.Hierarchy: groupSelection
growGroup(List<Integer>, Atom) - Static method in class ffx.potential.parameters.PolarizeType: A recursive method that checks all atoms bonded to the seed atom for inclusion in the polarization group.
GUA - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
GUANINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
guessRotamer(Residue) - Method in class ffx.potential.bonded.RotamerLibrary: Guess at what rotamer a residue is currently in.
guessTitrState - Variable in class ffx.potential.extended.ExtendedSystem
guided() - Static method in class edu.rit.pj.IntegerSchedule: Returns a self-guided schedule object with a minimum chunk size of 1.
guided() - Static method in class edu.rit.pj.LongSchedule: Returns a self-guided schedule object with a minimum chunk size of 1.
guided(int) - Static method in class edu.rit.pj.IntegerSchedule: Returns a self-guided schedule object with the given minimum chunk size.
guided(long) - Static method in class edu.rit.pj.LongSchedule: Returns a self-guided schedule object with the given minimum chunk size.

H

h - Variable in class ffx.crystal.HKL: The h-index of the reflection.
H - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
H - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
H - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
H - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
H - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
H2N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
H2O - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
H2U - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
HA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
HA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms
HA2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLY
HA2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
HA3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
halfBinComposite(double[], int, String) - Static method in class ffx.numerics.integrate.Integration: halfBinComposite.
HalfEdge - Class in ffx.numerics.quickhull: Represents the half-edges that surround each face in a counter-clockwise direction.
HalfEdge() - Constructor for class ffx.numerics.quickhull.HalfEdge: Constructs an uninitialized HalfEdge.
HalfEdge(Vertex, Face) - Constructor for class ffx.numerics.quickhull.HalfEdge: Constructs a HalfEdge with head vertex v and left-hand triangular face f.
halfStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic: The half-step temperature correction.
halfStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Berendsen: The half-step temperature correction.
halfStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Bussi: The half-step temperature correction.
halfStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: The half-step temperature correction.
halfWidthEnd - Variable in class ffx.numerics.integrate.FunctionDataCurve: If ends should have 1/2 regular separation.
halfWidthEnds() - Method in interface ffx.numerics.integrate.DataSet: Does this data set have half-width start/end bins.
halfWidthEnds() - Method in class ffx.numerics.integrate.DoublesDataSet: Does this data set have half-width start/end bins.
halfWidthEnds() - Method in class ffx.numerics.integrate.FunctionDataCurve: Does this data set have half-width start/end bins.
handleAbout() - Method in class ffx.ui.OSXAdapter
handleOpenFile(File) - Method in class ffx.ui.OSXAdapter
handlePrefs() - Method in class ffx.ui.OSXAdapter
handleQuit() - Method in class ffx.ui.OSXAdapter
HARMONIC - Enum constant in enum class ffx.potential.parameters.AngleType.AngleFunction
HARMONIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
HarmonicAngleForce - Class in ffx.openmm: This class implements an interaction between groups of three particles that varies harmonically with the angle between them.
HarmonicAngleForce() - Constructor for class ffx.openmm.HarmonicAngleForce: Create a new HarmonicAngleForce.
HarmonicBondForce - Class in ffx.openmm: This class implements an interaction between pairs of particles that varies harmonically with the distance between them.
HarmonicBondForce() - Constructor for class ffx.openmm.HarmonicBondForce: Create a new HarmonicBondForce.
HarmonicOscillatorsTestCase(double[], double[], double) - Constructor for class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
HARTREE_TO_KCAL_PER_MOL - Static variable in class ffx.utilities.Constants: Convert Hartree to kcal/mol.
hasAmoebaCavitationForce() - Method in class ffx.potential.openmm.OpenMMSystem
hasAttachedAtom(Atom, int) - Static method in class ffx.potential.bonded.BondedUtils: Checks if there is an Atom of a given atomic number bonded to the provided Atom.
hasContextPointer() - Method in class ffx.openmm.Context: Does the context have a pointer?
hasFlatBottom() - Method in enum class ffx.potential.parameters.BondType.BondFunction: Returns whether this BondFunction has a flat bottom.
hasFrontendCommunicator() - Method in class edu.rit.pj.cluster.JobBackend: Determine whether the frontend communicator exists in this job.
hashCode() - Method in class edu.rit.pj.io.StreamFile: Returns a hash code for this stream file.
hashCode() - Method in class edu.rit.util.LongRange: Returns a hash code for this range.
hashCode() - Method in class edu.rit.util.Range: Returns a hash code for this range.
hashCode() - Method in class ffx.crystal.Crystal
hashCode() - Method in class ffx.crystal.HKL
hashCode() - Method in class ffx.numerics.clustering.Cluster
hashCode() - Method in record class ffx.numerics.clustering.visualization.VCoord: Returns a hash code value for this object.
hashCode() - Method in record class ffx.numerics.fft.PassConstants: Returns a hash code value for this object.
hashCode() - Method in class ffx.potential.bonded.Atom
hashCode() - Method in class ffx.potential.bonded.BondedTerm
hashCode() - Method in class ffx.potential.bonded.Molecule
hashCode() - Method in class ffx.potential.bonded.MSNode
hashCode() - Method in class ffx.potential.bonded.MSRoot
hashCode() - Method in class ffx.potential.bonded.MultiResidue
hashCode() - Method in class ffx.potential.bonded.Polymer
hashCode() - Method in class ffx.potential.bonded.Residue
hashCode() - Method in class ffx.potential.bonded.ROLSP
hashCode() - Method in class ffx.potential.parameters.AngleTorsionType
hashCode() - Method in class ffx.potential.parameters.AngleType
hashCode() - Method in class ffx.potential.parameters.AtomType
hashCode() - Method in class ffx.potential.parameters.BioType
hashCode() - Method in class ffx.potential.parameters.BondType
hashCode() - Method in class ffx.potential.parameters.ImproperTorsionType
hashCode() - Method in class ffx.potential.parameters.MultipoleType
hashCode() - Method in class ffx.potential.parameters.OutOfPlaneBendType
hashCode() - Method in class ffx.potential.parameters.PiOrbitalTorsionType
hashCode() - Method in class ffx.potential.parameters.PolarizeType
hashCode() - Method in class ffx.potential.parameters.RelativeSolvationType
hashCode() - Method in class ffx.potential.parameters.SoluteType
hashCode() - Method in class ffx.potential.parameters.StretchBendType
hashCode() - Method in class ffx.potential.parameters.StretchTorsionType
hashCode() - Method in class ffx.potential.parameters.TorsionTorsionType
hashCode() - Method in class ffx.potential.parameters.TorsionType
hashCode() - Method in class ffx.potential.parameters.UreyBradleyType
hashCode() - Method in class ffx.potential.parameters.VDWPairType
hashCode() - Method in class ffx.potential.parameters.VDWType
hashCode() - Method in record class ffx.potential.UnmodifiableState: Returns a hash code value for this object.
hashCode() - Method in class ffx.ui.KeywordComponent
hashCode() - Method in record class ffx.utilities.DoubleIndexPair: Returns a hash code value for this object.
hashCode() - Method in record class ffx.utilities.IndexIndexPair: Returns a hash code value for this object.
hashCode() - Method in record class ffx.utilities.ObjectPair: Returns a hash code value for this object.
hasHKL(HKL) - Method in class ffx.crystal.ReflectionList: hasHKL
hasNext() - Method in class edu.rit.util.RandomSubset: Determine whether there are more integers in the random subset.
hasProperty(String) - Method in class ffx.potential.parameters.ForceField: Checks if a property was specified.
hasSoftcore() - Method in class ffx.potential.cli.AlchemicalOptions: If any softcore Atoms have been detected.
hasSoftcore() - Method in class ffx.potential.cli.TopologyOptions: If any softcore Atoms have been detected.
hasSubsystemThermostats() - Method in class ffx.openmm.NoseHooverIntegrator: Check if the integrator has subsystem thermostats.
hasVariable(String) - Method in class ffx.utilities.FFXBinding: Simple check for whether the context contains a particular variable or not.
HB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
HB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
HB1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ALA
HB11 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
HB12 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
HB13 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ALA
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYD
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYS
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYX
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.SER
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
HB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
HB2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
HB2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
HB2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HB21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
HB22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
HB23 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ALA
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYD
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYS
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYX
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.SER
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
HB3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
HB3 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
HB3 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
HB3 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
HD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
HD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
HD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
HD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
HD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
HD1 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
HD11 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HD11 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HD12 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HD12 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HD13 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HD13 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
HD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
HD2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
HD2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HD21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
HD21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HD22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
HD22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HD23 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HD3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HD3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HD3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HD3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HD3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
HD3 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
He - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
HE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
he0 - Variable in class ffx.numerics.quickhull.Face
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
HE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
HE1 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
HE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
HE2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
HE2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HE21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
HE22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
HE3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HE3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HE3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
HE3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HE3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HE3 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
head() - Method in class ffx.numerics.quickhull.HalfEdge: Returns the head vertex associated with this half-edge.
HEAD_METHOD - Static variable in class edu.rit.http.HttpRequest: The HEAD method string, "HEAD".
HeadlessMain - Class in ffx: The HeadlessMain class is the entry point to the command line version of Force Field X.
heavyAtoms - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
HELIX - Enum constant in enum class ffx.potential.bonded.Residue.SSType
help - Variable in class ffx.utilities.FFXCommand: -h or --help Prints a help message.
helpString() - Method in class ffx.utilities.FFXCommand: Default help information.
Hex - Class in edu.rit.util: Class Hex provides static methods for converting between hexadecimal strings and numbers of various kinds.
HEXAGONAL - Enum constant in enum class ffx.crystal.CrystalSystem: Hexagonal crystal system.
HEXAGONAL_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem: Hexagonal lattice system.
Hf - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Hg - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
HG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYS
HG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
HG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.SER
HG - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
HG1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
HG11 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
HG12 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HG12 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
HG13 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HG13 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
HG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
HG2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HG21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HG21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
HG21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
HG22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HG22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
HG22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
HG23 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
HG23 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
HG23 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
HG3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
HG3 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
HH11 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HH12 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HH2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HH21 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HH22 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
HHG - Enum constant in enum class ffx.potential.parameters.VDWType.EPSILON_RULE
HID - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
HID - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HisStates
HIDEHYDROGEN - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
HIDEVECTORS - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
HIDEVRML - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
HIDtoHIE - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
HIE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
HIE - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HisStates
hierarchicalClustering(List<double[]>, double) - Static method in class ffx.potential.utils.Clustering: This method performs hierarchical clustering on a distance matrix.
Hierarchy - Class in ffx.ui: The Hierarchy Class creates and manages a JTree view of the data structure.
HierarchyBuilder - Class in ffx.numerics.clustering: Performs agglomerative steps to build a clustering hierarchy from an initial set of singleton clusters and a map of pairwise distances.
HierarchyBuilder(List<Cluster>, DistanceMap) - Constructor for class ffx.numerics.clustering.HierarchyBuilder: Constructs a HierarchyBuilder with an initial set of clusters and inter-cluster distances.
highestOrderZeroDerivativeAtZeroBound() - Method in class ffx.numerics.switching.PowerSwitch: Power switch derivatives can be zero at the zero bound if the exponent is greater than the derivative order.
highestOrderZeroDerivativeAtZeroBound() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: Returns the highest-order, guaranteed-zero derivative at the zero bound.
highlightSelections - Static variable in class ffx.potential.bonded.RendererCache: Constant highlightSelections=false
HilbertCurveTransforms - Class in ffx.numerics.math: HilbertCurveTransforms is a class that provides static methods for converting between Hilbert indices and coordinates.
hilbertIndexToCoordinates(int, int, long) - Static method in class ffx.numerics.math.HilbertCurveTransforms: Convert a Hilbert index to coordinates.
HippoNonbondedForce - Class in ffx.openmm.amoeba: This class implements all nonbonded interactions in the HIPPO force field: electrostatics, induction, charge transfer, dispersion, and repulsion.
HippoNonbondedForce() - Constructor for class ffx.openmm.amoeba.HippoNonbondedForce: Create a new HippoNonbondedForce.
HIS - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
HIS - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HisStates
HISTIDINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
Histogram - Class in ffx.algorithms.commands: The Histogram script prints out a Orthogonal Space histogram from a *.his file.
Histogram() - Constructor for class ffx.algorithms.commands.Histogram: Histogram Constructor.
Histogram(FFXBinding) - Constructor for class ffx.algorithms.commands.Histogram: Histogram Constructor.
Histogram(String[]) - Constructor for class ffx.algorithms.commands.Histogram: Histogram constructor that sets the command line arguments.
HistogramData - Class in ffx.algorithms.thermodynamics
HistogramData() - Constructor for class ffx.algorithms.thermodynamics.HistogramData
HistogramXmlAdapter - Class in ffx.utilities: Write/read Histogram data to/from a String.
HistogramXmlAdapter() - Constructor for class ffx.utilities.HistogramXmlAdapter: Default constructor.
HIStoHID - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
HIStoHIE - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
HKL - Class in ffx.crystal: The HKL class represents a single reflection.
HKL() - Constructor for class ffx.crystal.HKL: Constructor for HKL.
HKL(int, int, int) - Constructor for class ffx.crystal.HKL: Constructor for HKL.
HKL(int, int, int, int, int) - Constructor for class ffx.crystal.HKL: Constructor for HKL.
hklList - Variable in class ffx.crystal.ReflectionList: The HKL list.
Ho - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
HOH - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
horizon - Variable in class ffx.numerics.quickhull.QuickHull3D
host - Variable in class edu.rit.pj.cluster.BackendInfo: The host name for SSH remote logins to the backend.
host() - Method in class edu.rit.pj.Comm: Obtain the host name of this communicator's backend processor.
hrConversion(double, double, double, double, double, double, SpaceGroup) - Static method in class ffx.crystal.SpaceGroupConversions: Convert between hexagonal and rhombohedral space groups.
hrConversion(Crystal) - Static method in class ffx.crystal.SpaceGroupConversions: Convert between hexagonal and rhombohedral space groups.
Hs - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
HTTP_1_0_VERSION - Static variable in class edu.rit.http.HttpRequest: The HTTP/1.0 version string "HTTP/1.0".
HTTP_1_1_VERSION - Static variable in class edu.rit.http.HttpRequest: The HTTP/1.1 version string, "HTTP/1.1".
HttpRequest - Class in edu.rit.http: Class HttpRequest encapsulates an HTTP request received from a web browser.
HttpRequest(Socket) - Constructor for class edu.rit.http.HttpRequest: Construct a new HTTP request.
HttpResponse - Class in edu.rit.http: Class HttpResponse encapsulates an HTTP response returned to a web browser.
HttpResponse(Socket) - Constructor for class edu.rit.http.HttpResponse: Construct a new HTTP response.
HttpResponse.Status - Enum Class in edu.rit.http: Enumeration HttpResponse.Status enumerates the status codes for an HTTP response message.
HttpServer - Class in edu.rit.http: Class HttpServer provides a lightweight HTTP/1.0 server.
HttpServer(InetSocketAddress) - Constructor for class edu.rit.http.HttpServer: Construct a new HTTP server.
HttpServer(InetSocketAddress, Logger) - Constructor for class edu.rit.http.HttpServer: Construct a new HTTP server.
Hybrid36 - Class in ffx.utilities: Java port of the hy36encode() and hy36decode() functions in the hybrid_36.py Python prototype/reference implementation.
HybridTeam - Class in edu.rit.pj: Class HybridTeam provides a team of threads, distributed across the processes of a cluster parallel program, for executing a WorkerRegion in parallel.
HybridTeam() - Constructor for class edu.rit.pj.HybridTeam: Construct a new hybrid team with the default number of threads per process and using the world communicator for message passing.
HybridTeam(int) - Constructor for class edu.rit.pj.HybridTeam: Construct a new hybrid team with the given number of threads per process and using the world communicator for message passing.
HybridTeam(int, Comm) - Constructor for class edu.rit.pj.HybridTeam: Construct a new hybrid team with the given number of threads per process and using the given communicator for message passing.
HybridTeam(Comm) - Constructor for class edu.rit.pj.HybridTeam: Construct a new hybrid team with the default number of threads per process and using the given communicator for message passing.
HYDROPHOBIC_PMF - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
HydrophobicPMFRegion - Class in ffx.potential.nonbonded.implicit: Initial implementation of a Hydrophobic PMF.
HydrophobicPMFRegion(Atom[], double[], double[], double[], boolean[], double[][][], int) - Constructor for class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
HZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
HZ1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HZ1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HZ1 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HZ2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
HZ2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HZ2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HZ2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
HZ3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
HZ3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
HZ3 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames

I

i - Variable in class ffx.potential.nonbonded.NeighborList.AtomIndex
I - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
I - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
I - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
I - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
i0() - Method in class ffx.crystal.ReflectionSpline: i0
i0(double) - Static method in class ffx.numerics.special.ModifiedBessel: Modified zero-order Bessel function.
i1() - Method in class ffx.crystal.ReflectionSpline: i1
i1(double) - Static method in class ffx.numerics.special.ModifiedBessel: Modified 1st-order Bessel function.
i1OverI0(double) - Static method in class ffx.numerics.special.ModifiedBessel: Compute the ratio of i1(x) to i0(x).
i2() - Method in class ffx.crystal.ReflectionSpline: i2
IAMOEBA_WATER - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
id - Variable in class ffx.potential.bonded.BondedTerm: ID of this BondedTerm.
id - Variable in class ffx.ui.behaviors.MouseBehavior
identifyHullAtoms(QuickHull3D, Atom[]) - Static method in class ffx.potential.utils.ConvexHullOps: UNTESTED: Identifies atoms forming the convex hull.
IdentifyRotamers - Class in ffx.algorithms.commands.test: The IdentifyRotamers script attempts to identify which rotamer each Residue in the system is in.
IdentifyRotamers() - Constructor for class ffx.algorithms.commands.test.IdentifyRotamers: IdentifyRotamers Constructor.
IdentifyRotamers(FFXBinding) - Constructor for class ffx.algorithms.commands.test.IdentifyRotamers: IdentifyRotamers Constructor.
IdentifyRotamers(String[]) - Constructor for class ffx.algorithms.commands.test.IdentifyRotamers: IdentifyRotamers constructor that sets the command line arguments.
IDLE - Enum constant in enum class edu.rit.pj.cluster.BackendInfo.State: The backend is available for jobs.
ifft(double[]) - Method in class ffx.numerics.fft.Complex3D: Compute the inverse 3D FFT.
ifft(double[]) - Method in class ffx.numerics.fft.Complex3DParallel: Compute the inverse 3D FFT in parallel.
ifft(double[]) - Method in class ffx.numerics.fft.Real3D: Compute the inverse 3D FFT.
ifft(double[]) - Method in class ffx.numerics.fft.Real3DParallel: Compute the inverse 3D FFT.
ifft(double[], int) - Method in class ffx.numerics.fft.Complex2D: Compute the 2D IFFT.
ifft(double[], int) - Method in class ffx.numerics.fft.Real: ifft
ifft(double[], int, int) - Method in class ffx.numerics.fft.Complex: Compute the (un-normalized) inverse FFT of data, leaving it in place.
ifft(double[], int, int, int) - Method in class ffx.numerics.fft.Complex: Compute the (un-normalized) inverse FFT of data, leaving it in place.
ii - Variable in class ffx.numerics.fft.MixedRadixFactor: The increment for input data within the inner loop.
ik - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Atom indices used only by LambdaFactorsESV::print.
il - Variable in class ffx.numerics.multipole.MultipoleTensor: Order plus one.
il - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Order plus one.
ILE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
im - Variable in class ffx.numerics.fft.MixedRadixFactor: The imaginary offset.
im - Variable in class ffx.numerics.multipole.MultipoleTensor: im = (Order plus one)^2.
im - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: im = (Order plus one)^2.
im() - Method in record class ffx.numerics.fft.PassConstants: Returns the value of the im record component.
im() - Method in class ffx.numerics.math.ComplexNumber: im
im(double) - Method in class ffx.numerics.math.ComplexNumber: im
image(double[]) - Method in class ffx.crystal.Crystal: Apply the minimum image convention.
image(double[], double[]) - Method in class ffx.crystal.Crystal: Apply the minimum image convention.
image(double, double, double) - Method in class ffx.crystal.Crystal: Apply the minimum image convention.
ImplicitSolvent - Enum constant in enum class ffx.utilities.PropertyGroup: Implicit solvent functional form.
ImportCIF - Class in ffx.potential.commands: Convert a CIF file to PDB/XYZ format.
ImportCIF() - Constructor for class ffx.potential.commands.ImportCIF
ImportCIF(FFXBinding) - Constructor for class ffx.potential.commands.ImportCIF
ImportCIF(String[]) - Constructor for class ffx.potential.commands.ImportCIF
IMPROPER - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
IMPROPER - Enum constant in enum class ffx.potential.parameters.TorsionType.TorsionMode
ImproperTorsion - Class in ffx.potential.bonded: The ImproperTorsion class represents an Improper Torsion.
improperTorsionForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Improper Torsion Force.
ImproperTorsionForce - Class in ffx.potential.openmm: OpenMM Improper Torsion Force.
ImproperTorsionForce(ImproperTorsionPotentialEnergy) - Constructor for class ffx.potential.openmm.ImproperTorsionForce: Create an OpenMM Improper Torsion Force.
ImproperTorsionForce(ImproperTorsionPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.ImproperTorsionForce: Create a Dual Topology OpenMM Improper Torsion Force.
improperTorsionForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Improper Torsion Force for topology 2.
ImproperTorsionPotentialEnergy - Class in ffx.potential.terms: Improper Torsion potential energy term using ImproperTorsion instances.
ImproperTorsionPotentialEnergy(String) - Constructor for class ffx.potential.terms.ImproperTorsionPotentialEnergy: Create an ImproperTorsionPotentialEnergy with the provided name.
ImproperTorsionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.ImproperTorsionPotentialEnergy: Create an ImproperTorsionPotentialEnergy with the provided name and force group.
ImproperTorsionPotentialEnergy(String, int, List<ImproperTorsion>) - Constructor for class ffx.potential.terms.ImproperTorsionPotentialEnergy: Create an ImproperTorsionPotentialEnergy initialized with a list of terms and force group.
ImproperTorsionPotentialEnergy(String, Collection<ImproperTorsion>) - Constructor for class ffx.potential.terms.ImproperTorsionPotentialEnergy: Create an ImproperTorsionPotentialEnergy initialized with a collection of terms.
improperTorsionTime - Static variable in class ffx.potential.bonded.MSGroup: Constant torsionTorsionTime=0
ImproperTorsionType - Class in ffx.potential.parameters: The ImproperTorsionType class defines an improper torsion.
ImproperTorsionType(int[], double, double, int) - Constructor for class ffx.potential.parameters.ImproperTorsionType: TorsionType Constructor.
improperType - Variable in class ffx.potential.bonded.ImproperTorsion: Force field parameters to compute the ImproperTorsion energy.
IMPTORS - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
impTorUnit - Variable in class ffx.potential.parameters.ImproperTorsionType: Convert angle bending energy to kcal/mole.
in - Variable in class edu.rit.pj.cluster.BackendFileReader: Input stream for reading from the job frontend's standard input.
in - Variable in class ffx.numerics.fft.PassData
in - Variable in class ffx.numerics.multipole.MultipoleTensor: in = (Order plus one)^3.
in - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: in = (Order plus one)^3.
in() - Static method in class edu.rit.io.Stdio: Get the standard input stream for the calling thread.
in(InputStream) - Static method in class edu.rit.io.Stdio: Set the standard input stream for the calling thread.
In - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
IN_PLANE - Enum constant in enum class ffx.potential.parameters.AngleType.AngleMode
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedByte: Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedCharacter: Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedDouble: Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedFloat: Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedInteger: Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedLong: Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedShort: Add one to this reduction variable and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedByteArray: Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedFloatArray: Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedLongArray: Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedShortArray: Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Add one to this matrix reduction variable at the given row and column and return the new value.
incrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Add one to this matrix reduction variable at the given row and column and return the new value.
incrementClasses(int) - Method in class ffx.potential.parameters.AngleTorsionType: incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.AngleType: incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.BondType: incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.ImproperTorsionType: incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.OutOfPlaneBendType: incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.PiOrbitalTorsionType: incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.StretchBendType: Increment the atom classes by a given value.
incrementClasses(int) - Method in class ffx.potential.parameters.StretchTorsionType: Increment the atom classes by a specified amount.
incrementClasses(int) - Method in class ffx.potential.parameters.TorsionTorsionType: Increment the atom classes by a value.
incrementClasses(int) - Method in class ffx.potential.parameters.TorsionType: Increment the atom classes by a specified amount.
incrementClasses(int) - Method in class ffx.potential.parameters.UreyBradleyType: Increment the atom classes by a specified amount.
incrementClasses(int) - Method in class ffx.potential.parameters.VDWPairType: Increment the atom classes by a specified amount.
incrementType(int) - Method in class ffx.potential.parameters.ChargeType: incrementType
INDEPENDENT - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
independentWrite() - Method in class ffx.algorithms.thermodynamics.HistogramData: Returns the value of independentWrite.
index - Variable in class ffx.crystal.HKL: The unique index of this reflection.
index - Variable in class ffx.potential.parameters.BioType: The index of this BioType.
index() - Method in record class ffx.utilities.DoubleIndexPair: Returns the value of the index record component.
index(int, int, int) - Method in class ffx.potential.nonbonded.SpatialDensityRegion: index
index3D(int, int, int, int, int, DataLayout3D) - Static method in class ffx.numerics.fft.Complex3D: Determine the index of the complex number in the blocked 1D array from the X, Y and Z indices.
INDEXED_FROM_ONE - Static variable in class ffx.numerics.quickhull.QuickHull3D: Specifies that (on output) the vertex indices for a face should be numbered starting from 1.
INDEXED_FROM_ZERO - Static variable in class ffx.numerics.quickhull.QuickHull3D: Specifies that (on output) the vertex indices for a face should be numbered starting from 0.
IndexIndexPair - Record Class in ffx.utilities: The IndexIndexPair record.
IndexIndexPair(int, int) - Constructor for record class ffx.utilities.IndexIndexPair: Creates an instance of a IndexIndexPair record class.
induced - Variable in class ffx.ui.commands.SimulationUpdate
inducedDipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.DirectRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.OPTRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.PermanentFieldRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.SORRegion: Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.ScfPredictor: Dimensions of [nsymm][nAtoms][3]
INDUCEDDIPOLE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
inducedDipoleCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.OPTRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.PermanentFieldRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.SORRegion
inducedDipoleCR - Variable in class ffx.potential.nonbonded.ScfPredictor
InducedDipoleFieldReduceRegion - Class in ffx.potential.nonbonded.pme: Parallel summation and reduction of components of the induced dipole field at each atom.
InducedDipoleFieldReduceRegion(int) - Constructor for class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
InducedDipoleFieldRegion - Class in ffx.potential.nonbonded.pme: Parallel calculation of the induced dipole field.
InducedDipoleFieldRegion(ParallelTeam, ForceField, boolean) - Constructor for class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
InducedFileFilter - Class in ffx.potential.parsers: The InducedFileFilter class is used to choose a TINKER induced dipole (*.IND) file.
InducedFileFilter() - Constructor for class ffx.potential.parsers.InducedFileFilter: Default Constructor.
InducedFilter - Class in ffx.potential.parsers: The InducedFilter class parses TINKER Induced Dipole (*.
InducedFilter(MolecularAssembly, File) - Constructor for class ffx.potential.parsers.InducedFilter: Constructor for InducedFilter.
InducedGKFieldRegion - Class in ffx.potential.nonbonded.implicit: Parallel calculation of the Generalized Kirkwood induced reaction field.
InducedGKFieldRegion(int, double, double, double) - Constructor for class ffx.potential.nonbonded.implicit.InducedGKFieldRegion: Compute the GK field due to induced dipoles.
inducedRealSpaceEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
inducedReciprocalEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
inducedSelfEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
info() - Method in class edu.rit.mp.Channel: Obtain this channel's information object.
info(Object) - Method in class edu.rit.mp.Channel: Set this channel's information object.
inInverseResSqRange(double) - Method in class ffx.crystal.Resolution: inInverseResSqRange
init() - Method in class ffx.algorithms.cli.AlgorithmsCommand: Initialize this Command based on the specified command line arguments.
init() - Method in class ffx.algorithms.cli.DynamicsOptions: Parse the thermostat and integrator.
init() - Method in class ffx.potential.cli.PotentialCommand: Initialize this Command based on the specified command line arguments.
init() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
init() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
init() - Method in class ffx.potential.nonbonded.pme.PMETimings
init() - Method in class ffx.utilities.FFXCommand: Initialize this Command based on the specified command line arguments.
init() - Method in class ffx.xray.cli.XrayOptions: Parse options.
init(boolean, boolean, Atom[], double[][][], MultipoleType.MultipoleFrameDefinition[], int[][], AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.pme.ReduceRegion
init(boolean, AlchemicalParameters, ExtendedSystem, Atom[], double[][][], Crystal, MultipoleType.MultipoleFrameDefinition[], int[][], double[][][], double[][][], double[][][], double[], double[], double[], double[], double[], boolean[], int[][][], int[][][], AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.pme.InitializationRegion
init(int[][], MultipoleType.MultipoleFrameDefinition[], double[][][]) - Method in class ffx.potential.nonbonded.pme.Torque
init(int, Atom[], double[], double[][][], double[][][], double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, boolean, GeneralizedKirkwood, EwaldParameters, double) - Method in class ffx.potential.nonbonded.pme.OPTRegion
init(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics: A version of init with the original method header.
init(long, double, double, double, String, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics: init
init(long, double, double, double, String, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: init
init(DistanceMatrix, MolecularAssembly, Residue[], AlgorithmListener, DistanceMatrix.NeighborDistances[][]) - Method in class ffx.algorithms.optimize.manybody.DistanceRegion
init(EnergyExpansion, Residue[], int[], boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
init(Atom[], boolean) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion: Initialize this VolumeRegion instance for an energy evaluation.
init(Atom[], double[][][], double[][][], boolean, GeneralizedKirkwood, EwaldParameters, double, double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
init(Atom[], double[][][], double[][][], double[][][], Crystal, double[][][], int[][][], boolean[], double, double[], double[], boolean, ParallelTeam, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray) - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
init(Atom[], double[][][], double[][][], Crystal, double[][][], int[][][], boolean[], double, double[], AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.InducedGKFieldRegion
init(Atom[], double[][][], double[], double[], double[], boolean[], Crystal, double[][][], double[][][], double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, EwaldParameters, double, ParallelTeam, IntegerSchedule, PMETimings) - Method in class ffx.potential.nonbonded.pme.PCGSolver
init(Atom[], double[][][], Crystal, double[][][], int[][][], boolean[], double, double[], AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.PermanentGKFieldRegion
init(Atom[], double[], double[][][], double[][][], double[][], double[][], double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, boolean, GeneralizedKirkwood, EwaldParameters) - Method in class ffx.potential.nonbonded.pme.SORRegion
init(Atom[], double[], double[][][], double[][], double) - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
init(Atom[], double[], double[][][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, boolean, GeneralizedKirkwood, EwaldParameters, double, double[][][], double[][][], double[][], double[][], double[][], double[][]) - Method in class ffx.potential.nonbonded.pme.DirectRegion
init(Atom[], Crystal, boolean[], int[][][], double[], double[], double[], double, boolean, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: Initialize the DispersionRegion for energy calculation.
init(Atom[], Crystal, boolean[], int[], double[], double[], double[][][], RealSpaceNeighborParameters, double[][][], double[][][], boolean, ReciprocalSpace, LambdaMode, EwaldParameters, AtomicDoubleArray3D, AtomicDoubleArray3D, PMETimings) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
init(Atom[], Crystal, boolean, boolean, boolean, boolean[], double[][][], double[][][], double[][][], double[][][], double[][], double[][], Polarization, double[][][], double[][][], double[][], double[][], double[][], double[][], ReciprocalSpace, AlchemicalParameters, ExtendedSystem, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, SharedDouble, SharedDouble) - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
init(Atom[], Crystal, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
init(Atom[], Crystal, double[][][], double[][][], double[][][], double[][][], int[][][], ScaleParameters, boolean[], int[], double[], double[], int[][], int[][], int[][], int[][], LambdaMode, boolean, ReciprocalSpace, EwaldParameters, PCGSolver, IntegerSchedule, RealSpaceNeighborParameters, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
init(Atom[], Crystal, double[][][], int[][][], double[], double[], double[], double[], double, boolean[], double, boolean, double[]) - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
init(Atom[], Crystal, double[][][], int[][][], double[], double[], double[], double[], double, double[], boolean[], double, boolean, double[], AtomicDoubleArray3D, AtomicDoubleArray) - Method in class ffx.potential.nonbonded.implicit.BornGradRegion
init(Atom[], Crystal, ExtendedSystem, boolean, double[][][], MultipoleType.MultipoleFrameDefinition[], int[][], double[][][], double[][][], double[][][], double[][][], double[][][], boolean[], int[], int[][], int[][], int[][], int[][], int[][], boolean[], double[], double[], RealSpaceNeighborParameters, boolean, boolean, boolean, LambdaMode, Polarization, EwaldParameters, ScaleParameters, AlchemicalParameters, long[], AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, SharedDouble, SharedDouble) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
init(Residue[], int, int, int, int, int, int, int[][], RotamerOptimization) - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion: Initializes a ParallelRegion to attempt the elimination of riA,rjC by riB,rjD.
init(GeneralizedKirkwood, Atom[], boolean, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray) - Method in class ffx.potential.nonbonded.implicit.InitializationRegion
init(ForceField) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters
init(String[]) - Static method in class edu.rit.pj.Comm: Initialize the PJ message passing middleware.
initBorn(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Initialize for computing Born chain-rule terms.
initBorn(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyQI: Initialize for computing Born chain-rule terms.
initBorn(DoubleVector[], DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Initialize for computing Born chain-rule terms.
initBorn(DoubleVector[], DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Initialize for computing Born chain-rule terms.
initBuffers(int) - Method in class ffx.numerics.quickhull.QuickHull3D: (Re)initializes internal buffers and lists for a hull build of nump points.
initEsvIndElec() - Method in class ffx.potential.extended.ExtendedSystem: Zero out each array element of the indElec ESV array
initEsvPermElec() - Method in class ffx.potential.extended.ExtendedSystem: Zero out each array element of the permElec ESV array
initEsvVdw() - Method in class ffx.potential.extended.ExtendedSystem: Zero out each array element of the vdW ESV array
initEwaldSource(int, double, double[]) - Static method in class ffx.numerics.multipole.EwaldTensorGlobal: Initialize the Ewald source terms.
initFraction(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization: Init fraction array
InitializationRegion - Class in ffx.potential.nonbonded.implicit: Parallel initialization of accumulation arrays for Generalized Kirkwood.
InitializationRegion - Class in ffx.potential.nonbonded.pme: Parallel initialization of accumulation arrays, expand atomic coordinates and rotation of multipoles into the global frame.
InitializationRegion(int) - Constructor for class ffx.potential.nonbonded.implicit.InitializationRegion
InitializationRegion(ParticleMeshEwald, int, ForceField) - Constructor for class ffx.potential.nonbonded.pme.InitializationRegion
initialize() - Method in class ffx.potential.Renderer
initialize() - Method in class ffx.ui.behaviors.MouseBehavior: initialize
initialize() - Method in class ffx.ui.behaviors.MouseOrbit: initialize
initialize() - Method in class ffx.ui.behaviors.MouseProperties: initialize
initialize() - Method in class ffx.ui.behaviors.MouseRotate: initialize
initialize() - Method in class ffx.ui.behaviors.MouseSelection: initialize
initialize() - Method in class ffx.ui.behaviors.MouseTranslate: initialize
initialize() - Method in class ffx.ui.behaviors.MouseZoom: initialize
initialize() - Method in class ffx.ui.behaviors.PickMouseBehavior: initialize
initialize() - Method in class ffx.ui.GraphicsEvents: initialize
initialize() - Method in class ffx.ui.MainPanel: initialize
initializeDefaultAtomicCoordinates() - Method in class ffx.potential.bonded.Residue: Initializes this (presumably nucleic acid) Residue's C1s, O4s, C4s, O3sNorth, and O3sSouth default coordinates based on default PDB atom locations; to preserve rotamer independence, this must be called before any NA rotamers are applied.
initializeDefaultAtomicCoordinates(Polymer[]) - Static method in class ffx.potential.bonded.RotamerLibrary: Initializes default coordinates (presently PDB coordinates) for key atoms in all nucleic acid Residues.
initialState - Variable in class ffx.algorithms.dynamics.MolecularDynamics: State of the system as of the last init call (and start of the last dynamics run).
initMain(String[], List<String>) - Static method in class ffx.Main: Process the input arguments into a List, start the logging, start Parallel Java and process the input command.
initPotential(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Initialize the potential.
initPotential(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyQI: Initialize the potential.
initPotential(DoubleVector[], DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Initialize the potential.
initPotential(DoubleVector[], DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Initialize the potential.
initRandomData(int, ParallelTeam) - Static method in class ffx.numerics.fft.Complex3DParallel: Initialize a 3D data for testing purposes.
initRotamerOptimization(RotamerOptimization, MolecularAssembly) - Method in class ffx.algorithms.cli.ManyBodyOptions: initRotamerOptimization.
initTiming() - Method in class ffx.numerics.fft.Complex3DParallel: Initialize the timing array.
initTimings() - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
initTimings() - Method in class ffx.potential.nonbonded.ReciprocalSpace: initTimings.
initVelocities - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Flag to indicate velocities should be initialized.
innerLoopLimit - Variable in class ffx.numerics.fft.MixedRadixFactor: The inner loop limit (product / factor).
inOffset - Variable in class ffx.numerics.fft.PassData
inPlaneAngleForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom In-Plane Angle Force
InPlaneAngleForce - Class in ffx.potential.openmm: OpenMM In-Plane Angle Force.
InPlaneAngleForce(AnglePotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.InPlaneAngleForce: Create a Dual Topology OpenMM Angle Force.
InPlaneAngleForce(AnglePotentialEnergy, OpenMMEnergy) - Constructor for class ffx.potential.openmm.InPlaneAngleForce: Create an OpenMM Angle Force.
inPlaneAngleForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom In-Plane Angle Force for topology 2.
input - Variable in class ffx.numerics.fft.Complex3DParallel: This is a reference to the input array for convenience.
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.FrontendFileReader: Close the given input file.
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontend: Close the given input file.
inputFileClose(JobBackendRef, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "input file close" message.
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Close the given input file.
inputFileClose(JobBackendRef, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Close the given input file.
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Close the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader: Report the result of closing the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of closing the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "input file close result" message.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of closing the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of closing the given input file.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.FrontendFileReader: Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.JobFrontend: Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "input file open" message.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Open the given input file for reading.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader: Report the result of opening the given input file.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of opening the given input file.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "input file open result" message.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of opening the given input file.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of opening the given input file.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.FrontendFileReader: Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.JobFrontend: Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "input file read" message.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Read bytes from the given input file.
inputFileReadResult(JobFrontendRef, int, byte[], int, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, byte[], int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, byte[], int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader: Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "input file read result" message.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.FrontendFileReader: Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.JobFrontend: Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "input file skip" message.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Skip bytes from the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader: Report the result of skipping the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of skipping the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "input file skip result" message.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of skipping the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of skipping the given input file.
inResolutionRange(double) - Method in class ffx.crystal.Resolution: inResolutionRange
insert(int) - Method in class ffx.openmm.IntSet: Insert a value into the set.
insertUpdate(DocumentEvent) - Method in class ffx.ui.KeywordComponent
Instance - Class in edu.rit.util: Class Instance provides static methods for creating instances of classes.
INT - Enum constant in enum class ffx.potential.Utilities.FileType
IntArray - Class in ffx.openmm: Int Array.
IntArray(int) - Constructor for class ffx.openmm.IntArray: Constructor.
Integer() - Constructor for class edu.rit.util.Searching.Integer
Integer() - Constructor for class edu.rit.util.Sorting.Integer
IntegerArrayBuf - Class in edu.rit.mp.buf: Class IntegerArrayBuf provides a buffer for an array of integer items sent or received using the Message Protocol (MP).
IntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.IntegerArrayBuf: Construct a new integer array buffer.
IntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class IntegerArrayBuf_1 provides a buffer for an array of integer items sent or received using the Message Protocol (MP).
IntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.IntegerArrayBuf_1: Construct a new integer array buffer.
IntegerBuf - Class in edu.rit.mp: Class IntegerBuf is the abstract base class for a buffer of integer items sent or received using the Message Protocol (MP).
IntegerBuf(int) - Constructor for class edu.rit.mp.IntegerBuf: Construct a new integer buffer.
IntegerForLoop - Class in edu.rit.pj: Class IntegerForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
IntegerForLoop() - Constructor for class edu.rit.pj.IntegerForLoop: Construct a new parallel for loop.
IntegerItemBuf - Class in edu.rit.mp.buf: Class IntegerItemBuf provides a buffer for a single integer item sent or received using the Message Protocol (MP).
IntegerItemBuf() - Constructor for class edu.rit.mp.buf.IntegerItemBuf: Construct a new integer item buffer.
IntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.IntegerItemBuf: Construct a new integer item buffer with the given initial value.
IntegerMatrixBuf - Class in edu.rit.mp.buf: Class IntegerMatrixBuf provides a buffer for a matrix of integer items sent or received using the Message Protocol (MP).
IntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.IntegerMatrixBuf: Construct a new integer matrix buffer.
IntegerMatrixBuf_1 - Class in edu.rit.mp.buf: Class IntegerMatrixBuf_1 provides a buffer for a matrix of integer items sent or received using the Message Protocol (MP).
IntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.IntegerMatrixBuf_1: Construct a new integer matrix buffer.
IntegerOp - Class in edu.rit.pj.reduction: Class IntegerOp is the abstract base class for a binary operation on integer values, used to do reduction in a parallel program.
IntegerOp() - Constructor for class edu.rit.pj.reduction.IntegerOp: Construct a new integer binary operation.
IntegerSchedule - Class in edu.rit.pj: Class IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.
IntegerSchedule() - Constructor for class edu.rit.pj.IntegerSchedule: Construct a new schedule object.
IntegerStrideForLoop - Class in edu.rit.pj: Class IntegerStrideForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
IntegerStrideForLoop() - Constructor for class edu.rit.pj.IntegerStrideForLoop: Construct a new parallel for loop.
integralAt(double) - Method in class ffx.numerics.integrate.CompositeCurve: Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.CosineWave: Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.FunctionDataCurve: Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.PolynomialCurve: Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.SinWave: Analytical integral at a point.
integrate(int) - Method in class ffx.potential.openmm.OpenMMContext: Use the Context / Integrator combination to take the requested number of steps.
Integrate1DNumeric - Class in ffx.numerics.integrate: This program integrates using four methods: rectangular integration, the trapezoidal method, Simpson's Three Point Integration, and Boole's Five Point Integration.
Integrate1DNumeric.IntegrationSide - Enum Class in ffx.numerics.integrate: Left vs right-hand integration; left-hand integration will start from the first available point, run right as far as possible, and then clean up any remaining points using finishIntegration, while right-hand integration will start from the last available point, run left as far as possible, and then clean up any remaining points using finishIntegration.
Integrate1DNumeric.IntegrationType - Enum Class in ffx.numerics.integrate: Enumeration of implemented integration methods, and the number of points required by them.
integrateByBins(DataSet, Integrate1DNumeric.IntegrationSide, Integrate1DNumeric.IntegrationType) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Returns the contribution of each bin to the overall integral as an array; will be most accurate at break-points for the integration type.
integrateData(DataSet, Integrate1DNumeric.IntegrationSide, Integrate1DNumeric.IntegrationType) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Generic caller for 1D integration schemes given an IntegrationType.
integrateTransforms() - Method in class ffx.ui.behaviors.GlobalBehavior: integrateTransforms
Integration - Class in ffx.numerics.integrate: This program integrates using three methods: the trapezoidal method, Simpson's Three Point Integration, and Boole's Five Point Integration
integrator - Variable in class ffx.algorithms.cli.DynamicsOptions: Integrator.
integrator - Variable in class ffx.openmm.Context: The integrator used for this context.
Integrator - Class in ffx.algorithms.dynamics.integrators: The Integrator class is responsible for propagation of degrees of freedom through time.
Integrator - Class in ffx.openmm: An Integrator defines a method for simulating a System by integrating the equations of motion.
Integrator(PointerByReference) - Constructor for class ffx.openmm.Integrator: Constructor.
Integrator(SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.Integrator: Constructor for Integrator.
IntegratorEnum - Enum Class in ffx.algorithms.dynamics.integrators: An enumeration of available integrators.
intensitiesToAmplitudes() - Method in class ffx.xray.DiffractionRefinementData: Generate amplitudes from intensities.
interfacialRadiusA - Variable in class ffx.crystal.Crystal: Interfacial radius in the direction of the A-axis.
interfacialRadiusB - Variable in class ffx.crystal.Crystal: Interfacial radius in the direction of the B-axis.
interfacialRadiusC - Variable in class ffx.crystal.Crystal: Interfacial radius in the direction of the C-axis.
interleaved(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor5: Handle factors of 5.
INTERLEAVED - Enum constant in enum class ffx.numerics.fft.DataLayout1D: Interleaved data layout.
INTERLEAVED - Enum constant in enum class ffx.numerics.fft.DataLayout2D: Interleaved data layout.
INTERLEAVED - Enum constant in enum class ffx.numerics.fft.DataLayout3D: Interleaved data layout.
interleavedIndex(int, int, int, int, int) - Static method in class ffx.numerics.fft.Complex3D: Determine the index of the complex number in the 1D array from the X, Y and Z indices.
intermolecular - Variable in class ffx.ui.commands.SimulationUpdate
InternalErrorException - Exception Class in ffx.numerics.quickhull: Exception thrown when QuickHull3D encounters an internal error.
InternalErrorException(String) - Constructor for exception class ffx.numerics.quickhull.InternalErrorException: Constructs an InternalErrorException with a message describing the error.
interResidueDistance(double[][], double[][], SymOp) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Calculates the minimum distance between two sets of coordinates in a given symmetry operator.
interrupt() - Method in class ffx.ui.SwingWorker: A new method that interrupts the worker thread.
INTFileFilter - Class in ffx.potential.parsers: The INTFileFilter class is used to choose TINKER Internal Coordinate (*.INT) files.
INTFileFilter() - Constructor for class ffx.potential.parsers.INTFileFilter: Default Constructor.
INTFilter - Class in ffx.potential.parsers: The INTFilter class parses TINKER internal coordinate (*.INT) files.
INTFilter(File, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.INTFilter: Constructor for INTFilter.
INTFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.INTFilter: Constructor for INTFilter.
IntplnErr - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Interpolation error occurred.
intra12Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: An intra-12-scale factor other than 0.0 is not supported and will cause FFX to exit.
intra13Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: An intra-13-scale factor other than 0.0 is not supported and will cause FFX to exit.
intra14Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: Provides a multiplicative scale factor that is applied to polarization interactions between 1-4 connected atoms located in the same polarization group.
intra15Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: An intra-15-scale factor other than 1.0 is not supported and will cause FFX to exit.
IntSet - Class in ffx.openmm: Int Set.
IntSet() - Constructor for class ffx.openmm.IntSet: Constructor.
intToProteinLibrary(int) - Static method in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary: Converts an integer to a corresponding ProteinLibrary.
intValue() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns this reduction variable's current value converted to type int.
intxyz(Atom, Atom, double, Atom, double, Atom, double, int) - Static method in class ffx.potential.bonded.BondedUtils: This routine was derived from a similar routine in TINKER.
InvalidMatrixFileException - Exception Class in edu.rit.io: Class InvalidMatrixFileException provides an exception thrown when the contents of a matrix file are invalid.
InvalidMatrixFileException() - Constructor for exception class edu.rit.io.InvalidMatrixFileException: Construct a new invalid matrix file exception with no detail message and no cause.
InvalidMatrixFileException(String) - Constructor for exception class edu.rit.io.InvalidMatrixFileException: Construct a new invalid matrix file exception with the given detail message and no cause.
InvalidMatrixFileException(String, Throwable) - Constructor for exception class edu.rit.io.InvalidMatrixFileException: Construct a new invalid matrix file exception with the given detail message and the given cause.
InvalidMatrixFileException(Throwable) - Constructor for exception class edu.rit.io.InvalidMatrixFileException: Construct a new invalid matrix file exception with the given cause and the default detail message.
inverse(double[], int) - Method in class ffx.numerics.fft.Real: inverse
inverse(double[], int, int) - Method in class ffx.numerics.fft.Complex: Compute the normalized inverse FFT of data, leaving it in place.
inverse(double[], int, int, int) - Method in class ffx.numerics.fft.Complex: Compute the normalized inverse FFT of data, leaving it in place.
inverseResSqLimit() - Method in class ffx.crystal.Resolution: inverseResSqLimit
invert - Variable in class ffx.ui.behaviors.MouseBehavior
INVERT_INPUT - Static variable in class ffx.ui.behaviors.MouseBehavior: Constant INVERT_INPUT=0x2
invertSymOp(SymOp) - Static method in class ffx.crystal.SymOp: Invert a symmetry operator.
INVISIBLE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
invoke(JobBackendRef, JobFrontendRef) - Method in class edu.rit.pj.cluster.JobBackendMessage: Invoke the method corresponding to this job backend message on the given Job Backend object.
invoke(JobFrontendRef, JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontendMessage: Invoke the method corresponding to this job frontend message on the given Job Frontend object.
invoke(JobFrontendRef, JobSchedulerRef) - Method in class edu.rit.pj.cluster.JobFrontendMessage: Invoke the method corresponding to this job frontend message on the given Job Frontend object.
invoke(JobSchedulerRef, JobFrontendRef) - Method in class edu.rit.pj.cluster.JobSchedulerMessage: Invoke the method corresponding to this job scheduler message on the given Job Scheduler object.
invressq(HKL) - Method in class ffx.crystal.Crystal: invressq
IORequest - Class in edu.rit.mp: Class IORequest encapsulates the state of a message being sent or received in the Message Protocol (MP).
IORequest() - Constructor for class edu.rit.mp.IORequest: Construct a new I/O request object.
ip11 - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Polarization groups.
ip11 - Variable in class ffx.potential.nonbonded.pme.PermanentFieldRegion: Polarization groups.
ip11 - Variable in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion: Polarization groups.
ip12 - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
ip13 - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Ir - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
iReal3D(int, int, int, int, int) - Static method in class ffx.numerics.fft.Real3D: Determine the index of the real number in the 1D array from the X, Y and Z indices.
is_1_3(Atom) - Method in class ffx.potential.bonded.Atom: is_1_3
is_1_4(Atom) - Method in class ffx.potential.bonded.Atom: Are these atoms 1-4 bonded?
is_1_5(Atom) - Method in class ffx.potential.bonded.Atom: Are these atoms 1-5 bonded?
is_1_6(Atom) - Method in class ffx.potential.bonded.Atom: Are these atoms 1-6 bonded?
is_1_7(Atom) - Method in class ffx.potential.bonded.Atom: Are these atoms 1-7 bonded?
is_1_8(Atom) - Method in class ffx.potential.bonded.Atom: Are these atoms 1-8 bonded?
is_12_or_13(Atom) - Method in class ffx.potential.bonded.Atom: is_12_or_13
isActive() - Method in class ffx.algorithms.dynamics.Barostat
isActive() - Method in class ffx.potential.bonded.Atom: If active, the coordinates of this atom can be modified.
isActive() - Method in class ffx.ui.KeywordComponent: isActive
isAlive() - Method in class ffx.ui.commands.FFXServer: isAlive
isAlive() - Method in class ffx.ui.FFXExec: isAlive
isARC(File) - Static method in class ffx.potential.parsers.ARCFileFilter: This is a static version of the accept method.
isArmed() - Method in class ffx.potential.Renderer: Check to see if a graphics operation is pending/executing
isAtomSelectionSet() - Method in class ffx.potential.cli.AtomSelectionOptions: Check if either the active or inactive atom selection is set.
isBonded(Atom) - Method in class ffx.potential.bonded.Atom: Checks to see if an Atom is bonded to this Atom
isCacheFull() - Method in class ffx.potential.Renderer: isCacheFull
isClosed() - Method in class ffx.ui.commands.FFXClient: isClosed
isClosing() - Method in class ffx.ui.FFXSystem: isClosing
isConnected() - Method in class ffx.ui.commands.FFXClient: isConnected
isConnected() - Method in class ffx.ui.SimulationLoader: isConnected
isConstantPhTautomer - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
isConstantPhTitratable - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
isConstrained() - Method in class ffx.potential.bonded.BondedTerm: Check if this BondedTerm is constrained.
isContinuous() - Method in class ffx.algorithms.mc.LambdaMove: If true, do continuous moves.
isCosine() - Method in class ffx.numerics.switching.SquaredTrigSwitch: Return true if a cos^2(ax) transform, false if a sin^2(ax) transform.
isDecompose() - Method in class ffx.algorithms.cli.ManyBodyOptions: -E or --decompose Print energy decomposition for the input structure (no optimization).
isDee() - Method in class ffx.algorithms.cli.ManyBodyOptions: Use dead-end elimination criteria instead of Goldstein criteria.
isDeuterium() - Method in class ffx.potential.bonded.Atom: isDeuterium
isDYN(File) - Static method in class ffx.potential.parsers.DYNFileFilter: This is a static version of the accept method.
isEmpty() - Method in class ffx.numerics.quickhull.FaceList: Returns true if this list is empty.
isExecutingInParallel() - Method in class edu.rit.pj.ParallelConstruct: Determine if a parallel team is executing this parallel construct.
isExecutingInParallel() - Method in class edu.rit.pj.ParallelTeam: Determine if this parallel team is executing a parallel region.
isExecutingInParallel() - Method in class edu.rit.pj.WorkerConstruct: Determine if a worker team is executing this worker construct.
isExecutingInParallel() - Method in class edu.rit.pj.WorkerTeam: Determine if this worker team is executing a worker region.
isFinalized() - Method in class ffx.potential.bonded.MSGroup: Returns true if the MultiScaleGroup is finalized.
isFinalized() - Method in class ffx.potential.bonded.MultiResidue: Returns true if the MultiScaleGroup is finalized.
isFinished() - Method in class edu.rit.mp.IORequest: Determine if this I/O request has finished.
isFinished() - Method in class edu.rit.pj.CommRequest: Determine if the message passing operation associated with this CommRequest object has finished.
isFixedSchedule() - Method in class edu.rit.pj.IntegerSchedule: Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class edu.rit.pj.LongSchedule: Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.potential.nonbonded.PairwiseSchedule: Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.potential.nonbonded.SpatialDensitySchedule: Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.xray.GradientSchedule: Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.xray.RowSchedule: Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.xray.SliceSchedule: Determine if this schedule is a fixed schedule.
isForceFieldType(String) - Static method in class ffx.potential.parameters.ForceField: Check if a keyword is a force field type.
isFreeR(int, int) - Method in class ffx.xray.DiffractionRefinementData: isFreeR
isHalogen() - Method in class ffx.potential.bonded.Atom: Check if this atom is a Halogen (F, Cl, Br, I)
isHeavy() - Method in class ffx.potential.bonded.Atom: isHeavy checks whether this Atom is a heavy (non-hydrogen) atom.
isHetero() - Method in class ffx.potential.bonded.Atom: isHetero
isHydrogen() - Method in class ffx.potential.bonded.Atom: isHydrogen
isHydrogenAngle(Angle) - Method in class ffx.potential.openmm.OpenMMSystem: Check to see if an angle is a hydrogen angle.
isIndependentWalkers() - Method in class ffx.algorithms.cli.OSTOptions: Enforces that each walker maintains their own histogram.
isINT(File) - Static method in class ffx.potential.parsers.INTFileFilter: This is a static version of the accept method.
isIsotropic() - Method in class ffx.algorithms.cli.BarostatOptions: Restrict the MC Barostat to isotropic moves.
isIsotropic() - Method in class ffx.algorithms.dynamics.Barostat: Restrict the MC Barostat to isotropic moves.
isKeyword(String) - Method in class ffx.ui.KeywordPanel: isKeyword
isLambdaScaled() - Method in class ffx.potential.bonded.BondedTerm: Check if this BondedTerm is lambda-sensitive (e.g., a softcore dihedral).
isLambdaScaled() - Method in class ffx.potential.bonded.RestrainDistance
isLeaf() - Method in class ffx.numerics.clustering.Cluster: Returns true if this cluster is a leaf (has no children).
isLocal() - Method in interface ffx.potential.utils.PotentialsFunctions: True if using a local implementation (not in a user interfaces module).
isLocal() - Method in class ffx.potential.utils.PotentialsUtils: True if using a local implementation (not in a user interfaces module).
isLocal() - Method in class ffx.ui.UIUtils
isMasterThread() - Method in class edu.rit.pj.WorkerConstruct: Determine if the calling thread is the master thread in the worker team executing this worker construct.
isMcHardWall() - Method in class ffx.algorithms.cli.OSTOptions: The Monte Carlo scheme can use a hard wall that rejects any sample (Lambda, dU/dL) located in an empty histogram bin.
isMetaDynamics() - Method in class ffx.algorithms.cli.OSTOptions: Use a MetaDynamics style bias.
isModRes() - Method in class ffx.potential.bonded.Atom: isModRes
isMonteCarlo() - Method in class ffx.algorithms.cli.OSTOptions: Checks if the use of the Monte Carlo algorithm has been specified.
isMtnPurine() - Method in class ffx.potential.parsers.PDBFilter.Mutation: Determine if the mutation residue is purine.
isMtnPyrimidine() - Method in class ffx.potential.parsers.PDBFilter.Mutation: Determine if the mutation residue is pyrimidine.
isNaN() - Method in class ffx.numerics.clustering.Distance: Checks whether the distance value is NaN or undefined.
isNeuralNetwork() - Method in class ffx.potential.bonded.Atom: If true, this atom is part of a molecule whose intramolecular interactions are handled by a neural network.
isNeuralNetwork() - Method in class ffx.potential.bonded.BondedTerm: This method returns true if any atom is marked as being part of a neural network.
isNeutron() - Method in class ffx.xray.parsers.DiffractionFile: is this a neutron dataset?
isNewer(SimulationMessage) - Method in class ffx.ui.commands.SimulationUpdate: isNewer
isNonAlchemicalAtom(String) - Method in class ffx.potential.parsers.PDBFilter.Mutation: Check to see if an atom is involved in the mutated base's glycosyl torsion.
isNoOriginal() - Method in class ffx.algorithms.cli.ManyBodyOptions: Do not include starting coordinates as their own rotamer.
ISOLEUCINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
isOptimize() - Method in class ffx.algorithms.cli.DynamicsOptions: Saves low-energy snapshots discovered (only for single topology simulations).
isPDB(File) - Static method in class ffx.potential.parsers.PDBFileFilter: This is a static version of the accept method.
isPickingActive() - Method in class ffx.ui.MainMenu: isPickingActive
isPrintName() - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Returns whether the node name should be drawn.
isqrt(double) - Static method in class ffx.numerics.math.SquareRoot: Compute the inverse square root 1.0/sqrt(x2) of the input value x2 using a look-up table and two iterations of Newton's method for finding roots of an equation.
isQuiet() - Method in enum class ffx.algorithms.dynamics.MDVerbosity
isRefineMolOcc() - Method in class ffx.xray.DiffractionData: isRefineMolOcc.
isReinitVelocities() - Method in class ffx.algorithms.cli.AnnealOptions: Forces simulated annealing to re-initialize velocities to the new temperature at each annealing step, rather than letting the thermostat shift temperature downwards.
isResetNumSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions: Ignores steps detected in .lam lambda-restart files.
isRevert() - Method in class ffx.algorithms.cli.ManyBodyOptions: Revert unfavorable changes.
isRing(Atom) - Method in class ffx.potential.bonded.Atom: Determine if atom is in a ring with second atom WARNING: Does not work for 8+ membered rings...
isSaveOutput() - Method in class ffx.algorithms.cli.ManyBodyOptions: Save eliminated singles and eliminated pairs to a text file (global and box optimization).
isSelected() - Method in class ffx.potential.bonded.MSNode: isSelected
isShowDistanceValues() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel: Returns whether linkage distance values should be rendered on the dendrogram.
isShowScale() - Method in class ffx.numerics.clustering.visualization.DendrogramPanel: Returns whether the X-axis scale should be drawn below the dendrogram.
isSohnckeGroup(int) - Static method in class ffx.crystal.SpaceGroupInfo: Sohncke groups respect chiral molecules (i.e., non-enantiogenic) and include space group numbers: 1, 3-5, 16-24, 75-80, 89-98, 143-146, 149-155, 168-173, 177-182, 195-199 and 207-214.
isSpecialPosition() - Method in class ffx.potential.bonded.Atom: If true, this atom is at a special position.
isSpecialPositionSymOp(int) - Method in class ffx.potential.bonded.Atom: If true, this atom is at a special position for the specified symmetry operation.
isStale() - Method in class ffx.potential.bonded.Atom: isStale
isStale() - Method in class ffx.ui.FFXSystem: isStale
isStarted() - Method in class edu.rit.util.Timer: Determine whether this timer is started.
isState - Variable in class ffx.potential.bonded.Rotamer: Flag to indicate the rotamer was initialized from a Residue state.
isStochastic(IntegratorEnum) - Static method in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
isStopped() - Method in class edu.rit.util.Timer: Determine whether this timer is stopped.
isSupported(Platform) - Method in enum class ffx.potential.nonbonded.pme.SCFAlgorithm: Checks if this platform is supported
isSynchronous() - Method in class ffx.algorithms.cli.MultiDynamicsOptions: Synchronous walker communication.
isTautomer(Residue) - Method in class ffx.potential.extended.ExtendedSystem: Returns the tautomerizibility of a residue
isTautomerizing(int) - Method in class ffx.potential.extended.ExtendedSystem: Returns whether an atom is tautomerizing
isTcpPortAvailable(int) - Static method in class ffx.utilities.PortUtils: Check if a port is available.
isThreeBody() - Method in class ffx.algorithms.cli.ManyBodyOptions: -T or --threeBody Include 3-Body interactions in the elimination criteria.
isTitratable(Residue) - Method in class ffx.potential.extended.ExtendedSystem: Returns the titratibility of the passed residue
isTitrateConformers() - Method in class ffx.potential.bonded.Residue
isTitrating - Variable in class ffx.potential.bonded.Rotamer: If this flag is set, application of a rotamer requires updating force field parameters.
isTitrating() - Method in class ffx.algorithms.cli.ManyBodyOptions
isTitrating(int) - Method in class ffx.potential.extended.ExtendedSystem: Returns whether an atom is titrating
isTitratingHeavy(int) - Method in class ffx.potential.extended.ExtendedSystem: Questions whether the current non-hydrogen atom's polarizability is changing in response to lambda being updated.
isTitratingHeavy(AminoAcidUtils.AminoAcid3, Atom) - Static method in class ffx.potential.parameters.TitrationUtils: Used to keep track of heavy atoms with changing polarizability.
isTitratingHydrogen(int) - Method in class ffx.potential.extended.ExtendedSystem: Questions whether the current hydrogen's polarizability is changing in response to lambda being updated.
isTitratingHydrogen(AminoAcidUtils.AminoAcid3, Atom) - Static method in class ffx.potential.parameters.TitrationUtils
isTreeComplete() - Method in class ffx.numerics.clustering.HierarchyBuilder: Returns true if only a single cluster remains (i.e., the hierarchy has a root).
isTriggered() - Method in class edu.rit.util.Timer: Determine whether this timer is triggered.
isTrigonal() - Method in class ffx.potential.bonded.Atom: isTrigonal
isTwoStep() - Method in class ffx.algorithms.cli.OSTOptions: Returns true if the 2-step option is enabled (not guaranteed to also mean that MC is enabled!).
isUpdateStep(long) - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Check if the non-equilibrium lambda value should be updated at a given MD step.
isUse_3g() - Method in class ffx.xray.DiffractionData: isUse_3g.
isValid() - Method in class edu.rit.http.HttpRequest: Determine if this HTTP request is valid.
isVirtualSite(int) - Method in class ffx.openmm.System: Check if a particle is a virtual site.
isVisible() - Method in class ffx.potential.bonded.Atom: isVisible
isVisible() - Method in class ffx.potential.MolecularAssembly: isVisible
isWtPurine() - Method in class ffx.potential.parsers.PDBFilter.Mutation: Determine if original (wild type) residue is purine.
isWtPyrimidine() - Method in class ffx.potential.parsers.PDBFilter.Mutation: Determine if original (wild type) residue is pyrimidine.
isXYZ(File) - Static method in class ffx.potential.parsers.XYZFileFilter: This is a static version of the accept method.
iSymm - Variable in class ffx.potential.nonbonded.NeighborList.AtomIndex
item - Variable in class edu.rit.mp.buf.BooleanItemBuf: Boolean item to be sent or received.
item - Variable in class edu.rit.mp.buf.ByteItemBuf: Byte item to be sent or received.
item - Variable in class edu.rit.mp.buf.CharacterItemBuf: Character item to be sent or received.
item - Variable in class edu.rit.mp.buf.DoubleItemBuf: Double item to be sent or received.
item - Variable in class edu.rit.mp.buf.FloatItemBuf: Float item to be sent or received.
item - Variable in class edu.rit.mp.buf.IntegerItemBuf: Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.LongItemBuf: Long item to be sent or received.
item - Variable in class edu.rit.mp.buf.ObjectItemBuf: Object item to be sent or received.
item - Variable in class edu.rit.mp.buf.ShortItemBuf: Short item to be sent or received.
item - Variable in class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Integer item to be sent or received.
iterativeClustering(List<double[]>, int, double) - Static method in class ffx.potential.utils.Clustering: Perform an iterative clustering for a specified number of clusters.
iterator() - Method in class edu.rit.pj.job.JobGenerator: Get an iterator for generating the jobs in the job group.

J

J - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
job - Variable in class edu.rit.pj.cluster.BackendInfo: The job that has reserved or is running on the backend.
Job - Class in edu.rit.pj.job: Class Job encapsulates a job and its attributes.
Job() - Constructor for class edu.rit.pj.job.Job: Construct a new uninitialized job.
Job(int, String, String) - Constructor for class edu.rit.pj.job.Job: Construct a new job.
JobBackend - Class in edu.rit.pj.cluster: Class JobBackend is the main program for a job backend process in the PJ cluster middleware.
JobBackendMessage - Class in edu.rit.pj.cluster: Class JobBackendMessage provides a message sent to a Job Backend process (interface JobBackendRef) in the PJ cluster middleware.
JobBackendMessage() - Constructor for class edu.rit.pj.cluster.JobBackendMessage: Construct a new job backend message.
JobBackendMessage(int) - Constructor for class edu.rit.pj.cluster.JobBackendMessage: Construct a new job backend message with the given message tag.
JobBackendProxy - Class in edu.rit.pj.cluster: Class JobBackendProxy provides a proxy object for sending messages to a PJ job backend process.
JobBackendProxy(ChannelGroup, Channel) - Constructor for class edu.rit.pj.cluster.JobBackendProxy: Construct a new job backend proxy.
JobBackendRef - Interface in edu.rit.pj.cluster: Interface JobBackendRef specifies the interface for the PJ job backend process.
jobCount() - Method in class edu.rit.pj.job.JobGenerator: Returns the number of jobs in the job group, N.
jobFinished(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobBackend: Report that the job finished.
jobFinished(JobFrontendRef) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "job finished" message.
jobFinished(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report that the job finished.
jobFinished(JobFrontendRef) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report that the job finished.
jobFinished(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobScheduler: Report that a job finished.
jobFinished(JobFrontendRef) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "job finished" message.
jobFinished(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Report that a job finished.
jobFinished(JobFrontendRef) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Report that a job finished.
JobFrontend - Class in edu.rit.pj.cluster: Class JobFrontend provides the message handler for the PJ job frontend process.
JobFrontend(String, int, int, int, boolean, String, String[]) - Constructor for class edu.rit.pj.cluster.JobFrontend: Construct a new job frontend object.
JobFrontendMessage - Class in edu.rit.pj.cluster: Class JobFrontendMessage provides a message sent to a Job Frontend process (interface JobFrontendRef) in the PJ cluster middleware.
JobFrontendMessage() - Constructor for class edu.rit.pj.cluster.JobFrontendMessage: Construct a new job frontend message.
JobFrontendMessage(int) - Constructor for class edu.rit.pj.cluster.JobFrontendMessage: Construct a new job frontend message with the given message tag.
JobFrontendProxy - Class in edu.rit.pj.cluster: Class JobFrontendProxy provides a proxy object for sending messages to a PJ job frontend process.
JobFrontendProxy(ChannelGroup, Channel) - Constructor for class edu.rit.pj.cluster.JobFrontendProxy: Construct a new job frontend proxy.
JobFrontendRef - Interface in edu.rit.pj.cluster: Interface JobFrontendRef specifies the interface for the PJ job frontend process.
JobGenerator - Class in edu.rit.pj.job: Class JobGenerator is the abstract base class for an object that generates a group of Jobs.
JobGenerator() - Constructor for class edu.rit.pj.job.JobGenerator: Construct a new job generator.
JobInfo - Class in edu.rit.pj.cluster: Class JobInfo provides a record of information about one job in a parallel computer in the PJ cluster middleware.
JobInfo(int, JobInfo.State, long, String, int, int, int, int, BackendInfo[], int[], int, JobFrontendRef, Timer, Timer, Timer) - Constructor for class edu.rit.pj.cluster.JobInfo: Construct a new job information record.
JobInfo.State - Enum Class in edu.rit.pj.cluster: The state of a job.
jobnum - Variable in class edu.rit.pj.cluster.JobInfo: The job number.
JobScheduler - Class in edu.rit.pj.cluster: Class JobScheduler is the main program for the PJ Job Scheduler Daemon process for a parallel computer.
JobSchedulerException - Exception Class in edu.rit.pj.cluster: Class JobSchedulerException is thrown to indicate that a job frontend process was unable to contact the Job Scheduler Daemon.
JobSchedulerException() - Constructor for exception class edu.rit.pj.cluster.JobSchedulerException: Create a new Job Scheduler exception with no detail message and no cause.
JobSchedulerException(String) - Constructor for exception class edu.rit.pj.cluster.JobSchedulerException: Create a new Job Scheduler exception with the given detail message and no cause.
JobSchedulerException(String, Throwable) - Constructor for exception class edu.rit.pj.cluster.JobSchedulerException: Create a new Job Scheduler exception with the given detail message and the given cause.
JobSchedulerException(Throwable) - Constructor for exception class edu.rit.pj.cluster.JobSchedulerException: Create a new Job Scheduler exception with no detail message and the given cause.
JobSchedulerMessage - Class in edu.rit.pj.cluster: Class JobSchedulerMessage provides a message sent to a Job Scheduler process (interface JobSchedulerRef) in the PJ cluster middleware.
JobSchedulerMessage() - Constructor for class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new job scheduler message.
JobSchedulerMessage(int) - Constructor for class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new job scheduler message with the given message tag.
JobSchedulerProxy - Class in edu.rit.pj.cluster: Class JobSchedulerProxy provides a proxy object for sending messages to a PJ job scheduler process.
JobSchedulerProxy(ChannelGroup, Channel) - Constructor for class edu.rit.pj.cluster.JobSchedulerProxy: Construct a new job scheduler proxy.
JobSchedulerRef - Interface in edu.rit.pj.cluster: Interface JobSchedulerRef specifies the interface for the PJ Job Scheduler Daemon process.
jobTimer - Variable in class edu.rit.pj.cluster.JobInfo: Maximum job time timer.
Joint - Class in ffx.potential.bonded: The Joint class contains the geometry produced by the FGroup Joiner method.
Joint() - Constructor for class ffx.potential.bonded.Joint: Default Constructor
Joint(MSGroup, MSGroup, MSNode, MSNode, MSNode, MSNode, MSNode, MSNode, MSNode, MSNode, MSNode, MSNode, MSNode) - Constructor for class ffx.potential.bonded.Joint: Constructs a Joint between Group 1 and Group 2.
Joint(String) - Constructor for class ffx.potential.bonded.Joint: Constructor for Joint.
JPEG - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
jstep - Variable in class ffx.numerics.fft.MixedRadixFactor: Increment for the inner loop.
jvm - Variable in class edu.rit.pj.cluster.BackendInfo: The full pathname for executing the Java Virtual Machine (JVM) on the backend.
jvmflags - Variable in class edu.rit.pj.cluster.BackendInfo: Array of command line flags for the JVM (zero or more).

K

k - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
k - Variable in class ffx.crystal.HKL: The k-index of the reflection.
k - Variable in class ffx.potential.parameters.ImproperTorsionType: Force constant in kcal/mol.
K - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
K - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
K - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
K_CD_SI - Static variable in class ffx.utilities.Constants: Luminous efficacy in lm/W, defining the lumen.
kB - Static variable in class ffx.utilities.Constants: Boltzmann/ideal gas constant in units of g*Ang^2/(mol*psec^2*K).
KCAL_TO_GRAM_ANG2_PER_PS2 - Static variable in class ffx.utilities.Constants: Conversion from kcal/mole to g*Ang**2/ps**2.
KCAL_TO_KJ - Static variable in class ffx.utilities.Constants: Constant KCAL_TO_KJ=4.184
key - Variable in class ffx.potential.parameters.BaseType: The look-up key for this term, which is usually a concatenation of atom classes or atom types.
key() - Method in record class ffx.utilities.ObjectPair: Returns the value of the key record component.
KeyFileEditor - Class in ffx.ui: The KeyFileEditor class is a wrapper for the KeywordPanel to create a stand alone Key File Editor (it needs updating).
KeyFileFilter - Class in ffx.potential.parsers: The KeyFileFilter class is used to choose a Force Field X keyword (*.KEY) or property (*.properties) file.
KeyFileFilter() - Constructor for class ffx.potential.parsers.KeyFileFilter: Default Constructor.
KeyFilter - Class in ffx.potential.parsers: The KeyFilter class parses Force Field X Keyword (*.KEY) and Property (*.PROPERTIES) files.
KeyFilter() - Constructor for class ffx.potential.parsers.KeyFilter: Constructor for KeyFilter.
keyPressed(KeyEvent) - Method in class ffx.ui.GraphicsFullScreen
keyReleased(KeyEvent) - Method in class ffx.ui.GraphicsFullScreen
keyTyped(KeyEvent) - Method in class ffx.ui.GraphicsFullScreen
Keyword - Class in ffx.utilities: The Keyword class holds a single Force Field X keyword entry.
Keyword(String) - Constructor for class ffx.utilities.Keyword: Constructor for Keyword.
Keyword(String, String) - Constructor for class ffx.utilities.Keyword: Constructor for Keyword.
Keyword(String, String[]) - Constructor for class ffx.utilities.Keyword: Constructor for Keyword.
KEYWORD - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
KeywordComponent - Class in ffx.ui: The KeywordComponent class is used to represent one TINKER keyword.
KeywordComponent.SwingRepresentation - Enum Class in ffx.ui
KeywordPanel - Class in ffx.ui: The KeywordPanel class provides a View and Control of TINKER Keyword (*.KEY) files.
keywords - Variable in class ffx.ui.commands.SimulationDefinition
KG_TO_GRAMS - Static variable in class ffx.utilities.Constants: Constant KG_TO_GRAMS=1000
KillRegion - Class in edu.rit.pj: Provides a mechanism to shut down a ParallelTeam's threads, enabling garbage collection.
KillRegion() - Constructor for class edu.rit.pj.KillRegion
kinetic - Variable in class ffx.ui.commands.SimulationUpdate
kineticEnergy - Variable in class ffx.potential.openmm.OpenMMState: Kinetic energy (kcal/mol).
kineticEnergy() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the kineticEnergy record component.
KJ_TO_KCAL - Static variable in class ffx.utilities.Constants: Constant KJ_TO_KCAL=1.0 / KCAL_TO_KJ
kMeansClustering(List<double[]>, int, int, long) - Static method in class ffx.potential.utils.Clustering: Perform a k-means clustering for a specified number of clusters.
Kr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ksbsGridOptimize() - Method in class ffx.xray.ScaleBulkMinimize: ksbsGridOptimize
kT - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat: The value of kT in kcal/mol at the target temperature.

L

l - Variable in class ffx.crystal.HKL: The l-index of the reflection.
L - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
L111 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 111.
L112 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 112.
L113 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 113.
L114 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 114.
L11T - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 11T.
L121 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 121.
L131 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 131.
L141 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 141.
L1T1 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 1T1.
L211 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 211.
L21U - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 21U.
L21V - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 21V.
L21W - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 21W.
L21X - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 21X.
L21Y - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 21Y.
L21Z - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 21Z.
L222 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 222.
L223 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 223.
L224 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 224.
L22U - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 22U.
L22V - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 22V.
L22W - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 22W.
L232 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 232.
L242 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 242.
l2Error(double[], double[]) - Method in class ffx.potential.nonbonded.octree.Octree: Compute the L2 error.
L311 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 311.
L31A - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 31A.
L31B - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 31B.
L31C - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 31C.
L31D - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 31D.
L322 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 322.
L32A - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32A.
L32B - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32B.
L32C - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32C.
L32D - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32D.
L32U - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32U.
L32V - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32V.
L32W - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32W.
L32X - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32X.
L32Y - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32Y.
L32Z - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 32Z.
L411 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 411.
L422 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System 422.
La - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
labelAtoms - Static variable in class ffx.potential.bonded.RendererCache: Constant labelAtoms=false
labelResidues - Static variable in class ffx.potential.bonded.RendererCache: Constant labelResidues=false
lAlpha - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: lAlpha = α*(1 - L)^2
lambda - Variable in class ffx.realspace.RealSpaceEnergy: Value of the lambda state variable.
lambda - Variable in class ffx.xray.XRayEnergy
lambdaAllBondedTerms - Variable in class ffx.potential.terms.EnergyTermRegion: Indicates all bonded energy terms should be evaluated if lambdaBondedTerms is true.
lambdaBins - Variable in class ffx.algorithms.thermodynamics.HistogramData: For continuous lambda: The first Lambda bin is centered on 0.0 (-0.0025 to 0.0025).
lambdaBinWidth_2 - Variable in class ffx.algorithms.thermodynamics.HistogramData: Half the width of a lambda bin, or zero for discrete lambda values.
lambdaBondedTerms - Variable in class ffx.potential.ForceFieldEnergy: Indicates only bonded energy terms effected by Lambda should be evaluated.
lambdaBondedTerms - Variable in class ffx.potential.terms.EnergyTermRegion: Indicates only bonded energy terms effected by Lambda should be evaluated.
LambdaData - Class in ffx.algorithms.thermodynamics
LambdaData() - Constructor for class ffx.algorithms.thermodynamics.LambdaData
LambdaDefaults - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: The defaults are effectively final, as the implementation of setFactors in the base class is always a no-op.
LambdaFactors() - Constructor for class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
LambdaFactors() - Constructor for class ffx.potential.nonbonded.VanDerWaals.LambdaFactors
LambdaFactorsESV() - Constructor for class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsESV
LambdaFactorsOST() - Constructor for class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsOST
LambdaFactorsOST() - Constructor for class ffx.potential.nonbonded.VanDerWaals.LambdaFactorsOST
LambdaGradient - Class in ffx.potential.commands.test: The LambdaGradient script tests numeric gradients w.r.t. lambda against numeric, finite-difference gradients
Usage:
ffxc test.LambdaGradient [options] <filename> [file2...]
LambdaGradient - Class in ffx.realspace.commands.test: The Real Space Annealing script.
LambdaGradient - Class in ffx.xray.commands.test: The X-ray test Lambda Gradient script.
LambdaGradient() - Constructor for class ffx.potential.commands.test.LambdaGradient: LambdaGradient Constructor
LambdaGradient() - Constructor for class ffx.realspace.commands.test.LambdaGradient: LambdaGradient constructor.
LambdaGradient() - Constructor for class ffx.xray.commands.test.LambdaGradient: LambdaGradient constructor.
LambdaGradient(FFXBinding) - Constructor for class ffx.potential.commands.test.LambdaGradient: LambdaGradient Constructor
LambdaGradient(FFXBinding) - Constructor for class ffx.realspace.commands.test.LambdaGradient: LambdaGradient constructor.
LambdaGradient(FFXBinding) - Constructor for class ffx.xray.commands.test.LambdaGradient: LambdaGradient constructor.
LambdaGradient(String[]) - Constructor for class ffx.potential.commands.test.LambdaGradient: LambdaGradient constructor that sets the command line arguments.
LambdaGradient(String[]) - Constructor for class ffx.realspace.commands.test.LambdaGradient: LambdaGradient constructor that sets the command line arguments.
LambdaGradient(String[]) - Constructor for class ffx.xray.commands.test.LambdaGradient: LambdaGradient constructor that sets the command line arguments.
LambdaInterface - Interface in ffx.potential.bonded: The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.
lambdaLadder - Variable in class ffx.algorithms.thermodynamics.HistogramData: Either the discrete lambda values used, or null (continuous lambda).
LambdaMode - Enum Class in ffx.potential.nonbonded.pme
LambdaMove - Class in ffx.algorithms.mc: Define an MC move to update lambda.
LambdaMove(int, OrthogonalSpaceTempering) - Constructor for class ffx.algorithms.mc.LambdaMove: Constructor for LambdaMove.
LambdaMove(OrthogonalSpaceTempering) - Constructor for class ffx.algorithms.mc.LambdaMove: Constructor for LambdaMove.
lambdaParticleOptions - Variable in class ffx.algorithms.commands.Thermodynamics
LambdaParticleOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that utilize a mobile lambda particle, such as Thermodynamics.
LambdaParticleOptions() - Constructor for class ffx.algorithms.cli.LambdaParticleOptions
lambdaPattern - Static variable in class ffx.potential.parsers.SystemFilter
lambdaProd - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: lambda * esvLambda[i] * esvLambda[k]
lambdaTerm - Variable in class ffx.potential.ForceFieldEnergy: Indicates use of the Lambda state variable.
lambdaVariance - Variable in class ffx.algorithms.thermodynamics.HistogramData: The variance for the Gaussian bias in the lambda dimension.
lamValues - Variable in class ffx.numerics.estimator.SequentialEstimator: The lambda values at which the samples were collected.
LANGEVIN - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
LANGEVIN_MTS - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
LangevinIntegrator - Class in ffx.openmm: This is an Integrator which simulates a System using Langevin dynamics.
LangevinIntegrator(double, double, double) - Constructor for class ffx.openmm.LangevinIntegrator: Create a LangevinIntegrator.
LangevinMiddleIntegrator - Class in ffx.openmm: This is an Integrator which simulates a System using Langevin dynamics, with the LFMiddle discretization (J.
LangevinMiddleIntegrator(double, double, double) - Constructor for class ffx.openmm.LangevinMiddleIntegrator: Create a LangevinMiddleIntegrator.
LAST_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
lastEnergy() - Method in class ffx.algorithms.mc.BoltzmannMC: Returns the energy as of the last step taken (not including any extra potential energy adjustments).
lastEnergy() - Method in interface ffx.algorithms.mc.MetropolisMC: Returns the energy as of the last step taken (not including any extra potential energy adjustments).
latticeSystem - Variable in class ffx.crystal.SpaceGroup: Lattice system.
LatticeSystem - Enum Class in ffx.crystal: Enumeration of the 7 lattice systems.
laueSystem - Variable in class ffx.crystal.SpaceGroup: Laue group
LaueSystem - Enum Class in ffx.crystal: Enumeration of the different Laue systems.
lb - Variable in class ffx.numerics.integrate.FunctionDataCurve: Lower bound.
lb() - Method in class edu.rit.util.LongRange: Returns this range's lower bound.
lb() - Method in class edu.rit.util.Range: Returns this range's lower bound.
LBFGS - Class in ffx.numerics.optimization: This class implements the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm for large-scale multidimensional unconstrained optimization problems.
LEASE_EXPIRE_INTERVAL - Static variable in class edu.rit.pj.cluster.Constants: The lease expiration interval (default is 150 seconds).
LEASE_RENEW_INTERVAL - Static variable in class edu.rit.pj.cluster.Constants: The lease renewal interval (default is 60 seconds).
leastSquaresOptimizer - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters
leastSquaresPredictor(LambdaMode, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters: The least-squares predictor with induced dipole information from 8-10 previous steps reduces the number SCF iterations by ~50%.
LEFT - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationSide: Left-hand integration.
leftBoole(double[]) - Static method in class ffx.numerics.integrate.Integration: leftBoole.
leftRectangularMethod(double[]) - Static method in class ffx.numerics.integrate.Integration: leftRectangularMethod.
leftSimpsons(double[]) - Static method in class ffx.numerics.integrate.Integration: leftSimpsons.
leftTrapInput(double[]) - Static method in class ffx.numerics.integrate.Integration: leftTrapInput.
length - Variable in class edu.rit.mp.Status: The actual number of items in the message that was received.
length - Variable in class edu.rit.pj.CommStatus: The actual number of items in the message that was received.
length - Variable in class ffx.potential.bonded.Rotamer: Number of chi/sigma values.
length() - Method in class edu.rit.mp.Buf: Obtain the number of items in this buffer.
length() - Method in class edu.rit.pj.reduction.SharedBooleanArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedByteArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedCharacterArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedDoubleArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedFloatArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedIntegerArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedLongArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedObjectArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedShortArray: Returns this array reduction variable's length.
length() - Method in class edu.rit.util.ByteSequence: Obtain the length of this byte sequence.
length() - Method in class edu.rit.util.LongRange: Returns this range's length.
length() - Method in class edu.rit.util.Range: Returns this range's length.
length() - Method in class ffx.numerics.math.Double3: Finds the length of this Double3.
length() - Method in class ffx.numerics.math.Float3: Finds the length of this Float3.
length() - Method in class ffx.numerics.quickhull.HalfEdge: Returns the length of this half-edge.
length(boolean[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given Boolean array.
length(byte[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given byte array.
length(char[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given character array.
length(double[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given double array.
length(double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the length of a vector.
length(float[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given float array.
length(float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the length of a vector.
length(int[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given integer array.
length(long[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given long array.
length(short[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given short array.
length(T[]) - Static method in class edu.rit.util.Arrays: Determine the number of elements in the given object array.
LENGTH - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of contiguous elements that will be read from the input data array.
LENGTH_128 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of contiguous elements that will be read from the input data array.
LENGTH_256 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of contiguous elements that will be read from the input data array.
LENGTH_512 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of contiguous elements that will be read from the input data array.
length2() - Method in class ffx.numerics.math.Double3: Finds the length of this Double3 squared.
length2() - Method in class ffx.numerics.math.Float3: Finds the length of this Float3 squared.
length2(double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the length^2 of a vector.
length2(float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the length of a vector squared.
lengthSquared() - Method in class ffx.numerics.quickhull.HalfEdge: Returns the length squared of this half-edge.
LENNARD_JONES - Enum constant in enum class ffx.potential.parameters.VDWType.VDW_TYPE
LEU - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
LEUCINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
lfAlpha - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Interatomic buffer distance: alpha*(1-lambda)*(1-lambda).
lfPowPerm - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Lambda to its permanent exponent.
lfPowPol - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Lambda to its polarization exponent.
Li - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
library - Variable in class ffx.algorithms.optimize.RotamerOptimization: RotamerLibrary instance.
likelihoodFree() - Method in class ffx.xray.DiffractionRefinementData: return the current likelihood
likelihoodWork() - Method in class ffx.xray.DiffractionRefinementData: return the current likelihood
linear - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
LINEAR - Enum constant in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules
LinearAnnealSchedule - Class in ffx.algorithms.optimize.anneal: Linear temperature schedule for simulated annealing
LinearAnnealSchedule(int, double, double) - Constructor for class ffx.algorithms.optimize.anneal.LinearAnnealSchedule: Creates an exponential annealing schedule that decays as tHigh-(n*(tHigh-tLow)).
LinearDerivativeSwitch - Class in ffx.numerics.switching: A LinearDerivativeSwitch interpolates between 0 and 1 vi f(x) = 2*x - x^2.
LinearDerivativeSwitch() - Constructor for class ffx.numerics.switching.LinearDerivativeSwitch: Constructor for the LinearDerivativeSwitch.
LineBufferedOutputStream - Class in edu.rit.io: Class LineBufferedOutputStream provides a line buffer layered on top of an underlying output stream.
LineBufferedOutputStream(OutputStream) - Constructor for class edu.rit.io.LineBufferedOutputStream: Construct a new line buffered output stream.
LINES - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
LineSearch - Class in ffx.numerics.optimization: This class implements an algorithm for uni-dimensional line search using parabolic extrapolation and cubic interpolation with both function and gradient values.
LineSearch.LineSearchResult - Enum Class in ffx.numerics.optimization: Enum representing the possible outcomes of a line search operation.
LinkageStrategy - Interface in ffx.numerics.clustering: Strategy interface for computing the inter-cluster distance used during agglomeration.
list() - Method in class ffx.numerics.clustering.DistanceMap: Returns a snapshot list of all cluster pairs currently stored.
list() - Method in class ffx.ui.properties.FFXLocale: list
listCommands(boolean, boolean) - Static method in class ffx.utilities.FFXCommand: List the embedded FFX Commands.
listen(InetSocketAddress) - Method in class edu.rit.mp.ChannelGroup: Listen for connection requests on the given host and port.
listen(ServerSocketChannel) - Method in class edu.rit.mp.ChannelGroup: Listen for connection requests using the given server socket channel.
listenAddress() - Method in class edu.rit.mp.ChannelGroup: Obtain this channel group's listen address.
LITERS_PER_CUBIC_ANGSTROM - Static variable in class ffx.utilities.Constants: Constant LITERS_PER_CUBIC_ANGSTROM=1E-27
LM3B - Enum constant in enum class ffx.crystal.LaueSystem: Laue System M3B.
LM3M - Enum constant in enum class ffx.crystal.LaueSystem: Laue System M3M.
lmn(int, int, int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Convenience method for writing out tensor indices.
lnI0(double) - Static method in class ffx.numerics.special.ModifiedBessel: Compute the natural log(i0(x)).
loadEnergyRestart - Variable in class ffx.algorithms.optimize.RotamerOptimization: If true, load an energy restart file.
loadEnergyRestart(File, Residue[]) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
loadEnergyRestart(File, Residue[], int, int[]) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
loadPlatform(Platform, ForceField) - Static method in class ffx.potential.openmm.OpenMMContext: Load an OpenMM Platform
loadPluginLibrary(String) - Static method in class ffx.openmm.Platform: Load a dynamic library that contains a plugin.
loadPluginsFromDirectory(String) - Static method in class ffx.openmm.Platform: Load plugins from a directory.
loadProperties(File) - Static method in class ffx.utilities.Keyword: This method sets up configuration properties in the following precedence * order:
loadTensor(int, int, int, HashMap<Integer, String>) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Load a tensor element into a SIMD register.
loadUpdate(SimulationUpdate) - Method in class ffx.ui.commands.FFXServer: loadUpdate
loadVRML() - Method in class ffx.potential.MolecularAssembly: loadVRML
LocalCoordinatesSite - Class in ffx.openmm: This is a VirtualSite that computes the particle location based on a local coordinate system.
LocalCoordinatesSite(int, int, int, OpenMM_Vec3, OpenMM_Vec3, OpenMM_Vec3, OpenMM_Vec3) - Constructor for class ffx.openmm.LocalCoordinatesSite: Create a LocalCoordinatesSite using specific particles and vectors to define the coordinate system.
LocalCoordinatesSite(PointerByReference, PointerByReference, PointerByReference, PointerByReference, OpenMM_Vec3) - Constructor for class ffx.openmm.LocalCoordinatesSite: Create a LocalCoordinatesSite using weighted averages to define the coordinate system.
LocalGeometryFunctionalForm - Enum constant in enum class ffx.utilities.PropertyGroup: Local geometry functional form.
locateDisulfideBonds(List<String>, MolecularAssembly, Map<String, String>) - Static method in class ffx.potential.bonded.PolymerUtils: Locate disulfide bonds based on SSBOND records.
Lock - Class in edu.rit.pj: Class Lock provides an object used for synchronizing parallel team threads in a critical region.
Lock() - Constructor for class edu.rit.pj.Lock: Construct a new lock.
log() - Method in class ffx.numerics.math.Double3: Log this Double3.
log() - Method in class ffx.numerics.math.Float3: Log this Float3.
log() - Method in class ffx.potential.bonded.Angle: Log details for this Angle energy term.
log() - Method in class ffx.potential.bonded.AngleTorsion: Log details for this Angle-Torsion energy term.
log() - Method in class ffx.potential.bonded.Bond: Log details for this Bond energy term.
log() - Method in class ffx.potential.bonded.ImproperTorsion: Log details for this Improper Torsion energy term.
log() - Method in class ffx.potential.bonded.OutOfPlaneBend: Log details for this Out-of-Plane Bend energy term.
log() - Method in class ffx.potential.bonded.PiOrbitalTorsion: Log details for this Pi-Orbital Torsion energy term.
log() - Method in class ffx.potential.bonded.RestrainDistance: Log details for this Bond energy term.
log() - Method in class ffx.potential.bonded.StretchBend: log
log() - Method in class ffx.potential.bonded.StretchTorsion: Log details for this Stretch-Torsional Angle energy term.
log() - Method in class ffx.potential.bonded.Torsion: Log details for this Torsional Angle energy term.
log() - Method in class ffx.potential.bonded.TorsionTorsion: Log details for this Torsion-Torsion energy term.
log() - Method in class ffx.potential.bonded.UreyBradley: log
log() - Method in class ffx.potential.parameters.BaseType: Log this type.
log() - Method in class ffx.potential.parameters.ForceField: log
log() - Method in class ffx.potential.terms.AnglePotentialEnergy: Log the details of Angle interactions.
log() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Log the details of Angle-Torsion interactions.
log() - Method in class ffx.potential.terms.BondPotentialEnergy: Log the details of Bond interactions.
log() - Method in class ffx.potential.terms.EnergyTerm: Log the details of this energy term.
log() - Method in class ffx.potential.terms.EnergyTermRegion: Log the details of the energy terms in this bonded region.
log() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Log the details of Improper interactions.
log() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Log the details of Out-of-Plane Bend interactions.
log() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Log the details of Pi-Orbital Torsion interactions.
log() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Log the details of Restrain Distance interactions.
log() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Log the details of Restrain Position interactions.
log() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Log the details of Restrain Torsion interactions.
log() - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Log the details of Stretch-Bend interactions.
log() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Log the details of Stretch-Torsion interactions.
log() - Method in class ffx.potential.terms.TorsionPotentialEnergy: Log the details of Torsion interactions.
log() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Log the details of Torsion-Torsion interactions.
log() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Log the details of Urey-Bradley interactions.
log(double[]) - Static method in class ffx.numerics.math.DoubleMath: logVector
log(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: log.
log(double[], String) - Static method in class ffx.numerics.math.DoubleMath: logVector.
log(float[]) - Static method in class ffx.numerics.math.FloatMath: logVector
log(float[], String) - Static method in class ffx.numerics.math.FloatMath: logVector.
log(long, String) - Method in interface edu.rit.util.Logger: Log the given date and message.
log(long, String) - Method in class edu.rit.util.PrintStreamLogger: Log the given date and message.
log(long, String, Throwable) - Method in interface edu.rit.util.Logger: Log the given date, message, and exception.
log(long, String, Throwable) - Method in class edu.rit.util.PrintStreamLogger: Log the given date, message, and exception.
log(long, Throwable) - Method in interface edu.rit.util.Logger: Log the given date and exception.
log(long, Throwable) - Method in class edu.rit.util.PrintStreamLogger: Log the given date and exception.
log(String) - Method in interface edu.rit.util.Logger: Log the given message.
log(String) - Method in class edu.rit.util.PrintStreamLogger: Log the given message.
log(String) - Method in class ffx.potential.parameters.ForceField: Prints any force field keyword to Standard.out.
log(String, Throwable) - Method in interface edu.rit.util.Logger: Log the given message and exception.
log(String, Throwable) - Method in class edu.rit.util.PrintStreamLogger: Log the given message and exception.
log(Throwable) - Method in interface edu.rit.util.Logger: Log the given exception.
log(Throwable) - Method in class edu.rit.util.PrintStreamLogger: Log the given exception.
log(Level) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Log the target temperature and current number of kT per degree of freedom (should be 0.5 kT at equilibrium).
logAllEnergyInformation() - Method in class ffx.algorithms.optimize.ConformationScan
logBindingEnergyCalculation(ConformationScan, ConformationScan, ConformationScan) - Static method in class ffx.algorithms.optimize.ConformationScan
logBondedTermsAndRestraints() - Method in class ffx.potential.ForceFieldEnergy: Log bonded energy terms and restraints.
logDevice(TornadoDevice) - Static method in class ffx.numerics.tornado.FFXTornado: List details about the passed TornadoDevice instance.
LogFormatter - Class in ffx.ui: A minor extension to the SimpleFormatter to reduce verbosity if debugging is not turned on.
logFrequency - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Time steps between logging information to the screen.
logger - Static variable in class ffx.numerics.clustering.DistanceMap
logger - Static variable in class ffx.potential.cli.AlchemicalOptions: The logger for this class.
logger - Static variable in class ffx.potential.cli.TopologyOptions: The logger for this class.
logger - Static variable in class ffx.potential.nonbonded.SpatialDensityRegion: Constant logger
logger - Static variable in interface ffx.potential.utils.PotentialsFunctions: Constant logger
logger - Static variable in class ffx.utilities.FFXCommand: The logger for this class.
logger - Static variable in class ffx.utilities.FFXTest: Constant logger
logger - Static variable in class ffx.utilities.HistogramXmlAdapter: The logger for this class.
logger - Static variable in class ffx.xray.BulkSolventRowRegion: Constant logger
logger - Static variable in class ffx.xray.BulkSolventSliceRegion: Constant logger
Logger - Interface in edu.rit.util: Interface Logger specifies the interface for an object that logs messages.
LogHandler - Class in ffx.ui: The default ConsoleHanlder publishes logging to System.err.
LogHandler() - Constructor for class ffx.ui.LogHandler: Construct the Force Field X Log Handler.
logIfRank0(String) - Method in class ffx.algorithms.optimize.RotamerOptimization
logIfRank0(String, Level) - Method in class ffx.algorithms.optimize.RotamerOptimization
logNoAngleType(Atom, Atom, Atom, ForceField) - Static method in class ffx.potential.bonded.Angle: Log that no AngleType exists.
logNoBondType(Atom, Atom, ForceField) - Static method in class ffx.potential.bonded.Bond: Log that no BondType exists.
logNoTorsionType(Atom, Atom, Atom, Atom, ForceField) - Static method in class ffx.potential.bonded.Torsion: Log that no TorsionType exists.
logOutputFiles(int) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
logResources() - Static method in class ffx.utilities.Resources: Log resources.
logTemp() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
logThermoForTime(long, long) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Checks if thermodynamics must be logged.
Long() - Constructor for class edu.rit.util.Searching.Long
Long() - Constructor for class edu.rit.util.Sorting.Long
LongArrayBuf - Class in edu.rit.mp.buf: Class LongArrayBuf provides a buffer for an array of long items sent or received using the Message Protocol (MP).
LongArrayBuf(long[], Range) - Constructor for class edu.rit.mp.buf.LongArrayBuf: Construct a new long array buffer.
LongArrayBuf_1 - Class in edu.rit.mp.buf: Class LongArrayBuf_1 provides a buffer for an array of long items sent or received using the Message Protocol (MP).
LongArrayBuf_1(long[], Range) - Constructor for class edu.rit.mp.buf.LongArrayBuf_1: Construct a new long array buffer.
LongBuf - Class in edu.rit.mp: Class LongBuf is the abstract base class for a buffer of long items sent or received using the Message Protocol (MP).
LongBuf(int) - Constructor for class edu.rit.mp.LongBuf: Construct a new long buffer.
LongForLoop - Class in edu.rit.pj: Class LongForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
LongForLoop() - Constructor for class edu.rit.pj.LongForLoop: Construct a new parallel for loop.
LongItemBuf - Class in edu.rit.mp.buf: Class LongItemBuf provides a buffer for a single long item sent or received using the Message Protocol (MP).
LongItemBuf() - Constructor for class edu.rit.mp.buf.LongItemBuf: Construct a new long item buffer.
LongItemBuf(long) - Constructor for class edu.rit.mp.buf.LongItemBuf: Construct a new long item buffer with the given initial value.
LongMatrixBuf - Class in edu.rit.mp.buf: Class LongMatrixBuf provides a buffer for a matrix of long items sent or received using the Message Protocol (MP).
LongMatrixBuf(long[][], Range, Range) - Constructor for class edu.rit.mp.buf.LongMatrixBuf: Construct a new long matrix buffer.
LongMatrixBuf_1 - Class in edu.rit.mp.buf: Class LongMatrixBuf_1 provides a buffer for a matrix of long items sent or received using the Message Protocol (MP).
LongMatrixBuf_1(long[][], Range, Range) - Constructor for class edu.rit.mp.buf.LongMatrixBuf_1: Construct a new long matrix buffer.
LongOp - Class in edu.rit.pj.reduction: Class LongOp is the abstract base class for a binary operation on long values, used to do reduction in a parallel program.
LongOp() - Constructor for class edu.rit.pj.reduction.LongOp: Construct a new long binary operation.
LongRange - Class in edu.rit.util: Class LongRange provides a range of type long.
LongRange() - Constructor for class edu.rit.util.LongRange: Construct a new range object representing an empty range.
LongRange(long, long) - Constructor for class edu.rit.util.LongRange: Construct a new range object with the given lower bound and upper bound.
LongRange(long, long, long) - Constructor for class edu.rit.util.LongRange: Construct a new range object with the given lower bound, upper bound, and stride.
LongRange(LongRange) - Constructor for class edu.rit.util.LongRange: Construct a new range object that is a copy of the given range object.
LongSchedule - Class in edu.rit.pj: Class LongSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.
LongSchedule() - Constructor for class edu.rit.pj.LongSchedule: Construct a new schedule object.
LongStrideForLoop - Class in edu.rit.pj: Class LongStrideForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
LongStrideForLoop() - Constructor for class edu.rit.pj.LongStrideForLoop: Construct a new parallel for loop.
longValue() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns this reduction variable's current value converted to type long.
looksLikeIon(String) - Static method in class ffx.utilities.StringUtils: Checks if a String matches a known monoatomic ion name.
looksLikeWater(String) - Static method in class ffx.utilities.StringUtils: Checks if a String matches a known water name.
Loop - Class in ffx.potential.utils: Loop class.
Loop(MolecularAssembly) - Constructor for class ffx.potential.utils.Loop: Constructor for Loop.
Loop(MolecularAssembly, int, int) - Constructor for class ffx.potential.utils.Loop: Constructor for Loop.
LOOP - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
LOOP_128 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
LOOP_256 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
LOOP_512 - Static variable in class ffx.numerics.fft.MixedRadixFactor: The number of complex elements that will be processed in each inner loop iteration.
loopbackChannel() - Method in class edu.rit.mp.ChannelGroup: Obtain this channel group's loopback channel.
LoopClosure - Class in ffx.potential.utils: LoopClosure class.
LoopClosure() - Constructor for class ffx.potential.utils.LoopClosure
lowerBound() - Method in interface ffx.numerics.integrate.DataSet: Lower bound of the points along x.
lowerBound() - Method in class ffx.numerics.integrate.DoublesDataSet: Lower bound of the points along x.
lowerBound() - Method in class ffx.numerics.integrate.FunctionDataCurve: Lower bound of the points along x.
lowestPairEnergy(Residue[], int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Return the lowest pair-energy for residue (i,ri) with residue j.
lowestSelfEnergy(Residue[], int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Return the lowest self-energy for residue i.
lPowPerm - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: lPowPerm = L^permanentLambdaExponent
lPowPol - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: lPowPol = L^polarizationLambdaExponent
Lr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
LS - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
LS - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
LT - Enum constant in enum class ffx.crystal.ASULimit: Less than operator.
LT11 - Enum constant in enum class ffx.crystal.LaueSystem: Laue System T11.
LTE - Enum constant in enum class ffx.crystal.ASULimit: Less than or equal to operator.
Lu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
LYD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
LYD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysStates
LYS - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
LYS - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysStates
LYSINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
LYStoLYD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration

M

m - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
M - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
m12scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between 1-2 multipoles is scaled by m12scale.
m13scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between 1-3 multipoles is scaled by m13scale.
m14scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between 1-4 multipoles is scaled by m14scale.
m15scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between 1-5 multipoles is scaled by m15scale.
M1MA - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
M2G - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
M2MG - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
M5MC - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
M5MU - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
M7MG - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
MACCALLUM_SPC - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
MACCALLUM_TIP4P - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
main(String[]) - Static method in class edu.rit.io.DoubleMatrixFile: Main program to combine a group of double matrix files into one double matrix file.
main(String[]) - Static method in class edu.rit.pj.cluster.JobBackend: Job Backend main program.
main(String[]) - Static method in class edu.rit.pj.cluster.JobScheduler: Job Scheduler main program.
main(String[]) - Static method in class edu.rit.pj.job.Runner: Main program.
main(String[]) - Static method in class ffx.Main: Create an instance of Force Field X
main(String[]) - Static method in class ffx.numerics.clustering.visualization.DendrogramFrame: Demo entry point that creates two frames with example dendrograms.
main(String[]) - Static method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: Example MBAR code usage and comparison with analytic answers for Harmonic Oscillators.
main(String[]) - Static method in class ffx.numerics.fft.Complex: Test the Complex FFT.
main(String[]) - Static method in class ffx.numerics.fft.Complex3DParallel: Test the Complex3DParallel FFT.
main(String[]) - Static method in class ffx.numerics.fft.Real3DParallel: Test the real 3D FFT.
main(String[]) - Static method in class ffx.numerics.integrate.Integration: main.
main(String[]) - Static method in class ffx.numerics.math.HilbertCurveTransforms: Main method for testing the Hilbert curve transforms.
main(String[]) - Static method in class ffx.numerics.math.SquareRoot: main.
main(String[]) - Static method in class ffx.numerics.math.SSETest: main.
main(String[]) - Static method in class ffx.potential.nonbonded.NeighborList: Debugging method.
main(String[]) - Static method in class ffx.potential.parsers.ForceFieldFilter: Parse a Force Field parameter file and echo the results with slashes.
main(String[]) - Static method in class ffx.potential.parsers.PDBMLFilter: Create an instance of the PDBML Filter
main(String[]) - Static method in class ffx.ui.KeyFileEditor: main
Main - Class in ffx: The Main class is the entry point to the graphical user interface version of Force Field X.
Main(File, List<String>) - Constructor for class ffx.Main: Main does some window initializations.
mainLoop(long, boolean) - Method in class ffx.algorithms.thermodynamics.RepExOST: Executes the main loop of RepExOST.
MainMenu - Class in ffx.ui: The MainMenu class creates the Force Field X Menu Bar
MainMenu(MainPanel) - Constructor for class ffx.ui.MainMenu: Constructor for MainMenu.
mainPanel - Variable in class ffx.HeadlessMain: This is the main application container for both the GUI and CLI.
mainPanel - Static variable in class ffx.Main: This is the main application wrapper.
MainPanel - Class in ffx.ui: The MainPanel class is the main container for Force Field X, handles file input/output and is used to pass references among the various sub-Panels.
MainPanel() - Constructor for class ffx.ui.MainPanel: Constructor for MainPanel.
MainPanel(JFrame) - Constructor for class ffx.ui.MainPanel: MainPanel Constructor
manageFilesAndRestart(File) - Method in class ffx.algorithms.dynamics.PhReplicaExchange: This deals with anything having to do with restarts and backup files.
MANUAL_WAKEUP - Static variable in class ffx.ui.behaviors.MouseBehavior: Constant MANUAL_WAKEUP=0x1
ManyBody - Class in ffx.algorithms.commands: The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
ManyBody - Class in ffx.realspace.commands: The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
ManyBody - Class in ffx.xray.commands: The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
ManyBody() - Constructor for class ffx.algorithms.commands.ManyBody: ManyBody Constructor.
ManyBody() - Constructor for class ffx.realspace.commands.ManyBody: ManyBody constructor.
ManyBody() - Constructor for class ffx.xray.commands.ManyBody: ManyBody constructor.
ManyBody(FFXBinding) - Constructor for class ffx.algorithms.commands.ManyBody: ManyBody Constructor.
ManyBody(FFXBinding) - Constructor for class ffx.realspace.commands.ManyBody: ManyBody constructor.
ManyBody(FFXBinding) - Constructor for class ffx.xray.commands.ManyBody: ManyBody constructor.
ManyBody(String[]) - Constructor for class ffx.algorithms.commands.ManyBody: ManyBody constructor that sets the command line arguments.
ManyBody(String[]) - Constructor for class ffx.realspace.commands.ManyBody: ManyBody constructor that sets the command line arguments.
ManyBody(String[]) - Constructor for class ffx.xray.commands.ManyBody: ManyBody constructor that sets the command line arguments.
ManyBodyCell - Class in ffx.algorithms.optimize.manybody: A cell used for optimization of a subdomain, its residues, its extent in fractional coordinates, its overall (linear) index, and its indices along the a, b, and c axes.
ManyBodyCell(double[], int[], int) - Constructor for class ffx.algorithms.optimize.manybody.ManyBodyCell: Constructs a ManyBodyCell instance, which takes up a set of fractional coordinates within the Crystal, the Residues contained within, and the index of the cell along the crystal's a, b, and c axes.
ManyBodyOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that use a many-body expansion for global optimization.
ManyBodyOptions() - Constructor for class ffx.algorithms.cli.ManyBodyOptions
ManyBodyPhScan - Class in ffx.algorithms.commands.test: The ManyBodyPhScan script runs a pH scan with ManyBody optimization by executing another FFXScript multiple times across a pH range.
ManyBodyPhScan() - Constructor for class ffx.algorithms.commands.test.ManyBodyPhScan: ManyBodyPhScan Constructor.
ManyBodyPhScan(FFXBinding) - Constructor for class ffx.algorithms.commands.test.ManyBodyPhScan: ManyBodyPhScan Constructor.
ManyBodyPhScan(String[]) - Constructor for class ffx.algorithms.commands.test.ManyBodyPhScan: ManyBodyPhScan constructor that sets the command line arguments.
mapLambda(double) - Method in class ffx.potential.bonded.RestrainTorsion
mapToDualTopologyIndex(int, int) - Method in class ffx.potential.DualTopologyEnergy: Map an atomic index from a single topology to the overall dual-topology atom array.
mark - Variable in class ffx.numerics.quickhull.Face
marshal(double[][]) - Method in class ffx.utilities.HistogramXmlAdapter: Convert the 2D histogram double array into a String.
marshal(Double) - Method in class ffx.utilities.DoubleXMLAdapter
MaskingInterface - Interface in ffx.potential.nonbonded: By implementing the MaskingInterface interface, interaction pairs can be excluded during NeighborList construction.
mass - Variable in class ffx.potential.SystemState: Mass for each degree of freedom.
mass - Variable in class ffx.ui.commands.SimulationDefinition
mass() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the mass record component.
masterRank() - Method in class edu.rit.pj.WorkerTeam: Determine the rank of the process that contains the master thread.
mat3Inverse(double[][]) - Static method in class ffx.numerics.math.MatrixMath: inverse of a 3x3 matrix.
mat3Inverse(double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: mat3inverse
mat3Mat3(double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: Matrix times a matrix.
mat3Mat3(double[][], double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: mat3mat3
mat3SymVec6(double[][], double[]) - Static method in class ffx.numerics.math.MatrixMath: matrix times a vector representation of a symmetric 3x3 matrix
mat3SymVec6(double[][], double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath: mat3SymVec6
mat3Vec3(double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath: matrix times a vector
mat3Vec3(double[], double[][], double[]) - Static method in class ffx.numerics.math.MatrixMath: mat3vec3
mat4Mat4(double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: Matrix times a matrix (both 4x4).
mat4Mat4(double[][], double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: Multiply two 4x4 matrices.
Mathe - Class in edu.rit.util: Class Mathe provides useful mathematical operations.
matrix - Variable in class ffx.ui.GraphicsAxis
MatrixMath - Class in ffx.numerics.math: The MatrixMath class is a simple matrix math library used mainly by the X-ray package.
matrixToString(double[][], int, String) - Static method in class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Parse values of a matrix into a string.
max - Variable in class ffx.numerics.math.BootStrapStatistics: The maximum value.
max - Variable in class ffx.numerics.math.SummaryStatistics: Maximum value.
MAX_BORN_RADIUS - Static variable in class ffx.potential.nonbonded.implicit.BornTanhRescaling: Maximum Born radius.
MAX_COVALENT_RADIUS - Static variable in class ffx.potential.parsers.CIFFilter: Maximum atomic covalent radius for CDK Rebonder Tool
MAX_TCP_PORT - Static variable in class ffx.utilities.PortUtils: The maximum TCP Port.
maxDebugGradient - Variable in class ffx.potential.ForceFieldEnergy: If the absolute value of a gradient component is greater than "maxDebugGradient", verbose logging results.
maxDist(QuickHull3D) - Static method in class ffx.potential.utils.ConvexHullOps: Find the maximum pairwise distance between vertex points on a convex hull.
maxDist(Atom[]) - Static method in class ffx.potential.utils.ConvexHullOps: Maximum pairwise distance between atoms in an array.
MAXIMUM - Static variable in class edu.rit.pj.reduction.ByteOp: The byte maximum binary operation.
MAXIMUM - Static variable in class edu.rit.pj.reduction.CharacterOp: The character maximum binary operation.
MAXIMUM - Static variable in class edu.rit.pj.reduction.DoubleOp: The double maximum binary operation.
MAXIMUM - Static variable in class edu.rit.pj.reduction.FloatOp: The float maximum binary operation.
MAXIMUM - Static variable in class edu.rit.pj.reduction.IntegerOp: The integer maximum binary operation.
MAXIMUM - Static variable in class edu.rit.pj.reduction.LongOp: The long maximum binary operation.
MAXIMUM - Static variable in class edu.rit.pj.reduction.ShortOp: The short maximum binary operation.
MaxLengthScale - Static variable in interface ffx.potential.bonded.ROLS: Constant MaxLengthScale=5
maxwell() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Reset velocities from a Maxwell-Boltzmann distribution based on the current target temperature of thermostat.
maxwell(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Reset velocities from a Maxwell-Boltzmann distribution of momenta based on the supplied target temperature.
maxwellIndividual(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Return 3 velocities from a Maxwell-Boltzmann distribution of momenta.
maxWindowLength() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Returns the longest window to be used (normalized to the number of MD steps in a "regular" window).
maxWindowLength() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
maxWindowLength() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
maxWindowLength() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
mbar - Variable in class ffx.algorithms.commands.MBAR
MBAR - Class in ffx.algorithms.commands: Perform MBAR calculation or necessary energy evaluations.
MBAR() - Constructor for class ffx.algorithms.commands.MBAR: MBAR Constructor.
MBAR(FFXBinding) - Constructor for class ffx.algorithms.commands.MBAR: MBAR Constructor.
MBAR(String[]) - Constructor for class ffx.algorithms.commands.MBAR: MBAR constructor that sets the command line arguments.
MBARFilter - Class in ffx.numerics.estimator: The MBARFilter class parses mbar (*.mbar or *.bar) files.
MBARFilter(File, boolean) - Constructor for class ffx.numerics.estimator.MBARFilter: Constructor for MBARFilter.
Mcg1Random - Class in edu.rit.util: Class Mcg1Random provides a default pseudorandom number generator (PRNG) designed for use in parallel scientific programming.
Mcg1Random(long) - Constructor for class edu.rit.util.Mcg1Random: Construct a new PRNG with the given seed.
MCLoop - Class in ffx.algorithms.mc: MCLoop class.
MCMove - Interface in ffx.algorithms.mc: The MCMove interface defines the basic functionality of a Monte Carlo move; that it can apply its move and revert it.
mcStep(MCMove) - Method in class ffx.algorithms.mc.BoltzmannMC: Calculates the current system energy and performs an MCMove.
mcStep(MCMove) - Method in interface ffx.algorithms.mc.MetropolisMC: Calculates the current system energy and performs an MCMove.
mcStep(MCMove, double) - Method in class ffx.algorithms.mc.BoltzmannMC: Performs an MCMove.
mcStep(MCMove, double) - Method in interface ffx.algorithms.mc.MetropolisMC: Performs an MCMove.
mcStep(List<MCMove>) - Method in class ffx.algorithms.mc.BoltzmannMC: Calculates the current system energy and performs a series of moves sequentially as a single hybrid step.
mcStep(List<MCMove>) - Method in interface ffx.algorithms.mc.MetropolisMC: Calculates the current system energy and performs a series of moves sequentially as a single hybrid step.
mcStep(List<MCMove>, double) - Method in class ffx.algorithms.mc.BoltzmannMC: Performs a series of moves sequentially, as a single hybrid step.
mcStep(List<MCMove>, double) - Method in interface ffx.algorithms.mc.MetropolisMC: Performs a series of moves sequentially, as a single hybrid step.
mcUpdate(double) - Method in class ffx.algorithms.mc.MCLoop: After a successful step or interval of an algorithm, this method of the listener will be called.
mcUpdate(double) - Method in interface ffx.algorithms.mc.MonteCarloListener: After a successful step or interval of an algorithm, this method of the listener will be called.
mcUpdate(double) - Method in class ffx.algorithms.mc.RosenbluthCBMC: After a successful step or interval of an algorithm, this method of the listener will be called.
mcUpdate(double) - Method in class ffx.algorithms.mc.RosenbluthOBMC: After a successful step or interval of an algorithm, this method of the listener will be called.
md(int, double, double, double, double, boolean, File) - Method in class ffx.ui.ModelingShell: md
md(MolecularAssembly, int, double, double, double, double, boolean, File) - Method in interface ffx.algorithms.AlgorithmFunctions: Runs molecular dynamics on an assembly.
md(MolecularAssembly, int, double, double, double, double, boolean, File) - Method in class ffx.algorithms.AlgorithmUtils: Runs molecular dynamics on an assembly.
md(MolecularAssembly, int, double, double, double, double, boolean, File) - Method in class ffx.ui.UIUtils
Md - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
MDEngine - Enum Class in ffx.algorithms.dynamics: Enumerates available molecular dynamics engines; presently limited to the FFX reference engine and the OpenMM engine.
MDMove - Class in ffx.algorithms.mc: Use MD as a coordinate based MC move.
MDMove(MolecularAssembly, Potential, AlgorithmListener, DynamicsOptions, long, File) - Constructor for class ffx.algorithms.mc.MDMove: Constructor for MDMove.
MDVerbosity - Enum Class in ffx.algorithms.dynamics: Define the verbosity of the MolecularDynamics class.
MDWriteAction - Enum Class in ffx.algorithms.dynamics: Describe actions taken by writeFilesForStep.
mean - Variable in class ffx.numerics.math.BootStrapStatistics: The mean value.
mean - Variable in class ffx.numerics.math.SummaryStatistics: Mean value.
measure() - Method in class ffx.potential.bonded.Torsion: Compute the torsional angle in degrees.
measureAARotamer(Residue, double[], boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: Measures the torsions of an amino acid Residue's current configuration.
MEASUREANGLE - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
measureDelta(Residue) - Static method in class ffx.potential.bonded.RotamerLibrary: Measures the delta torsion (sugar pucker) of a nucleic acid Residue.
MEASUREDIHEDRAL - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
MEASUREDISTANCE - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
measureRotamer(Residue, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: Measures the torsional angles of a residue's side chain.
measureRotamer(Residue, double[], boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: Measures the torsion angles of a Residue.
measureRotamers(List<Residue>, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: Measures the torsions in a list of Residues.
merge(Joint) - Method in class ffx.potential.bonded.Joint: merge
merge(MSNode[]) - Method in class ffx.ui.MainPanel: merge
mergeAdjacentFace(HalfEdge, Face[]) - Method in class ffx.numerics.quickhull.Face: Merges this face with the adjacent face across the specified half-edge if possible.
MergeFilter - Class in ffx.potential.parsers: The MergeFilter class allows Force Field X to treat merging of Systems just like opening a file from a hard disk or socket.
MergeFilter(MolecularAssembly, ArrayList<Atom>, ArrayList<Bond>) - Constructor for class ffx.potential.parsers.MergeFilter: Constructor for MergeFilter.
Message - Class in edu.rit.pj.cluster: Class Message is the abstract base class for a message sent to a process in the PJ cluster middleware.
Message() - Constructor for class edu.rit.pj.cluster.Message: Construct a new message.
Message(int) - Constructor for class edu.rit.pj.cluster.Message: Construct a new message with the given message tag.
MET - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
METERS_TO_ANG - Static variable in class ffx.utilities.Constants: Constant METERS_TO_ANG=1E10
METHIONINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
MetropolisMC - Interface in ffx.algorithms.mc: The MetropolisMC interface defines the basic methods of a Metropolis Monte Carlo application.
mevent - Variable in class ffx.ui.behaviors.PickMouseBehavior
Mg - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
MG - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
MG2 - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
MIDDLE_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
middlewareAddress - Variable in class edu.rit.pj.cluster.ProcessInfo: Host/port to which the job backend process is listening for middleware messages.
min - Variable in class ffx.numerics.math.BootStrapStatistics: The minimum value.
min - Variable in class ffx.numerics.math.SummaryStatistics: Minimum value.
MIN_BOND_DISTANCE - Static variable in class ffx.potential.parsers.CIFFilter: Minimum bond distance for CDK Rebonder Tool
minDist() - Method in class ffx.numerics.clustering.DistanceMap: Peek at the minimal linkage distance currently in the map.
minDistOverSymOps(double[], double[]) - Method in class ffx.crystal.Crystal: Minimum distance between two coordinates over all symmetry operators.
minEnergy - Variable in class ffx.potential.commands.test.PhGradient
MinimizationReporter - Class in ffx.openmm: A MinimizationReporter can be passed to LocalEnergyMinimizer::minimize() to provide periodic information on the progress of minimization, and to give you the chance to stop minimization early.
MinimizationReporter() - Constructor for class ffx.openmm.MinimizationReporter: Constructor.
minimize() - Method in class ffx.algorithms.optimize.Minimize: minimize
minimize() - Method in class ffx.xray.RefinementMinimize: minimize assuming an eps of 1.0 and Integer.MAX_VALUE cycles
minimize() - Method in class ffx.xray.ScaleBulkMinimize: minimize
minimize() - Method in class ffx.xray.SigmaAMinimize: minimize
minimize() - Method in class ffx.xray.SplineMinimize: minimize
minimize(double) - Method in class ffx.algorithms.optimize.Minimize: minimize
minimize(double) - Method in class ffx.xray.RefinementMinimize: minimize assuming Integer.MAX_VALUE cycles
minimize(double) - Method in class ffx.xray.ScaleBulkMinimize: minimize
minimize(double) - Method in class ffx.xray.SigmaAMinimize: minimize
minimize(double) - Method in class ffx.xray.SplineMinimize: minimize
minimize(double, int) - Method in class ffx.algorithms.optimize.Minimize: minimize
minimize(double, int) - Method in class ffx.algorithms.optimize.MinimizeOpenMM: minimize
minimize(double, int) - Method in class ffx.xray.RefinementMinimize: minimize with input eps and cycles
minimize(int) - Method in class ffx.xray.RefinementMinimize: minimize assuming an eps of 1.0 and limited cycles
minimize(int, double) - Method in class ffx.xray.ScaleBulkMinimize: minimize
minimize(int, double) - Method in class ffx.xray.SigmaAMinimize: minimize
minimize(int, double) - Method in class ffx.xray.SplineMinimize: minimize
minimize(int, double, int) - Method in class ffx.algorithms.optimize.CrystalMinimize: minimize
minimize(int, double, int) - Method in class ffx.algorithms.optimize.Minimize: minimize
minimize(int, double, int) - Method in class ffx.algorithms.optimize.MinimizeOpenMM: Note the OpenMM L-BFGS minimizer does not accept the parameter "m" for the number of previous steps used to estimate the Hessian.
minimize(int, double, int) - Method in class ffx.xray.RefinementMinimize: minimize with input cycles for matrix conditioning, eps and cycles
minimize(int, int, double[], double, double[], double, int, OptimizationInterface, OptimizationListener) - Static method in class ffx.numerics.optimization.LBFGS: This method solves the unconstrained minimization problem
minimize(int, int, double[], double, double[], double, OptimizationInterface, OptimizationListener) - Static method in class ffx.numerics.optimization.LBFGS: This method solves the unconstrained minimization problem
minimize(MolecularAssembly, double) - Method in interface ffx.algorithms.AlgorithmFunctions: Relax the coordinates of a MolecularAssembly and minimize its potential energy
minimize(MolecularAssembly, double) - Method in class ffx.algorithms.AlgorithmUtils: Relax the coordinates of a MolecularAssembly and minimize its potential energy
minimize(MolecularAssembly, double) - Method in class ffx.ui.UIUtils
Minimize - Class in ffx.algorithms.commands: The Minimize script uses a limited-memory BFGS algorithm to minimize the energy of a molecular system.
Minimize - Class in ffx.algorithms.optimize: Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.
Minimize - Class in ffx.realspace.commands: The Real Space Minimize script.
Minimize - Class in ffx.xray.commands: The X-ray Minimize script.
Minimize() - Constructor for class ffx.algorithms.commands.Minimize: Minimize Constructor.
Minimize() - Constructor for class ffx.realspace.commands.Minimize: Minimize constructor.
Minimize() - Constructor for class ffx.xray.commands.Minimize: Minimize constructor.
Minimize(MolecularAssembly, AlgorithmListener) - Constructor for class ffx.algorithms.optimize.Minimize: Constructor for Minimize.
Minimize(MolecularAssembly, Potential, AlgorithmListener) - Constructor for class ffx.algorithms.optimize.Minimize: Constructor for Minimize.
Minimize(FFXBinding) - Constructor for class ffx.algorithms.commands.Minimize: Minimize Constructor.
Minimize(FFXBinding) - Constructor for class ffx.realspace.commands.Minimize: Minimize constructor.
Minimize(FFXBinding) - Constructor for class ffx.xray.commands.Minimize: Minimize constructor.
Minimize(String[]) - Constructor for class ffx.algorithms.commands.Minimize: Minimize constructor that sets the command line arguments.
Minimize(String[]) - Constructor for class ffx.realspace.commands.Minimize: Minimize constructor that sets the command line arguments.
Minimize(String[]) - Constructor for class ffx.xray.commands.Minimize: Minimize constructor that sets the command line arguments.
Minimize.MinimizationEngine - Enum Class in ffx.algorithms.optimize: Enumerates available molecular minimization engines; presently limited to the FFX reference engine and the OpenMM engine.
minimizeCoordinates() - Method in class ffx.algorithms.optimize.PhMinimize: minimize
minimizeCoordinates(double) - Method in class ffx.algorithms.optimize.PhMinimize: minimize
minimizeCoordinates(double, int) - Method in class ffx.algorithms.optimize.PhMinimize: minimize
minimizeCoordinates(int, double, int) - Method in class ffx.algorithms.optimize.PhMinimize: minimize
MinimizeCrystals - Class in ffx.algorithms.commands: The MinimizeCrystals script uses a limited-memory BFGS algorithm to minimize the energy of a crystal, including both coordinates and unit cell parameters.
MinimizeCrystals() - Constructor for class ffx.algorithms.commands.MinimizeCrystals: CrystalMin Constructor.
MinimizeCrystals(FFXBinding) - Constructor for class ffx.algorithms.commands.MinimizeCrystals: CrystalMin Constructor.
MinimizeCrystals(String[]) - Constructor for class ffx.algorithms.commands.MinimizeCrystals: MinimizeCrystals constructor that sets the command line arguments.
minimizeFactory(MolecularAssembly, Potential, AlgorithmListener, Minimize.MinimizationEngine) - Static method in class ffx.algorithms.optimize.Minimize: dynamicsFactory.
MinimizeOpenMM - Class in ffx.algorithms.commands: The Minimize script uses OpenMM accelerated L-BFGS algorithm to minimize the energy of a molecular system.
MinimizeOpenMM - Class in ffx.algorithms.optimize: Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy.
MinimizeOpenMM() - Constructor for class ffx.algorithms.commands.MinimizeOpenMM: MinimizeOpenMM Constructor.
MinimizeOpenMM(MolecularAssembly) - Constructor for class ffx.algorithms.optimize.MinimizeOpenMM: MinimizeOpenMM constructor.
MinimizeOpenMM(MolecularAssembly, OpenMMEnergy) - Constructor for class ffx.algorithms.optimize.MinimizeOpenMM: MinimizeOpenMM constructor.
MinimizeOpenMM(MolecularAssembly, OpenMMEnergy, AlgorithmListener) - Constructor for class ffx.algorithms.optimize.MinimizeOpenMM: MinimizeOpenMM constructor.
MinimizeOpenMM(FFXBinding) - Constructor for class ffx.algorithms.commands.MinimizeOpenMM: MinimizeOpenMM Constructor.
MinimizeOpenMM(String[]) - Constructor for class ffx.algorithms.commands.MinimizeOpenMM: MinimizeOpenMM constructor that sets the command line arguments.
MinimizeOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that involve local energy minimization.
MinimizeOptions() - Constructor for class ffx.algorithms.cli.MinimizeOptions
MinimizePh - Class in ffx.algorithms.commands.test: The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.
MinimizePh() - Constructor for class ffx.algorithms.commands.test.MinimizePh: MinimizePh Constructor.
MinimizePh(FFXBinding) - Constructor for class ffx.algorithms.commands.test.MinimizePh: MinimizePh Constructor.
MinimizePh(String[]) - Constructor for class ffx.algorithms.commands.test.MinimizePh: MinimizePh constructor that sets the command line arguments.
minimizeTitration(double, int) - Method in class ffx.algorithms.optimize.PhMinimize: minimize
minimizeTitration(int, double, int) - Method in class ffx.algorithms.optimize.PhMinimize: minimize
MINIMUM - Static variable in class edu.rit.pj.reduction.ByteOp: The byte minimum binary operation.
MINIMUM - Static variable in class edu.rit.pj.reduction.CharacterOp: The character minimum binary operation.
MINIMUM - Static variable in class edu.rit.pj.reduction.DoubleOp: The double minimum binary operation.
MINIMUM - Static variable in class edu.rit.pj.reduction.FloatOp: The float minimum binary operation.
MINIMUM - Static variable in class edu.rit.pj.reduction.IntegerOp: The integer minimum binary operation.
MINIMUM - Static variable in class edu.rit.pj.reduction.LongOp: The long minimum binary operation.
MINIMUM - Static variable in class edu.rit.pj.reduction.ShortOp: The short minimum binary operation.
minLambda - Variable in class ffx.algorithms.thermodynamics.HistogramData: The minimum value of the first lambda bin.
minLambdaList - Variable in class ffx.potential.commands.test.PhGradient
minMaxE2(Residue[], double[], int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Calculates the minimum and maximum summations over additional residues for some pair ri-rj.
minMaxPairEnergy(Residue[], double[], int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes the maximum and minimum energy i,ri might have with j, and optionally (if three-body energies in use) third residues k.
minus(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is (this - b).
minusIP(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: minusIP
minWindowLength() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Returns the shortest window to be used (normalized to the number of MD steps in a "regular" window).
minWindowLength() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
minWindowLength() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
minWindowLength() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
mirror(Random, double, double) - Static method in class ffx.algorithms.mc.LambdaMove: Applies 0-1 mirroring conditions to lam + dL.
mirrorDegrees(double) - Static method in class ffx.numerics.math.ScalarMath: Reflect proposed angles to be within 0 and 180 degrees.
mirrorRadians(double) - Static method in class ffx.numerics.math.ScalarMath: Reflect proposed angles to be within 0 and 180 degrees.
MissingAtomTypeException(Residue, Atom) - Constructor for exception class ffx.potential.bonded.BondedUtils.MissingAtomTypeException
MissingHeavyAtomException(String, AtomType, Atom) - Constructor for exception class ffx.potential.bonded.BondedUtils.MissingHeavyAtomException
MixedRadixFactor - Class in ffx.numerics.fft: Mixed radix factor is extended by the pass classes to apply the mixed radix factor.
MixedRadixFactor(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactor: Constructor for the mixed radix factor.
MixedRadixFactor2 - Class in ffx.numerics.fft: The MixedRadixFactor2 class handles factors of 2 in the FFT.
MixedRadixFactor2(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactor2: Create a new MixedRadixFactor2 instance.
MixedRadixFactor3 - Class in ffx.numerics.fft: The MixedRadixFactor3 class handles factors of 3 in the FFT.
MixedRadixFactor3(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactor3: Create a new MixedRadixFactor3 instance.
MixedRadixFactor4 - Class in ffx.numerics.fft: The MixedRadixFactor4 class handles factors of 4 in the FFT.
MixedRadixFactor4(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactor4: Construct a MixedRadixFactor4.
MixedRadixFactor5 - Class in ffx.numerics.fft: The MixedRadixFactor5 class handles factors of 5 in the FFT.
MixedRadixFactor5(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactor5: Construct a MixedRadixFactor5.
MixedRadixFactor6 - Class in ffx.numerics.fft: The MixedRadixFactor6 class handles factors of 6 in the FFT.
MixedRadixFactor6(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactor6: Construct a MixedRadixFactor6.
MixedRadixFactor7 - Class in ffx.numerics.fft: The MixedRadixFactor7 class handles factors of 7 in the FFT.
MixedRadixFactor7(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactor7: Construct a MixedRadixFactor7.
MixedRadixFactorPrime - Class in ffx.numerics.fft: The MixedRadixFactorPrime class handles prime factors in the FFT.
MixedRadixFactorPrime(PassConstants) - Constructor for class ffx.numerics.fft.MixedRadixFactorPrime: Construct a MixedRadixFactorPrime.
Mn - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Mo - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
mod(double, double) - Static method in class ffx.numerics.math.ScalarMath: This is an atypical mod function used by crystallography methods.
mod(int, int) - Static method in class ffx.numerics.math.ScalarMath: This is an atypical mod function used by crystallography methods.
mode - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: The alchemical mode to use.
ModelingPanel - Class in ffx.ui: The ModelingPanel class encapsulates functionality needed to run FFX Modeling Commands.
ModelingPanel(MainPanel) - Constructor for class ffx.ui.ModelingPanel: Constructor
ModelingShell - Class in ffx.ui: The ModelingShell is used to script Multiscale Modeling Routines via the Groovy scripting language.
ModelingShell(MainPanel) - Constructor for class ffx.ui.ModelingShell: Constructor for ModelingShell.
ModelvsData - Class in ffx.xray.commands: The X-ray ModelvsData script.
ModelvsData() - Constructor for class ffx.xray.commands.ModelvsData: ModelvsData constructor.
ModelvsData(FFXBinding) - Constructor for class ffx.xray.commands.ModelvsData: ModelvsData constructor.
ModelvsData(String[]) - Constructor for class ffx.xray.commands.ModelvsData: ModelvsData constructor that sets the command line arguments.
ModifiedBessel - Class in ffx.numerics.special: Implementation of the modified Bessel function of the first kind using Chebyshev polynomials.
modToRange(double, double, double) - Static method in class ffx.numerics.math.ScalarMath: Atypical mod function used to move a value into the range lb <= value < ub, assuming the domain is periodic with a period of (ub - lb).
mola - Variable in class ffx.potential.commands.PhEnergy
molDyn - Variable in class ffx.algorithms.commands.Dynamics
molecularAssemblies - Variable in class ffx.potential.commands.MoveIntoUnitCell: Save a reference to the MolecularAssembly instances to destroy their potentials.
molecularAssembly - Variable in class ffx.algorithms.dynamics.MolecularDynamics: MolecularAssembly to run dynamics on.
molecularAssembly - Variable in class ffx.algorithms.optimize.Minimize: The MolecularAssembly being operated on.
molecularAssembly - Variable in class ffx.algorithms.optimize.PhMinimize: The MolecularAssembly being operated on.
molecularAssembly - Variable in class ffx.algorithms.optimize.RotamerOptimization: MolecularAssembly to perform rotamer optimization on.
molecularAssembly - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: The MolecularAssembly being simulated.
molecularAssembly - Variable in class ffx.potential.ForceFieldEnergy: The MolecularAssembly associated with this force field energy.
MolecularAssembly - Class in ffx.potential: The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
MolecularAssembly(String) - Constructor for class ffx.potential.MolecularAssembly: Constructor for MolecularAssembly.
MolecularAssembly(String, MSNode) - Constructor for class ffx.potential.MolecularAssembly: Constructor for MolecularAssembly.
MolecularAssembly(String, MSNode, CompositeConfiguration) - Constructor for class ffx.potential.MolecularAssembly: Constructor for MolecularAssembly.
MolecularAssembly.FractionalMode - Enum Class in ffx.potential
molecularDynamics - Variable in class ffx.algorithms.commands.test.PhDynamics
MolecularDynamics - Class in ffx.algorithms.dynamics: Run NVE, NVT, or NPT molecular dynamics.
MolecularDynamics(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum) - Constructor for class ffx.algorithms.dynamics.MolecularDynamics: Constructor for MolecularDynamics.
MolecularDynamicsOpenMM - Class in ffx.algorithms.dynamics: Runs Molecular Dynamics using OpenMM implementation
MolecularDynamicsOpenMM(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum) - Constructor for class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: Constructs a MolecularDynamicsOpenMM object, to perform molecular dynamics using native OpenMM routines, avoiding the cost of communicating coordinates, gradients, and energies back and forth across the PCI bus.
MolecularMC - Class in ffx.algorithms.mc: The MolecularMC class is a framework to take Monte Carlo steps on a molecular system.
MolecularMC(MolecularAssembly) - Constructor for class ffx.algorithms.mc.MolecularMC: Constructs a DefaultMC instance with a molecular assembly and its PotentialEnergy.
MolecularMC(MolecularAssembly, Potential) - Constructor for class ffx.algorithms.mc.MolecularMC: Constructs a DefaultMC instance with a molecular assembly and a specific Potential.
Molecule - Class in ffx.potential.bonded: The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.
Molecule(String) - Constructor for class ffx.potential.bonded.Molecule: Constructor for Molecule.
Molecule(String, int, Character, String) - Constructor for class ffx.potential.bonded.Molecule: Constructor for Molecule.
MOLECULE - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
MOLECULE - Enum constant in enum class ffx.potential.MolecularAssembly.FractionalMode
moleculeName - Variable in class ffx.potential.parameters.BioType: The PDB molecule name for this BioType.
momentsOfInertia(double[], double[], boolean, boolean, boolean) - Static method in class ffx.potential.utils.StructureMetrics: Compute the moments of inertia.
momentsOfInertia(double[], double[], double[], double[], boolean, boolean, boolean) - Static method in class ffx.potential.utils.StructureMetrics: Compute the moments of inertia
momentsOfInertia(Atom[], boolean, boolean, boolean) - Static method in class ffx.potential.utils.StructureMetrics: Compute the moments of inertia for all atoms in the supplied array.
MONOCHROME - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
MONOCLINIC - Enum constant in enum class ffx.crystal.CrystalSystem: Monoclinic crystal system.
MONOCLINIC_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem: Monoclinic lattice system.
MONOPHOSPHATE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
MONOPOLE - Enum constant in enum class ffx.numerics.multipole.GKMultipoleOrder: Monopole potential.
monopoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Permanent multipole energy and gradient using the GK monopole tensor.
monopoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Permanent multipole energy and gradient using the GK monopole tensor.
monopoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Permanent multipole energy and gradient using the GK monopole tensor.
monopoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Permanent multipole energy and gradient using the GK monopole tensor.
monopolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Monopole Polarization Energy and Gradient.
monopolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Monopole Polarization Energy and Gradient.
monopolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Monopole Polarization Energy and Gradient.
monopolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Monopole Polarization Energy and Gradient.
MonteCarloAnisotropicBarostat - Class in ffx.openmm: This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure.
MonteCarloAnisotropicBarostat(OpenMM_Vec3, double, int, int, int, int) - Constructor for class ffx.openmm.MonteCarloAnisotropicBarostat: Create a MonteCarloAnisotropicBarostat.
monteCarloBarostat - Variable in class ffx.potential.openmm.OpenMMSystem: Barostat to be added if NPT (isothermal-isobaric) dynamics is requested.
MonteCarloBarostat - Class in ffx.openmm: This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure.
MonteCarloBarostat(double, double, int) - Constructor for class ffx.openmm.MonteCarloBarostat: Create a MonteCarloBarostat.
MonteCarloFlexibleBarostat - Class in ffx.openmm: This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure.
MonteCarloFlexibleBarostat(double, double, int, int) - Constructor for class ffx.openmm.MonteCarloFlexibleBarostat: Create a MonteCarloFlexibleBarostat.
MonteCarloListener - Interface in ffx.algorithms.mc: The MonteCarloListener will be notified at regular intervals during an MC algorithm.
MonteCarloMembraneBarostat - Class in ffx.openmm: This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure and surface tension on a membrane system.
MonteCarloMembraneBarostat(double, double, double, int, int, int) - Constructor for class ffx.openmm.MonteCarloMembraneBarostat: Create a MonteCarloMembraneBarostat.
MonteCarloOST - Class in ffx.algorithms.thermodynamics: Sample a thermodynamic path using the OST method, with the time-dependent bias built up using Metropolis Monte Carlo steps.
MonteCarloOST(Potential, OrthogonalSpaceTempering, MolecularAssembly, CompositeConfiguration, AlgorithmListener, DynamicsOptions, boolean, int, File) - Constructor for class ffx.algorithms.thermodynamics.MonteCarloOST: Constructor for MonteCarloOST.
MostBar - Class in ffx.algorithms.commands.test: The MostBar script uses a single set of archive file(s) from a Metropolized Orthogonal Space Tempering run to evaluate free energy via the Bennett Acceptance Ratio
Usage:
ffxc test.MostBar [options] <structures1>
MostBar() - Constructor for class ffx.algorithms.commands.test.MostBar: MostBar Constructor.
MostBar(FFXBinding) - Constructor for class ffx.algorithms.commands.test.MostBar: MostBar Constructor.
MostBar(String[]) - Constructor for class ffx.algorithms.commands.test.MostBar: MostBar constructor that sets the command line arguments.
MouseBehavior - Class in ffx.ui.behaviors: The MouseBehavior class is the Base class for all mouse manipulators.
MouseBehavior(int, TransformGroup) - Constructor for class ffx.ui.behaviors.MouseBehavior: Constructor for MouseBehavior.
MouseBehavior(int, TransformGroup, Behavior, int) - Constructor for class ffx.ui.behaviors.MouseBehavior: Constructor for MouseBehavior.
MouseBehaviorCallback - Interface in ffx.ui.behaviors: The MouseBehaviorCallback interface is implemented by classes that want to receive callbacks when transforms are updated.
mouseClicked(MouseEvent) - Method in class ffx.ui.GraphicsSplitPane
mouseClicked(MouseEvent) - Method in class ffx.ui.KeywordComponent
mouseClicked(MouseEvent) - Method in class ffx.ui.ModelingPanel: Mouse events are used to trigger status bar updates.
mouseCriterion - Variable in class ffx.ui.behaviors.MouseBehavior
mouseDragged(MouseEvent) - Method in class ffx.ui.GraphicsSplitPane
mouseEntered(MouseEvent) - Method in class ffx.ui.GraphicsSplitPane
mouseEntered(MouseEvent) - Method in class ffx.ui.KeywordComponent
mouseEntered(MouseEvent) - Method in class ffx.ui.ModelingPanel
mouseEvents - Variable in class ffx.ui.behaviors.MouseBehavior
mouseExited(MouseEvent) - Method in class ffx.ui.GraphicsSplitPane
mouseExited(MouseEvent) - Method in class ffx.ui.KeywordComponent
mouseExited(MouseEvent) - Method in class ffx.ui.ModelingPanel
mouseMoved(MouseEvent) - Method in class ffx.ui.GraphicsSplitPane
MouseOrbit - Class in ffx.ui.behaviors: The MouseOrbit class implements a mouse orbit behavior.
MouseOrbit(int, TransformGroup) - Constructor for class ffx.ui.behaviors.MouseOrbit: Constructor for MouseOrbit.
mousePressed(MouseEvent) - Method in class ffx.ui.GraphicsSplitPane
mousePressed(MouseEvent) - Method in class ffx.ui.KeywordComponent
mousePressed(MouseEvent) - Method in class ffx.ui.ModelingPanel
MouseProperties - Class in ffx.ui.behaviors: The MouseProperties class is simple extension of MouseBehavior.
MouseProperties(int, TransformGroup) - Constructor for class ffx.ui.behaviors.MouseProperties: Constructor for MouseProperties.
mouseReleased(MouseEvent) - Method in class ffx.ui.GraphicsSplitPane
mouseReleased(MouseEvent) - Method in class ffx.ui.KeywordComponent
mouseReleased(MouseEvent) - Method in class ffx.ui.ModelingPanel
MouseRotate - Class in ffx.ui.behaviors: The MouseRotate class implements a mouse rotation behavior.
MouseRotate(int, TransformGroup) - Constructor for class ffx.ui.behaviors.MouseRotate: Constructor for MouseRotate.
MouseRotate(int, TransformGroup, Behavior, int, int) - Constructor for class ffx.ui.behaviors.MouseRotate: Constructor for MouseRotate.
MouseSelection - Class in ffx.ui.behaviors: The MouseSelection class implements a mouse selection behavior.
MouseSelection(int, TransformGroup) - Constructor for class ffx.ui.behaviors.MouseSelection: Constructor for MouseSelection.
MouseTranslate - Class in ffx.ui.behaviors: The MouseTranslate class implements a mouse translate behavior.
MouseTranslate(int, TransformGroup) - Constructor for class ffx.ui.behaviors.MouseTranslate: Constructor for MouseTranslate.
MouseTranslate(int, TransformGroup, Behavior, int, int) - Constructor for class ffx.ui.behaviors.MouseTranslate: Constructor for MouseTranslate.
MouseZoom - Class in ffx.ui.behaviors: The MouseZoom class implements a Mouse Zoom behavior.
MouseZoom(int, TransformGroup) - Constructor for class ffx.ui.behaviors.MouseZoom: Constructor for MouseZoom.
MouseZoom(int, TransformGroup, Behavior, int, int) - Constructor for class ffx.ui.behaviors.MouseZoom: Constructor for MouseZoom.
move() - Method in class ffx.algorithms.mc.LambdaMove: Performs the move associated with this MCMove.
move() - Method in interface ffx.algorithms.mc.MCMove: Performs the move associated with this MCMove.
move() - Method in class ffx.algorithms.mc.MDMove: Performs the move associated with this MCMove.
move() - Method in class ffx.algorithms.mc.RosenbluthChi0Move: Performs the move associated with this MCMove.
move() - Method in class ffx.algorithms.mc.RosenbluthChiAllMove: Performs the move associated with this MCMove.
move() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMove
move(double[]) - Method in class ffx.potential.bonded.Atom: Add a vector to the Atom's current position vector
move(MDVerbosity) - Method in class ffx.algorithms.mc.MDMove: Performs an MDMove.
moveAllIntoUnitCell() - Method in class ffx.potential.MolecularAssembly: Moves the center of all chemical entities into the primary unit cell.
moveCenter(double[]) - Method in class ffx.potential.MolecularAssembly: moveCenter
MoveIntoUnitCell - Class in ffx.potential.commands: Move the center of mass of each molecule into the unit cell.
MoveIntoUnitCell() - Constructor for class ffx.potential.commands.MoveIntoUnitCell
MoveIntoUnitCell(FFXBinding) - Constructor for class ffx.potential.commands.MoveIntoUnitCell
MoveIntoUnitCell(String[]) - Constructor for class ffx.potential.commands.MoveIntoUnitCell
moveTo(double[]) - Method in class ffx.potential.bonded.Atom: Moves the atom to the specified location
moveTo(double, double, double) - Method in class ffx.potential.bonded.Atom: moveTo
moveTo(Vector3d) - Method in class ffx.potential.bonded.Atom: moveTo
moveToFractionalCoordinates() - Method in class ffx.potential.MolecularAssembly: Move to fractional coordinates.
moveValuesBetweenZeroAndOne(double[]) - Static method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Moves an array of doubles to be within 0.0 and 1.0 by addition or subtraction of a multiple of 1.0.
MP1 - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
MSGroup - Class in ffx.potential.bonded: The MSGroup class has one sub-node containing atoms, and one that contains molecular mechanics/geometry terms.
MSGroup() - Constructor for class ffx.potential.bonded.MSGroup: Default Constructor initializes a MultiScaleGroup and a few of its sub-nodes.
MSGroup(String) - Constructor for class ffx.potential.bonded.MSGroup: Constructs a MultiScaleGroup object with name n.
MSGroup(String, MSNode) - Constructor for class ffx.potential.bonded.MSGroup: Constructs a MultiScaleGroup object with name n and sets its AtomGroup node equals to node.
MSNode - Class in ffx.potential.bonded: The MSNode class forms the basic unit that all data classes extend.
MSNode() - Constructor for class ffx.potential.bonded.MSNode: Default MSNode Constructor
MSNode(String) - Constructor for class ffx.potential.bonded.MSNode: Constructs a MSNode with the name n.
MSNode(String, int) - Constructor for class ffx.potential.bonded.MSNode: Constructor for MSNode.
MSRoot - Class in ffx.potential.bonded: The MSRoot class is the root of the Force Field X data structure.
MSRoot() - Constructor for class ffx.potential.bonded.MSRoot: Default MSRoot Constructor
Mt - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
MTS - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
MTZFileFilter - Class in ffx.xray.parsers: The MTZFileFilter class is used to choose CCP4 MTZ files
MTZFileFilter() - Constructor for class ffx.xray.parsers.MTZFileFilter: Default Constructor.
MTZFilter - Class in ffx.xray.parsers: This class parses CCP4 MTZ files.
MTZFilter() - Constructor for class ffx.xray.parsers.MTZFilter: Constructor for MTZFilter.
MTZInfo - Class in ffx.xray.commands: The MTZInfo script prints out MTZ reflection file header info.
MTZInfo() - Constructor for class ffx.xray.commands.MTZInfo: MTZInfo constructor.
MTZInfo(FFXBinding) - Constructor for class ffx.xray.commands.MTZInfo: MTZInfo constructor.
MTZInfo(String[]) - Constructor for class ffx.xray.commands.MTZInfo: MTZInfo constructor that sets the command line arguments.
MTZWriter - Class in ffx.xray.parsers: MTZWriter class.
MTZWriter(ReflectionList, DiffractionRefinementData, String) - Constructor for class ffx.xray.parsers.MTZWriter: Constructor for MTZWriter.
MTZWriter(ReflectionList, DiffractionRefinementData, String, int) - Constructor for class ffx.xray.parsers.MTZWriter: Constructor for MTZWriter.
MTZWriter.MTZType - Interface in ffx.xray.parsers: The possible output "styles".
MULTI - Enum constant in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl: Each thread has its own array, and reduction is performed by the user.
MultiDoubleArray - Class in ffx.numerics.atomic: The MultiDoubleArray avoids the need for Atomic variables, but at the cost of storing a full size double array for each thread.
MultiDoubleArray(int, int) - Constructor for class ffx.numerics.atomic.MultiDoubleArray: Constructor for MultiDoubleArray.
multiDynamicsOptions - Variable in class ffx.algorithms.commands.Thermodynamics
MultiDynamicsOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that can create multiple walkers, such as multi-walker OST.
MultiDynamicsOptions() - Constructor for class ffx.algorithms.cli.MultiDynamicsOptions
MultipleParallelException - Exception Class in edu.rit.pj: Class MultipleParallelException is thrown to indicate that multiple threads in a parallel team threw exceptions while executing a parallel construct.
MultipleParallelException() - Constructor for exception class edu.rit.pj.MultipleParallelException: Create a new multiple parallel exception with no detail message and no exception map.
MultipleParallelException(String) - Constructor for exception class edu.rit.pj.MultipleParallelException: Create a new multiple parallel exception with the given detail message and no exception map.
MultipleParallelException(String, ConcurrentHashMap<Integer, Throwable>) - Constructor for exception class edu.rit.pj.MultipleParallelException: Create a new multiple parallel exception with the given detail message and the given exception map.
MultipleParallelException(ConcurrentHashMap<Integer, Throwable>) - Constructor for exception class edu.rit.pj.MultipleParallelException: Create a new multiple parallel exception with no detail message and the given exception map.
MultiplicativeSwitch - Class in ffx.numerics.switching: The 6 coefficients of the multiplicative polynomial switch are unique given the distances "a" and "b".
MultiplicativeSwitch() - Constructor for class ffx.numerics.switching.MultiplicativeSwitch: Constructs a MultiplicativeSwitch that starts at f(0)=1 and ends at f(1)=0.
MultiplicativeSwitch(double, double) - Constructor for class ffx.numerics.switching.MultiplicativeSwitch: Constructs a MultiplicativeSwitch that starts at f(a)=1 and ends at f(b)=0.
multiplyAndStore(double, double, double, double, double[], int, int) - Static method in class ffx.numerics.fft.MixedRadixFactor: Multiply two complex numbers [x_r, x_i] and [w_r, w_i] and store the result.
MULTIPOLE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
MULTIPOLE - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
multipoleEnergy(PolarizableMultipole) - Method in class ffx.numerics.multipole.MultipoleTensor: Contract a multipole with the potential and its derivatives.
multipoleEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Compute the multipole energy.
multipoleEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKEnergyQI: Compute the multipole energy.
multipoleEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Permanent multipole energy.
multipoleEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorQI: GK Permanent multipole energy.
multipoleEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.MultipoleTensor: Permanent multipole energy.
multipoleEnergy(PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Contract a multipole with the potential and its derivatives.
multipoleEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Compute the multipole energy.
multipoleEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Compute the multipole energy.
multipoleEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Permanent multipole energy.
multipoleEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Permanent multipole energy.
multipoleEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Contract a multipole with the potential and its derivatives.
multipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Compute the multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKEnergyQI: Compute the multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Permanent multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: GK Permanent multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Permanent multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Compute the multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Compute the multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Permanent multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Permanent multipole energy and gradient.
multipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Permanent multipole energy and gradient.
multipoleEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Compute the Born chain-rule term for the multipole energy.
multipoleEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKEnergyQI: Compute the Born chain-rule term for the multipole energy.
multipoleEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Permanent multipole Born grad.
multipoleEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorQI: GK Permanent multipole Born grad.
multipoleEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Compute the Born chain-rule term for the multipole energy.
multipoleEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Compute the Born chain-rule term for the multipole energy.
multipoleEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Permanent multipole Born grad.
multipoleEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Permanent multipole Born grad.
MultipoleForce - Class in ffx.openmm.amoeba: This class implements the Amoeba multipole interaction.
MultipoleForce() - Constructor for class ffx.openmm.amoeba.MultipoleForce
multipoleGradient(PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the permanent multipole gradient.
multipoleGradient(PolarizableMultipoleSIMD, DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the permanent multipole gradient.
multipoleIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to multipole I at site K.
multipoleIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to multipole I at site K.
multipoleIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to multipole I at site K.
multipoleIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the field components due to site I multipole at site K.
multipoleIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the field components due to site I multipole at site K.
multipoleIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the field components due to site I multipole at site K.
multipoleKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to multipole K at site I.
multipoleKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to multipole K at site I.
multipoleKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to multipole K at site I.
multipoleKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the field components due to site K multipole at site I.
multipoleKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the field components due to site K multipole at site I.
multipoleKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the field components due to site K multipole at site I.
multipoleOrder - Variable in class ffx.numerics.multipole.GKTensorGlobal: The GK tensor can be constructed for monopoles (GB), dipoles or quadrupoles.
multipoleOrder - Variable in class ffx.numerics.multipole.GKTensorGlobalSIMD: The GK tensor can be constructed for monopoles (GB), dipoles or quadrupoles.
multipoleOrder - Variable in class ffx.numerics.multipole.GKTensorQI: The GK tensor can be constructed for monopoles (GB), dipoles or quadrupoles.
multipoleOrder - Variable in class ffx.numerics.multipole.GKTensorQISIMD: The GK tensor can be constructed for monopoles (GB), dipoles or quadrupoles.
MultipoleTensor - Class in ffx.numerics.multipole: The abstract MultipoleTensor is extended by classes that compute derivatives of 1/|r| via recursion to arbitrary order using Cartesian multipoles in either a global frame or a quasi-internal frame.
MultipoleTensor(CoordinateSystem, int) - Constructor for class ffx.numerics.multipole.MultipoleTensor: Constructor for MultipoleTensor.
MultipoleTensorSIMD - Class in ffx.numerics.multipole: The abstract MultipoleTensorSIMD is extended by classes that compute derivatives of 1/|r| via recursion to arbitrary order using Cartesian multipoles in either a global frame or a quasi-internal frame.
MultipoleTensorSIMD(CoordinateSystem, int) - Constructor for class ffx.numerics.multipole.MultipoleTensorSIMD: Constructor for MultipoleTensor.
multipoleTorque(PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the torque on a permanent multipole.
multipoleTorque(PolarizableMultipoleSIMD, DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the torque on a permanent multipole.
MultipoleType - Class in ffx.potential.parameters: The MultipoleType class defines a multipole in its local frame.
MultipoleType(double[], int[], MultipoleType.MultipoleFrameDefinition, boolean) - Constructor for class ffx.potential.parameters.MultipoleType: Multipole Constructor.
MultipoleType(double, double[], double[][], int[], MultipoleType.MultipoleFrameDefinition, boolean) - Constructor for class ffx.potential.parameters.MultipoleType: Constructor for MultipoleType.
MultipoleType(MultipoleType, double[]) - Constructor for class ffx.potential.parameters.MultipoleType: Construct a MultipoleType from a reference type and updated coefficients.
MultipoleType.MultipoleFrameDefinition - Enum Class in ffx.potential.parameters: The local multipole frame is defined by the Z-then-X or Bisector convention.
multipoleTypeFactory(ForceField.ELEC_FORM, Atom, ForceField) - Static method in class ffx.potential.parameters.MultipoleType: multipoleTypeFactory.
MultipoleUtilities - Class in ffx.numerics.multipole
MultipoleUtilities() - Constructor for class ffx.numerics.multipole.MultipoleUtilities
MultiResidue - Class in ffx.potential.bonded: The MultiResidue class allows switching between residues for uses such as sequence optimization.
MultiResidue(Residue, ForceField) - Constructor for class ffx.potential.bonded.MultiResidue: Constructor for MultiResidue.
MultiScaleLevel - Static variable in class ffx.ui.FFXSystem: Constant MultiScaleLevel=4
MultistateBennettAcceptanceRatio - Class in ffx.numerics.estimator: The MultistateBennettAcceptanceRatio class defines a statistical estimator based on a generalization to the Bennett Acceptance Ratio (BAR) method for multiple lambda windows.
MultistateBennettAcceptanceRatio(double[], double[][][], double[]) - Constructor for class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: Constructor for MBAR estimator.
MultistateBennettAcceptanceRatio(double[], double[][][], double[], double, MultistateBennettAcceptanceRatio.SeedType) - Constructor for class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: Constructor for MBAR estimator.
MultistateBennettAcceptanceRatio(double[], int[], double[][], double[], double, MultistateBennettAcceptanceRatio.SeedType) - Constructor for class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase - Class in ffx.numerics.estimator: Harmonic oscillators test case generates data for testing the MBAR implementation
MultistateBennettAcceptanceRatio.SeedType - Enum Class in ffx.numerics.estimator: Enum of MBAR seed types.
mutate(List<PDBFilter.Mutation>) - Method in class ffx.potential.parsers.PDBFilter: Mutate residue(s) as the PDB file is being parsed.
MutatePDB - Class in ffx.algorithms.commands: The MutatePDB script mutates residue(s) of a PDB file.
MutatePDB() - Constructor for class ffx.algorithms.commands.MutatePDB: MutatePDB Constructor.
MutatePDB(FFXBinding) - Constructor for class ffx.algorithms.commands.MutatePDB: MutatePDB Constructor.
MutatePDB(String[]) - Constructor for class ffx.algorithms.commands.MutatePDB: MutatePDB constructor that sets the command line arguments.
Mutation(int, char, String) - Constructor for class ffx.potential.parsers.PDBFilter.Mutation
MUTUAL - Enum constant in enum class ffx.potential.nonbonded.pme.Polarization
mutualPolarizationEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Mutual Polarization Contribution to the Born grad.
mutualPolarizationEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorQI: GK Mutual Polarization Contribution to the Born grad.
mutualPolarizationEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Mutual Polarization Contribution to the Born grad.
mutualPolarizationEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Mutual Polarization Contribution to the Born grad.
myBuf - Variable in class edu.rit.mp.IORequest: Source or destination of message items.
myChannel - Variable in class edu.rit.mp.IORequest: Channel on which to send or receive message.
myLength - Variable in class edu.rit.mp.Buf: Number of items in this buffer.
mySerializedItems - Variable in class edu.rit.mp.ObjectBuf: Byte array containing this buffer's object items in serialized form.
myStatus - Variable in class edu.rit.mp.IORequest: Status of a received message.
myTagLb - Variable in class edu.rit.mp.IORequest: Message tag range lower bound.
myTagUb - Variable in class edu.rit.mp.IORequest: Message tag range upper bound.

N

n - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
n - Variable in class ffx.algorithms.optimize.Minimize: Number of variables.
n - Variable in class ffx.algorithms.optimize.PhMinimize: Number of variables.
n - Variable in class ffx.numerics.fft.MixedRadixFactor: The size of the input.
n - Variable in class ffx.xray.DiffractionRefinementData: Number of reflections in the data set.
n() - Method in record class ffx.numerics.fft.PassConstants: Returns the value of the n record component.
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms
N - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
nA - Variable in class ffx.potential.nonbonded.SpatialDensityRegion: The number of divisions along the A-axis.
Na - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
NA - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
NA - Enum constant in enum class ffx.potential.bonded.Residue.ResidueType
NA_C1 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_C1
NA_C2 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_C2
NA_C3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_C3
NA_C4 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_C4
NA_C5 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_C5
NA_H1 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_H1
NA_H21 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_H21
NA_H22 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_H22
NA_H3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_H3
NA_H4 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_H4
NA_H51 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_H51
NA_H52 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_H52
NA_HO3T - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Should be NA_HO3' (' replaced by T in the name).
NA_HO5T - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Should be NA_HO5' (' replaced by T in the name).
NA_O2 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_O2
NA_O3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_O3
NA_O4 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_O4
NA_O5 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Biotype keys for nucleic acid backbone atom types.
NA_OP - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_OP
NA_P - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA_P
NA1toNA3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant NA1toNA3
name - Variable in class edu.rit.pj.cluster.BackendInfo: The backend's name.
name - Variable in class edu.rit.pj.cluster.ProcessInfo: The job backend node's name.
name - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat: The identity of this Thermostat.
name - Variable in class ffx.potential.parameters.AtomType: Short name (ie CH3/CH2 etc).
name - Variable in class ffx.potential.terms.EnergyTerm: Optional name for this energy term (for reporting/logging).
name - Variable in class ffx.ui.commands.SimulationDefinition
name() - Method in interface ffx.potential.bonded.AminoAcidUtils.SideChainType: This is already implemented by all enum instances.
name() - Element in annotation interface ffx.utilities.FFXProperty: The name of this FFXProperty.
nameAcetylCap(Residue, Atom) - Static method in class ffx.potential.bonded.NamingUtils: Names the atoms in an N-terminal acetyl ACE capping group.
NamingUtils - Class in ffx.potential.bonded: Utilities for importing atoms from PDB files and checking their names.
NamingUtils() - Constructor for class ffx.potential.bonded.NamingUtils
NamingUtils.HetAtoms - Enum Class in ffx.potential.bonded: Common HETATOM labels for water and ions.
NAPATTERN - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Repeating atomic numbers of a nucleic acid chain.
nAtoms - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: The number of atoms in the system.
nAtoms - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
nB - Variable in class ffx.potential.nonbonded.SpatialDensityRegion: The number of divisions along the B-axis.
Nb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
nBins - Variable in class ffx.crystal.ReflectionList: For binning reflections based on resolution
nC - Variable in class ffx.potential.nonbonded.SpatialDensityRegion: The number of divisions along the C-Axis.
NCSCrystal - Class in ffx.crystal: The NCSCrystal class extends Crystal to support non-crystallographic symmetry (NCS).
NCSCrystalFactory(Crystal, List<SymOp>) - Static method in class ffx.crystal.NCSCrystal: Returns an NCSCrystal by expanding the orignal unit cell with the symmetry operators provided by the BIOMT records in the PDB files.
NCSRestraint - Class in ffx.potential.nonbonded: Given unit cell parameters and symmetry operators, NCS copies are restrained to the asymmetric unit atoms.
NCSRestraint(Atom[], ForceField, Crystal) - Constructor for class ffx.potential.nonbonded.NCSRestraint: This NCSRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
Nd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ND1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
ND1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
ND1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
ND1 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
ND2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
nd2EdL2Failures - Variable in class ffx.potential.commands.test.LambdaGradient
ndEdLFailures - Variable in class ffx.potential.commands.test.LambdaGradient
ndEdXdLFailures - Variable in class ffx.potential.commands.test.LambdaGradient
ndEdXFailures - Variable in class ffx.potential.commands.test.LambdaGradient
Ne - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
NE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
NE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
NE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
NE2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
nearEndAddress() - Method in class edu.rit.mp.Channel: Obtain this channel's near end address.
nearEndChannelGroupId() - Method in class edu.rit.mp.Channel: Obtain the channel group ID of this channel's near end channel group.
nearEndConnected(ChannelGroup, Channel) - Method in interface edu.rit.mp.ConnectListener: Report that a channel was connected in the given channel group, initiated by the near end.
NeckIntegral - Class in ffx.potential.nonbonded.implicit: This class is used to compute interstitial space integrals of the form 1/r^6.
NeckIntegral() - Constructor for class ffx.potential.nonbonded.implicit.NeckIntegral
needUpdate() - Method in class ffx.ui.commands.FFXServer: needUpdate
neg() - Method in class ffx.crystal.HKL: Negate the reflection.
NEGATE_IM - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the imaginary members of the vector via multiplication.
NEGATE_IM_128 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the imaginary members of the vector via multiplication.
NEGATE_IM_256 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the imaginary members of the vector via multiplication.
NEGATE_IM_512 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the imaginary members of the vector via multiplication.
NEGATE_RE - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the real members of the vector via multiplication.
NEGATE_RE_128 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the real members of the vector via multiplication.
NEGATE_RE_256 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the real members of the vector via multiplication.
NEGATE_RE_512 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Vector used to change the sign of the real members of the vector via multiplication.
NeighborDistances(int, int) - Constructor for class ffx.algorithms.optimize.manybody.DistanceMatrix.NeighborDistances: Constructor.
NeighborList - Class in ffx.potential.nonbonded: The NeighborList class builds Verlet lists in parallel via a spatial decomposition.
NeighborList(Crystal, Atom[], double, double, ParallelTeam) - Constructor for class ffx.potential.nonbonded.NeighborList: Constructor for the NeighborList class.
NeighborList.AtomIndex - Class in ffx.potential.nonbonded: Hold the atom index and its symmetry operator.
NeighborList.Cell - Class in ffx.potential.nonbonded: Hold the atoms in each cell.
neighborLists - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Neighbor lists, including atoms beyond the real space cutoff.
NEQ - Enum constant in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm
nESV - Variable in class ffx.algorithms.optimize.PhMinimize: Number of Extended System variables.
nESVFailures - Variable in class ffx.potential.commands.test.PhGradient
NeutronFormFactor - Class in ffx.xray: This implementation uses the coefficients from International Tables, Vol.
NeutronFormFactor(Atom) - Constructor for class ffx.xray.NeutronFormFactor: Constructor for NeutronFormFactor.
NeutronFormFactor(Atom, double) - Constructor for class ffx.xray.NeutronFormFactor: Constructor for NeutronFormFactor.
NeutronFormFactor(Atom, double, double[]) - Constructor for class ffx.xray.NeutronFormFactor: Constructor for NeutronFormFactor.
newInstance(String) - Static method in class edu.rit.util.Instance: Create a new instance of a class as specified by the given string.
next - Variable in class ffx.numerics.quickhull.Face
next - Variable in class ffx.numerics.quickhull.HalfEdge: Next half-edge in the triangle.
next() - Method in class edu.rit.util.DefaultRandom: Return the next 64-bit pseudorandom value in this PRNG's sequence.
next() - Method in class edu.rit.util.Mcg1Random: Return the next 64-bit pseudorandom value in this PRNG's sequence.
next() - Method in class edu.rit.util.Random: Return the next 64-bit pseudorandom value in this PRNG's sequence.
next() - Method in class edu.rit.util.RandomSubset: Returns the next integer in the random subset.
next(int) - Method in class edu.rit.pj.IntegerSchedule: Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class edu.rit.pj.LongSchedule: Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.potential.nonbonded.PairwiseSchedule: Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.potential.nonbonded.SpatialDensitySchedule: Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.xray.GradientSchedule: Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.xray.RowSchedule: Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.xray.SliceSchedule: Obtain the next chunk of iterations for the given thread index.
next(long) - Method in class edu.rit.util.DefaultRandom: Return the 64-bit pseudorandom value the given number of positions ahead in this PRNG's sequence.
next(long) - Method in class edu.rit.util.Mcg1Random: Return the 64-bit pseudorandom value the given number of positions ahead in this PRNG's sequence.
next(long) - Method in class edu.rit.util.Random: Return the 64-bit pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextBoolean() - Method in class edu.rit.util.Random: Return the Boolean value from the next pseudorandom value in this PRNG's sequence.
nextBoolean(long) - Method in class edu.rit.util.Random: Return the Boolean value from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextByte() - Method in class edu.rit.util.Random: Return the byte value from the next pseudorandom value in this PRNG's sequence.
nextByte(long) - Method in class edu.rit.util.Random: Return the byte value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextCharacter() - Method in class edu.rit.util.Random: Return the character value from the next pseudorandom value in this PRNG's sequence.
nextCharacter(long) - Method in class edu.rit.util.Random: Return the character value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextDouble() - Method in class edu.rit.util.Random: Return the double precision floating point value from the next pseudorandom value in this PRNG's sequence.
nextDouble(long) - Method in class edu.rit.util.Random: Return the double precision floating point value from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextFloat() - Method in class edu.rit.util.Random: Return the single precision floating point value from the next pseudorandom value in this PRNG's sequence.
nextFloat(long) - Method in class edu.rit.util.Random: Return the single precision floating point value from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextInput - Variable in class ffx.numerics.fft.MixedRadixFactor: The next input (n / factor).
nextInt(int) - Method in class edu.rit.util.Random: Return the integer value in the given range from the next pseudorandom value in this PRNG's sequence.
nextInt(int, long) - Method in class edu.rit.util.Random: Return the integer value in the given range from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextInteger() - Method in class edu.rit.util.Random: Return the integer value from the next pseudorandom value in this PRNG's sequence.
nextInteger(long) - Method in class edu.rit.util.Random: Return the integer value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextLong() - Method in class edu.rit.util.Random: Return the long value from the next pseudorandom value in this PRNG's sequence.
nextLong(long) - Method in class edu.rit.util.Random: Return the long value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextPointToAdd() - Method in class ffx.numerics.quickhull.QuickHull3D: Selects the next vertex to add: the farthest point above some face that currently has outside points claimed.
nextShort() - Method in class edu.rit.util.Random: Return the short value from the next pseudorandom value in this PRNG's sequence.
nextShort(long) - Method in class edu.rit.util.Random: Return the short value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextUnsignedByte() - Method in class edu.rit.util.Random: Return the unsigned byte value from the next pseudorandom value in this PRNG's sequence.
nextUnsignedByte(long) - Method in class edu.rit.util.Random: Return the unsigned byte value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextUnsignedShort() - Method in class edu.rit.util.Random: Return the unsigned short value from the next pseudorandom value in this PRNG's sequence.
nextUnsignedShort(long) - Method in class edu.rit.util.Random: Return the unsigned short value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nFailures - Variable in class ffx.algorithms.commands.test.OSTGradient
nFailures - Variable in class ffx.potential.commands.test.Gradient
nFailures - Variable in class ffx.potential.commands.test.PhGradient
nFFTs - Variable in class ffx.numerics.fft.MixedRadixFactor: The number of FFTs to process (default = 1).
nFFTs() - Method in record class ffx.numerics.fft.PassConstants: Returns the value of the nFFTs record component.
nh - Variable in class ffx.potential.bonded.Angle: Number of hydrogen on the central atom that are not part of this Angle.
NH1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
NH2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
NH2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
Ni - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
NM_TO_ANG - Static variable in class ffx.utilities.Constants: Constant NM_TO_ANG=10
NME - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
Nn - Variable in class edu.rit.pj.cluster.JobInfo: The number of backend nodes in the job.
No - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
NO_PICK - Static variable in interface ffx.ui.behaviors.PickingCallback: The user made a selection but nothing was actually picked
NO_WAIT - Static variable in class edu.rit.pj.BarrierAction: Do not do a barrier wait.
noCutoffFactory() - Static method in class ffx.potential.nonbonded.NonbondedCutoff: Returns a NonbondedCutoff that does not cut off anything.
nodeCount - Variable in class edu.rit.pj.cluster.JobInfo: The number of nodes that have been assigned to the job so far.
NON_CONVEX - Static variable in class ffx.numerics.quickhull.Face
NonbondedCutoff - Class in ffx.potential.nonbonded: This class contains fields and methods for maintaining details of non-bonded cutoffs.
NonbondedCutoff(double, double, double) - Constructor for class ffx.potential.nonbonded.NonbondedCutoff: Non-bonded Cutoff constructor.
NonBondedCutoff - Enum constant in enum class ffx.utilities.PropertyGroup: Non-bonded cutoff.
NonbondedForce - Class in ffx.openmm: This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions.
NonbondedForce() - Constructor for class ffx.openmm.NonbondedForce: Create a new NonbondedForce.
None - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary
NONE - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
NONE - Enum constant in enum class ffx.potential.bonded.Residue.SSType
NONE - Enum constant in enum class ffx.potential.bonded.ROLSP.PARALLELMETHOD
NONE - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
NONE - Enum constant in enum class ffx.potential.nonbonded.pme.Polarization
NONE - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
NONE - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
NONE - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
NONE - Enum constant in enum class ffx.potential.parsers.SystemFilter.Versioning
NONE - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: Do not model solvent scattering.
NONE - Static variable in class ffx.ui.commands.SimulationUpdate: Constant NONE=0
NonEquilbriumDynamics - Class in ffx.algorithms.dynamics: NonEquilbriumDynamics is a class that contains methods to control non-equilibrium molecular dynamics simulations.
NonEquilbriumDynamics(int, boolean) - Constructor for class ffx.algorithms.dynamics.NonEquilbriumDynamics: Constructor for NonEquilbriumDynamics.
NonPjJobFrontend - Class in edu.rit.pj.cluster: Class NonPjJobFrontend provides the message handler for a job frontend process that communicates with the Job Scheduler to allocate backend nodes but does not run a PJ program.
NonPjJobFrontend(String, int) - Constructor for class edu.rit.pj.cluster.NonPjJobFrontend: Construct a new non-PJ job frontend object.
nonPolarModel - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion
nonStandardProtonation - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
norm() - Method in class ffx.numerics.quickhull.Vector3d: Returns the 2 norm of this vector.
NORMAL - Enum constant in enum class ffx.potential.parameters.AngleType.AngleMode
NORMAL - Enum constant in enum class ffx.potential.parameters.TorsionType.TorsionMode
NORMAL - Enum constant in enum class ffx.potential.parameters.VDWType.VDWMode
normalize() - Method in class ffx.numerics.math.Double3: Normalize this Double3.
normalize() - Method in class ffx.numerics.math.Float3: Normalize this Float3.
normalize() - Method in class ffx.numerics.quickhull.Vector3d: Normalizes this vector in place.
normalize(double[]) - Static method in class ffx.numerics.math.DoubleMath: Normalizes a vector.
normalize(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Normalizes a vector.
normalize(float[]) - Static method in class ffx.numerics.math.FloatMath: Normalizes a vector.
normalize(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Normalizes a vector.
normalizeI() - Method in class ffx.numerics.math.Double3: Normalize this Double3 in place.
normalizeI() - Method in class ffx.numerics.math.Float3: Normalize this Float3 in place.
normalizeVec(DoubleVector[], DoubleVector[]) - Static method in class ffx.numerics.multipole.QIFrameSIMD: Normalize a vector.
normSquared() - Method in class ffx.numerics.quickhull.Vector3d: Returns the square of the 2 norm of this vector.
NoseHooverIntegrator - Class in ffx.openmm: This is an Integrator which simulates a System using one or more Nose Hoover chain thermostats, using the "middle" leapfrog propagation algorithm described in J.
NoseHooverIntegrator(double) - Constructor for class ffx.openmm.NoseHooverIntegrator: Create a NoseHooverIntegrator with a single thermostat.
NoseHooverIntegrator(double, double, double, int, int, int) - Constructor for class ffx.openmm.NoseHooverIntegrator: Create a NoseHooverIntegrator with detailed thermostat parameters.
NoseHooverIntegrator(PointerByReference) - Constructor for class ffx.openmm.NoseHooverIntegrator: Create a NoseHooverIntegrator with a single thermostat.
noStorageRecursion(double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
NOT_STARTED - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State: The job backend process has not started yet.
noZeroClasses() - Method in class ffx.potential.parameters.ImproperTorsionType: Check if this Improper Torsion Type is defined by 1 or more atom classes equal to zero.
Np - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Np - Variable in class edu.rit.pj.cluster.JobInfo: The number of processes in the job.
NS2SEC - Static variable in class ffx.utilities.Constants: Convert nanoseconds to seconds.
nSamples - Variable in class ffx.numerics.estimator.SequentialEstimator: The number of samples for each lambda state.
nStates - Variable in class ffx.numerics.estimator.SequentialEstimator: The number of states from which samples were collected.
nSteps - Variable in class ffx.algorithms.optimize.Minimize: The number of optimization steps taken.
nSteps - Variable in class ffx.algorithms.optimize.PhMinimize: The number of optimization steps taken.
nSymm - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
Nt - Variable in class edu.rit.pj.cluster.JobInfo: The number of CPUs per process in the job.
Nt - Variable in class edu.rit.pj.cluster.ProcessInfo: Number of CPUs assigned to the job backend process.
nthDerivative(double, int) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
nthDerivative(double, int) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction: N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.BellCurveSwitch: N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.CompositeSwitch
nthDerivative(double, int) - Method in class ffx.numerics.switching.ConstantSwitch: N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.LinearDerivativeSwitch: N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.MultiplicativeSwitch: N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.PowerSwitch: N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.SquaredTrigSwitch: N'th order derivative at a point.
nThreads - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
NUCLEICACID - Enum constant in enum class ffx.potential.Utilities.PolymerType
nucleicAcid3 - Variable in class ffx.potential.bonded.Rotamer: The N.A. name of this residue (or null for a A.A.).
NucleicAcidAnalysis - Class in ffx.potential.commands: Calculates nucleic acid torsions as well as information regarding the sugar pucker.
NucleicAcidAnalysis() - Constructor for class ffx.potential.commands.NucleicAcidAnalysis
NucleicAcidAnalysis(FFXBinding) - Constructor for class ffx.potential.commands.NucleicAcidAnalysis
NucleicAcidAnalysis(String[]) - Constructor for class ffx.potential.commands.NucleicAcidAnalysis
nucleicAcidList - Static variable in class ffx.potential.bonded.NucleicAcidUtils: Constant nucleicAcidList
NucleicAcidUtils - Class in ffx.potential.bonded: Utilities for creating Nucleic Acid residues.
NucleicAcidUtils() - Constructor for class ffx.potential.bonded.NucleicAcidUtils
NucleicAcidUtils.NA - Enum Class in ffx.potential.bonded: The 4 RNA bases, 4 DNA bases, and mono- di- and triphosphate.
NucleicAcidUtils.NucleicAcid1 - Enum Class in ffx.potential.bonded
NucleicAcidUtils.NucleicAcid3 - Enum Class in ffx.potential.bonded: Since enumeration values must start with a letter, an 'M' is added to modified bases whose IUPAC name starts with an integer.
numatoms - Variable in class ffx.ui.commands.SimulationDefinition
numatoms - Variable in class ffx.ui.commands.SimulationUpdate
number - Variable in class ffx.crystal.SpaceGroup: Space group number.
numberAtoms(MolecularAssembly) - Static method in class ffx.potential.bonded.BondedUtils: Re-number atoms, especially if missing atoms were created.
numberCreated - Variable in class ffx.potential.commands.PrepareSpaceGroups: Number of directories created.
numberOfVariables - Variable in class ffx.potential.SystemState: Number of dynamics variables.
numFaces - Variable in class ffx.numerics.quickhull.QuickHull3D
numkeys - Variable in class ffx.ui.commands.SimulationDefinition
numPoints - Variable in class ffx.numerics.quickhull.QuickHull3D
numPoints() - Method in interface ffx.numerics.integrate.DataSet: Number of points along x.
numPoints() - Method in class ffx.numerics.integrate.DoublesDataSet: Number of points along x.
numPoints() - Method in class ffx.numerics.integrate.FunctionDataCurve: Number of points along x.
numPrimitiveSymEquiv - Variable in class ffx.crystal.SpaceGroup: Number of primitive symmetry equivalents.
numThreads - Variable in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters
numVertices - Variable in class ffx.numerics.quickhull.QuickHull3D
numVertices() - Method in class ffx.numerics.quickhull.Face: Returns the number of vertices (half-edges) bounding this face.
numVerts - Variable in class ffx.numerics.quickhull.Face
nVariables - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Number of variables.
nx - Variable in class ffx.potential.parameters.TorsionTorsionType: Number of points along x.
ny - Variable in class ffx.potential.parameters.TorsionTorsionType: Number of point along y.
NZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
NZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
NZ - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames

O

o - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
O - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
O - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
O - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
O - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms
O - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
O - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
o1 - Variable in class ffx.numerics.multipole.MultipoleTensor: Order plus 1.
o1 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Order plus 1.
Object() - Constructor for class edu.rit.util.Searching.Object
Object() - Constructor for class edu.rit.util.Sorting.Object
ObjectArrayBuf<T> - Class in edu.rit.mp.buf: Class ObjectArrayBuf provides a buffer for an array of object items sent or received using the Message Protocol (MP).
ObjectArrayBuf(T[], Range) - Constructor for class edu.rit.mp.buf.ObjectArrayBuf: Construct a new object array buffer.
ObjectArrayBuf_1<T> - Class in edu.rit.mp.buf: Class ObjectArrayBuf_1 provides a buffer for an array of object items sent or received using the Message Protocol (MP).
ObjectArrayBuf_1(T[], Range) - Constructor for class edu.rit.mp.buf.ObjectArrayBuf_1: Construct a new object array buffer.
ObjectBuf<T> - Class in edu.rit.mp: Class ObjectBuf is the abstract base class for a buffer of object items sent or received using the Message Protocol (MP).
ObjectBuf(int) - Constructor for class edu.rit.mp.ObjectBuf: Construct a new object buffer.
objectBuffer(T[]) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for the entire given object array.
objectBuffer(T[][]) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for the entire given object matrix.
ObjectItemBuf<T> - Class in edu.rit.mp.buf: Class ObjectItemBuf provides a buffer for a single object item sent or received using the Message Protocol (MP).
ObjectItemBuf() - Constructor for class edu.rit.mp.buf.ObjectItemBuf: Construct a new object item buffer.
ObjectItemBuf(T) - Constructor for class edu.rit.mp.buf.ObjectItemBuf: Construct a new object item buffer with the given initial value.
ObjectMatrixBuf<T> - Class in edu.rit.mp.buf: Class ObjectMatrixBuf provides a buffer for a matrix of object items sent or received using the Message Protocol (MP).
ObjectMatrixBuf(T[][], Range, Range) - Constructor for class edu.rit.mp.buf.ObjectMatrixBuf: Construct a new object matrix buffer.
ObjectMatrixBuf_1<T> - Class in edu.rit.mp.buf: Class ObjectMatrixBuf_1 provides a buffer for a matrix of object items sent or received using the Message Protocol (MP).
ObjectMatrixBuf_1(T[][], Range, Range) - Constructor for class edu.rit.mp.buf.ObjectMatrixBuf_1: Construct a new object matrix buffer.
ObjectOp<T> - Class in edu.rit.pj.reduction: Class ObjectOp is the abstract base class for a binary operation on object values, used to do reduction in a parallel program.
ObjectOp() - Constructor for class edu.rit.pj.reduction.ObjectOp: Construct a new object binary operation.
ObjectPair<T,S> - Record Class in ffx.utilities: ObjectPair record.
ObjectPair(T, S) - Constructor for record class ffx.utilities.ObjectPair: Creates an instance of a ObjectPair record class.
OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine occupancies only (alternate conformers are constrained)
Octree - Class in ffx.potential.nonbonded.octree: Octree method presented in the Fast Multipole Method (FMM) tutorial from the Barba Group: https://github.com/barbagroup/FMM_tutorial
Octree(int, ArrayList<OctreeParticle>) - Constructor for class ffx.potential.nonbonded.octree.Octree: Constructor allowing the specification of nCritical, default theta value
Octree(int, ArrayList<OctreeParticle>, double) - Constructor for class ffx.potential.nonbonded.octree.Octree: Constructor allowing the specification of nCritical and theta
Octree(ArrayList<OctreeParticle>) - Constructor for class ffx.potential.nonbonded.octree.Octree: Default constructor: only need to pass in a list of particles nCritical and theta set to defaults
OctreeCell - Class in ffx.potential.nonbonded.octree: OctreeCell: Object class for Octree method presented in the Fast Multipole Method (FMM) tutorial from the Barba Group: https://github.com/barbagroup/FMM_tutorial
OctreeCell(int) - Constructor for class ffx.potential.nonbonded.octree.OctreeCell
OctreeParticle - Class in ffx.potential.nonbonded.octree: OctreeParticle: Object class for Octree method presented in the Fast Multipole Method (FMM) tutorial from the Barba Group: https://github.com/barbagroup/FMM_tutorial
OctreeParticle(double[], double, double) - Constructor for class ffx.potential.nonbonded.octree.OctreeParticle
OctreePoint - Class in ffx.potential.nonbonded.octree: OctreePoint: Object class for Octree method presented in the Fast Multipole Method (FMM) tutorial from the Barba Group: https://github.com/barbagroup/FMM_tutorial
OctreePoint(double[], double) - Constructor for class ffx.potential.nonbonded.octree.OctreePoint
OD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
OD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
OD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
OD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
OD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
OD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
OD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
OE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
OE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
OE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
OE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
OE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
OE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
OE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
OE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
off - Variable in class ffx.potential.nonbonded.NonbondedCutoff: All vdW interactions are 0 at the distance "off".
off - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
OFF - Enum constant in enum class ffx.potential.MolecularAssembly.FractionalMode
OFF - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
off2 - Variable in class ffx.potential.nonbonded.NonbondedCutoff: The distance off squared.
off2 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
offset - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
OG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.SER
OG1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
OH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
OH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
OK - Static variable in class ffx.ui.commands.SimulationMessage: Constant OK=3
OMC - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
OMG - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
omit(Set<Integer>) - Method in class edu.rit.pj.job.JobGenerator: Omit the job numbers in the given set when generating jobs.
OMM - Enum constant in enum class ffx.algorithms.dynamics.MDEngine
OMM - Enum constant in enum class ffx.potential.Platform: An alias for the best GPU implementation (OMM_CUDA or OMM_OPENCL).
OMM_CPU - Enum constant in enum class ffx.potential.Platform: Optimized OpenMM CPU implementation (no AMOEBA support).
OMM_CUDA - Enum constant in enum class ffx.potential.Platform: OpenMM CUDA implementation.
OMM_OPENCL - Enum constant in enum class ffx.potential.Platform: OpenMM OpenCL implementation.
OMM_REF - Enum constant in enum class ffx.potential.Platform: OpenMM reference implementation.
oneThird - Static variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion: Constant factor used with quadrupoles.
onlyPrunedPairs - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Pruned rotamer pairs.
onlyPrunedSingles - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Pruned rotamers.
op(boolean, boolean) - Method in class edu.rit.pj.reduction.BooleanOp: Perform this binary operation.
op(byte, byte) - Method in class edu.rit.pj.reduction.ByteOp: Perform this binary operation.
op(char, char) - Method in class edu.rit.pj.reduction.CharacterOp: Perform this binary operation.
op(double, double) - Method in class edu.rit.pj.reduction.DoubleOp: Perform this binary operation.
op(float, float) - Method in class edu.rit.pj.reduction.FloatOp: Perform this binary operation.
op(int, int) - Method in class edu.rit.pj.reduction.IntegerOp: Perform this binary operation.
op(long, long) - Method in class edu.rit.pj.reduction.LongOp: Perform this binary operation.
op(short, short) - Method in class edu.rit.pj.reduction.ShortOp: Perform this binary operation.
op(T, T) - Method in class edu.rit.pj.reduction.ObjectOp: Perform this binary operation.
Op - Class in edu.rit.pj.reduction: Class Op is the abstract base class for a binary operation used to do reduction in a parallel program.
OPBEND - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
opBendUnit - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Convert Out-of-Plane bending energy to kcal/mole.
open(File) - Method in class edu.rit.pj.cluster.BackendFileReader: Open a backend file input stream on the given file.
open(File) - Static method in class ffx.potential.parsers.KeyFilter: open
open(File) - Method in class ffx.potential.utils.PotentialsUtils: Return one MolecularAssembly.
open(File, boolean) - Method in class edu.rit.pj.cluster.BackendFileWriter: Open a backend file output stream on the given file.
open(File, String) - Method in class ffx.ui.MainPanel
open(File, Hashtable<String, Keyword>) - Static method in class ffx.potential.parsers.KeyFilter: open
open(String) - Method in interface ffx.potential.utils.PotentialsFunctions: open.
open(String) - Method in class ffx.potential.utils.PotentialsUtils: open.
open(String) - Method in class ffx.ui.MainPanel: open
open(String) - Method in class ffx.ui.UIUtils
open(String[]) - Method in class ffx.ui.MainPanel: open
open(String[], int) - Method in interface ffx.potential.utils.PotentialsFunctions: Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
open(String[], int) - Method in class ffx.potential.utils.PotentialsUtils: Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
open(String[], int) - Method in class ffx.ui.UIUtils
open(List<File>, String) - Method in class ffx.ui.MainPanel
openAll(String) - Method in interface ffx.potential.utils.PotentialsFunctions: Opens a file and returns all created MolecularAssembly objects.
openAll(String) - Method in class ffx.potential.utils.PotentialsUtils: Opens a file and returns all created MolecularAssembly objects.
openAll(String) - Method in class ffx.ui.UIUtils
openAll(String[]) - Method in interface ffx.potential.utils.PotentialsFunctions: Opens an array of files and returns the created MolecularAssembly objects.
openAll(String[]) - Method in class ffx.potential.utils.PotentialsUtils: Opens an array of files and returns the created MolecularAssembly objects.
openAll(String[]) - Method in class ffx.ui.UIUtils
openAll(String, int) - Method in interface ffx.potential.utils.PotentialsFunctions: Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
openAll(String, int) - Method in class ffx.potential.utils.PotentialsUtils: Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
openAll(String, int) - Method in class ffx.ui.UIUtils
openFile(AlgorithmFunctions, TopologyOptions, int, String, int, AlchemicalOptions, File, int) - Method in class ffx.algorithms.cli.MultiDynamicsOptions: Opens a file and processes it.
openFile(PotentialsFunctions, TopologyOptions, int, String, int) - Method in class ffx.potential.cli.AlchemicalOptions: Opens a File to a MolecularAssembly for alchemistry.
OPENMM - Enum constant in enum class ffx.algorithms.dynamics.MDEngine
OPENMM - Enum constant in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine
OpenMMContext - Class in ffx.potential.openmm: Creates and manage an OpenMM Context.
OpenMMContext(Platform, OpenMMSystem, Atom[]) - Constructor for class ffx.potential.openmm.OpenMMContext: Create an OpenMM Context for a single topology OpenMM system.
OpenMMDualTopologyEnergy - Class in ffx.potential.openmm
OpenMMDualTopologyEnergy(MolecularAssembly, MolecularAssembly, UnivariateSwitchingFunction, Platform) - Constructor for class ffx.potential.openmm.OpenMMDualTopologyEnergy: Constructor for DualTopologyEnergy.
OpenMMDualTopologySystem - Class in ffx.potential.openmm: Create and manage an OpenMM Dual-Topology System.
OpenMMDualTopologySystem(OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMMDualTopologyEnergy constructor.
OpenMMEnergy - Class in ffx.potential.openmm: Compute the potential energy and derivatives using OpenMM.
OpenMMEnergy(MolecularAssembly, Platform, int) - Constructor for class ffx.potential.openmm.OpenMMEnergy: ForceFieldEnergyOpenMM constructor; offloads heavy-duty computation to an OpenMM Platform while keeping track of information locally.
OpenMMIntegrator - Class in ffx.potential.openmm: Create and manage an OpenMM Integrator.
OpenMMPotential - Interface in ffx.potential.openmm: An interface for classes that provide an OpenMM potential energy implementation.
OpenMMState - Class in ffx.potential.openmm: Retrieve state information from an OpenMM Simulation.
OpenMMState(PointerByReference) - Constructor for class ffx.potential.openmm.OpenMMState: Construct an OpenMM State with the requested information.
OpenMMSystem - Class in ffx.potential.openmm: Create and manage an OpenMM System.
OpenMMSystem() - Constructor for class ffx.potential.openmm.OpenMMSystem: OpenMMSystem constructor.
OpenMMSystem(OpenMMEnergy) - Constructor for class ffx.potential.openmm.OpenMMSystem: OpenMMSystem constructor.
OpenMMXmlFilter - Class in ffx.potential.parsers: The OpenMMXmlFilter class creates an OpenMM-style XML file from a ForceField object.
OpenMMXmlFilter(ForceField) - Constructor for class ffx.potential.parsers.OpenMMXmlFilter: Constructor for outputting XML.
OpenMMXmlFilter(ForceField, String) - Constructor for class ffx.potential.parsers.OpenMMXmlFilter: Constructor for outputting XML with output path specified.
openQuietly(String) - Method in class ffx.potential.utils.PotentialsUtils: Open one filename string without printing all the header material.
openWaitUtils(String) - Method in class ffx.ui.MainPanel
openWithMutations(File, List<PDBFilter.Mutation>) - Method in class ffx.potential.utils.PotentialsUtils: Mutates file on-the-fly as it is being opened.
openWithMutations(File, List<PDBFilter.Mutation>) - Method in class ffx.ui.UIUtils: Mutates file on-the-fly as it is being opened.
operator - Variable in class ffx.numerics.multipole.MultipoleTensor: The OPERATOR in use.
operator - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: The OPERATOR in use.
Operator - Enum Class in ffx.numerics.multipole: Operators that are supported.
OPLS_AA_2008 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
OPLS_AAL - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
OPLS_EXPLICIT - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
OPLS_GK - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
oppFaceDistance(HalfEdge) - Method in class ffx.numerics.quickhull.QuickHull3D: Computes the signed distance from the centroid of the opposite face across this edge to the plane of this edge's face.
opposite - Variable in class ffx.numerics.quickhull.HalfEdge: Half-edge associated with the opposite triangle adjacent to this edge.
oppositeFace() - Method in class ffx.numerics.quickhull.HalfEdge: Returns the opposite triangular face associated with this half-edge.
optCoefficients - Variable in class ffx.potential.nonbonded.pme.OPTRegion
optDipole - Variable in class ffx.potential.nonbonded.pme.OPTRegion
optDipoleCR - Variable in class ffx.potential.nonbonded.pme.OPTRegion
OPTIMIZATION - Static variable in class ffx.ui.commands.SimulationUpdate: Constant OPTIMIZATION=2
OptimizationInterface - Interface in ffx.numerics: The OptimizationInterface defines methods required by an optimizer.
OptimizationListener - Interface in ffx.numerics.optimization: This interface allows the optimizer to notify registered instances of successful steps.
optimizationScaling - Variable in class ffx.potential.ForceFieldEnergy: Optimization scaling value to use for each degree of freedom.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in class ffx.algorithms.optimize.Minimize: This method is called by the optimizer after each step.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in class ffx.algorithms.optimize.MinimizeOpenMM: MinimizeOpenMM does not support the OptimizationListener interface.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in class ffx.algorithms.optimize.PhMinimize: This method is called by the optimizer after each step.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in interface ffx.numerics.optimization.OptimizationListener: This method is called by the optimizer after each step.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in class ffx.xray.RefinementMinimize: This method is called by the optimizer after each step.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in class ffx.xray.ScaleBulkMinimize: This method is called by the optimizer after each step.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in class ffx.xray.SigmaAMinimize: This method is called by the optimizer after each step.
optimizationUpdate(int, int, int, double, double, double, double, double, LineSearch.LineSearchResult) - Method in class ffx.xray.SplineMinimize: This method is called by the optimizer after each step.
optimize() - Method in class ffx.algorithms.optimize.RotamerOptimization: Execute the rotamer optimization.
optimize(double, double[], double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters: Run a local optimization.
optimize(double, int) - Method in class ffx.potential.openmm.OpenMMContext: Use the Context to optimize the system to the requested tolerance.
optimize(RotamerOptimization.Algorithm) - Method in class ffx.algorithms.optimize.RotamerOptimization: Perform the rotamer optimization using the specified algorithm.
optimum - Variable in class ffx.algorithms.optimize.RotamerOptimization: This is the optimal rotamers corresponding to residueList.
optimumSubset - Variable in class ffx.algorithms.optimize.RotamerOptimization: The array of optimum rotamers for the subset of residues being optimized during box or window optimization.
optOrder - Variable in class ffx.potential.nonbonded.pme.OPTRegion: Induced dipoles for extrapolated perturbation theory.
OPTRegion - Class in ffx.potential.nonbonded.pme: Parallel computation of the OPT induced dipoles.
OPTRegion(int) - Constructor for class ffx.potential.nonbonded.pme.OPTRegion
or(Class<? extends Object>, String) - Method in class ffx.ui.Selection: or
OR - Static variable in class edu.rit.pj.reduction.BooleanOp: The Boolean logical "or" binary operation.
OR - Static variable in class edu.rit.pj.reduction.ByteOp: The byte bitwise "or" binary operation.
OR - Static variable in class edu.rit.pj.reduction.CharacterOp: The character bitwise "or" binary operation.
OR - Static variable in class edu.rit.pj.reduction.IntegerOp: The integer bitwise "or" binary operation.
OR - Static variable in class edu.rit.pj.reduction.LongOp: The long bitwise "or" binary operation.
OR - Static variable in class edu.rit.pj.reduction.ShortOp: The short bitwise "or" binary operation.
orbit - Variable in class ffx.ui.behaviors.PickOrbitBehavior
ORBIT - Static variable in interface ffx.ui.behaviors.MouseBehaviorCallback: Constant ORBIT=6
ORBIT - Static variable in interface ffx.ui.behaviors.PickingCallback: Constant ORBIT=6
order - Variable in class ffx.numerics.multipole.MultipoleTensor: Order of the tensor recursion (5th is needed for AMOEBA forces).
order - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Order of the tensor recursion (5th is needed for AMOEBA forces).
order1() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Hard coded computation of the Cartesian multipole tensors up to 1st order.
order1() - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
order1() - Method in class ffx.numerics.multipole.CoulombTensorQI: Hard coded computation of the Cartesian multipole tensors up to 1st order.
order1() - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Hard coded tensor computation up to 1st order.
order1() - Method in class ffx.numerics.multipole.MultipoleTensor: Hard coded computation of the Cartesian multipole tensors up to 1st order.
order1() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Hard coded tensor computation up to 1st order.
order2() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Hard coded computation of the Cartesian multipole tensors up to 2nd order.
order2() - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
order2() - Method in class ffx.numerics.multipole.CoulombTensorQI: Hard coded computation of the Cartesian multipole tensors up to 2nd order.
order2() - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Hard coded tensor computation up to 2nd order.
order2() - Method in class ffx.numerics.multipole.MultipoleTensor: Hard coded computation of the Cartesian multipole tensors up to 2nd order.
order2() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Hard coded tensor computation up to 2nd order.
order3() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Hard coded computation of the Cartesian multipole tensors up to 3rd order.
order3() - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
order3() - Method in class ffx.numerics.multipole.CoulombTensorQI: Hard coded computation of the Cartesian multipole tensors up to 3rd order.
order3() - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Hard coded tensor computation up to 3rd order.
order3() - Method in class ffx.numerics.multipole.MultipoleTensor: Hard coded computation of the Cartesian multipole tensors up to 3rd order.
order3() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Hard coded tensor computation up to 3rd order.
order4() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Hard coded computation of the Cartesian multipole tensors up to 4th order.
order4() - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
order4() - Method in class ffx.numerics.multipole.CoulombTensorQI: Hard coded computation of the Cartesian multipole tensors up to 4th order.
order4() - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Hard coded tensor computation up to 4th order.
order4() - Method in class ffx.numerics.multipole.MultipoleTensor: Hard coded computation of the Cartesian multipole tensors up to 4th order.
order4() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Hard coded tensor computation up to 4th order.
order5() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Hard coded computation of the Cartesian multipole tensors up to 5th order, which is needed for quadrupole-quadrupole forces.
order5() - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
order5() - Method in class ffx.numerics.multipole.CoulombTensorQI: Hard coded computation of the Cartesian multipole tensors up to 5th order, which is needed for quadrupole-quadrupole forces.
order5() - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Hard coded tensor computation up to 5th order.
order5() - Method in class ffx.numerics.multipole.MultipoleTensor: Hard coded computation of the Cartesian multipole tensors up to 5th order, which is needed for quadrupole-quadrupole forces.
order5() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Hard coded tensor computation up to 5th order.
order6() - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Hard coded computation of the Cartesian multipole tensors up to 6th order, which is needed for quadrupole-quadrupole forces and orthogonal space sampling.
order6() - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
order6() - Method in class ffx.numerics.multipole.CoulombTensorQI: Hard coded computation of the Cartesian multipole tensors up to 6th order, which is needed for quadrupole-quadrupole forces and orthogonal space sampling.
order6() - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Hard coded tensor computation up to 6th order.
order6() - Method in class ffx.numerics.multipole.MultipoleTensor: Hard coded computation of the Cartesian multipole tensors up to 6th order, which is needed for quadrupole-quadrupole forces and orthogonal space sampling.
order6() - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Hard coded tensor computation up to 6th order.
ordered(ParallelSection) - Method in class edu.rit.pj.IntegerForLoop: Execute the given section of code in order of the loop indexes.
ordered(ParallelSection) - Method in class edu.rit.pj.IntegerStrideForLoop: Execute the given section of code in order of the loop indexes.
ordered(ParallelSection) - Method in class edu.rit.pj.LongForLoop: Execute the given section of code in order of the loop indexes.
ordered(ParallelSection) - Method in class edu.rit.pj.LongStrideForLoop: Execute the given section of code in order of the loop indexes.
ordered(ParallelSection) - Method in class edu.rit.pj.ParallelIteration: Execute the given section of code in the items' iteration order.
ordinal(double) - Method in class ffx.crystal.ReflectionList: ordinal
origCoordinates - Variable in class ffx.potential.commands.MoveIntoUnitCell: Original Cartesian coordinates before moving into the unit cell.
originalState - Variable in class ffx.potential.bonded.Rotamer: Residue state used to initialize the rotamer.
ORN - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
orthogonalSpaceTempering - Variable in class ffx.algorithms.commands.Thermodynamics
OrthogonalSpaceTempering - Class in ffx.algorithms.thermodynamics: An implementation of the Orthogonal Space Tempering algorithm.
OrthogonalSpaceTempering(LambdaInterface, CrystalPotential, HistogramData, LambdaData, CompositeConfiguration, DynamicsOptions, LambdaParticleOptions, AlgorithmListener) - Constructor for class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: OST Constructor.
OrthogonalSpaceTempering.Histogram - Class in ffx.algorithms.thermodynamics: Store and operate on a 2D Histogram of (Lambda, dU/dL) observations to produce an OST bias.
OrthogonalSpaceTempering.OptimizationParameters - Class in ffx.algorithms.thermodynamics: Parameters for running local optimizations during OST sampling.
ORTHORHOMBIC - Enum constant in enum class ffx.crystal.CrystalSystem: Orthorhombic crystal system.
ORTHORHOMBIC_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem: Orthorhombic lattice system.
Os - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
OST - Enum constant in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm
OST - Enum constant in enum class ffx.potential.nonbonded.pme.AlchemicalParameters.AlchemicalMode
OSTGradient - Class in ffx.algorithms.commands.test: OSTGradient tests the Orthogonal Space Tempering Potential.
OSTGradient() - Constructor for class ffx.algorithms.commands.test.OSTGradient: OSTGradient Constructor.
OSTGradient(FFXBinding) - Constructor for class ffx.algorithms.commands.test.OSTGradient: OSTGradient Constructor.
OSTGradient(String[]) - Constructor for class ffx.algorithms.commands.test.OSTGradient: OSTGradient constructor that sets the command line arguments.
ostOptions - Variable in class ffx.algorithms.commands.Thermodynamics
OSTOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that utilize variants of the Orthogonal Space Tempering (OST) algorithm.
OSTOptions() - Constructor for class ffx.algorithms.cli.OSTOptions
OSXAdapter - Class in ffx.ui: The OSXAdapter class was developed by following an example supplied on the OS X site.
OSXAdapter(MainPanel) - Constructor for class ffx.ui.OSXAdapter
OTHER - Enum constant in enum class ffx.numerics.Potential.VARIABLE_TYPE: Other variable type.
out - Variable in class edu.rit.pj.cluster.BackendFileWriter: Print stream for printing on the job frontend's standard output.
out - Variable in class ffx.numerics.fft.PassData
out() - Static method in class edu.rit.io.Stdio: Get the standard output stream for the calling thread.
out(PrintStream) - Static method in class edu.rit.io.Stdio: Set the standard output stream for the calling thread.
outerLoopLimit - Variable in class ffx.numerics.fft.MixedRadixFactor: The outer loop limit (n / product).
outOffset - Variable in class ffx.numerics.fft.PassData
OutOfPlaneBend - Class in ffx.potential.bonded: The OutOfPlaneBend class represents an Out-Of-Plane Bend.
OutOfPlaneBend(Angle, Atom) - Constructor for class ffx.potential.bonded.OutOfPlaneBend: OutOfPlaneBend constructor.
outOfPlaneBendFactory(Angle, ForceField) - Static method in class ffx.potential.bonded.OutOfPlaneBend: Attempt to create a new OutOfPlaneBend instance for a given Angle and Force Field.
outOfPlaneBendForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom Out-of-Plane Bend Force
OutOfPlaneBendForce - Class in ffx.potential.openmm: OpenMM Out-of-Plane Bend Force.
OutOfPlaneBendForce(OutOfPlaneBendPotentialEnergy) - Constructor for class ffx.potential.openmm.OutOfPlaneBendForce: Create an Out-of-Plane Bend Force.
OutOfPlaneBendForce(OutOfPlaneBendPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.OutOfPlaneBendForce: Create an Out-of-Plane Bend Force for Dual Topology.
outOfPlaneBendForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Out-of-Plane Bend Force for topology 2.
OutOfPlaneBendPotentialEnergy - Class in ffx.potential.terms: Out-of-Plane Bend potential energy term using OutOfPlaneBend instances.
OutOfPlaneBendPotentialEnergy(String) - Constructor for class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Create an OutOfPlaneBendPotentialEnergy with the provided name.
OutOfPlaneBendPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Create an OutOfPlaneBendPotentialEnergy with the provided name and force group.
OutOfPlaneBendPotentialEnergy(String, int, List<OutOfPlaneBend>) - Constructor for class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Create an OutOfPlaneBendPotentialEnergy initialized with a list of terms and force group.
OutOfPlaneBendPotentialEnergy(String, Collection<OutOfPlaneBend>) - Constructor for class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Create an OutOfPlaneBendPotentialEnergy initialized with a collection of terms.
outOfPlaneBendTime - Static variable in class ffx.potential.bonded.MSGroup: Constant outOfPlaneBendTime=0
outOfPlaneBendType - Variable in class ffx.potential.bonded.OutOfPlaneBend: Force field parameters to compute the Out-of-Plane Bend energy.
OutOfPlaneBendType - Class in ffx.potential.parameters: The OutOfPlaneBendType class defines one Allinger style out-of-plane angle bending energy type.
OutOfPlaneBendType(int[], double) - Constructor for class ffx.potential.parameters.OutOfPlaneBendType: OutOfPlaneBendType Constructor.
OutOfPlaneSite - Class in ffx.openmm: This is a VirtualSite that computes the particle location based on three other particles' locations.
OutOfPlaneSite(int, int, int, double, double, double) - Constructor for class ffx.openmm.OutOfPlaneSite: Create an OutOfPlaneSite.
outputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.FrontendFileWriter: Close the given output file.
outputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontend: Close the given output file.
outputFileClose(JobBackendRef, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "output file close" message.
outputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Close the given output file.
outputFileClose(JobBackendRef, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Close the given output file.
outputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Close the given output file.
outputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileWriter: Report the result of closing the given output file.
outputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of closing the given output file.
outputFileCloseResult(JobFrontendRef, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "output file close result" message.
outputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of closing the given output file.
outputFileCloseResult(JobFrontendRef, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of closing the given output file.
outputFileFlush(JobBackendRef, int) - Method in class edu.rit.pj.cluster.FrontendFileWriter: Flush accumulated bytes to the given output file.
outputFileFlush(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontend: Flush accumulated bytes to the given output file.
outputFileFlush(JobBackendRef, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "output file flush" message.
outputFileFlush(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Flush accumulated bytes to the given output file.
outputFileFlush(JobBackendRef, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Flush accumulated bytes to the given output file.
outputFileFlush(JobBackendRef, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Flush accumulated bytes to the given output file.
outputFileFlushResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileWriter: Report the result of flushing the given output file.
outputFileFlushResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of flushing the given output file.
outputFileFlushResult(JobFrontendRef, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "output file flush result" message.
outputFileFlushResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of flushing the given output file.
outputFileFlushResult(JobFrontendRef, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of flushing the given output file.
outputFileOpen(JobBackendRef, int, File, boolean) - Method in class edu.rit.pj.cluster.FrontendFileWriter: Open the given output file for writing or appending.
outputFileOpen(JobBackendRef, int, File, boolean) - Method in class edu.rit.pj.cluster.JobFrontend: Open the given output file for writing or appending.
outputFileOpen(JobBackendRef, int, File, boolean) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "output file open" message.
outputFileOpen(JobBackendRef, int, File, boolean) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Open the given output file for writing or appending.
outputFileOpen(JobBackendRef, int, File, boolean) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Open the given output file for writing or appending.
outputFileOpen(JobBackendRef, int, File, boolean) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Open the given output file for writing or appending.
outputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileWriter: Report the result of opening the given output file.
outputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of opening the given output file.
outputFileOpenResult(JobFrontendRef, int, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "output file open result" message.
outputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of opening the given output file.
outputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of opening the given output file.
outputFileWrite(JobBackendRef, int, byte[], int, int) - Method in class edu.rit.pj.cluster.JobFrontend: Write the given bytes to the given output file.
outputFileWrite(JobBackendRef, int, byte[], int, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Write the given bytes to the given output file.
outputFileWrite(JobBackendRef, int, byte[], int, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Write the given bytes to the given output file.
outputFileWrite(JobBackendRef, int, byte[], int, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Write the given bytes to the given output file.
outputFileWrite(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.FrontendFileWriter: Write the given bytes to the given output file.
outputFileWrite(JobBackendRef, int, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "output file write" message.
outputFileWriteResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileWriter: Report the result of writing the given output file.
outputFileWriteResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend: Report the result of writing the given output file.
outputFileWriteResult(JobFrontendRef, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "output file write result" message.
outputFileWriteResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the result of writing the given output file.
outputFileWriteResult(JobFrontendRef, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the result of writing the given output file.
outside - Variable in class ffx.numerics.quickhull.Face
overlapSource(double, double, double, double, double, double[]) - Static method in class ffx.numerics.multipole.AmoebaPlusOverlapTensorGlobal: Generate source terms for the Challacombe et al. recursion.

P

p - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
P - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
P - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
p12scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between a permanent multipole and polarizable site that are 1-2 is scaled by p12scale.
p13scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between a permanent multipole and polarizable site that are 1-3 is scaled by p13scale.
p14scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between a permanent multipole and polarizable site that are 1-4 is scaled by p14scale.
p15scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters: The interaction energy between a permanent multipole and polarizable site that are 1-5 is scaled by p15scale.
Pa - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Packing - Class in edu.rit.util: Class Packing provides static methods for packing and unpacking arrays of bytes into and out of integers, long integers, and arrays thereof.
packIntBigEndian(byte[], int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into an integer in big-endian order.
packIntBigEndian(byte[], int, int[], int, int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into the given array of integers in big-endian order.
packIntLittleEndian(byte[], int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into an integer in little-endian order.
packIntLittleEndian(byte[], int, int[], int, int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into the given array of integers in little-endian order.
packLongBigEndian(byte[], int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into a long integer in big-endian order.
packLongBigEndian(byte[], int, long[], int, int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into the given array of long integers in big-endian order.
packLongLittleEndian(byte[], int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into a long integer in little-endian order.
packLongLittleEndian(byte[], int, long[], int, int) - Static method in class edu.rit.util.Packing: Pack bytes from the given array into the given array of long integers in little-endian order.
padLeft(String, int) - Static method in class ffx.utilities.StringUtils: padLeft
padRight(String, int) - Static method in class ffx.utilities.StringUtils: padRight
paint(Graphics) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
paint(Graphics) - Method in class ffx.ui.GraphicsCanvas
paint(Graphics2D, int, int, double, double, boolean) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Paints this visual component onto the provided Graphics2D context.
paint(Graphics2D, int, int, double, double, boolean) - Method in interface ffx.numerics.clustering.visualization.Paintable: Paints this visual component onto the provided Graphics2D context.
Paintable - Interface in ffx.numerics.clustering.visualization: Implemented by visual components of the dendrogram.
pairsToSingleElimination(Residue[], int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Method to check if pairs elimination for some residue pair has enabled a singles rotamer elimination by eliminating all ri-rj for some ri or some rj.
PairwiseSchedule - Class in ffx.potential.nonbonded: A fixed schedule that balances pairwise work across threads.
PairwiseSchedule(int, int, Range[]) - Constructor for class ffx.potential.nonbonded.PairwiseSchedule: Constructor for PairwiseSchedule.
PAM - Enum constant in enum class ffx.potential.parameters.ForceField.ELEC_FORM
ParallelConstruct - Class in edu.rit.pj: Class ParallelConstruct is the common base class for all parallel constructs that are executed by a ParallelTeam.
ParallelConstruct() - Constructor for class edu.rit.pj.ParallelConstruct: Construct a new parallel construct.
ParallelForLoop - Class in edu.rit.pj: Class ParallelForLoop is the abstract base class for a parallel for loop that is executed inside a ParallelRegion.
ParallelForLoop() - Constructor for class edu.rit.pj.ParallelForLoop: Construct a new parallel for loop.
ParallelIteration<T> - Class in edu.rit.pj: Class ParallelIteration is the abstract base class for a parallel iteration that is executed inside a ParallelRegion.
ParallelIteration() - Constructor for class edu.rit.pj.ParallelIteration: Construct a new parallel iteration.
parallelNotDone - Static variable in class ffx.potential.bonded.ROLSP: Constant parallelNotDone=0
ParallelRegion - Class in edu.rit.pj: Class ParallelRegion is the abstract base class for a parallel region that is executed by a ParallelTeam of threads.
ParallelRegion() - Constructor for class edu.rit.pj.ParallelRegion: Construct a new parallel region.
ParallelSection - Class in edu.rit.pj: Class ParallelSection is the abstract base class for a section of code to be executed in parallel.
ParallelSection() - Constructor for class edu.rit.pj.ParallelSection: Construct a new parallel section.
ParallelStateEnergy - Class in ffx.algorithms: The ParallelStateEnergy class evaluates the energy of a system at different lambda values.
ParallelStateEnergy(int, double[], MolecularAssembly[], Potential, String[][], SystemFilter[]) - Constructor for class ffx.algorithms.ParallelStateEnergy: The ParallelEnergy constructor.
ParallelTeam - Class in edu.rit.pj: Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
ParallelTeam() - Constructor for class edu.rit.pj.ParallelTeam: Construct a new parallel team with the default number of threads.
ParallelTeam(int) - Constructor for class edu.rit.pj.ParallelTeam: Construct a new parallel team with the given number of threads.
parse() - Method in class ffx.potential.parsers.ForceFieldFilter: parse
parse(String) - Static method in class edu.rit.pj.IntegerSchedule: Returns a schedule object of a type determined by parsing the given string.
parse(String) - Static method in class edu.rit.pj.LongSchedule: Returns a schedule object of a type determined by parsing the given string.
parse(String) - Static method in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm: Parse a String to a corresponding thermodynamics algorithm, recognizing aliases.
parse(String) - Static method in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules: Attempt to parse a String to a Schedules in a case-insensitive, alias-recognizing fashion.
parse(String) - Static method in class ffx.crystal.SymOp: Create a SymOp from an input String.
parse(String) - Static method in enum class ffx.potential.bonded.NamingUtils.HetAtoms: Slightly more robust parsing function that ignores case and trailing numbers, -, and +
parse(String) - Static method in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3: Best-guess parse of a String to an NA3.
parse(String, String[]) - Static method in class ffx.potential.parameters.AngleTorsionType: Construct an AngleTorsionType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.AngleType: Construct an AngleType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.AtomType: Construct an AtomType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.BioType: Construct an BioType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.BondType: Construct a BondType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.ImproperTorsionType: Construct an ImproperTorsionType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.MultipoleType: Parse a single line multipole.
parse(String, String[]) - Static method in class ffx.potential.parameters.OutOfPlaneBendType: Construct an OutOfPlaneBendType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.PiOrbitalTorsionType: Construct a PiTorsionType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.PolarizeType: Construct a PolarizeType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.RelativeSolvationType: Construct a RelativeSolvationType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.SoluteType: Construct a SoluteType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.StretchBendType: Construct a StretchBendType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.StretchTorsionType: Construct an StretchTorsionType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.TorsionTorsionType: Construct a TorsionTorsionType from a single input line.
parse(String, String[]) - Static method in class ffx.potential.parameters.TorsionType: Construct a TorsionType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.UreyBradleyType: Construct a UreyBradleyType from an input string.
parse(String, String[]) - Static method in class ffx.potential.parameters.VDWPairType: Construct a VDWPairType from multiple input lines.
parse(String, String[]) - Static method in class ffx.potential.parameters.VDWType: Construct a VDWType from multiple input lines.
parse(String, String[], BufferedReader) - Static method in class ffx.potential.parameters.MultipoleType: Parse a single line multipole.
parse(String, String[], BufferedReader) - Static method in class ffx.potential.parameters.TorsionTorsionType: Construct a TorsionTorsionType from multiple input lines.
parseAtomRange(String, String, int) - Static method in class ffx.utilities.StringUtils: Parses a numerical argument for an atom-specific flag.
parseAtomRanges(String, String, int) - Static method in class ffx.utilities.StringUtils: Parses a list of atom ranges for a per atom flag.
parseChargeType(String, String[]) - Static method in class ffx.potential.parameters.MultipoleType: Map charge parameters to a Multipole instance.
parseImproper(String, String[]) - Static method in class ffx.potential.parameters.TorsionType: Construct a TorsionType with TorsionMode.IMPROPER from an input string.
parseInPlane(String, String[]) - Static method in class ffx.potential.parameters.AngleType: Construct an In-Plane AngleType from an input string.
parseIntegrator(String) - Static method in class ffx.algorithms.dynamics.integrators.Integrator: Parse an integrator String into an instance of the IntegratorEnum enum.
parseMessage(Exception) - Method in class ffx.potential.parsers.PDBMLFilter: parseMessage.
parseMode(String) - Static method in class ffx.xray.RefinementMinimize: Parse a string into a refinement mode.
parseResidueString(String, String, int) - Static method in class ffx.utilities.StringUtils: Parses a list of residue (ChainResid) for a per residue flag.
parseRestrainPosition(String, Atom[], boolean) - Static method in class ffx.potential.bonded.RestrainPosition: Parse a Restrain-Position line and return a RestrainPosition instance.
parseRestrainPositions(MolecularAssembly) - Static method in class ffx.potential.bonded.RestrainPosition
parseResult - Variable in class ffx.utilities.FFXCommand: Parse Result.
parseSolventModel(String) - Static method in class ffx.xray.CrystalReciprocalSpace: Parse a solvent model string and return a SolventModel enum.
parseThermostat(String) - Static method in class ffx.algorithms.dynamics.thermostats.Thermostat: Parse a string into a Thermostat enumeration.
parseTinkerAtomList(List<String>, int, int) - Static method in class ffx.utilities.TinkerUtils: Parse a Tinker selection list.
parseUSF(String[]) - Static method in class ffx.numerics.switching.UnivariateFunctionFactory: Parse an array of Strings describing a univariate switching function.
parseUSF(String[], int) - Static method in class ffx.numerics.switching.UnivariateFunctionFactory: Parse an array of Strings terminating in the description of a univariate switching function.
parseVDW14(String, String[]) - Static method in class ffx.potential.parameters.VDWType: Construct a 1-4 VDWType from multiple input lines.
PARTIALCHARGE - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
ParticleMeshEwald - Class in ffx.potential.nonbonded: This Particle Mesh Ewald class implements PME for the AMOEBA polarizable mutlipole force field in parallel using a NeighborList for any Crystal space group.
ParticleMeshEwald - Enum constant in enum class ffx.utilities.PropertyGroup: Particle-mesh Ewald parameters.
ParticleMeshEwald(Atom[], int[], ForceField, Crystal, NeighborList, ForceField.ELEC_FORM, double, double, ParallelTeam) - Constructor for class ffx.potential.nonbonded.ParticleMeshEwald: ParticleMeshEwald constructor.
ParticleMeshEwald.LambdaFactors - Class in ffx.potential.nonbonded: The setFactors(i,k,lambdaMode) method is called every time through the inner PME loops, avoiding an "if (esv)" branch statement.
ParticleMeshEwald.LambdaFactorsESV - Class in ffx.potential.nonbonded
ParticleMeshEwald.LambdaFactorsOST - Class in ffx.potential.nonbonded
partitionFunction(Residue[], int, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: A global optimization over side-chain rotamers using a recursive algorithm and information about eliminated rotamers, rotamer pairs and rotamer triples.
PassConstants - Record Class in ffx.numerics.fft: Constant factors needed for each pass.
PassConstants(int, int, int, int, int, double[][]) - Constructor for record class ffx.numerics.fft.PassConstants: Creates an instance of a PassConstants record class.
PassData - Class in ffx.numerics.fft
PassData(int, double[], int, double[], int) - Constructor for class ffx.numerics.fft.PassData: References to the input and output data arrays.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor: Apply the mixed radix factor using scalar operations.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor2: Handle factors of 2.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor3: Handle factors of 3.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor4: Handle factors of 4.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor5: Handle factors of 5.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor6: Handle factors of 6.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor7: Handle factors of 7.
passScalar(PassData) - Method in class ffx.numerics.fft.MixedRadixFactorPrime: Handle a general prime number.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor: Apply the mixed radix factor using SIMD operations.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor2: Handle factors of 2 using SIMD vectors.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor3: Handle factors of 3 using SIMD vectors.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor4: Handle factors of 4 using SIMD vectors.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor5: Handle factors of 5 using SIMD vectors.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor6: Handle factors of 6 using SIMD vectors.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactor7: Handle factors of 6 using SIMD vectors.
passSIMD(PassData) - Method in class ffx.numerics.fft.MixedRadixFactorPrime: There is no SIMD support for general prime numbers, so the scalar method is used.
patchBuffer(boolean[][], Range, Range) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for one patch of the given Boolean matrix.
patchBuffer(byte[][], Range, Range) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for one patch of the given byte matrix.
patchBuffer(char[][], Range, Range) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for one patch of the given character matrix.
patchBuffer(double[][], Range, Range) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for one patch of the given double matrix.
patchBuffer(float[][], Range, Range) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for one patch of the given float matrix.
patchBuffer(int[][], Range, Range) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for one patch of the given integer matrix.
patchBuffer(int[][], Range, Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for one patch of the given integer matrix.
patchBuffer(int[][], Range, Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for one patch of the given integer matrix.
patchBuffer(int[][], Range, Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for one patch of the given integer matrix.
patchBuffer(int[][], Range, Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for one patch of the given integer matrix.
patchBuffer(long[][], Range, Range) - Static method in class edu.rit.mp.LongBuf: Create a buffer for one patch of the given long matrix.
patchBuffer(short[][], Range, Range) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for one patch of the given short matrix.
patchBuffer(T[][], Range, Range) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for one patch of the given object matrix.
patchBuffers(boolean[][], Range[], Range[]) - Static method in class edu.rit.mp.BooleanBuf: Create an array of buffers for multiple patches of the given Boolean matrix.
patchBuffers(byte[][], Range[], Range[]) - Static method in class edu.rit.mp.ByteBuf: Create an array of buffers for multiple patches of the given byte matrix.
patchBuffers(char[][], Range[], Range[]) - Static method in class edu.rit.mp.CharacterBuf: Create an array of buffers for multiple patches of the given character matrix.
patchBuffers(double[][], Range[], Range[]) - Static method in class edu.rit.mp.DoubleBuf: Create an array of buffers for multiple patches of the given double matrix.
patchBuffers(float[][], Range[], Range[]) - Static method in class edu.rit.mp.FloatBuf: Create an array of buffers for multiple patches of the given float matrix.
patchBuffers(int[][], Range[], Range[]) - Static method in class edu.rit.mp.IntegerBuf: Create an array of buffers for multiple patches of the given integer matrix.
patchBuffers(int[][], Range[], Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an array of buffers for multiple patches of the given integer matrix.
patchBuffers(int[][], Range[], Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an array of buffers for multiple patches of the given integer matrix.
patchBuffers(int[][], Range[], Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an array of buffers for multiple patches of the given integer matrix.
patchBuffers(int[][], Range[], Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an array of buffers for multiple patches of the given integer matrix.
patchBuffers(long[][], Range[], Range[]) - Static method in class edu.rit.mp.LongBuf: Create an array of buffers for multiple patches of the given long matrix.
patchBuffers(short[][], Range[], Range[]) - Static method in class edu.rit.mp.ShortBuf: Create an array of buffers for multiple patches of the given short matrix.
patchBuffers(T[][], Range[], Range[]) - Static method in class edu.rit.mp.ObjectBuf: Create an array of buffers for multiple patches of the given object matrix.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.AngleTorsionType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.AngleType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.BondType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.ImproperTorsionType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.OutOfPlaneBendType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.PiOrbitalTorsionType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.StretchBendType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.StretchTorsionType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.TorsionTorsionType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.TorsionType: Remap new atom classes to known internal ones.
patchClasses(HashMap<AtomType, AtomType>) - Method in class ffx.potential.parameters.UreyBradleyType: Remap new atom classes to known internal ones.
Pb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
pbDiameter - Variable in class ffx.potential.parameters.SoluteType: Solute atomic diameter for PB.
PCA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
PCGSolver - Class in ffx.potential.nonbonded.pme: Parallel pre-conditioned conjugate gradient solver for the self-consistent field.
PCGSolver(int, double, ForceField, int) - Constructor for class ffx.potential.nonbonded.pme.PCGSolver: Constructor the PCG solver.
Pd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
pdamp - Variable in class ffx.potential.parameters.PolarizeType: Value of polarizability scale factor.
PDB - Enum constant in enum class ffx.potential.Utilities.FileType
pdb2ShortName(String) - Static method in class ffx.crystal.SpaceGroupInfo: Returns the space group name for the given PDB name.
PDBFileFilter - Class in ffx.potential.parsers: The PDBFileFilter class is used to choose a Protein Databank (*.PDB) file.
PDBFileFilter() - Constructor for class ffx.potential.parsers.PDBFileFilter: Public Constructor.
PDBFilter - Class in ffx.potential.parsers: The PDBFilter class parses data from a Protein DataBank (*.PDB) file.
PDBFilter(File, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.PDBFilter: Parse the PDB File from a URL.
PDBFilter(File, MolecularAssembly, ForceField, CompositeConfiguration, List<Integer>) - Constructor for class ffx.potential.parsers.PDBFilter: Constructor for PDBFilter with residue numbers.
PDBFilter(File, List<MolecularAssembly>, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.PDBFilter: Parse the PDB File from a URL.
PDBFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.PDBFilter: Constructor for PDBFilter.
PDBFilter.Mutation - Class in ffx.potential.parsers
PDBFilter.PDBFileStandard - Enum Class in ffx.potential.parsers: Presently, VERSION3_3 is default, and VERSION3_2 is anything non-standard.
pdbForID(String) - Static method in class ffx.utilities.StringUtils: pdbForID
PDBMLFileFilter - Class in ffx.potential.parsers: The PDBXFileFilter class is used to choose a PDBML File (*.XML).
PDBMLFileFilter() - Constructor for class ffx.potential.parsers.PDBMLFileFilter: Public Constructor.
PDBMLFilter - Class in ffx.potential.parsers: PDBMLFilter class.
PDBMLFilter() - Constructor for class ffx.potential.parsers.PDBMLFilter: PDBML Constructor.
pdbName - Variable in class ffx.crystal.SpaceGroup: Space group name under the PDB convention.
pdbSpaceGroupNames - Static variable in class ffx.crystal.SpaceGroupInfo: PDB space group names.
PDistClusteringAlgorithm - Class in ffx.numerics.clustering: Clustering algorithm that consumes a condensed (pdist-style) upper-triangular distance array to produce hierarchical agglomerative clusters.
PDistClusteringAlgorithm() - Constructor for class ffx.numerics.clustering.PDistClusteringAlgorithm
pentic - Variable in class ffx.potential.parameters.AngleType: Pentic coefficient in angle bending potential.
pentic - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Quintic coefficient in out-of-plane angle bending potential.
performClustering(double[][], String[], LinkageStrategy) - Method in interface ffx.numerics.clustering.ClusteringAlgorithm: Performs hierarchical agglomerative clustering on a square distance matrix.
performClustering(double[][], String[], LinkageStrategy) - Method in class ffx.numerics.clustering.DefaultClusteringAlgorithm: Performs hierarchical agglomerative clustering using a full N x N distance matrix.
performClustering(double[][], String[], LinkageStrategy) - Method in class ffx.numerics.clustering.PDistClusteringAlgorithm: Performs hierarchical agglomerative clustering using a condensed pdist-like matrix.
performConvolution() - Method in class ffx.potential.nonbonded.ReciprocalSpace: Compute the reciprocal space field using a convolution.
performFlatClustering(double[][], String[], LinkageStrategy, Double) - Method in interface ffx.numerics.clustering.ClusteringAlgorithm: Performs a flat clustering by agglomerating until the next linkage distance would exceed the provided threshold, and returns the list of clusters at that cut.
performFlatClustering(double[][], String[], LinkageStrategy, Double) - Method in class ffx.numerics.clustering.DefaultClusteringAlgorithm: Produces a flat clustering by agglomerating until the next merge would exceed the threshold.
performFlatClustering(double[][], String[], LinkageStrategy, Double) - Method in class ffx.numerics.clustering.PDistClusteringAlgorithm: Produces a flat clustering from a condensed distance matrix by agglomerating until the threshold is exceeded.
performWeightedClustering(double[][], String[], double[], LinkageStrategy) - Method in interface ffx.numerics.clustering.ClusteringAlgorithm: Performs hierarchical clustering when each initial element has an associated weight.
performWeightedClustering(double[][], String[], double[], LinkageStrategy) - Method in class ffx.numerics.clustering.DefaultClusteringAlgorithm: Performs hierarchical clustering when each element has an associated weight.
performWeightedClustering(double[][], String[], double[], LinkageStrategy) - Method in class ffx.numerics.clustering.PDistClusteringAlgorithm: Weighted variant for condensed inputs; currently delegates to unweighted clustering as weights are not applied with condensed input in this implementation.
periodicity - Variable in class ffx.potential.parameters.ImproperTorsionType: Periodicity (should be 2 for an Improper Torsion).
periodicity - Variable in class ffx.potential.parameters.TorsionType: Periodicity of the Fourier series.
PeriodicTorsionForce - Class in ffx.openmm: This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them.
PeriodicTorsionForce() - Constructor for class ffx.openmm.PeriodicTorsionForce: Create a new PeriodicTorsionForce.
permanentChargeCorrectionEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
PermanentFieldRegion - Class in ffx.potential.nonbonded.pme: Parallel computation of the permanent field.
PermanentFieldRegion(ParallelTeam, ForceField, boolean) - Constructor for class ffx.potential.nonbonded.pme.PermanentFieldRegion
PermanentGKFieldRegion - Class in ffx.potential.nonbonded.implicit: Parallel computation of the Generalized Kirkwood permanent reaction field.
PermanentGKFieldRegion(int, double, double, double) - Constructor for class ffx.potential.nonbonded.implicit.PermanentGKFieldRegion: Compute the GK field due to the permanent multipoles.
permanentMultipoleEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Permanent multipole energy = permanentRealSpaceEnergy + permanentSelfEnergy + permanentReciprocalEnergy.
permanentRealSpaceEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
permanentReciprocalEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
permanentScale - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
permanentSelfEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
permLambda - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: The permanent Lambda value goes from 0.0 .. 1.0 as the global lambda value varies between permLambdaStart .. permLambdaEnd.
permLambdaAlpha - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Constant α in: r' = sqrt(r^2 + α*(1 - L)^2)
permLambdaEnd - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Finish turning on permanent multipoles at Lambda = 1.0;
permLambdaExponent - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Power on L in front of the pairwise multipole potential.
permLambdaStart - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Begin turning on permanent multipoles at Lambda = 0.4;
perturbCellVectors(double[][]) - Method in class ffx.crystal.Crystal: Strain the unit cell vectors.
phase - Variable in class ffx.potential.parameters.ImproperTorsionType: Phases in degrees.
phase - Variable in class ffx.potential.parameters.TorsionType: Phases of the Fourier series in degrees.
phase() - Method in class ffx.numerics.math.ComplexNumber: phase
phaseShift(double) - Method in class ffx.numerics.math.ComplexNumber: phaseShift
phaseShift(ComplexNumber, double) - Static method in class ffx.numerics.math.ComplexNumber: Static version of phaseShift.
phaseShiftIP(double) - Method in class ffx.numerics.math.ComplexNumber: phaseShiftIP
PhDynamics - Class in ffx.algorithms.commands.test: The PhDynamics command implements constant pH molecular dynamics.
PhDynamics() - Constructor for class ffx.algorithms.commands.test.PhDynamics: PhDynamics Constructor.
PhDynamics(FFXBinding) - Constructor for class ffx.algorithms.commands.test.PhDynamics: PhDynamics Constructor.
PhDynamics(String[]) - Constructor for class ffx.algorithms.commands.test.PhDynamics: PhDynamics constructor that sets the command line arguments.
PHE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
PhEnergy - Class in ffx.potential.commands: The Energy script evaluates the energy of a system.
PhEnergy() - Constructor for class ffx.potential.commands.PhEnergy: Energy constructor.
PhEnergy(FFXBinding) - Constructor for class ffx.potential.commands.PhEnergy: Energy constructor.
PhEnergy(String[]) - Constructor for class ffx.potential.commands.PhEnergy: PhEnergy constructor that sets the command line arguments.
PHENYLALANINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
PhGradient - Class in ffx.potential.commands.test: The Gradient script evaluates the consistency of the energy and gradient for CpHMD.
PhGradient() - Constructor for class ffx.potential.commands.test.PhGradient: Default constructor.
PhGradient(FFXBinding) - Constructor for class ffx.potential.commands.test.PhGradient: Constructor with Binding.
PhGradient(String[]) - Constructor for class ffx.potential.commands.test.PhGradient: Constructor that sets command-line args.
PhMinimize - Class in ffx.algorithms.optimize: Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.
PhMinimize(MolecularAssembly, AlgorithmListener, ExtendedSystem) - Constructor for class ffx.algorithms.optimize.PhMinimize: Constructor for Minimize.
PhMinimize(MolecularAssembly, Potential, AlgorithmListener, ExtendedSystem) - Constructor for class ffx.algorithms.optimize.PhMinimize: Constructor for Minimize.
PhReplicaExchange - Class in ffx.algorithms.dynamics: The PhReplicaExchange implements pH replica exchange.
PhReplicaExchange(MolecularDynamics, File, double, double[], double, ExtendedSystem, double[], int) - Constructor for class ffx.algorithms.dynamics.PhReplicaExchange: pHReplicaExchange constructor.
PhReplicaExchange(MolecularDynamics, File, double, double[], double, ExtendedSystem, double[], MolecularDynamicsOpenMM, Potential, int) - Constructor for class ffx.algorithms.dynamics.PhReplicaExchange: OpenMM cycled pHReplicaExchange constructor.
PICK - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
PICKANGLE - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
PICKATOM - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
PICKBOND - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
pickCanvas - Variable in class ffx.ui.behaviors.PickMouseBehavior
PICKDIHEDRAL - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
PickingCallback - Interface in ffx.ui.behaviors: The PickingCallback interface is implemented by classes wishing to recieve notification that a picked object has moved.
pickingColor - Static variable in class ffx.potential.bonded.RendererCache: Constant pickingColor
PICKMOLECULE - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
PickMouseBehavior - Class in ffx.ui.behaviors: The PickMouseBehavior class is the base class for mouse picking behaviors.
PickMouseBehavior(Canvas3D, BranchGroup, Bounds) - Constructor for class ffx.ui.behaviors.PickMouseBehavior: Creates a PickMouseBehavior given current canvas, root of the tree to operate on, and the bounds.
PickOrbitBehavior - Class in ffx.ui.behaviors: The PickOrbitBehavior class implements a mouse orbit behavior.
PickOrbitBehavior(BranchGroup, Canvas3D, Bounds, TransformGroup, int) - Constructor for class ffx.ui.behaviors.PickOrbitBehavior: Constructor for PickOrbitBehavior.
PICKPOLYMER - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
PickPropertiesBehavior - Class in ffx.ui.behaviors: The PickPropertiesBehavior class.
PickPropertiesBehavior(BranchGroup, Canvas3D, Bounds, TransformGroup, int) - Constructor for class ffx.ui.behaviors.PickPropertiesBehavior: Constructor for PickPropertiesBehavior.
PICKRESIDUE - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
PickRotateBehavior - Class in ffx.ui.behaviors: The PickRotateBehavior class implements a mouse rotate behavior on a picked object.
PickRotateBehavior(BranchGroup, Canvas3D, Bounds, TransformGroup, int) - Constructor for class ffx.ui.behaviors.PickRotateBehavior: Constructor for PickRotateBehavior.
PickSelectionBehavior - Class in ffx.ui.behaviors: The PickSelectionBehavior class implements a mouse based selections behavior.
PickSelectionBehavior(BranchGroup, Canvas3D, Bounds, TransformGroup, int) - Constructor for class ffx.ui.behaviors.PickSelectionBehavior: Constructor for PickSelectionBehavior.
PICKSYSTEM - Enum constant in enum class ffx.ui.GraphicsPicking.PickLevel
PickTranslateBehavior - Class in ffx.ui.behaviors: The PickTranslateBehavior class implements a translation behavior on a picked scenegraph object.
PickTranslateBehavior(BranchGroup, Canvas3D, Bounds, TransformGroup, int) - Constructor for class ffx.ui.behaviors.PickTranslateBehavior: Constructor for PickTranslateBehavior.
PickZoomBehavior - Class in ffx.ui.behaviors: The PickZoomBehavior class implements a scaling behavior on a picked scenegraph object.
PickZoomBehavior(BranchGroup, Canvas3D, Bounds, TransformGroup, int) - Constructor for class ffx.ui.behaviors.PickZoomBehavior: Constructor for PickZoomBehavior.
PiOrbitalTorsion - Class in ffx.potential.bonded: The Pi-Orbital Torsion class.
PiOrbitalTorsion(Bond) - Constructor for class ffx.potential.bonded.PiOrbitalTorsion: Pi-Orbital Torsion constructor.
piOrbitalTorsionFactory(Bond, ForceField) - Static method in class ffx.potential.bonded.PiOrbitalTorsion: Attempt to create a new PiOrbitalTorsion based on the supplied bond and forceField.
piOrbitalTorsionForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom Pi-Torsion Force
PiOrbitalTorsionForce - Class in ffx.potential.openmm: OpenMM Pi-Orbital Torsion Force.
PiOrbitalTorsionForce(PiOrbitalTorsionPotentialEnergy) - Constructor for class ffx.potential.openmm.PiOrbitalTorsionForce: Create a Pi-Orbital Torsion Force.
PiOrbitalTorsionForce(PiOrbitalTorsionPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.PiOrbitalTorsionForce: Create an Pi-Orbital Torsion Force for Dual Topology.
piOrbitalTorsionForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Pi-Orbital Torsion Force for topology 2.
PiOrbitalTorsionPotentialEnergy - Class in ffx.potential.terms: Pi-Orbital Torsion potential energy term using PiOrbitalTorsion instances.
PiOrbitalTorsionPotentialEnergy(String) - Constructor for class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Create a PiOrbitalTorsionPotentialEnergy with the provided name.
PiOrbitalTorsionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Create a PiOrbitalTorsionPotentialEnergy with the provided name and force group.
PiOrbitalTorsionPotentialEnergy(String, int, List<PiOrbitalTorsion>) - Constructor for class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Create a PiOrbitalTorsionPotentialEnergy initialized with a list of terms and force group.
PiOrbitalTorsionPotentialEnergy(String, Collection<PiOrbitalTorsion>) - Constructor for class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Create a PiOrbitalTorsionPotentialEnergy initialized with a collection of terms.
piOrbitalTorsionTime - Static variable in class ffx.potential.bonded.MSGroup: Constant piOrbitalTorsionTime=0
piOrbitalTorsionType - Variable in class ffx.potential.bonded.PiOrbitalTorsion: A reference to the Pi-Torsion type in use.
PiOrbitalTorsionType - Class in ffx.potential.parameters: The PiOrbitalTorsionType class defines a Pi-Orbital Torsion energy term.
PiOrbitalTorsionType(int[], double) - Constructor for class ffx.potential.parameters.PiOrbitalTorsionType: PiTorsionType Constructor.
PITORS - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
piTorsUnit - Variable in class ffx.potential.parameters.PiOrbitalTorsionType: Convert Pi-Torsion energy to kcal/mole.
PJ - Enum constant in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl: Parallel Java edu.rit.pj.reduction.SharedDoubleArray implementation.
PJ_PORT - Static variable in class edu.rit.pj.cluster.Constants: The default port number to which the Job Scheduler listens for connections from job frontend processes (20617).
PJ_VERSION - Static variable in class edu.rit.pj.Version: The Parallel Java Library version.
PJDoubleArray - Class in ffx.numerics.atomic: PJDoubleArray implements the AtomicDoubleArray interface using the Parallel Java class SharedDoubleArray.
PJDoubleArray(int) - Constructor for class ffx.numerics.atomic.PJDoubleArray: Constructor: Initialize the size and array.
PJProperties - Class in edu.rit.pj: Class PJProperties provides static methods for reading Java system properties that control the behavior of Parallel Java.
pKa - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
PLANCK_CONSTANT_SI - Static variable in class ffx.utilities.Constants: Planck constant in J*s, defining the kilogram (by defining the derived Joule).
planeOffset - Variable in class ffx.numerics.quickhull.Face
platform - Variable in class ffx.openmm.Context: The platform used for this context.
Platform - Class in ffx.openmm: A Platform defines an implementation of all the kernels needed to perform some calculation.
Platform - Enum Class in ffx.potential: Platform describes a set of force field implementations that include a pure Java reference implementation (FFX), and OpenMM implementations (Reference, CUDA and OpenCL).
Platform() - Constructor for class ffx.openmm.Platform: Default constructor.
Platform(PointerByReference) - Constructor for class ffx.openmm.Platform: OpenMM Platform constructor.
Platform(String) - Constructor for class ffx.openmm.Platform: OpenMM Platform constructor.
plus(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is (this + b).
plusIP(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: plusIP
Pm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
PMETimings - Class in ffx.potential.nonbonded.pme
PMETimings(int) - Constructor for class ffx.potential.nonbonded.pme.PMETimings
PNG - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
Po - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
POINT_RELATIVE - Static variable in class ffx.numerics.quickhull.QuickHull3D: Specifies that (on output) the vertex indices for a face should be numbered with respect to the original input points.
Point3d - Class in ffx.numerics.quickhull: A three-element spatial point.
Point3d() - Constructor for class ffx.numerics.quickhull.Point3d: Creates a Point3d and initializes it to zero.
Point3d(double, double, double) - Constructor for class ffx.numerics.quickhull.Point3d: Creates a Point3d with the supplied element values.
Point3d(Vector3d) - Constructor for class ffx.numerics.quickhull.Point3d: Creates a Point3d by copying a vector
pointBuffer - Variable in class ffx.numerics.quickhull.QuickHull3D
pointer - Variable in class ffx.openmm.Force: The forcePointer is allocated and deallocated by classes that extend OpenMMForce.
pointer - Variable in class ffx.openmm.Integrator: OpenMM Integrator pointer.
pointer - Variable in class ffx.openmm.TabulatedFunction: The pointer is allocated and deallocated by classes that extend TabulatedFunction.
pointer - Variable in class ffx.openmm.VirtualSite: The pointer is allocated and deallocated by classes that extend VirtualSite.
pointGroupName - Variable in class ffx.crystal.SpaceGroup: Point group name.
points - Variable in class ffx.numerics.integrate.FunctionDataCurve: Function values.
POINTS - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
pointsNeeded() - Method in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType: Returns the number of points required for integration.
polarizability - Variable in class ffx.potential.parameters.PolarizeType: Isotropic polarizability in units of Angstroms^3.
PolarizableMultipole - Class in ffx.numerics.multipole: The PolarizableMultipole class defines a polarizable multipole.
PolarizableMultipole() - Constructor for class ffx.numerics.multipole.PolarizableMultipole: PolarizableMultipole constructor with zero moments.
PolarizableMultipole(double[], double[], double[]) - Constructor for class ffx.numerics.multipole.PolarizableMultipole: PolarizableMultipole constructor.
PolarizableMultipole(double[], double[], double[], double) - Constructor for class ffx.numerics.multipole.PolarizableMultipole: PolarizableMultipole constructor.
PolarizableMultipoleSIMD - Class in ffx.numerics.multipole: The PolarizableMultipole class defines a polarizable multipole.
PolarizableMultipoleSIMD() - Constructor for class ffx.numerics.multipole.PolarizableMultipoleSIMD: PolarizableMultipole constructor with zero moments.
PolarizableMultipoleSIMD(double[][], double[][], double[][]) - Constructor for class ffx.numerics.multipole.PolarizableMultipoleSIMD: PolarizableMultipole constructor.
polarization - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion: Treatment of polarization.
polarization - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Polarization modes include "direct", in which induced dipoles do not interact, and "mutual" that converges the self-consistent field to a tolerance specified by the "polar-eps" keyword.
Polarization - Enum Class in ffx.potential.nonbonded.pme
polarizationEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Polarization energy = inducedRealSpaceEnergy + inducedSelfEnergy + inducedReciprocalEnergy.
polarizationEnergy(PolarizableMultipole) - Method in class ffx.numerics.multipole.MultipoleTensor: Contract an induced dipole with the potential and its derivatives.
polarizationEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Compute the polarization energy.
polarizationEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKEnergyQI: Compute the polarization energy.
polarizationEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Polarization Energy.
polarizationEnergy(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorQI: GK Polarization Energy.
polarizationEnergy(PolarizableMultipole, PolarizableMultipole, double) - Method in class ffx.numerics.multipole.GKTensorQI: GK Polarization Energy.
polarizationEnergy(PolarizableMultipole, PolarizableMultipole, double) - Method in class ffx.numerics.multipole.MultipoleTensor: Polarization Energy.
polarizationEnergy(PolarizableMultipole, PolarizableMultipole, DoubleVector) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Polarization Energy.
polarizationEnergy(PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Contract an induced dipole with the potential and its derivatives.
polarizationEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Compute the polarization energy.
polarizationEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Compute the polarization energy.
polarizationEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Polarization Energy.
polarizationEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Polarization Energy.
polarizationEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Polarization Energy.
polarizationEnergy(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Polarization Energy.
polarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Compute the polarization energy and gradient.
polarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKEnergyQI: Compute the polarization energy and gradient.
polarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Polarization Energy and Gradient.
polarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Polarization Energy and Gradient.
polarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Polarization Energy and Gradient.
polarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Compute the polarization energy and gradient.
polarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Compute the polarization energy and gradient.
polarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Polarization Energy and Gradient.
polarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Polarization Energy and Gradient.
polarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Polarization Energy and Gradient.
polarizationEnergyBorn(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Polarization Energy.
polarizationEnergyBorn(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorQI: GK Polarization Energy.
polarizationEnergyBorn(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Polarization Energy.
polarizationEnergyBorn(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Polarization Energy.
polarizationEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorGlobal: GK Direct Polarization Born grad.
polarizationEnergyBornGrad(PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.GKTensorQI: GK Direct Polarization Born grad.
polarizationEnergyBornGrad(PolarizableMultipole, PolarizableMultipole, boolean) - Method in class ffx.numerics.multipole.GKEnergyGlobal: Compute the Born chain-rule term for the polarization energy.
polarizationEnergyBornGrad(PolarizableMultipole, PolarizableMultipole, boolean) - Method in class ffx.numerics.multipole.GKEnergyQI: Compute the Born chain-rule term for the polarization energy.
polarizationEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: GK Direct Polarization Born grad.
polarizationEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.GKTensorQISIMD: GK Direct Polarization Born grad.
polarizationEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, boolean) - Method in class ffx.numerics.multipole.GKEnergyGlobalSIMD: Compute the Born chain-rule term for the polarization energy.
polarizationEnergyBornGrad(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, boolean) - Method in class ffx.numerics.multipole.GKEnergyQISIMD: Compute the Born chain-rule term for the polarization energy.
PolarizationEnergyRegion - Class in ffx.potential.nonbonded.pme: Parallel computation of the polarization energy as sum over atomic contributions (-1/2 u.E).
PolarizationEnergyRegion(int, double) - Constructor for class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
polarizationEnergyS(PolarizableMultipole) - Method in class ffx.numerics.multipole.MultipoleTensor: Contract an induced dipole with the potential and its derivatives.
polarizationEnergyS(PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Contract an induced dipole with the potential and its derivatives.
polarizationGroup - Variable in class ffx.potential.parameters.PolarizeType: Connected types in the polarization group of each atom (can be null).
polarizationScale - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: When computing the polarization energy at L there are 3 pieces.
POLARIZE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
PolarizeType - Class in ffx.potential.parameters: The PolarizeType class defines an isotropic atomic polarizability.
PolarizeType(int, double, double, double, int[]) - Constructor for class ffx.potential.parameters.PolarizeType: PolarizeType Constructor.
PolarizeType(PolarizeType, double) - Constructor for class ffx.potential.parameters.PolarizeType: Construct a PolarizeType from a reference type and updated polarizability.
polLambda - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: The polarization Lambda value goes from 0.0 .. 1.0 as the global lambda value varies between polLambdaStart .. polLambadEnd.
polLambdaEnd - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
polLambdaExponent - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Power on L in front of the polarization energy.
polLambdaStart - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Start turning on polarization later in the Lambda path to prevent SCF convergence problems when atoms nearly overlap.
POLY - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
POLY - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
Polymer - Class in ffx.potential.bonded: The Polymer class encapsulates a peptide or nucleotide chain.
Polymer(Character, String) - Constructor for class ffx.potential.bonded.Polymer: Polymer constructor.
Polymer(Character, String, boolean) - Constructor for class ffx.potential.bonded.Polymer: Polymer constructor.
Polymer(Character, String, MSNode) - Constructor for class ffx.potential.bonded.Polymer: Polymer Constructor.
POLYMER - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
PolymerUtils - Class in ffx.potential.bonded: Utilities for creating polymers.
PolymerUtils() - Constructor for class ffx.potential.bonded.PolymerUtils
polyMul1(double[], double[], int, int, double[], int[]) - Method in class ffx.potential.utils.LoopClosure: Polynomial multiply 1.
polyMul2(double[][], double[][], int[], int[], double[][], int[]) - Method in class ffx.potential.utils.LoopClosure: Polynomial multiplication 2.
polyMulSub1(double[], double[], double[], double[], int, int, int, int, double[], int[]) - Method in class ffx.potential.utils.LoopClosure: Polynomial multiply subtraction 1.
polyMulSub2(double[][], double[][], double[][], double[][], int[], int[], int[], int[], double[][], int[]) - Method in class ffx.potential.utils.LoopClosure: Polynomial multiplication subtraction 2.
POLYNOMIAL - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: Smooth the boundar of the classic model using a cubic polynomial switch (default).
PolynomialCurve - Class in ffx.numerics.integrate: A PolynomialCurve describes points along a polynomial function.
PolynomialCurve(double[], boolean, double[]) - Constructor for class ffx.numerics.integrate.PolynomialCurve: Default constructor, assumes constant-width bins.
PolynomialCurve(double[], double[]) - Constructor for class ffx.numerics.integrate.PolynomialCurve: Default constructor, assumes constant-width bins.
polynomialPredictor(LambdaMode, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Polynomial predictor for the mutual induced dipoles.
polySub1(double[], double[], int[], int[], double[], int[]) - Method in class ffx.potential.utils.LoopClosure: Polynomial subtraction 1.
polySub2(double[][], double[][], int[], int[], double[][], int[]) - Method in class ffx.potential.utils.LoopClosure: Polynomial subtraction 2.
PonderAndRichards - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary
PortUtils - Class in ffx.utilities: Port Utilities.
POST_METHOD - Static variable in class edu.rit.http.HttpRequest: The POST method string, "POST".
postCriterion - Variable in class ffx.ui.behaviors.MouseBehavior
poster - Variable in class ffx.ui.behaviors.MouseBehavior
POSTFIX - Enum constant in enum class ffx.potential.parsers.SystemFilter.Versioning
POSTFIX_ABSOLUTE - Enum constant in enum class ffx.potential.parsers.SystemFilter.Versioning
postForce() - Method in class ffx.potential.extended.ExtendedSystem: Applies a chain rule term to the derivative to account for taking a derivative of lambda = sin(theta)^2
postForce(double[]) - Method in class ffx.algorithms.dynamics.integrators.BetterBeeman: Integrator post-force evaluation operation.
postForce(double[]) - Method in class ffx.algorithms.dynamics.integrators.Integrator: Integrator post-force evaluation operation.
postForce(double[]) - Method in class ffx.algorithms.dynamics.integrators.Respa: Integrator post-force evaluation operation.
postForce(double[]) - Method in class ffx.algorithms.dynamics.integrators.Stochastic: Integrator post-force evaluation operation.
postForce(double[]) - Method in class ffx.algorithms.dynamics.integrators.VelocityVerlet: Integrator post-force evaluation operation.
postForce1(MolecularAssembly, double) - Method in class ffx.algorithms.dynamics.integrators.Rattle: postForce1.
postForce2(double) - Method in class ffx.algorithms.dynamics.integrators.Rattle: postForce2.
postRender() - Method in class ffx.ui.GraphicsCanvas
postSwap() - Method in class ffx.ui.GraphicsCanvas
potential - Variable in class ffx.algorithms.commands.Dynamics: Creation of a public field to try and make the JUnit test work, original code does not declare this as a public field.
potential - Variable in class ffx.algorithms.commands.test.FindRestraints: Creation of a public field to try and make the JUnit test work, original code does not declare this as a public field.
potential - Variable in class ffx.algorithms.commands.Thermodynamics
potential - Variable in class ffx.algorithms.optimize.Minimize: The potential energy to optimize.
potential - Variable in class ffx.algorithms.optimize.PhMinimize: The potential energy to optimize.
potential - Variable in class ffx.algorithms.optimize.RotamerOptimization: The Potential to evaluate during rotamer optimization.
potential - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: The potential energy of the system.
potential - Variable in class ffx.ui.commands.SimulationUpdate
Potential - Interface in ffx.numerics: The Potential interface defines methods required by an optimizer or molecular dynamics.
POTENTIAL - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
POTENTIAL - Enum constant in enum class ffx.numerics.multipole.GKTensorMode: The tensor is for the GK potential energy.
Potential.STATE - Enum Class in ffx.numerics: Set the state of the Potential to include FAST varying energy terms, SLOW varying energy terms or BOTH.
Potential.VARIABLE_TYPE - Enum Class in ffx.numerics: Recognized variables currently include Cartesian coordinates and OTHER.
PotentialCommand - Class in ffx.potential.cli: Base class for scripts in the Potentials package, providing some key functions.
PotentialCommand() - Constructor for class ffx.potential.cli.PotentialCommand: Default constructor.
PotentialCommand(FFXBinding) - Constructor for class ffx.potential.cli.PotentialCommand: Create a Script using the supplied Binding.
PotentialCommand(String[]) - Constructor for class ffx.potential.cli.PotentialCommand: Create a Script using the supplied command line arguments.
potentialEnergy - Variable in class ffx.potential.openmm.OpenMMState: Potential energy (kcal/mol).
potentialEnergy() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the potentialEnergy record component.
PotentialFunctionParameter - Enum constant in enum class ffx.utilities.PropertyGroup: Potential function parameter.
potentialFunctions - Variable in class ffx.potential.cli.PotentialCommand: An instance of PotentialFunctions passed into the current context.
PotentialFunctionSelection - Enum constant in enum class ffx.utilities.PropertyGroup: Potential function selection.
potentialMultipoleI(PolarizableMultipole, double[], int, int, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Collect the field at R due to Q multipole moments at the origin (site I).
potentialScript - Variable in class ffx.potential.utils.PotentialTest
PotentialsFileOpener - Class in ffx.potential.utils: The PotentialsFileOpener class specifies a Runnable object which is constructed with a File and, when run, allows returning any opened MolecularAssembly objects and their associated properties.
PotentialsFileOpener(File) - Constructor for class ffx.potential.utils.PotentialsFileOpener: Constructor for PotentialsFileOpener.
PotentialsFunctions - Interface in ffx.potential.utils: PotentialsFunctions describes core functionality for many Force Field X algorithms and scripts, such as opening and closing structure files, basic force field energy evaluations, etc.
PotentialsUtils - Class in ffx.potential.utils: PotentialsUtils implements core functionality for many Force Field X algorithms and scripts, such as opening and closing structure files, basic force field evaluations, etc.
PotentialsUtils() - Constructor for class ffx.potential.utils.PotentialsUtils: Constructor for PotentialsUtils.
PotentialTest - Class in ffx.potential.utils: PotentialTest extends BaseFFXTest to include support for:
1) Creating a Binding before each test.
PotentialTest() - Constructor for class ffx.potential.utils.PotentialTest
PowerSwitch - Class in ffx.numerics.switching: A PowerSwitch interpolates between 0 and 1 vi f(x) = (ax)^beta, where x must be between 0 and 1/a.
PowerSwitch() - Constructor for class ffx.numerics.switching.PowerSwitch: Default Constructor of the PowerSwitch: constructs a linear switch.
PowerSwitch(double, double) - Constructor for class ffx.numerics.switching.PowerSwitch: Constructor of the PowerSwitch.
Pr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
predictHillCoeffandPka(double[], double[]) - Static method in class ffx.potential.parameters.TitrationUtils: Predict pKa from a set of residue fractions (deprotonated / (deprotonated + protonated)).
predictorCount - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Induced dipole predictor count.
predictorInducedDipole - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Dimensions of [mode][predictorOrder][nAtoms][3]
predictorInducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Dimensions of [mode][predictorOrder][nAtoms][3]
predictorOrder - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Induced dipole predictor order.
predictorStartIndex - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Induced dipole predictor index.
preferredDimension(int) - Static method in class ffx.numerics.fft.Complex: Check if a dimension is a preferred dimension.
PREFIX - Enum constant in enum class ffx.potential.parsers.SystemFilter.Versioning
PREFIX_ABSOLUTE - Enum constant in enum class ffx.potential.parsers.SystemFilter.Versioning
preForce() - Method in class ffx.potential.extended.ExtendedSystem: Processes lambda values based on propagation of theta value from Stochastic integrator in Molecular dynamics
preForce(Potential) - Method in class ffx.algorithms.dynamics.integrators.BetterBeeman: Integrator pre-force evaluation operation.
preForce(Potential) - Method in class ffx.algorithms.dynamics.integrators.Integrator: Integrator pre-force evaluation operation.
preForce(Potential) - Method in class ffx.algorithms.dynamics.integrators.Respa: Integrator pre-force evaluation operation.
preForce(Potential) - Method in class ffx.algorithms.dynamics.integrators.Stochastic: Integrator pre-force evaluation operation.
preForce(Potential) - Method in class ffx.algorithms.dynamics.integrators.VelocityVerlet: Integrator pre-force evaluation operation.
PrepareSpaceGroups - Class in ffx.potential.commands: Create sub-directories for selected space groups.
PrepareSpaceGroups() - Constructor for class ffx.potential.commands.PrepareSpaceGroups
PrepareSpaceGroups(FFXBinding) - Constructor for class ffx.potential.commands.PrepareSpaceGroups
PrepareSpaceGroups(String[]) - Constructor for class ffx.potential.commands.PrepareSpaceGroups
prepareToRead(InputStream) - Method in class edu.rit.io.DoubleMatrixFile: Prepare to read this matrix file from the given input stream.
prepareToWrite(OutputStream) - Method in class edu.rit.io.DoubleMatrixFile: Prepare to write this matrix file to the given output stream.
prepend(SymOp) - Method in class ffx.crystal.SymOp: Return the combined SymOp that is equivalent to first applying the argument and then this SymOp.
prePrunePairs(Residue[]) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Pre-prunes any pairs that have a pair-energy of Double.NaN before pruning and eliminations happen.
prePruneSelves(Residue[]) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Pre-prunes any selves that have a self-energy of Double.NaN before pruning and eliminations happen.
preSaveOperations(ForceFieldEnergy) - Method in class ffx.potential.cli.SaveOptions: Performs key operations prior to saving to disc, such as application of geometric constraints.
preSaveOperations(MolecularAssembly) - Method in class ffx.potential.cli.SaveOptions: Performs key operations prior to saving to disc, such as application of geometric constraints.
PRESCON - Static variable in class ffx.utilities.Constants: Conversion from kcal/mol/Ang^3 to Atm.
pressure - Variable in class ffx.ui.commands.SimulationUpdate
prev - Variable in class ffx.numerics.quickhull.HalfEdge: Previous half-edge in the triangle.
previousVersion(File) - Static method in class ffx.potential.parsers.SystemFilter: previousVersion
previousVersion(File) - Static method in class ffx.utilities.TinkerUtils: Get the previous file based on the TINKER scheme.
print - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Print detailed energy information.
print() - Method in class ffx.potential.bonded.Atom: Prints the MSNode's name
print() - Method in class ffx.potential.bonded.BondedTerm: Prints the MSNode's name
print() - Method in class ffx.potential.bonded.MSGroup: Prints the MSNode's name
print() - Method in class ffx.potential.bonded.MSNode: Prints the MSNode's name
print() - Method in class ffx.potential.bonded.Residue: Prints the MSNode's name
print() - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
print() - Method in class ffx.potential.parameters.BaseType: Print this to System.out.
print() - Method in class ffx.potential.parameters.ForceField: print
print() - Method in class ffx.ui.commands.SimulationDefinition: print
print() - Method in class ffx.ui.commands.SimulationMessage: print
print() - Method in class ffx.ui.commands.SimulationUpdate: print
print() - Method in class ffx.utilities.Keyword: print
print(PrintStream) - Method in class ffx.numerics.quickhull.QuickHull3D: Prints the vertices and faces of this hull to the stream ps.
print(PrintStream, int) - Method in class ffx.numerics.quickhull.QuickHull3D: Prints the vertices and faces of this hull to the stream ps.
print(String) - Method in class ffx.potential.parameters.ForceField: print
print(Level) - Method in class ffx.potential.bonded.Atom
printEnergyUpdate() - Method in class ffx.realspace.RealSpaceData: printEnergyUpdate
printEnergyUpdate() - Method in interface ffx.xray.DataContainer: printEnergyUpdate
printEnergyUpdate() - Method in class ffx.xray.DiffractionData: printEnergyUpdate
printFiles - Variable in class ffx.algorithms.optimize.RotamerOptimization: Sets whether files should be printed; true for standalone applications, false for some applications which use rotamer optimization as part of a larger process.
printHeader() - Method in class ffx.xray.parsers.MTZFilter: printHeader
printOptimizationHeader() - Method in class ffx.realspace.RealSpaceData: printOptimizationHeader
printOptimizationHeader() - Method in interface ffx.xray.DataContainer: printOptimizationHeader
printOptimizationHeader() - Method in class ffx.xray.DiffractionData: printOptimizationHeader
printOptimizationUpdate() - Method in class ffx.realspace.RealSpaceData: printOptimizationUpdate
printOptimizationUpdate() - Method in interface ffx.xray.DataContainer: printOptimizationUpdate
printOptimizationUpdate() - Method in class ffx.xray.DiffractionData: printOptimizationUpdate
printPoints(PrintStream) - Method in class ffx.numerics.quickhull.QuickHull3D: print all points to the print stream (very point a line)
printProtonationRatios() - Method in class ffx.potential.extended.ExtendedSystem: Calculate the Deprotonation Fraction from the ESV histogram
printRealSpaceTimings(int, PermanentFieldRegion, RealSpaceEnergyRegion) - Method in class ffx.potential.nonbonded.pme.PMETimings
printScaleAndR() - Method in class ffx.xray.DiffractionData: Print scale and R statistics for all datasets associated with the model.
printStackTrace(PrintStream) - Method in exception class edu.rit.pj.MultipleParallelException: Print this throwable and its backtrace to the specified print stream.
printStackTrace(PrintWriter) - Method in exception class edu.rit.pj.MultipleParallelException: Print this throwable and its backtrace to the specified print writer.
printStats() - Method in class ffx.xray.DiffractionData: Print all statistics for all datasets associated with the model.
PrintStreamLogger - Class in edu.rit.util: Class PrintStreamLogger provides an object that logs messages to a print stream.
PrintStreamLogger() - Constructor for class edu.rit.util.PrintStreamLogger: Construct a new print stream logger that logs to System.err.
PrintStreamLogger(PrintStream) - Constructor for class edu.rit.util.PrintStreamLogger: Construct a new print stream logger that logs to the given print stream.
printTensor() - Method in class ffx.algorithms.optimize.CrystalMinimize: Print out the partial derivatives of the Energy with respect to components of the 3 vectors that define the primitive cell.
printTimings() - Method in class ffx.potential.nonbonded.ReciprocalSpace: printTimings.
PrmToProperty - Class in ffx.potential.commands.test: The PrmToProperty script converts a TINKER *.prm file to Java properties.
PrmToProperty() - Constructor for class ffx.potential.commands.test.PrmToProperty: PrmToProperty Constructor.
PrmToProperty(FFXBinding) - Constructor for class ffx.potential.commands.test.PrmToProperty: PrmToProperty Constructor.
PrmToProperty(String[]) - Constructor for class ffx.potential.commands.test.PrmToProperty: PrmToProperty constructor that sets the command line arguments.
PRO - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
probe - Variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Water probe radius.
process(HttpRequest, HttpResponse) - Method in class edu.rit.http.HttpServer: Process the given HTTP request.
process(Set<? extends TypeElement>, RoundEnvironment) - Method in class ffx.utilities.PropertyProcessor: Processes a set of annotation types on type elements originating from the prior round and returns whether these annotations are claimed by this processor.
processData(List<String>, MolecularAssembly) - Method in class ffx.realspace.cli.RealSpaceOptions: Process input to collect Real Space Files.
processData(List<String>, MolecularAssembly[]) - Method in class ffx.xray.cli.XrayOptions: Process input to collect Diffraction Files.
processFile(TopologyOptions, MolecularAssembly, int) - Method in class ffx.potential.cli.AlchemicalOptions: Performs processing on a MolecularAssembly for alchemistry.
ProcessInfo - Class in edu.rit.pj.cluster: Class ProcessInfo provides a record of information about one job backend process in the PJ cluster middleware.
ProcessInfo(ProcessInfo.State, String, int, JobBackendRef, InetSocketAddress, InetSocketAddress, InetSocketAddress, Timer, Timer, int) - Constructor for class edu.rit.pj.cluster.ProcessInfo: Construct a new job information record.
ProcessInfo.State - Enum Class in edu.rit.pj.cluster: The state of a job backend process.
processMouseEvent(MouseEvent) - Method in class ffx.ui.behaviors.MouseBehavior: processMouseEvent
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.potential.Renderer
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.MouseBehavior
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.MouseOrbit
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.MouseProperties
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.MouseRotate
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.MouseSelection
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.MouseTranslate
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.MouseZoom
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.behaviors.PickMouseBehavior
processStimulus(Iterator<WakeupCriterion>) - Method in class ffx.ui.GraphicsEvents: Most of the logic for mouse interaction with the Scenegraph is here.
product - Variable in class ffx.numerics.fft.MixedRadixFactor: The product of all factors applied so far.
product() - Method in record class ffx.numerics.fft.PassConstants: Returns the value of the product record component.
PRODUCT - Static variable in class edu.rit.pj.reduction.ByteOp: The byte product binary operation.
PRODUCT - Static variable in class edu.rit.pj.reduction.DoubleOp: The double product binary operation.
PRODUCT - Static variable in class edu.rit.pj.reduction.FloatOp: The float product binary operation.
PRODUCT - Static variable in class edu.rit.pj.reduction.IntegerOp: The integer product binary operation.
PRODUCT - Static variable in class edu.rit.pj.reduction.LongOp: The long product binary operation.
PRODUCT - Static variable in class edu.rit.pj.reduction.ShortOp: The short product binary operation.
ProgressiveAlignmentOfCrystals - Class in ffx.potential.utils: Class ProgressiveAlignmentOfCrystals holds the majority of the functionality necessary to quantify crystal similarity following the PAC method.
ProgressiveAlignmentOfCrystals(SystemFilter, SystemFilter, boolean) - Constructor for class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Constructor for the ProgressiveAlignmentOfCrystals class.
PROLINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
properties - Variable in class ffx.potential.parsers.SystemFilter: Properties associated with this file.
PROPERTIES - Static variable in interface ffx.ui.behaviors.MouseBehaviorCallback: Constant PROPERTIES=5
PROPERTIES - Static variable in interface ffx.ui.behaviors.PickingCallback: Constant PROPERTIES=5
propertyGroup() - Element in annotation interface ffx.utilities.FFXProperty: The Property Group this FFXKeyword belongs to.
PropertyGroup - Enum Class in ffx.utilities: The Keyword Group for an FFX Keyword.
PropertyProcessor - Class in ffx.utilities: Log out FFXProperty Annotations for documentation purposes.
PropertyProcessor() - Constructor for class ffx.utilities.PropertyProcessor: Default constructor.
protForm - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
Proxy - Class in edu.rit.pj.cluster: Class Proxy is the abstract base class for a proxy object for sending messages to a PJ process.
Proxy(ChannelGroup, Channel) - Constructor for class edu.rit.pj.cluster.Proxy: Construct a new proxy.
prunePairClashes(Residue[]) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Prunes rotamer ri of residue i if all ri-j pair energies are worse than the best i-j pair by some threshold value; additionally prunes ri-rj pairs if they exceed the best i-j pair by a greater threshold value; additionally performs this in reverse (searches over j-i).
pruneSingleClashes(Residue[]) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Uses calculated energies to prune rotamers based on a threshold distance from that residue's minimum energy rotamer (by default 20 kcal/mol).
PSEC_TO_FSEC - Static variable in class ffx.utilities.Constants: Constant PSEC_TO_FSEC=1000
PSU - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
Pt - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Pu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
publish(LogRecord) - Method in class ffx.ui.LogHandler
put(int, boolean) - Method in class edu.rit.mp.BooleanBuf: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.BooleanArrayBuf: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.BooleanItemBuf: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.BooleanMatrixBuf: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.EmptyBooleanBuf: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf: Store the given item in this buffer.
put(int, boolean) - Method in class edu.rit.mp.buf.SharedBooleanBuf: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.ByteArrayBuf_1: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.ByteArrayBuf: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.ByteItemBuf: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.ByteMatrixBuf: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.EmptyByteBuf: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.SharedByteArrayBuf: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.buf.SharedByteBuf: Store the given item in this buffer.
put(int, byte) - Method in class edu.rit.mp.ByteBuf: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.CharacterArrayBuf: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.CharacterItemBuf: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.CharacterMatrixBuf: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.EmptyCharacterBuf: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.buf.SharedCharacterBuf: Store the given item in this buffer.
put(int, char) - Method in class edu.rit.mp.CharacterBuf: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.DoubleArrayBuf: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.DoubleItemBuf: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.DoubleMatrixBuf: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.EmptyDoubleBuf: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.buf.SharedDoubleBuf: Store the given item in this buffer.
put(int, double) - Method in class edu.rit.mp.DoubleBuf: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.EmptyFloatBuf: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.FloatArrayBuf_1: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.FloatArrayBuf: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.FloatItemBuf: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.FloatMatrixBuf: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.buf.SharedFloatBuf: Store the given item in this buffer.
put(int, float) - Method in class edu.rit.mp.FloatBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.EmptyIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.IntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.IntegerItemBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.IntegerMatrixBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.IntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.Signed16BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.Signed8BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf: Store the given item in this buffer.
put(int, int) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.EmptyLongBuf: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.LongArrayBuf_1: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.LongArrayBuf: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.LongItemBuf: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.LongMatrixBuf_1: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.LongMatrixBuf: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.SharedLongArrayBuf: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.buf.SharedLongBuf: Store the given item in this buffer.
put(int, long) - Method in class edu.rit.mp.LongBuf: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.EmptyShortBuf: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.SharedShortArrayBuf: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.SharedShortBuf: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.ShortArrayBuf_1: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.ShortArrayBuf: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.ShortItemBuf: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.buf.ShortMatrixBuf: Store the given item in this buffer.
put(int, short) - Method in class edu.rit.mp.ShortBuf: Store the given item in this buffer.
put(int, Object) - Method in class edu.rit.mp.buf.EmptyObjectBuf: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.ObjectArrayBuf_1: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.ObjectArrayBuf: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.ObjectItemBuf: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.ObjectMatrixBuf_1: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.ObjectMatrixBuf: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf_1: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.buf.SharedObjectBuf: Store the given item in this buffer.
put(int, T) - Method in class edu.rit.mp.ObjectBuf: Store the given item in this buffer.
put(String, byte[]) - Method in class edu.rit.pj.cluster.ResourceCache: Store the given resource content under the given resource name in this resource cache.
px - Variable in class ffx.numerics.multipole.PolarizableMultipole: Induced dipole chain rule x-component.
px - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Induced dipole chain rule x-component.
py - Variable in class ffx.numerics.multipole.PolarizableMultipole: Induced dipole chain rule y-component.
py - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Induced dipole chain rule y-component.
pz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Induced dipole chain rule z-component.
pz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Induced dipole chain rule z-component.

Q

q - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
q - Variable in class ffx.numerics.multipole.PolarizableMultipole: Partial charge.
q - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Partial charge.
Q - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
QI - Enum constant in enum class ffx.numerics.multipole.CoordinateSystem: Quasi-internal coordinate system.
QIFrame - Class in ffx.numerics.multipole: The QIFrame class defines a quasi-internal frame between two atoms.
QIFrame() - Constructor for class ffx.numerics.multipole.QIFrame: QIFrame constructor
QIFrame(double[]) - Constructor for class ffx.numerics.multipole.QIFrame: QIFrame constructor.
QIFrame(double, double, double) - Constructor for class ffx.numerics.multipole.QIFrame: QIFrame constructor.
QIFrameSIMD - Class in ffx.numerics.multipole: The QIFrame class defines a quasi-internal frame between two atoms.
QIFrameSIMD() - Constructor for class ffx.numerics.multipole.QIFrameSIMD: QIFrame constructor
QIFrameSIMD(DoubleVector[]) - Constructor for class ffx.numerics.multipole.QIFrameSIMD: QIFrame constructor.
QIFrameSIMD(DoubleVector, DoubleVector, DoubleVector) - Constructor for class ffx.numerics.multipole.QIFrameSIMD: QIFrame constructor.
quadForm(double[][]) - Method in class ffx.crystal.HKL: quadForm
quadForm(double[], double[][]) - Static method in class ffx.numerics.math.ScalarMath: quadForm
quadratic - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
quadrupole - Variable in class ffx.potential.parameters.MultipoleType: Atomic quadrupole. 3 x 3 (e Angstroms^2).
QUADRUPOLE - Enum constant in enum class ffx.numerics.multipole.GKMultipoleOrder: Quadrupole potential.
quadrupoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Permanent multipole energy and gradient using the GK quadrupole tensor.
quadrupoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Permanent multipole energy and gradient using the GK quadrupole tensor.
quadrupoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Permanent multipole energy and gradient using the GK quadrupole tensor.
quadrupoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Permanent multipole energy and gradient using the GK quadrupole tensor.
quadrupoleIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to quadrupole I at site K.
quadrupoleIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to quadrupole I at site K.
quadrupoleIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to quadrupole I at site K.
quadrupoleIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the field components due to site I quadrupole at site K.
quadrupoleIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the field components due to site I quadrupole at site K.
quadrupoleIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the field components due to site I quadrupole at site K.
quadrupoleKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to multipole K at site I.
quadrupoleKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to multipole K at site I.
quadrupoleKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to multipole K at site I.
quadrupoleKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD: Compute the field components due to site K quadrupole at site I.
quadrupoleKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Compute the field components due to site K quadrupole at site I.
quadrupoleKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the field components due to site K quadrupole at site I.
quadrupolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Quadrupole Polarization Energy and Gradient.
quadrupolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Quadrupole Polarization Energy and Gradient.
quadrupolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Quadrupole Polarization Energy and Gradient.
quadrupolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Quadrupole Polarization Energy and Gradient.
quadrupoleTorque(PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the torque on a permanent quadrupole.
quadrupoleTorque(PolarizableMultipoleSIMD, DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Compute the torque on a permanent quadrupole.
QuadTopologyEnergy - Class in ffx.potential: Implements an error-canceling quad topology, where two large dual-topology simulation legs are run simultaneously to arrive at a small sum.
QuadTopologyEnergy(DualTopologyEnergy, DualTopologyEnergy) - Constructor for class ffx.potential.QuadTopologyEnergy: General structure: first layer will be the "A/B" layer, consisting of the two dual topologies.
QuadTopologyEnergy(DualTopologyEnergy, DualTopologyEnergy, List<Integer>, List<Integer>) - Constructor for class ffx.potential.QuadTopologyEnergy: General structure: first layer will be the "A/B" layer, consisting of the two dual topologies.
quartic - Variable in class ffx.potential.parameters.AngleType: Quartic coefficient in angle bending potential.
quartic - Variable in class ffx.potential.parameters.BondType: Quartic coefficient in bond stretch potential.
quartic - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Quartic coefficient in out-of-plane angle bending potential.
quartic - Variable in class ffx.potential.parameters.UreyBradleyType: Quartic coefficient in bond stretch potential.
QUARTIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
QuasiLinearThetaMap - Class in ffx.numerics.func1d: A QuasiLinearThetaMap implements a map of theta[-pi, +pi] to lambda[0,1] in a mostly-linear fashion (i.e. rectangular sampling of theta produces roughly rectangular sampling of lambda).
QuasiLinearThetaMap() - Constructor for class ffx.numerics.func1d.QuasiLinearThetaMap: Constructs a QuasiLinearThetaMap with a theta0 of 0.1.
QuasiLinearThetaMap(double) - Constructor for class ffx.numerics.func1d.QuasiLinearThetaMap: Constructs a QuasiLinearThetaMap which is roughly V-shaped from [-pi,+pi], is periodic, and uses trigonometric functions to spline between the linear ranges (theta0-pi, -theta0), (+theta0, pi-theta0) and the trigonometric interpolating regions [-pi, theta0-pi], [-theta0,+theta0] and [pi-theta0, pi].
QuickHull3D - Class in ffx.numerics.quickhull: Computes the convex hull of a set of three dimensional points.
QuickHull3D() - Constructor for class ffx.numerics.quickhull.QuickHull3D: Creates an empty convex hull object.
QuickHull3D(double[]) - Constructor for class ffx.numerics.quickhull.QuickHull3D: Creates a convex hull object and initializes it to the convex hull of a set of points whose coordinates are given by an array of doubles.
QuickHull3D(Point3d[]) - Constructor for class ffx.numerics.quickhull.QuickHull3D: Creates a convex hull object and initializes it to the convex hull of a set of points.
QUIET - Enum constant in enum class ffx.algorithms.dynamics.MDVerbosity
qxx - Variable in class ffx.numerics.multipole.PolarizableMultipole: Quadrupole xx-component multiplied by 1/3.
qxx - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Quadrupole xx-component multiplied by 1/3.
qxy - Variable in class ffx.numerics.multipole.PolarizableMultipole: Quadrupole xy-component multiplied by 2/3.
qxy - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Quadrupole xy-component multiplied by 2/3.
qxz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Quadrupole xz-component multiplied by 2/3.
qxz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Quadrupole xz-component multiplied by 2/3.
qyy - Variable in class ffx.numerics.multipole.PolarizableMultipole: Quadrupole yy-component multiplied by 1/3.
qyy - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Quadrupole yy-component multiplied by 1/3.
qyz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Quadrupole xz-component multiplied by 2/3.
qyz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Quadrupole xz-component multiplied by 2/3.
qzz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Quadrupole zz-component multiplied by 1/3.
qzz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Quadrupole zz-component multiplied by 1/3.

R

R - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
R - Variable in class ffx.numerics.multipole.MultipoleTensor: Separation distance.
R - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Separation distance.
R - Static variable in class ffx.utilities.Constants: Ideal gas constant in kcal/(mol*K) R = BOLTZMANN_SI * AVOGADRO * 0.001 * KJ_TO_KCAL R = 0.0019872042586408316
R_MIN - Enum constant in enum class ffx.potential.parameters.VDWType.RADIUS_TYPE
R000 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R001 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R002 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R003 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R004 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R005 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R006 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R010 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R011 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R012 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R013 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R014 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R015 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R020 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R021 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R022 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R023 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R024 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R030 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R031 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R032 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R033 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R040 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R041 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R042 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R050 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R051 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R060 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R100 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R101 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R102 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R103 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R104 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R105 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R110 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R111 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R112 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R113 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R114 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R120 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R121 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R122 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R123 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R130 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R131 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R132 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R140 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R141 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R150 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
r2 - Variable in class ffx.numerics.multipole.MultipoleTensor: Separation distance squared.
r2 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Separation distance squared.
R200 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R201 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R202 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R203 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R204 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R210 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R211 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R212 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R213 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R220 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R221 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R222 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R230 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R231 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R240 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R300 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R301 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R302 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R303 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R310 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R311 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R312 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R320 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R321 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R330 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R400 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R401 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R402 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R410 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R411 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R420 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R500 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R501 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R510 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
R600 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
Ra - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
radius - Static variable in class ffx.potential.bonded.RendererCache: Constant radius=1.0d
radius - Variable in class ffx.potential.parameters.VDWPairType: The radius of the minimum well depth energy (angstroms).
radius - Variable in class ffx.potential.parameters.VDWType: The radius of the minimum well depth energy (angstroms).
RADIUS - Enum constant in enum class ffx.potential.parameters.VDWType.RADIUS_SIZE
RADIUS_OF_GYRATION - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
radiusOfGyration(double[], double[]) - Static method in class ffx.potential.utils.StructureMetrics: Compute the average radius of gyration.
radiusOfGyration(double[], double[], double[], double[]) - Static method in class ffx.potential.utils.StructureMetrics: Compute the average radius of gyration.
radiusOfGyration(Atom[]) - Static method in class ffx.potential.utils.StructureMetrics: Compute the radius of gyration for all atoms in the supplied array.
radiusOfGyrationComponents(double[], double[], boolean) - Static method in class ffx.potential.utils.StructureMetrics: Compute the components that make up the radius of gyration about yz-, xz-, xy-planes.
radiusOfGyrationComponents(double[], double[], double[], double[], boolean) - Static method in class ffx.potential.utils.StructureMetrics: Compute the components that make up the radius of gyration tensor about yz-, xz-, xy-planes.
radiusOfGyrationComponents(Atom[]) - Static method in class ffx.potential.utils.StructureMetrics: Compute the radius of gyration for all atoms in the supplied array.
radiusRule - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Radius combining rule.
radiusSize - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Radius size in the parameter file (radius or diameter).
radiusType - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Radius type in the parameter file (R-Min or Sigma).
Ramachandran - Static variable in class ffx.potential.bonded.Residue: Constant Ramachandran="new String[17]"
random - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat: The random number generator that the Thermostat will use to initialize velocities.
random - Variable in class ffx.algorithms.mc.BoltzmannMC
Random - Class in edu.rit.util: Class Random is the abstract base class for a pseudorandom number generator (PRNG) designed for use in parallel scientific programming.
Random() - Constructor for class edu.rit.util.Random: Construct a new PRNG.
randomize(MolecularAssembly) - Method in class ffx.algorithms.cli.RandomUnitCellOptions: Randomize the unit cell for a MolecularAssembly.
randomParameters(double, double) - Method in class ffx.crystal.Crystal: Randomly set the unit cell vectors respecting the specified density.
randomParameters(double, double) - Method in class ffx.crystal.ReplicatesCrystal: Update the ReplicatesCrystal using random parameters with the target density.
RandomSample - Class in edu.rit.util: Class RandomSample provides objects that generate random samples from discrete sets.
RandomSubset - Class in edu.rit.util: Class RandomSubset provides an object that generates a random subset of a set of integers.
RandomSubset(Random, int) - Constructor for class edu.rit.util.RandomSubset: Construct a new random subset object for the original set consisting of the integers from 0 through N−1 inclusive.
RandomSubset(Random, int, boolean) - Constructor for class edu.rit.util.RandomSubset: Construct a new random subset object for the original set consisting of the integers from 0 through N−1 inclusive.
randomSymOpFactory(double) - Static method in class ffx.crystal.SymOp: Generate a random Cartesian Symmetry Operator.
randomSymOpFactory(double[]) - Static method in class ffx.crystal.SymOp: Generate a random Cartesian Symmetry Operator.
randomSymopOptions - Variable in class ffx.algorithms.commands.Thermodynamics
RandomUnitCellOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that create randomized unit cells.
RandomUnitCellOptions() - Constructor for class ffx.algorithms.cli.RandomUnitCellOptions
Range - Class in edu.rit.util: Class Range provides a range of type int.
Range() - Constructor for class edu.rit.util.Range: Construct a new range object representing an empty range.
Range(int, int) - Constructor for class edu.rit.util.Range: Construct a new range object with the given lower bound and upper bound.
Range(int, int, int) - Constructor for class edu.rit.util.Range: Construct a new range object with the given lower bound, upper bound, and stride.
Range(Range) - Constructor for class edu.rit.util.Range: Construct a new range object that is a copy of the given range object.
rangeRegEx - Static variable in class ffx.potential.cli.AlchemicalOptions: A regular expression used to parse ranges of atoms.
rank - Variable in class edu.rit.pj.cluster.ProcessInfo: The job backend process's rank.
rank - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: Rank of this process.
rank - Variable in class ffx.algorithms.thermodynamics.SendSynchronous: Rank of this process.
rank - Static variable in class ffx.crystal.SpaceGroupInfo: PDB space group ranking (as of Feb. 2017).
rank() - Method in class edu.rit.pj.Comm: Obtain the current process's rank in this communicator.
rank0 - Variable in class ffx.algorithms.optimize.RotamerOptimization: Flag to indicate if this is the master process.
RaoBlackwellEstimator - Class in ffx.algorithms.commands.test: Use the Rao-Blackwell Estimator to estimate a free energy difference of protonation for a CpHMD system.
RaoBlackwellEstimator() - Constructor for class ffx.algorithms.commands.test.RaoBlackwellEstimator: RaoBlackwellEstimator Constructor.
RaoBlackwellEstimator(FFXBinding) - Constructor for class ffx.algorithms.commands.test.RaoBlackwellEstimator: RaoBlackwellEstimator Constructor.
RaoBlackwellEstimator(String[]) - Constructor for class ffx.algorithms.commands.test.RaoBlackwellEstimator: RaoBlackwellEstimator constructor that sets the command line arguments.
Rattle - Class in ffx.algorithms.dynamics.integrators: The Rattle classes implements the RATTLE distance constraint method.
Rattle(int, MolecularAssembly, double[]) - Constructor for class ffx.algorithms.dynamics.integrators.Rattle: Constructor for Rattle.
Rb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
RBTorsionForce - Class in ffx.openmm: This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential.
RBTorsionForce() - Constructor for class ffx.openmm.RBTorsionForce: Create a new RBTorsionForce.
re() - Method in class ffx.numerics.math.ComplexNumber: re
re(double) - Method in class ffx.numerics.math.ComplexNumber: re
Re - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
read - Variable in class ffx.ui.commands.SimulationDefinition
read - Variable in class ffx.ui.commands.SimulationUpdate
read() - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read all matrix element segments from the input stream.
read() - Method in class edu.rit.pj.cluster.BackendFileInputStream: Read a byte from this input stream.
read() - Method in class ffx.potential.parsers.InducedFilter: read
read(byte[]) - Method in class edu.rit.pj.cluster.BackendFileInputStream: Read the given byte array from this input stream.
read(byte[], int, int) - Method in class edu.rit.pj.cluster.BackendFileInputStream: Read a portion of the given byte array from this input stream.
readBoolean() - Method in class edu.rit.io.DataInputStream: Read a Boolean value from this data input stream.
readByte() - Method in class edu.rit.io.DataInputStream: Read a byte value from this data input stream.
readChar() - Method in class edu.rit.io.DataInputStream: Read a character value from this data input stream.
readColSlice(Range) - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read all matrix element segments from the input stream, storing only the matrix elements in the given column slice.
readDistanceMatrix(String, int, int) - Method in class ffx.potential.parsers.DistanceMatrixFilter: Read in the distance matrix from a file.
readDistanceMatrix(String, List<double[]>) - Method in class ffx.potential.parsers.DistanceMatrixFilter: Read in the distance matrix from a file.
readDouble() - Method in class edu.rit.io.DataInputStream: Read a double value from this data input stream.
readDYN(File, Crystal, double[], double[], double[], double[]) - Method in class ffx.potential.parsers.DYNFilter: readDYN
readESV(File, double[], double[], double[], int[][][]) - Method in class ffx.potential.parsers.ESVFilter: readDYN
readESVInfoFrom(File) - Method in class ffx.potential.extended.ExtendedSystem: Method overwrites whatever is in the extended system at the time with the read data.
readExternal(ObjectInput) - Method in class edu.rit.pj.cluster.JobBackendMessage: Read this job backend message from the given object input stream.
readExternal(ObjectInput) - Method in class edu.rit.pj.cluster.JobFrontendMessage: Read this job frontend message from the given object input stream.
readExternal(ObjectInput) - Method in class edu.rit.pj.cluster.JobSchedulerMessage: Read this job scheduler message from the given object input stream.
readExternal(ObjectInput) - Method in class edu.rit.pj.job.Job: Read this job from the given object input stream.
readExternal(ObjectInput) - Method in class edu.rit.util.LongRange: Read this range from the given object input stream.
readExternal(ObjectInput) - Method in class edu.rit.util.Range: Read this range from the given object input stream.
readFile() - Method in class ffx.potential.parsers.BARFilter: Read TINKER bar files and parse the snapshots into energy arrays
readFile() - Method in class ffx.potential.parsers.CIFFilter: This method is different for each subclass and must be overridden.
readFile() - Method in class ffx.potential.parsers.INTFilter: This method is different for each subclass and must be overridden.
readFile() - Method in class ffx.potential.parsers.MergeFilter: This method is different for each subclass and must be overridden.
readFile() - Method in class ffx.potential.parsers.PDBFilter: Parse the PDB File
readFile() - Method in class ffx.potential.parsers.SystemFilter: This method is different for each subclass and must be overridden.
readFile() - Method in class ffx.potential.parsers.XPHFilter: This method is different for each subclass and must be overridden.
readFile() - Method in class ffx.potential.parsers.XYZFilter: This method is different for each subclass and must be overridden.
readFile() - Method in class ffx.ui.commands.SimulationFilter: This method is different for each subclass and must be overridden.
readFile(File, ReflectionList, DiffractionRefinementData, CompositeConfiguration) - Method in class ffx.xray.parsers.CIFFilter: Read in reflection file.
readFile(File, ReflectionList, DiffractionRefinementData, CompositeConfiguration) - Method in class ffx.xray.parsers.CNSFilter: Read in reflection file.
readFile(File, ReflectionList, DiffractionRefinementData, CompositeConfiguration) - Method in interface ffx.xray.parsers.DiffractionFileFilter: Read in reflection file.
readFile(File, ReflectionList, DiffractionRefinementData, CompositeConfiguration) - Method in class ffx.xray.parsers.MTZFilter: Read in reflection file.
readFile(String, RealSpaceRefinementData, CompositeConfiguration) - Method in class ffx.realspace.parsers.CCP4MapFilter: Read in a Real Space file.
readFile(String, RealSpaceRefinementData, CompositeConfiguration) - Method in interface ffx.realspace.parsers.RealSpaceFileFilter: Read in a Real Space file.
readFloat() - Method in class edu.rit.io.DataInputStream: Read a float value from this data input stream.
readHistogram(File) - Static method in class ffx.algorithms.thermodynamics.HistogramData: Unmarshall the histogram data.
readInt() - Method in class edu.rit.io.DataInputStream: Read an integer value from this data input stream.
readLambdaData(File) - Static method in class ffx.algorithms.thermodynamics.LambdaData: Unmarshall the histogram data.
readLong() - Method in class edu.rit.io.DataInputStream: Read a long value from this data input stream.
readNext() - Method in class ffx.potential.parsers.CIFFilter: Reads the next snapshot of an archive into the activeMolecularAssembly.
readNext() - Method in class ffx.potential.parsers.INTFilter: Reads the next model if applicable (currently, ARC and PDB files only).
readNext() - Method in class ffx.potential.parsers.MergeFilter: Reads the next model if applicable (currently, ARC and PDB files only).
readNext() - Method in class ffx.potential.parsers.PDBFilter: Reads the next model if applicable (currently, ARC and PDB files only).
readNext() - Method in class ffx.potential.parsers.SystemFilter: Reads the next model if applicable (currently, ARC and PDB files only).
readNext() - Method in class ffx.potential.parsers.XPHFilter: Reads the next model if applicable (currently, ARC and PDB files only).
readNext() - Method in class ffx.potential.parsers.XYZFilter: Reads the next model if applicable (currently, ARC and PDB files only).
readNext() - Method in class ffx.ui.commands.SimulationFilter
readNext(boolean) - Method in class ffx.potential.parsers.CIFFilter: Reads the next snapshot of an archive into the activeMolecularAssembly.
readNext(boolean) - Method in class ffx.potential.parsers.INTFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean) - Method in class ffx.potential.parsers.MergeFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean) - Method in class ffx.potential.parsers.PDBFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean) - Method in class ffx.potential.parsers.SystemFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean) - Method in class ffx.potential.parsers.XPHFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean) - Method in class ffx.potential.parsers.XYZFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean) - Method in class ffx.ui.commands.SimulationFilter
readNext(boolean, boolean) - Method in class ffx.potential.parsers.CIFFilter: Reads the next snapshot of an archive into the activeMolecularAssembly.
readNext(boolean, boolean) - Method in class ffx.potential.parsers.INTFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean) - Method in class ffx.potential.parsers.MergeFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean) - Method in class ffx.potential.parsers.PDBFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean) - Method in class ffx.potential.parsers.SystemFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean) - Method in class ffx.potential.parsers.XPHFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean) - Method in class ffx.potential.parsers.XYZFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean) - Method in class ffx.ui.commands.SimulationFilter
readNext(boolean, boolean, boolean) - Method in class ffx.potential.parsers.CIFFilter: Reads the next snapshot of an archive into the activeMolecularAssembly.
readNext(boolean, boolean, boolean) - Method in class ffx.potential.parsers.INTFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean, boolean) - Method in class ffx.potential.parsers.MergeFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean, boolean) - Method in class ffx.potential.parsers.PDBFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean, boolean) - Method in class ffx.potential.parsers.SystemFilter: Reads the next model if applicable (currently, ARC files only).
readNext(boolean, boolean, boolean) - Method in class ffx.potential.parsers.XPHFilter: Reads the next snap-shot of an archive into the activeMolecularAssembly.
readNext(boolean, boolean, boolean) - Method in class ffx.potential.parsers.XYZFilter: Reads the next snapshot of an archive into the activeMolecularAssembly.
readNext(boolean, boolean, boolean) - Method in class ffx.ui.commands.SimulationFilter
readObservableData(boolean, boolean, boolean) - Method in class ffx.numerics.estimator.MBARFilter: Read in observable data, try to leave as many fields in-tact as possible.
readOnto(File, MolecularAssembly) - Static method in class ffx.potential.parsers.XPHFilter: readOnto
readOnto(File, MolecularAssembly) - Static method in class ffx.potential.parsers.XYZFilter: readOnto
readPatch(Range, Range) - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read all matrix element segments from the input stream, storing only the matrix elements in the given patch.
readRotFile(File, MolecularAssembly) - Static method in class ffx.potential.bonded.RotamerLibrary
readRowSlice(Range) - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read all matrix element segments from the input stream, storing only the matrix elements in the given row slice.
readSegment() - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read the next matrix element segment from the input stream.
readSegmentColSlice(Range) - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read the next matrix element segment from the input stream, storing only the matrix elements in the given column slice.
readSegmentPatch(Range, Range) - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read the next matrix element segment from the input stream, storing only the matrix elements in the given patch.
readSegmentRowSlice(Range) - Method in class edu.rit.io.DoubleMatrixFile.Reader: Read the next matrix element segment from the input stream, storing only the matrix elements in the given row slice.
readShort() - Method in class edu.rit.io.DataInputStream: Read a short value from this data input stream.
readSocket() - Method in class ffx.ui.commands.FFXClient: readSocket
readString() - Method in class edu.rit.io.DataInputStream: Read a string value from this data input stream.
readUnsignedByte() - Method in class edu.rit.io.DataInputStream: Read an unsigned byte value from this data input stream.
readUnsignedChar() - Method in class edu.rit.io.DataInputStream: Read an unsigned character value from this data input stream.
readUnsignedInt() - Method in class edu.rit.io.DataInputStream: Read an unsigned integer value from this data input stream.
readUnsignedLong() - Method in class edu.rit.io.DataInputStream: Read an unsigned long value from this data input stream.
readUnsignedShort() - Method in class edu.rit.io.DataInputStream: Read an unsigned short value from this data input stream.
Real - Class in ffx.numerics.fft: Compute the FFT of real, double precision data of arbitrary length n using a Complex transform.
Real(int) - Constructor for class ffx.numerics.fft.Real: Constructs a Complex FFT of length (n / 2) for real data of length n.
Real3D - Class in ffx.numerics.fft: Compute the 3D FFT of real, double precision input of arbitrary dimensions.
Real3D(int, int, int) - Constructor for class ffx.numerics.fft.Real3D: Initialize the 3D FFT for complex 3D matrix.
Real3DParallel - Class in ffx.numerics.fft: Compute the 3D FFT of real, double precision input of arbitrary dimensions in parallel.
Real3DParallel(int, int, int, ParallelTeam) - Constructor for class ffx.numerics.fft.Real3DParallel: Initialize the FFT for real input.
Real3DParallel(int, int, int, ParallelTeam, IntegerSchedule) - Constructor for class ffx.numerics.fft.Real3DParallel: Initialize the FFT for real input.
realSpaceCounts - Variable in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters: Number of neighboring atoms within the real space cutoff.
RealSpaceData - Class in ffx.realspace: RealSpaceData class.
RealSpaceData(MolecularAssembly[], CompositeConfiguration, ParallelTeam, RealSpaceFile...) - Constructor for class ffx.realspace.RealSpaceData: Construct a real space data molecularAssemblies.
RealSpaceData(MolecularAssembly[], CompositeConfiguration, ParallelTeam, DiffractionData) - Constructor for class ffx.realspace.RealSpaceData: Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecularAssemblies.
RealSpaceData(MolecularAssembly, CompositeConfiguration, ParallelTeam) - Constructor for class ffx.realspace.RealSpaceData: Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies.
RealSpaceData(MolecularAssembly, CompositeConfiguration, ParallelTeam, RealSpaceFile...) - Constructor for class ffx.realspace.RealSpaceData: Construct a real space data molecularAssemblies.
RealSpaceData(MolecularAssembly, CompositeConfiguration, ParallelTeam, DiffractionData) - Constructor for class ffx.realspace.RealSpaceData: Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies.
RealSpaceEnergy - Class in ffx.realspace: Combine the Real Space target and chemical potential energy.
RealSpaceEnergy(RealSpaceData, int, int, int, RefinementMinimize.RefinementMode) - Constructor for class ffx.realspace.RealSpaceEnergy: Diffraction data energy target
RealSpaceEnergyRegion - Class in ffx.potential.nonbonded.pme: Parallel evaluation of the PME real space energy and gradient.
RealSpaceEnergyRegion(ForceField.ELEC_FORM, int, ForceField, boolean, double) - Constructor for class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
realSpaceEnergyTime - Variable in class ffx.potential.nonbonded.pme.PMETimings
realSpaceEnergyTotal - Variable in class ffx.potential.nonbonded.pme.PMETimings
RealSpaceFile - Class in ffx.realspace.parsers: RealSpaceFile class.
RealSpaceFile(MolecularAssembly) - Constructor for class ffx.realspace.parsers.RealSpaceFile: Read in a Real Space density file based on the molecular assembly filename, using a weight of 1.0.
RealSpaceFile(MolecularAssembly[]) - Constructor for class ffx.realspace.parsers.RealSpaceFile: Read in a Real Space density file based on the molecular assembly filename, using a weight of 1.0 and neutron value of false.
RealSpaceFile(MolecularAssembly, double) - Constructor for class ffx.realspace.parsers.RealSpaceFile: Read in a Real Space density file based on the molecular assembly filename, using a weight of 1.0.
RealSpaceFile(String) - Constructor for class ffx.realspace.parsers.RealSpaceFile: Read in a Real Space density file and set weight set to 1.0.
RealSpaceFile(String, double) - Constructor for class ffx.realspace.parsers.RealSpaceFile: Read in a Real Space density file.
RealSpaceFileFilter - Interface in ffx.realspace.parsers: RealSpaceFileFilter interface.
realSpaceLists - Variable in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters: Neighbor lists, without atoms beyond the real space cutoff.
RealSpaceNeighborParameters - Class in ffx.potential.nonbonded.pme
RealSpaceNeighborParameters(int) - Constructor for class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters
RealSpaceOptions - Class in ffx.realspace.cli: Represents command line options for scripts that utilize a real-space density map.
RealSpaceOptions() - Constructor for class ffx.realspace.cli.RealSpaceOptions
realSpaceRanges - Variable in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters: Optimal pairwise ranges.
RealSpaceRefinementData - Class in ffx.realspace: RealSpaceRefinementData class.
realSpaceSCFTime - Variable in class ffx.potential.nonbonded.pme.PMETimings
realSpaceSCFTotalTime - Variable in class ffx.potential.nonbonded.pme.PMETimings
realSpaceSchedule - Variable in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters: Pairwise schedule for load balancing.
rebuildList - Variable in class ffx.potential.nonbonded.RowLoop
rebuildList - Variable in class ffx.potential.nonbonded.SliceLoop
receive(Buf) - Method in class edu.rit.pj.cluster.Proxy: Receive a message from this proxy's far end process.
receive(Channel, int, Buf) - Method in class edu.rit.mp.ChannelGroup: Receive a message from the given channel with the given tag.
receive(Channel, Buf) - Method in class edu.rit.mp.ChannelGroup: Receive a message from the given channel.
receive(Channel, Range, Buf) - Method in class edu.rit.mp.ChannelGroup: Receive a message from the given channel with the given range of tags.
receive(Integer, int, Buf) - Method in class edu.rit.pj.Comm: Receive a message from the process at the given rank in this communicator with the given message tag.
receive(Integer, int, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Receive a message from the process at the given rank in this communicator with the given message tag (non-blocking).
receive(Integer, Buf) - Method in class edu.rit.pj.cluster.Proxy: Receive a message with the given tag from this proxy's far end process.
receive(Integer, Buf) - Method in class edu.rit.pj.Comm: Receive a message from the process at the given rank in this communicator.
receive(Integer, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Receive a message from the process at the given rank in this communicator (non-blocking).
receive(Integer, Range, Buf) - Method in class edu.rit.pj.Comm: Receive a message from the process at the given rank in this communicator with the given message tag range.
receive(Integer, Range, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Receive a message from the process at the given rank in this communicator with the given message tag range (non-blocking).
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyBooleanBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyByteBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyCharacterBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyDoubleBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyFloatBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyLongBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyShortBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.LongArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.LongArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.LongItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.LongMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.LongMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.Buf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveItems(int, int, ByteBuffer) - Method in class edu.rit.mp.ObjectBuf: Receive as many items as possible from the given byte buffer to this buffer.
receiveNoWait(Channel, int, Buf, IORequest) - Method in class edu.rit.mp.ChannelGroup: Receive (non-blocking) a message from the given channel with the given tag.
receiveNoWait(Channel, Buf, IORequest) - Method in class edu.rit.mp.ChannelGroup: Receive (non-blocking) a message from the given channel.
receiveNoWait(Channel, Range, Buf, IORequest) - Method in class edu.rit.mp.ChannelGroup: Receive (non-blocking) a message from the given channel with the given range of tags.
receiveTaskInput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongForLoop: Receive additional input data associated with a task.
receiveTaskInput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongStrideForLoop: Receive additional input data associated with a task.
receiveTaskInput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerForLoop: Receive additional input data associated with a task.
receiveTaskInput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Receive additional input data associated with a task.
receiveTaskInput(T, Comm, int, int) - Method in class edu.rit.pj.WorkerIteration: Receive input data associated with a task.
receiveTaskOutput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongForLoop: Receive additional output data associated with a task.
receiveTaskOutput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongStrideForLoop: Receive additional output data associated with a task.
receiveTaskOutput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerForLoop: Receive additional output data associated with a task.
receiveTaskOutput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Receive additional output data associated with a task.
receiveTaskOutput(T, Comm, int, int) - Method in class edu.rit.pj.WorkerIteration: Receive additional output data associated with a task.
reciprocal() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the reciprocal of this.
ReciprocalEnergyRegion - Class in ffx.potential.nonbonded.pme: Parallel evaluation of the PME reciprocal space energy and gradient.
ReciprocalEnergyRegion(int, double, double) - Constructor for class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
reciprocalIP() - Method in class ffx.numerics.math.ComplexNumber: reciprocalIP
ReciprocalSpace - Class in ffx.potential.nonbonded: The Reciprocal Space class computes the reciprocal space contribution to ParticleMeshEwald for the AMOEBA force field.
ReciprocalSpace(ParticleMeshEwald, Crystal, ForceField, Atom[], double, ParallelTeam, ParallelTeam) - Constructor for class ffx.potential.nonbonded.ReciprocalSpace: Reciprocal Space PME contribution.
ReciprocalSpace.BSplineRegion - Class in ffx.potential.nonbonded: The class computes b-Splines that are used to spline multipoles and induced dipoles onto the PME grid.
ReciprocalSpace.BSplineRegion.BSplineLoop - Class in ffx.potential.nonbonded
ReciprocalSpace.GridMethod - Enum Class in ffx.potential.nonbonded
rectangular(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using rectangular integration.
rectangular(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using rectangular integration.
RECTANGULAR - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType: Rectangular integration, requiring 1 point.
rectangularEnds(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Treats half-width bins at the ends of a DataSet using rectangular integration.
rectangularParallel(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using parallelized rectangular integration.
rectangularParallel(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using rectangular integration.
recursion(double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: This method is a driver to collect elements of the Cartesian multipole tensor using recursion relationships and storing intermediate values.
recursion(double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This method is a driver to collect elements of the Cartesian multipole tensor using recursion relationships and storing intermediate values.
recursion(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: This method is a driver to collect elements of the Cartesian multipole tensor using recursion relationships and storing intermediate values.
recursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: This method is a driver to collect elements of the Cartesian multipole tensor using recursion relationships and storing intermediate values.
recursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This method is a driver to collect elements of the Cartesian multipole tensor using recursion relationships and storing intermediate values.
recursion(double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: This method is a driver to collect elements of the Cartesian multipole tensor using recursion relationships and storing intermediate values.
reduce(boolean) - Method in class edu.rit.pj.replica.ReplicatedBoolean: Update this replicated, shared reduction variable's current value.
reduce(boolean[][], Range, Range, boolean[][], Range, Range, BooleanOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one Boolean matrix with a range of elements in another Boolean matrix.
reduce(boolean[], BooleanOp) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Combine this array reduction variable with the given array using the given operation.
reduce(boolean[], Range, boolean[], Range, BooleanOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one Boolean array with a range of elements in another Boolean array.
reduce(boolean, BooleanOp) - Method in class edu.rit.pj.reduction.SharedBoolean: Combine this reduction variable with the given value using the given operation.
reduce(byte) - Method in class edu.rit.pj.replica.ReplicatedByte: Update this replicated, shared reduction variable's current value.
reduce(byte[][], Range, Range, byte[][], Range, Range, ByteOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one byte matrix with a range of elements in another byte matrix.
reduce(byte[], ByteOp) - Method in class edu.rit.pj.reduction.SharedByteArray: Combine this array reduction variable with the given array using the given operation.
reduce(byte[], Range, byte[], Range, ByteOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one byte array with a range of elements in another byte array.
reduce(byte, ByteOp) - Method in class edu.rit.pj.reduction.SharedByte: Combine this reduction variable with the given value using the given operation.
reduce(char) - Method in class edu.rit.pj.replica.ReplicatedCharacter: Update this replicated, shared reduction variable's current value.
reduce(char[][], Range, Range, char[][], Range, Range, CharacterOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one character matrix with a range of elements in another character matrix.
reduce(char[], CharacterOp) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Combine this array reduction variable with the given array using the given operation.
reduce(char[], Range, char[], Range, CharacterOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one character array with a range of elements in another character array.
reduce(char, CharacterOp) - Method in class edu.rit.pj.reduction.SharedCharacter: Combine this reduction variable with the given value using the given operation.
reduce(double) - Method in class edu.rit.pj.replica.ReplicatedDouble: Update this replicated, shared reduction variable's current value.
reduce(double[][], Range, Range, double[][], Range, Range, DoubleOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one double matrix with a range of elements in another double matrix.
reduce(double[], DoubleOp) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Combine this array reduction variable with the given array using the given operation.
reduce(double[], Range, double[], Range, DoubleOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one double array with a range of elements in another double array.
reduce(double, DoubleOp) - Method in class edu.rit.pj.reduction.SharedDouble: Combine this reduction variable with the given value using the given operation.
reduce(float) - Method in class edu.rit.pj.replica.ReplicatedFloat: Update this replicated, shared reduction variable's current value.
reduce(float[][], Range, Range, float[][], Range, Range, FloatOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one float matrix with a range of elements in another float matrix.
reduce(float[], FloatOp) - Method in class edu.rit.pj.reduction.SharedFloatArray: Combine this array reduction variable with the given array using the given operation.
reduce(float[], Range, float[], Range, FloatOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one float array with a range of elements in another float array.
reduce(float, FloatOp) - Method in class edu.rit.pj.reduction.SharedFloat: Combine this reduction variable with the given value using the given operation.
reduce(int) - Method in class edu.rit.pj.replica.ReplicatedInteger: Update this replicated, shared reduction variable's current value.
reduce(int[][], IntegerOp) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Combine this matrix reduction variable with the given matrix using the given operation.
reduce(int[][], Range, Range, int[][], Range, Range, IntegerOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one integer matrix with a range of elements in another integer matrix.
reduce(int[], IntegerOp) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Combine this array reduction variable with the given array using the given operation.
reduce(int[], Range, int[], Range, IntegerOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one integer array with a range of elements in another integer array.
reduce(int, boolean[], int, int, BooleanOp) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, boolean, BooleanOp) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, byte[], int, int, ByteOp) - Method in class edu.rit.pj.reduction.SharedByteArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, byte, ByteOp) - Method in class edu.rit.pj.reduction.SharedByteArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, char[], int, int, CharacterOp) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, char, CharacterOp) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, double[], int, int, DoubleOp) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, double, DoubleOp) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, float[], int, int, FloatOp) - Method in class edu.rit.pj.reduction.SharedFloatArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, float, FloatOp) - Method in class edu.rit.pj.reduction.SharedFloatArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, int) - Method in class ffx.numerics.atomic.AdderDoubleArray: The AtomicDoubleArray handles the reduction automatically, so this method does nothing.
reduce(int, int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Perform reduction between the given lower and upper bounds, if necessary.
reduce(int, int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Perform reduction between the given lower bound (lb) and upper bound (up) if necessary.
reduce(int, int) - Method in class ffx.numerics.atomic.MultiDoubleArray: Reduce contributions from each thread into the main thread's array.
reduce(int, int) - Method in class ffx.numerics.atomic.PJDoubleArray: Perform reduction between the given lower and upper bounds, if necessary.
reduce(int, int[], int, int, IntegerOp) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, int, int[][], int, int, int, int, IntegerOp) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Combine a portion of this matrix reduction variable with a portion of the given matrix using the given operation.
reduce(int, int, int, IntegerOp) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Combine this matrix reduction variable at the given row and column with the given value using the given operation.
reduce(int, int, long[][], int, int, int, int, LongOp) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Combine a portion of this matrix reduction variable with a portion of the given matrix using the given operation.
reduce(int, int, long, LongOp) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Combine this matrix reduction variable at the given row and column with the given value using the given operation.
reduce(int, int, Buf, Op) - Method in class edu.rit.pj.Comm: Perform a reduction on all processes in this communicator using the given message tag.
reduce(int, int, IntegerOp) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, long[], int, int, LongOp) - Method in class edu.rit.pj.reduction.SharedLongArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, long, LongOp) - Method in class edu.rit.pj.reduction.SharedLongArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, short[], int, int, ShortOp) - Method in class edu.rit.pj.reduction.SharedShortArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, short, ShortOp) - Method in class edu.rit.pj.reduction.SharedShortArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(int, Buf, Op) - Method in class edu.rit.pj.Comm: Perform a reduction on all processes in this communicator.
reduce(int, IntegerOp) - Method in class edu.rit.pj.reduction.SharedInteger: Combine this reduction variable with the given value using the given operation.
reduce(int, T[], int, int, ObjectOp<T>) - Method in class edu.rit.pj.reduction.SharedObjectArray: Combine a portion of this array reduction variable with a portion of the given array using the given operation.
reduce(int, T, ObjectOp<T>) - Method in class edu.rit.pj.reduction.SharedObjectArray: Combine this array reduction variable at the given index with the given value using the given operation.
reduce(long) - Method in class edu.rit.pj.replica.ReplicatedLong: Update this replicated, shared reduction variable's current value.
reduce(long[][], LongOp) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Combine this matrix reduction variable with the given matrix using the given operation.
reduce(long[][], Range, Range, long[][], Range, Range, LongOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one long matrix with a range of elements in another long matrix.
reduce(long[], LongOp) - Method in class edu.rit.pj.reduction.SharedLongArray: Combine this array reduction variable with the given array using the given operation.
reduce(long[], Range, long[], Range, LongOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one long array with a range of elements in another long array.
reduce(long, LongOp) - Method in class edu.rit.pj.reduction.SharedLong: Combine this reduction variable with the given value using the given operation.
reduce(short) - Method in class edu.rit.pj.replica.ReplicatedShort: Update this replicated, shared reduction variable's current value.
reduce(short[][], Range, Range, short[][], Range, Range, ShortOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one short matrix with a range of elements in another short matrix.
reduce(short[], ShortOp) - Method in class edu.rit.pj.reduction.SharedShortArray: Combine this array reduction variable with the given array using the given operation.
reduce(short[], Range, short[], Range, ShortOp) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one short array with a range of elements in another short array.
reduce(short, ShortOp) - Method in class edu.rit.pj.reduction.SharedShort: Combine this reduction variable with the given value using the given operation.
reduce(ParallelTeam) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Perform a reduction on the entire array.
reduce(ParallelTeam, int, int) - Method in class ffx.numerics.atomic.AdderDoubleArray: The AtomicDoubleArray handles the reduction automatically, so this method does nothing.
reduce(ParallelTeam, int, int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Perform reduction between the given bounds using a ParallelTeam.
reduce(ParallelTeam, int, int) - Method in class ffx.numerics.atomic.MultiDoubleArray: Perform reduction between the given bounds using a ParallelTeam.
reduce(ParallelTeam, int, int) - Method in class ffx.numerics.atomic.PJDoubleArray: Perform reduction between the given bounds using a ParallelTeam.
reduce(AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
reduce(ST[][], Range, Range, DT[][], Range, Range, ObjectOp<DT>) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one object matrix with a range of elements in another object matrix.
reduce(ST[], Range, DT[], Range, ObjectOp<DT>) - Static method in class edu.rit.pj.reduction.ReduceArrays: Combine a range of elements from one object array with a range of elements in another object array.
reduce(T) - Method in class edu.rit.pj.replica.ReplicatedObject: Update this replicated, shared reduction variable's current value.
reduce(T[], ObjectOp<T>) - Method in class edu.rit.pj.reduction.SharedObjectArray: Combine this array reduction variable with the given array using the given operation.
reduce(T, ObjectOp<T>) - Method in class edu.rit.pj.reduction.SharedObject: Combine this reduction variable with the given value using the given operation.
ReduceArrays - Class in edu.rit.pj.reduction: Class ReduceArrays provides static methods for reduction operations on arrays and matrices of primitive types and object types.
ReduceRegion - Class in ffx.potential.nonbonded.pme: Parallel conversion of torques into forces, and then reduce them.
ReduceRegion(int, ForceField) - Constructor for class ffx.potential.nonbonded.pme.ReduceRegion
reductionFactor - Variable in class ffx.potential.parameters.VDWType: Reduction factor for evaluating van der Waals pairs.
referenceIndex() - Method in record class ffx.utilities.IndexIndexPair: Returns the value of the referenceIndex record component.
refinementData - Variable in class ffx.xray.SigmaAMinimize
refinementEnergy - Variable in class ffx.xray.RefinementMinimize
RefinementEnergy - Class in ffx.xray: Combine the X-ray target and chemical potential energy using the CrystalPotential interface
RefinementEnergy(DataContainer, RefinementMinimize.RefinementMode) - Constructor for class ffx.xray.RefinementEnergy: RefinementEnergy Constructor.
RefinementEnergy(DataContainer, RefinementMinimize.RefinementMode, double[]) - Constructor for class ffx.xray.RefinementEnergy: RefinementEnergy Constructor.
RefinementMinimize - Class in ffx.xray: Refinement minimization class using OptimizationListener interface, constructs a RefinementEnergy object for this purpose
RefinementMinimize(DataContainer) - Constructor for class ffx.xray.RefinementMinimize: constructor for refinement, assumes coordinates and B factor optimization
RefinementMinimize(DataContainer, RefinementMinimize.RefinementMode) - Constructor for class ffx.xray.RefinementMinimize: constructor for refinement
RefinementMinimize(DataContainer, RefinementMinimize.RefinementMode, AlgorithmListener) - Constructor for class ffx.xray.RefinementMinimize: constructor for refinement
RefinementMinimize.RefinementMode - Enum Class in ffx.xray: Different refinement mode selection types.
refinementMode - Variable in class ffx.realspace.cli.RealSpaceOptions: The refinement mode to use.
refinementMode - Variable in class ffx.xray.cli.DataRefinementOptions: The refinement mode to use.
refinementMode - Variable in class ffx.xray.cli.XrayOptions: The refinement mode to use.
RefinementModel - Class in ffx.xray: RefinementModel class.
RefinementModel(MolecularAssembly[]) - Constructor for class ffx.xray.RefinementModel: Constructor for RefinementModel.
RefinementModel(MolecularAssembly[], boolean) - Constructor for class ffx.xray.RefinementModel: Constructor for RefinementModel.
ReflectionList - Class in ffx.crystal: Class to represent a reflection list.
ReflectionList(double, double, double, double, double, double, String, double) - Constructor for class ffx.crystal.ReflectionList: Constructor for ReflectionList.
ReflectionList(Crystal, Resolution) - Constructor for class ffx.crystal.ReflectionList: Constructor for ReflectionList.
ReflectionList(Crystal, Resolution, CompositeConfiguration) - Constructor for class ffx.crystal.ReflectionList: Constructor for ReflectionList.
ReflectionSpline - Class in ffx.crystal: The ReflectionSpline class represents a reflection spline basis.
ReflectionSpline(ReflectionList, int) - Constructor for class ffx.crystal.ReflectionSpline: Constructor for ReflectionSpline.
region() - Method in class edu.rit.pj.ParallelConstruct: Returns the parallel region of code within which a parallel team is executing this parallel construct.
region() - Method in class edu.rit.pj.ParallelTeam: Returns the parallel region of code that this parallel team is executing.
region() - Method in class edu.rit.pj.WorkerConstruct: Returns the worker region of code within which a worker team is executing this worker construct.
region() - Method in class edu.rit.pj.WorkerTeam: Returns the worker region of code that this worker team is executing.
registerPlatform(Platform) - Static method in class ffx.openmm.Platform: Register a new platform.
registerTemporaryDirectory() - Method in class ffx.utilities.FFXTest: Create temporary testing directory that will be deleted after the current test.
reGuessLambdas() - Method in class ffx.potential.extended.ExtendedSystem: Reset initialized lambdas to a naive guess based on the model pKa for each extended residue
reindexFacesAndVertices() - Method in class ffx.numerics.quickhull.QuickHull3D: Removes deleted faces, marks active vertices, and assigns new contiguous indices to both faces and vertices for compact output.
reinitialize(int) - Method in class ffx.openmm.Context: When a Context is created, it caches information about the System being simulated and the Force objects contained in it.
RELATIVE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
relativePathTo(File) - Static method in class ffx.utilities.FileUtils: Constructs a relative path from the present working directory to a file.
RELATIVESOLV - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
RelativeSolvation - Class in ffx.potential.bonded: A relative solvation term for chemical perturbations.
RelativeSolvation(RelativeSolvation.SolvationLibrary, ForceField) - Constructor for class ffx.potential.bonded.RelativeSolvation: Constructor for RelativeSolvation.
RelativeSolvation.SolvationLibrary - Enum Class in ffx.potential.bonded: Citations: Wolfenden et al: Wolfenden, R., Andersson, L., Cullis, P.
RelativeSolvationType - Class in ffx.potential.parameters: A BaseType for relative solvation energies (intended for nonstandard amino acids).
RelativeSolvationType(String, double) - Constructor for class ffx.potential.parameters.RelativeSolvationType: Constructor for RelativeSolvationType.
release() - Method in class ffx.ui.commands.FFXClient: release
release() - Method in class ffx.ui.SimulationLoader: release
remove() - Method in class edu.rit.util.RandomSubset: Unsupported operation.
remove(int) - Method in class edu.rit.util.RandomSubset: Remove the given integer from the original set.
remove(ClusterPair) - Method in class ffx.numerics.clustering.DistanceMap: Marks the given ClusterPair as removed (lazy removal) and drops it from the hash index.
remove(String) - Method in class edu.rit.pj.cluster.ResourceCache: Remove the resource content for the given resource name from this resource cache.
removeAngle(Angle) - Method in class ffx.potential.terms.AnglePotentialEnergy: Remove an Angle from this term.
removeAngleTorsion(AngleTorsion) - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy: Remove an AngleTorsion from this term.
removeBond(Bond) - Method in class ffx.potential.terms.BondPotentialEnergy: Remove a Bond from this term.
removeChild(MSNode) - Method in class ffx.potential.bonded.MSNode: removeChild.
removeConstraint(int) - Method in class ffx.openmm.System: Remove a constraint from the system.
removeEnergyTerm(EnergyTerm) - Method in class ffx.potential.terms.EnergyTermRegion: Remove an EnergyTerm from this bonded region.
removeExcessHydrogens() - Method in class ffx.potential.parsers.PDBFilter
removeFirst() - Method in class ffx.numerics.clustering.DistanceMap: Removes and returns the minimal-distance pair (according to priority queue ordering).
removeForce(int) - Method in class ffx.openmm.System: Remove a force from the system.
removeForce(Force) - Method in class ffx.potential.openmm.OpenMMSystem: Remove a force from the OpenMM System.
removeFromParent() - Method in class ffx.potential.bonded.Atom
removeFromParent() - Method in class ffx.potential.bonded.Bond
removeH1_H2_H3(AminoAcidUtils.AminoAcid3, Residue) - Static method in class ffx.potential.bonded.AminoAcidUtils: Only the first nitrogen should have H1, H2 and H3 atoms, unless it's an NME cap.
removeImproperTorsion(ImproperTorsion) - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy: Remove an ImproperTorsion from this term.
removeKeyword(Keyword) - Method in class ffx.ui.FFXSystem: removeKeyword
removeLeaves() - Method in class ffx.potential.bonded.MSGroup: removeLeaves
removeLeaves() - Method in class ffx.potential.MolecularAssembly: removeLeaves
removeMask(int, boolean[], double[]...) - Method in interface ffx.potential.nonbonded.MaskingInterface: After calling removeMask, all entries in the mask array should be 1 and is14 array false.
removeMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion: Remove permanent field masking rules.
removeMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
removeMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.VanDerWaals: After calling removeMask, all entries in the mask array should be 1 and is14 array false.
removeNeuralNetworkTerms(List<T>) - Static method in class ffx.potential.bonded.BondedTerm: This method removes terms from a list that are marked as being part of a neural network.
removeOutOfPlaneBend(OutOfPlaneBend) - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy: Remove an OutOfPlaneBend from this term.
removeOXT_OT2(Residue) - Static method in class ffx.potential.bonded.AminoAcidUtils: Only the last residue in a chain should have an OXT/OT2 atom.
removePiOrbitalTorsion(PiOrbitalTorsion) - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Remove a PiOrbitalTorsion from this term.
removeRestrainDistance(RestrainDistance) - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy: Remove a RestrainDistance from this term.
removeRestrainPosition(RestrainPosition) - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy: Remove a RestrainPosition from this term.
removeRestrainTorsion(Torsion) - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy: Remove a restrain torsion.
removeSelections(ArrayList<MSNode>) - Method in class ffx.ui.Hierarchy: removeSelections
removeStretchBend(StretchBend) - Method in class ffx.potential.terms.StretchBendPotentialEnergy: Remove a StretchBend from this term.
removeStretchTorsion(StretchTorsion) - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy: Remove a StretchTorsion from this term.
removeTorsion(Torsion) - Method in class ffx.potential.terms.TorsionPotentialEnergy: Remove a Torsion from this term.
removeTorsionTorsion(TorsionTorsion) - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Remove a TorsionTorsion from this term.
removeUpdate(DocumentEvent) - Method in class ffx.ui.KeywordComponent
removeUreyBradley(UreyBradley) - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy: Remove a UreyBradley from this term.
removeVariable(String) - Method in class ffx.utilities.FFXBinding: Remove the variable with the specified name.
renameAlkyl(Atom, Atom, int, char) - Static method in class ffx.potential.bonded.NamingUtils: Renames an atom, its bonded hydrogen, and returns the next atom in the chain.
renameAminoAcidToPDBStandard(Residue) - Static method in class ffx.potential.bonded.NamingUtils: Renames the Atoms in an amino acid to PDB standard.
renameArginineHydrogen(Residue, List<Atom>) - Static method in class ffx.potential.bonded.NamingUtils: renameArginineHydrogen.
renameAsparagineHydrogen(Residue, List<Atom>) - Static method in class ffx.potential.bonded.NamingUtils: renameAsparagineHydrogen.
renameAtomsToPDBStandard(MolecularAssembly) - Static method in class ffx.potential.bonded.NamingUtils: Renames Atoms to PDB standard using bonding patterns, atomic numbers, and residue types.
renameBetaHydrogen(Residue, List<Atom>, int) - Static method in class ffx.potential.bonded.NamingUtils: renameBetaHydrogen.
renameBranchedAlkyl(Atom, Atom, int, int, char) - Static method in class ffx.potential.bonded.NamingUtils: Renames a numbered carbon, its bonded hydrogen, and returns the next atom in the chain.
renameCommonAminoAcids(Residue, AminoAcidUtils.AminoAcid3, Atom, Atom) - Static method in class ffx.potential.bonded.NamingUtils: Renames atoms in common amino acids to PDB standard.
renameCommonNucleicAcid(Residue, NucleicAcidUtils.NucleicAcid3) - Static method in class ffx.potential.bonded.NamingUtils: Renames atoms in common nucleic acids to PDB standard.
renameCommonNucleobase(Atom, Atom, NucleicAcidUtils.NucleicAcid3) - Static method in class ffx.potential.bonded.NamingUtils: Renames the atoms of the common nucleobases (A, C, G, T, U, and deoxy variants).
renameCommonPurine(Atom, Atom) - Static method in class ffx.potential.bonded.NamingUtils: Renames atoms common to all standard purines (A, G)
renameCommonPyrimidine(Atom, Atom) - Static method in class ffx.potential.bonded.NamingUtils: Renames atoms common to all standard pyrimidines (C, T, U)
renameDeltaHydrogen(Residue, List<Atom>, int) - Static method in class ffx.potential.bonded.NamingUtils: renameDeltaHydrogen.
renameEpsilonHydrogen(Residue, List<Atom>, int) - Static method in class ffx.potential.bonded.NamingUtils: renameEpsilonHydrogen.
renameGammaHydrogen(Residue, List<Atom>, int) - Static method in class ffx.potential.bonded.NamingUtils: renameGammaHydrogen.
renameGlutamineHydrogen(Residue, List<Atom>) - Static method in class ffx.potential.bonded.NamingUtils: renameGlutamineHydrogen.
renameGlycineAlphaHydrogen(Residue, List<Atom>) - Static method in class ffx.potential.bonded.NamingUtils: renameGlycineAlphaHydrogen.
renameIsoleucineHydrogen(Residue, List<Atom>) - Static method in class ffx.potential.bonded.NamingUtils: renameIsoleucineHydrogen.
renameNTerminusHydrogen(Residue) - Static method in class ffx.potential.bonded.NamingUtils: renameNTerminusHydrogen.
renameNucleicAcidToPDBStandard(Residue) - Static method in class ffx.potential.bonded.NamingUtils: Renames the Atoms in a nucleic acid to PDB standard.
renameZetaHydrogen(Residue, List<Atom>, int) - Static method in class ffx.potential.bonded.NamingUtils: renameZetaHydrogen.
Renderer - Class in ffx.potential: The Renderer class attempts to maximize throughput of graphics operations on MolecularAssembly instances.
Renderer(Bounds, JLabel) - Constructor for class ffx.potential.Renderer: Constructor
RendererCache - Class in ffx.potential.bonded: The RendererCache class defines constants related to rendering modes and caches primitives for the Renderer.
RendererCache() - Constructor for class ffx.potential.bonded.RendererCache: Constructor for RendererCache.
RendererCache.ColorModel - Enum Class in ffx.potential.bonded
RendererCache.ViewModel - Enum Class in ffx.potential.bonded
renewLease(JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontend: Renew the lease on the job.
renewLease(JobBackendRef) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "renew lease" message.
renewLease(JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Renew the lease on the job.
renewLease(JobBackendRef) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Renew the lease on the job.
renewLease(JobBackendRef) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Renew the lease on the job.
renewLease(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobBackend: Renew the lease on the job.
renewLease(JobFrontendRef) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "renew lease" message.
renewLease(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobBackendProxy: Renew the lease on the job.
renewLease(JobFrontendRef) - Method in interface edu.rit.pj.cluster.JobBackendRef: Renew the lease on the job.
renewLease(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobScheduler: Renew the lease on a job.
renewLease(JobFrontendRef) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "renew lease" message.
renewLease(JobFrontendRef) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Renew the lease on a job.
renewLease(JobFrontendRef) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Renew the lease on a job.
renewLease(JobSchedulerRef) - Method in class edu.rit.pj.cluster.JobFrontend: Renew the lease on the job.
renewLease(JobSchedulerRef) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "renew lease" message.
renewLease(JobSchedulerRef) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Renew the lease on the job.
renewLease(JobSchedulerRef) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Renew the lease on the job.
renewLease(JobSchedulerRef) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Renew the lease on the job.
renewTimer - Variable in class edu.rit.pj.cluster.JobInfo: Lease renewal timer.
renewTimer - Variable in class edu.rit.pj.cluster.ProcessInfo: Lease renewal timer.
renumberForceField(int, int, int) - Method in class ffx.potential.parameters.ForceField: Renumber ForceField class, type and biotype values.
reOrderAtoms() - Method in class ffx.potential.bonded.MSGroup: reOrderAtoms
reOrderAtoms() - Method in class ffx.potential.bonded.MultiResidue: reOrderAtoms
ReorderAtoms - Class in ffx.potential.commands.test: The ReorderAtoms script sorts the atoms within an XYZ file based on atomic weight.
ReorderAtoms() - Constructor for class ffx.potential.commands.test.ReorderAtoms: Constructor.
ReorderAtoms(FFXBinding) - Constructor for class ffx.potential.commands.test.ReorderAtoms: Constructor using Binding.
ReorderAtoms(String[]) - Constructor for class ffx.potential.commands.test.ReorderAtoms: Constructor using args.
repexMC(OrthogonalSpaceTempering, MonteCarloOST, DynamicsOptions, OSTOptions, CompositeConfiguration, String, boolean, double) - Static method in class ffx.algorithms.thermodynamics.RepExOST: Construct a RepExOST for Monte Carlo orthogonal space tempering.
repexMD(OrthogonalSpaceTempering, MolecularDynamics, DynamicsOptions, OSTOptions, CompositeConfiguration, String, double) - Static method in class ffx.algorithms.thermodynamics.RepExOST: Construct a RepExOST for Molecular Dynamics orthogonal space tempering.
RepExOptions - Class in ffx.algorithms.cli
RepExOptions() - Constructor for class ffx.algorithms.cli.RepExOptions
RepExOST - Class in ffx.algorithms.thermodynamics: An implementation of RepEx between Orthogonal Space Tempering potentials.
RepexOSTOptions - Class in ffx.algorithms.cli
RepexOSTOptions() - Constructor for class ffx.algorithms.cli.RepexOSTOptions
RepexThermo - Class in ffx.algorithms.commands.test: The RepexThermo command uses the Orthogonal Space Tempering with histogram replica exchange to estimate a free energy difference.
RepexThermo() - Constructor for class ffx.algorithms.commands.test.RepexThermo: RepexThermo Constructor.
RepexThermo(FFXBinding) - Constructor for class ffx.algorithms.commands.test.RepexThermo: RepexThermo Constructor.
RepexThermo(String[]) - Constructor for class ffx.algorithms.commands.test.RepexThermo: RepexThermo constructor that sets the command line arguments.
ReplicaExchange - Class in ffx.algorithms.dynamics: The ReplicaExchange implements temperature and lambda replica exchange methods.
ReplicaExchange(MolecularDynamics, AlgorithmListener, double, double, boolean) - Constructor for class ffx.algorithms.dynamics.ReplicaExchange: ReplicaExchange constructor.
ReplicatedBoolean - Class in edu.rit.pj.replica: Class ReplicatedBoolean provides a replicated, shared reduction variable for a value of type boolean.
ReplicatedBoolean(BooleanOp) - Constructor for class edu.rit.pj.replica.ReplicatedBoolean: Construct a new replicated, shared Boolean reduction variable with the given reduction operator.
ReplicatedBoolean(BooleanOp, boolean) - Constructor for class edu.rit.pj.replica.ReplicatedBoolean: Construct a new replicated, shared Boolean reduction variable with the given reduction operator and initial value.
ReplicatedBoolean(BooleanOp, boolean, int) - Constructor for class edu.rit.pj.replica.ReplicatedBoolean: Construct a new replicated, shared Boolean reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedBoolean(BooleanOp, boolean, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedBoolean: Construct a new replicated, shared Boolean reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedByte - Class in edu.rit.pj.replica: Class ReplicatedByte provides a replicated, shared reduction variable for a value of type byte.
ReplicatedByte(ByteOp) - Constructor for class edu.rit.pj.replica.ReplicatedByte: Construct a new replicated, shared byte reduction variable with the given reduction operator.
ReplicatedByte(ByteOp, byte) - Constructor for class edu.rit.pj.replica.ReplicatedByte: Construct a new replicated, shared byte reduction variable with the given reduction operator and initial value.
ReplicatedByte(ByteOp, byte, int) - Constructor for class edu.rit.pj.replica.ReplicatedByte: Construct a new replicated, shared byte reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedByte(ByteOp, byte, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedByte: Construct a new replicated, shared byte reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedCharacter - Class in edu.rit.pj.replica: Class ReplicatedCharacter provides a replicated, shared reduction variable for a value of type char.
ReplicatedCharacter(CharacterOp) - Constructor for class edu.rit.pj.replica.ReplicatedCharacter: Construct a new replicated, shared character reduction variable with the given reduction operator.
ReplicatedCharacter(CharacterOp, char) - Constructor for class edu.rit.pj.replica.ReplicatedCharacter: Construct a new replicated, shared character reduction variable with the given reduction operator and initial value.
ReplicatedCharacter(CharacterOp, char, int) - Constructor for class edu.rit.pj.replica.ReplicatedCharacter: Construct a new replicated, shared character reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedCharacter(CharacterOp, char, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedCharacter: Construct a new replicated, shared character reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedDouble - Class in edu.rit.pj.replica: Class ReplicatedDouble provides a replicated, shared reduction variable for a value of type double.
ReplicatedDouble(DoubleOp) - Constructor for class edu.rit.pj.replica.ReplicatedDouble: Construct a new replicated, shared double reduction variable with the given reduction operator.
ReplicatedDouble(DoubleOp, double) - Constructor for class edu.rit.pj.replica.ReplicatedDouble: Construct a new replicated, shared double reduction variable with the given reduction operator and initial value.
ReplicatedDouble(DoubleOp, double, int) - Constructor for class edu.rit.pj.replica.ReplicatedDouble: Construct a new replicated, shared double reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedDouble(DoubleOp, double, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedDouble: Construct a new replicated, shared double reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedFloat - Class in edu.rit.pj.replica: Class ReplicatedFloat provides a replicated, shared reduction variable for a value of type float.
ReplicatedFloat(FloatOp) - Constructor for class edu.rit.pj.replica.ReplicatedFloat: Construct a new replicated, shared float reduction variable with the given reduction operator.
ReplicatedFloat(FloatOp, float) - Constructor for class edu.rit.pj.replica.ReplicatedFloat: Construct a new replicated, shared float reduction variable with the given reduction operator and initial value.
ReplicatedFloat(FloatOp, float, int) - Constructor for class edu.rit.pj.replica.ReplicatedFloat: Construct a new replicated, shared float reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedFloat(FloatOp, float, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedFloat: Construct a new replicated, shared float reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedInteger - Class in edu.rit.pj.replica: Class ReplicatedInteger provides a replicated, shared reduction variable for a value of type int.
ReplicatedInteger(IntegerOp) - Constructor for class edu.rit.pj.replica.ReplicatedInteger: Construct a new replicated, shared integer reduction variable with the given reduction operator.
ReplicatedInteger(IntegerOp, int) - Constructor for class edu.rit.pj.replica.ReplicatedInteger: Construct a new replicated, shared integer reduction variable with the given reduction operator and initial value.
ReplicatedInteger(IntegerOp, int, int) - Constructor for class edu.rit.pj.replica.ReplicatedInteger: Construct a new replicated, shared integer reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedInteger(IntegerOp, int, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedInteger: Construct a new replicated, shared integer reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedLong - Class in edu.rit.pj.replica: Class ReplicatedLong provides a replicated, shared reduction variable for a value of type long.
ReplicatedLong(LongOp) - Constructor for class edu.rit.pj.replica.ReplicatedLong: Construct a new replicated, shared long reduction variable with the given reduction operator.
ReplicatedLong(LongOp, long) - Constructor for class edu.rit.pj.replica.ReplicatedLong: Construct a new replicated, shared long reduction variable with the given reduction operator and initial value.
ReplicatedLong(LongOp, long, int) - Constructor for class edu.rit.pj.replica.ReplicatedLong: Construct a new replicated, shared long reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedLong(LongOp, long, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedLong: Construct a new replicated, shared long reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedObject<T> - Class in edu.rit.pj.replica: Class ReplicatedObject provides a replicated, shared reduction variable for a value of type T (a nonprimitive type).
ReplicatedObject(ObjectOp<T>) - Constructor for class edu.rit.pj.replica.ReplicatedObject: Construct a new replicated, shared object reduction variable with the given reduction operator.
ReplicatedObject(ObjectOp<T>, T) - Constructor for class edu.rit.pj.replica.ReplicatedObject: Construct a new replicated, shared object reduction variable with the given reduction operator and initial value.
ReplicatedObject(ObjectOp<T>, T, int) - Constructor for class edu.rit.pj.replica.ReplicatedObject: Construct a new replicated, shared object reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedObject(ObjectOp<T>, T, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedObject: Construct a new replicated, shared object reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatedShort - Class in edu.rit.pj.replica: Class ReplicatedShort provides a replicated, shared reduction variable for a value of type short.
ReplicatedShort(ShortOp) - Constructor for class edu.rit.pj.replica.ReplicatedShort: Construct a new replicated, shared short reduction variable with the given reduction operator.
ReplicatedShort(ShortOp, short) - Constructor for class edu.rit.pj.replica.ReplicatedShort: Construct a new replicated, shared short reduction variable with the given reduction operator and initial value.
ReplicatedShort(ShortOp, short, int) - Constructor for class edu.rit.pj.replica.ReplicatedShort: Construct a new replicated, shared short reduction variable with the given reduction operator, initial value, and message tag.
ReplicatedShort(ShortOp, short, int, Comm) - Constructor for class edu.rit.pj.replica.ReplicatedShort: Construct a new replicated, shared short reduction variable with the given reduction operator, initial value, message tag, and communicator.
ReplicatesCrystal - Class in ffx.crystal: The ReplicatesCrystal class extends Crystal to generate additional symmetry operators needed to describe a "replicated" super-cell.
ReplicatesCrystal(Crystal, int, int, int, double) - Constructor for class ffx.crystal.ReplicatesCrystal: Constructor for a ReplicatesCrystal.
replicatesCrystalFactory(Crystal, double) - Static method in class ffx.crystal.ReplicatesCrystal: Returns a ReplicatesCrystal large enough to satisfy the minimum image convention for the specified unit cell and cutoff criteria.
replicatesCrystalFactory(Crystal, double, int[]) - Static method in class ffx.crystal.ReplicatesCrystal: Returns a ReplicatesCrystal large enough to satisfy the minimum image convention for the specified unit cell and cutoff criteria.
replicatesVector - Variable in class ffx.crystal.SymOp: Replicates position for the given symmetry operator (LxMxN).
report() - Method in class ffx.numerics.estimator.FreeEnergyDifferenceReporter: Report the free energy differences.
reportComment(JobBackendRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontend: Report a comment for a process.
reportComment(JobBackendRef, int, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "report comment" message.
reportComment(JobBackendRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Report a comment for a process.
reportComment(JobBackendRef, int, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Report a comment for a process.
reportComment(JobBackendRef, int, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Report a comment for a process.
reportComment(JobFrontendRef, int, String) - Method in class edu.rit.pj.cluster.JobScheduler: Report a comment for a process.
reportComment(JobFrontendRef, int, String) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "report comment" message.
reportComment(JobFrontendRef, int, String) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Report a comment for a process.
reportComment(JobFrontendRef, int, String) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Report a comment for a process.
reportFailure(IOException) - Method in class edu.rit.mp.IORequest: Report that this I/O request failed with an I/O exception.
reportResource(JobFrontendRef, String, byte[]) - Method in class edu.rit.pj.cluster.JobBackend: Report the content for a previously-requested resource.
reportResource(JobFrontendRef, String, byte[]) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "report resource" message.
reportResource(JobFrontendRef, String, byte[]) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the content for a previously-requested resource.
reportResource(JobFrontendRef, String, byte[]) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the content for a previously-requested resource.
reportResource(JobFrontendRef, String, ByteSequence) - Method in class edu.rit.pj.cluster.JobBackend: Report the content for a previously-requested resource.
reportResource(JobFrontendRef, String, ByteSequence) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "report resource" message.
reportResource(JobFrontendRef, String, ByteSequence) - Method in class edu.rit.pj.cluster.JobBackendProxy: Report the content for a previously-requested resource.
reportResource(JobFrontendRef, String, ByteSequence) - Method in interface edu.rit.pj.cluster.JobBackendRef: Report the content for a previously-requested resource.
reportSuccess() - Method in class edu.rit.mp.IORequest: Report that this I/O request succeeded.
requestJob(JobFrontendRef, String, int, int, int) - Method in class edu.rit.pj.cluster.JobScheduler: Request that a job be scheduled.
requestJob(JobFrontendRef, String, int, int, int) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "request job" message.
requestJob(JobFrontendRef, String, int, int, int) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Request that a job be scheduled.
requestJob(JobFrontendRef, String, int, int, int) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Request that a job be scheduled.
requestResource(JobBackendRef, String) - Method in class edu.rit.pj.cluster.JobFrontend: Request the given resource from this job frontend's class loader.
requestResource(JobBackendRef, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "request resource" message.
requestResource(JobBackendRef, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Request the given resource from this job frontend's class loader.
requestResource(JobBackendRef, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Request the given resource from this job frontend's class loader.
requestResource(JobBackendRef, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Request the given resource from this job frontend's class loader.
res(HKL) - Method in class ffx.crystal.Crystal: res
ReSearch - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Search was restarted.
RESERVED - Enum constant in enum class edu.rit.pj.cluster.BackendInfo.State: The backend is reserved for a job that has not yet started running.
reset - Variable in class ffx.ui.behaviors.MouseBehavior
reset() - Method in class edu.rit.mp.ObjectBuf: Reset this buffer.
reset() - Method in class ffx.numerics.math.RunningStatistics: Add a RunningStatistics object to this one.
reset() - Method in class ffx.ui.MainPanel: reset
reset(int, int, int) - Method in class ffx.numerics.atomic.AdderDoubleArray: Reset the double array values to zero within the specified bounds.
reset(int, int, int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Reset the double array values to zero within the specified bounds.
reset(int, int, int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Reset the double array to Zero.
reset(int, int, int) - Method in class ffx.numerics.atomic.MultiDoubleArray: Reset the double array values to zero within the specified bounds.
reset(int, int, int) - Method in class ffx.numerics.atomic.PJDoubleArray: Reset the double array values to zero within the specified bounds.
reset(ParallelTeam) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Reset the double array to Zero.
reset(ParallelTeam, int, int) - Method in class ffx.numerics.atomic.AdderDoubleArray: Reset the double array values to zero within the specified bounds using a ParallelTeam.
reset(ParallelTeam, int, int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Reset the double array values to zero within the specified bounds using a ParallelTeam.
reset(ParallelTeam, int, int) - Method in class ffx.numerics.atomic.MultiDoubleArray: Reset the double array values to zero within the specified bounds using a ParallelTeam.
reset(ParallelTeam, int, int) - Method in class ffx.numerics.atomic.PJDoubleArray: Reset the double array values to zero within the specified bounds using a ParallelTeam.
resetHistogramAtLambda() - Method in class ffx.algorithms.thermodynamics.HistogramData
resetSource() - Method in class ffx.numerics.multipole.CombinedTensorGlobal: Reset the source terms.
resetUnitCellParams() - Method in enum class ffx.crystal.LatticeSystem: Reset lattice parameters for the given lattice systems.
residual(boolean, boolean) - Method in class ffx.potential.nonbonded.COMRestraint: residual.
residual(boolean, boolean) - Method in class ffx.potential.nonbonded.NCSRestraint: residual.
residue - Variable in exception class ffx.potential.bonded.BondedUtils.MissingAtomTypeException
Residue - Class in ffx.potential.bonded: The Residue class represents individual amino acids or nucleic acid bases.
Residue(int, Residue.ResidueType) - Constructor for class ffx.potential.bonded.Residue: Default Constructor where num is this Residue's position in the Polymer.
Residue(String, int, MSNode, Residue.ResidueType, ForceField) - Constructor for class ffx.potential.bonded.Residue: As above, with atoms being a MSNode with this Residue's atoms as child nodes
Residue(String, int, Residue.ResidueType) - Constructor for class ffx.potential.bonded.Residue: Name is the residue's 3 letter abbreviation and num is its position in the Polymer.
Residue(String, int, Residue.ResidueType, Character, String) - Constructor for class ffx.potential.bonded.Residue: Name is the residue's 3 letter abbreviation and num is its position in the Polymer.
Residue(String, Residue.ResidueType) - Constructor for class ffx.potential.bonded.Residue: Constructor for Residue.
RESIDUE - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.DistanceMethod
RESIDUE - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
RESIDUE_DISTANCE - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
Residue.ResidueType - Enum Class in ffx.potential.bonded: Residue type [NA, AA, UNK].
Residue.SSType - Enum Class in ffx.potential.bonded
residueInsideCell(Residue, Crystal, SymOp, boolean) - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Checks if a Residue is inside this BoxOptCell.
residueNames - Variable in class ffx.potential.extended.ExtendedSystem: Array of AminoAcid3 initialized to match the number of atoms in the system.
ResidueState - Class in ffx.potential.bonded: The ResidueState class encodes the current chemical and coordinate state of a Residue, particularly a MultiResidue, for ease of reverting coordinates.
ResidueState(Residue) - Constructor for class ffx.potential.bonded.ResidueState: Constructor for ResidueState.
ResidueState(Residue, Residue) - Constructor for class ffx.potential.bonded.ResidueState: Constructor for ResidueState.
resize(int) - Method in class ffx.openmm.BondArray: Resize the bond array.
resize(int) - Method in class ffx.openmm.DoubleArray: Resize the array.
resize(int) - Method in class ffx.openmm.IntArray: Resize the array.
resize(int) - Method in class ffx.openmm.StringArray: Resize the String Array.
resize(int) - Method in class ffx.openmm.Vec3Array: Resize the Vec3Array.
Resnum_Name - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
resolution - Variable in class ffx.crystal.ReflectionList: Resolution instance.
resolution - Variable in class ffx.crystal.Resolution: The resolution of the data set.
Resolution - Class in ffx.crystal: The Resolution class encapsulates the sampling limits and resolution limits for a given crystal and/or data set.
Resolution(double) - Constructor for class ffx.crystal.Resolution: Constructor for Resolution.
Resolution(double, double) - Constructor for class ffx.crystal.Resolution: Constructor for Resolution.
resolutionLimit() - Method in class ffx.crystal.Resolution: resolutionLimit
resolveEntity(String, String) - Method in class ffx.ui.commands.DTDResolver
resolvePolymerLinks(List<MSNode>, MolecularAssembly, List<Bond>) - Static method in class ffx.potential.bonded.PolymerUtils: Resolves links between polymeric hetero groups; presently only functional for cyclic molecules.
resolveUnclaimedPoints(FaceList) - Method in class ffx.numerics.quickhull.QuickHull3D: Assigns previously unclaimed vertices to the newly created faces most distant above them.
ResourceCache - Class in edu.rit.pj.cluster: Class ResourceCache provides a cache of resources, indexed by resource name.
ResourceCache() - Constructor for class edu.rit.pj.cluster.ResourceCache: Construct a new resource cache.
Resources - Class in ffx.utilities: Log resources.
Respa - Class in ffx.algorithms.dynamics.integrators: Respa performs multiple time step molecular dynamics using the reversible reference system propagation algorithm (r-RESPA) via a Verlet core with the potential split into fast- and slow-evolving portions.
Respa(SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.Respa: Initialize Respa multiple time step molecular dynamics.
RESPA - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
respectsChirality - Variable in class ffx.crystal.SpaceGroup: True for a Sohncke group (non-enantiogenic).
respectsChirality() - Method in class ffx.crystal.SpaceGroup: Check if the space group maintains chirality.
restart() - Method in class edu.rit.util.RandomSubset: Restart this random subset's iteration.
RESTART - Enum constant in enum class ffx.algorithms.dynamics.MDWriteAction
restartFrequency - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Time steps between writing out restart/checkpoint files.
restartInterval - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Time between writing out restart/checkpoint files in picoseconds.
RestrainDistance - Class in ffx.potential.bonded: RestraintDistance class.
RestrainDistance(Atom, Atom, Crystal, boolean, double, double, UnivariateSwitchingFunction) - Constructor for class ffx.potential.bonded.RestrainDistance: Creates a distance restraint between two Atoms.
RestrainDistanceForce - Class in ffx.potential.openmm: Restrain-Distance Force.
RestrainDistanceForce(BondType.BondFunction, RestrainDistancePotentialEnergy) - Constructor for class ffx.potential.openmm.RestrainDistanceForce: Restrain Bond Force constructor.
RestrainDistancePotentialEnergy - Class in ffx.potential.terms: Restrain-Distance potential energy term using RestrainDistance instances.
RestrainDistancePotentialEnergy(String) - Constructor for class ffx.potential.terms.RestrainDistancePotentialEnergy: Create a RestrainDistancePotentialEnergy with the provided name.
RestrainDistancePotentialEnergy(String, int) - Constructor for class ffx.potential.terms.RestrainDistancePotentialEnergy: Create a RestrainDistancePotentialEnergy with the provided name and force group.
RestrainDistancePotentialEnergy(String, int, List<RestrainDistance>) - Constructor for class ffx.potential.terms.RestrainDistancePotentialEnergy: Create a RestrainDistancePotentialEnergy initialized with a list of terms and force group.
RestrainDistancePotentialEnergy(String, Collection<RestrainDistance>) - Constructor for class ffx.potential.terms.RestrainDistancePotentialEnergy: Create a RestrainDistancePotentialEnergy initialized with a collection of terms.
RestrainGroups - Class in ffx.potential.nonbonded: Apply a restraint between groups.
RestrainGroups(MolecularAssembly) - Constructor for class ffx.potential.nonbonded.RestrainGroups: Group Restraint Constructor.
restrainGroupsForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Restrain-Groups Force.
RestrainGroupsForce - Class in ffx.potential.openmm: Restrain Groups Force.
RestrainGroupsForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.RestrainGroupsForce: Restrain Groups Force constructor.
RestrainPosition - Class in ffx.potential.bonded: Restrain the position of atoms to their initial coordinates.
RestrainPosition(Atom[], double[][], double, double, boolean) - Constructor for class ffx.potential.bonded.RestrainPosition: Restrain atoms to a position in the global coordinate frame.
RestrainPositionPotentialEnergy - Class in ffx.potential.terms: Restrain-Position potential energy term using RestrainPosition instances.
RestrainPositionPotentialEnergy(String) - Constructor for class ffx.potential.terms.RestrainPositionPotentialEnergy: Create a RestrainPositionPotentialEnergy with the provided name.
RestrainPositionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.RestrainPositionPotentialEnergy: Create a RestrainPositionPotentialEnergy with the provided name and force group.
RestrainPositionPotentialEnergy(String, int, List<RestrainPosition>) - Constructor for class ffx.potential.terms.RestrainPositionPotentialEnergy: Create a RestrainPositionPotentialEnergy initialized with a list of terms and force group.
RestrainPositionPotentialEnergy(String, Collection<RestrainPosition>) - Constructor for class ffx.potential.terms.RestrainPositionPotentialEnergy: Create a RestrainPositionPotentialEnergy initialized with a collection of terms.
restrainPositionsForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Restrain-Position Force.
RestrainPositionsForce - Class in ffx.potential.openmm: Restrain Positions Force.
RestrainPositionsForce(RestrainPositionPotentialEnergy) - Constructor for class ffx.potential.openmm.RestrainPositionsForce: Restrain Positions Force constructor.
RestrainTorsion - Class in ffx.potential.bonded: RestraintTorsion is a class that restrains the torsion angle defined by four atoms.
RestrainTorsion(Atom, Atom, Atom, Atom, TorsionType, boolean, boolean, double) - Constructor for class ffx.potential.bonded.RestrainTorsion: Constructor for RestrainTorsion.
RestrainTorsionPotentialEnergy - Class in ffx.potential.terms: Restrain-Torsion potential energy term using Torsion instances.
RestrainTorsionPotentialEnergy(String) - Constructor for class ffx.potential.terms.RestrainTorsionPotentialEnergy: Create a RestrainTorsionPotentialEnergy with the provided name.
RestrainTorsionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.RestrainTorsionPotentialEnergy: Create a RestrainTorsionPotentialEnergy with the provided name and force group.
RestrainTorsionPotentialEnergy(String, int, List<Torsion>) - Constructor for class ffx.potential.terms.RestrainTorsionPotentialEnergy: Create a RestrainTorsionPotentialEnergy initialized with a list of torsions and force group.
RestrainTorsionPotentialEnergy(String, Collection<Torsion>) - Constructor for class ffx.potential.terms.RestrainTorsionPotentialEnergy: Create a RestrainTorsionPotentialEnergy initialized with a collection of torsions.
restrainTorsionsForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Restraint-Torsion Force.
RestrainTorsionsForce - Class in ffx.potential.openmm: Restrain Torsions Force.
RestrainTorsionsForce(RestrainTorsionPotentialEnergy) - Constructor for class ffx.potential.openmm.RestrainTorsionsForce: Restrain Torsion Force constructor.
RestrainTorsionsForce(RestrainTorsionPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.RestrainTorsionsForce: Restrain Torsion Force constructor for Dual Topology.
restrainTorsionsForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Restrain Torsion Force for topology 2.
RESTRICT - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
returnEnergy(MolecularAssembly) - Method in interface ffx.potential.utils.PotentialsFunctions: Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluation
returnEnergy(MolecularAssembly) - Method in class ffx.potential.utils.PotentialsUtils: Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluation
returnEnergy(MolecularAssembly) - Method in class ffx.ui.UIUtils
reverse() - Method in class ffx.numerics.clustering.ClusterPair: Creates a new ClusterPair with left and right clusters swapped.
reverseKey(int[]) - Static method in class ffx.potential.parameters.TorsionTorsionType: Reversed key for the Torsion-Torsion lookup.
reversible - Variable in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
revert - Variable in class ffx.algorithms.optimize.RotamerOptimization: In sliding window, whether to revert an unfavorable change.
REVERT - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
revertAllCoordinates(List<Residue>, ResidueState[]) - Static method in class ffx.potential.bonded.ResidueState: revertAllCoordinates.
revertAtomicCoordinates(Atom[], double[][]) - Static method in class ffx.potential.bonded.ResidueState: Uses a double[nAtoms][3] to revert the coordinates of an array of atoms.
revertMove() - Method in class ffx.algorithms.mc.LambdaMove: Reverts the last applied move() call.
revertMove() - Method in interface ffx.algorithms.mc.MCMove: Reverts the last applied move() call.
revertMove() - Method in class ffx.algorithms.mc.MDMove: Reverts the last applied move() call.
revertMove() - Method in class ffx.algorithms.mc.RosenbluthChi0Move: Reverts the last applied move() call.
revertMove() - Method in class ffx.algorithms.mc.RosenbluthChiAllMove: Reverts the last applied move() call.
revertMove() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMove
revertState() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Revert the state of the MolecularDynamics instance to the stored MDState.
revertState() - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
revertState() - Method in class ffx.potential.AssemblyState: Revert the state of the associated MolecularAssembly, assuming no chemical changes were made except to MultiResidues.
revertState(ResidueState) - Method in class ffx.potential.bonded.MultiResidue
revertState(ResidueState) - Method in class ffx.potential.bonded.Residue: revertState.
revertState(UnmodifiableState) - Method in class ffx.potential.SystemState: Revert the current state to the passed UnmodifiableState.
revertStep() - Method in interface ffx.algorithms.mc.MetropolisMC: If possible, reverts the last successful Monte Carlo step taken.
revertStep() - Method in class ffx.algorithms.mc.MolecularMC: If possible, reverts the last successful Monte Carlo step taken.
revertStep() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMC
revertStep() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: If possible, reverts the last successful Monte Carlo step taken.
Rf - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
rFreeFlag - Variable in class ffx.xray.DiffractionRefinementData: Duplicated settings - these are also in DiffractionData, but duplicated here until settings are put in their own class.
Rh - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
rho(double, double, double) - Method in class ffx.xray.SolventBinaryFormFactor: rho
rho(double, double, double) - Method in class ffx.xray.SolventGaussFormFactor: rho
rho(double, double, double) - Method in class ffx.xray.SolventPolyFormFactor: rho
rho(double, double, double[]) - Method in interface ffx.xray.FormFactor: Compute the real space density rho
rho(double, double, double[]) - Method in class ffx.xray.NeutronFormFactor: Compute the real space density rho
rho(double, double, double[]) - Method in class ffx.xray.SolventBinaryFormFactor: Compute the real space density rho
rho(double, double, double[]) - Method in class ffx.xray.SolventGaussFormFactor: Compute the real space density rho
rho(double, double, double[]) - Method in class ffx.xray.SolventPolyFormFactor: Compute the real space density rho
rho(double, double, double[]) - Method in class ffx.xray.XRayFormFactor: Compute the real space density rho
rhoGrad(double[], double, RefinementMinimize.RefinementMode) - Method in interface ffx.xray.FormFactor: Compute the real space gradient
rhoGrad(double[], double, RefinementMinimize.RefinementMode) - Method in class ffx.xray.NeutronFormFactor: Compute the real space gradient
rhoGrad(double[], double, RefinementMinimize.RefinementMode) - Method in class ffx.xray.SolventBinaryFormFactor: Derivatives are zero or infinite for the binary model.
rhoGrad(double[], double, RefinementMinimize.RefinementMode) - Method in class ffx.xray.SolventGaussFormFactor: Compute the real space gradient
rhoGrad(double[], double, RefinementMinimize.RefinementMode) - Method in class ffx.xray.SolventPolyFormFactor: Compute the real space gradient
rhoGrad(double[], double, RefinementMinimize.RefinementMode) - Method in class ffx.xray.XRayFormFactor: Compute the real space gradient
RHOMBOHEDRAL_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem: Rhombohedral lattice system.
RIBBON - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
Richardson - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary
RICHARDSON - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.NucleicAcidLibrary
RIGHT - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationSide: Right-hand integration.
rightBoole(double[]) - Static method in class ffx.numerics.integrate.Integration: rightBoole.
rightRectangularMethod(double[]) - Static method in class ffx.numerics.integrate.Integration: rightRectangularMethod.
rightSimpsons(double[]) - Static method in class ffx.numerics.integrate.Integration: rightSimpsons.
rightTrapInput(double[]) - Static method in class ffx.numerics.integrate.Integration: rightTrapInput.
rlmn(int, int, int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Convenience method for writing out tensor indices.
RMIN - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
RMSCoordDev(MolecularAssembly, MolecularAssembly) - Static method in class ffx.potential.Utilities: Finds the RMS deviation between the atoms of MolecularAssembly m1 and m2 provided they have the same number of atoms.
rmsd(double[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: Compute the RMSD for superimposed atom pairs.
RMSD - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
RMSDForce - Class in ffx.openmm: This is a force whose energy equals the root mean squared deviation (RMSD) between the current coordinates and a reference structure.
RMSDForce(PointerByReference, PointerByReference) - Constructor for class ffx.openmm.RMSDForce: Create an RMSDForce.
Rn - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ROLS - Interface in ffx.potential.bonded: The ROLS Interace defines "Recursive Over Length Scales" (ROLS) Methods.
ROLSP - Class in ffx.potential.bonded: The ROLSP class is used for Proof-Of-Concept Parallel Recusive Over Length Scales (ROLS) Methods (currently only on shared memory systems).
ROLSP() - Constructor for class ffx.potential.bonded.ROLSP: Constructor for ROLSP.
ROLSP.PARALLELMETHOD - Enum Class in ffx.potential.bonded
ROOM_TEMPERATURE - Static variable in class ffx.utilities.Constants: Room temperature ~= 298.15 Kelvins.
RosenbluthCBMC - Class in ffx.algorithms.mc: Conformational Biased Monte Carlo (applied to ALL torsions of a peptide side-chain).
RosenbluthCBMC(MolecularAssembly, ForceFieldEnergy, Thermostat, List<Residue>, int, int, boolean) - Constructor for class ffx.algorithms.mc.RosenbluthCBMC: RRMC constructor.
RosenbluthChi0Move - Class in ffx.algorithms.mc: Represents a random chi[0] spin of the target residue.
RosenbluthChiAllMove - Class in ffx.algorithms.mc: Represents a Boltzmann-drawn spin of all residue torsions for use with RosenbluthCBMC (Configurational-Bias Monte Carlo).
RosenbluthChiAllMove.MODE - Enum Class in ffx.algorithms.mc: Mode of the RosenbluthChiAllMove instance.
RosenbluthOBMC - Class in ffx.algorithms.mc: Orientational Biased Monte Carlo (as applied to chi0 torsion of peptide side-chains).
RosenbluthOBMC(MolecularAssembly, ForceFieldEnergy, Thermostat, List<Residue>, int, int) - Constructor for class ffx.algorithms.mc.RosenbluthOBMC: RRMC constructor.
RosenbluthOBMC(MolecularAssembly, ForceFieldEnergy, Thermostat, List<Residue>, int, int, boolean) - Constructor for class ffx.algorithms.mc.RosenbluthOBMC: Constructor for RosenbluthOBMC.
rot - Variable in class ffx.crystal.SymOp: The rotation matrix in fractional coordinates.
Rotamer - Class in ffx.potential.bonded: The Rotamer Class usually represents one immutable amino acid Rotamer.
Rotamer(double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for unknown residue types.
Rotamer(AminoAcidUtils.AminoAcid3, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for Rotamer.
Rotamer(AminoAcidUtils.AminoAcid3, ResidueState, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for Rotamer.
Rotamer(AminoAcidUtils.AminoAcid3, ResidueState, TitrationUtils, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for Rotamer.
Rotamer(AminoAcidUtils.AminoAcid3, TitrationUtils, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for Rotamer.
Rotamer(NucleicAcidUtils.NucleicAcid3, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for Rotamer.
Rotamer(NucleicAcidUtils.NucleicAcid3, ResidueState, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for Rotamer.
Rotamer(NucleicAcidUtils.NucleicAcid3, ResidueState, TitrationUtils, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for Rotamer.
Rotamer(ResidueState, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for unknown residue types.
Rotamer(ResidueState, TitrationUtils, double...) - Constructor for class ffx.potential.bonded.Rotamer: Constructor for unknown residue types.
ROTAMER - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.DistanceMethod
RotamerLibrary - Class in ffx.potential.bonded: The Rotamer Library Class manages a library of side-chain Rotamers for amino acids, and a library of backbone Rotamers for nucleic acids.
RotamerLibrary(boolean) - Constructor for class ffx.potential.bonded.RotamerLibrary: Constructor for RotamerLibrary.
RotamerLibrary(RotamerLibrary.NucleicAcidLibrary, boolean) - Constructor for class ffx.potential.bonded.RotamerLibrary: Constructor for RotamerLibrary.
RotamerLibrary(RotamerLibrary.ProteinLibrary, boolean) - Constructor for class ffx.potential.bonded.RotamerLibrary: Constructor for RotamerLibrary.
RotamerLibrary(RotamerLibrary.ProteinLibrary, RotamerLibrary.NucleicAcidLibrary, boolean) - Constructor for class ffx.potential.bonded.RotamerLibrary: Constructor for RotamerLibrary.
RotamerLibrary.NucleicAcidLibrary - Enum Class in ffx.potential.bonded
RotamerLibrary.NucleicSugarPucker - Enum Class in ffx.potential.bonded
RotamerLibrary.ProteinLibrary - Enum Class in ffx.potential.bonded
RotamerLibrary.RotamerGuess - Class in ffx.potential.bonded
RotamerMatrixMC - Class in ffx.algorithms.optimize.manybody: Monte Carlo driver for DEE-MC.
RotamerMatrixMC(int[], Residue[], boolean, RotamerOptimization) - Constructor for class ffx.algorithms.optimize.manybody.RotamerMatrixMC: The Rotamers array must be the same array as passed to any MCMove objects used (and not a copy).
RotamerMatrixMove - Class in ffx.algorithms.optimize.manybody: This implements single-rotamer changes in the framework of the rotamer energy matrices.
RotamerMatrixMove(boolean, int[], Residue[], RotamerOptimization, EliminatedRotamers, boolean) - Constructor for class ffx.algorithms.optimize.manybody.RotamerMatrixMove: Constructs the RotamerMatrixMove set; at present, a new object must be made if rotamers or residues are changed outside the scope of this class.
rotamerOptimization(MolecularAssembly, Residue[], int, double, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: A brute-force global optimization over side-chain rotamers using a recursive algorithm.
RotamerOptimization - Class in ffx.algorithms.optimize: Optimize protein side-chain conformations and nucleic acid backbone conformations using rotamers.
RotamerOptimization(MolecularAssembly, Potential, AlgorithmListener) - Constructor for class ffx.algorithms.optimize.RotamerOptimization: RotamerOptimization constructor.
RotamerOptimization.Algorithm - Enum Class in ffx.algorithms.optimize: Rotamer Optimization Methods.
RotamerOptimization.Direction - Enum Class in ffx.algorithms.optimize
RotamerOptimization.DistanceMethod - Enum Class in ffx.algorithms.optimize: Allows get2BodyDistance to find the shortest distance between any two rotamers or two residues.
rotate(double[][]) - Method in class ffx.potential.bonded.Atom: Applies a rotation matrix to the atom's coordinates.
rotate(double[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: Minimize the RMS distance between two sets of atoms using quaternions.
ROTATE - Enum constant in enum class ffx.ui.GraphicsCanvas.LeftButtonMode
ROTATE - Static variable in interface ffx.ui.behaviors.MouseBehaviorCallback: Constant ROTATE=0
ROTATE - Static variable in interface ffx.ui.behaviors.PickingCallback: Constant ROTATE=0
rotateAbout(Vector3d) - Method in class ffx.potential.MolecularAssembly: Rotate about a point in given in the System's Local Coordinates
rotateDipole(double[][], double[], double[]) - Static method in class ffx.potential.parameters.MultipoleType: Rotate a dipole vector using a rotation matrix.
rotateInducedDipoles(PolarizableMultipole) - Method in class ffx.numerics.multipole.QIFrame: Rotate the induced dipoles components.
rotateInducedDipoles(PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.QIFrameSIMD: Rotate the induced dipoles components.
rotateMultipole(double[][], double[], double[][], double[], double[][]) - Static method in class ffx.potential.parameters.MultipoleType: Rotate a multipole using a rotation matrix.
rotatePermanentMultipole(PolarizableMultipole) - Method in class ffx.numerics.multipole.QIFrame: Rotate the permanent multipole.
rotatePermanentMultipole(PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.QIFrameSIMD: Rotate the permanent multipole.
rotatePolarizableMultipole(PolarizableMultipole) - Method in class ffx.numerics.multipole.QIFrame: Rotate the permanent multipole and induced dipole.
rotatePolarizableMultipole(PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.QIFrameSIMD: Rotate the permanent multipole and induced dipole.
ROW - Enum constant in enum class ffx.potential.nonbonded.ReciprocalSpace.GridMethod
ROW - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.GridMethod
rowIndexForYZ(int, int) - Method in class ffx.potential.nonbonded.RowRegion: rowIndexForYZ.
rowLength(boolean[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given Boolean matrix.
rowLength(byte[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given byte matrix.
rowLength(char[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given character matrix.
rowLength(double[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given double matrix.
rowLength(float[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given float matrix.
rowLength(int[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given integer matrix.
rowLength(long[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given long matrix.
rowLength(short[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given short matrix.
rowLength(T[][]) - Static method in class edu.rit.util.Arrays: Determine the number of rows in the given object matrix.
rowLoop - Variable in class ffx.potential.nonbonded.RowRegion
RowLoop - Class in ffx.potential.nonbonded: The RowLoop class is used to parallelize placing onto a 3D grid
RowLoop(int, int, RowRegion) - Constructor for class ffx.potential.nonbonded.RowLoop: Constructor for RowLoop.
rowRegion - Variable in class ffx.potential.nonbonded.RowLoop
RowRegion - Class in ffx.potential.nonbonded: The RowRegion class is used to parallelize placing onto a 3D grid
RowRegion(int, int, int, double[], int, int, Atom[], double[][][]) - Constructor for class ffx.potential.nonbonded.RowRegion: Constructor for RowRegion.
rows() - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Returns the number of rows in this matrix reduction variable.
rows() - Method in class edu.rit.pj.reduction.SharedLongMatrix: Returns the number of rows in this matrix reduction variable.
RowSchedule - Class in ffx.xray: RowSchedule class.
RowSchedule(int, int, int) - Constructor for class ffx.xray.RowSchedule: Constructor for RowSchedule.
rowSliceBuffer(boolean[][], Range) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for one row slice of the given Boolean matrix.
rowSliceBuffer(byte[][], Range) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for one row slice of the given byte matrix.
rowSliceBuffer(char[][], Range) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for one row slice of the given character matrix.
rowSliceBuffer(double[][], Range) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for one row slice of the given double matrix.
rowSliceBuffer(float[][], Range) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for one row slice of the given float matrix.
rowSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for one row slice of the given integer matrix.
rowSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for one row slice of the given integer matrix.
rowSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for one row slice of the given integer matrix.
rowSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for one row slice of the given integer matrix.
rowSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for one row slice of the given integer matrix.
rowSliceBuffer(long[][], Range) - Static method in class edu.rit.mp.LongBuf: Create a buffer for one row slice of the given long matrix.
rowSliceBuffer(short[][], Range) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for one row slice of the given short matrix.
rowSliceBuffer(T[][], Range) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for one row slice of the given object matrix.
rowSliceBuffers(boolean[][], Range[]) - Static method in class edu.rit.mp.BooleanBuf: Create an array of buffers for multiple row slices of the given Boolean matrix.
rowSliceBuffers(byte[][], Range[]) - Static method in class edu.rit.mp.ByteBuf: Create an array of buffers for multiple row slices of the given byte matrix.
rowSliceBuffers(char[][], Range[]) - Static method in class edu.rit.mp.CharacterBuf: Create an array of buffers for multiple row slices of the given character matrix.
rowSliceBuffers(double[][], Range[]) - Static method in class edu.rit.mp.DoubleBuf: Create an array of buffers for multiple row slices of the given double matrix.
rowSliceBuffers(float[][], Range[]) - Static method in class edu.rit.mp.FloatBuf: Create an array of buffers for multiple row slices of the given float matrix.
rowSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.IntegerBuf: Create an array of buffers for multiple row slices of the given integer matrix.
rowSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an array of buffers for multiple row slices of the given integer matrix.
rowSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an array of buffers for multiple row slices of the given integer matrix.
rowSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an array of buffers for multiple row slices of the given integer matrix.
rowSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an array of buffers for multiple row slices of the given integer matrix.
rowSliceBuffers(long[][], Range[]) - Static method in class edu.rit.mp.LongBuf: Create an array of buffers for multiple row slices of the given long matrix.
rowSliceBuffers(short[][], Range[]) - Static method in class edu.rit.mp.ShortBuf: Create an array of buffers for multiple row slices of the given short matrix.
rowSliceBuffers(T[][], Range[]) - Static method in class edu.rit.mp.ObjectBuf: Create an array of buffers for multiple row slices of the given object matrix.
rtValues - Variable in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
Ru - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
run() - Method in class edu.rit.pj.BarrierAction: Execute this barrier action.
run() - Method in class edu.rit.pj.cluster.JobBackend: Run this Job Backend.
run() - Method in class edu.rit.pj.cluster.JobFrontend: Run this Job Frontend.
run() - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Run this Non-PJ Job Frontend.
run() - Method in class edu.rit.pj.job.Job: Run this job.
run() - Method in class edu.rit.pj.KillRegion: Execute parallel code.
run() - Method in class edu.rit.pj.ParallelRegion: Execute parallel code.
run() - Method in class edu.rit.pj.ParallelSection: Execute this parallel section.
run() - Method in class edu.rit.pj.WorkerRegion: Execute parallel code.
run() - Method in class edu.rit.util.TimerThread: Perform this timer thread's processing.
run() - Method in class ffx.algorithms.commands.AnalyzeNEQ: Execute this Command.
run() - Method in class ffx.algorithms.commands.Anneal: Execute this Command.
run() - Method in class ffx.algorithms.commands.BAR: Execute this Command.
run() - Method in class ffx.algorithms.commands.Cluster: Execute the script.
run() - Method in class ffx.algorithms.commands.Dynamics: Execute this Command.
run() - Method in class ffx.algorithms.commands.ForEachFile: Execute this Command.
run() - Method in class ffx.algorithms.commands.GenZ: Execute this Command.
run() - Method in class ffx.algorithms.commands.Histogram: Execute this Command.
run() - Method in class ffx.algorithms.commands.ManyBody: Execute this Command.
run() - Method in class ffx.algorithms.commands.MBAR: Execute this Command.
run() - Method in class ffx.algorithms.commands.Minimize: Execute this Command.
run() - Method in class ffx.algorithms.commands.MinimizeCrystals: Execute this Command.
run() - Method in class ffx.algorithms.commands.MinimizeOpenMM: Execute this Command.
run() - Method in class ffx.algorithms.commands.MutatePDB: Execute the script.
run() - Method in class ffx.algorithms.commands.SaveRotamers
run() - Method in class ffx.algorithms.commands.Scheduler: Execute this Command.
run() - Method in class ffx.algorithms.commands.SortArc
run() - Method in class ffx.algorithms.commands.Superpose: Execute the script.
run() - Method in class ffx.algorithms.commands.SuperposeCrystals
run() - Method in class ffx.algorithms.commands.test.ApplyTorsions: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.CoformerBindingSearch: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.CreateRotamers: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.CrystalSearch: Execute the script.
run() - Method in class ffx.algorithms.commands.test.FindRestraints: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.Freefix: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.IdentifyRotamers: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.ManyBodyPhScan: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.MinimizePh: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.MostBar: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.OSTGradient: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.PhDynamics: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.RaoBlackwellEstimator
run() - Method in class ffx.algorithms.commands.test.RepexThermo: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.SortXPH: Execute this Command.
run() - Method in class ffx.algorithms.commands.test.WeightedEnsemble: Execute this Command.
run() - Method in class ffx.algorithms.commands.Thermodynamics: Execute this Command.
run() - Method in class ffx.algorithms.commands.TorsionScan
run() - Method in class ffx.algorithms.dynamics.MolecularDynamics
run() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
run() - Method in class ffx.algorithms.optimize.manybody.DistanceRegion
run() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
run() - Method in class ffx.algorithms.optimize.manybody.FourBodyEnergyRegion
run() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
run() - Method in class ffx.algorithms.optimize.manybody.SelfEnergyRegion
run() - Method in class ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
run() - Method in class ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
run() - Method in class ffx.potential.bonded.ROLSP
run() - Method in class ffx.potential.commands.Biotype
run() - Method in class ffx.potential.commands.Cart2Frac
run() - Method in class ffx.potential.commands.ChainBreaks
run() - Method in class ffx.potential.commands.Density
run() - Method in class ffx.potential.commands.Energy
run() - Method in class ffx.potential.commands.ExportQE
run() - Method in class ffx.potential.commands.Fasta
run() - Method in class ffx.potential.commands.FeatureMap
run() - Method in class ffx.potential.commands.FFtoXML
run() - Method in class ffx.potential.commands.Frac2Cart
run() - Method in class ffx.potential.commands.ImportCIF
run() - Method in class ffx.potential.commands.MoveIntoUnitCell
run() - Method in class ffx.potential.commands.NucleicAcidAnalysis
run() - Method in class ffx.potential.commands.PhEnergy: Execute the script.
run() - Method in class ffx.potential.commands.PrepareSpaceGroups
run() - Method in class ffx.potential.commands.SaveAsP1
run() - Method in class ffx.potential.commands.SaveAsPDB
run() - Method in class ffx.potential.commands.SaveAsXYZ
run() - Method in class ffx.potential.commands.Solvator
run() - Method in class ffx.potential.commands.test.Gradient: Execute the script.
run() - Method in class ffx.potential.commands.test.LambdaGradient: Script run method.
run() - Method in class ffx.potential.commands.test.PhGradient: Execute the script.
run() - Method in class ffx.potential.commands.test.PrmToProperty: Execute the script.
run() - Method in class ffx.potential.commands.test.ReorderAtoms
run() - Method in class ffx.potential.commands.test.SaveAsConstantPhPDB: Execute the script.
run() - Method in class ffx.potential.commands.Timer
run() - Method in class ffx.potential.commands.Volume
run() - Method in class ffx.potential.commands.VolumeArc
run() - Method in class ffx.potential.commands.WriteRestraints
run() - Method in class ffx.potential.nonbonded.implicit.BornGradRegion
run() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
run() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
run() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: Execute parallel code.
run() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
run() - Method in class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
run() - Method in class ffx.potential.nonbonded.implicit.InducedGKFieldRegion
run() - Method in class ffx.potential.nonbonded.implicit.InitializationRegion
run() - Method in class ffx.potential.nonbonded.implicit.PermanentGKFieldRegion
run() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
run() - Method in class ffx.potential.nonbonded.NeighborList: Execute parallel code.
run() - Method in class ffx.potential.nonbonded.pme.DirectRegion
run() - Method in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
run() - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
run() - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
run() - Method in class ffx.potential.nonbonded.pme.InitializationRegion
run() - Method in class ffx.potential.nonbonded.pme.OPTRegion
run() - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
run() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
run() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
run() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
run() - Method in class ffx.potential.nonbonded.pme.ReduceRegion
run() - Method in class ffx.potential.nonbonded.pme.SORRegion
run() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion
run() - Method in class ffx.potential.nonbonded.RowRegion: Execute parallel code.
run() - Method in class ffx.potential.nonbonded.SliceRegion: Execute parallel code.
run() - Method in class ffx.potential.nonbonded.SpatialDensityRegion: Execute parallel code.
run() - Method in interface ffx.potential.parsers.FileOpener
run() - Method in class ffx.potential.terms.EnergyTermRegion
run() - Method in class ffx.potential.utils.PotentialsFileOpener
run() - Method in class ffx.realspace.commands.Anneal
run() - Method in class ffx.realspace.commands.Dynamics
run() - Method in class ffx.realspace.commands.GenZ: Execute this Command.
run() - Method in class ffx.realspace.commands.ManyBody
run() - Method in class ffx.realspace.commands.Minimize
run() - Method in class ffx.realspace.commands.test.Alchemical
run() - Method in class ffx.realspace.commands.test.LambdaGradient
run() - Method in class ffx.ui.commands.FFXServer: run
run() - Method in class ffx.ui.FFXExec: Executes the native call to "System()" and notifies the ResultPanel upon completion.
run() - Method in class ffx.ui.ModelingShell: Configure the Swing GUI for the shell.
run() - Method in class ffx.ui.UIFileCloser
run() - Method in class ffx.ui.UIFileOpener
run() - Method in class ffx.utilities.FFXCommand: Execute this Command.
run() - Method in class ffx.xray.BulkSolventDensityRegion: Execute parallel code.
run() - Method in class ffx.xray.BulkSolventList: Execute parallel code.
run() - Method in class ffx.xray.BulkSolventRowRegion: Execute parallel code.
run() - Method in class ffx.xray.BulkSolventSliceRegion: Execute parallel code.
run() - Method in class ffx.xray.commands.Anneal
run() - Method in class ffx.xray.commands.AverageMTZ
run() - Method in class ffx.xray.commands.CIFtoMTZ: Execute the script.
run() - Method in class ffx.xray.commands.ComputeFc
run() - Method in class ffx.xray.commands.Deuterate: Execute the script.
run() - Method in class ffx.xray.commands.Dynamics
run() - Method in class ffx.xray.commands.GenZ: Execute this Command.
run() - Method in class ffx.xray.commands.ManyBody
run() - Method in class ffx.xray.commands.Minimize
run() - Method in class ffx.xray.commands.ModelvsData
run() - Method in class ffx.xray.commands.MTZInfo: Execute the script.
run() - Method in class ffx.xray.commands.SaveConformerPDB
run() - Method in class ffx.xray.commands.test.Alchemical
run() - Method in class ffx.xray.commands.test.LambdaGradient: Execute this Command.
run() - Method in class ffx.xray.commands.Timer: Execute this Command.
run(int, int) - Method in class edu.rit.pj.IntegerForLoop: Execute one chunk of iterations of this parallel for loop.
run(int, int) - Method in class edu.rit.pj.WorkerIntegerForLoop: Execute one chunk of iterations of this worker for loop.
run(int, int) - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
run(int, int) - Method in class ffx.potential.nonbonded.RowLoop: Execute one chunk of iterations of this parallel for loop.
run(int, int) - Method in class ffx.potential.nonbonded.SliceLoop: Execute one chunk of iterations of this parallel for loop.
run(int, int) - Method in class ffx.potential.nonbonded.SpatialDensityLoop: Execute one chunk of iterations of this parallel for loop.
run(int, int, int) - Method in class edu.rit.pj.IntegerStrideForLoop: Execute one chunk of iterations of this parallel for loop.
run(int, int, int) - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Execute one chunk of iterations of this worker for loop.
run(long, long) - Method in class edu.rit.pj.LongForLoop: Execute one chunk of iterations of this parallel for loop.
run(long, long) - Method in class edu.rit.pj.WorkerLongForLoop: Execute one chunk of iterations of this worker for loop.
run(long, long, double, double) - Method in class ffx.algorithms.dynamics.WeightedEnsembleManager: Run the Weighted Ensemble algorithm.
run(long, long, long) - Method in class edu.rit.pj.LongStrideForLoop: Execute one chunk of iterations of this parallel for loop.
run(long, long, long) - Method in class edu.rit.pj.WorkerLongStrideForLoop: Execute one chunk of iterations of this worker for loop.
run(LambdaMode) - Method in class ffx.potential.nonbonded.ScfPredictor: run.
run(T) - Method in class edu.rit.pj.ParallelIteration: Process one item in this parallel iteration.
run(T) - Method in class edu.rit.pj.WorkerIteration: Process one item in this worker iteration.
runFFXScript(File, List<String>) - Method in class ffx.ui.ModelingShell: runFFXScript - Execute a FFX script.
runFFXScript(Class<? extends FFXCommand>, List<String>) - Method in class ffx.ui.ModelingShell: runFFXScript - Execute a compiled FFX command.
runFixedAlchemy(MolecularAssembly[], CrystalPotential, DynamicsOptions, WriteoutOptions, File, AlgorithmListener) - Method in class ffx.algorithms.cli.ThermodynamicsOptions: Run an alchemical free energy window.
runNEQ(MolecularAssembly[], CrystalPotential, DynamicsOptions, WriteoutOptions, File, AlgorithmListener) - Method in class ffx.algorithms.cli.ThermodynamicsOptions: Run a non-equilibrium alchemical free energy simulation.
Runner - Class in edu.rit.pj.job: Class Runner is a parallel program that runs, in parallel, a group of Jobs created by a JobGenerator.
RUNNING - Enum constant in enum class edu.rit.pj.cluster.BackendInfo.State: The backend is running a job.
RUNNING - Enum constant in enum class edu.rit.pj.cluster.JobInfo.State: The job is running.
RUNNING - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State: The job backend process is running.
runningStatistics - Variable in class ffx.algorithms.commands.SuperposeCrystals
RunningStatistics - Class in ffx.numerics.math: The RunningStatistics class uses online, stable algorithms to calculate summary statistics from a source of doubles, including mean, variance, standard deviation, max, min, sum, and count.
RunningStatistics() - Constructor for class ffx.numerics.math.RunningStatistics: Constructs new running statistics accumulator.
runNonGroovyScript(File, List<String>) - Method in class ffx.ui.ModelingShell: runPythonScript - Execute a Python script.
runScript(ModelingShell, File, List<String>) - Static method in class ffx.Main
runtime() - Static method in class edu.rit.pj.IntegerSchedule: Returns a schedule object of a type determined at run time.
runtime() - Static method in class edu.rit.pj.LongSchedule: Returns a schedule object of a type determined at run time.
runtime(IntegerSchedule) - Static method in class edu.rit.pj.IntegerSchedule: Returns a schedule object of a type determined at run time, using the given default schedule.
runtime(LongSchedule) - Static method in class edu.rit.pj.LongSchedule: Returns a schedule object of a type determined at run time, using the given default schedule.
runVolume() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion: Execute the VolumeRegion with a private, single threaded ParallelTeam.
runWorker() - Method in class ffx.algorithms.optimize.TorsionSearch: Runs this worker with the indices assigned to it by the buildWorker() method.

S

S - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
S - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
sample(int[], String, Long) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase: Sample from harmonic oscillator with gaussian and standard deviation.
sample(int, long, double, double, double) - Method in class ffx.algorithms.dynamics.ReplicaExchange: Sample.
sample(int, long, double, double, double, int) - Method in class ffx.algorithms.dynamics.PhReplicaExchange: Sample.
sample(int, long, long, double, double, double, int) - Method in class ffx.algorithms.dynamics.PhReplicaExchange
sampleOneStep() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: The goal is to sample lambda and coordinates (X) simultaneously to converge the ensemble average dU/dL for every state (lambda) along the thermodynamic path.
sampleTwoStep() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: The goal is to sample lambda and coordinates (X) separately to converge the ensemble average dU/dL for every state (lambda) along the thermodynamic path.
sampling - Variable in class ffx.crystal.Resolution: The sampling limit for the data set.
samplingLimit() - Method in class ffx.crystal.Resolution: samplingLimit
save(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions: Saves the current state of a MolecularAssembly to an XYZ file.
save(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils: Saves the current state of a MolecularAssembly to an XYZ file.
save(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
SaveAsConstantPhPDB - Class in ffx.potential.commands.test: Save a PDB file that includes all titrating tautomer hydrogen atoms.
SaveAsConstantPhPDB() - Constructor for class ffx.potential.commands.test.SaveAsConstantPhPDB: SaveAsConstantPhPDB constructor.
SaveAsConstantPhPDB(FFXBinding) - Constructor for class ffx.potential.commands.test.SaveAsConstantPhPDB: SaveAsConstantPhPDB constructor.
SaveAsConstantPhPDB(String[]) - Constructor for class ffx.potential.commands.test.SaveAsConstantPhPDB: SaveAsConstantPhPDB constructor that sets the command line arguments.
SaveAsP1 - Class in ffx.potential.commands: Expand the system to P1 and then save it.
SaveAsP1() - Constructor for class ffx.potential.commands.SaveAsP1
SaveAsP1(FFXBinding) - Constructor for class ffx.potential.commands.SaveAsP1
SaveAsP1(String[]) - Constructor for class ffx.potential.commands.SaveAsP1
saveAsPDB(MolecularAssembly[], File) - Method in interface ffx.potential.utils.PotentialsFunctions: Saves the current state of an array of MolecularAssembly instances to a PDB file.
saveAsPDB(MolecularAssembly[], File) - Method in class ffx.potential.utils.PotentialsUtils: Saves the current state of an array of MolecularAssembly instances to a PDB file.
saveAsPDB(MolecularAssembly[], File) - Method in class ffx.ui.UIUtils
saveAsPDB(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions: Saves the current state of a MolecularAssembly to a PDB file.
saveAsPDB(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils: Saves the current state of a MolecularAssembly to a PDB file.
saveAsPDB(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
saveAsPDB(MolecularAssembly, File, boolean, boolean) - Method in interface ffx.potential.utils.PotentialsFunctions
saveAsPDB(MolecularAssembly, File, boolean, boolean) - Method in class ffx.potential.utils.PotentialsUtils
saveAsPDB(MolecularAssembly, File, boolean, boolean) - Method in class ffx.ui.UIUtils
SaveAsPDB - Class in ffx.potential.commands: Save the system as a PDB file.
SaveAsPDB() - Constructor for class ffx.potential.commands.SaveAsPDB
SaveAsPDB(FFXBinding) - Constructor for class ffx.potential.commands.SaveAsPDB
SaveAsPDB(String[]) - Constructor for class ffx.potential.commands.SaveAsPDB
saveAsPDBinP1(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions: Saves the symmetry mates of a MolecularAssembly to PDB files.
saveAsPDBinP1(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils: Saves the symmetry mates of a MolecularAssembly to PDB files.
saveAsPDBinP1(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
saveAsPDBinP1(MolecularAssembly, File, int[]) - Method in class ffx.potential.utils.PotentialsUtils
saveAsXYZ(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions: Saves the current state of a MolecularAssembly to an XYZ file.
saveAsXYZ(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils: Saves the current state of a MolecularAssembly to an XYZ file.
saveAsXYZ(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
SaveAsXYZ - Class in ffx.potential.commands: Save the system as an XYZ (or ARC) file.
SaveAsXYZ() - Constructor for class ffx.potential.commands.SaveAsXYZ
SaveAsXYZ(FFXBinding) - Constructor for class ffx.potential.commands.SaveAsXYZ
SaveAsXYZ(String[]) - Constructor for class ffx.potential.commands.SaveAsXYZ
saveAsXYZasReplicates(MolecularAssembly, File, int[]) - Method in interface ffx.potential.utils.PotentialsFunctions: Saves the current state of a MolecularAssembly to an XYZ file as a replicates crystal.
saveAsXYZasReplicates(MolecularAssembly, File, int[]) - Method in class ffx.potential.utils.PotentialsUtils: Saves the current state of a MolecularAssembly to an XYZ file as a replicates crystal.
saveAsXYZinP1(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions: Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.
saveAsXYZinP1(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils: Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.
saveAsXYZinP1(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
SaveConformerPDB - Class in ffx.xray.commands: The SaveConformerPDB script saves alternate conformers with proper alt loc labels.
SaveConformerPDB() - Constructor for class ffx.xray.commands.SaveConformerPDB: SaveConformerPDB constructor.
SaveConformerPDB(FFXBinding) - Constructor for class ffx.xray.commands.SaveConformerPDB: SaveConformerPDB constructor.
SaveConformerPDB(String[]) - Constructor for class ffx.xray.commands.SaveConformerPDB: SaveConformerPDB constructor that sets the command line arguments.
saveDirFile(File) - Method in class ffx.algorithms.cli.AlgorithmsCommand: Return a File in the base directory with the same name as the input file.
saveFeatures(Residue, double, boolean, boolean, boolean) - Method in class ffx.potential.utils.GetProteinFeatures: Make a string array of surface area and additional selected features (phi,psi,omega,and structure annotations)
saveFile(String, PotentialsFunctions, MolecularAssembly) - Method in class ffx.potential.cli.WriteoutOptions: Saves a single-snapshot file to either .xyz or .pdb, depending on the value of fileType.
saveKeywordFile(File) - Method in class ffx.ui.MainPanel
saveMutualInducedDipoles(double[][][], double[][][], double[][], double[][]) - Method in class ffx.potential.nonbonded.ScfPredictor: Save the current converged mutual induced dipoles.
saveMutualInducedDipoles(LambdaMode, double[][][], double[][][], double[][], double[][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Save the current converged mutual induced dipoles.
SaveOptions - Class in ffx.potential.cli: Represents command line options for scripts that save a structure to disc.
SaveOptions() - Constructor for class ffx.potential.cli.SaveOptions
SaveRotamers - Class in ffx.algorithms.commands: The SaveRotamers script saves out rotamers.
SaveRotamers() - Constructor for class ffx.algorithms.commands.SaveRotamers
SaveRotamers(FFXBinding) - Constructor for class ffx.algorithms.commands.SaveRotamers
SaveRotamers(String[]) - Constructor for class ffx.algorithms.commands.SaveRotamers
saveZValues(int[][]) - Method in class ffx.potential.nonbonded.SliceLoop: saveZValues.
saveZYValues(int[][][]) - Method in class ffx.potential.nonbonded.RowLoop: saveZYValues.
Sb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Sc - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
scalarMat3Mat3(double, double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: scalar times a matrix times a matrix.
scalarMat3Mat3(double, double[][], double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: scalarMat3mat3
ScalarMath - Class in ffx.numerics.math: The ScalarMath class is a simple math library that operates on single variables
scale(double) - Method in class ffx.numerics.math.Double3: Scales a Double3.
scale(double) - Method in class ffx.numerics.quickhull.Vector3d: Scales the elements of this vector by s.
scale(double[], double) - Static method in class ffx.numerics.math.DoubleMath: Scales a vector.
scale(double[], double[]) - Static method in class ffx.potential.parameters.MultipoleType: Scale a multipole by the charge, dipole, and quadrupole scales.
scale(double[], double, double[]) - Static method in class ffx.numerics.math.DoubleMath: Scales a vector.
scale(double, Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Scales the elements of vector v1 by s and places the results in this vector.
scale(float) - Method in class ffx.numerics.math.Float3: Scales a Float3.
scale(float[], float) - Static method in class ffx.numerics.math.FloatMath: Scales a vector.
scale(float[], float, float[]) - Static method in class ffx.numerics.math.FloatMath: Scales a vector.
scale(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray: Scale the value of the double array at the specified index.
scale(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Scale the value of the double array at the specified index.
scale(int, int, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Scale the double arrays at the specified index to the given values.
scale(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray: Scale the value of the double array at the specified index.
scale(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray: Scale the value of the double array at the specified index.
scale(MultipoleType, double[]) - Static method in class ffx.potential.parameters.MultipoleType: Scale a multipole by the charge, dipole, and quadrupole scales.
SCALE - Enum constant in enum class ffx.potential.nonbonded.pme.AlchemicalParameters.AlchemicalMode
scale12 - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Define scale factors between 1-2 atoms.
scale13 - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Define scale factors between 1-3 atoms.
scale14 - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Define scale factors between 1-4 atoms.
scaleB - Variable in class ffx.crystal.Crystal: Anisotropic bulk solvent B-factor scaling (0 or 1 for each component).
ScaleBulkEnergy - Class in ffx.xray: Fit bulk solvent and aniso B scaling terms to correct calculated structure factors against data
scaleBulkFit() - Method in class ffx.xray.DiffractionData: Scale model and fit bulk solvent to all data.
scaleBulkFit(int) - Method in class ffx.xray.DiffractionData: Scale model and fit bulk solvent to dataset i of n.
ScaleBulkMinimize - Class in ffx.xray: ScaleBulkMinimize class.
ScaleBulkMinimize(ReflectionList, DiffractionRefinementData, CrystalReciprocalSpace, ParallelTeam) - Constructor for class ffx.xray.ScaleBulkMinimize: Constructor for ScaleBulkMinimize.
scaleCoordinates(double[]) - Method in interface ffx.numerics.OptimizationInterface: Default method to scale coordinates.
scaleCoordinatesAndGradient(double[], double[]) - Method in interface ffx.numerics.OptimizationInterface: Default method to unscale coordinates.
scaleFactor - Variable in class ffx.potential.bonded.ImproperTorsion: Scale factor.
scaleI(double) - Method in class ffx.numerics.math.Double3: Scales a Double3 in place.
scaleI(float) - Method in class ffx.numerics.math.Float3: Scales a Float3 in place.
scaleN - Variable in class ffx.crystal.Crystal: Number of bulk solvent B-factor components.
ScaleParameters - Class in ffx.potential.nonbonded.pme: Scale factors and masking rules for electrostatics.
ScaleParameters(ForceField.ELEC_FORM, ForceField) - Constructor for class ffx.potential.nonbonded.pme.ScaleParameters
ScaleStep - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Step size was scaled down.
scaleVec(DoubleVector[], DoubleVector, DoubleVector[]) - Static method in class ffx.numerics.multipole.QIFrameSIMD: Scale a vector by a scalar.
scaling - Variable in class ffx.algorithms.optimize.Minimize: Scaling applied to each variable.
scaling - Variable in class ffx.algorithms.optimize.PhMinimize: Scaling applied to each variable.
scan() - Method in class ffx.algorithms.optimize.ConformationScan
scan(int, Buf, Op) - Method in class edu.rit.pj.Comm: Perform a scan on all processes in this communicator using the given message tag.
scan(Buf, Op) - Method in class edu.rit.pj.Comm: Perform a scan on all processes in this communicator.
scatter(int, int, Buf[], Buf) - Method in class edu.rit.pj.Comm: Scatter messages to all processes in this communicator using the given message tag.
scatter(int, Buf[], Buf) - Method in class edu.rit.pj.Comm: Scatter messages to all processes in this communicator.
sceneGraphChange(List<BranchGroup>) - Method in class ffx.potential.MolecularAssembly: sceneGraphChange
scfAlgorithm - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
SCFAlgorithm - Enum Class in ffx.potential.nonbonded.pme: Describes available SCF algorithms, and whether they are supported by the FFX and/or CUDA implementations.
scfByPCG(boolean, long, ParticleMeshEwald) - Method in class ffx.potential.nonbonded.pme.PCGSolver
scfPredictor - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters
ScfPredictor - Class in ffx.potential.nonbonded: Predict Mutual Induced Dipoles based on previous steps.
ScfPredictor(ScfPredictor.PredictorMode, int, ForceField) - Constructor for class ffx.potential.nonbonded.ScfPredictor: Constructor for ScfPredictor.
SCFPredictor - Enum Class in ffx.potential.nonbonded.pme
ScfPredictor.PredictorMode - Enum Class in ffx.potential.nonbonded
SCFPredictorParameters - Class in ffx.potential.nonbonded.pme
SCFPredictorParameters(SCFPredictor, int) - Constructor for class ffx.potential.nonbonded.pme.SCFPredictorParameters
schedule() - Method in class edu.rit.pj.IntegerForLoop: Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.IntegerStrideForLoop: Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.LongForLoop: Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.LongStrideForLoop: Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerIntegerForLoop: Determine this worker for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Determine this worker for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerLongForLoop: Determine this worker for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerLongStrideForLoop: Determine this worker for loop's schedule.
schedule() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
schedule() - Method in class ffx.potential.nonbonded.SpatialDensityLoop: Determine this parallel for loop's schedule.
Schedule - Class in edu.rit.pj: Class Schedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.
Scheduler - Class in ffx.algorithms.commands: Run a Parallel Java Job Scheduler on a cluster with multiple nodes.
Scheduler() - Constructor for class ffx.algorithms.commands.Scheduler: Scheduler Constructor.
Scheduler(FFXBinding) - Constructor for class ffx.algorithms.commands.Scheduler: Scheduler Constructor.
Scheduler(String[]) - Constructor for class ffx.algorithms.commands.Scheduler: Scheduler constructor that sets the command line arguments.
SCREENED_COULOMB - Enum constant in enum class ffx.numerics.multipole.Operator: Screened Coulomb operator.
sd - Variable in class ffx.numerics.math.BootStrapStatistics: The standard deviation.
sd - Variable in class ffx.numerics.math.SummaryStatistics: Sample standard deviation.
SD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
sdPopulation - Variable in class ffx.numerics.math.BootStrapStatistics: The population standard deviation.
sdPopulation - Variable in class ffx.numerics.math.SummaryStatistics: Population standard deviation.
Se - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
search(int, double[], double, double[], double[], double[], double, LineSearch.LineSearchResult[], int[], OptimizationInterface) - Method in class ffx.numerics.optimization.LineSearch: Minimize a function along a search direction.
Searching - Class in edu.rit.util: Class Searching provides static methods for searching arrays of primitive types and object types.
Searching.Byte - Class in edu.rit.util: Class Searching.Byte is the base class for a helper object used to search an array of type byte[].
Searching.Character - Class in edu.rit.util: Class Searching.Character is the base class for a helper object used to search an array of type char[].
Searching.Double - Class in edu.rit.util: Class Searching.Double is the base class for a helper object used to search an array of type double[].
Searching.Float - Class in edu.rit.util: Class Searching.Float is the base class for a helper object used to search an array of type float[].
Searching.Integer - Class in edu.rit.util: Class Searching.Integer is the base class for a helper object used to search an array of type int[].
Searching.Long - Class in edu.rit.util: Class Searching.Long is the base class for a helper object used to search an array of type long[].
Searching.Object<T> - Class in edu.rit.util: Class Searching.Object is the base class for a helper object used to search an array of type T[].
Searching.Short - Class in edu.rit.util: Class Searching.Short is the base class for a helper object used to search an array of type short[].
searchSorted(byte[], byte, Searching.Byte) - Static method in class edu.rit.util.Searching: Search the given ordered array of type byte[] for the given element.
searchSorted(char[], char, Searching.Character) - Static method in class edu.rit.util.Searching: Search the given ordered array of type char[] for the given element.
searchSorted(double[], double, Searching.Double) - Static method in class edu.rit.util.Searching: Search the given ordered array of type double[] for the given element.
searchSorted(float[], float, Searching.Float) - Static method in class edu.rit.util.Searching: Search the given ordered array of type float[] for the given element.
searchSorted(int[], int, Searching.Integer) - Static method in class edu.rit.util.Searching: Search the given ordered array of type int[] for the given element.
searchSorted(long[], long, Searching.Long) - Static method in class edu.rit.util.Searching: Search the given ordered array of type long[] for the given element.
searchSorted(short[], short, Searching.Short) - Static method in class edu.rit.util.Searching: Search the given ordered array of type short[] for the given element.
searchSorted(T[], T) - Static method in class edu.rit.util.Searching: Search the given ordered array of type T[] for the given element.
searchSorted(T[], T, Searching.Object<T>) - Static method in class edu.rit.util.Searching: Search the given ordered array of type T[] for the given element.
searchSorted(T[], T, Comparator<T>) - Static method in class edu.rit.util.Searching: Search the given ordered array of type T[] for the given element.
searchUnsorted(byte[], byte, Searching.Byte) - Static method in class edu.rit.util.Searching: Search the given unordered array of type byte[] for the given element.
searchUnsorted(char[], char, Searching.Character) - Static method in class edu.rit.util.Searching: Search the given unordered array of type char[] for the given element.
searchUnsorted(double[], double, Searching.Double) - Static method in class edu.rit.util.Searching: Search the given unordered array of type double[] for the given element.
searchUnsorted(float[], float, Searching.Float) - Static method in class edu.rit.util.Searching: Search the given unordered array of type float[] for the given element.
searchUnsorted(int[], int, Searching.Integer) - Static method in class edu.rit.util.Searching: Search the given unordered array of type int[] for the given element.
searchUnsorted(long[], long, Searching.Long) - Static method in class edu.rit.util.Searching: Search the given unordered array of type long[] for the given element.
searchUnsorted(short[], short, Searching.Short) - Static method in class edu.rit.util.Searching: Search the given unordered array of type short[] for the given element.
searchUnsorted(T[], T) - Static method in class edu.rit.util.Searching: Search the given unordered array of type T[] for the given element.
searchUnsorted(T[], T, Searching.Object<T>) - Static method in class edu.rit.util.Searching: Search the given unordered array of type T[] for the given element.
searchUnsorted(T[], T, Comparator<T>) - Static method in class edu.rit.util.Searching: Search the given unordered array of type T[] for the given element.
SEC_TO_PSEC - Static variable in class ffx.utilities.Constants: Constant SEC_TO_PSEC=1E12
secondDerivative(double) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
secondDerivative(double) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction: Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.BellCurveSwitch: Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.CompositeSwitch
secondDerivative(double) - Method in class ffx.numerics.switching.ConstantSwitch: Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.LinearDerivativeSwitch: Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.PowerSwitch: Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.SquaredTrigSwitch: Second derivative at a point.
select - Variable in class ffx.potential.nonbonded.RowRegion
select - Variable in class ffx.potential.nonbonded.SliceRegion
select - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
select(MSNode) - Method in class ffx.ui.ModelingShell: select
select(MSNode, Class<? extends Object>, String) - Static method in class ffx.ui.Selection: select
select(MSNode, String, String) - Static method in class ffx.ui.Selection: select
SELECT - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
selectAtoms() - Method in class ffx.potential.nonbonded.RowRegion: Select atoms that should be included.
selectAtoms() - Method in class ffx.potential.nonbonded.SliceRegion: Select atoms that should be included.
selectAtoms() - Method in class ffx.potential.nonbonded.SpatialDensityRegion: Select atoms that should be assigned to cells.
selectAtoms() - Method in class ffx.xray.BulkSolventDensityRegion: Select atoms that should be assigned to cells.
selectAtoms() - Method in class ffx.xray.BulkSolventRowRegion: Select atoms that should be included.
selectAtoms() - Method in class ffx.xray.BulkSolventSliceRegion: Select atoms that should be included.
selected - Variable in class ffx.potential.bonded.MSNode: True if this node is selected.
selected() - Method in class ffx.ui.GraphicsCanvas: selected
selected() - Method in class ffx.ui.KeywordPanel: selected
selected() - Method in class ffx.ui.ModelingPanel: Selected.
selectInclusionResidues(List<Residue>, int, boolean, double) - Method in class ffx.algorithms.cli.ManyBodyOptions
Selection - Class in ffx.ui: The Selection class will be used to make recursive multiscale selections, however its implementation is not yet complete.
SELECTION - Static variable in interface ffx.ui.behaviors.MouseBehaviorCallback: Constant SELECTION=4
SELECTION - Static variable in interface ffx.ui.behaviors.PickingCallback: Constant SELECTION=4
selectionColor - Static variable in class ffx.potential.bonded.RendererCache: Constant selectionColor
selfEnergy(PolarizableMultipole, double, double, double) - Static method in class ffx.numerics.multipole.GKSource: Compute the self-energy of a polarizable multipole.
SelfEnergyRegion - Class in ffx.algorithms.optimize.manybody: Compute residue self-energy values in parallel across nodes.
SelfEnergyRegion(RotamerOptimization, EnergyExpansion, EliminatedRotamers, Residue[], BufferedWriter, Comm, int, boolean, boolean, int, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.manybody.SelfEnergyRegion
send(double, double, double) - Method in class ffx.algorithms.thermodynamics.SendSynchronous: Send an OST count to all other processes while also receiving an OST count from all other processes.
send(int, int, Buf) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator with the given message tag.
send(int, int, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator with the given message tag (non-blocking).
send(int, Buf) - Method in class edu.rit.pj.cluster.Proxy: Send a message with the given tag and items to this proxy's far end process.
send(int, Buf) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator.
send(int, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator (non-blocking).
send(Channel, int, Buf) - Method in class edu.rit.mp.ChannelGroup: Send a message to the given channel with the given tag.
send(Channel, Buf) - Method in class edu.rit.mp.ChannelGroup: Send a message to the given channel.
send(Message) - Method in class edu.rit.pj.cluster.Proxy: Send the given message to this proxy's far end process.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyBooleanBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyByteBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyCharacterBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyDoubleBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyFloatBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyLongBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyShortBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.Buf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf: Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.ObjectBuf: Send as many items as possible from this buffer to the given byte buffer.
sendNoWait(Channel, int, Buf, IORequest) - Method in class edu.rit.mp.ChannelGroup: Send (non-blocking) a message to the given channel with the given tag.
sendNoWait(Channel, Buf, IORequest) - Method in class edu.rit.mp.ChannelGroup: Send (non-blocking) a message to the given channel.
sendReceive(int, int, Buf, int, int, Buf) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator with the given message tag, and receive a message from the process at the given rank in this communicator with the given message tag.
sendReceive(int, int, Buf, int, int, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator with the given message tag, and receive a message from the process at the given rank in this communicator with the given message tag (non-blocking).
sendReceive(int, Buf, int, Buf) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator, and receive a message from the process at the given rank in this communicator.
sendReceive(int, Buf, int, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Send a message to the process at the given rank in this communicator, and receive a message from the process at the given rank in this communicator (non-blocking).
SendSynchronous - Class in ffx.algorithms.thermodynamics: Synchronous (blocking) communication of OST counts.
SendSynchronous(OrthogonalSpaceTempering.Histogram[], int[]) - Constructor for class ffx.algorithms.thermodynamics.SendSynchronous: Synchronous Communication Constructor.
sendTaskInput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongForLoop: Send additional input data associated with a task.
sendTaskInput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongStrideForLoop: Send additional input data associated with a task.
sendTaskInput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerForLoop: Send additional input data associated with a task.
sendTaskInput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Send additional input data associated with a task.
sendTaskInput(T, Comm, int, int) - Method in class edu.rit.pj.WorkerIteration: Send additional input data associated with a task.
sendTaskOutput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongForLoop: Send additional output data associated with a task.
sendTaskOutput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongStrideForLoop: Send additional output data associated with a task.
sendTaskOutput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerForLoop: Send additional output data associated with a task.
sendTaskOutput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Send additional output data associated with a task.
sendTaskOutput(T, Comm, int, int) - Method in class edu.rit.pj.WorkerIteration: Send additional output data associated with a task.
SequentialEstimator - Class in ffx.numerics.estimator: The SequentialEstimator abstract class defines a statistical estimator based on perturbative potential energy differences between adjacent windows (e.g. exponential free energy perturbation, Bennett Acceptance Ratio, etc).
SequentialEstimator(double[], double[][][], double[]) - Constructor for class ffx.numerics.estimator.SequentialEstimator: The SequentialEstimator constructor largely just copies its parameters into local variables.
SequentialEstimator(double[], double[][], double[][], double[][], double[]) - Constructor for class ffx.numerics.estimator.SequentialEstimator: The SequentialEstimator constructor largely just copies its parameters into local variables.
SequentialEstimator(double[], int[], double[][], double[]) - Constructor for class ffx.numerics.estimator.SequentialEstimator: Simpler constructor for when data provided is already flattened (although it adds uncertainty about snap counts, they are all set to the same number).
SER - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
SERINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
set(boolean) - Method in class edu.rit.pj.reduction.SharedBoolean: Set this reduction variable to the given value.
set(byte) - Method in class edu.rit.pj.reduction.SharedByte: Set this reduction variable to the given value.
set(char) - Method in class edu.rit.pj.reduction.SharedCharacter: Set this reduction variable to the given value.
set(double) - Method in class edu.rit.pj.reduction.SharedDouble: Set this reduction variable to the given value.
set(double[]) - Method in class ffx.numerics.math.Double3: Set the value of this Double3.
set(double[][], double[][], double[][]) - Method in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Set the permanent multipole.
set(double[], double[], double[]) - Method in class ffx.numerics.multipole.PolarizableMultipole: Set the permanent multipole.
set(double, double, double) - Method in class ffx.numerics.math.Double3: Set the value of this Double3.
set(double, double, double) - Method in class ffx.numerics.quickhull.Vector3d: Sets the elements of this vector to the prescribed values.
set(float) - Method in class edu.rit.pj.reduction.SharedFloat: Set this reduction variable to the given value.
set(float[]) - Method in class ffx.numerics.math.Float3: Set the value of this Float3.
set(float, float, float) - Method in class ffx.numerics.math.Float3: Set the value of this Float3.
set(int) - Method in class edu.rit.pj.reduction.SharedInteger: Set this reduction variable to the given value.
set(int, boolean) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Set this array reduction variable at the given index to the given value.
set(int, byte) - Method in class edu.rit.pj.reduction.SharedByteArray: Set this array reduction variable at the given index to the given value.
set(int, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Set this array reduction variable at the given index to the given value.
set(int, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Set this array reduction variable at the given index to the given value.
set(int, double) - Method in class ffx.numerics.quickhull.Vector3d: Sets a single element of this vector.
set(int, double) - Method in class ffx.openmm.DoubleArray: Set a value in the array.
set(int, float) - Method in class edu.rit.pj.reduction.SharedFloatArray: Set this array reduction variable at the given index to the given value.
set(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Set this array reduction variable at the given index to the given value.
set(int, int) - Method in class ffx.openmm.IntArray: Set a value in the array.
set(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray: Set the value of the double array at the specified index.
set(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Set the value of the double array at the specified index.
set(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray: Set the value of the double array at the specified index.
set(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray: Set the value of the double array at the specified index.
set(int, int, double, double, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Set the double arrays at the specified index to the given values.
set(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Set this matrix reduction variable at the given row and column to the given value.
set(int, int, int) - Method in class ffx.openmm.BondArray: Set the bond at index to i1 and i2.
set(int, int, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Set this matrix reduction variable at the given row and column to the given value.
set(int, int, Double3) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Set the double arrays at the specified index to the given Double3.
set(int, int, DoubleArray) - Method in class ffx.openmm.amoeba.DoubleArray3D: Set the value of the array at the given index.
set(int, long) - Method in class edu.rit.pj.reduction.SharedLongArray: Set this array reduction variable at the given index to the given value.
set(int, short) - Method in class edu.rit.pj.reduction.SharedShortArray: Set this array reduction variable at the given index to the given value.
set(int, OpenMM_Vec3.ByValue) - Method in class ffx.openmm.Vec3Array: Set a Vec3 in the Vec3Array.
set(int, String) - Method in class ffx.openmm.StringArray: Set the String at index i.
set(int, T) - Method in class edu.rit.pj.reduction.SharedObjectArray: Set this array reduction variable at the given index to the given value.
set(long) - Method in class edu.rit.pj.reduction.SharedLong: Set this reduction variable to the given value.
set(short) - Method in class edu.rit.pj.reduction.SharedShort: Set this reduction variable to the given value.
set(Double3) - Method in class ffx.numerics.math.Double3: Set the value of this Double3.
set(Float3) - Method in class ffx.numerics.math.Float3: Set the value of this Float3.
set(Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Sets the values of this vector to those of v1.
set(T) - Method in class edu.rit.pj.reduction.SharedObject: Set this reduction variable to the given value.
set2Body(int, int, int, int, double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
set2Body(int, int, int, int, double, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Store a pair energy in the pairs energy matrix.
set3Body(Residue[], int, int, int, int, int, int, double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: set3Body.
set3Body(Residue[], int, int, int, int, int, int, double, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Stores a triple energy in the triples energy matrix.
setAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat: setAcceleration.
setAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: setAcceleration.
setAcceleration(double[]) - Method in interface ffx.numerics.Potential: setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
setAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field acceleration.
setAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy: setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
setAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy: setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy: setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.XtalEnergy: setAcceleration.
setAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy: setAcceleration.
setAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy: setAcceleration.
setAcceleration(double[]) - Method in class ffx.xray.XRayEnergy: setAcceleration.
setAcceleration(double, double, double) - Method in class ffx.potential.bonded.Atom: Setter for the field acceleration.
setAccelerations(double[]) - Method in class ffx.potential.SystemState: Set the accelerations via a copy of the passed array into the internal array.
setAcceptorParameters(int, int, int, int, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Set the parameters for an acceptor.
setActive(boolean) - Method in class ffx.algorithms.dynamics.Barostat: Setter for the field active.
setActive(boolean) - Method in class ffx.potential.bonded.Atom: If active, the coordinates of this atom can be modified.
setActive(int) - Method in class ffx.ui.Hierarchy: setActive
setActive(FFXSystem) - Method in class ffx.ui.Hierarchy: Sets the FFXSystem s to be active.
setActiveAssembly(MolecularAssembly) - Method in class ffx.algorithms.cli.AlgorithmsCommand: Set the Active Assembly.
setActiveAssembly(MolecularAssembly) - Method in class ffx.potential.cli.PotentialCommand: Set the Active Assembly.
setActiveAtoms() - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Update active atoms.
setActiveAtoms() - Method in class ffx.potential.openmm.OpenMMEnergy: Update active atoms.
setActiveAtoms() - Method in interface ffx.potential.openmm.OpenMMPotential: Update active atoms.
setActiveAtoms(MolecularAssembly) - Method in class ffx.potential.cli.AtomSelectionOptions: Set active atoms for a MolecularAssembly.
setActiveResidue(int) - Method in class ffx.potential.bonded.MultiResidue: Request the ith residue be set active.
setActiveResidue(AminoAcidUtils.AminoAcid3) - Method in class ffx.potential.bonded.MultiResidue: Method may be redundant with requestSetActiveResidue.
setActiveResidue(Residue) - Method in class ffx.potential.bonded.MultiResidue: Setter for the field activeResidue.
setAEwald(double) - Method in class ffx.openmm.amoeba.MultipoleForce: Deprecated.
This method exists only for backward compatibility. Use setPMEParameters() instead.
setAlchemicalAtoms(MolecularAssembly, String, String) - Static method in class ffx.potential.cli.AlchemicalOptions: Sets the alchemical atoms for a MolecularAssembly.
setAlchemicalMethod(int) - Method in class ffx.openmm.amoeba.VdwForce: Set the alchemical method.
setAlchemicalProperties() - Method in class ffx.potential.cli.AlchemicalOptions: Set system properties for alchemical simulations.
setAlchemicalProperties(int) - Method in class ffx.potential.cli.TopologyOptions: Relative free energies via the DualTopologyEnergy class require different default OST parameters than absolute free energies.
setAlgorithm(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setAllowed(int) - Method in class ffx.crystal.HKL: setAllowed
setAlternateClassLoader(ClassLoader) - Method in class edu.rit.mp.ChannelGroup: Specify an alternate class loader for this channel group.
setAlternateLocation(Character) - Method in class ffx.potential.MolecularAssembly: Set the alternate location.
setAltID(MolecularAssembly, Character) - Method in class ffx.potential.parsers.PDBFilter: Specify the alternate location.
setAltLoc(Character) - Method in class ffx.potential.bonded.Atom: Setter for the field altLoc.
setAndRotate(double[], PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.QIFrame: Update the QIFrame rotation matrix and rotate the multipoles.
setAndRotate(double, double, double, PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.QIFrame: Update the QIFrame rotation matrix and rotate the multipoles.
setAndRotate(DoubleVector[], PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.QIFrameSIMD: Update the QIFrame rotation matrix and rotate the multipoles.
setAndRotate(DoubleVector, DoubleVector, DoubleVector, PolarizableMultipoleSIMD, PolarizableMultipoleSIMD) - Method in class ffx.numerics.multipole.QIFrameSIMD: Update the QIFrame rotation matrix and rotate the multipoles.
setAngle(Angle) - Method in class ffx.potential.bonded.Atom: setAngle
setAngleFunction(AngleType.AngleFunction) - Method in class ffx.potential.parameters.AngleType: Set the AngleFunction.
setAngleFunction(AngleType.AngleFunction) - Method in class ffx.potential.parameters.ForceField: The AngleFunction in use by this ForceField.
setAngleParameters(int, int, int, int, double, double) - Method in class ffx.openmm.HarmonicAngleForce: Set the force field parameters for an angle term.
setAngleParameters(int, int, int, int, DoubleArray) - Method in class ffx.openmm.CustomAngleForce: Set the parameters for one angle in the OpenMM System.
setAngles(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the Angles node to t.
setAngles(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the Angles node to t.
setAngleTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the MultiScaleGroup's angle-torsion node to t.
setAngleType(AngleType) - Method in class ffx.potential.bonded.Angle: Set a reference to the force field parameters for this Angle.
setAnisou(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field anisou.
setAnisouAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field anisouAcceleration.
setAnisouGradient(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field anisouGradient.
setAnisouPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field anisouPreviousAcceleration.
setAnisouVelocity(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field anisouVelocity.
setAperiodic(boolean) - Method in class ffx.crystal.Crystal: Is this a finite system without periodic boundary conditions.
setApplyLambda(boolean) - Method in class ffx.potential.bonded.Atom: setApplyLambda
setApproxBoxLength(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setApproxBoxLength(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the approximate dimensions of boxes, over-riding numXYZBoxes in determining box size.
setArchiveFile(File) - Method in class ffx.potential.MolecularAssembly: Set the File for writing out an archive.
setArchiveFiles(File[]) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Set the archive file for each MolecularAssembly.
setArgList(List<String>) - Method in class ffx.ui.ModelingShell: setArgList
setAsynchronous(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
setAtomInitial(Atom) - Method in class ffx.potential.bonded.Residue
setAtomNode(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the Moieties node to t.
setAtomNode(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the Moieties node to t.
setAtoms(int) - Method in class ffx.potential.nonbonded.PairwiseSchedule: setAtoms.
setAtoms(Atom[]) - Method in class ffx.potential.bonded.BondedTerm: Add a constituent Atom to the Term.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.NeighborList: The NeighborList will be re-configured, if necessary, for the supplied atom list.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.RowRegion: Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.SliceRegion: Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.SpatialDensityRegion: setAtoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.VanDerWaalsTornado: Setter for the field atoms.
setAtoms(Atom[], int[]) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
setAtoms(Atom[], int[], boolean[]) - Method in class ffx.potential.nonbonded.VanDerWaals: Set the atoms and molecule arrays, and rebuild the neighbor list.
setAtomType(AtomType) - Method in class ffx.potential.bonded.Atom: Setter for the field atomType.
setAtomTypes(AtomTypeFactory, IAtom) - Static method in class ffx.potential.parsers.CIFFilter: Specify the atom types for atoms created by factory.
setAutomaticWriteouts(boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Enable or disable automatic writeout of trajectory snapshots and restart files.
setAutomaticWriteouts(boolean) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
setAwater(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the water density parameter.
setAxisAtoms(Atom...) - Method in class ffx.potential.bonded.Atom: Setter for the field axisAtoms.
setAxisShowing(boolean) - Method in class ffx.ui.MainMenu: setAxisShowing
setBackboneEnergy(double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
setBarInt(int) - Method in class ffx.algorithms.cli.BarostatOptions
setBarostat(Barostat) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: Set the barostat for this MolecularDynamicsOpenMM instance.
setBarostatPrintFrequency(int) - Method in class ffx.algorithms.dynamics.Barostat: Set the Barostat print frequency.
setBaseDir(File) - Method in class ffx.algorithms.cli.AlgorithmsCommand: Sets the directory this script should save files to.
setBaselineAARes(AminoAcidUtils.AminoAcid3) - Method in class ffx.algorithms.misc.GenerateRotamers: Sets a standard amino acid to be the baseline for rotamer generation.
setBeta0(double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
setBeta1(double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
setBeta2(double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
setBiasData(double[][]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
setBiasData(double[][][], boolean) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: Weight observable by exp(bias/RT) prior to computing expectation when set.
setBiasMag(double) - Method in class ffx.algorithms.thermodynamics.HistogramData: Set the bias magnitude.
setBiasMag(double[]) - Method in class ffx.algorithms.cli.OSTOptions
setBin(int) - Method in class ffx.crystal.HKL: Set the bin number of this reflection, which is used for resolution dependent R/Rfree.
setBinding(FFXBinding) - Method in class ffx.utilities.FFXCommand: Set the Binding that provides variables to this Command.
setBond(Bond) - Method in class ffx.potential.bonded.Atom: Specify that this Atom is part of a Bond
setBondFunction(BondType.BondFunction) - Method in class ffx.potential.parameters.BondType
setBondFunction(BondType.BondFunction) - Method in class ffx.potential.parameters.ForceField: The BondFunction in use by this ForceField.
setBondParameters(int, int, int, double, double) - Method in class ffx.openmm.HarmonicBondForce: Set the force field parameters for a bond term.
setBondParameters(int, int, int, DoubleArray) - Method in class ffx.openmm.CustomBondForce: Set the parameters for one bond in the OpenMM System.
setBondParameters(int, IntArray, DoubleArray) - Method in class ffx.openmm.CustomCentroidBondForce: Set the properties of a bond.
setBondParameters(int, IntArray, DoubleArray) - Method in class ffx.openmm.CustomCompoundBondForce: Set the parameters for a bond.
setBonds(Bond[]) - Method in class ffx.potential.bonded.BondedTerm: Add constituent Bonds to the Term.
setBonds(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the Bonds node to t.
setBonds(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the Bonds node to t.
setBondTolerance(double) - Method in class ffx.potential.parsers.CIFFilter: Set buffer value when bonding atoms together.
setBondType(BondType) - Method in class ffx.potential.bonded.Bond: Set a reference to the force field parameters.
setBondType(BondType) - Method in class ffx.potential.bonded.RestrainDistance: Set a reference to the force field parameters.
setBorderBottom(int) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setBorderLeft(int) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setBorderRight(int) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setBorderTop(int) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setBoxBorderSize(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setBoxBorderSize(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the amount of overlap between adjacent boxes for box optimization.
setBoxEnd(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the ending box index.
setBoxInclusionCriterion(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setBoxInclusionCriterion(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets behavior for how Residues are added to boxOptCells; 1 uses just reference atom (C alpha for protein, N1/9 for nucleic acids), 2 uses any atom, 3 uses any atom in any rotamer.
setBoxStart(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the starting box index.
setBoxTitration(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setBuilt(boolean) - Method in class ffx.potential.bonded.Atom: Setter for the field built.
setCaptures(boolean) - Method in class ffx.ui.GraphicsCanvas: setCaptures
setCellVectors(double[][]) - Method in class ffx.crystal.Crystal: Set the unit cell vectors.
setCellVectors(double[][]) - Method in class ffx.crystal.ReplicatesCrystal: Change the cell vectors for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
setCellVectorsAndVolume(double[][], double) - Method in class ffx.crystal.Crystal: Set the unit cell vectors.
setCellVectorsAndVolume(double[][], double) - Method in class ffx.crystal.ReplicatesCrystal: Change the cell vectors and volume for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
setCenter(double[]) - Method in class ffx.potential.bonded.MSGroup: Set the value of Center to d.
setCenter(double[]) - Method in class ffx.potential.bonded.MultiResidue: Set the value of Center to d.
setChain(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
setChainID(Character) - Method in class ffx.potential.bonded.Atom: Set the chain name.
setChainID(Character) - Method in class ffx.potential.bonded.Molecule: Setter for the field chainID.
setChainID(Character) - Method in class ffx.potential.bonded.Polymer: Set the Polymer chainID.
setChainID(Character) - Method in class ffx.potential.bonded.Residue: Setter for the field chainID.
setChainIDAndRenumberMolecules(Character) - Method in class ffx.potential.MolecularAssembly: This method sets all HETATM molecules, including water and ions, to use the given chainID and then renumbers the molecules.
setChannelGroupId(int) - Method in class edu.rit.mp.ChannelGroup: Set this channel group's channel group ID.
setCharge(double) - Method in class ffx.potential.nonbonded.octree.OctreeParticle
setCharset(Charset) - Method in class edu.rit.http.HttpResponse: Set this HTTP response's character set.
setCheckAlchemicalAtoms(boolean) - Method in class ffx.potential.terms.EnergyTermRegion
setCheckpoint(double) - Method in class ffx.algorithms.cli.DynamicsOptions
setCheckRestrictions(boolean) - Method in class ffx.crystal.Crystal: Set whether to check space group restrictions.
setCheckRestrictions(boolean) - Method in class ffx.crystal.ReplicatesCrystal: Set whether to check space group restrictions.
setChildren(int, int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
setChildren(List<Cluster>) - Method in class ffx.numerics.clustering.Cluster: Sets the list of child clusters for this node.
setChildren(List<ClusterComponent>) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Sets the list of child visual components.
setClashThreshold(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setClosing(boolean) - Method in class ffx.ui.FFXSystem: Setter for the field closing.
setCluster(Cluster) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Sets the Cluster model represented by this component.
setCollisionFrequency(double, int) - Method in class ffx.openmm.NoseHooverIntegrator: Set the collision frequency for a thermostat.
setColor(Atom) - Method in class ffx.potential.bonded.Bond: Set the color of this Bond's Java3D shapes based on the passed Atom.
setColor(RendererCache.ColorModel) - Method in class ffx.potential.bonded.Joint: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.Atom: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.BondedTerm: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.MSGroup: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.MSNode: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.MultiResidue: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.Polymer: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.Residue: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in interface ffx.potential.bonded.ROLS: setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.MolecularAssembly: setColor
setColor(String) - Method in class ffx.ui.GraphicsCanvas: setColor
setColorModel(String, MSNode) - Method in class ffx.ui.GraphicsCanvas: Operates on the passed node.
setCommand(String) - Method in class ffx.ui.ModelingPanel: setCommand
setCommandDescription(String) - Method in class ffx.ui.FFXSystem: Setter for the field commandDescription.
setComment(String) - Method in class edu.rit.pj.cluster.JobBackend: Set the comment string for this job backend process.
setComputedValueParameters(int, String, String) - Method in class ffx.openmm.CustomNonbondedForce: Set the parameters for a computed value.
setComputedValueParameters(int, String, String, int) - Method in class ffx.openmm.CustomGBForce: Set the parameters for a computed value.
setConnectListener(ConnectListener) - Method in class edu.rit.mp.ChannelGroup: Register the given connect listener with this channel group.
setConstantPh(double) - Method in class ffx.potential.extended.ExtendedSystem: setConstantPh.
setConstantPH(boolean) - Method in class ffx.potential.parsers.PDBFilter
setConstraint(Constraint) - Method in class ffx.potential.bonded.Angle
setConstraint(Constraint) - Method in class ffx.potential.bonded.BondedTerm: Sets the Constraint on this bond (clearing it if null).
setConstraintParameters(int, int, int, double) - Method in class ffx.openmm.System: Set the parameters defining a constraint.
setConstraintTolerance(double) - Method in class ffx.openmm.CompoundIntegrator: Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
setConstraintTolerance(double) - Method in class ffx.openmm.Integrator: Set the tolerance within which constraints must be satisfied during the simulation.
setContentLength(int) - Method in class edu.rit.http.HttpResponse: Set this HTTP response's content length.
setContentType(String) - Method in class edu.rit.http.HttpResponse: Set this HTTP response's content type.
setContinuous(boolean) - Method in class ffx.algorithms.mc.LambdaMove: If true, do continuous moves.
setCoordinates(double[]) - Method in class ffx.algorithms.dynamics.Barostat: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Set the coordinates.
setCoordinates(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
setCoordinates(double[]) - Method in interface ffx.numerics.OptimizationInterface: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.potential.ANIEnergy
setCoordinates(double[]) - Method in class ffx.potential.DualTopologyEnergy: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.potential.extended.ExtendedSystem
setCoordinates(double[]) - Method in class ffx.potential.ForceFieldEnergy: The coordinate array should only contain active atoms.
setCoordinates(double[]) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Coordinates for active atoms in units of Angstroms.
setCoordinates(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: Coordinates for active atoms in units of Angstroms.
setCoordinates(double[]) - Method in class ffx.potential.QuadTopologyEnergy: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.potential.SystemState: Set the coordinates via a copy of the passed array into the internal array.
setCoordinates(double[]) - Method in class ffx.potential.XtalEnergy: Sets atomic coordinates and lattice parameters.
setCoordinates(double[]) - Method in class ffx.realspace.RealSpaceEnergy: Set atomic coordinates positions.
setCoordinates(double[]) - Method in class ffx.xray.CrystalReciprocalSpace: Set atomic coordinates.
setCoordinates(double[]) - Method in class ffx.xray.RefinementEnergy: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.xray.ScaleBulkEnergy: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.xray.SigmaAEnergy: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.xray.SplineEnergy: Set the current value of the parameters.
setCoordinates(double[]) - Method in class ffx.xray.XRayEnergy: set atomic xyz coordinates based on current position
setCoordinatesToEnsemble(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: setCoordinatesToEnsemble.
setCountInterval(int) - Method in class ffx.algorithms.cli.OSTOptions
setCountInterval(int) - Method in class ffx.algorithms.thermodynamics.HistogramData
setCovalentMap(int, int, IntArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the covalent map.
setCrossOver(double) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
setCrystal(Crystal) - Method in class ffx.algorithms.dynamics.Barostat: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in interface ffx.crystal.CrystalPotential: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.potential.DualTopologyEnergy: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.potential.ForceFieldEnergy: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.potential.MolecularAssembly: Set the Crystal for the Potential of this MolecularAssembly.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Setter for the field crystal.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.NeighborList: The NeighborList will be re-configured, if necessary, for the supplied Crystal.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.ReciprocalSpace: Setter for the field crystal.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.VanDerWaals: If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.VanDerWaalsTornado: If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated.
setCrystal(Crystal) - Method in class ffx.potential.openmm.OpenMMEnergy: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.potential.QuadTopologyEnergy: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.realspace.RealSpaceEnergy: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.xray.RefinementEnergy: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal) - Method in class ffx.xray.XRayEnergy: Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
setCrystal(Crystal[]) - Method in class ffx.realspace.RealSpaceData: Setter for the field crystal.
setCrystal(Crystal, boolean) - Method in class ffx.potential.ForceFieldEnergy: Set the boundary conditions for this calculation.
setCrystal(Crystal, int, int, int) - Method in class ffx.potential.nonbonded.RowRegion: Setter for the field crystal.
setCrystal(Crystal, int, int, int) - Method in class ffx.potential.nonbonded.SliceRegion: Setter for the field crystal.
setCrystal(Crystal, int, int, int) - Method in class ffx.potential.nonbonded.SpatialDensityRegion: Setter for the field crystal.
setCurrentCycle(int) - Method in class ffx.potential.bonded.Atom: setCurrentCycle
setCurrentCycle(int) - Method in class ffx.potential.MolecularAssembly: Setter for the field currentCycle.
setCurrentIntegrator(int) - Method in class ffx.openmm.CompoundIntegrator: Set the current Integrator.
setCutoff(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setCutoff(double) - Method in class ffx.openmm.amoeba.VdwForce: Deprecated.
This method exists only for backward compatibility. Use setCutoffDistance() instead.
setCutoff(double) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Setter for the field cutoff.
setCutoffDistance(double) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the cutoff distance (in nm) being used for nonbonded interactions.
setCutoffDistance(double) - Method in class ffx.openmm.amoeba.VdwForce: Set the cutoff distance (in nm) being used for nonbonded interactions.
setCutoffDistance(double) - Method in class ffx.openmm.CustomGBForce: Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.CustomHbondForce: Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.CustomManyParticleForce: Set the cutoff distance (in nm) being used for interactions.
setCutoffDistance(double) - Method in class ffx.openmm.CustomNonbondedForce: Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.GayBerneForce: Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.GBSAOBCForce: Set the cutoff distance (in nm) being used for nonbonded interactions.
setCutoffDistance(double) - Method in class ffx.openmm.NonbondedForce: Set the cutoff distance.
setCycles(int) - Method in class ffx.potential.MolecularAssembly: Setter for the field cycles.
setDanglingAtoms(List<Atom>) - Method in class ffx.potential.bonded.MSGroup: Sets the MultiScaleGroup's danglingAtoms member to a.
setDanglingAtoms(List<Atom>) - Method in class ffx.potential.bonded.MultiResidue: Sets the MultiScaleGroup's danglingAtoms member to a.
setData(double[]) - Method in class ffx.realspace.RealSpaceRefinementData: Setter for the field data.
setDecompose(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setDecomposeOriginal(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the decompose-original flag.
setDee(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setDefaultCollisionFrequency(double) - Method in class ffx.openmm.AndersenThermostat: Set the default collision frequency.
setDefaultPeriodicBoxVectors() - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Set the default values of the vectors defining the axes of the periodic box (measured in nm).
setDefaultPeriodicBoxVectors() - Method in class ffx.potential.openmm.OpenMMSystem: Set the default values of the vectors defining the axes of the periodic box (measured in nm).
setDefaultPeriodicBoxVectors(OpenMM_Vec3, OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.System: Set the default periodic box vectors.
setDefaultPressure(double) - Method in class ffx.openmm.MonteCarloBarostat: Set the default pressure acting on the system.
setDefaultPressure(double) - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Set the default pressure acting on the system (in bar).
setDefaultPressure(double) - Method in class ffx.openmm.MonteCarloMembraneBarostat: Set the default pressure acting on the system (in bar).
setDefaultPressure(OpenMM_Vec3) - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Set the default pressure acting on each axis (in bar).
setDefaultSurfaceTension(double) - Method in class ffx.openmm.MonteCarloMembraneBarostat: Set the default surface tension acting on the membrane (in bar*nm).
setDefaultTemperature(double) - Method in class ffx.openmm.AndersenThermostat: Set the default temperature of the heat bath.
setDefaultTemperature(double) - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Set the default temperature at which the system is being maintained (in Kelvin).
setDefaultTemperature(double) - Method in class ffx.openmm.MonteCarloBarostat: Set the default temperature at which the system is being maintained.
setDefaultTemperature(double) - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Set the default temperature at which the system is being maintained (in Kelvin).
setDefaultTemperature(double) - Method in class ffx.openmm.MonteCarloMembraneBarostat: Set the default temperature at which the system is being maintained (in Kelvin).
setDensity(double) - Method in class ffx.algorithms.dynamics.Barostat: setDensity.
setDensity(double, double) - Method in class ffx.crystal.Crystal: Set the unit cell vectors.
setDensity(double, double) - Method in class ffx.crystal.ReplicatesCrystal: Update the ReplicatesCrystal dimensions to the target density.
setDensityLoop(RowLoop[]) - Method in class ffx.potential.nonbonded.RowRegion: setDensityLoop.
setDensityLoop(SliceLoop[]) - Method in class ffx.potential.nonbonded.SliceRegion: setDensityLoop.
setDensityLoop(SpatialDensityLoop[]) - Method in class ffx.potential.nonbonded.SpatialDensityRegion: setDensityLoop
setDepth(int, int) - Method in class ffx.algorithms.misc.GenerateRotamers: Set which torsions to work on.
setDescreenOffset(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the descreen offset.
setDielectricOffset(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the dielectric offset.
setDirection(RotamerOptimization.Direction) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the optimization direction to forward or backward.
setDisableUpdates(boolean) - Method in class ffx.potential.nonbonded.NeighborList: If disableUpdates true, disable updating the neighbor list upon motion.
setDiscreteLambda(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
setDispersionOffest(double) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: The dispersion integral begins offset from the vdW radius.
setDispersionOverlapFactor(double) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: Set the dispersion overlap HCT scale factor.
setDispoff(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the dispersion offset.
setDistance(Distance) - Method in class ffx.numerics.clustering.Cluster: Sets the Distance metadata for this cluster.
setDistance(Double) - Method in class ffx.numerics.clustering.Distance: Sets the distance value.
setDistanceCutoff(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the cut-off distance for inclusion of residues in sliding box and window methods.
setDistributeWalkersString(String) - Method in class ffx.algorithms.cli.MultiDynamicsOptions
setDomain(double) - Method in class ffx.potential.nonbonded.octree.OctreeParticle
setDomain(double) - Method in class ffx.potential.nonbonded.octree.OctreePoint
setDonorParameters(int, int, int, int, PointerByReference) - Method in class ffx.openmm.CustomHbondForce: Set the parameters for a donor.
setDotRadius(int) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Sets the radius of node dots in pixels.
setDPMEParameters(double, int, int, int) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the DPME parameters.
setDrudeFriction(double) - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Set the friction coefficient which determines how strongly the internal coordinates of Drude particles are coupled to the heat bath (in inverse ps).
setDrudeTemperature(double) - Method in class ffx.openmm.drude.DrudeIntegrator: Set the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).
setDt(double) - Method in class ffx.algorithms.cli.DynamicsOptions
setdUdLBinWidth(double) - Method in class ffx.algorithms.thermodynamics.HistogramData
setElectrostatics(boolean) - Method in class ffx.potential.bonded.Atom: Setter for the field electrostatics.
setElectrostatics(String) - Method in class ffx.algorithms.misc.GenerateRotamers: Inactivates electrostatics for atom sets defined by 'start-end,start-end,...'.
setElementHCTScaleFactors(HashMap<Integer, Double>) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Setter for element-specific HCT overlap scale factors
setEnable(boolean) - Method in class ffx.ui.behaviors.GlobalBehavior
setEndSnapshot(int) - Method in class ffx.numerics.estimator.MBARFilter: Set the end snapshot.
setEnergy(double) - Method in class ffx.potential.terms.EnergyTerm: Set the total potential energy of this term.
setEnergyExpansion(EnergyExpansion) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
setEnergyFunction(Pointer) - Method in class ffx.openmm.ATMForce: Set the energy function.
setEnergyFunction(Pointer) - Method in class ffx.openmm.CustomCVForce: Set the energy function.
setEnergyFunction(Pointer) - Method in class ffx.openmm.CustomHbondForce: Set the energy expression for the force.
setEnergyFunction(Pointer) - Method in class ffx.openmm.CustomManyParticleForce: Set the algebraic expression that gives the interaction energy for each set of particles.
setEnergyFunction(Pointer) - Method in class ffx.openmm.CustomTorsionForce: Set the algebraic expression that gives the interaction energy of each torsion.
setEnergyFunction(Pointer) - Method in class ffx.openmm.CustomVolumeForce: Set the algebraic expression that defines the energy.
setEnergyFunction(String) - Method in class ffx.openmm.ATMForce: Set the energy function.
setEnergyFunction(String) - Method in class ffx.openmm.CustomAngleForce: Set the energy function expression.
setEnergyFunction(String) - Method in class ffx.openmm.CustomBondForce: Set the energy function expression.
setEnergyFunction(String) - Method in class ffx.openmm.CustomCentroidBondForce: Set the algebraic expression that gives the interaction energy of each bond
setEnergyFunction(String) - Method in class ffx.openmm.CustomCompoundBondForce: Set the energy expression for the force.
setEnergyFunction(String) - Method in class ffx.openmm.CustomCVForce: Set the energy function.
setEnergyFunction(String) - Method in class ffx.openmm.CustomExternalForce: Set the energy expression for the force.
setEnergyFunction(String) - Method in class ffx.openmm.CustomHbondForce: Set the energy expression for the force.
setEnergyFunction(String) - Method in class ffx.openmm.CustomManyParticleForce: Set the algebraic expression that gives the interaction energy for each set of particles.
setEnergyFunction(String) - Method in class ffx.openmm.CustomNonbondedForce: Set the energy expression for the force.
setEnergyFunction(String) - Method in class ffx.openmm.CustomTorsionForce: Set the algebraic expression that gives the interaction energy of each torsion.
setEnergyFunction(String) - Method in class ffx.openmm.CustomVolumeForce: Set the algebraic expression that defines the energy.
setEnergyRestart(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
setEnergyRestartFile(File) - Method in class ffx.algorithms.optimize.RotamerOptimization: Setter for the field energyRestartFile.
setEnergyTermParameters(int, String, int) - Method in class ffx.openmm.CustomGBForce: Set the parameters for an energy term.
setEnergyTermState(Potential.STATE) - Method in class ffx.algorithms.dynamics.Barostat: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in interface ffx.numerics.Potential: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.ANIEnergy
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.DualTopologyEnergy: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.extended.ExtendedSystem
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.ForceFieldEnergy: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.QuadTopologyEnergy: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.XtalEnergy: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.realspace.RealSpaceEnergy: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.xray.RefinementEnergy: Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.xray.XRayEnergy: Set the Potential Energy terms that should be active.
setEngineString(String) - Method in class ffx.algorithms.cli.DynamicsOptions
setEnsemble(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: setEnsemble.
setEnsemble(int, double) - Method in class ffx.algorithms.optimize.RotamerOptimization: setEnsemble.
setEps(double) - Method in class ffx.algorithms.cli.MinimizeOptions
setEpsh(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the water hydrogen epsilon parameter.
setEpsilon(int) - Method in class ffx.crystal.HKL: setEpsilon
setEpsilonCombiningRule(String) - Method in class ffx.openmm.amoeba.VdwForce: Set the epsilon combining rule.
setEpso(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the water oxygen epsilon parameter.
setEquilibration(boolean) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Sets the value of the boolean equilibration variables to true or false to either allow an equilibration step or skip it.
setEquilibrationSteps(long) - Method in class ffx.algorithms.cli.ThermodynamicsOptions
setErrorTolerance(double) - Method in class ffx.openmm.VariableLangevinIntegrator: Set the error tolerance for adaptive step sizing.
setErrorTolerance(double) - Method in class ffx.openmm.VariableVerletIntegrator: Set the error tolerance for adaptive step sizing.
setESVLambda(double, ExtendedSystem) - Static method in class ffx.potential.commands.PhEnergy: Sets lambda values for the extended system.
setESVTautomer(double, ExtendedSystem) - Static method in class ffx.potential.commands.PhEnergy: Sets tautomer values for the extended system.
setEvenSpacePhLadder(double, double, int) - Static method in class ffx.algorithms.dynamics.PhReplicaExchange: Sets an even pH ladder based on the pH gap.
setEwaldErrorTolerance(double) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the Ewald error tolerance.
setEwaldErrorTolerance(double) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the error tolerance for Ewald summation.
setEwaldParameters(double, double) - Method in class ffx.potential.nonbonded.pme.EwaldParameters: Determine the real space Ewald parameters and permanent multipole self energy.
setExceptionParameters(int, int, int, double, double) - Method in class ffx.openmm.GayBerneForce: Set the parameters for an exception.
setExceptionParameters(int, int, int, double, double, double) - Method in class ffx.openmm.NonbondedForce: Set the exception parameters.
setExceptionParameters(int, int, int, double, double, double, double, double, double) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the scale factors for an interaction that should be calculated differently from others.
setExclude(double) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
setExcludeAtoms(Set<Atom>) - Method in class ffx.algorithms.optimize.TitrationManyBody
setExclusionParticles(int, int, int) - Method in class ffx.openmm.CustomGBForce: Set the particles in an exclusion.
setExclusionParticles(int, int, int) - Method in class ffx.openmm.CustomHbondForce: Set the particles in an exclusion.
setExclusionParticles(int, int, int) - Method in class ffx.openmm.CustomManyParticleForce: Set the particles in an exclusion.
setExclusionParticles(int, int, int) - Method in class ffx.openmm.CustomNonbondedForce: Set the particles in an exclusion.
setExplicitDistanceTolerance(double) - Method in class ffx.numerics.quickhull.QuickHull3D: Sets an explicit distance tolerance for convexity tests.
setExponent(double) - Method in class ffx.algorithms.cli.RepExOptions
setExponentialTemperatureLadder(double, double) - Method in class ffx.algorithms.dynamics.ReplicaExchange: setExponentialTemperatureLadder.
setExtendedSystem(ExtendedSystem) - Method in class ffx.potential.parsers.XPHFilter
setExtent(int, int, int) - Method in class ffx.realspace.RealSpaceRefinementData: Setter for the field extent.
setExtrapolationCoefficients(PointerByReference) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the extrapolation coefficients.
setExtrapolationCoefficients(DoubleArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Set extrapolation coefficients.
setF(int, double) - Method in class ffx.xray.DiffractionRefinementData: Set amplitude (F).
setFactor(double) - Method in class ffx.ui.behaviors.MouseOrbit: Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseProperties: Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseRotate: Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseSelection: Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseTranslate: Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseZoom: Set the y-axis movement multipler with factor.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseOrbit: Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseProperties: Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseRotate: Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseSelection: Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseTranslate: Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactors() - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Overriden by the OST version which updates only during setLambda().
setFactors() - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsOST
setFactors() - Method in class ffx.potential.nonbonded.VanDerWaals.LambdaFactors: Overriden by the OST version which updates only during setLambda().
setFactors() - Method in class ffx.potential.nonbonded.VanDerWaals.LambdaFactorsOST
setFactors(int, int, LambdaMode) - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Overriden by the ESV version which updates with every softcore interaction.
setFactors(int, int, LambdaMode) - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsESV
setFallbackDynFile(File) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Sets the "fallback" .dyn file to write to if none is passed to the dynamic method.
setFc(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData: set complex Fc
setFcTot(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData: setFcTot
setFile(File) - Method in class ffx.potential.MolecularAssembly: Setter for the field file.
setFile(File) - Method in class ffx.potential.parsers.SystemFilter: setFile
setFileRead(boolean) - Method in class ffx.potential.parsers.SystemFilter: Setter for the field fileRead.
setFiles(List<File>) - Method in class ffx.potential.parsers.SystemFilter: Setter for the field files.
setFileType(String) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Method to set file type from groovy scripts.
setFileType(String) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: Method to set file type from groovy scripts.
setFinalized(boolean) - Method in class ffx.potential.bonded.MSGroup: Specifies whether the MultiScaleGroup has been finalized.
setFinalized(boolean) - Method in class ffx.potential.bonded.MultiResidue: Specifies whether the MultiScaleGroup has been finalized.
setFinish(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setFirstDir(int) - Method in class ffx.algorithms.cli.MultiDynamicsOptions
setFirstSystemAlchemistry(MolecularAssembly) - Method in class ffx.potential.cli.AlchemicalOptions: Set the alchemical atoms for this molecularAssembly.
setFirstSystemUnchargedAtoms(MolecularAssembly) - Method in class ffx.potential.cli.AlchemicalOptions: Set uncharged atoms for this molecularAssembly.
setFixedTautomerState(boolean) - Method in class ffx.potential.extended.ExtendedSystem: Does not allow for changes to the tautomer states of tautomerizing residues
setFixedTitrationState(boolean) - Method in class ffx.potential.extended.ExtendedSystem: Does not allow for changes to the tautomer states of titrating residues
setFixLattice(boolean) - Method in class ffx.potential.parsers.CIFFilter: Determine whether lattice parameters can be manipulated to follow lattice system constraints.
setFoFc1(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData: setFoFc1
setFoFc2(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData: setFoFc2
setForceField(ForceField) - Method in class ffx.potential.MolecularAssembly: Setter for the field forceField.
setForceField(ForceField) - Method in class ffx.potential.parsers.SystemFilter: Setter for the field forceField.
setForceGroup(int) - Method in class ffx.openmm.Force: Set the force group.
setForceGroup(int) - Method in class ffx.potential.terms.EnergyTerm: Set the force group identifier.
setForceIndex(int) - Method in class ffx.openmm.Force: Set the force index.
setFormFactorIndex(int) - Method in class ffx.potential.bonded.Atom: Setter for the field formFactorIndex.
setFormFactorWidth(double) - Method in class ffx.potential.bonded.Atom: Setter for the field formFactorWidth.
setFractionalCoordinateMode(MolecularAssembly.FractionalMode) - Method in class ffx.potential.XtalEnergy: setFractionalCoordinateMode.
setFractionalMode(MolecularAssembly.FractionalMode) - Method in class ffx.potential.MolecularAssembly: Setter for the field fractionalMode.
setFrame(int) - Method in class ffx.ui.Trajectory: setFrame
setFreeR(int, int) - Method in class ffx.xray.DiffractionRefinementData: Set FreeR value flag of a reflection.
setFreeRFlag(int) - Method in class ffx.xray.DiffractionRefinementData: Set FreeR value flag.
setFrequency(int) - Method in class ffx.openmm.CMMotionRemover: Set the frequency (in time steps) at which center of mass motion should be removed.
setFrequency(int) - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
setFrequency(int) - Method in class ffx.openmm.MonteCarloBarostat: Set the frequency.
setFrequency(int) - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
setFrequency(int) - Method in class ffx.openmm.MonteCarloMembraneBarostat: Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.
setFriction(double) - Method in class ffx.openmm.BrownianIntegrator: Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps).
setFriction(double) - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Set the friction coefficient which determines how strongly the system is coupled to the main heat bath (in inverse ps).
setFriction(double) - Method in class ffx.openmm.LangevinMiddleIntegrator: Set the friction coefficient.
setFriction(double) - Method in class ffx.openmm.VariableLangevinIntegrator: Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in 1/ps).
setFs(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData: setFs
setFSigF(int, double, double) - Method in class ffx.xray.DiffractionRefinementData: Set amplitude and sigF.
setFunctionParameters(int, int, int, PointerByReference) - Method in class ffx.openmm.Discrete3DFunction: Set the parameters for the tabulated function.
setFunctionParameters(int, int, PointerByReference) - Method in class ffx.openmm.Discrete2DFunction: Set the parameters for the tabulated function.
setFunctionParameters(int, Pointer, PointerByReference, double, double) - Method in class ffx.openmm.CustomHbondForce: Set the parameters for a tabulated function.
setFunctionParameters(int, String, PointerByReference, double, double) - Method in class ffx.openmm.CustomCompoundBondForce: Set the parameters for a tabulated function.
setFunctionParameters(int, String, PointerByReference, double, double) - Method in class ffx.openmm.CustomGBForce: Set the parameters for a tabulated function.
setFunctionParameters(int, String, PointerByReference, double, double) - Method in class ffx.openmm.CustomHbondForce: Set the parameters for a tabulated function.
setFunctionParameters(int, String, PointerByReference, double, double) - Method in class ffx.openmm.CustomNonbondedForce: Set the parameters for a tabulated function.
setFunctionParameters(PointerByReference) - Method in class ffx.openmm.Discrete1DFunction: Set the parameters for the tabulated function.
setFunctionParameters(PointerByReference, double, double) - Method in class ffx.openmm.Continuous1DFunction: Set the parameters for the tabulated function.
setFunctionParameters(PointerByReference, int, int, double, double, double, double) - Method in class ffx.openmm.Continuous2DFunction: Set the parameters for the tabulated function.
setFunctionParameters(PointerByReference, int, int, int, double, double, double, double, double, double) - Method in class ffx.openmm.Continuous3DFunction: Set the parameters for the tabulated function.
setGlobalCenter(double[]) - Method in class ffx.ui.GraphicsEvents: setGlobalCenter
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.ATMForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomAngleForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomBondForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomCentroidBondForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomCompoundBondForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomCVForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomExternalForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomGBForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomHbondForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomManyParticleForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomNonbondedForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomTorsionForce: Set the default value of a global parameter.
setGlobalParameterDefaultValue(int, double) - Method in class ffx.openmm.CustomVolumeForce: Set the default value of a global parameter.
setGlobalParameterName(int, Pointer) - Method in class ffx.openmm.ATMForce: Set the name of a global parameter.
setGlobalParameterName(int, Pointer) - Method in class ffx.openmm.CustomCVForce: Set the name of a global parameter.
setGlobalParameterName(int, Pointer) - Method in class ffx.openmm.CustomHbondForce: Set the name of a global parameter.
setGlobalParameterName(int, Pointer) - Method in class ffx.openmm.CustomManyParticleForce: Set the name of a global parameter.
setGlobalParameterName(int, Pointer) - Method in class ffx.openmm.CustomTorsionForce: Set the name of a global parameter.
setGlobalParameterName(int, Pointer) - Method in class ffx.openmm.CustomVolumeForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.ATMForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomAngleForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomBondForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomCentroidBondForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomCompoundBondForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomCVForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomExternalForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomGBForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomHbondForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomManyParticleForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomNonbondedForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomTorsionForce: Set the name of a global parameter.
setGlobalParameterName(int, String) - Method in class ffx.openmm.CustomVolumeForce: Set the name of a global parameter.
setGlobalVariable(int, double) - Method in class ffx.openmm.CustomIntegrator: Set the value of a global variable.
setGlobalVariableByName(String, double) - Method in class ffx.openmm.CustomIntegrator: Set the value of a global variable, specified by name.
setGradient(boolean) - Method in class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
setGradient(boolean) - Method in class ffx.potential.terms.EnergyTermRegion: Set whether the gradient will be computed.
setGroupParameters(int, IntArray, DoubleArray) - Method in class ffx.openmm.CustomCentroidBondForce: Set the properties of a group.
setGroupSize(int) - Method in class ffx.potential.nonbonded.NeighborList: Set the group size for group-based Verlet lists.
setH(int) - Method in class ffx.crystal.HKL: Set the h-index of the reflection.
setHardWallConstraint(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: If this flag is true, (lambda, dU/dL) Monte Carlo samples that have no weight in the Histogram are rejected.
setHeader(String, String) - Method in class edu.rit.http.HttpResponse: Set the given header in this HTTP response.
setHetero(boolean) - Method in class ffx.potential.bonded.Atom: setHetero
setHistogramFile(File) - Method in class ffx.algorithms.thermodynamics.HistogramData
setHistogramIndex(int) - Method in class ffx.algorithms.thermodynamics.LambdaData
setHistogramRead(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
setHistograms(OrthogonalSpaceTempering.Histogram[], int[]) - Method in class ffx.algorithms.thermodynamics.SendSynchronous: Update the synchronous communication histograms.
setHull(double[], int, int[][], int) - Method in class ffx.numerics.quickhull.QuickHull3D: Initializes the hull from precomputed face indices and point coordinates.
setID(String) - Method in class ffx.potential.bonded.BondedTerm: Sets the Term's id.
setID_Key(boolean) - Method in class ffx.potential.bonded.BondedTerm: setID_Key
setImproperTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the ImproperTorsion node to t.
setInactiveAtoms(String) - Method in class ffx.algorithms.misc.GenerateRotamers: Inactivates atom sets defined by 'start-end,start-end,...'.
setIncludeCavityTerm(int) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the include cavity term.
setInclusionCutoff(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setIncrement(double) - Method in class ffx.algorithms.misc.GenerateRotamers: Sets the angle to change torsions by.
setIncrement(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setIncrement(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the residue increment for sliding window.
setIndependentWalkers(boolean) - Method in class ffx.algorithms.cli.OSTOptions
setIndependentWalkers(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData: Sets the value of independentWalkers; if true, it also sets writeIndependent to true.
setIndex(int) - Method in class ffx.crystal.HKL: Set the index of this reflection.
setInducedDipole(double[][], double[][]) - Method in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Set the induced dipole.
setInducedDipole(double[], double[]) - Method in class ffx.numerics.multipole.PolarizableMultipole: Set the induced dipole.
setInducedDipoleReferences(double[][][], double[][][], boolean) - Method in class ffx.potential.nonbonded.ScfPredictor: To be called upon initialization and update of inducedDipole arrays in parent.
setInitAtomGradients(boolean) - Method in class ffx.potential.terms.EnergyTermRegion
setInitPoint(VCoord) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Sets the virtual coordinate at which this node is drawn.
setInitValue(double) - Method in class ffx.potential.nonbonded.RowRegion: Setter for the field initValue.
setInitValue(double) - Method in class ffx.potential.nonbonded.SliceRegion: Setter for the field initValue.
setInitValue(double) - Method in class ffx.potential.nonbonded.SpatialDensityRegion: Setter for the field initValue.
setInnerTimeSteps(int) - Method in class ffx.algorithms.dynamics.integrators.Respa: Set inner Respa number of time steps.
setIntegrationForceGroups(int) - Method in class ffx.openmm.CompoundIntegrator: Set which force groups to use for integration.
setIntegrationForceGroups(int) - Method in class ffx.openmm.Integrator: Set the force groups this integrator acts on.
setIntegrator(IntegratorEnum) - Method in class ffx.algorithms.cli.DynamicsOptions: Set the integrator.
setIntegratorString(String) - Method in class ffx.algorithms.cli.DynamicsOptions
setInteractionGroupParameters(int, PointerByReference, PointerByReference) - Method in class ffx.openmm.CustomNonbondedForce: Set the parameters for an interaction group.
setInterestedResidue(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setIntermolecular(boolean) - Method in class ffx.potential.nonbonded.NeighborList: Setter for the field intermolecular.
setIntervalSteps(int) - Method in class ffx.algorithms.dynamics.MolecularDynamics: No-op; FFX does not need to occasionally return information from FFX.
setIntervalSteps(int) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: Setter for the field intervalSteps.
setIsotropic(boolean) - Method in class ffx.algorithms.cli.BarostatOptions
setIsotropic(boolean) - Method in class ffx.algorithms.dynamics.Barostat: Restrict the MC Barostat to isotropic moves.
setIterations(int) - Method in class ffx.algorithms.cli.MinimizeOptions
setIterations(int) - Method in class ffx.algorithms.mc.MCLoop: Setter for the field iterations.
setK(int) - Method in class ffx.crystal.HKL: Set the k-index of the reflection.
setKey(int[]) - Method in class ffx.potential.parameters.BaseType: Setter for the field key.
setKey(String) - Method in class ffx.potential.parameters.BaseType: Setter for the field key.
setKeyFile(File) - Method in class ffx.ui.FFXSystem: Setter for the field keyFile.
setKeywordGroup(String) - Method in class ffx.ui.KeywordPanel: Make the passed Keyword Group active in the editor.
setKeywords(Hashtable<String, Keyword>) - Method in class ffx.ui.FFXSystem: Setter for the field keywords.
setKeywordValue(String, String) - Method in class ffx.ui.KeywordPanel: Load a value into a KeywordComponent.
setKineticEnergy(double) - Method in class ffx.potential.SystemState: Set the kinetic energy.
setKineticEnergyExpression(String) - Method in class ffx.openmm.CustomIntegrator: Set the expression used to compute the kinetic energy.
setKTScale(double) - Method in class ffx.xray.RefinementEnergy: set the current kT scaling weight
setL(int) - Method in class ffx.crystal.HKL: Set the l-index of the reflection.
setLambda(double) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Calls on the OST method set lambda to update lambda to the current value in this class
setLambda(double) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Setter for the field lambda.
setLambda(double) - Method in class ffx.potential.ANIEnergy
setLambda(double) - Method in class ffx.potential.bonded.AngleTorsion: Set the current value of the state variable.
setLambda(double) - Method in interface ffx.potential.bonded.LambdaInterface: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.PiOrbitalTorsion: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.RestrainDistance: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.RestrainPosition: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.RestrainTorsion
setLambda(double) - Method in class ffx.potential.bonded.StretchTorsion: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.Torsion: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.TorsionTorsion: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.DualTopologyEnergy: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.ForceFieldEnergy: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.COMRestraint: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.NCSRestraint: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.VanDerWaals: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.openmm.OpenMMEnergy: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.QuadTopologyEnergy: Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy: Set the lambda value for all Pi-Orbital Torsions in this term.
setLambda(double) - Method in class ffx.potential.terms.TorsionPotentialEnergy: Set the lambda value for all Torsions in this term.
setLambda(double) - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy: Set the lambda value for all TorsionTorsions in this term.
setLambda(double) - Method in class ffx.realspace.RealSpaceData: Set the current value of the state variable.
setLambda(double) - Method in class ffx.realspace.RealSpaceEnergy: Set the current value of the state variable.
setLambda(double) - Method in class ffx.xray.RefinementEnergy: Set the current value of the state variable.
setLambda(double) - Method in class ffx.xray.XRayEnergy: Set the current value of the state variable.
setLambdaAllBondedTerms(boolean) - Method in class ffx.potential.terms.EnergyTermRegion
setLambdaBinWidth(double) - Method in class ffx.algorithms.thermodynamics.HistogramData: Sets lambdaBinWidth; if an invalid value is provided (not 0-1), resets it to default 0.005.
setLambdaBondedTerms(boolean) - Method in class ffx.potential.terms.EnergyTermRegion
setLambdaFile(File) - Method in class ffx.algorithms.thermodynamics.LambdaData
setLambdaFriction(double) - Method in class ffx.algorithms.cli.LambdaParticleOptions
setLambdaMass(double) - Method in class ffx.algorithms.cli.LambdaParticleOptions
setLambdaName(String) - Method in class ffx.openmm.amoeba.VdwForce: Set the lambda parameter name.
setLambdaRead(boolean) - Method in class ffx.algorithms.thermodynamics.LambdaData
setLambdaStdDev(double) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Calls on LambdaMove class method setLambdaStdDev to update the lambda standard deviation to the current value in this class
setLambdaTerm(boolean) - Method in class ffx.potential.ForceFieldEnergy: Set the lambdaTerm flag.
setLambdaTerm(boolean) - Method in class ffx.potential.nonbonded.COMRestraint: Setter for the field lambdaTerm.
setLambdaWriteOut(double) - Method in class ffx.algorithms.cli.OSTOptions
setLambdaXYZGradient(double, double, double) - Method in class ffx.potential.bonded.Atom: setLambdaXYZGradient
setLastReceiveddUdL(double) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
setLastReceivedLambda(double) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
setlCluster(Cluster) - Method in class ffx.numerics.clustering.ClusterPair: Sets the left cluster.
setLeaf(int, int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
setLibrary(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setLineColor(Color) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setLink(boolean) - Method in class ffx.potential.bonded.Polymer: Setter for the field link.
setLinkageDistance(Double) - Method in class ffx.numerics.clustering.ClusterPair: Sets the linkage distance.
setLinkPoint(VCoord) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Sets the virtual coordinate where this node connects to its parent.
setListResidues(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
setLMN(int[]) - Method in class ffx.potential.parsers.PDBFilter
setLocale(String, String) - Method in class ffx.ui.properties.FFXLocale: setLocale
setLogFile(File) - Method in class ffx.ui.FFXSystem: Setter for the field logFile.
setLogMode(String) - Method in class ffx.ui.ModelingPanel
setLogWrites(boolean) - Method in class ffx.potential.parsers.PDBFilter: Sets whether this PDBFilter should log each time it saves to a file.
setLow(double) - Method in class ffx.algorithms.cli.AnnealOptions
setMainPanel(MainPanel) - Method in class ffx.ui.LogHandler: A reference to the Force Field X MainPanel container to shut down if we encounter a fatal (SEVERE) exception.
setMapParameters(int, int, PointerByReference) - Method in class ffx.openmm.CMAPTorsionForce: Set the energy values of a map.
setMass(double) - Method in class ffx.potential.bonded.Atom: Set the Atomic Mass.
setMass(double[]) - Method in class ffx.potential.SystemState: Set the mass of each degree of freedom.
setMatrix(int, int, double[][]) - Method in class edu.rit.io.DoubleMatrixFile: Set this matrix file's number of rows, number of columns, and underlying matrix.
setMaxAM(double) - Method in class ffx.algorithms.cli.BarostatOptions
setMaxAngleMove(double) - Method in class ffx.algorithms.dynamics.Barostat: Setter for the field maxAngleMove.
setMaxD(double) - Method in class ffx.algorithms.cli.BarostatOptions
setMaxDensity(double) - Method in class ffx.algorithms.dynamics.Barostat: Setter for the field maxDensity.
setMaxDrudeDistance(double) - Method in class ffx.openmm.drude.DrudeIntegrator: Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm.
setMaxDrudeDistance(double) - Method in class ffx.openmm.drude.DrudeNoseHooverIntegrator: Set the maximum allowed distance between Drude particles and their parent atoms.
setMaximumPairDistance(double) - Method in class ffx.openmm.NoseHooverIntegrator: Set the maximum pair distance for neighbor list updates.
setMaximumStepSize(double) - Method in class ffx.openmm.VariableLangevinIntegrator: Set the maximum step size the integrator is allowed to use (in ps).
setMaximumStepSize(double) - Method in class ffx.openmm.VariableVerletIntegrator: Set the maximum step size the integrator is allowed to use (in ps).
setMaxRotCheckDepth(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Control the depth of self-consistency checking with a rotamer is eliminated.
setMaxV(double) - Method in class ffx.algorithms.cli.BarostatOptions
setMaxVolumeMove(double) - Method in class ffx.algorithms.dynamics.Barostat: Setter for the field maxVolumeMove.
setMcHardWall(boolean) - Method in class ffx.algorithms.cli.OSTOptions
setMcLambdaStdDev(double) - Method in class ffx.algorithms.cli.OSTOptions
setMcMDSteps(int) - Method in class ffx.algorithms.cli.OSTOptions
setMDIntervalSteps(int) - Method in class ffx.algorithms.mc.MDMove
setMDSteps(long) - Method in class ffx.algorithms.dynamics.NonEquilbriumDynamics: Configure increments of the non-equilibrium lambda values based on the total number of MD steps.
setMeanBarostatInterval(int) - Method in class ffx.algorithms.dynamics.Barostat: Setter for the field meanBarostatInterval.
setMessage(int) - Method in class ffx.ui.commands.SimulationMessage: Setter for the field message.
setMetaDynamics(boolean) - Method in class ffx.algorithms.cli.OSTOptions
setMetaDynamics(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
setMinD(double) - Method in class ffx.algorithms.cli.BarostatOptions
setMinDensity(double) - Method in class ffx.algorithms.dynamics.Barostat: Setter for the field minDensity.
setMinimizationErrorTolerance(double) - Method in class ffx.openmm.drude.DrudeSCFIntegrator: Set the error tolerance to use when minimizing the potential energy.
setMinimumNumberAcceptedNARotamers(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the minimum number of accepted nucleic acid rotamers.
setMinSIMDLoopLength(int) - Method in class ffx.numerics.fft.Complex: Configure the minimum SIMD inner loop length.
setModel(Cluster) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setModelNumbering(int) - Method in class ffx.potential.parsers.PDBFilter: setModelNumbering.
setModRes(boolean) - Method in class ffx.potential.bonded.Atom: setModRes
setMolecularAssembly(MolecularAssembly) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
setMoleculeNumber(int) - Method in class ffx.potential.bonded.Atom: Setter for the field moleculeNumber.
setMonteCarlo(boolean) - Method in class ffx.algorithms.cli.OSTOptions
setMonteCarlo(boolean) - Method in class ffx.algorithms.cli.RepExOptions
setMonteCarlo(boolean, int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the option to use a number of Monte Carlo steps for final optimization.
setMonteCarlo(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setMonteCarloTesting(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the monteCarloTesting boolean in RotamerOptimization.java to true or false.
setMouseButton(int) - Method in class ffx.ui.behaviors.MouseTranslate: Setter for the field mouseButton.
setMouseButton(int) - Method in class ffx.ui.behaviors.MouseZoom: Setter for the field mouseButton.
setMoveSize(double) - Method in class ffx.algorithms.mc.LambdaMove: Get the Lambda move size, which is a standard deviation for continuous moves or step size for discrete moves.
setMultipoleParameters(int, double, DoubleArray, DoubleArray, int, int, int, int, double, double, double) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the multipole parameters for a particle.
setMultipoleType(MultipoleType) - Method in class ffx.potential.bonded.Atom: Setter for the field multipoleType.
setMutualInducedMaxIterations(int) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the mutual induced target maximum number of iterations.
setMutualInducedTargetEpsilon(double) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the mutual induced target epsilon.
setNaLibraryName(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
setName(String) - Method in class ffx.numerics.clustering.Cluster: Sets the name of this cluster.
setName(String) - Method in class ffx.openmm.Force: Set the name of the force.
setName(String) - Method in class ffx.potential.bonded.Molecule: Sets the name of this NodeObject to n.
setName(String) - Method in class ffx.potential.bonded.MSNode: Sets the name of this NodeObject to n.
setName(String) - Method in class ffx.potential.bonded.Residue
setName(String) - Method in class ffx.potential.terms.EnergyTerm: Set the name of this energy term.
setNamePadding(int) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Sets the pixel padding between a leaf node and its name text.
setNB(int) - Method in class ffx.xray.XRayEnergy: set the number of B factor parameters
setNBFGS(int) - Method in class ffx.algorithms.cli.MinimizeOptions
setnChild(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
setnCritical(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
setNeighborList(int[][][]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Setter for the field neighborLists.
setNeuralNetwork(boolean) - Method in class ffx.potential.bonded.Atom: If true, this atom is part of a molecule whose intramolecular interactions are handled by a neural network.
setNext(HalfEdge) - Method in class ffx.numerics.quickhull.HalfEdge: Sets the value of the next edge adjacent (counter-clockwise) to this one within the triangle.
setNI(int, int, int) - Method in class ffx.realspace.RealSpaceRefinementData: setNI.
setNOcc(int) - Method in class ffx.xray.XRayEnergy: set the number of occupancy parameters
setNonbondedMethod(int) - Method in class ffx.openmm.amoeba.GKCavitationForce: Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the nonbonded method for the multipole force.
setNonbondedMethod(int) - Method in class ffx.openmm.amoeba.VdwForce: Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.CustomGBForce: Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.CustomHbondForce: Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.CustomManyParticleForce: Set the method used for handling long range nonbonded interactions.
setNonbondedMethod(int) - Method in class ffx.openmm.CustomNonbondedForce: Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.GayBerneForce: Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.GBSAOBCForce: Set the method used for handling long range nonbonded interactions.
setNonbondedMethod(int) - Method in class ffx.openmm.NonbondedForce: Set the nonbonded method.
setNonEquilibriumLambda(boolean, int, boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Enables non-equilibrium lambda dynamics.
setNoOriginal(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setNsymm(int) - Method in class ffx.potential.nonbonded.RowLoop: setNsymm
setNsymm(int) - Method in class ffx.potential.nonbonded.SliceLoop: setNsymm
setNsymm(int) - Method in class ffx.potential.nonbonded.SpatialDensityLoop: setNsymm
setNucleicCorrectionThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: The nucleic acid correction threshold.
setNucleicPruningFactor(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Also sets derivative pruning factors.
setNumber(int) - Method in class ffx.potential.bonded.Residue: setNumber
setNumBoxes(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
setNumLeaves(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
setNumXYZBoxes(int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the number of boxes in the x, y, and z axes if the box optimization is to be carried out.
setNXYZ(int) - Method in class ffx.xray.XRayEnergy: set the number of xyz parameters
setObservableData(double[][][], boolean, boolean) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
setObservableData(double[][], boolean) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
setObtainVelAcc(boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Not meaningful for FFX dynamics (no need to obtain velocities/accelerations from a different program, especially one running on a GPU).
setObtainVelAcc(boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: Sets whether to obtain all variables (velocities, gradients) from OpenMM, or just positions and energies.
setOccupancies(double[]) - Method in class ffx.xray.XRayEnergy: set atom occupancies based on current position
setOccupancy(double) - Method in class ffx.potential.bonded.Atom: Setter for the field occupancy.
setOccupancyAcceleration(double) - Method in class ffx.potential.bonded.Atom: Setter for the field occupancyAcceleration.
setOccupancyGradient(double) - Method in class ffx.potential.bonded.Atom: Setter for the field occupancyGradient.
setOccupancyPreviousAcceleration(double) - Method in class ffx.potential.bonded.Atom: Setter for the field occupancyPreviousAcceleration.
setOccupancyVelocity(double) - Method in class ffx.potential.bonded.Atom: Setter for the field occupancyVelocity.
setOctant(int) - Method in class ffx.potential.nonbonded.SpatialDensityLoop: Setter for the field octant.
setOffset(Vector3d) - Method in class ffx.potential.MolecularAssembly: Setter for the field offset.
setOnlyTitration(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setOpposite(HalfEdge) - Method in class ffx.numerics.quickhull.HalfEdge: Sets the half-edge opposite to this half-edge.
setOptimization(boolean, MolecularAssembly) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters: setOptimization.
setOptimize(boolean) - Method in class ffx.algorithms.cli.DynamicsOptions
setOrigin(int, int, int) - Method in class ffx.realspace.RealSpaceRefinementData: Setter for the field origin.
setOriginalCoordinates(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setOSXProperties() - Static method in class ffx.ui.OSXAdapter: Set Mac OS X Systems Properties to promote native integration.
setOutOfPlaneBends(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the Out-of-Plane Bend node to t.
setOutOfPlaneBends(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the Out-of-Plane Bend node to t.
setOutOfPlaneBendType(OutOfPlaneBendType) - Method in class ffx.potential.bonded.OutOfPlaneBend: Set a reference to the force field parameters for this Angle.
setPackFFTs(boolean) - Method in class ffx.numerics.fft.Complex2D: Set the 2D transform to pack FFTs into a contiguous array to compute all FFTs at once.
setPackFFTs(boolean) - Method in class ffx.numerics.fft.Complex3D: Set the 2D transform to pack FFTs.
setPackFFTs(boolean) - Method in class ffx.numerics.fft.Complex3DParallel: Pack the FFTs for optimal use of SIMD instructions.
setPairClashThreshold(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setPairClashThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Setter for the field pairClashThreshold.
setParallel(boolean) - Method in class ffx.potential.DualTopologyEnergy: setParallel.
setParallel(boolean) - Method in class ffx.potential.QuadTopologyEnergy: setParallel.
setParameter(Pointer, double) - Method in class ffx.openmm.Context: Set the value of an adjustable parameter defined by a Force object in the System.
setParameter(String, double) - Method in class ffx.openmm.Context: Set the value of an adjustable parameter defined by a Force object in the System.
setParent(Cluster) - Method in class ffx.numerics.clustering.Cluster: Sets the parent cluster of this node.
setParentIndex(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
setParticleExclusions(int, IntArray) - Method in class ffx.openmm.amoeba.VdwForce: Set the particle exclusions.
setParticleMass(int, double) - Method in class ffx.openmm.System: Set the mass (in atomic mass units) of a particle.
setParticleParameters(int, double, double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the force field parameters for a WCA dispersion particle.
setParticleParameters(int, double, double, double) - Method in class ffx.openmm.GBSAOBCForce: Set the force field parameters for a particle.
setParticleParameters(int, double, double, double) - Method in class ffx.openmm.NonbondedForce: Set the particle parameters.
setParticleParameters(int, double, double, double, double, double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the force field parameters for a particle.
setParticleParameters(int, double, double, int) - Method in class ffx.openmm.amoeba.GKCavitationForce: Set the parameters for an atom in the Cavitation force.
setParticleParameters(int, double, double, int, int, double, double, double, double, double, double) - Method in class ffx.openmm.GayBerneForce: Set the parameters for a particle.
setParticleParameters(int, double, PointerByReference, PointerByReference, double, double, double, double, double, double, double, double, double, int, int, int, int) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the nonbonded force parameters for a particle.
setParticleParameters(int, int, double, double, double, int, int, double) - Method in class ffx.openmm.amoeba.VdwForce: Set the particle parameters.
setParticleParameters(int, int, int, int, int, int, double, double, double, double) - Method in class ffx.openmm.drude.DrudeForce: Set the parameters for a Drude particle.
setParticleParameters(int, int, DoubleArray) - Method in class ffx.openmm.CustomExternalForce: Set the parameters for a particle.
setParticleParameters(int, PointerByReference) - Method in class ffx.openmm.CustomNonbondedForce: Set the parameters for a particle.
setParticleParameters(int, PointerByReference, int) - Method in class ffx.openmm.CustomManyParticleForce: Set the parameters for a particle.
setParticleParameters(int, OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.ATMForce: Set the parameters for a particle
setParticleParameters(int, DoubleArray) - Method in class ffx.openmm.CustomGBForce: Set the parameters for a particle.
setParticles(PointerByReference) - Method in class ffx.openmm.RMSDForce: Set the indices of the particles to use when computing the RMSD.
setParticleTypeParameters(int, double, double) - Method in class ffx.openmm.amoeba.VdwForce: Set the particle type parameters.
setPerAcceptorParameterName(int, Pointer) - Method in class ffx.openmm.CustomHbondForce: Set the name of a per-acceptor parameter.
setPerAcceptorParameterName(int, String) - Method in class ffx.openmm.CustomHbondForce: Set the name of a per-acceptor parameter.
setPerAngleParameterName(int, String) - Method in class ffx.openmm.CustomAngleForce: Set the name of a per-angle parameter.
setPerBondParameterName(int, String) - Method in class ffx.openmm.CustomBondForce: Set the name of a per-bond parameter.
setPerBondParameterName(int, String) - Method in class ffx.openmm.CustomCentroidBondForce: Set the name of a per-bond parameter.
setPerBondParameterName(int, String) - Method in class ffx.openmm.CustomCompoundBondForce: Set the name of a per-bond parameter.
setPerDofVariable(int, PointerByReference) - Method in class ffx.openmm.CustomIntegrator: Set the values of a per-DOF variable.
setPerDofVariableByName(String, PointerByReference) - Method in class ffx.openmm.CustomIntegrator: Set the values of a per-DOF variable, specified by name.
setPerDonorParameterName(int, Pointer) - Method in class ffx.openmm.CustomHbondForce: Set the name of a per-donor parameter.
setPerDonorParameterName(int, String) - Method in class ffx.openmm.CustomHbondForce: Set the name of a per-donor parameter.
setPeriodicBoxVectors(OpenMM_Vec3, OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.Context: Set the vectors defining the axes of the periodic box (measured in nm).
setPeriodicBoxVectors(Crystal) - Method in class ffx.potential.openmm.OpenMMContext: Set the periodic box vectors for a context based on the crystal instance.
setPermanentMultipole(double[]) - Method in class ffx.numerics.multipole.PolarizableMultipole: Set the permanent multipole.
setPermanentMultipole(double[][]) - Method in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Set the permanent multipole.
setPermutationMode(int) - Method in class ffx.openmm.CustomManyParticleForce: Set the permutation mode.
setPerParticleParameterName(int, Pointer) - Method in class ffx.openmm.CustomManyParticleForce: Set the name of a per-particle parameter.
setPerParticleParameterName(int, String) - Method in class ffx.openmm.CustomExternalForce: Set the name of a per-particle parameter.
setPerParticleParameterName(int, String) - Method in class ffx.openmm.CustomGBForce: Set the name of a per-particle parameter.
setPerParticleParameterName(int, String) - Method in class ffx.openmm.CustomManyParticleForce: Set the name of a per-particle parameter.
setPerParticleParameterName(int, String) - Method in class ffx.openmm.CustomNonbondedForce: Set the name of a per-particle parameter.
setPerTorsionParameterName(int, Pointer) - Method in class ffx.openmm.CustomTorsionForce: Set the name of a per-torsion parameter.
setPerTorsionParameterName(int, String) - Method in class ffx.openmm.CustomTorsionForce: Set the name of a per-torsion parameter.
setpH(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the environment pH
setPHRestraint(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setPHRestraint(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the K for the harmonic pH restraint
setPicking(boolean) - Method in class ffx.ui.GraphicsPicking: Setter for the field picking.
setPickMode(int) - Method in class ffx.ui.behaviors.PickOrbitBehavior: Sets the pickMode component of this PickTranslateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickPropertiesBehavior: setPickMode
setPickMode(int) - Method in class ffx.ui.behaviors.PickRotateBehavior: Sets the pickMode component of this PickRotateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickSelectionBehavior: Sets the pickMode component of this PickRotateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickTranslateBehavior: Sets the pickMode component of this PickTranslateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickZoomBehavior: Sets the pickMode component of this PickTranslateBehavior to the value of the passed pickMode.
setPiOrbitalTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.
setPiOrbitalTorsions(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.
setPiOrbitalTorsionType(PiOrbitalTorsionType) - Method in class ffx.potential.bonded.PiOrbitalTorsion: Set the PiOrbitalTorsionType.
setPmeGridDimensions(IntArray) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the PME grid dimensions for the multipole force.
setPMEParameters(double, int, int, int) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the PME parameters.
setPMEParameters(double, int, int, int) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the parameters to use for PME calculations.
setPMEParameters(double, int, int, int) - Method in class ffx.openmm.NonbondedForce: Set the PME parameters.
setPointer(PointerByReference) - Method in class ffx.openmm.Integrator: Set the OpenMM Integrator pointer.
setPointer(PointerByReference) - Method in class ffx.openmm.System: Set the pointer to the system.
setPoints(double[], int) - Method in class ffx.numerics.quickhull.QuickHull3D: Populates the internal vertex buffer from a flat coordinate array.
setPoints(Point3d[], int) - Method in class ffx.numerics.quickhull.QuickHull3D: Populates the internal vertex buffer from an array of Point3d.
setPolarization(Polarization) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Setter for the field polarization.
setPolarizationEnergy(double) - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion: Set the current polarization energy.
setPolarizationType(int) - Method in class ffx.openmm.amoeba.MultipoleForce: Set the polarization method.
setPolarizeType(PolarizeType) - Method in class ffx.potential.bonded.Atom: Setter for the field polarizeType.
setPosition() - Method in class ffx.ui.GraphicsCanvas: setPosition
setPosition(MSNode) - Method in class ffx.ui.GraphicsCanvas: setPosition
setPositions(double[]) - Method in class ffx.openmm.Context: Set the positions of all particles in the System (measured in nm).
setPositions(double[]) - Method in class ffx.potential.openmm.OpenMMContext: The array x should contain atomic coordinates for all atoms in units of Angstroms.
setPotential(ForceFieldEnergy) - Method in class ffx.potential.MolecularAssembly: setPotential
setPotentialEnergy(double) - Method in class ffx.potential.SystemState: Set the potential energy.
setPotentialFunction(int) - Method in class ffx.openmm.amoeba.VdwForce: Set the potential function.
setPressure(double) - Method in class ffx.algorithms.cli.BarostatOptions
setPressure(double) - Method in class ffx.algorithms.dynamics.Barostat: Setter for the field pressure.
setPrev(HalfEdge) - Method in class ffx.numerics.quickhull.HalfEdge: Sets the value of the previous edge adjacent (clockwise) to this one within the triangle.
setPreviousAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in interface ffx.numerics.Potential: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
setPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field previousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
setPreviousAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.XtalEnergy: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy: setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.xray.XRayEnergy: setPreviousAcceleration.
setPreviousAccelerations(double[]) - Method in class ffx.potential.SystemState: Set the previous accelerations via a copy of the passed array into the internal array.
setPrint(boolean) - Method in class ffx.algorithms.mc.BoltzmannMC: Sets whether the implementation prints its own messages.
setPrint(boolean) - Method in interface ffx.algorithms.mc.MetropolisMC: Sets whether the implementation prints its own messages.
setPrint(boolean) - Method in class ffx.algorithms.misc.GenerateRotamers: Sets algorithm to log all torsions/energies (not just to file).
setPrintFiles(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets whether rotamer optimization should print out any files, or act solely to optimize a structure in memory.
setPrintInt(int) - Method in class ffx.algorithms.cli.BarostatOptions
setPrintInterval(double) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: Setter for the field printInterval.
setPrintName(boolean) - Method in class ffx.numerics.clustering.visualization.ClusterComponent: Sets whether the node name should be drawn.
setPrintOnFailure(boolean, boolean) - Method in class ffx.potential.DualTopologyEnergy: Sets the printOnFailure flag; if override is true, over-rides any existing property.
setPrintOnFailure(boolean, boolean) - Method in class ffx.potential.ForceFieldEnergy: Sets the printOnFailure flag; if override is true, over-rides any existing property.
setPrintOnFailure(boolean, boolean) - Method in class ffx.potential.QuadTopologyEnergy: Sets the printOnFailure flag; if override is true, over-rides any existing property.
setPrintOnFailure(boolean, boolean) - Method in class ffx.xray.RefinementEnergy: Sets the printOnFailure flag; if override is true, over-rides any existing property.
setProbe(double) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
setProbeRadius(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the probe radius.
setPropagateLambda(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Indicate if the Lambda extended system particle should be propagated using Langevin dynamics.
setProperties(CompositeConfiguration) - Method in class ffx.algorithms.commands.SortArc: Sets an optional Configuration with additional properties.
setProperties(CompositeConfiguration) - Method in class ffx.algorithms.commands.test.MostBar
setProperties(CompositeConfiguration) - Method in class ffx.algorithms.commands.test.SortXPH: Sets an optional Configuration with additional properties.
setProperties(CompositeConfiguration) - Method in class ffx.potential.parsers.SystemFilter: Setter for the field properties.
setProperties(Configuration) - Method in class ffx.algorithms.commands.BAR: Sets an optional Configuration with additional properties.
setProperties(Configuration) - Method in class ffx.algorithms.commands.Thermodynamics: Sets an optional Configuration with additional properties.
setProperties(Configuration) - Method in class ffx.potential.commands.Solvator
setProperties(CommandLine.ParseResult, CompositeConfiguration) - Method in class ffx.xray.cli.XrayOptions: setProperties.
setPropertyDefaultValue(String, String) - Method in class ffx.openmm.Platform: Set the default value of a platform property.
setPropertyValue(Context, String, String) - Method in class ffx.openmm.Platform: Set the value of a context-specific platform property.
setPrune(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setPruning(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets level of pruning: 0 for fully off, 1 for only singles, 2 for single and pair pruning.
setQIVector(double[]) - Method in class ffx.numerics.multipole.QIFrame: Update the QIFrame rotation matrix.
setQIVector(double, double, double) - Method in class ffx.numerics.multipole.QIFrame: Update the QIFrame rotation matrix.
setQIVector(DoubleVector[]) - Method in class ffx.numerics.multipole.QIFrameSIMD: Update the QIFrame rotation matrix.
setQIVector(DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.QIFrameSIMD: Update the QIFrame rotation matrix.
setQuiet(boolean) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Setter for the field quiet.
setR(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell: Sets cell radius
setR(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Set the separation vector.
setR(double, double, double) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Set the separation vector.
setR(double, double, double) - Method in class ffx.numerics.multipole.CoulombTensorQI: Set the separation vector.
setR(double, double, double) - Method in class ffx.numerics.multipole.MultipoleTensor: Set the separation vector.
setR(DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Set the separation vector.
setR(DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
setR(DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Set the separation vector.
setR(DoubleVector, DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Set the separation vector.
setRandom(double, double, Random) - Method in class ffx.numerics.quickhull.Vector3d: Sets the elements of this vector to uniformly distributed random values in a specified range, using a supplied random number generator.
setRandomNumberSeed(int) - Method in class ffx.openmm.AndersenThermostat: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.BrownianIntegrator: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.CustomIntegrator: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.drude.DrudeIntegrator: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.LangevinMiddleIntegrator: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.MonteCarloBarostat: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.MonteCarloMembraneBarostat: Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.VariableLangevinIntegrator: Set the random number seed.
setRandomSeed(int) - Method in class ffx.algorithms.mc.BoltzmannMC: Set the random seed.
setRandomSeed(long) - Method in class ffx.algorithms.dynamics.integrators.Stochastic: Initialize the Random number generator used to apply random forces to the particles.
setRandomSeed(long) - Method in class ffx.algorithms.dynamics.thermostats.Bussi: The setRandomSeed method is used to initialize the Random number generator to the same starting state, such that separate runs produce the same Maxwell-Boltzmann initial velocities. same
setRandomSeed(long) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: The setRandomSeed method is used to initialize the Random number generator to the same starting state, such that separate runs produce the same Maxwell-Boltzmann initial velocities. same
setRandomSymOp(double) - Method in class ffx.algorithms.cli.RandomUnitCellOptions
setRandomUnitCell(double) - Method in class ffx.algorithms.cli.RandomUnitCellOptions
setRate(int) - Method in class ffx.ui.Trajectory: setRate
setrCluster(Cluster) - Method in class ffx.numerics.clustering.ClusterPair: Sets the right cluster.
setRecip(double[]) - Method in class ffx.numerics.fft.Complex3D: Setter for the field recip.
setRecip(double[]) - Method in class ffx.numerics.fft.Complex3DParallel: Setter for the field recip.
setRecip(double[]) - Method in class ffx.numerics.fft.Real3D: Setter for the field recip.
setRecip(double[]) - Method in class ffx.numerics.fft.Real3DParallel: Setter for the field recip.
setRecomputeSelf(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets to recompute self energies at a different pH using an energy restart file
setRedXYZ(double[]) - Method in class ffx.potential.bonded.Atom: setXYZ
setReferencePositions(PointerByReference) - Method in class ffx.openmm.RMSDForce: Set the reference positions to compute the deviation from.
setRefinementData(RealSpaceRefinementData[]) - Method in class ffx.realspace.RealSpaceData: Setter for the field refinementData.
setRefinementMode(RefinementMinimize.RefinementMode) - Method in class ffx.realspace.RealSpaceEnergy: Setter for the field refinementMode.
setRefinementMode(RefinementMinimize.RefinementMode) - Method in class ffx.xray.XRayEnergy: Setter for the field refinementMode.
setRegion(SpatialDensityRegion) - Method in class ffx.potential.nonbonded.SpatialDensityLoop: setRegion.
setReinitVelocities(boolean) - Method in class ffx.algorithms.cli.AnnealOptions
setRelativeCollisionFrequency(double, int) - Method in class ffx.openmm.NoseHooverIntegrator: Set the relative collision frequency for a thermostat.
setRelativeTemperature(double, int) - Method in class ffx.openmm.NoseHooverIntegrator: Set the relative temperature for a thermostat.
setRemoveCenterOfMassMotion(boolean) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: If center of mass motion is being removed, then the mean kinetic energy of the system will be 3 kT/2 less than if center of mass motion is allowed.
setRepEx(boolean) - Method in class ffx.algorithms.cli.RepExOptions
setRepexFrequency(double) - Method in class ffx.algorithms.cli.RepexOSTOptions
setReplicaSteps(int) - Method in class ffx.algorithms.cli.RepExOptions
setReport(double) - Method in class ffx.algorithms.cli.DynamicsOptions
setResetHistogramAtLambda(double) - Method in class ffx.algorithms.thermodynamics.HistogramData: Set the lambda value at which to reset the histogram.
setResetNumSteps(boolean) - Method in class ffx.algorithms.cli.ThermodynamicsOptions
setResidueNum(int) - Method in class ffx.potential.bonded.Molecule: Setter for the field residueNum.
setResidueNumber(int) - Method in class ffx.potential.bonded.Atom: setResidueNumber
setResidues(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the residue list.
setResiduesIgnoreNull(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization: Accepts a list of residues but throws out null residues.
setResName(String) - Method in class ffx.potential.bonded.Atom: Setter for the field resName.
setResolution(Atom.Resolution) - Method in class ffx.potential.bonded.Atom: Setter for the field resolution.
setRestartFile(File) - Method in class ffx.potential.extended.ExtendedSystem: Sets the restartFile field of this extended system to the passed file.
setRestartFrequency(double) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Method to set the Restart Frequency.
setRestartFrequency(double) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: Method to set the Restart Frequency.
setRevert(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setRevert(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the algorithm to revert to starting coordinates if the energy increases.
setRigidScale(double) - Method in class ffx.potential.bonded.Angle: Setter for the field rigidScale.
setRigidScale(double) - Method in class ffx.potential.bonded.Bond: Setter for the field rigidScale.
setRigidScale(double) - Method in class ffx.potential.bonded.StretchBend: Setter for the field rigidScale.
setRigidScale(double) - Method in class ffx.potential.bonded.UreyBradley: Setter for the field rigidScale.
setRminh(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the water hydrogen radius parameter.
setRmino(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the water oxygen radius parameter.
setRMSD(double) - Method in class ffx.potential.terms.EnergyTerm: Set the RMSD accumulator value for this term.
setRotamer(Rotamer) - Method in class ffx.potential.bonded.Residue: Set the current rotamer.
setRotamerLibrary(RotamerLibrary) - Method in class ffx.algorithms.optimize.RotamerOptimization
setRotamerPhBias(double, double) - Method in class ffx.potential.parameters.TitrationUtils
setRotamers() - Method in class ffx.potential.bonded.Residue: Sets the original coordinate rotamers for titratable residues RotamerLibrary's original coordinates rotamer flag has been set.
setRotamers(RotamerLibrary) - Method in class ffx.potential.bonded.MultiResidue: Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.
setRotamers(RotamerLibrary) - Method in class ffx.potential.bonded.Residue: Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.
setRotamerTitration(boolean) - Method in class ffx.potential.parsers.PDBFilter
setSaveFrequency(double) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: Sets the frequency of writing to the trajectory file.
setSaveOutput(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setScaleMoleculesAsRigid(int) - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Set whether molecules should be scaled as rigid bodies.
setScalePadding(int) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel: Sets the padding (pixels) between the dendrogram and the scale axis.
setScaleTickLength(int) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setScaleValueDecimals(int) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setScaleValueInterval(double) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel
setScaling(double[]) - Method in class ffx.algorithms.dynamics.Barostat: Scale the problem.
setScaling(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Scale the problem.
setScaling(double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
setScaling(double[]) - Method in interface ffx.numerics.OptimizationInterface: Scale the problem.
setScaling(double[]) - Method in class ffx.potential.ANIEnergy
setScaling(double[]) - Method in class ffx.potential.DualTopologyEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.potential.extended.ExtendedSystem
setScaling(double[]) - Method in class ffx.potential.ForceFieldEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.potential.QuadTopologyEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.potential.XtalEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.realspace.RealSpaceEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.xray.RefinementEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.xray.ScaleBulkEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.xray.SigmaAEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.xray.SplineEnergy: Scale the problem.
setScaling(double[]) - Method in class ffx.xray.XRayEnergy: Scale the problem.
setScreenedPairParameters(int, int, int, double) - Method in class ffx.openmm.drude.DrudeForce: Set the force field parameters for a screened pair.
setSearchWidth(double) - Method in class ffx.algorithms.misc.GenerateRotamers: Sets the width around each torsion to search (+/-, so 10 degree width will search a 20 degree arc).
setSecondSystemAlchemistry(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions: Set the alchemical atoms for this topology.
setSecondSystemUnchargedAtoms(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions: Set uncharged atoms for this topology.
setSeed(long) - Method in class edu.rit.util.DefaultRandom: Set this PRNG's seed.
setSeed(long) - Method in class edu.rit.util.Mcg1Random: Set this PRNG's seed.
setSeed(long) - Method in class edu.rit.util.Random: Set this PRNG's seed.
setSegID(String) - Method in class ffx.potential.bonded.Atom: Set this atom's seg ID.
setSegID(String) - Method in class ffx.potential.bonded.Polymer: Set the Polymer segID.
setSegID(String) - Method in class ffx.potential.bonded.Residue: Setter for the field segID.
setSelected(boolean) - Method in class ffx.potential.bonded.Atom: Setter for the field selected.
setSelected(boolean) - Method in class ffx.potential.bonded.BondedTerm: Setter for the field selected.
setSelected(boolean) - Method in class ffx.potential.bonded.MSNode: Setter for the field selected.
setSelf(int, int, double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
setSelf(int, int, double, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Stores a self energy in the self energy matrix.
setSgName(String) - Method in class ffx.potential.parsers.CIFFilter: Override the space group of a CIF conversion based on space group name.
setSgNum(int) - Method in class ffx.potential.parsers.CIFFilter: Override the space group of a CIF conversion based on space group number.
setShctd(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the overlap factor.
setShowDistances(boolean) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel: Sets whether linkage distance values should be rendered on the dendrogram.
setShowScale(boolean) - Method in class ffx.numerics.clustering.visualization.DendrogramPanel: Sets whether the X-axis scale should be drawn below the dendrogram.
setSigF(int, double) - Method in class ffx.xray.DiffractionRefinementData: Set amplitude sigma (sigF).
setSigmaCombiningRule(String) - Method in class ffx.openmm.amoeba.VdwForce: Set the sigma combining rule.
setSingletonClashThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: setSingletonClashThreshold.
setSlevy(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Set the Levy parameter.
setSneck(double) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
setSoftcoreAlpha(double) - Method in class ffx.openmm.amoeba.VdwForce: Set the softcore alpha.
setSoftcorePower(int) - Method in class ffx.openmm.amoeba.VdwForce: Set the softcore power.
setSoluteDielectric(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the solute dielectric constant.
setSoluteDielectric(double) - Method in class ffx.openmm.GBSAOBCForce: Set the dielectric constant for the solute.
setSoluteOffset(double) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
setSoluteRadii(ForceField, Atom[], SoluteType.SOLUTE_RADII_TYPE) - Static method in class ffx.potential.parameters.SoluteType
setSoluteType(SoluteType) - Method in class ffx.potential.bonded.Atom: setSoluteType
setSolventAB(double, double) - Method in class ffx.xray.DiffractionData: set the bulk solvent parameters for a given bulk solvent model
setSolventDielectric(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the solvent dielectric constant.
setSolventDielectric(double) - Method in class ffx.openmm.GBSAOBCForce: Set the dielectric constant for the solvent.
setSolventPressure(double) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
setSpecialPositionCutoff(double) - Method in class ffx.crystal.Crystal: Setter for the field specialPositionCutoff.
setSpecialPositionSymOps(List<Integer>) - Method in class ffx.potential.bonded.Atom: Set the symmetry operations that leave this atom's molecule at a special position.
setStart(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setStartSnapshot(int) - Method in class ffx.numerics.estimator.MBARFilter: Set the start snapshot.
setState(Potential.STATE) - Method in class ffx.potential.terms.EnergyTermRegion: Set the state of the potential energy term.
setState(State) - Method in class ffx.openmm.Context: Copy information from a State object into this Context.
setStatusCode(HttpResponse.Status) - Method in class edu.rit.http.HttpResponse: Set this HTTP response's status code.
setStep(int) - Method in class ffx.ui.commands.SimulationMessage: Setter for the field step.
setStepCount(long) - Method in class ffx.openmm.Context: Set the current step count.
setSteps(long) - Method in class ffx.algorithms.cli.DynamicsOptions
setStepSize(double) - Method in class ffx.openmm.CompoundIntegrator: Set the size of each time step, in picoseconds.
setStepSize(double) - Method in class ffx.openmm.Integrator: Set the size of each time step, in picoseconds.
setStepsTaken(int) - Method in class ffx.algorithms.thermodynamics.LambdaData
setStretchBends(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the Stretch-Bends node to t.
setStretchBends(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the Stretch-Bends node to t.
setStretchBendType(StretchBendType) - Method in class ffx.potential.bonded.StretchBend: Setter for the field stretchBendType.
setStretchTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the MultiScaleGroup's stretch-torsion node to t.
setStride(int) - Method in class ffx.xray.parsers.CCP4MapWriter: Set the stepping across the array (e.g. 2 if data is separated by 1 space)
setSuperpositionThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Setter for the field superpositionThreshold.
setSurfaceAreaEnergy(double) - Method in class ffx.openmm.GBSAOBCForce: Set the energy scale for the surface area term, measured in kJ/mol/nmˆ2.
setSurfaceAreaFactor(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the surface area factor.
setSurfaceTension(double) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
setSurfaceTension(double) - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
setSwitchingDistance(double) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Set the switching distance.
setSwitchingDistance(double) - Method in class ffx.openmm.CustomNonbondedForce: Set the switching distance.
setSwitchingDistance(double) - Method in class ffx.openmm.GayBerneForce: Set the switching distance.
setSwitchingDistance(double) - Method in class ffx.openmm.NonbondedForce: Set the switching distance.
setSymOp(int) - Method in class ffx.potential.parsers.PDBFilter: setSymOp.
setSynchronous(boolean) - Method in class ffx.algorithms.cli.MultiDynamicsOptions
setTanhBetas(double[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
setTanhParameters(double, double, double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the tanh parameters.
setTanhRescaling(int) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Set the tanh rescaling.
setTargetTemperature(double) - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic: Set the target temperature.
setTargetTemperature(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Set the target temperature.
setTau(double) - Method in class ffx.algorithms.dynamics.thermostats.Berendsen: Setter for the field tau.
setTau(double) - Method in class ffx.algorithms.dynamics.thermostats.Bussi: Setter for the field tau.
setTautomerLambda(Residue, double) - Method in class ffx.potential.extended.ExtendedSystem: Set the tautomer lambda of a residue and update corresponding theta
setTautomerLambda(Residue, double, boolean) - Method in class ffx.potential.extended.ExtendedSystem: Set the tautomer lambda of a residue and update corresponding theta if desired
setTemperAfter(int) - Method in class ffx.algorithms.cli.AnnealOptions
setTemperature(double) - Method in class ffx.algorithms.cli.DynamicsOptions
setTemperature(double) - Method in class ffx.algorithms.dynamics.Barostat: Set the Metropolis Monte Carlo temperature.
setTemperature(double) - Method in class ffx.algorithms.dynamics.integrators.Stochastic: Setter for the field temperature.
setTemperature(double) - Method in class ffx.algorithms.mc.BoltzmannMC: Sets temperature of Monte Carlo criterion.
setTemperature(double) - Method in interface ffx.algorithms.mc.MetropolisMC: Sets temperature of Monte Carlo criterion.
setTemperature(double) - Method in class ffx.openmm.BrownianIntegrator: Set the temperature of the heat bath (in Kelvin).
setTemperature(double) - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Set the temperature of the main heat bath (in Kelvin).
setTemperature(double) - Method in class ffx.openmm.LangevinMiddleIntegrator: Set the temperature.
setTemperature(double) - Method in class ffx.openmm.VariableLangevinIntegrator: Set the temperature of the heat bath (in Kelvin).
setTemperature(double) - Method in class ffx.potential.extended.ExtendedSystem: setTemperature.
setTemperature(double) - Method in class ffx.potential.SystemState: Set the temperature.
setTemperature(double, int) - Method in class ffx.openmm.NoseHooverIntegrator: Set the temperature for a thermostat.
setTemperatures(double[]) - Method in class ffx.algorithms.dynamics.ReplicaExchange: Setter for the field temperatures.
setTemperBefore(int) - Method in class ffx.algorithms.cli.AnnealOptions
setTemperingFactor(double) - Method in class ffx.algorithms.thermodynamics.HistogramData
setTemperingOffset(double) - Method in class ffx.algorithms.thermodynamics.HistogramData: Sets an explicit tempering offset in kcal/mol.
setTemperingRate(double[]) - Method in class ffx.algorithms.cli.OSTOptions
setTemperingThreshold(double[]) - Method in class ffx.algorithms.cli.OSTOptions
setTemperString(String) - Method in class ffx.algorithms.cli.AnnealOptions
setTempFactor(double) - Method in class ffx.potential.bonded.Atom: Setter for the field tempFactor.
setTempFactorAcceleration(double) - Method in class ffx.potential.bonded.Atom: Setter for the field tempFactorAcceleration.
setTempFactorGradient(double) - Method in class ffx.potential.bonded.Atom: Setter for the field tempFactorGradient.
setTempFactorPreviousAcceleration(double) - Method in class ffx.potential.bonded.Atom: Setter for the field tempFactorPreviousAcceleration.
setTempFactorVelocity(double) - Method in class ffx.potential.bonded.Atom: Setter for the field tempFactorVelocity.
setTensor(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Set the tensor components.
setTerms(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the MultiScaleGroup's terms node to t.
setTerms(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the MultiScaleGroup's terms node to t.
setTestingParametersAndExchangeOnce() - Method in class ffx.algorithms.dynamics.PhReplicaExchange
setThermoAlgoString(String) - Method in class ffx.algorithms.cli.ThermodynamicsOptions
setThermostat(Thermostat) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Setter for the field thermostat.
setThermostat(Thermostat) - Method in class ffx.xray.RefinementEnergy: Setter for the field thermostat.
setThermostat(ThermostatEnum) - Method in class ffx.algorithms.cli.DynamicsOptions: Set the thermostat.
setThermostatString(String) - Method in class ffx.algorithms.cli.DynamicsOptions
setThole(double, double) - Method in class ffx.numerics.multipole.TholeTensorGlobal: Set Thole damping parameters
setThole(double, double) - Method in class ffx.numerics.multipole.TholeTensorQI: Set Thole damping parameters
setThole(DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.TholeTensorGlobalSIMD: Set Thole damping parameters
setThole(DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.TholeTensorQISIMD: Set Thole damping parameters
setThreeBody(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
setThreeBodyCutoff(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setThreeBodyCutoff(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the threeBodyCutoffDist.
setThreeBodyEnergy(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Flag to control use of 3-body energy terms.
setTime(double) - Method in class ffx.openmm.Context: Set the current time of the simulation (in picoseconds).
setTime(double) - Method in class ffx.ui.commands.SimulationMessage: Setter for the field time.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.BetterBeeman: Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.Integrator: Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.Respa: Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.Stochastic: Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.VelocityVerlet: Set the time step.
setTitrateConformers(boolean) - Method in class ffx.potential.bonded.Residue
setTitrationBoxes(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets titratble residues to be the center of the box.
setTitrationBoxSize(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the size around the titratable residues.
setTitrationLambda(Residue, double) - Method in class ffx.potential.extended.ExtendedSystem: Set the titration lambda of a residue and update corresponding theta
setTitrationLambda(Residue, double, boolean) - Method in class ffx.potential.extended.ExtendedSystem: Set the titration lambda of a residue and update corresponding theta if desired
setTitrationPH(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setTitrationUtils(TitrationUtils) - Method in class ffx.potential.bonded.Residue
SettleConstraint - Class in ffx.potential.constraint: SETTLE triatomic distance constraints, intended for rigid water models.
settleFactory(Angle) - Static method in class ffx.potential.constraint.SettleConstraint: Constructs a SETTLE constraint from an angle and its two bonds.
setTolerance(float) - Method in class ffx.ui.behaviors.PickMouseBehavior: setTolerance
setTopologyAtomIndex(int) - Method in class ffx.potential.bonded.Atom: Dual-topology atom index.
setTopologyIndex(int) - Method in class ffx.potential.bonded.Atom: Set the topology index of this atom.
setTorsion(Torsion) - Method in class ffx.potential.bonded.Atom: setTorsion
setTorsionParameters(int, int, int, int, int, double, double, double, double, double, double) - Method in class ffx.openmm.RBTorsionForce: Set the parameters for a torsion.
setTorsionParameters(int, int, int, int, int, int, double, double) - Method in class ffx.openmm.PeriodicTorsionForce: Set the parameters for a torsion.
setTorsionParameters(int, int, int, int, int, int, int, int, int, int) - Method in class ffx.openmm.CMAPTorsionForce: Set the force field parameters for a CMAP torsion term.
setTorsionParameters(int, int, int, int, int, PointerByReference) - Method in class ffx.openmm.CustomTorsionForce: Set the force field parameters for a torsion.
setTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the MultiScaleGroup's torsion node to t.
setTorsions(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the MultiScaleGroup's torsion node to t.
setTorsionScale(double) - Method in class ffx.potential.bonded.Torsion: Set the torsion scale up factor.
setTorsionTorsionGrid(int, PointerByReference) - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Set the torsion-torsion grid at the specified index
setTorsionTorsionParameters(int, int, int, int, int, int, int, int) - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Set the force field parameters for a torsion-torsion term.
setTorsionTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the MultiScaleGroup's Torsion-Torsion node to t.
setTorsionTorsions(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the MultiScaleGroup's Torsion-Torsion node to t.
setTorsionType(TorsionType) - Method in class ffx.potential.bonded.Torsion: Set the torsion type.
setTotalSteps(long) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Sets the next number of steps MC-OST should run.
setTrajectory(Trajectory) - Method in class ffx.ui.FFXSystem: Setter for the field trajectory.
setTrajectorySteps(int) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: Sets the number of steps to use per OpenMM cycle.
setTrajSteps(int) - Method in class ffx.algorithms.cli.DynamicsOptions
setTransformGroup(TransformGroup) - Method in class ffx.ui.behaviors.MouseBehavior: Setter for the field transformGroup.
setTransformGroups(TransformGroup, TransformGroup) - Method in class ffx.ui.behaviors.MouseOrbit: setTransformGroups
setTransformGroups(TransformGroup, TransformGroup) - Method in class ffx.ui.behaviors.PickOrbitBehavior: setTransformGroups
setTwoBodyCutoff(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
setTwoBodyCutoff(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Sets the twoBodyCutoffDist.
setTwoStep(boolean) - Method in class ffx.algorithms.cli.OSTOptions
setType(int) - Method in class ffx.ui.commands.SimulationMessage: Setter for the field type.
setType(Utilities.FileType) - Method in class ffx.potential.parsers.SystemFilter: setType
setTypeFilter(int, PointerByReference) - Method in class ffx.openmm.CustomManyParticleForce: Set the type filter for the specified type.
setTypePairParameters(int, int, int, double, double) - Method in class ffx.openmm.amoeba.VdwForce: Set the type pair parameters.
setUnchargedAtoms(MolecularAssembly, String) - Static method in class ffx.potential.cli.AlchemicalOptions: Sets the uncharged atoms for a MolecularAssembly.
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseOrbit: The transformChanged method in the callback class will be called every time the transform is updated
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseProperties: The transformChanged method in the callback class will be called every time the transform is updated
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseRotate: setupCallback
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseSelection: The transformChanged method in the callback class will be called every time the transform is updated
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseTranslate: The transformChanged method in the callback class will be called every time the transform is updated.
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseZoom: The transformChanged method in the callback class will be called every time the transform is updated.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickOrbitBehavior: Register the class @param callback to be called each time the picked object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickPropertiesBehavior: Register the class @param callback to be called each time the picked object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickRotateBehavior: Register the class @param callback to be called each time the picked object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickSelectionBehavior: Register the class @param callback to be called each time the picked * object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickTranslateBehavior: Register the class @param callback to be called each time the picked object moves
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickZoomBehavior: Register the class @param callback to be called each time the picked object moves.
setUpCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.GlobalBehavior: setUpCallback
setUpdateBondedTerms(boolean) - Method in class ffx.potential.openmm.OpenMMSystem
setUpdated() - Method in class ffx.ui.commands.FFXServer: setUpdated
setUpHydrogenAngleConstraints() - Method in class ffx.potential.openmm.OpenMMSystem: Add a constraint to every angle that includes two hydrogen atoms.
setupMCOST(OrthogonalSpaceTempering, MolecularAssembly[], DynamicsOptions, ThermodynamicsOptions, boolean, File, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions: setupMCOST.
setUpper(double) - Method in class ffx.algorithms.cli.AnnealOptions
setUreyBradleys(MSNode) - Method in class ffx.potential.bonded.MSGroup: Sets the Urey-Bradley node to t.
setUreyBradleys(MSNode) - Method in class ffx.potential.bonded.MultiResidue: Sets the Urey-Bradley node to t.
setUse(boolean) - Method in class ffx.potential.bonded.Atom: If true, this atom should be used in potential energy functions.
setUse(boolean[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Setter for the field use.
setUseDispersionCorrection(boolean) - Method in class ffx.openmm.amoeba.VdwForce: Set whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.
setUseDispersionCorrection(int) - Method in class ffx.openmm.NonbondedForce: Set if a dispersion correction will be used.
setUseGoldstein(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Specify use of Goldstein optimization.
setUseLongRangeCorrection(int) - Method in class ffx.openmm.CustomNonbondedForce: Set whether to use the long range correction.
setUseOrigCoordsRotamer(boolean) - Method in class ffx.potential.bonded.RotamerLibrary: Setter for the field useOrigCoordsRotamer.
setUseSIMD(boolean) - Method in class ffx.numerics.fft.Complex: Configure use of SIMD operators.
setUseSIMD(boolean) - Method in class ffx.numerics.fft.Complex2D: Set the 2D transform to use SIMD instructions.
setUseSIMD(boolean) - Method in class ffx.numerics.fft.Complex3D: Set the 2D transform to use SIMD instructions.
setUseSIMD(boolean) - Method in class ffx.numerics.fft.Complex3DParallel: Use SIMD instructions if available.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.CMAPTorsionForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.CustomAngleForce: Set whether this force uses periodic boundary conditions.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.CustomBondForce: Set whether this force uses periodic boundary conditions.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.CustomCompoundBondForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.CustomTorsionForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.drude.DrudeForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.HarmonicAngleForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.HarmonicBondForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.PeriodicTorsionForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(boolean) - Method in class ffx.openmm.RBTorsionForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUsesPeriodicBoundaryConditions(int) - Method in class ffx.openmm.CustomCentroidBondForce: Set whether this force should apply periodic boundary conditions when calculating displacements.
setUseSwitchingFunction(int) - Method in class ffx.openmm.CustomNonbondedForce: Set whether to use a switching function.
setUseSwitchingFunction(int) - Method in class ffx.openmm.GayBerneForce: Set whether to use a switching function.
setUseSwitchingFunction(int) - Method in class ffx.openmm.NonbondedForce: Set if a switching function will be used.
setValue(double) - Method in class ffx.potential.bonded.BondedTerm: Sets the Term's value.
setVariable(String, Object) - Method in class ffx.utilities.FFXBinding: Sets the value of the given variable
setVariables(Map<String, Object>) - Method in class ffx.utilities.FFXBinding: Set the Map of all variables.
setVDWType(VDWType) - Method in class ffx.potential.bonded.Atom: setVDWType
setVelocities(double[]) - Method in class ffx.openmm.Context: Set the velocities of all particles in the System (measured in nm/picosecond).
setVelocities(double[]) - Method in class ffx.potential.openmm.OpenMMContext: The array v contains velocity values for all atomic coordinates in units of Angstroms/psec.
setVelocities(double[]) - Method in class ffx.potential.SystemState: Set the velocities via a copy of the passed array into the internal array.
setVelocitiesToTemperature(double, int) - Method in class ffx.openmm.Context: Set the velocities of all particles in the System to random values chosen from a Boltzmann distribution at a given temperature.
setVelocity(double[]) - Method in class ffx.algorithms.dynamics.Barostat: setVelocity.
setVelocity(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: setVelocity.
setVelocity(double[]) - Method in interface ffx.numerics.Potential: setVelocity.
setVelocity(double[]) - Method in class ffx.potential.ANIEnergy
setVelocity(double[]) - Method in class ffx.potential.bonded.Atom: Setter for the field velocity.
setVelocity(double[]) - Method in class ffx.potential.DualTopologyEnergy: setVelocity.
setVelocity(double[]) - Method in class ffx.potential.extended.ExtendedSystem
setVelocity(double[]) - Method in class ffx.potential.ForceFieldEnergy: setVelocity.
setVelocity(double[]) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Velocities for active atoms in units of Angstroms.
setVelocity(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy: Velocities for active atoms in units of Angstroms.
setVelocity(double[]) - Method in class ffx.potential.QuadTopologyEnergy: setVelocity.
setVelocity(double[]) - Method in class ffx.potential.XtalEnergy: setVelocity.
setVelocity(double[]) - Method in class ffx.realspace.RealSpaceEnergy: setVelocity.
setVelocity(double[]) - Method in class ffx.xray.RefinementEnergy: setVelocity.
setVelocity(double[]) - Method in class ffx.xray.XRayEnergy: setVelocity.
setVelocity(double, double, double) - Method in class ffx.potential.bonded.Atom: Setter for the field velocity.
setVerbosityLevel(MDVerbosity) - Method in class ffx.algorithms.dynamics.MolecularDynamics
setVersioning(SystemFilter.Versioning) - Static method in class ffx.potential.parsers.SystemFilter: Negative: prefix a version number; Positive: postfix; Zero: TINKER-style.
setVideo(String) - Method in class ffx.algorithms.misc.GenerateRotamers: Null file indicates to not write a video.
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Atom: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Bond: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.BondedTerm: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Joint: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.MSGroup: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.MSNode: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.MultiResidue: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Polymer: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in interface ffx.potential.bonded.ROLS: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.ROLSP: setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.MolecularAssembly: setView
setView(String) - Method in class ffx.ui.GraphicsCanvas
SETVIEW - Enum constant in enum class ffx.potential.bonded.ROLSP.PARALLELMETHOD
setViewModel(String, MSNode) - Method in class ffx.ui.GraphicsCanvas: Operates on the supplied node.
setVirtualSite(int, VirtualSite) - Method in class ffx.openmm.System: Set a particle to be a virtual site.
setVisible(boolean) - Method in class ffx.ui.GraphicsPanel
setWeight(double) - Method in class ffx.realspace.RealSpaceData: setWeight
setWeight(double) - Method in class ffx.xray.CrystalReciprocalSpace: set the dataset weight
setWeight(double) - Method in interface ffx.xray.DataContainer: setWeight
setWeight(double) - Method in class ffx.xray.DiffractionData: setWeight
setWeight(Double) - Method in class ffx.numerics.clustering.Distance: Sets the weight.
setWiggle(double) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion: Apply a random perturbation to the atomic coordinates to avoid numerical instabilities for various linear, planar and symmetric structures.
setWindow(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
setWindows(int) - Method in class ffx.algorithms.cli.AnnealOptions
setWindowSize(int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Setter for the field windowSize.
setWire(LineArray, int) - Method in class ffx.potential.bonded.Bond: setWire
setWireWidth(float) - Method in class ffx.potential.MolecularAssembly: setWireWidth
setWrite(double) - Method in class ffx.algorithms.cli.DynamicsOptions
setWriteEnergyRestart(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Set the writeEnergyRestart flag.
setWriteIndependent(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData: Sets the value of writeIndependent.
setX(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell: Sets x coordinate of center of cell
setXYMode(int) - Method in class ffx.openmm.MonteCarloMembraneBarostat: Set the mode for scaling the XY dimensions.
setXYZ(double[]) - Method in class ffx.potential.bonded.Atom: setXYZ
setXYZGradient(double, double, double) - Method in class ffx.potential.bonded.Atom: setXYZGradient
setXyzIndex(int) - Method in class ffx.potential.bonded.Atom: Setter for the field xyzIndex.
setY(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell: Sets y coordinate of center of cell
setZ(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell: Sets z coordinate of center of cell
setZero() - Method in class ffx.numerics.quickhull.Vector3d: Sets the elements of this vector to zero.
setZMode(int) - Method in class ffx.openmm.MonteCarloMembraneBarostat: Set the mode for scaling the Z dimension.
setZprime(int) - Method in class ffx.potential.parsers.CIFFilter: Override the number of copies in the asymmetric unit (Z').
SEV_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
sextic - Variable in class ffx.potential.parameters.AngleType: Sextic coefficient in angle bending potential.
sextic - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Sextic coefficient in out-of-plane angle bending potential.
SEXTIC - Enum constant in enum class ffx.potential.parameters.AngleType.AngleFunction
Sg - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
SG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYD
SG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYS
SG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYX
SG - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
ShakeChargeConstraint - Class in ffx.potential.constraint
ShakeChargeConstraint(int, int, double) - Constructor for class ffx.potential.constraint.ShakeChargeConstraint
SharedBoolean - Class in edu.rit.pj.reduction: Class SharedBoolean provides a reduction variable for a value of type boolean.
SharedBoolean() - Constructor for class edu.rit.pj.reduction.SharedBoolean: Construct a new Boolean reduction variable with the initial value false.
SharedBoolean(boolean) - Constructor for class edu.rit.pj.reduction.SharedBoolean: Construct a new Boolean reduction variable with the given initial value.
SharedBooleanArray - Class in edu.rit.pj.reduction: Class SharedBooleanArray provides an array reduction variable with elements of type boolean.
SharedBooleanArray(boolean[]) - Constructor for class edu.rit.pj.reduction.SharedBooleanArray: Construct a new Boolean array reduction variable whose elements are copied from the given array.
SharedBooleanArray(int) - Constructor for class edu.rit.pj.reduction.SharedBooleanArray: Construct a new Boolean array reduction variable with the given length.
SharedBooleanArrayBuf - Class in edu.rit.mp.buf: Class SharedBooleanArrayBuf provides a buffer for a multiple thread safe array of Boolean items sent or received using the Message Protocol (MP).
SharedBooleanArrayBuf(SharedBooleanArray, Range) - Constructor for class edu.rit.mp.buf.SharedBooleanArrayBuf: Construct a new shared Boolean array buffer.
SharedBooleanArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedBooleanArrayBuf_1 provides a buffer for a multiple thread safe array of Boolean items sent or received using the Message Protocol (MP).
SharedBooleanArrayBuf_1(SharedBooleanArray, Range) - Constructor for class edu.rit.mp.buf.SharedBooleanArrayBuf_1: Construct a new shared Boolean array buffer.
SharedBooleanBuf - Class in edu.rit.mp.buf: Class SharedBooleanBuf provides a buffer for a multiple thread safe Boolean item sent or received using the Message Protocol (MP).
SharedBooleanBuf(SharedBoolean) - Constructor for class edu.rit.mp.buf.SharedBooleanBuf: Construct a new shared Boolean buffer.
SharedByte - Class in edu.rit.pj.reduction: Class SharedByte provides a reduction variable for a value of type byte.
SharedByte() - Constructor for class edu.rit.pj.reduction.SharedByte: Construct a new byte reduction variable with the initial value 0.
SharedByte(byte) - Constructor for class edu.rit.pj.reduction.SharedByte: Construct a new byte reduction variable with the given initial value.
SharedByteArray - Class in edu.rit.pj.reduction: Class SharedByteArray provides an array reduction variable with elements of type byte.
SharedByteArray(byte[]) - Constructor for class edu.rit.pj.reduction.SharedByteArray: Construct a new byte array reduction variable whose elements are copied from the given array.
SharedByteArray(int) - Constructor for class edu.rit.pj.reduction.SharedByteArray: Construct a new byte array reduction variable with the given length.
SharedByteArrayBuf - Class in edu.rit.mp.buf: Class SharedByteArrayBuf provides a buffer for a multiple thread safe array of byte items sent or received using the Message Protocol (MP).
SharedByteArrayBuf(SharedByteArray, Range) - Constructor for class edu.rit.mp.buf.SharedByteArrayBuf: Construct a new shared byte array buffer.
SharedByteArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedByteArrayBuf_1 provides a buffer for a multiple thread safe array of byte items sent or received using the Message Protocol (MP).
SharedByteArrayBuf_1(SharedByteArray, Range) - Constructor for class edu.rit.mp.buf.SharedByteArrayBuf_1: Construct a new shared byte array buffer.
SharedByteBuf - Class in edu.rit.mp.buf: Class SharedByteBuf provides a buffer for a multiple thread safe byte item sent or received using the Message Protocol (MP).
SharedByteBuf(SharedByte) - Constructor for class edu.rit.mp.buf.SharedByteBuf: Construct a new shared byte buffer.
SharedCharacter - Class in edu.rit.pj.reduction: Class SharedCharacter provides a reduction variable for a value of type char.
SharedCharacter() - Constructor for class edu.rit.pj.reduction.SharedCharacter: Construct a new character reduction variable with the initial value 0.
SharedCharacter(char) - Constructor for class edu.rit.pj.reduction.SharedCharacter: Construct a new character reduction variable with the given initial value.
SharedCharacterArray - Class in edu.rit.pj.reduction: Class SharedCharacterArray provides an array reduction variable with elements of type char.
SharedCharacterArray(char[]) - Constructor for class edu.rit.pj.reduction.SharedCharacterArray: Construct a new character array reduction variable whose elements are copied from the given array.
SharedCharacterArray(int) - Constructor for class edu.rit.pj.reduction.SharedCharacterArray: Construct a new character array reduction variable with the given length.
SharedCharacterArrayBuf - Class in edu.rit.mp.buf: Class SharedCharacterArrayBuf provides a buffer for a multiple thread safe array of character items sent or received using the Message Protocol (MP).
SharedCharacterArrayBuf(SharedCharacterArray, Range) - Constructor for class edu.rit.mp.buf.SharedCharacterArrayBuf: Construct a new shared character array buffer.
SharedCharacterArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedCharacterArrayBuf_1 provides a buffer for a multiple thread safe array of character items sent or received using the Message Protocol (MP).
SharedCharacterArrayBuf_1(SharedCharacterArray, Range) - Constructor for class edu.rit.mp.buf.SharedCharacterArrayBuf_1: Construct a new shared character array buffer.
SharedCharacterBuf - Class in edu.rit.mp.buf: Class SharedCharacterBuf provides a buffer for a shared character item sent or received using the Message Protocol (MP).
SharedCharacterBuf(SharedCharacter) - Constructor for class edu.rit.mp.buf.SharedCharacterBuf: Construct a new shared character buffer.
SharedDouble - Class in edu.rit.pj.reduction: Class SharedDouble provides a reduction variable for a value of type double.
SharedDouble() - Constructor for class edu.rit.pj.reduction.SharedDouble: Construct a new double reduction variable with the initial value 0.
SharedDouble(double) - Constructor for class edu.rit.pj.reduction.SharedDouble: Construct a new double reduction variable with the given initial value.
SharedDoubleArray - Class in edu.rit.pj.reduction: Class SharedDoubleArray provides an array reduction variable with elements of type double.
SharedDoubleArray(double[]) - Constructor for class edu.rit.pj.reduction.SharedDoubleArray: Construct a new double array reduction variable whose elements are copied from the given array.
SharedDoubleArray(int) - Constructor for class edu.rit.pj.reduction.SharedDoubleArray: Construct a new double array reduction variable with the given length.
SharedDoubleArrayBuf - Class in edu.rit.mp.buf: Class SharedDoubleArrayBuf provides a buffer for a multiple thread safe array of double items sent or received using the Message Protocol (MP).
SharedDoubleArrayBuf(SharedDoubleArray, Range) - Constructor for class edu.rit.mp.buf.SharedDoubleArrayBuf: Construct a new shared double array buffer.
SharedDoubleArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedDoubleArrayBuf_1 provides a buffer for a multiple thread safe array of double items sent or received using the Message Protocol (MP).
SharedDoubleArrayBuf_1(SharedDoubleArray, Range) - Constructor for class edu.rit.mp.buf.SharedDoubleArrayBuf_1: Construct a new shared double array buffer.
SharedDoubleBuf - Class in edu.rit.mp.buf: Class SharedDoubleBuf provides a buffer for a shared double item sent or received using the Message Protocol (MP).
SharedDoubleBuf(SharedDouble) - Constructor for class edu.rit.mp.buf.SharedDoubleBuf: Construct a new shared double buffer.
SharedFloat - Class in edu.rit.pj.reduction: Class SharedFloat provides a reduction variable for a value of type float.
SharedFloat() - Constructor for class edu.rit.pj.reduction.SharedFloat: Construct a new float reduction variable with the initial value 0.
SharedFloat(float) - Constructor for class edu.rit.pj.reduction.SharedFloat: Construct a new float reduction variable with the given initial value.
SharedFloatArray - Class in edu.rit.pj.reduction: Class SharedFloatArray provides an array reduction variable with elements of type float.
SharedFloatArray(float[]) - Constructor for class edu.rit.pj.reduction.SharedFloatArray: Construct a new float array reduction variable whose elements are copied from the given array.
SharedFloatArray(int) - Constructor for class edu.rit.pj.reduction.SharedFloatArray: Construct a new float array reduction variable with the given length.
SharedFloatArrayBuf - Class in edu.rit.mp.buf: Class SharedFloatArrayBuf provides a buffer for a multiple thread safe array of float items sent or received using the Message Protocol (MP).
SharedFloatArrayBuf(SharedFloatArray, Range) - Constructor for class edu.rit.mp.buf.SharedFloatArrayBuf: Construct a new shared float array buffer.
SharedFloatArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedFloatArrayBuf_1 provides a buffer for a multiple thread safe array of float items sent or received using the Message Protocol (MP).
SharedFloatArrayBuf_1(SharedFloatArray, Range) - Constructor for class edu.rit.mp.buf.SharedFloatArrayBuf_1: Construct a new shared float array buffer.
SharedFloatBuf - Class in edu.rit.mp.buf: Class SharedFloatBuf provides a buffer for a shared float item sent or received using the Message Protocol (MP).
SharedFloatBuf(SharedFloat) - Constructor for class edu.rit.mp.buf.SharedFloatBuf: Construct a new shared float buffer.
SharedInteger - Class in edu.rit.pj.reduction: Class SharedInteger provides a reduction variable for a value of type int.
SharedInteger() - Constructor for class edu.rit.pj.reduction.SharedInteger: Construct a new integer reduction variable with the initial value 0.
SharedInteger(int) - Constructor for class edu.rit.pj.reduction.SharedInteger: Construct a new integer reduction variable with the given initial value.
SharedIntegerArray - Class in edu.rit.pj.reduction: Class SharedIntegerArray provides an array reduction variable with elements of type int.
SharedIntegerArray(int) - Constructor for class edu.rit.pj.reduction.SharedIntegerArray: Construct a new integer array reduction variable with the given length.
SharedIntegerArray(int[]) - Constructor for class edu.rit.pj.reduction.SharedIntegerArray: Construct a new integer array reduction variable whose elements are copied from the given array.
SharedIntegerArrayBuf - Class in edu.rit.mp.buf: Class SharedIntegerArrayBuf provides a buffer for a multiple thread safe array of integer items sent or received using the Message Protocol (MP).
SharedIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedIntegerArrayBuf: Construct a new shared integer array buffer.
SharedIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of integer items sent or received using the Message Protocol (MP).
SharedIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedIntegerArrayBuf_1: Construct a new shared integer array buffer.
SharedIntegerBuf - Class in edu.rit.mp.buf: Class SharedIntegerBuf provides a buffer for a shared integer item sent or received using the Message Protocol (MP).
SharedIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedIntegerBuf: Construct a new shared integer buffer.
SharedIntegerMatrix - Class in edu.rit.pj.reduction: Class SharedIntegerMatrix provides a matrix reduction variable with elements of type int.
SharedIntegerMatrix(int[][]) - Constructor for class edu.rit.pj.reduction.SharedIntegerMatrix: Construct a new integer matrix reduction variable whose elements are copied from the given matrix.
SharedIntegerMatrix(int, int) - Constructor for class edu.rit.pj.reduction.SharedIntegerMatrix: Construct a new integer matrix reduction variable with the given number of rows and columns.
SharedLong - Class in edu.rit.pj.reduction: Class SharedLong provides a reduction variable for a value of type long.
SharedLong() - Constructor for class edu.rit.pj.reduction.SharedLong: Construct a new long reduction variable with the initial value 0.
SharedLong(long) - Constructor for class edu.rit.pj.reduction.SharedLong: Construct a new long reduction variable with the given initial value.
SharedLongArray - Class in edu.rit.pj.reduction: Class SharedLongArray provides an array reduction variable with elements of type long.
SharedLongArray(int) - Constructor for class edu.rit.pj.reduction.SharedLongArray: Construct a new long array reduction variable with the given length.
SharedLongArray(long[]) - Constructor for class edu.rit.pj.reduction.SharedLongArray: Construct a new long array reduction variable whose elements are copied from the given array.
SharedLongArrayBuf - Class in edu.rit.mp.buf: Class SharedLongArrayBuf provides a buffer for a multiple thread safe array of long items sent or received using the Message Protocol (MP).
SharedLongArrayBuf(SharedLongArray, Range) - Constructor for class edu.rit.mp.buf.SharedLongArrayBuf: Construct a new shared long array buffer.
SharedLongArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedLongArrayBuf_1 provides a buffer for a multiple thread safe array of long items sent or received using the Message Protocol (MP).
SharedLongArrayBuf_1(SharedLongArray, Range) - Constructor for class edu.rit.mp.buf.SharedLongArrayBuf_1: Construct a new shared long array buffer.
SharedLongBuf - Class in edu.rit.mp.buf: Class SharedLongBuf provides a buffer for a shared long item sent or received using the Message Protocol (MP).
SharedLongBuf(SharedLong) - Constructor for class edu.rit.mp.buf.SharedLongBuf: Construct a new shared long buffer.
SharedLongMatrix - Class in edu.rit.pj.reduction: Class SharedLongMatrix provides a matrix reduction variable with elements of type long.
SharedLongMatrix(int, int) - Constructor for class edu.rit.pj.reduction.SharedLongMatrix: Construct a new long matrix reduction variable with the given number of rows and columns.
SharedLongMatrix(long[][]) - Constructor for class edu.rit.pj.reduction.SharedLongMatrix: Construct a new long matrix reduction variable whose elements are copied from the given matrix.
SharedObject<T> - Class in edu.rit.pj.reduction: Class SharedObject provides a reduction variable for a value of an object type.
SharedObject() - Constructor for class edu.rit.pj.reduction.SharedObject: Construct a new object reduction variable with the initial value null.
SharedObject(T) - Constructor for class edu.rit.pj.reduction.SharedObject: Construct a new object reduction variable with the given initial value.
SharedObjectArray<T> - Class in edu.rit.pj.reduction: Class SharedObjectArray provides an array reduction variable with elements of an object type.
SharedObjectArray(int) - Constructor for class edu.rit.pj.reduction.SharedObjectArray: Construct a new object array reduction variable with the given length.
SharedObjectArray(T[]) - Constructor for class edu.rit.pj.reduction.SharedObjectArray: Construct a new object array reduction variable whose elements are copied from the given array.
SharedObjectArrayBuf<T> - Class in edu.rit.mp.buf: Class SharedObjectArrayBuf provides a buffer for a multiple thread safe array of object items sent or received using the Message Protocol (MP).
SharedObjectArrayBuf(SharedObjectArray<T>, Range) - Constructor for class edu.rit.mp.buf.SharedObjectArrayBuf: Construct a new shared object array buffer.
SharedObjectArrayBuf_1<T> - Class in edu.rit.mp.buf: Class SharedObjectArrayBuf_1 provides a buffer for a multiple thread safe array of object items sent or received using the Message Protocol (MP).
SharedObjectArrayBuf_1(SharedObjectArray<T>, Range) - Constructor for class edu.rit.mp.buf.SharedObjectArrayBuf_1: Construct a new shared object array buffer.
SharedObjectBuf<T> - Class in edu.rit.mp.buf: Class SharedObjectBuf provides a buffer for a shared object item sent or received using the Message Protocol (MP).
SharedObjectBuf(SharedObject<T>) - Constructor for class edu.rit.mp.buf.SharedObjectBuf: Construct a new shared object buffer.
SharedShort - Class in edu.rit.pj.reduction: Class SharedShort provides a reduction variable for a value of type short.
SharedShort() - Constructor for class edu.rit.pj.reduction.SharedShort: Construct a new short reduction variable with the initial value 0.
SharedShort(short) - Constructor for class edu.rit.pj.reduction.SharedShort: Construct a new short reduction variable with the given initial value.
SharedShortArray - Class in edu.rit.pj.reduction: Class SharedShortArray provides an array reduction variable with elements of type short.
SharedShortArray(int) - Constructor for class edu.rit.pj.reduction.SharedShortArray: Construct a new short array reduction variable with the given length.
SharedShortArray(short[]) - Constructor for class edu.rit.pj.reduction.SharedShortArray: Construct a new short array reduction variable whose elements are copied from the given array.
SharedShortArrayBuf - Class in edu.rit.mp.buf: Class SharedShortArrayBuf provides a buffer for a multiple thread safe array of short items sent or received using the Message Protocol (MP).
SharedShortArrayBuf(SharedShortArray, Range) - Constructor for class edu.rit.mp.buf.SharedShortArrayBuf: Construct a new shared short array buffer.
SharedShortArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedShortArrayBuf_1 provides a buffer for a multiple thread safe array of short items sent or received using the Message Protocol (MP).
SharedShortArrayBuf_1(SharedShortArray, Range) - Constructor for class edu.rit.mp.buf.SharedShortArrayBuf_1: Construct a new shared short array buffer.
SharedShortBuf - Class in edu.rit.mp.buf: Class SharedShortBuf provides a buffer for a shared short item sent or received using the Message Protocol (MP).
SharedShortBuf(SharedShort) - Constructor for class edu.rit.mp.buf.SharedShortBuf: Construct a new shared short buffer.
SharedSigned16BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class SharedSigned16BitIntegerArrayBuf provides a buffer for a multiple thread safe array of signed 16-bit integer items sent or received using the Message Protocol (MP).
SharedSigned16BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf: Construct a new shared signed 16-bit integer array buffer.
SharedSigned16BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedSigned16BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of signed 16-bit integer items sent or received using the Message Protocol (MP).
SharedSigned16BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1: Construct a new shared signed 16-bit integer array buffer.
SharedSigned16BitIntegerBuf - Class in edu.rit.mp.buf: Class SharedSigned16BitIntegerBuf provides a buffer for a single signed 16-bit integer item sent or received using the Message Protocol (MP).
SharedSigned16BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedSigned16BitIntegerBuf: Construct a new shared signed 16-bit integer buffer.
SharedSigned8BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class SharedSigned8BitIntegerArrayBuf provides a buffer for a multiple thread safe array of signed 8-bit integer items sent or received using the Message Protocol (MP).
SharedSigned8BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf: Construct a new shared signed 8-bit integer array buffer.
SharedSigned8BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedSigned8BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of signed 8-bit integer items sent or received using the Message Protocol (MP).
SharedSigned8BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1: Construct a new shared signed 8-bit integer array buffer.
SharedSigned8BitIntegerBuf - Class in edu.rit.mp.buf: Class SharedSigned8BitIntegerBuf provides a buffer for a shared signed 8-bit integer item sent or received using the Message Protocol (MP).
SharedSigned8BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedSigned8BitIntegerBuf: Construct a new shared signed 8-bit integer buffer.
SharedUnsigned16BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class SharedUnsigned16BitIntegerArrayBuf provides a buffer for a multiple thread safe array of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned16BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf: Construct a new shared unsigned 16-bit integer array buffer.
SharedUnsigned16BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedUnsigned16BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned16BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1: Construct a new shared unsigned 16-bit integer array buffer.
SharedUnsigned16BitIntegerBuf - Class in edu.rit.mp.buf: Class SharedUnsigned16BitIntegerBuf provides a buffer for a shared unsigned 16-bit integer item sent or received using the Message Protocol (MP).
SharedUnsigned16BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf: Construct a new shared unsigned 16-bit integer buffer.
SharedUnsigned8BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class SharedUnsigned8BitIntegerArrayBuf provides a buffer for a multiple thread safe array of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned8BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf: Construct a new shared unsigned 8-bit integer array buffer.
SharedUnsigned8BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class SharedUnsigned8BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned8BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1: Construct a new shared unsigned 8-bit integer array buffer.
SharedUnsigned8BitIntegerBuf - Class in edu.rit.mp.buf: Class SharedUnsigned8BitIntegerBuf provides a buffer for a single unsigned 8-bit integer item sent or received using the Message Protocol (MP).
SharedUnsigned8BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf: Construct a new shared unsigned 8-bit integer buffer.
SHEET - Enum constant in enum class ffx.potential.bonded.Residue.SSType
shellCommand - Variable in class edu.rit.pj.cluster.BackendInfo: Shell command string on the backend.
shiftButton - Variable in class ffx.ui.behaviors.PickMouseBehavior
Short() - Constructor for class edu.rit.util.Searching.Short
Short() - Constructor for class edu.rit.util.Sorting.Short
ShortArrayBuf - Class in edu.rit.mp.buf: Class ShortArrayBuf provides a buffer for an array of short items sent or received using the Message Protocol (MP).
ShortArrayBuf(short[], Range) - Constructor for class edu.rit.mp.buf.ShortArrayBuf: Construct a new short array buffer.
ShortArrayBuf_1 - Class in edu.rit.mp.buf: Class ShortArrayBuf_1 provides a buffer for an array of short items sent or received using the Message Protocol (MP).
ShortArrayBuf_1(short[], Range) - Constructor for class edu.rit.mp.buf.ShortArrayBuf_1: Construct a new short array buffer.
ShortBuf - Class in edu.rit.mp: Class ShortBuf is the abstract base class for a buffer of short items sent or received using the Message Protocol (MP).
ShortBuf(int) - Constructor for class edu.rit.mp.ShortBuf: Construct a new short buffer.
ShortItemBuf - Class in edu.rit.mp.buf: Class ShortItemBuf provides a buffer for a single short item sent or received using the Message Protocol (MP).
ShortItemBuf() - Constructor for class edu.rit.mp.buf.ShortItemBuf: Construct a new short item buffer.
ShortItemBuf(short) - Constructor for class edu.rit.mp.buf.ShortItemBuf: Construct a new short item buffer with the given initial value.
ShortMatrixBuf - Class in edu.rit.mp.buf: Class ShortMatrixBuf provides a buffer for a matrix of short items sent or received using the Message Protocol (MP).
ShortMatrixBuf(short[][], Range, Range) - Constructor for class edu.rit.mp.buf.ShortMatrixBuf: Construct a new short matrix buffer.
ShortMatrixBuf_1 - Class in edu.rit.mp.buf: Class ShortMatrixBuf_1 provides a buffer for a matrix of short items sent or received using the Message Protocol (MP).
ShortMatrixBuf_1(short[][], Range, Range) - Constructor for class edu.rit.mp.buf.ShortMatrixBuf_1: Construct a new short matrix buffer.
shortName - Variable in class ffx.crystal.SpaceGroup: Space group name.
ShortOp - Class in edu.rit.pj.reduction: Class ShortOp is the abstract base class for a binary operation on short values, used to do reduction in a parallel program.
ShortOp() - Constructor for class edu.rit.pj.reduction.ShortOp: Construct a new short binary operation.
showAbout() - Method in class ffx.ui.ModelingShell
showAbout(EventObject) - Method in class ffx.ui.ModelingShell
SHOWHYDROGEN - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
SHOWVRML - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
SHUFFLE_RE_IM - Static variable in class ffx.numerics.fft.MixedRadixFactor: Shuffle used to swap real and imaginary members of the vector.
SHUFFLE_RE_IM_128 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Shuffle used to swap real and imaginary members of the vector.
SHUFFLE_RE_IM_256 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Shuffle used to swap real and imaginary members of the vector.
SHUFFLE_RE_IM_512 - Static variable in class ffx.numerics.fft.MixedRadixFactor: Shuffle used to swap real and imaginary members of the vector.
shutdown() - Method in class edu.rit.pj.ParallelTeam: Kills the team's threads run() methods so that they are no longer GC roots.
shutdown() - Method in class edu.rit.util.TimerThread: Shut down this timer thread.
Si - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
sidechainStoichiometry - Static variable in class ffx.potential.bonded.AminoAcidUtils: Stoichiometry of side chains can be used for identification, accept for a couple cases:
SIGMA - Enum constant in enum class ffx.potential.parameters.VDWType.RADIUS_TYPE
sigmaA - Variable in class ffx.xray.DiffractionRefinementData: SigmaA coefficient - s.
SigmaAEnergy - Class in ffx.xray: Optimize SigmaA coefficients (using spline coefficients) and structure factor derivatives using a likelihood target function.
SigmaAMinimize - Class in ffx.xray: SigmaAMinimize class.
sigmas - Variable in class ffx.potential.bonded.Rotamer: An array of sigmas for each chi angle.
sigmaW - Variable in class ffx.xray.DiffractionRefinementData: SigmaA coefficient - w.
sign - Variable in class ffx.numerics.fft.PassData
Signed16BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class Signed16BitIntegerArrayBuf provides a buffer for an array of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerArrayBuf: Construct a new signed 16-bit integer array buffer.
Signed16BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class Signed16BitIntegerArrayBuf_1 provides a buffer for an array of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1: Construct a new signed 16-bit integer array buffer.
Signed16BitIntegerBuf - Class in edu.rit.mp: Class Signed16BitIntegerBuf is the abstract base class for a buffer of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerBuf(int) - Constructor for class edu.rit.mp.Signed16BitIntegerBuf: Construct a new signed 16-bit integer buffer.
Signed16BitIntegerItemBuf - Class in edu.rit.mp.buf: Class Signed16BitIntegerItemBuf provides a buffer for a single signed 16-bit integer item sent or received using the Message Protocol (MP).
Signed16BitIntegerItemBuf() - Constructor for class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Construct a new signed 16-bit integer item buffer.
Signed16BitIntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerItemBuf: Construct a new signed 16-bit integer item buffer with the given initial value.
Signed16BitIntegerMatrixBuf - Class in edu.rit.mp.buf: Class Signed16BitIntegerMatrixBuf provides a buffer for a matrix of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf: Construct a new signed 16-bit integer matrix buffer.
Signed16BitIntegerMatrixBuf_1 - Class in edu.rit.mp.buf: Class Signed16BitIntegerMatrixBuf_1 provides a buffer for a matrix of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1: Construct a new signed 16-bit integer matrix buffer.
Signed8BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class Signed8BitIntegerArrayBuf provides a buffer for an array of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerArrayBuf: Construct a new signed 8-bit integer array buffer.
Signed8BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class Signed8BitIntegerArrayBuf_1 provides a buffer for an array of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1: Construct a new signed 8-bit integer array buffer.
Signed8BitIntegerBuf - Class in edu.rit.mp: Class Signed8BitIntegerBuf is the abstract base class for a buffer of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerBuf(int) - Constructor for class edu.rit.mp.Signed8BitIntegerBuf: Construct a new signed 8-bit integer buffer.
Signed8BitIntegerItemBuf - Class in edu.rit.mp.buf: Class Signed8BitIntegerItemBuf provides a buffer for a single signed 8-bit integer item sent or received using the Message Protocol (MP).
Signed8BitIntegerItemBuf() - Constructor for class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Construct a new signed 8-bit integer item buffer.
Signed8BitIntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerItemBuf: Construct a new signed 8-bit integer item buffer with the given initial value.
Signed8BitIntegerMatrixBuf - Class in edu.rit.mp.buf: Class Signed8BitIntegerMatrixBuf provides a buffer for a matrix of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf: Construct a new signed 8-bit integer matrix buffer.
Signed8BitIntegerMatrixBuf_1 - Class in edu.rit.mp.buf: Class Signed8BitIntegerMatrixBuf_1 provides a buffer for a matrix of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1: Construct a new signed 8-bit integer matrix buffer.
SILENT - Enum constant in enum class ffx.algorithms.dynamics.MDVerbosity
SIM - Enum constant in enum class ffx.potential.Utilities.FileType
simpsons(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using Simpson's rule.
simpsons(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using Simpson's rule.
SIMPSONS - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType: Simpson's Three Point Integration, requiring 3 points.
simpsonsParallel(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using Boole's rule.
simpsonsParallel(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using Simpson's rule.
SimulatedAnnealing - Class in ffx.algorithms.optimize.anneal: Run NVT molecular dynamics at a series of temperatures to optimize a structure.
SimulatedAnnealing(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum, AnnealingSchedule, long, double, boolean, File) - Constructor for class ffx.algorithms.optimize.anneal.SimulatedAnnealing: Constructor for SimulatedAnnealing.
SimulatedAnnealing.Schedules - Enum Class in ffx.algorithms.optimize.anneal: Represents non-composite AnnealingSchedules known (i.e. not FlatEndAnnealSchedule).
SIMULATION - Static variable in class ffx.ui.commands.SimulationUpdate: Constant SIMULATION=1
SimulationDefinition - Class in ffx.ui.commands: The SimulationDefinition class is a serializable wrapper that specifies an FFX simulation.
SimulationDefinition(int, int) - Constructor for class ffx.ui.commands.SimulationDefinition: Constructor that allocates space for a simulation definition.
SimulationFilter - Class in ffx.ui.commands: The SimulationFilter class parses system data sent by FFXServer to FFXClient.
SimulationFilter(SimulationDefinition, MolecularAssembly) - Constructor for class ffx.ui.commands.SimulationFilter: Constructor for SimulationFilter.
SimulationLoader - Class in ffx.ui: This SimulationLoader class oversees loading information from an executing FFX instance program this instance of Force Field X.
SimulationLoader(FFXSystem, Thread, MainPanel, InetSocketAddress) - Constructor for class ffx.ui.SimulationLoader: Constructor for SimulationLoader.
SimulationMessage - Class in ffx.ui.commands: The SimulationMessage class is used to pass simple messages between an FFXServer and its FFXClient(s).
SimulationMessage(int) - Constructor for class ffx.ui.commands.SimulationMessage: Constructor for SimulationMessage.
SimulationUpdate - Class in ffx.ui.commands: The SimulationUpdate class is a serializable wrapper for FFX simulation data that changes during a simulation.
SimulationUpdate(int, int, boolean) - Constructor for class ffx.ui.commands.SimulationUpdate: Constructor for SimulationUpdate.
sin - Variable in class ffx.potential.parameters.ImproperTorsionType: Value of sin(toRadians(phase)).
sin() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the complex sine of this.
sine - Variable in class ffx.potential.parameters.TorsionType: Sine of the phase angle.
SINGLE_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
SingleLinkageStrategy - Class in ffx.numerics.clustering: Linkage strategy that uses the minimum of pairwise distances between cluster members (single-linkage / nearest-neighbor).
SingleLinkageStrategy() - Constructor for class ffx.numerics.clustering.SingleLinkageStrategy
SinWave - Class in ffx.numerics.integrate: A SinWave describes points along a sine wave of f(x) = a*sin(jx).
SinWave(double[], boolean, double, double) - Constructor for class ffx.numerics.integrate.SinWave: Constructs f(x) = a*sin(nx).
SinWave(double[], double, double) - Constructor for class ffx.numerics.integrate.SinWave: Constructs f(x) = a*sin(nx).
size - Variable in class ffx.numerics.multipole.MultipoleTensor: Size = (order + 1) * (order + 2) * (order + 3) / 6;
size - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Size = (order + 1) * (order + 2) * (order + 3) / 6;
size() - Method in class edu.rit.pj.Comm: Obtain the number of processes in this communicator.
size() - Method in class ffx.numerics.atomic.AdderDoubleArray: Get the current size of the array.
size() - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Get the current size of the array.
size() - Method in class ffx.numerics.atomic.MultiDoubleArray: Get the current size of the array.
size() - Method in class ffx.numerics.atomic.PJDoubleArray: Get the current size of the array.
skip() - Method in class edu.rit.util.Random: Skip one position ahead in this PRNG's sequence.
skip(long) - Method in class edu.rit.pj.cluster.BackendFileInputStream: Skip the given number of bytes from this input stream.
skip(long) - Method in class edu.rit.util.Random: Skip the given number of positions ahead in this PRNG's sequence.
SLICE - Enum constant in enum class ffx.potential.nonbonded.ReciprocalSpace.GridMethod
SLICE - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.GridMethod
sliceBuffer(boolean[], Range) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for one slice of the given Boolean array.
sliceBuffer(byte[], Range) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for one slice of the given byte array.
sliceBuffer(char[], Range) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for one slice of the given character array.
sliceBuffer(double[], Range) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for one slice of the given double array.
sliceBuffer(float[], Range) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for one slice of the given float array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for one slice of the given integer array.
sliceBuffer(long[], Range) - Static method in class edu.rit.mp.LongBuf: Create a buffer for one slice of the given long array.
sliceBuffer(short[], Range) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for one slice of the given short array.
sliceBuffer(SharedBooleanArray, Range) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for one slice of the given shared Boolean array.
sliceBuffer(SharedByteArray, Range) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for one slice of the given shared byte array.
sliceBuffer(SharedCharacterArray, Range) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for one slice of the given shared character array.
sliceBuffer(SharedDoubleArray, Range) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for one slice of the given shared double array.
sliceBuffer(SharedFloatArray, Range) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for one slice of the given shared float array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedLongArray, Range) - Static method in class edu.rit.mp.LongBuf: Create a buffer for one slice of the given shared long array.
sliceBuffer(SharedObjectArray<T>, Range) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for one slice of the given shared object array.
sliceBuffer(SharedShortArray, Range) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for one slice of the given shared short array.
sliceBuffer(T[], Range) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for one slice of the given object array.
sliceBuffers(boolean[], Range[]) - Static method in class edu.rit.mp.BooleanBuf: Create an array of buffers for multiple slices of the given Boolean array.
sliceBuffers(byte[], Range[]) - Static method in class edu.rit.mp.ByteBuf: Create an array of buffers for multiple slices of the given byte array.
sliceBuffers(char[], Range[]) - Static method in class edu.rit.mp.CharacterBuf: Create an array of buffers for multiple slices of the given character array.
sliceBuffers(double[], Range[]) - Static method in class edu.rit.mp.DoubleBuf: Create an array of buffers for multiple slices of the given double array.
sliceBuffers(float[], Range[]) - Static method in class edu.rit.mp.FloatBuf: Create an array of buffers for multiple slices of the given float array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.IntegerBuf: Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(long[], Range[]) - Static method in class edu.rit.mp.LongBuf: Create an array of buffers for multiple slices of the given long array.
sliceBuffers(short[], Range[]) - Static method in class edu.rit.mp.ShortBuf: Create an array of buffers for multiple slices of the given short array.
sliceBuffers(SharedBooleanArray, Range[]) - Static method in class edu.rit.mp.BooleanBuf: Create an array of buffers for multiple slices of the given shared Boolean array.
sliceBuffers(SharedByteArray, Range[]) - Static method in class edu.rit.mp.ByteBuf: Create an array of buffers for multiple slices of the given shared byte array.
sliceBuffers(SharedCharacterArray, Range[]) - Static method in class edu.rit.mp.CharacterBuf: Create an array of buffers for multiple slices of the given shared character array.
sliceBuffers(SharedDoubleArray, Range[]) - Static method in class edu.rit.mp.DoubleBuf: Create an array of buffers for multiple slices of the given shared double array.
sliceBuffers(SharedFloatArray, Range[]) - Static method in class edu.rit.mp.FloatBuf: Create an array of buffers for multiple slices of the given shared float array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.IntegerBuf: Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedLongArray, Range[]) - Static method in class edu.rit.mp.LongBuf: Create an array of buffers for multiple slices of the given shared long array.
sliceBuffers(SharedObjectArray<T>, Range[]) - Static method in class edu.rit.mp.ObjectBuf: Create an array of buffers for multiple slices of the given shared object array.
sliceBuffers(SharedShortArray, Range[]) - Static method in class edu.rit.mp.ShortBuf: Create an array of buffers for multiple slices of the given shared short array.
sliceBuffers(T[], Range[]) - Static method in class edu.rit.mp.ObjectBuf: Create an array of buffers for multiple slices of the given object array.
sliceLoop - Variable in class ffx.potential.nonbonded.SliceRegion
SliceLoop - Class in ffx.potential.nonbonded: The SliceLoop class is used to parallelize placing onto a 3D grid
SliceLoop(int, int, SliceRegion) - Constructor for class ffx.potential.nonbonded.SliceLoop: Constructor for SliceLoop.
sliceRegion - Variable in class ffx.potential.nonbonded.SliceLoop
SliceRegion - Class in ffx.potential.nonbonded: The SliceLoop class is used to parallelize placing onto a 3D grid
SliceRegion(int, int, int, double[], int, int, Atom[], double[][][]) - Constructor for class ffx.potential.nonbonded.SliceRegion: Constructor for SliceRegion.
SliceSchedule - Class in ffx.xray: SliceSchedule class.
SliceSchedule(int, int) - Constructor for class ffx.xray.SliceSchedule: Constructor for SliceSchedule.
slidingWindowCentered(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization
SLOW - Enum constant in enum class ffx.numerics.Potential.STATE: Include SLOW varying energy terms.
Sm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Sn - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
SNAPSHOT - Enum constant in enum class ffx.algorithms.dynamics.MDWriteAction
sneck - Variable in class ffx.potential.parameters.SoluteType: Sneck scaling factor to use with interstitial space corrections
softcoreCreated - Variable in class ffx.potential.openmm.OpenMMSystem: Fixed charge softcore vdW force boolean.
SOLUTE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
SOLUTE - Enum constant in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE
soluteDielectric - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: The requested permittivity for the solute.
SoluteType - Class in ffx.potential.parameters: The SoluteType class defines one implicit solvent radius.
SoluteType(int, double) - Constructor for class ffx.potential.parameters.SoluteType: Constructor for SoluteType.
SoluteType(int, double, double, double) - Constructor for class ffx.potential.parameters.SoluteType: Constructor for SoluteType.
SoluteType(int, double, double, double, double) - Constructor for class ffx.potential.parameters.SoluteType: Constructor for SoluteType.
SoluteType(int, String, double, double, double) - Constructor for class ffx.potential.parameters.SoluteType: Constructor for SoluteType.
SoluteType.SOLUTE_RADII_TYPE - Enum Class in ffx.potential.parameters
solvationEnergy(boolean, boolean) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: solvationEnergy
solvationEnergy(double, boolean, boolean) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: solvationEnergy
Solvator - Class in ffx.potential.commands: The Solvator script puts a box of solvent around a solute.
Solvator() - Constructor for class ffx.potential.commands.Solvator
Solvator(FFXBinding) - Constructor for class ffx.potential.commands.Solvator
Solvator(String[]) - Constructor for class ffx.potential.commands.Solvator
solve3PepPoly(double[], double[], double[], double[], double[][][], double[][][], double[][][]) - Method in class ffx.potential.utils.LoopClosure: Close a 3-residue loop by filling in the backbone atom coordinates and return the possible solution set.
SolventBinaryFormFactor - Class in ffx.xray: SolventBinaryFormFactor class.
SolventBinaryFormFactor(Atom, double) - Constructor for class ffx.xray.SolventBinaryFormFactor: Constructor for SolventBinaryFormFactor.
SolventBinaryFormFactor(Atom, double, double[]) - Constructor for class ffx.xray.SolventBinaryFormFactor: Constructor for SolventBinaryFormFactor.
SolventGaussFormFactor - Class in ffx.xray: SolventGaussFormFactor class.
SolventGaussFormFactor(Atom, double) - Constructor for class ffx.xray.SolventGaussFormFactor: Constructor for SolventGaussFormFactor.
SolventGaussFormFactor(Atom, double, double[]) - Constructor for class ffx.xray.SolventGaussFormFactor: Constructor for SolventGaussFormFactor.
solventModel - Variable in class ffx.xray.cli.XrayOptions: The SolventModel to use.
solventModel - Variable in class ffx.xray.CrystalReciprocalSpace
SolventPolyFormFactor - Class in ffx.xray: SolventPolyFormFactor class.
SolventPolyFormFactor(Atom, double, double) - Constructor for class ffx.xray.SolventPolyFormFactor: Constructor for SolventPolyFormFactor.
SolventPolyFormFactor(Atom, double, double, double[]) - Constructor for class ffx.xray.SolventPolyFormFactor: Constructor for SolventPolyFormFactor.
solveSturm(int, double[], double[]) - Method in class ffx.potential.bonded.SturmMethod: Solve using the Sturm method.
SOR - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
SORRegion - Class in ffx.potential.nonbonded.pme: Parallel successive over-relaxation (SOR) solver for the self-consistent field.
SORRegion(int, ForceField) - Constructor for class ffx.potential.nonbonded.pme.SORRegion
sort(byte[], Sorting.Byte) - Static method in class edu.rit.util.Sorting: Sort the given array of type byte[].
sort(char[], Sorting.Character) - Static method in class edu.rit.util.Sorting: Sort the given array of type char[].
sort(double[], Sorting.Double) - Static method in class edu.rit.util.Sorting: Sort the given array of type double[].
sort(float[], Sorting.Float) - Static method in class edu.rit.util.Sorting: Sort the given array of type float[].
sort(int[], Sorting.Integer) - Static method in class edu.rit.util.Sorting: Sort the given array of type int[].
sort(long[], Sorting.Long) - Static method in class edu.rit.util.Sorting: Sort the given array of type long[].
sort(short[], Sorting.Short) - Static method in class edu.rit.util.Sorting: Sort the given array of type short[].
sort(T[], Sorting.Object<T>) - Static method in class edu.rit.util.Sorting: Sort the given object array of type T[].
sortAndReturn(List<ObjectPair<U, V>>) - Static method in record class ffx.utilities.ObjectPair: sortAndReturn.
SortArc - Class in ffx.algorithms.commands: The SortArc script sort Monte Carlo archive files by lambda value.
SortArc() - Constructor for class ffx.algorithms.commands.SortArc: SortArc Constructor.
SortArc(FFXBinding) - Constructor for class ffx.algorithms.commands.SortArc: SortArc Constructor.
SortArc(String[]) - Constructor for class ffx.algorithms.commands.SortArc: SortArc constructor that sets the command line arguments.
sortAtomsByDistance(Atom, Atom[]) - Static method in class ffx.potential.bonded.BondedUtils: In-place sorts toCompare by distance to the reference Atom.
sortAtomsByDistance(Atom, List<Atom>) - Static method in class ffx.potential.bonded.BondedUtils: Sorts toCompare by distance to the reference Atom, returning a sorted array.
sortCellResidues() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Sorts residues in the box.
sortedIndex() - Method in record class ffx.utilities.IndexIndexPair: Returns the value of the sortedIndex record component.
Sorting - Class in edu.rit.util: Class Sorting provides static methods for sorting arrays of primitive types and object types.
Sorting.Byte - Class in edu.rit.util: Class Sorting.Byte is the base class for a helper object used to sort an array of type byte[].
Sorting.Character - Class in edu.rit.util: Class Sorting.Character is the base class for a helper object used to sort an array of type char[].
Sorting.Double - Class in edu.rit.util: Class Sorting.Double is the base class for a helper object used to sort an array of type double[].
Sorting.Float - Class in edu.rit.util: Class Sorting.Float is the base class for a helper object used to sort an array of type float[].
Sorting.Integer - Class in edu.rit.util: Class Sorting.Integer is the base class for a helper object used to sort an array of type int[].
Sorting.Long - Class in edu.rit.util: Class Sorting.Long is the base class for a helper object used to sort an array of type long[].
Sorting.Object<T> - Class in edu.rit.util: Class Sorting.Object is the abstract base class for a helper object used to sort an array of objects of type T[].
Sorting.Short - Class in edu.rit.util: Class Sorting.Short is the base class for a helper object used to sort an array of type short[].
sortKey(int[]) - Static method in class ffx.potential.parameters.AngleTorsionType: This method sorts the atom classes for the angle-torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.AngleType: This method sorts the atom classes as: min, c[1], max
sortKey(int[]) - Static method in class ffx.potential.parameters.BondType: This method sorts the atom classes as: min, max
sortKey(int[]) - Static method in class ffx.potential.parameters.ImproperTorsionType: This method sorts the atom classes for the improper torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.OutOfPlaneBendType: This method sorts the atom classes for the out-of-plane angle bending type.
sortKey(int[]) - Static method in class ffx.potential.parameters.PiOrbitalTorsionType: This method sorts the atom classes as: min, max
sortKey(int[]) - Static method in class ffx.potential.parameters.StretchBendType: This method sorts the atom classes as: min, c[1], max
sortKey(int[]) - Static method in class ffx.potential.parameters.StretchTorsionType: This method sorts the atom classes for the torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.TorsionTorsionType: No sorting is done for the Torsion-Torsion lookup.
sortKey(int[]) - Static method in class ffx.potential.parameters.TorsionType: This method sorts the atom classes for the torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.UreyBradleyType: This method sorts the atom classes as: min, c[1], max
sortKey(int[]) - Static method in class ffx.potential.parameters.VDWPairType: This method sorts the atom classes as: min, max
sortMyArc(File, int, double, int) - Static method in class ffx.algorithms.commands.test.PhDynamics: Sort archive files by pH with string parsing
SortXPH - Class in ffx.algorithms.commands.test: The SortXPH command unwinds .ARC files from CpHMD runs.
SortXPH() - Constructor for class ffx.algorithms.commands.test.SortXPH: SortXPH Constructor.
SortXPH(FFXBinding) - Constructor for class ffx.algorithms.commands.test.SortXPH: SortXPH Constructor.
SortXPH(String[]) - Constructor for class ffx.algorithms.commands.test.SortXPH: SortXPH constructor that sets the command line arguments.
source(double[]) - Method in class ffx.numerics.multipole.AmoebaPlusDampTensorGlobal: Generate source terms for the Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.AmoebaPlusOverlapTensorGlobal: Generate source terms for the Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.CombinedTensorGlobal: Generate source terms for the Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Generate source terms for the Coulomb Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: Generate source terms for the Coulomb Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.EwaldTensorGlobal: Generate source terms for the Ewald Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.EwaldTensorQI: Generate source terms for the Ewald Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Generate source terms for the Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.TholeTensorGlobal: Generate source terms for the Challacombe et al. recursion.
source(double[]) - Method in class ffx.numerics.multipole.TholeTensorQI: Generate source terms for the Challacombe et al. recursion.
source(double[], GKMultipoleOrder) - Method in class ffx.numerics.multipole.GKSource: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
source(DoubleVector[]) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD: Generate source terms for the Coulomb Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.EwaldTensorGlobalSIMD: Generate source terms for the Ewald Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.EwaldTensorQISIMD: Generate source terms for the Ewald Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: Generate source terms for the Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.TholeTensorGlobalSIMD: Generate source terms for the Challacombe et al. recursion.
source(DoubleVector[]) - Method in class ffx.numerics.multipole.TholeTensorQISIMD: Generate source terms for the Challacombe et al. recursion.
source(DoubleVector[], GKMultipoleOrder) - Method in class ffx.numerics.multipole.GKSourceSIMD: Generate source terms for the Kirkwood version of the Challacombe et al. recursion.
SPACEFILL - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
spaceGroup - Variable in class ffx.crystal.Crystal: The space group of the crystal.
spaceGroup - Variable in class ffx.crystal.ReflectionList: The space group.
SpaceGroup - Class in ffx.crystal: The Spacegroup class defines the symmetry of a crystal.
SpaceGroup(int, int, int, String, String, String, CrystalSystem, LatticeSystem, LaueSystem, ASULimit[], double[], SymOp...) - Constructor for class ffx.crystal.SpaceGroup: Immutable SpaceGroup instances are made available only through the factory method so this constructor is private.
SpaceGroupConversions - Class in ffx.crystal: This class holds the functionality to convert between equivalent space groups.
SpaceGroupDefinitions - Class in ffx.crystal: The SpaceGroupDefinitions class defines the 230 distinct space groups in three dimensions.
spaceGroupFactory(int) - Static method in class ffx.crystal.SpaceGroupDefinitions: Returns a SpaceGroup instance corresponding to the number parameter.
spaceGroupFactory(String) - Static method in class ffx.crystal.SpaceGroupDefinitions: Return a SpaceGroup based on its name.
SpaceGroupInfo - Class in ffx.crystal: Information about the 230 space groups.
spaceGroupNames - Static variable in class ffx.crystal.SpaceGroupInfo: Names of the 230 three-dimensional space groups.
spaceGroupNumber(String) - Static method in class ffx.crystal.SpaceGroupDefinitions: Returns the space group number for a given space group name.
SPATIAL - Enum constant in enum class ffx.potential.nonbonded.ReciprocalSpace.GridMethod
SPATIAL - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.GridMethod
spatialDensityLoop - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
SpatialDensityLoop - Class in ffx.potential.nonbonded: Loop over a list of atoms and assign their density to a grid.
SpatialDensityLoop(SpatialDensityRegion, int, int[]) - Constructor for class ffx.potential.nonbonded.SpatialDensityLoop: Constructor for SpatialDensityLoop.
SpatialDensityRegion - Class in ffx.potential.nonbonded: This class implements a spatial decomposition based on partitioning a grid into octants.
SpatialDensityRegion(int, int, int, double[], int, int, int, int, Crystal, Atom[], double[][][]) - Constructor for class ffx.potential.nonbonded.SpatialDensityRegion: Constructor for SpatialDensityRegion.
SpatialDensitySchedule - Class in ffx.potential.nonbonded: A fixed schedule that load balances work chunks across threads.
SPEED_OF_LIGHT_SI - Static variable in class ffx.utilities.Constants: Speed of light in m/s, defining the meter.
spinTorsions() - Method in class ffx.algorithms.optimize.TorsionSearch: Scanning through nTorsionsPerBond^nTorsionsPerBond (nTorsionsPerBond x nTorsionsPerBond x nTorsionsPerBond x ...)
spinTorsions(long, long) - Method in class ffx.algorithms.optimize.TorsionSearch: Similar to above, but with a limited number of hilbert indices to run through with this worker alone.
spline - Variable in class ffx.xray.DiffractionRefinementData: Spine scaling coefficients.
spline(double, double, double, double[][][], double[]) - Method in class ffx.numerics.spline.TriCubicSpline: Determine the spline value at a given point.
SplineEnergy - Class in ffx.xray: Fit structure factors using spline coefficients
SplineEnergy.Type - Interface in ffx.xray
splineInducedDipoles(double[][][], double[][][], boolean[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: Place the induced dipoles onto the FFT grid for the atoms in use.
SplineMinimize - Class in ffx.xray: SplineMinimize class.
SplineMinimize(ReflectionList, DiffractionRefinementData, double[], int) - Constructor for class ffx.xray.SplineMinimize: Constructor for SplineMinimize.
splinePermanentMultipoles(double[][][], double[][][], boolean[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: Use b-Splines to place the permanent multipoles onto the FFT grid for the atoms in use.
sqrt() - Method in class ffx.numerics.math.Double3: Square roots values in Double3.
sqrt() - Method in class ffx.numerics.math.Float3: Square roots values in Float3.
sqrt(double) - Static method in class ffx.numerics.math.SquareRoot: Compute the square root of the input value x.
sqrt(int) - Static method in class edu.rit.util.Mathe: Compute the integer square root of the integer x.
sqrtI() - Method in class ffx.numerics.math.Double3: Square roots values in Double3 in place.
sqrtI() - Method in class ffx.numerics.math.Float3: Square roots values in Float3 in place.
square() - Method in class ffx.numerics.math.Double3: Squares values in Double3.
square() - Method in class ffx.numerics.math.Float3: Squares values in Float3.
square(double[]) - Static method in class ffx.numerics.math.DoubleMath: Squares values of a vector.
square(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Squares values of a vector.
square(float[]) - Static method in class ffx.numerics.math.FloatMath: Squares values of a vector.
square(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Squares values of a vector.
SquaredTrigSwitch - Class in ffx.numerics.switching: A SquaredTrigSwitch implements a 0-1 switch of form f(x) = sin^2(ax) or of form f(x) = cos^2(ax).
SquaredTrigSwitch(boolean) - Constructor for class ffx.numerics.switching.SquaredTrigSwitch: Default constructor, creating a switch sin^2(pi*x/2), or cos^2 if flag set.
SquaredTrigSwitch(double, boolean) - Constructor for class ffx.numerics.switching.SquaredTrigSwitch: Constructor permitting a custom frequency "a" in the form sin^2(a*x) or cos^2(a*x).
squareI() - Method in class ffx.numerics.math.Double3: Squares values in Double3 in place.
squareI() - Method in class ffx.numerics.math.Float3: Squares values in Float3 in place.
squareRoot(double[]) - Static method in class ffx.numerics.math.DoubleMath: Square root values of a vector.
squareRoot(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Square root values of a vector.
squareRoot(float[]) - Static method in class ffx.numerics.math.FloatMath: Square root values of a vector.
squareRoot(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Square root values of a vector.
SquareRoot - Class in ffx.numerics.math: Software based computation of square root and inverse square root.
Sr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
SSETest - Class in ffx.numerics.math: java -cp target/numerics-1.0.0.jar -XX:+UnlockDiagnosticVMOptions -XX:+PrintAssembly -Djava.library.path=hsdis-amd64.dylib ffx.numerics.math.SSETest
stackTraceToString(Throwable) - Static method in class ffx.potential.Utilities: Gets the stack trace for an exception and converts it to a String.
STANDARD_WATER_NAME - Static variable in class ffx.utilities.StringUtils: Constant STANDARD_WATER_NAME="HOH"
standardizeAtomNames - Variable in class ffx.potential.parsers.SystemFilter: Standardize atom names to PDB standard by default.
start() - Method in class edu.rit.pj.IntegerForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.IntegerStrideForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.LongForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.LongStrideForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.ParallelIteration: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.ParallelRegion: Perform initialization actions before parallel execution begins.
start() - Method in class edu.rit.pj.WorkerIntegerForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerIteration: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerLongForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerLongStrideForLoop: Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerRegion: Perform initialization actions before parallel execution begins.
start() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
start() - Method in class ffx.algorithms.optimize.manybody.FourBodyEnergyRegion
start() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
start() - Method in class ffx.algorithms.optimize.manybody.SelfEnergyRegion
start() - Method in class ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
start() - Method in class ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
start() - Method in class ffx.potential.nonbonded.implicit.BornGradRegion
start() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
start() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
start() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: Perform initialization actions before parallel execution begins.
start() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
start() - Method in class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
start() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
start() - Method in class ffx.potential.nonbonded.NeighborList: Perform initialization actions before parallel execution begins.
start() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
start() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
start() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
start() - Method in class ffx.potential.nonbonded.pme.SORRegion
start() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
start() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion
start() - Method in class ffx.potential.nonbonded.RowRegion: Perform initialization actions before parallel execution begins.
start() - Method in class ffx.potential.nonbonded.SliceRegion: Perform initialization actions before parallel execution begins.
start() - Method in class ffx.potential.terms.EnergyTermRegion
start() - Method in class ffx.ui.commands.FFXServer: start
start() - Method in class ffx.ui.SwingWorker: Start the worker thread.
start() - Method in class ffx.ui.Trajectory: start
start() - Method in class ffx.xray.BulkSolventList: Perform initialization actions before parallel execution begins.
start(int, LongRange) - Method in class edu.rit.pj.LongSchedule: Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class edu.rit.pj.IntegerSchedule: Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.potential.nonbonded.PairwiseSchedule: Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.potential.nonbonded.SpatialDensitySchedule: Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.xray.GradientSchedule: Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.xray.RowSchedule: Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.xray.SliceSchedule: Start generating chunks of iterations for a parallel for loop using this schedule.
start(long) - Method in class edu.rit.util.Timer: Start this timer with a one-shot timeout at the given interval from now.
start(long, long) - Method in class edu.rit.util.Timer: Start this timer with a periodic fixed-rate timeout starting at the given interval from now.
start(Date) - Method in class edu.rit.util.Timer: Start this timer with a one-shot timeout at the given absolute time.
start(Date, long) - Method in class edu.rit.util.Timer: Start this timer with a periodic fixed-rate timeout starting at the given absolute time.
startFixedIntervalTimeout(long, long) - Method in class edu.rit.util.Timer: Start this timer with a periodic fixed-interval timeout starting at the given interval from now.
startFixedIntervalTimeout(Date, long) - Method in class edu.rit.util.Timer: Start this timer with a periodic fixed-interval timeout starting at the given absolute time.
startListening() - Method in class edu.rit.mp.ChannelGroup: Start actively listening for connection requests.
startTime() - Method in class ffx.potential.terms.EnergyTerm: Set the starting time for the energy computation.
state - Variable in class edu.rit.pj.cluster.BackendInfo: The backend's state.
state - Variable in class edu.rit.pj.cluster.JobInfo: The job's state.
state - Variable in class edu.rit.pj.cluster.ProcessInfo: The job backend process's state.
state - Variable in class ffx.algorithms.dynamics.integrators.Integrator: The MDState class contains the current state of the Molecular Dynamics simulation.
state - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Stores the current molecular dynamics state.
state - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat: The molecular dynamics state to be used.
state - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Are FAST varying energy terms being computed, SLOW varying energy terms, or BOTH.
State - Class in ffx.openmm: A State object records a snapshot of the current state of a simulation at a point in time.
State(PointerByReference) - Constructor for class ffx.openmm.State: Constructor.
stateChanged(ChangeEvent) - Method in class ffx.ui.KeywordComponent
stateChanged(ChangeEvent) - Method in class ffx.ui.MainPanel
stateTime - Variable in class edu.rit.pj.cluster.BackendInfo: The time when the backend entered its current state (milliseconds since midnight 01-Jan-1970 GMT).
stateTime - Variable in class edu.rit.pj.cluster.JobInfo: The time when the job entered its current state (milliseconds since midnight 01-Jan-1970 GMT).
staticAnalysis(int, double) - Method in class ffx.algorithms.optimize.TorsionSearch: Static analysis of torsional bonds.
StatisticalEstimator - Interface in ffx.numerics.estimator: The StatisticalEstimator interface defines a free energy estimator in the most generic sense.
status - Variable in class ffx.algorithms.optimize.Minimize: The return status of the optimization.
status - Variable in class ffx.algorithms.optimize.PhMinimize: The return status of the optimization.
Status - Class in edu.rit.mp: Class Status provides the result of receiving a message in the Message Protocol (MP).
STATUS_200_OK - Enum constant in enum class edu.rit.http.HttpResponse.Status: The request has succeeded.
STATUS_201_CREATED - Enum constant in enum class edu.rit.http.HttpResponse.Status: The request has been fulfilled and resulted in a new resource being created.
STATUS_202_ACCEPTED - Enum constant in enum class edu.rit.http.HttpResponse.Status: The request has been accepted for processing, but the processing has not been completed.
STATUS_204_NO_CONTENT - Enum constant in enum class edu.rit.http.HttpResponse.Status: The server has fulfilled the request but there is no new information to send back.
STATUS_301_MOVED_PERMANENTLY - Enum constant in enum class edu.rit.http.HttpResponse.Status: The requested resource has been assigned a new permanent URL and any future references to this resource should be done using that URL.
STATUS_302_MOVED_TEMPORARILY - Enum constant in enum class edu.rit.http.HttpResponse.Status: The requested resource resides temporarily under a different URL.
STATUS_304_NOT_MODIFIED - Enum constant in enum class edu.rit.http.HttpResponse.Status: If the client has performed a conditional GET request and access is allowed, but the document has not been modified since the date and time specified in the If-Modified-Since field, the server must respond with this status code and not send an Entity-Body to the client.
STATUS_400_BAD_REQUEST - Enum constant in enum class edu.rit.http.HttpResponse.Status: The request could not be understood by the server due to malformed syntax.
STATUS_401_UNAUTHORIZED - Enum constant in enum class edu.rit.http.HttpResponse.Status: The request requires user authentication.
STATUS_403_FORBIDDEN - Enum constant in enum class edu.rit.http.HttpResponse.Status: The server understood the request, but is refusing to fulfill it.
STATUS_404_NOT_FOUND - Enum constant in enum class edu.rit.http.HttpResponse.Status: The server has not found anything matching the Request-URI.
STATUS_500_INTERNAL_SERVER_ERROR - Enum constant in enum class edu.rit.http.HttpResponse.Status: The server encountered an unexpected condition which prevented it from fulfilling the request.
STATUS_501_NOT_IMPLEMENTED - Enum constant in enum class edu.rit.http.HttpResponse.Status: The server does not support the functionality required to fulfill the request.
STATUS_502_BAD_GATEWAY - Enum constant in enum class edu.rit.http.HttpResponse.Status: The server, while acting as a gateway or proxy, received an invalid response from the upstream server it accessed in attempting to fulfill the request.
STATUS_503_SERVICE_UNAVAILABLE - Enum constant in enum class edu.rit.http.HttpResponse.Status: The server is currently unable to handle the request due to a temporary overloading or maintenance of the server.
STD_CONVERSION - Static variable in class ffx.algorithms.commands.test.Freefix
stderrAppendToFile(File) - Method in class edu.rit.pj.job.Job: Append this job's standard error to the end of the given file.
stderrToFile(File) - Method in class edu.rit.pj.job.Job: Store this job's standard error in the given file.
stderrToStdout() - Method in class edu.rit.pj.job.Job: Redirect this job's standard error to the same place as this job's standard output.
stdinFromFile(File) - Method in class edu.rit.pj.job.Job: Read this job's standard input from the given file.
Stdio - Class in edu.rit.io: Class Stdio provides standard I/O streams that can be redirected on a per-thread basis.
stdoutAppendToFile(File) - Method in class edu.rit.pj.job.Job: Append this job's standard output to the end of the given file.
stdoutToFile(File) - Method in class edu.rit.pj.job.Job: Store this job's standard output in the given file.
step - Variable in class ffx.ui.commands.SimulationUpdate
step(int) - Method in class ffx.openmm.BrownianIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.CompoundIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.CustomIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.drude.DrudeIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.drude.DrudeLangevinIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.drude.DrudeSCFIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.Integrator: Integrate the system forward in time by the specified number of time steps.
step(int) - Method in class ffx.openmm.LangevinMiddleIntegrator: Step the integrator.
step(int) - Method in class ffx.openmm.NoseHooverIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.VariableLangevinIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.VariableVerletIntegrator: Advance a simulation through time by taking a series of time steps.
step(int) - Method in class ffx.openmm.VerletIntegrator: Step the integrator.
stepTo(double) - Method in class ffx.openmm.VariableLangevinIntegrator: Advance the simulation by integrating until a specified time is reached.
stepTo(double) - Method in class ffx.openmm.VariableVerletIntegrator: Advance the simulation by integrating until a specified time is reached.
Stochastic - Class in ffx.algorithms.dynamics.integrators: Stochastic dynamics time step via a velocity Verlet integration algorithm.
Stochastic(double, SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.Stochastic: Constructor for Stochastic Dynamics.
STOCHASTIC - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
STOCHASTIC_MTS - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
stop() - Method in class edu.rit.util.Timer: Stop this timer.
stop() - Method in class ffx.ui.commands.FFXServer: stop
stop() - Method in class ffx.ui.MainPanel: stop
stop() - Method in class ffx.ui.Trajectory: stop
stopLoop() - Method in class edu.rit.pj.IntegerForLoop: Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.IntegerStrideForLoop: Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.LongForLoop: Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.LongStrideForLoop: Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.ParallelIteration: Stop this parallel iteration.
stopTime() - Method in class ffx.potential.terms.EnergyTerm: Stop the timer for the energy computation.
store(FFXSystem) - Method in class ffx.ui.KeywordPanel: Store the KeywordPanel's current keyword content into sys.
storeAllCoordinates(Residue[]) - Static method in class ffx.potential.bonded.ResidueState: storeAllCoordinates.
storeAllCoordinates(List<Residue>) - Static method in class ffx.potential.bonded.ResidueState: storeAllCoordinates.
storeAtomicCoordinates(Atom[]) - Static method in class ffx.potential.bonded.ResidueState: Returns a new double[nAtoms][3] with the coordinates of an array of atoms.
storeCoordinateArray() - Method in class ffx.potential.bonded.Residue: Returns the coordinates of all atoms in this Residue as a 2D array.
storeDistance(int, int, double) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix.NeighborDistances: Store a distance.
storePotential(String, int, int, int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Code to store an electrostatic potential element into an array.
storePotentialNeg(String, int, int, int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Code to store a negated electrostatic potential element into an array.
storeState() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Store the current state of the molecular dynamics simulation in a MDState record.
storeState() - Method in class ffx.algorithms.mc.BoltzmannMC: Store the state for reverting a move.
storeState() - Method in class ffx.algorithms.mc.MolecularMC: Store the state for reverting a move.
storeState() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMC
storeState() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Store the state for reverting a move.
storeState() - Method in class ffx.potential.bonded.MultiResidue: storeState.
storeState() - Method in class ffx.potential.bonded.Residue: storeState.
story - Variable in class ffx.ui.commands.SimulationDefinition
STRBND - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
strbndunit - Variable in class ffx.potential.parameters.StretchBendType
StreamFile - Class in edu.rit.pj.io: Class StreamFile represents a file that resides in the user's account in the job frontend process of a PJ cluster parallel program.
StreamFile(File) - Constructor for class edu.rit.pj.io.StreamFile: Construct a new stream file that refers to the given file in the frontend processor.
StretchBend - Class in ffx.potential.bonded: The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.
StretchBend(Angle) - Constructor for class ffx.potential.bonded.StretchBend: Constructor for the Stretch-Bend class.
stretchBendForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom Stretch-Bend Force
StretchBendForce - Class in ffx.potential.openmm: OpenMM Stretch-Bend Force.
StretchBendForce(StretchBendPotentialEnergy) - Constructor for class ffx.potential.openmm.StretchBendForce: Create an OpenMM Stretch-Bend Force.
StretchBendForce(StretchBendPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.StretchBendForce: Create an OpenMM Stretch-Bend Force for Dual Topology.
stretchBendForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Stetch-Bend Force for topology 2.
StretchBendPotentialEnergy - Class in ffx.potential.terms: Stretch-Bend potential energy term using StretchBend instances.
StretchBendPotentialEnergy(String) - Constructor for class ffx.potential.terms.StretchBendPotentialEnergy: Create a StretchBendPotentialEnergy with the provided name.
StretchBendPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.StretchBendPotentialEnergy: Create a StretchBendPotentialEnergy with the provided name and force group.
StretchBendPotentialEnergy(String, int, List<StretchBend>) - Constructor for class ffx.potential.terms.StretchBendPotentialEnergy: Create a StretchBendPotentialEnergy initialized with a list of stretch-bends and force group.
StretchBendPotentialEnergy(String, Collection<StretchBend>) - Constructor for class ffx.potential.terms.StretchBendPotentialEnergy: Create a StretchBendPotentialEnergy initialized with a collection of stretch-bends.
stretchBendTime - Static variable in class ffx.potential.bonded.MSGroup: Constant stretchBendTime=0
StretchBendType - Class in ffx.potential.parameters: The StretchBendType class defines one out-of-plane angle bending energy type.
StretchBendType(int[], double[]) - Constructor for class ffx.potential.parameters.StretchBendType: StretchBendType Constructor.
StretchTorsion - Class in ffx.potential.bonded: The StretchTorsion class represents a coupling between a torsional angle and the three bonds contained in the torsion, as defined in the 2017 AMOEBA nucleic acid force field.
stretchTorsionFactory(Torsion, ForceField) - Static method in class ffx.potential.bonded.StretchTorsion: Attempt to create a new StretchTorsion based on the supplied torsion.
stretchTorsionForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Stretch-Torsion Force.
StretchTorsionForce - Class in ffx.potential.openmm: OpenMM Stretch-Torsion Force.
StretchTorsionForce(StretchTorsionPotentialEnergy) - Constructor for class ffx.potential.openmm.StretchTorsionForce: Create an OpenMM Stretch-Torsion Force.
StretchTorsionForce(StretchTorsionPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.StretchTorsionForce: Create a Dual Topology OpenMM Stretch-Torsion Force.
stretchTorsionForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Stretch-Torsion Force for topology 2.
stretchTorsionForm() - Static method in class ffx.potential.bonded.StretchTorsion: Returns the mathematical form of a stretch-torsion as an OpenMM-parsable String.
StretchTorsionPotentialEnergy - Class in ffx.potential.terms: Stretch-Torsion potential energy term using StretchTorsion instances.
StretchTorsionPotentialEnergy(String) - Constructor for class ffx.potential.terms.StretchTorsionPotentialEnergy: Create a StretchTorsionPotentialEnergy with the provided name.
StretchTorsionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.StretchTorsionPotentialEnergy: Create a StretchTorsionPotentialEnergy with the provided name and force group.
StretchTorsionPotentialEnergy(String, int, List<StretchTorsion>) - Constructor for class ffx.potential.terms.StretchTorsionPotentialEnergy: Create a StretchTorsionPotentialEnergy initialized with a list of terms and force group.
StretchTorsionPotentialEnergy(String, Collection<StretchTorsion>) - Constructor for class ffx.potential.terms.StretchTorsionPotentialEnergy: Create a StretchTorsionPotentialEnergy initialized with a collection of terms.
stretchTorsionTime - Static variable in class ffx.potential.bonded.MSGroup: Constant stretchTorsionTime=0
StretchTorsionType - Class in ffx.potential.parameters: The StretchTorsionType class defines one stretch-torsion energy type.
StretchTorsionType(int[], double[]) - Constructor for class ffx.potential.parameters.StretchTorsionType: StretchTorsionType Constructor.
stride() - Method in class edu.rit.util.LongRange: Returns this range's stride.
stride() - Method in class edu.rit.util.Range: Returns this range's stride.
StringArray - Class in ffx.openmm: String Array.
StringArray(int) - Constructor for class ffx.openmm.StringArray: OpenMM String Array constructor.
StringArray(PointerByReference) - Constructor for class ffx.openmm.StringArray: OpenMM String Array constructor.
StringOutputStream - Class in ffx.utilities: StringOutputStream class.
StringOutputStream(ByteArrayOutputStream) - Constructor for class ffx.utilities.StringOutputStream: Constructor for StringOutputStream.
StringOutputStream(ByteArrayOutputStream, Charset) - Constructor for class ffx.utilities.StringOutputStream: Constructor for StringOutputStream.
StringUtils - Class in ffx.utilities: StringUtils class.
STRTORS - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
strTorUnit - Variable in class ffx.potential.parameters.StretchTorsionType: Unit conversion.
StructuralRefinement - Enum constant in enum class ffx.utilities.PropertyGroup: Refinement parameters.
STRUCTURE - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
StructureMetrics - Class in ffx.potential.utils: Structure Metrics contains functionality to calculate characteristics of coordinate systems.
StructureMetrics() - Constructor for class ffx.potential.utils.StructureMetrics
SturmMethod - Class in ffx.potential.bonded: SturmMethod class.
SturmMethod() - Constructor for class ffx.potential.bonded.SturmMethod: SturmMethod constructor with termination criteria for polynomial solver.
sub(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the difference between two vectors.
sub(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the difference between two vectors.
sub(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the difference between two vectors.
sub(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the difference between two vectors
sub(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray: Subtract a value from the double array at the specified index.
sub(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Subtract a value from the double array at the specified index.
sub(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray: Subtract a value from the double array at the specified index.
sub(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray: Subtract a value from the double array at the specified index.
sub(int, int, double, double, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Subtracts from the double arrays at the specified index the given values.
sub(int, int, Double3) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Subtracts from the double arrays at the specified index the given Double3.
sub(Double3) - Method in class ffx.numerics.math.Double3: Finds the difference between two vectors.
sub(Float3) - Method in class ffx.numerics.math.Float3: Finds the difference between two vectors.
sub(Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Subtracts v1 from this vector and places the result in this vector.
sub(Vector3d, Vector3d) - Method in class ffx.numerics.quickhull.Vector3d: Subtracts vector v1 from v2 and places the result in this vector.
subI(Double3) - Method in class ffx.numerics.math.Double3: Finds the difference between two vectors.
subI(Float3) - Method in class ffx.numerics.math.Float3: Finds the difference between two vectors.
subrange(int, int) - Method in class edu.rit.util.LongRange: Partition this range and return one subrange.
subrange(int, int) - Method in class edu.rit.util.Range: Partition this range and return one subrange.
subranges(int) - Method in class edu.rit.util.LongRange: Partition this range and return all the subranges.
subranges(int) - Method in class edu.rit.util.Range: Partition this range and return all the subranges.
subVec(DoubleVector[], DoubleVector[], DoubleVector[]) - Static method in class ffx.numerics.multipole.QIFrameSIMD: Subtract two vectors.
Success - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Successful line search.
sum - Variable in class ffx.numerics.math.BootStrapStatistics: The sum of all values.
sum - Variable in class ffx.numerics.math.SummaryStatistics: Sum of observations.
SUM - Static variable in class edu.rit.pj.reduction.ByteOp: The byte sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.DoubleOp: The double sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.FloatOp: The float sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.IntegerOp: The integer sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.LongOp: The long sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.ShortOp: The short sum binary operation.
SummaryStatistics - Class in ffx.numerics.math: The SummaryStatistics class uses online, stable algorithms to calculate summary statistics from double arrays/lists, including mean, variance, standard deviation, max, min, sum, and count.
SummaryStatistics(double[]) - Constructor for class ffx.numerics.math.SummaryStatistics: Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], double[], int, int, int) - Constructor for class ffx.numerics.math.SummaryStatistics: Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], int) - Constructor for class ffx.numerics.math.SummaryStatistics: Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], int, int) - Constructor for class ffx.numerics.math.SummaryStatistics: Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], int, int, int) - Constructor for class ffx.numerics.math.SummaryStatistics: Constructs a static summary of a statistic from provided values.
SummaryStatistics(RunningStatistics) - Constructor for class ffx.numerics.math.SummaryStatistics: Builds a static view of a running statistic.
sumWeights - Variable in class ffx.numerics.math.BootStrapStatistics: The sum of all weights.
sumWeights - Variable in class ffx.numerics.math.SummaryStatistics: Sum of weights.
superpose(double[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: This method completes the following superposition operations and returns an RMSD: 1) translates the x1 coordinates to the origin. 2) translates the x2 coordinates to the origin. 3) rotates x2 onto x1. 4) computes and return the RMSD.
Superpose - Class in ffx.algorithms.commands: The Superpose script superposes molecules in an arc/multiple model pdb file (all versus all or one versus all) or in two pdb/xyz files.
Superpose - Class in ffx.potential.utils
Superpose() - Constructor for class ffx.algorithms.commands.Superpose: Superpose Constructor.
Superpose(SystemFilter, SystemFilter, boolean) - Constructor for class ffx.potential.utils.Superpose
Superpose(FFXBinding) - Constructor for class ffx.algorithms.commands.Superpose: Superpose Constructor.
Superpose(String[]) - Constructor for class ffx.algorithms.commands.Superpose: Superpose constructor that sets the command line arguments.
SuperposeCrystals - Class in ffx.algorithms.commands
SuperposeCrystals() - Constructor for class ffx.algorithms.commands.SuperposeCrystals
SuperposeCrystals(FFXBinding) - Constructor for class ffx.algorithms.commands.SuperposeCrystals
SuperposeCrystals(String[]) - Constructor for class ffx.algorithms.commands.SuperposeCrystals
supportsDoublePrecision() - Method in class ffx.openmm.Platform: Determine whether this Platform supports double precision arithmetic.
supportsKernels(StringArray) - Method in class ffx.openmm.Platform: Determine whether this Platform supports a specified set of kernels.
supportsPlatform(Platform) - Method in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine: Checks if this energy Platform is supported by this DynamicsEngine
SurfaceAreaRegion - Class in ffx.potential.nonbonded.implicit: SurfaceAreaRegion performs an analytical computation of the weighted solvent accessible surface area of each atom and the first derivatives of the area with respect to Cartesian coordinates
SurfaceAreaRegion(Atom[], double[], double[], double[], boolean[], int[][][], AtomicDoubleArray3D, int, double, double) - Constructor for class ffx.potential.nonbonded.implicit.SurfaceAreaRegion: This class is a port of the Cavitation code in TINKER.
surfaceTension - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion: Cavitation surface tension coefficient (kcal/mol/A^2).
swap(byte[], int, int) - Method in class edu.rit.util.Sorting.Byte: Swap two elements in the given array.
swap(char[], int, int) - Method in class edu.rit.util.Sorting.Character: Swap two elements in the given array.
swap(double) - Static method in class ffx.utilities.ByteSwap: Byte swap a single double value.
swap(double[]) - Static method in class ffx.utilities.ByteSwap: Byte swap an array of doubles.
swap(double[], int, int) - Method in class edu.rit.util.Sorting.Double: Swap two elements in the given array.
swap(float) - Static method in class ffx.utilities.ByteSwap: Byte swap a single float value.
swap(float[]) - Static method in class ffx.utilities.ByteSwap: Byte swap an array of floats.
swap(float[], int, int) - Method in class edu.rit.util.Sorting.Float: Swap two elements in the given array.
swap(int) - Static method in class ffx.utilities.ByteSwap: Byte swap a single int value.
swap(int[]) - Static method in class ffx.utilities.ByteSwap: Byte swap an array of ints.
swap(int[], int, int) - Method in class edu.rit.util.Sorting.Integer: Swap two elements in the given array.
swap(long) - Static method in class ffx.utilities.ByteSwap: Byte swap a single long value.
swap(long[]) - Static method in class ffx.utilities.ByteSwap: Byte swap an array of longs.
swap(long[], int, int) - Method in class edu.rit.util.Sorting.Long: Swap two elements in the given array.
swap(short) - Static method in class ffx.utilities.ByteSwap: Byte swap a single short value.
swap(short[]) - Static method in class ffx.utilities.ByteSwap: Byte swap an array of shorts.
swap(short[], int, int) - Method in class edu.rit.util.Sorting.Short: Swap two elements in the given array.
swap(T[], int, int) - Method in class edu.rit.util.Sorting.Object: Swap two elements in the given array.
SwingWorker - Class in ffx.ui: This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class ffx.ui.SwingWorker: Start a thread that will call the construct method and then exit.
switchHistogram(int) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Switch to an alternate Histogram.
sx - Variable in class ffx.numerics.multipole.PolarizableMultipole: Averaged induced dipole + induced dipole chain-rule x-component: sx = 0.5 * (ux + px).
sx - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Averaged induced dipole + induced dipole chain-rule x-component: sx = 0.5 * (ux + px).
sy - Variable in class ffx.numerics.multipole.PolarizableMultipole: Averaged induced dipole + induced dipole chain-rule y-component: sy = 0.5 * (uy + py).
sy - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Averaged induced dipole + induced dipole chain-rule y-component: sy = 0.5 * (uy + py).
symmetricToUnity() - Method in class ffx.numerics.switching.BellCurveSwitch: True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.CompositeSwitch
symmetricToUnity() - Method in class ffx.numerics.switching.ConstantSwitch: True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.LinearDerivativeSwitch: True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.MultiplicativeSwitch: True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.PowerSwitch: True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.SquaredTrigSwitch: True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
SymOp - Class in ffx.crystal: The SymOp class defines the rotation and translation of a single symmetry operator.
SymOp(double[][]) - Constructor for class ffx.crystal.SymOp: The SymOp constructor using a 4x4 matrix.
SymOp(double[][], double[]) - Constructor for class ffx.crystal.SymOp: The SymOp constructor using a rotation matrix and translation vector.
SymOp(double[][], double[], int[]) - Constructor for class ffx.crystal.SymOp: The SymOp constructor using a rotation matrix and translation vector.
symOps - Variable in class ffx.crystal.SpaceGroup: A List of SymOp instances.
symOpsA - Variable in class ffx.algorithms.commands.SuperposeCrystals
symOpsB - Variable in class ffx.algorithms.commands.SuperposeCrystals
symPhaseShift(double[]) - Method in class ffx.crystal.SymOp: symPhaseShift
symPhaseShift(HKL) - Method in class ffx.crystal.SymOp: symPhaseShift
symVec6Mat3(double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath: vector representation of a symmetric 3x3 matrix times a matrix
symVec6Mat3(double[], double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: symVec6mat3
sysAbs() - Method in class ffx.crystal.HKL: Is this reflection a systematic absence?
System - Class in ffx.openmm: This class represents a molecular system.
System() - Constructor for class ffx.openmm.System: Constructor.
System(PointerByReference) - Constructor for class ffx.openmm.System: Constructor.
SYSTEM - Static variable in class ffx.ui.commands.SimulationMessage: Constant SYSTEM=0
SYSTEMBELOWMOUSE - Enum constant in enum class ffx.ui.GraphicsCanvas.MouseMode
SystemFilter - Class in ffx.potential.parsers: The SystemFilter class is the base class for most Force Field X file parsers.
SystemFilter(File, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.SystemFilter: Constructor for SystemFilter.
SystemFilter(File, List<MolecularAssembly>, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.SystemFilter: Constructor for SystemFilter.
SystemFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.SystemFilter: Constructor for SystemFilter.
SystemFilter.Versioning - Enum Class in ffx.potential.parsers
systems - Variable in class ffx.potential.parsers.SystemFilter: All MolecularAssembly instances defined.
SystemState - Class in ffx.potential: The current state of the molecular dynamics simulation.
SystemState(int) - Constructor for class ffx.potential.SystemState: Constructor for MDState.
sz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Averaged induced dipole + induced dipole chain-rule z-component: sz = 0.5 * (uz + pz).
sz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Averaged induced dipole + induced dipole chain-rule z-component: sz = 0.5 * (uz + pz).

T

t - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
T - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
T - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
t000 - Variable in class ffx.numerics.multipole.MultipoleTensor: No derivatives.
t000 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: No derivatives.
t000 - Static variable in class ffx.potential.parameters.MultipoleType: Constant chrg=t000
T000 - Variable in class ffx.numerics.multipole.MultipoleTensor: Store the auxiliary tensor memory to avoid memory consumption.
t001 - Variable in class ffx.numerics.multipole.MultipoleTensor: First derivative with respect to z.
t001 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: First derivative with respect to z.
t001 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t001=3
t002 - Variable in class ffx.numerics.multipole.MultipoleTensor: Second derivative with respect to z.
t002 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Second derivative with respect to z.
t002 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t002=6
t003 - Variable in class ffx.numerics.multipole.MultipoleTensor: Third derivative with respect to z.
t003 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Third derivative with respect to z.
t003 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t003=12
t004 - Variable in class ffx.numerics.multipole.MultipoleTensor: Fourth derivative with respect to z.
t004 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Fourth derivative with respect to z.
t005 - Variable in class ffx.numerics.multipole.MultipoleTensor: Fifth derivative with respect to z.
t005 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Fifth derivative with respect to z.
t006 - Variable in class ffx.numerics.multipole.MultipoleTensor: Sixth derivative with respect to z.
t006 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Sixth derivative with respect to z.
t010 - Variable in class ffx.numerics.multipole.MultipoleTensor: First derivative with respect to y.
t010 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: First derivative with respect to y.
t010 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t010=2
t011 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t011 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t011 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t011=9
t012 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t012 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t012 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t012=18
t013 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t013 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t014 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t014 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t015 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t015 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t020 - Variable in class ffx.numerics.multipole.MultipoleTensor: Second derivative with respect to y.
t020 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Second derivative with respect to y.
t020 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t020=5
t021 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t021 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t021 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t021=16
t022 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t022 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t023 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t023 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t024 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t024 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t030 - Variable in class ffx.numerics.multipole.MultipoleTensor: Third derivative with respect to y.
t030 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Third derivative with respect to y.
t030 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t030=11
t031 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t031 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t032 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t032 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t033 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t033 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t040 - Variable in class ffx.numerics.multipole.MultipoleTensor: Fourth derivative with respect to y.
t040 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Fourth derivative with respect to y.
t041 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t041 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t042 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t042 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t050 - Variable in class ffx.numerics.multipole.MultipoleTensor: Fifth derivative with respect to y.
t050 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Fifth derivative with respect to y.
t051 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to y and z.
t051 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to y and z.
t060 - Variable in class ffx.numerics.multipole.MultipoleTensor: Sixth derivative with respect to y.
t060 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Sixth derivative with respect to y.
t100 - Variable in class ffx.numerics.multipole.MultipoleTensor: First derivative with respect to x.
t100 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: First derivative with respect to x.
t100 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t100=1
t101 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t101 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t101 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t101=8
t102 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t102 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t102 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t102=17
t103 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t103 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t104 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t104 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t105 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t105 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t110 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t110 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t110 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t110=7
t111 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t111 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t111 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t111=19
t112 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t112 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t113 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t113 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t114 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t114 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t120 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t120 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t120 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t120=15
t121 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t121 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t122 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t122 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t123 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t123 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t130 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t130 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t131 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t131 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t132 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t132 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t140 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t140 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t141 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t141 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t150 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t150 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t200 - Variable in class ffx.numerics.multipole.MultipoleTensor: Second derivative with respect to x.
t200 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Second derivative with respect to x.
t200 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t200=4
t201 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t201 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t201 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t201=14
t202 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t202 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t203 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t203 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t204 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t204 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t210 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t210 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t210 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t210=13
t211 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t211 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t212 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t212 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t213 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t213 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t220 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t220 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t221 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t221 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t222 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t222 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t230 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t230 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t231 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t231 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t240 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t240 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t300 - Variable in class ffx.numerics.multipole.MultipoleTensor: Third derivative with respect to x.
t300 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Third derivative with respect to x.
t300 - Static variable in class ffx.potential.parameters.MultipoleType: Constant t300=10
t301 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t301 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t302 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t302 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t303 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t303 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t310 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t310 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t311 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t311 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t312 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t312 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t320 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t320 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t321 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t321 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t330 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t330 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t400 - Variable in class ffx.numerics.multipole.MultipoleTensor: Fourth derivative with respect to x.
t400 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Fourth derivative with respect to x.
t401 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t401 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t402 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t402 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t410 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t410 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t411 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x, y and z.
t411 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x, y and z.
t420 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t420 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t500 - Variable in class ffx.numerics.multipole.MultipoleTensor: Fifth derivative with respect to x.
t500 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Fifth derivative with respect to x.
t501 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and z.
t501 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and z.
t510 - Variable in class ffx.numerics.multipole.MultipoleTensor: Derivatives with respect to x and y.
t510 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Derivatives with respect to x and y.
t600 - Variable in class ffx.numerics.multipole.MultipoleTensor: Sixth derivative with respect to x.
t600 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Sixth derivative with respect to x.
Ta - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
TabulatedFunction - Class in ffx.openmm: A TabulatedFunction uses a set of tabulated values to define a mathematical function.
TabulatedFunction(PointerByReference) - Constructor for class ffx.openmm.TabulatedFunction: Constructor for TabulatedFunction.
tag - Variable in class edu.rit.mp.Status: The tag from the message that was received.
tag - Variable in class edu.rit.pj.CommStatus: The tag from the message that was received.
tagOffset() - Method in class edu.rit.pj.WorkerIntegerForLoop: Returns the tag offset for this worker for loop.
tagOffset() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Returns the tag offset for this worker for loop.
tagOffset() - Method in class edu.rit.pj.WorkerIteration: Returns the tag offset for this worker for loop.
tagOffset() - Method in class edu.rit.pj.WorkerLongForLoop: Returns the tag offset for this worker for loop.
tagOffset() - Method in class edu.rit.pj.WorkerLongStrideForLoop: Returns the tag offset for this worker for loop.
tail() - Method in class ffx.numerics.quickhull.HalfEdge: Returns the tail vertex associated with this half-edge.
tan() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the complex tangent of this.
tanhRescaling(double, double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling: Rescale the Born radius integral to account for interstitial spaces.
tanhRescalingChainRule(double, double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling: The chain rule derivative for rescaling the Born radius integral to account for interstitial spaces.
taper(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: Value of the switching function at r.
taper(double, double, double, double, double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: Value of the switching function at r.
target(double[], double[], boolean, boolean) - Method in class ffx.xray.ScaleBulkEnergy: target
target(double[], double[], boolean, boolean) - Method in class ffx.xray.SigmaAEnergy: target
target(double[], double[], boolean, boolean) - Method in class ffx.xray.SplineEnergy: target
tautomerDirections - Variable in class ffx.potential.extended.ExtendedSystem: Array of ints that is initialized to match the number of atoms in the molecular assembly. 1 indicates that the tautomer lambda direction is normal
Tb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Tc - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
tcpPortValid(int) - Static method in class ffx.utilities.PortUtils: Check if an int matches a valid TCP port (i.e. is a 16-bit unsigned integer).
Te - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
team() - Method in class edu.rit.pj.ParallelConstruct: Returns the parallel team that is executing this parallel construct.
team() - Method in class edu.rit.pj.WorkerConstruct: Returns the worker team that is executing this worker construct.
temperature - Variable in class ffx.ui.commands.SimulationUpdate
temperature() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the temperature record component.
temperatures - Variable in class ffx.numerics.estimator.SequentialEstimator: The temperatures at which the samples were collected.
tensorCount(int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Returns the number of tensors for derivatives to the given order.
term(int, int, int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Convenience method for writing out intermediate terms in the recursion.
term(int, int, int, int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: Convenience method for writing out intermediate terms in the recursion.
Terminatable - Interface in ffx.algorithms: Algorithms that can be gracefully terminated early should implement this interface.
terminate - Variable in class ffx.algorithms.optimize.Minimize: A flag to indicate the algorithm should be terminated.
terminate - Variable in class ffx.algorithms.optimize.PhMinimize: A flag to indicate the algorithm should be terminated.
terminate() - Method in class ffx.algorithms.dynamics.MolecularDynamics: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.algorithms.dynamics.PhReplicaExchange: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.algorithms.dynamics.ReplicaExchange: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.algorithms.optimize.Minimize: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.algorithms.optimize.PhMinimize: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.algorithms.optimize.RotamerOptimization: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in interface ffx.algorithms.Terminatable: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.xray.RefinementMinimize: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.xray.ScaleBulkMinimize: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.xray.SigmaAMinimize: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminate() - Method in class ffx.xray.SplineMinimize: This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.
terminateJobFinished(int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Terminate this Non-PJ Job Frontend immediately, sending a "job finished" message to the Job Scheduler.
terms - Variable in class ffx.potential.parameters.TorsionType: Number of terms in the Fourier series.
testGradient(GradientOptions) - Method in class ffx.potential.utils.GradientUtils: Test the gradient of the Potential.
testMBARMethods() - Static method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio: Test all MBAR methods individually with a simple Harmonic Oscillator test case with an excess of samples.
testResidueTypes(Residue) - Method in class ffx.potential.parameters.TitrationUtils
TETRAGONAL - Enum constant in enum class ffx.crystal.CrystalSystem: Tetragonal crystal system.
TETRAGONAL_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem: Tetragonal lattice system.
TEXTFIELD - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
Th - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Thermodynamics - Class in ffx.algorithms.commands: The Thermodynamics script uses the Transition-Tempered Orthogonal Space Random Walk algorithm to estimate a free energy.
Thermodynamics() - Constructor for class ffx.algorithms.commands.Thermodynamics: Thermodynamics Constructor.
Thermodynamics(FFXBinding) - Constructor for class ffx.algorithms.commands.Thermodynamics: Thermodynamics Constructor.
Thermodynamics(String[]) - Constructor for class ffx.algorithms.commands.Thermodynamics: Thermodynamics constructor that sets the command line arguments.
thermodynamicsOptions - Variable in class ffx.algorithms.commands.Thermodynamics
ThermodynamicsOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that calculate thermodynamics.
ThermodynamicsOptions() - Constructor for class ffx.algorithms.cli.ThermodynamicsOptions
ThermodynamicsOptions.ThermodynamicsAlgorithm - Enum Class in ffx.algorithms.cli: Represents categories of thermodynamics algorithms that must be handled differently.
thermostat - Variable in class ffx.algorithms.cli.DynamicsOptions: Thermostat.
thermostat - Variable in class ffx.xray.RefinementEnergy: A thermostat instance.
Thermostat - Class in ffx.algorithms.dynamics.thermostats: The abstract Thermostat class implements methods common to all thermostats for initializing velocities from a Maxwell-Boltzmann distribution and computing the instantaneous temperature.
Thermostat(SystemState, Potential.VARIABLE_TYPE[], double) - Constructor for class ffx.algorithms.dynamics.thermostats.Thermostat: Constructor for Thermostat.
Thermostat(SystemState, Potential.VARIABLE_TYPE[], double, List<Constraint>) - Constructor for class ffx.algorithms.dynamics.thermostats.Thermostat
ThermostatEnum - Enum Class in ffx.algorithms.dynamics.thermostats: An enumeration of available Thermostats.
theta - Variable in class ffx.algorithms.mc.RosenbluthChi0Move: The value of theta.
theta - Variable in class ffx.algorithms.optimize.PhMinimize: Current value of each Extended System variable.
thole - Variable in class ffx.potential.parameters.PolarizeType: Thole damping factor.
THOLE_DIRECT_FIELD - Enum constant in enum class ffx.numerics.multipole.Operator: IndDipole-Mpole Interaction for Amoeba+
THOLE_FIELD - Enum constant in enum class ffx.numerics.multipole.Operator: Thole field operator.
tholeSource(double, double, double, boolean, double[]) - Static method in class ffx.numerics.multipole.TholeTensorGlobal: Generate source terms for the Challacombe et al. recursion.
tholeSource(DoubleVector, DoubleVector, DoubleVector, DoubleVector[]) - Static method in class ffx.numerics.multipole.TholeTensorGlobalSIMD: Generate source terms for the Challacombe et al. recursion.
TholeTensorGlobal - Class in ffx.numerics.multipole: The TholeTensorGlobal class computes derivatives of Thole damping via recursion to order <= 4 for Cartesian multipoles in either a global frame.
TholeTensorGlobal(int, double, double) - Constructor for class ffx.numerics.multipole.TholeTensorGlobal: Constructor for EwaldMultipoleTensorGlobal.
TholeTensorGlobal(int, double, double, boolean) - Constructor for class ffx.numerics.multipole.TholeTensorGlobal
TholeTensorGlobalSIMD - Class in ffx.numerics.multipole: The TholeTensorGlobal class computes derivatives of Thole damping via recursion to order <= 4 for Cartesian multipoles in either a global frame.
TholeTensorGlobalSIMD(int, DoubleVector, DoubleVector) - Constructor for class ffx.numerics.multipole.TholeTensorGlobalSIMD: Constructor for EwaldMultipoleTensorGlobal.
TholeTensorQI - Class in ffx.numerics.multipole: The TholeTensorQI class computes derivatives of Thole damping via recursion to order <= 4 for Cartesian multipoles in a quasi-internal frame.
TholeTensorQI(int, double, double) - Constructor for class ffx.numerics.multipole.TholeTensorQI: Constructor for TholeTensorQI.
TholeTensorQISIMD - Class in ffx.numerics.multipole: The TholeTensorQI class computes derivatives of Thole damping via recursion to order <= 4 for Cartesian multipoles in a quasi-internal frame.
TholeTensorQISIMD(int, DoubleVector, DoubleVector) - Constructor for class ffx.numerics.multipole.TholeTensorQISIMD: Constructor for TholeTensorQI.
THR - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ThreeBodyEnergyRegion - Class in ffx.algorithms.optimize.manybody: Compute 3-Body energy values in parallel across nodes.
ThreeBodyEnergyRegion(RotamerOptimization, DistanceMatrix, EnergyExpansion, EliminatedRotamers, Residue[], List<Residue>, BufferedWriter, Comm, int, double, boolean, int, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
THREEFOLD - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
ThreeParticleAverageSite - Class in ffx.openmm: This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations.
ThreeParticleAverageSite(int, int, int, double, double, double) - Constructor for class ffx.openmm.ThreeParticleAverageSite: Create a new ThreeParticleAverageSite virtual site.
THREONINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
THY - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
THYMINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
ti(int, int, int) - Method in class ffx.numerics.multipole.MultipoleTensor: The index is based on the idea of filling tetrahedron.
ti(int, int, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD: The index is based on the idea of filling tetrahedron.
ti(int, int, int, int) - Static method in class ffx.numerics.multipole.MultipoleUtilities: The index is based on the idea of filling tetrahedron.
Ti - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
time - Variable in class ffx.algorithms.optimize.Minimize: Minimization time in nanoseconds.
time - Variable in class ffx.algorithms.optimize.PhMinimize: Minimization time in nanoseconds.
time - Variable in class ffx.ui.commands.SimulationUpdate
time() - Method in class ffx.algorithms.AlgorithmUtils: Logs time elapsed since last call.
time() - Method in interface ffx.potential.utils.PotentialsFunctions: Logs time elapsed since last call.
time() - Method in class ffx.potential.utils.PotentialsUtils: Logs time elapsed since last call.
time() - Method in class ffx.ui.ModelingShell: time
time() - Method in class ffx.ui.UIUtils
Timer - Class in edu.rit.util: Class Timer controls the execution of a TimerTask's timed actions.
Timer - Class in ffx.potential.commands: The Timer command evaluates the wall clock time for energy and forces.
Timer - Class in ffx.xray.commands: The X-ray Timer script.
Timer() - Constructor for class ffx.potential.commands.Timer
Timer() - Constructor for class ffx.xray.commands.Timer: Timer constructor.
Timer(FFXBinding) - Constructor for class ffx.potential.commands.Timer
Timer(FFXBinding) - Constructor for class ffx.xray.commands.Timer: Timer constructor.
Timer(String[]) - Constructor for class ffx.potential.commands.Timer
Timer(String[]) - Constructor for class ffx.xray.commands.Timer: Timer constructor that sets the command line arguments.
TimerOptions - Class in ffx.potential.cli: Represents command line options for scripts that perform timings for energy and optionally gradients.
TimerOptions() - Constructor for class ffx.potential.cli.TimerOptions
TimerTask - Interface in edu.rit.util: Interface TimerTask specifies the interface for an object that performs timed actions under the control of a Timer.
TimerThread - Class in edu.rit.util: Class TimerThread encapsulates a thread that does the timing for Timers and performs TimerTasks' actions when timeouts occur.
TimerThread() - Constructor for class edu.rit.util.TimerThread: Construct a new timer thread.
times(double) - Method in class ffx.numerics.math.ComplexNumber: Return a new object whose value is (this * alpha).
times(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is (this * b).
timesIP(double) - Method in class ffx.numerics.math.ComplexNumber: timesIP
timesIP(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: timesIP
timings() - Method in class ffx.xray.DiffractionData: Perform 10 Fc calculations for the purposes of timings.
timingString() - Method in class ffx.numerics.fft.Complex3DParallel: Get the timing string.
TINKER - Enum constant in enum class ffx.potential.parsers.SystemFilter.Versioning
TinkerUtils - Class in ffx.utilities: A collection of Utility methods for compatibility with Tinker.
title - Static variable in class ffx.ui.MainPanel: Constant
TitrationManyBody - Class in ffx.algorithms.optimize
TitrationManyBody(String, ForceField, List<Integer>, double) - Constructor for class ffx.algorithms.optimize.TitrationManyBody
TitrationManyBody(String, ForceField, List<Integer>, double, ManyBodyOptions) - Constructor for class ffx.algorithms.optimize.TitrationManyBody
TitrationUtils - Class in ffx.potential.parameters: Utilities for interpolating between Amino Acid protonation and tautomer states.
TitrationUtils(ForceField) - Constructor for class ffx.potential.parameters.TitrationUtils
TitrationUtils(ForceField, double, boolean) - Constructor for class ffx.potential.parameters.TitrationUtils
TitrationUtils.CysStates - Enum Class in ffx.potential.parameters
TitrationUtils.CysteineAtomNames - Enum Class in ffx.potential.parameters: Constant CysteineAtoms
TitrationUtils.HisStates - Enum Class in ffx.potential.parameters
TitrationUtils.HistidineAtomNames - Enum Class in ffx.potential.parameters: Constant HistidineAtoms
TitrationUtils.LysineAtomNames - Enum Class in ffx.potential.parameters: Constant lysineAtoms
TitrationUtils.LysStates - Enum Class in ffx.potential.parameters
TitrationUtils.Titration - Enum Class in ffx.potential.parameters: Amino acid protonation reactions.
Tl - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Tlmnj(int, int, int, int, double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: This routine implements the recurrence relations for computation of any Cartesian multipole tensor in ~O(L^8) time, where L is the total order l + m + n, given the auxiliary elements T0000.
Tlmnj(int, int, int, int, double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This routine implements the recurrence relations for computation of any Cartesian multipole tensor in ~O(L^8) time, where L is the total order l + m + n, given the auxiliary elements T0000.
Tlmnj(int, int, int, int, double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: This routine implements the recurrence relations for computation of any Cartesian multipole tensor in ~O(L^8) time, where L is the total order l + m + n, given the auxiliary elements T0000.
Tm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
toAngleString() - Method in class ffx.potential.bonded.Rotamer: toAngleString.
toArchiveExtension(String) - Static method in class ffx.potential.cli.WriteoutOptions
toByte(String) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to a byte value.
toByteArray() - Method in class edu.rit.util.ByteSequence: Obtain a byte array with a copy of this byte sequence's contents.
toByteArray(String) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to a sequence of bytes stored in a new byte array.
toByteArray(String, byte[]) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to a sequence of bytes stored in the given byte array.
toByteArray(String, byte[], int, int) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to a sequence of bytes stored in a portion of the given byte array.
toCartesianCoordinates(double[], double[]) - Method in class ffx.crystal.Crystal: toCartesianCoordinates
toCartesianCoordinates(int, double[], double[]) - Method in class ffx.crystal.Crystal: toCartesianCoordinates
toCartesianCoordinates(int, double[], double[], double[], double[], double[], double[]) - Method in class ffx.crystal.Crystal: toCartesianCoordinates
toChar(String) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to a char value.
toConsole(int) - Method in class ffx.numerics.clustering.Cluster: Prints this cluster and its subtree to the console with indentation.
toCRYST1() - Method in class ffx.crystal.Crystal: Return a CRYST1 record useful for writing a PDB file.
toDistanceMatrixString(double[][]) - Static method in class ffx.potential.parsers.DistanceMatrixFilter: Convert a distance matrix to a String.
toDistanceMatrixString(List<double[]>) - Static method in class ffx.potential.parsers.DistanceMatrixFilter: Convert a distance matrix to a String.
toEnumForm(String) - Static method in class ffx.potential.parameters.ForceField: Enums are uppercase with underscores, but property files use lower case with dashes.
toFFString() - Method in class ffx.ui.FFXSystem: toFFString
toFileString() - Method in class ffx.ui.FFXSystem: toFileString
toFormattedString(boolean, boolean) - Method in class ffx.potential.bonded.Residue: Formats this residue with some optional inclusions.
toFractionalCoordinates(double[], double[]) - Method in class ffx.crystal.Crystal: toFractionalCoordinates
toFractionalCoordinates(int, double[], double[]) - Method in class ffx.crystal.Crystal: toFractionalCoordinates
toFractionalCoordinates(int, double[], double[], double[], double[], double[], double[]) - Method in class ffx.crystal.Crystal: toFractionalCoordinates
toFractionalDipole(double[], double[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: Convert a dipole in the global frame into a factional dipole.
toggleFullScreen() - Method in class ffx.ui.GraphicsFullScreen: toggleFullScreen
toggleSelections(ArrayList<MSNode>) - Method in class ffx.ui.Hierarchy: toggleSelections
toggleSystemShowing() - Method in class ffx.ui.MainMenu: toggleSystemShowing
toGlobal(double[]) - Method in class ffx.numerics.multipole.QIFrame: Rotate a vector in the QI frame into the global frame.
toGlobal(DoubleVector[]) - Method in class ffx.numerics.multipole.QIFrameSIMD: Rotate a vector in the QI frame into the global frame.
toInt(String) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to an int value.
tolerance - Variable in class ffx.numerics.quickhull.QuickHull3D
toLong(String) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to a long value.
toMathematicalForm() - Method in enum class ffx.potential.parameters.BondType.BondFunction: Returns the form of this bond as a mathematical expression parsable by OpenMM.
toNewickString(int) - Method in class ffx.numerics.clustering.Cluster: Serializes this cluster subtree into a simple Newick-like string.
toPDBAtomLine(Atom) - Static method in class ffx.potential.parsers.PDBFilter: Simple method useful for converting files to PDB format.
toPDBString() - Method in class ffx.potential.terms.AnglePotentialEnergy
toPDBString() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.BondPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.EnergyTerm: Get a PDB-style REMARK representation of this energy term.
toPDBString() - Method in class ffx.potential.terms.EnergyTermRegion: String representation for PDB Headers
toPDBString() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy
toPDBString() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.StretchBendPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.TorsionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy
toPDBString() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy
topologies - Variable in class ffx.algorithms.commands.Thermodynamics
topologyOptions - Variable in class ffx.algorithms.commands.Thermodynamics
TopologyOptions - Class in ffx.potential.cli: Represents command line options for scripts that utilize multiple physical topologies.
TopologyOptions() - Constructor for class ffx.potential.cli.TopologyOptions
toPrimaryCell(double[], double[]) - Method in class ffx.crystal.Crystal: toPrimaryCell
toPropertyForm(String) - Static method in class ffx.potential.parameters.ForceField: Enums are uppercase with underscores, but property files use lower case with dashes.
toRealSpaceEnergy(List<String>, MolecularAssembly[]) - Method in class ffx.realspace.cli.RealSpaceOptions: Process input from opened molecular assemblies to a RefinementEnergy
TornadoDFT - Class in ffx.numerics.fft: Proof-of-concept use of the TornadoVM for parallelization of Java code.
TornadoDFT(int) - Constructor for class ffx.numerics.fft.TornadoDFT: Constructor.
torque(int, int, double[], int[], double[][]) - Method in class ffx.potential.nonbonded.pme.Torque
Torque - Class in ffx.potential.nonbonded.pme: The torque values on a single site defined by a local coordinate frame are converted to Cartesian forces on the original site and sites specifying the local frame.
Torque() - Constructor for class ffx.potential.nonbonded.pme.Torque
Torsion - Class in ffx.potential.bonded: The Torsion class represents a torsional angle formed between four bonded atoms.
Torsion(Bond, Bond, Bond) - Constructor for class ffx.potential.bonded.Torsion: Create a Torsion from 3 connected bonds (no error checking)
TORSION - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
torsionForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM AMOEBA Torsion Force.
TorsionForce - Class in ffx.potential.openmm: Torsion Force.
TorsionForce(TorsionPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.TorsionForce: Torsion Force constructor for Dual Topology.
TorsionForce(TorsionPotentialEnergy, OpenMMEnergy) - Constructor for class ffx.potential.openmm.TorsionForce: Torsion Force constructor.
torsionForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Torsion Force for topology 2.
TorsionPotentialEnergy - Class in ffx.potential.terms: Torsion potential energy term using Torsion instances.
TorsionPotentialEnergy(String) - Constructor for class ffx.potential.terms.TorsionPotentialEnergy: Create a TorsionPotentialEnergy with the provided name.
TorsionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.TorsionPotentialEnergy: Create a TorsionPotentialEnergy with the provided name and force group.
TorsionPotentialEnergy(String, int, List<Torsion>) - Constructor for class ffx.potential.terms.TorsionPotentialEnergy: Create a TorsionPotentialEnergy initialized with a list of torsions and force group.
TorsionPotentialEnergy(String, Collection<Torsion>) - Constructor for class ffx.potential.terms.TorsionPotentialEnergy: Create a TorsionPotentialEnergy initialized with a collection of torsions.
torsions - Variable in class ffx.potential.bonded.TorsionTorsion: The two torsions that are coupled.
TorsionScan - Class in ffx.algorithms.commands: The TorsionSearch command enumerates conformations of a molecule using torsional scans around rotatable bonds.
TorsionScan() - Constructor for class ffx.algorithms.commands.TorsionScan
TorsionScan(FFXBinding) - Constructor for class ffx.algorithms.commands.TorsionScan
TorsionScan(String[]) - Constructor for class ffx.algorithms.commands.TorsionScan
TorsionSearch - Class in ffx.algorithms.optimize: TorsionSearch class for performing a torsion scan on a molecule in a molecular assembly.
TorsionSearch(MolecularAssembly, Molecule, int, int) - Constructor for class ffx.algorithms.optimize.TorsionSearch
torsionTime - Static variable in class ffx.potential.bonded.MSGroup: Constant torsionTime=0
TorsionTorsion - Class in ffx.potential.bonded: The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.
TorsionTorsion(Bond, Angle, Bond, boolean) - Constructor for class ffx.potential.bonded.TorsionTorsion: Torsion-Torsion constructor.
torsionTorsionFactory(Bond, Angle, Bond, ForceField) - Static method in class ffx.potential.bonded.TorsionTorsion: torsionTorsionFactory.
TorsionTorsionForce - Class in ffx.openmm.amoeba: This class implements the Amoeba torsion-torsion interaction.
TorsionTorsionForce() - Constructor for class ffx.openmm.amoeba.TorsionTorsionForce: Create an AmoebaTorsionTorsionForce.
TorsionTorsionPotentialEnergy - Class in ffx.potential.terms: Torsion-Torsion potential energy term using TorsionTorsion instances.
TorsionTorsionPotentialEnergy(String) - Constructor for class ffx.potential.terms.TorsionTorsionPotentialEnergy: Create a TorsionTorsionPotentialEnergy with the provided name.
TorsionTorsionPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.TorsionTorsionPotentialEnergy: Create a TorsionTorsionPotentialEnergy with the provided name and force group.
TorsionTorsionPotentialEnergy(String, int, List<TorsionTorsion>) - Constructor for class ffx.potential.terms.TorsionTorsionPotentialEnergy: Create a TorsionTorsionPotentialEnergy initialized with a list of terms and force group.
TorsionTorsionPotentialEnergy(String, Collection<TorsionTorsion>) - Constructor for class ffx.potential.terms.TorsionTorsionPotentialEnergy: Create a TorsionTorsionPotentialEnergy initialized with a collection of terms.
torsionTorsionTime - Static variable in class ffx.potential.bonded.MSGroup: Constant torsionTorsionTime=0
torsionTorsionType - Variable in class ffx.potential.bonded.TorsionTorsion: The force field Torsion-Torsion type in use.
TorsionTorsionType - Class in ffx.potential.parameters: The TorsionTorsionType class defines a Torsion-Torsion spline.
TorsionTorsionType(int[], int[], double[], double[], double[]) - Constructor for class ffx.potential.parameters.TorsionTorsionType: Constructor for TorsionTorsionType.
torsionType - Variable in class ffx.potential.bonded.RestrainTorsion
torsionType - Variable in class ffx.potential.bonded.Torsion: The force field Torsion type in use.
TorsionType - Class in ffx.potential.parameters: The TorsionType class defines a torsional angle.
TorsionType(int[], double[], double[], int[]) - Constructor for class ffx.potential.parameters.TorsionType: TorsionType Constructor.
TorsionType(int[], double[], double[], int[], TorsionType.TorsionMode) - Constructor for class ffx.potential.parameters.TorsionType: TorsionType Constructor.
TorsionType.TorsionMode - Enum Class in ffx.potential.parameters: Torsion modes include Normal or In-Plane
torsionUnit - Variable in class ffx.potential.parameters.TorsionType: Unit conversion.
TORTORS - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
torTorUnit - Variable in class ffx.potential.parameters.TorsionTorsionType: Convert Torsion-Torsion energy to kcal/mole.
toShort(String) - Static method in class edu.rit.util.Hex: Convert the given hexadecimal string to a short value.
toShortString() - Method in class ffx.crystal.Crystal: A String containing the unit cell parameters.
toShortString() - Method in class ffx.crystal.ReplicatesCrystal: A String containing the replicated unit cell parameters.
toString() - Method in enum class edu.rit.http.HttpResponse.Status: Returns a string version of this Status value.
toString() - Method in class edu.rit.mp.Channel: Returns a string version of this channel.
toString() - Method in class edu.rit.mp.IORequest: Returns a string version of this I/O request.
toString() - Method in enum class edu.rit.pj.cluster.BackendInfo.State: Returns a string version of this State value.
toString() - Method in enum class edu.rit.pj.cluster.JobInfo.State: Returns a string version of this State value.
toString() - Method in enum class edu.rit.pj.cluster.ProcessInfo.State: Returns a string version of this State value.
toString() - Method in class edu.rit.pj.Comm: Returns a string version of this communicator.
toString() - Method in class edu.rit.pj.io.StreamFile: Returns a string version of this stream file.
toString() - Method in class edu.rit.pj.reduction.SharedBoolean: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedBooleanArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedByte: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedByteArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedCharacterArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedDouble: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedDoubleArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedFloat: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedFloatArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedInteger: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedIntegerArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedLong: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedLongArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedObject: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedObjectArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedShort: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.reduction.SharedShortArray: Returns a string version of this array reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedBoolean: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedObject: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns a string version of this reduction variable.
toString() - Method in class edu.rit.util.LongRange: Returns a string version of this range.
toString() - Method in class edu.rit.util.Range: Returns a string version of this range.
toString() - Method in class ffx.algorithms.commands.Minimize
toString() - Method in class ffx.algorithms.dynamics.integrators.BetterBeeman
toString() - Method in class ffx.algorithms.dynamics.integrators.Respa
toString() - Method in class ffx.algorithms.dynamics.integrators.Stochastic
toString() - Method in class ffx.algorithms.dynamics.integrators.VelocityVerlet
toString() - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic
toString() - Method in class ffx.algorithms.dynamics.thermostats.Berendsen
toString() - Method in class ffx.algorithms.dynamics.thermostats.Bussi
toString() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
toString() - Method in class ffx.algorithms.mc.MolecularMC
toString() - Method in class ffx.algorithms.mc.RosenbluthChi0Move
toString() - Method in class ffx.algorithms.mc.RosenbluthChiAllMove
toString() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
toString() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
toString() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
toString() - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
toString() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell: Returns a string representation of this BoxOptCell.
toString() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMove
toString() - Method in class ffx.algorithms.optimize.Minimize
toString() - Method in class ffx.algorithms.optimize.RotamerOptimization
toString() - Method in class ffx.algorithms.thermodynamics.HistogramData
toString() - Method in class ffx.crystal.Crystal
toString() - Method in class ffx.crystal.HKL
toString() - Method in class ffx.crystal.NCSCrystal
toString() - Method in class ffx.crystal.ReflectionList
toString() - Method in class ffx.crystal.ReplicatesCrystal
toString() - Method in class ffx.crystal.SymOp
toString() - Method in class ffx.HeadlessMain
toString() - Method in class ffx.Main
toString() - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Return a String for entire Array, with one 3D vector per line.
toString() - Method in class ffx.numerics.clustering.Cluster
toString() - Method in class ffx.numerics.clustering.ClusterPair
toString() - Method in class ffx.numerics.clustering.Distance: Returns a string containing distance and weight values.
toString() - Method in class ffx.numerics.clustering.DistanceMap
toString() - Method in record class ffx.numerics.clustering.visualization.VCoord: Returns a string representation of this coordinate in the form "Coord(x,y)" with values formatted to three decimal places.
toString() - Method in class ffx.numerics.fft.Complex: String representation of the Complex FFT.
toString() - Method in class ffx.numerics.fft.Complex3DParallel
toString() - Method in class ffx.numerics.fft.MixedRadixFactor: Return a string representation of the mixed radix factor.
toString() - Method in record class ffx.numerics.fft.PassConstants: Returns a string representation of this record class.
toString() - Method in class ffx.numerics.integrate.CompositeCurve
toString() - Method in class ffx.numerics.integrate.CosineWave
toString() - Method in class ffx.numerics.integrate.DoublesDataSet
toString() - Method in class ffx.numerics.integrate.FunctionDataCurve
toString() - Method in class ffx.numerics.integrate.PolynomialCurve
toString() - Method in class ffx.numerics.integrate.SinWave
toString() - Method in class ffx.numerics.math.BootStrapStatistics: $
toString() - Method in class ffx.numerics.math.ComplexNumber
toString() - Method in class ffx.numerics.math.Double3: Describe this Double3 in a String.
toString() - Method in class ffx.numerics.math.Float3: Describe this Float3 in a String.
toString() - Method in class ffx.numerics.math.SummaryStatistics: $
toString() - Method in class ffx.numerics.quickhull.Vector3d: Returns a string representation of this vector, consisting of the x, y, and z coordinates.
toString() - Method in class ffx.numerics.switching.BellCurveSwitch
toString() - Method in class ffx.numerics.switching.CompositeSwitch
toString() - Method in class ffx.numerics.switching.ConstantSwitch
toString() - Method in class ffx.numerics.switching.LinearDerivativeSwitch
toString() - Method in class ffx.numerics.switching.MultiplicativeSwitch
toString() - Method in class ffx.numerics.switching.PowerSwitch
toString() - Method in class ffx.numerics.switching.SquaredTrigSwitch
toString() - Method in class ffx.potential.bonded.Angle
toString() - Method in class ffx.potential.bonded.AngleTorsion
toString() - Method in class ffx.potential.bonded.Atom
toString() - Method in class ffx.potential.bonded.BondedTerm
toString() - Method in exception class ffx.potential.bonded.BondedUtils.MissingAtomTypeException
toString() - Method in exception class ffx.potential.bonded.BondedUtils.MissingHeavyAtomException
toString() - Method in class ffx.potential.bonded.ImproperTorsion
toString() - Method in class ffx.potential.bonded.Joint
toString() - Method in class ffx.potential.bonded.MSGroup
toString() - Method in class ffx.potential.bonded.MSNode
toString() - Method in class ffx.potential.bonded.MSRoot
toString() - Method in class ffx.potential.bonded.MultiResidue
toString() - Method in class ffx.potential.bonded.OutOfPlaneBend
toString() - Method in class ffx.potential.bonded.PiOrbitalTorsion
toString() - Method in class ffx.potential.bonded.RelativeSolvation
toString() - Method in class ffx.potential.bonded.Residue
toString() - Method in class ffx.potential.bonded.ResidueState
toString() - Method in class ffx.potential.bonded.RestrainDistance
toString() - Method in class ffx.potential.bonded.RestrainTorsion
toString() - Method in class ffx.potential.bonded.ROLSP
toString() - Method in class ffx.potential.bonded.Rotamer
toString() - Method in class ffx.potential.bonded.RotamerLibrary.RotamerGuess
toString() - Method in class ffx.potential.bonded.StretchBend
toString() - Method in class ffx.potential.bonded.StretchTorsion
toString() - Method in class ffx.potential.bonded.Torsion
toString() - Method in class ffx.potential.bonded.TorsionTorsion
toString() - Method in class ffx.potential.ForceFieldEnergy
toString() - Method in class ffx.potential.nonbonded.pme.AlchemicalParameters
toString() - Method in class ffx.potential.nonbonded.ScfPredictor
toString() - Method in class ffx.potential.nonbonded.VanDerWaals
toString() - Method in class ffx.potential.nonbonded.VanDerWaalsTornado
toString() - Method in class ffx.potential.openmm.OpenMMContext
toString() - Method in class ffx.potential.parameters.AngleTorsionType
toString() - Method in class ffx.potential.parameters.AngleType
toString() - Method in class ffx.potential.parameters.AtomType
toString() - Method in class ffx.potential.parameters.BaseType
toString() - Method in class ffx.potential.parameters.BioType
toString() - Method in class ffx.potential.parameters.BondType
toString() - Method in class ffx.potential.parameters.ChargeType
toString() - Method in class ffx.potential.parameters.ForceField
toString() - Method in class ffx.potential.parameters.ImproperTorsionType
toString() - Method in class ffx.potential.parameters.MultipoleType
toString() - Method in class ffx.potential.parameters.OutOfPlaneBendType
toString() - Method in class ffx.potential.parameters.PiOrbitalTorsionType
toString() - Method in class ffx.potential.parameters.PolarizeType
toString() - Method in class ffx.potential.parameters.RelativeSolvationType
toString() - Method in class ffx.potential.parameters.SoluteType
toString() - Method in class ffx.potential.parameters.StretchBendType
toString() - Method in class ffx.potential.parameters.StretchTorsionType
toString() - Method in class ffx.potential.parameters.TorsionTorsionType
toString() - Method in class ffx.potential.parameters.TorsionType
toString() - Method in class ffx.potential.parameters.UreyBradleyType
toString() - Method in class ffx.potential.parameters.VDWPairType
toString() - Method in enum class ffx.potential.parameters.VDWType.EPSILON_RULE
toString() - Method in enum class ffx.potential.parameters.VDWType.RADIUS_RULE
toString() - Method in enum class ffx.potential.parameters.VDWType.RADIUS_TYPE
toString() - Method in class ffx.potential.parameters.VDWType
toString() - Method in enum class ffx.potential.parameters.VDWType.VDW_TYPE
toString() - Method in class ffx.potential.terms.AnglePotentialEnergy
toString() - Method in class ffx.potential.terms.AngleTorsionPotentialEnergy
toString() - Method in class ffx.potential.terms.BondPotentialEnergy
toString() - Method in class ffx.potential.terms.EnergyTerm: Get a string representation of this energy term.
toString() - Method in class ffx.potential.terms.EnergyTermRegion: String representation of this EnergyTermRegion.
toString() - Method in class ffx.potential.terms.ImproperTorsionPotentialEnergy
toString() - Method in class ffx.potential.terms.OutOfPlaneBendPotentialEnergy
toString() - Method in class ffx.potential.terms.PiOrbitalTorsionPotentialEnergy
toString() - Method in class ffx.potential.terms.RestrainDistancePotentialEnergy
toString() - Method in class ffx.potential.terms.RestrainPositionPotentialEnergy
toString() - Method in class ffx.potential.terms.RestrainTorsionPotentialEnergy
toString() - Method in class ffx.potential.terms.StretchBendPotentialEnergy
toString() - Method in class ffx.potential.terms.StretchTorsionPotentialEnergy
toString() - Method in class ffx.potential.terms.TorsionPotentialEnergy
toString() - Method in class ffx.potential.terms.TorsionTorsionPotentialEnergy
toString() - Method in class ffx.potential.terms.UreyBradleyPotentialEnergy
toString() - Method in record class ffx.potential.UnmodifiableState: Returns a string representation of this record class.
toString() - Method in class ffx.ui.commands.SimulationDefinition: toString
toString() - Method in class ffx.ui.commands.SimulationMessage: toString
toString() - Method in class ffx.ui.FFXExec
toString() - Method in class ffx.ui.FFXSystem
toString() - Method in class ffx.ui.GraphicsCanvas
toString() - Method in class ffx.ui.Hierarchy
toString() - Method in class ffx.ui.KeywordComponent
toString() - Method in class ffx.ui.KeywordPanel
toString() - Method in class ffx.ui.MainPanel
toString() - Method in class ffx.ui.ModelingPanel: toString
toString() - Method in class ffx.ui.ModelingShell
toString() - Method in class ffx.ui.OSXAdapter
toString() - Method in record class ffx.utilities.DoubleIndexPair: Returns a string containing the index and double value.
toString() - Method in record class ffx.utilities.IndexIndexPair: Returns a string representation of this record class.
toString() - Method in class ffx.utilities.Keyword
toString() - Method in record class ffx.utilities.ObjectPair: Returns a string representation of this record class.
toString() - Method in class ffx.utilities.StringOutputStream: toString.
toString(byte) - Static method in class edu.rit.util.Hex: Convert the given byte value to a two-digit hexadecimal string.
toString(byte[]) - Static method in class edu.rit.util.Hex: Convert the given byte array to a hexadecimal string.
toString(byte[], int, int) - Static method in class edu.rit.util.Hex: Convert a portion of the given byte array to a hexadecimal string.
toString(char) - Static method in class edu.rit.util.Hex: Convert the given char value to a four-digit hexadecimal string.
toString(double[]) - Static method in class ffx.numerics.math.DoubleMath: logVector.
toString(double[], String) - Static method in class ffx.numerics.math.DoubleMath: vectorToString.
toString(float[]) - Static method in class ffx.numerics.math.FloatMath: logVector.
toString(float[], String) - Static method in class ffx.numerics.math.FloatMath: vectorToString.
toString(int) - Static method in class edu.rit.util.Hex: Convert the given int value to an eight-digit hexadecimal string.
toString(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Return a string for given index.
toString(int, String) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Return a string for given index.
toString(long) - Static method in class edu.rit.util.Hex: Convert the given long value to a sixteen-digit hexadecimal string.
toString(short) - Static method in class edu.rit.util.Hex: Convert the given short value to a four-digit hexadecimal string.
toString(Rotamer) - Method in class ffx.potential.bonded.Residue: A descriptive string based on a given rotamer.
toString(ForceField.ForceFieldType) - Method in class ffx.potential.parameters.ForceField: Return a String for any Force Field keyword.
toString(String) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Return a String for entire Array, with one 3D vector per line.
toString(String) - Method in class ffx.potential.parameters.ForceField: toString
toStringBuffer() - Method in class ffx.potential.parameters.ForceField: toStringBuffer
toStringPrecise() - Method in class ffx.crystal.SymOp: Print the symmetry operator with double precision.
totalCpus - Variable in class edu.rit.pj.cluster.BackendInfo: The total number of CPUs in the backend.
totalEnergy - Variable in class ffx.potential.openmm.OpenMMState: Total energy (kcal/mol).
totalEnergy(PolarizableMultipole, PolarizableMultipole, double, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Permanent Multipole + Polarization Energy.
totalMultipoleEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Total multipole energy = permanentMultipoleEnergy + polarizationEnergy.
totalSimTime - Variable in class ffx.algorithms.dynamics.MolecularDynamics: The total simulation time.
totalSurfaceArea - Variable in class ffx.potential.commands.Volume
totalSurfaceArea - Variable in class ffx.potential.commands.VolumeArc
totalVolume - Variable in class ffx.potential.commands.Volume: JUnit Testing Variables.
totalVolume - Variable in class ffx.potential.commands.VolumeArc: JUnit Testing Variables.
totalWindowLength() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Returns the sum of window lengths to be used (normalized to the number of MD steps in a "regular" window).
totalWindowLength() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
totalWindowLength() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
totalWindowLength() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
toThermostatString() - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic: Add Thermostat details to the kinetic energy and temperature details.
toThermostatString() - Method in class ffx.algorithms.dynamics.thermostats.Berendsen: Add Thermostat details to the kinetic energy and temperature details.
toThermostatString() - Method in class ffx.algorithms.dynamics.thermostats.Bussi: Add Thermostat details to the kinetic energy and temperature details.
toVec3Array(double[]) - Static method in class ffx.openmm.Vec3Array: Convert a double array to a Vec3Array.
toXML() - Method in class ffx.potential.parameters.ForceField: Uses OpenMMXmlFilter to create an XML file of the force field usable by OpenMM.
toXML() - Method in class ffx.potential.parsers.OpenMMXmlFilter: Create an OpenMM XML file for the given force field.
toXML(Document) - Method in class ffx.potential.parameters.AngleTorsionType: Write AngleTorsionType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.AngleType: Write AngleType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.AtomType: Write AtomType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.BondType: Write BondType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.MultipoleType: Write MultipoleType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.OutOfPlaneBendType: Write OutOfPlaneBendType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.PiOrbitalTorsionType: Write PiOrbitalTorsionType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.PolarizeType: Write PolarizeType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.StretchBendType: Write StretchBendType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.StretchTorsionType: Write StretchTorsionType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.UreyBradleyType: Write UreyBradleyType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.VDWPairType: Write VDWPairType to OpenMM XML format.
toXML(Document) - Method in class ffx.potential.parameters.VDWType: Write VDWType to OpenMM XML format.
toXML(Document, Double) - Method in class ffx.potential.parameters.TorsionType: Write TorsionType (Proper) to OpenMM XML format.
toXML(Document, Element, int) - Method in class ffx.potential.parameters.TorsionTorsionType: Write TorsionTorsionType to OpenMM XML format.
toXrayEnergy(DiffractionData) - Method in class ffx.xray.cli.XrayOptions: Process input from opened molecular assemblies and diffraction data to a RefinementEnergy.
toXYZString() - Method in class ffx.crystal.SymOp: toXYZString
TP3 - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
tr - Variable in class ffx.crystal.SymOp: The translation vector in fractional coordinates.
Tr_0_0_0 - Static variable in class ffx.crystal.SymOp: Constant Tr_0_0_0={ZERO, ZERO, ZERO}
Trajectory - Class in ffx.ui: The Trajectory class controls playback of a TINKER trajectory.
Trajectory(MolecularAssembly, MainPanel) - Constructor for class ffx.ui.Trajectory: Constructor for Trajectory.
trajectoryFrequency - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Time steps between adding a frame to the trajectory file.
transformChanged(int, Transform3D) - Method in interface ffx.ui.behaviors.MouseBehaviorCallback: transformChanged
transformChanged(int, Transform3D) - Method in class ffx.ui.behaviors.PickOrbitBehavior: Callback method from MouseOrbit This is used when the Picking callback is enabled.
transformChanged(int, Transform3D) - Method in class ffx.ui.behaviors.PickPropertiesBehavior: transformChanged
transformChanged(int, Transform3D) - Method in class ffx.ui.behaviors.PickRotateBehavior: Callback method from MouseRotate This is used when the Picking callback is enabled.
transformChanged(int, Transform3D) - Method in class ffx.ui.behaviors.PickSelectionBehavior: transformChanged
transformChanged(int, Transform3D) - Method in class ffx.ui.behaviors.PickTranslateBehavior: transformChanged
transformChanged(int, Transform3D) - Method in class ffx.ui.behaviors.PickZoomBehavior: transformChanged
transformChanged(int, Transform3D) - Method in class ffx.ui.GraphicsAxis: transformChanged
transformChanged(int, TransformGroup) - Method in interface ffx.ui.behaviors.PickingCallback: Called by the Pick Behavior with which this callback is registered each time the Picked object is moved.
transformChanged(Transform3D) - Method in class ffx.ui.behaviors.MouseOrbit: transformChanged
transformChanged(Transform3D) - Method in class ffx.ui.behaviors.MouseProperties: transformChanged
transformChanged(Transform3D) - Method in class ffx.ui.behaviors.MouseRotate: transformChanged
transformChanged(Transform3D) - Method in class ffx.ui.behaviors.MouseSelection: transformChanged
transformChanged(Transform3D) - Method in class ffx.ui.behaviors.MouseTranslate: transformChanged
transformChanged(Transform3D) - Method in class ffx.ui.behaviors.MouseZoom: transformChanged
transformClicked(int, Transform3D) - Method in interface ffx.ui.behaviors.MouseBehaviorCallback: transformClicked
transformClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickOrbitBehavior: transformClicked
transformClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickPropertiesBehavior: transformClicked
transformClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickRotateBehavior: transformClicked
transformClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickSelectionBehavior: transformClicked
transformClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickTranslateBehavior: transformClicked
transformClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickZoomBehavior: transformClicked
transformClicked(int, Transform3D) - Method in class ffx.ui.GraphicsAxis: transformClicked
transformClicked(int, TransformGroup) - Method in interface ffx.ui.behaviors.PickingCallback: transformClicked
transformDoubleClicked(int, Transform3D) - Method in interface ffx.ui.behaviors.MouseBehaviorCallback: transformDoubleClicked
transformDoubleClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickOrbitBehavior: transformDoubleClicked
transformDoubleClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickPropertiesBehavior: transformDoubleClicked
transformDoubleClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickRotateBehavior: transformDoubleClicked
transformDoubleClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickSelectionBehavior: transformDoubleClicked
transformDoubleClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickTranslateBehavior: transformDoubleClicked
transformDoubleClicked(int, Transform3D) - Method in class ffx.ui.behaviors.PickZoomBehavior: transformDoubleClicked
transformDoubleClicked(int, Transform3D) - Method in class ffx.ui.GraphicsAxis: transformDoubleClicked
transformDoubleClicked(int, TransformGroup) - Method in interface ffx.ui.behaviors.PickingCallback: transformDoubleClicked
transformGroup - Variable in class ffx.ui.behaviors.MouseBehavior
transformX - Variable in class ffx.ui.behaviors.MouseBehavior
transformY - Variable in class ffx.ui.behaviors.MouseBehavior
translate - Variable in class ffx.ui.behaviors.PickTranslateBehavior
translate(double[], double[]) - Static method in class ffx.potential.utils.Superpose: Move the center of mass for a set of atoms to the origin.
translate(double[], double[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: Move the center of mass for both sets of atoms to the origin.
TRANSLATE - Enum constant in enum class ffx.ui.GraphicsCanvas.LeftButtonMode
TRANSLATE - Static variable in interface ffx.ui.behaviors.MouseBehaviorCallback: Constant TRANSLATE=1
TRANSLATE - Static variable in interface ffx.ui.behaviors.PickingCallback: Constant TRANSLATE=1
transpose3(double[][]) - Static method in class ffx.numerics.math.MatrixMath: transpose3
transpose3(double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath: transpose3
trapezoidal(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using trapezoidal integration.
trapezoidal(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using trapezoidal integration.
TRAPEZOIDAL - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType: Trapezoidal integration, requiring 2 points.
trapezoidalEnds(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Treats half-width bins at the ends of a DataSet using trapezoidal integration.
trapezoidalParallel(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using trapezoidal integration.
trapezoidalParallel(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using trapezoidal integration.
traverseFiles(File, int, String) - Static method in class ffx.utilities.FileUtils: Traverse a directory to find files matching the given regex pattern.
treeNodesChanged(TreeModelEvent) - Method in class ffx.ui.Hierarchy
treeNodesInserted(TreeModelEvent) - Method in class ffx.ui.Hierarchy
treeNodesRemoved(TreeModelEvent) - Method in class ffx.ui.Hierarchy
treeStructureChanged(TreeModelEvent) - Method in class ffx.ui.Hierarchy
triangulate() - Method in class ffx.numerics.quickhull.QuickHull3D: Triangulates any non-triangular hull faces.
triangulate(FaceList, double) - Method in class ffx.numerics.quickhull.Face: Triangulates this (convex polygonal) face into a fan of triangles sharing the first vertex.
TRICLINIC - Enum constant in enum class ffx.crystal.CrystalSystem: Triclinic crystal system.
TRICLINIC_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem: Triclinic lattice system.
TriCubicSpline - Class in ffx.numerics.spline: TriCubicSpline class.
TriCubicSpline() - Constructor for class ffx.numerics.spline.TriCubicSpline: Initialize Spline function.
TRIGONAL - Enum constant in enum class ffx.crystal.CrystalSystem: Trigonal crystal system.
Trim - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
TRIPHOSPHATE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
TRP - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
tryParseIon(String) - Static method in class ffx.utilities.StringUtils: Checks if a String looks like a known ion.
tryParseWater(String) - Static method in class ffx.utilities.StringUtils: Checks if a String looks like a water molecule.
TRYPTOPHAN - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
tryRotamers() - Method in class ffx.algorithms.misc.GenerateRotamers: Main driver method; spins torsions, evaluates energy, and prints to file.
TUBE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
TURN - Enum constant in enum class ffx.potential.bonded.Residue.SSType
turnOffAllResidues(Residue[]) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
turnOffAllResidues(Residue[]) - Method in class ffx.algorithms.optimize.RotamerOptimization
turnOffResidue(Residue) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
turnOffResidue(Residue) - Method in class ffx.algorithms.optimize.RotamerOptimization
turnOnAllResidues(Residue[]) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
turnOnAllResidues(Residue[]) - Method in class ffx.algorithms.optimize.RotamerOptimization
turnOnResidue(Residue, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
turnOnResidue(Residue, int) - Method in class ffx.algorithms.optimize.RotamerOptimization
turnRotamerPairEliminationOff() - Method in class ffx.algorithms.optimize.RotamerOptimization: ONLY FOR UNIT TESTING.
turnRotamerSingleEliminationOff() - Method in class ffx.algorithms.optimize.RotamerOptimization: ONLY FOR UNIT TESTING.
twiddles - Variable in class ffx.numerics.fft.MixedRadixFactor: The twiddle factors for this pass.
twiddles() - Method in record class ffx.numerics.fft.PassConstants: Returns the value of the twiddles record component.
TwoBodyEnergyRegion - Class in ffx.algorithms.optimize.manybody: Compute 2-Body energy values in parallel across nodes.
TwoBodyEnergyRegion(RotamerOptimization, DistanceMatrix, EnergyExpansion, EliminatedRotamers, Residue[], List<Residue>, BufferedWriter, Comm, int, boolean, double, boolean, int, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
TwoParticleAverageSite - Class in ffx.openmm: This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations.
TwoParticleAverageSite(int, int, double, double) - Constructor for class ffx.openmm.TwoParticleAverageSite: Create a new TwoParticleAverageSite virtual site.
tx - Variable in class ffx.potential.parameters.TorsionTorsionType: Torsion values along x.
ty - Variable in class ffx.potential.parameters.TorsionTorsionType: Torsion values along y.
TYD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
type - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat: The type of each variable.
type - Variable in class ffx.potential.parameters.AtomType: Atom type.
type - Variable in class ffx.potential.parameters.PolarizeType: Atom type number.
type - Variable in class ffx.ui.commands.SimulationUpdate
types - Variable in class ffx.ui.commands.SimulationDefinition
TYR - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
TYROSINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA

U

U - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
U - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
U - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
u2b(double) - Static method in class ffx.numerics.math.ScalarMath: u2b
ub - Variable in class ffx.numerics.integrate.FunctionDataCurve: Upper bound.
ub() - Method in class edu.rit.util.LongRange: Returns this range's upper bound.
ub() - Method in class edu.rit.util.Range: Returns this range's upper bound.
udpateSoluteParameters(int) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Update GK solute parameters for a given atom.
UIFileCloser - Class in ffx.ui: The UIFileCloser class wraps the closing of an FFXSystem within a thread.
UIFileCloser(FFXSystem) - Constructor for class ffx.ui.UIFileCloser: Constructor for FileCloser.
UIFileOpener - Class in ffx.ui: The UIFileOpener class opens a file into Force Field X using a filter from the ffx.potential.parsers package.
UIUtils - Class in ffx.ui: UIUtils implements core and extended functionality for many Force Field X algorithms and scripts, such as opening and closing structure files, basic force field evaluations, molecular dynamics, etc.
UIUtils(ModelingShell, MainPanel) - Constructor for class ffx.ui.UIUtils
UniformBSpline - Class in ffx.numerics.spline: Static methods to generate and differentiate uniform b-Splines.
UNIT - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
UnitCellAndSpaceGroup - Enum constant in enum class ffx.utilities.PropertyGroup: Unit cell and space group.
unitCellCoordinates - Variable in class ffx.potential.commands.MoveIntoUnitCell: Cartesian coordinates after moving into the unit cell.
units - Variable in class ffx.potential.bonded.RestrainTorsion
UnivariateDiffFunction - Interface in ffx.numerics.func1d: A UnivariateDiffFunction describes a function of a single value (often lambda).
UnivariateFunctionFactory - Class in ffx.numerics.switching: Static class responsible for parsing String arrays into univariate switching functions.
UnivariateSwitchingFunction - Interface in ffx.numerics.switching: A UnivariateSwitchingFunction describes a function of a single value (often lambda), where f(lb) = 0, f(ub) = 1, and df(x)/dx >= 0 for all x lb-ub.
UNK - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
UNK - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
UNK - Enum constant in enum class ffx.potential.bonded.Residue.ResidueType
UNK - Enum constant in enum class ffx.potential.Utilities.FileType
UNKNOWN - Enum constant in enum class ffx.potential.Utilities.PolymerType
unmarshal(String) - Method in class ffx.utilities.DoubleXMLAdapter: Unmarshel the Double
unmarshal(String) - Method in class ffx.utilities.HistogramXmlAdapter: Convert the histogram data string to a 2D double array.
UnmodifiableState - Record Class in ffx.potential: A record class to hold the state of a system.
UnmodifiableState(double[], double[], double[], double[], double[], double[], double, double, double) - Constructor for record class ffx.potential.UnmodifiableState: This constructor does a defensive copy of all arrays.
UnmodifiableState(SystemState) - Constructor for record class ffx.potential.UnmodifiableState: This constructor does a defensive copy of all arrays.
unpackIntBigEndian(int[], int, byte[], int, int) - Static method in class edu.rit.util.Packing: Unpack integers from the given array into the given array of bytes in big-endian order.
unpackIntBigEndian(int, byte[], int) - Static method in class edu.rit.util.Packing: Unpack the given integer into the given array of bytes in big-endian order.
unpackIntLittleEndian(int[], int, byte[], int, int) - Static method in class edu.rit.util.Packing: Unpack integers from the given array into the given array of bytes in little-endian order.
unpackIntLittleEndian(int, byte[], int) - Static method in class edu.rit.util.Packing: Unpack the given integer into the given array of bytes in little-endian order.
unpackLongBigEndian(long[], int, byte[], int, int) - Static method in class edu.rit.util.Packing: Unpack long integers from the given array into the given array of bytes in big-endian order.
unpackLongBigEndian(long, byte[], int) - Static method in class edu.rit.util.Packing: Unpack the given long integer into the given array of bytes in big-endian order.
unpackLongLittleEndian(long[], int, byte[], int, int) - Static method in class edu.rit.util.Packing: Unpack long integers from the given array into the given array of bytes in little-endian order.
unpackLongLittleEndian(long, byte[], int) - Static method in class edu.rit.util.Packing: Unpack the given long integer into the given array of bytes in little-endian order.
unscaleCoordinates(double[]) - Method in interface ffx.numerics.OptimizationInterface: Default method to unscale coordinates.
Unsigned16BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class Unsigned16BitIntegerArrayBuf provides a buffer for an array of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
Unsigned16BitIntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf: Construct a new unsigned 16-bit integer array buffer.
Unsigned16BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class Unsigned16BitIntegerArrayBuf_1 provides a buffer for an array of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
Unsigned16BitIntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1: Construct a new unsigned 16-bit integer array buffer.
Unsigned16BitIntegerBuf - Class in edu.rit.mp: Class Unsigned16BitIntegerBuf is the abstract base class for a buffer of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
Unsigned16BitIntegerBuf(int) - Constructor for class edu.rit.mp.Unsigned16BitIntegerBuf: Construct a new unsigned 16-bit integer buffer.
Unsigned16BitIntegerItemBuf - Class in edu.rit.mp.buf: Class Unsigned16BitIntegerItemBuf provides a buffer for a single unsigned 16-bit integer item sent or received using the Message Protocol (MP).
Unsigned16BitIntegerItemBuf() - Constructor for class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Construct a new unsigned 16-bit integer item buffer.
Unsigned16BitIntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf: Construct a new unsigned 16-bit integer item buffer with the given initial value.
Unsigned16BitIntegerMatrixBuf - Class in edu.rit.mp.buf: Class Unsigned16BitIntegerMatrixBuf provides a buffer for a matrix of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
Unsigned16BitIntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf: Construct a new unsigned 16-bit integer matrix buffer.
Unsigned16BitIntegerMatrixBuf_1 - Class in edu.rit.mp.buf: Class Unsigned16BitIntegerMatrixBuf_1 provides a buffer for a matrix of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
Unsigned16BitIntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1: Construct a new unsigned 16-bit integer matrix buffer.
Unsigned8BitIntegerArrayBuf - Class in edu.rit.mp.buf: Class Unsigned8BitIntegerArrayBuf provides a buffer for an array of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
Unsigned8BitIntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf: Construct a new unsigned 8-bit integer array buffer.
Unsigned8BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf: Class Unsigned8BitIntegerArrayBuf_1 provides a buffer for an array of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
Unsigned8BitIntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1: Construct a new unsigned 8-bit integer array buffer.
Unsigned8BitIntegerBuf - Class in edu.rit.mp: Class Unsigned8BitIntegerBuf is the abstract base class for a buffer of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
Unsigned8BitIntegerBuf(int) - Constructor for class edu.rit.mp.Unsigned8BitIntegerBuf: Construct a new signed 8-bit integer buffer.
Unsigned8BitIntegerItemBuf - Class in edu.rit.mp.buf: Class Unsigned8BitIntegerItemBuf provides a buffer for a single unsigned 8-bit integer item sent or received using the Message Protocol (MP).
Unsigned8BitIntegerItemBuf() - Constructor for class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Construct a new unsigned 8-bit integer item buffer.
Unsigned8BitIntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf: Construct a new unsigned 8-bit integer item buffer with the given initial value.
Unsigned8BitIntegerMatrixBuf - Class in edu.rit.mp.buf: Class Unsigned8BitIntegerMatrixBuf provides a buffer for a matrix of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
Unsigned8BitIntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf: Construct a new unsigned 8-bit integer matrix buffer.
Unsigned8BitIntegerMatrixBuf_1 - Class in edu.rit.mp.buf: Class Unsigned8BitIntegerMatrixBuf_1 provides a buffer for a matrix of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
Unsigned8BitIntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1: Construct a new unsigned 8-bit integer matrix buffer.
update() - Method in class ffx.potential.bonded.Atom: update
update() - Method in class ffx.potential.bonded.Bond: update
update() - Method in interface ffx.potential.bonded.BondedEnergy: update.
update() - Method in class ffx.potential.bonded.MSGroup: update
update() - Method in class ffx.potential.bonded.MSNode: update
update() - Method in class ffx.potential.bonded.MultiResidue: update
update() - Method in interface ffx.potential.bonded.ROLS: update
update() - Method in class ffx.potential.openmm.OpenMMContext: Update the Context if necessary.
update(double) - Method in class ffx.potential.nonbonded.pme.AlchemicalParameters
update(double[]) - Method in interface ffx.xray.FormFactor: update the coordinates to the current position
update(double[]) - Method in class ffx.xray.NeutronFormFactor: update the coordinates to the current position
update(double[]) - Method in class ffx.xray.SolventBinaryFormFactor: update the coordinates to the current position
update(double[]) - Method in class ffx.xray.SolventGaussFormFactor: update the coordinates to the current position
update(double[]) - Method in class ffx.xray.SolventPolyFormFactor: update the coordinates to the current position
update(double[]) - Method in class ffx.xray.XRayFormFactor: update the coordinates to the current position
update(double[], double) - Method in interface ffx.xray.FormFactor: update the coordinates to the current position and Badd
update(double[], double) - Method in class ffx.xray.NeutronFormFactor: update the coordinates to the current position and Badd
update(double[], double) - Method in class ffx.xray.SolventBinaryFormFactor: update the coordinates to the current position and Badd
update(double[], double) - Method in class ffx.xray.SolventGaussFormFactor: update the coordinates to the current position and Badd
update(double[], double) - Method in class ffx.xray.SolventPolyFormFactor: update the coordinates to the current position and Badd
update(double[], double) - Method in class ffx.xray.XRayFormFactor: update the coordinates to the current position and Badd
update(String, double, double, boolean) - Method in class ffx.potential.openmm.OpenMMContext: Update the Context in which to run a simulation.
UPDATE - Static variable in class ffx.ui.commands.SimulationMessage: Constant UPDATE=1
updateAtom(int) - Method in class ffx.potential.nonbonded.implicit.GaussVol
updateAtomMass() - Method in class ffx.potential.openmm.OpenMMSystem: This method sets the mass of inactive atoms to zero.
updateAtoms() - Method in class ffx.potential.bonded.MSGroup: updateAtoms
updateAtoms() - Method in class ffx.potential.bonded.MultiResidue: updateAtoms
updateBondedTerms - Variable in class ffx.potential.openmm.OpenMMSystem: This flag indicates bonded force constants and equilibria are updated (e.g. during ManyBody titration).
updateBonds() - Method in class ffx.potential.bonded.MSGroup: updateBonds
updateBonds() - Method in class ffx.potential.bonded.MultiResidue: updateBonds
updateContext(System, Integrator, Platform) - Method in class ffx.openmm.Context: Update the context.
updateContext(String, double, double, boolean) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Create an OpenMM Context.
updateContext(String, double, double, boolean) - Method in class ffx.potential.openmm.OpenMMEnergy: Create an OpenMM Context.
updateContext(String, double, double, boolean) - Method in interface ffx.potential.openmm.OpenMMPotential: Update the OpenMM Context.
updateCrystal() - Method in class ffx.crystal.Crystal: Update all Crystal variables that are a function of unit cell parameters.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.AngleForce: Update an existing angle force for the OpenMM System.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.AngleTorsionForce: Update the Dual Topology Angle-Torsion Force.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.BondForce: Update an existing bond force for the OpenMM System.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.ImproperTorsionForce: Update the Dual Topology Improper Torsion force.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.InPlaneAngleForce: Update an existing angle force for the Dual Topology OpenMM System.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.OutOfPlaneBendForce: Update an existing angle force for the Dual-Topology OpenMM System.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.PiOrbitalTorsionForce: Update the Pi-Orbital Torsion force.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.RestrainTorsionsForce: Update the Restraint-Torsion force.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.StretchBendForce: Update existing Stretch-Bend Force for the Dual-Topology OpenMM System.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.StretchTorsionForce: Update the Dual Topology Stretch-Torsion Force.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.TorsionForce: Update the Torsion force.
updateForce(int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.UreyBradleyForce: Update the Urey-Bradley parameters in the OpenMM Context.
updateForce(Atom[], int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.AmoebaMultipoleForce: Update the force parameters for the AMOEBA Multipole Force in a dual topology system.
updateForce(Atom[], int, OpenMMDualTopologyEnergy) - Method in class ffx.potential.openmm.AmoebaVdwForce: Update the vdW force.
updateForce(Atom[], OpenMMEnergy) - Method in class ffx.potential.openmm.AmoebaGeneralizedKirkwoodForce: Update the force.
updateForce(Atom[], OpenMMEnergy) - Method in class ffx.potential.openmm.AmoebaGKCavitationForce: Update the Cavitation force.
updateForce(Atom[], OpenMMEnergy) - Method in class ffx.potential.openmm.AmoebaMultipoleForce: Update the force parameters for the AMOEBA Multipole Force.
updateForce(Atom[], OpenMMEnergy) - Method in class ffx.potential.openmm.AmoebaVdwForce: Update the vdW force.
updateForce(Atom[], OpenMMEnergy) - Method in class ffx.potential.openmm.AmoebaWcaDispersionForce: Update the WCA force.
updateForce(Atom[], OpenMMEnergy) - Method in class ffx.potential.openmm.FixedChargeGBForce: Update the GB force.
updateForce(Atom[], OpenMMEnergy) - Method in class ffx.potential.openmm.FixedChargeNonbondedForce: Update an existing non-bonded force for the OpenMM System.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.AngleForce: Update an existing angle force for the OpenMM System.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.BondForce: Update an existing bond force for the OpenMM System.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.ImproperTorsionForce: Update the Improper Torsion force.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.InPlaneAngleForce: Update an existing angle force for the OpenMM System.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.OutOfPlaneBendForce: Update an existing angle force for the OpenMM System.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.PiOrbitalTorsionForce: Update the Pi-Orbital Torsion force.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.RestrainTorsionsForce: Update the Restraint-Torsion force.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.StretchBendForce: Update this Stretch-Bend Force.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.TorsionForce: Update the Torsion force.
updateForce(OpenMMEnergy) - Method in class ffx.potential.openmm.UreyBradleyForce: Update the Urey-Bradley parameters in the OpenMM Context.
updateFreeEnergyDifference(boolean, boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
updateMetaDynamicsFreeEnergyDifference(boolean, boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: Update the free energy estimate for Meta Dynamics.
updateOSTFreeEnergyDifference(boolean, boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: Eqs. 7 and 8 from the 2012 Crystal Thermodynamics paper.
updateParameters(Atom[]) - Method in class ffx.potential.openmm.OpenMMDualTopologyEnergy: Update parameters if the Use flags and/or Lambda value has changed.
updateParameters(Atom[]) - Method in class ffx.potential.openmm.OpenMMDualTopologySystem: Update parameters if the Use flags and/or Lambda value has changed.
updateParameters(Atom[]) - Method in class ffx.potential.openmm.OpenMMEnergy: Update parameters if the Use flags and/or Lambda value has changed.
updateParameters(Atom[]) - Method in interface ffx.potential.openmm.OpenMMPotential: Update parameters if the Use flags and/or Lambda value has changed.
updateParameters(Atom[]) - Method in class ffx.potential.openmm.OpenMMSystem: Update parameters if the Use flags and/or Lambda value has changed.
updateParameters(Residue) - Method in class ffx.potential.bonded.Rotamer: Update force field parameters for force field dependent rotamers.
updateParametersInContext(Context) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Update the parameters in the context.
updateParametersInContext(Context) - Method in class ffx.openmm.amoeba.GKCavitationForce: Update the parameters in the context.
updateParametersInContext(Context) - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Update the parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.amoeba.MultipoleForce: Update the parameters in the context.
updateParametersInContext(Context) - Method in class ffx.openmm.amoeba.VdwForce: Update the per-particle parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.amoeba.WcaDispersionForce: Update the per-particle parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.ATMForce: Update the per-particle parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.CMAPTorsionForce: Update the map and torsion parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomAngleForce: Update the parameters in the OpenMM Context.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomBondForce: Update the parameters in the OpenMM Context.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomCentroidBondForce: Update the per-bond parameters and tabulated functions in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomCompoundBondForce: Update the parameters in the context.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomCVForce: Update the parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomExternalForce: Update the parameters in the context.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomGBForce: Update the parameters in the context.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomHbondForce: Update the parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomManyParticleForce: Update the per-particle parameters and tabulated functions in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomNonbondedForce: Update the per-particle parameters and tabulated functions in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.CustomTorsionForce: Update the per-torsion parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.drude.DrudeForce: Update the particle and screened pair parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.GayBerneForce: Update the parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.GBSAOBCForce: Update the particle parameters in a Context to match those stored in this Force object.
updateParametersInContext(Context) - Method in class ffx.openmm.HarmonicAngleForce: Update the parameters in the OpenMM Context.
updateParametersInContext(Context) - Method in class ffx.openmm.HarmonicBondForce: Update the parameters in the OpenMM Context.
updateParametersInContext(Context) - Method in class ffx.openmm.NonbondedForce: Update the parameters in the context.
updateParametersInContext(Context) - Method in class ffx.openmm.PeriodicTorsionForce: Update the parameters in the OpenMM Context.
updateParametersInContext(Context) - Method in class ffx.openmm.RBTorsionForce: Update the parameters in the OpenMM Context.
updateParametersInContext(Context) - Method in class ffx.openmm.RMSDForce: Update the reference positions and particle indices in a Context to match those stored in this Force object.
updateRanks(int[]) - Method in class ffx.algorithms.thermodynamics.SendSynchronous: Update the map of rank-to-histogram.
updateResidueParameters(Residue, Rotamer) - Method in class ffx.potential.parameters.TitrationUtils: Update force field parameters for the side-chain atoms of the given residue based on the rotamer amino acid type.
updateScene(int, int) - Method in class ffx.ui.behaviors.PickMouseBehavior: Subclasses shall implement this update function.
updateScene(int, int) - Method in class ffx.ui.behaviors.PickOrbitBehavior: Update the scene to manipulate any nodes.
updateScene(int, int) - Method in class ffx.ui.behaviors.PickPropertiesBehavior: Update the scene to manipulate any nodes.
updateScene(int, int) - Method in class ffx.ui.behaviors.PickRotateBehavior: Update the scene to manipulate any nodes.
updateScene(int, int) - Method in class ffx.ui.behaviors.PickSelectionBehavior: Update the scene to manipulate any nodes.
updateScene(int, int) - Method in class ffx.ui.behaviors.PickTranslateBehavior: Update the scene to manipulate any nodes.
updateScene(int, int) - Method in class ffx.ui.behaviors.PickZoomBehavior: Update the scene to manipulate any nodes.
updateScene(int, int) - Method in class ffx.ui.GraphicsPicking: Subclasses shall implement this update function.
updateScene(MSNode, boolean, boolean, RendererCache.ViewModel, boolean, RendererCache.ColorModel) - Method in class ffx.ui.GraphicsCanvas: updateScene
updateScene(ArrayList<MSNode>, boolean, boolean, RendererCache.ViewModel, boolean, RendererCache.ColorModel) - Method in class ffx.ui.GraphicsCanvas: updateScene
updateTitle() - Method in class ffx.ui.ModelingShell
updateTitle(double) - Method in class ffx.algorithms.cli.AlgorithmsCommand: Update the title line of the structure with Energy and Density.
upperBound() - Method in interface ffx.numerics.integrate.DataSet: Upper bound of the points along x.
upperBound() - Method in class ffx.numerics.integrate.DoublesDataSet: Upper bound of the points along x.
upperBound() - Method in class ffx.numerics.integrate.FunctionDataCurve: Upper bound of the points along x.
upwardSweep() - Method in class ffx.potential.nonbonded.octree.Octree: Update sweep.
URACIL - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
UREYBRAD - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
UreyBradley - Class in ffx.potential.bonded: The UreyBradley class.
UreyBradley(Angle, UreyBradleyType) - Constructor for class ffx.potential.bonded.UreyBradley: Constructor for the UreyBradley class.
ureyBradleyForce - Variable in class ffx.potential.openmm.OpenMMSystem: OpenMM Custom Urey-Bradley Force
UreyBradleyForce - Class in ffx.potential.openmm: Urey-Bradley Force.
UreyBradleyForce(UreyBradleyPotentialEnergy) - Constructor for class ffx.potential.openmm.UreyBradleyForce: Urey-Bradly Force constructor.
UreyBradleyForce(UreyBradleyPotentialEnergy, int, OpenMMDualTopologyEnergy) - Constructor for class ffx.potential.openmm.UreyBradleyForce: Urey-Bradly Force constructor.
ureyBradleyForce2 - Variable in class ffx.potential.openmm.OpenMMDualTopologySystem: OpenMM Custom Urey-Bradley Force for topology 2.
UreyBradleyPotentialEnergy - Class in ffx.potential.terms: Urey-Bradley potential energy term using UreyBradley instances.
UreyBradleyPotentialEnergy(String) - Constructor for class ffx.potential.terms.UreyBradleyPotentialEnergy: Create a UreyBradleyPotentialEnergy with the provided name.
UreyBradleyPotentialEnergy(String, int) - Constructor for class ffx.potential.terms.UreyBradleyPotentialEnergy: Create a UreyBradleyPotentialEnergy with the provided name and force group.
UreyBradleyPotentialEnergy(String, int, List<UreyBradley>) - Constructor for class ffx.potential.terms.UreyBradleyPotentialEnergy: Create a UreyBradleyPotentialEnergy initialized with a list of UreyBradleys and force group.
UreyBradleyPotentialEnergy(String, Collection<UreyBradley>) - Constructor for class ffx.potential.terms.UreyBradleyPotentialEnergy: Create a UreyBradleyPotentialEnergy initialized with a collection of UreyBradleys.
ureyBradleyTime - Static variable in class ffx.potential.bonded.MSGroup: Constant ureyBradleyTime=0
ureyBradleyType - Variable in class ffx.potential.bonded.UreyBradley: Force field parameters to compute the Stretch-Bend energy.
UreyBradleyType - Class in ffx.potential.parameters: The UreyBradleyType class defines one harmonic UreyBradley cross term.
UreyBradleyType(int[], double, double) - Constructor for class ffx.potential.parameters.UreyBradleyType: UreyBradleyType constructor.
ureyBradlyFactory(Angle, ForceField) - Static method in class ffx.potential.bonded.UreyBradley: Attempt to create a new UreyBradley for the specified Angle.
ureyUnit - Variable in class ffx.potential.parameters.UreyBradleyType: Convert Urey-Bradley stretch energy to kcal/mole.
URI - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
useConstraints - Variable in class ffx.algorithms.dynamics.integrators.Integrator: If there are constraints present.
userColor - Static variable in class ffx.potential.bonded.RendererCache: Constant userColor
USERCOLOR - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
username - Variable in class edu.rit.pj.cluster.JobInfo: The job's user name.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.amoeba.HippoNonbondedForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.amoeba.MultipoleForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.amoeba.TorsionTorsionForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.amoeba.VdwForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.amoeba.WcaDispersionForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.AndersenThermostat: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.ATMForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CMAPTorsionForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CMMotionRemover: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomAngleForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomBondForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomCentroidBondForce: Returns whether this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomCompoundBondForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomCVForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomExternalForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomGBForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomHbondForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomManyParticleForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomNonbondedForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomTorsionForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.CustomVolumeForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.drude.DrudeForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.Force: Check if the force use periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.GayBerneForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.GBSAOBCForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.HarmonicAngleForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.HarmonicBondForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.MonteCarloAnisotropicBarostat: Returns whether this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.MonteCarloBarostat: Does the force use periodic boundary conditions?
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.MonteCarloFlexibleBarostat: Returns whether this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.MonteCarloMembraneBarostat: Returns whether this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.NonbondedForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.PeriodicTorsionForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.RBTorsionForce: Check if the force uses periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.RMSDForce: Returns whether or not this force makes use of periodic boundary conditions.
usesPeriodicBoundaryConditions() - Method in class ffx.openmm.System: Check if the system uses periodic boundary conditions.
useTotalChargeCorrection - Variable in class ffx.potential.extended.ExtendedSystem
useWithMultiResidue - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
usingBoxOptimization - Variable in class ffx.algorithms.optimize.RotamerOptimization: Flag to indicate use of box optimization.
Utilities - Class in ffx.potential: The Utilities class provides methods to locate functional units of an organic system.
Utilities() - Constructor for class ffx.potential.Utilities
Utilities.FileType - Enum Class in ffx.potential: An enumeration of recognized file types.
Utilities.PolymerType - Enum Class in ffx.potential: An enumeration of recognized organic polymers.
ux - Variable in class ffx.numerics.multipole.PolarizableMultipole: Induced dipole x-component.
ux - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Induced dipole x-component.
uy - Variable in class ffx.numerics.multipole.PolarizableMultipole: Induced dipole y-component.
uy - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Induced dipole y-component.
uz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Induced dipole z-component.
uz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD: Induced dipole z-component.

V

v - Variable in class ffx.potential.SystemState: Velocities.
v() - Method in class ffx.potential.SystemState: Get a reference to the internal velocities array.
v() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the v record component.
V - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
V - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
vacuumDirectDipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Vacuum induced dipoles
vacuumDirectDipoleCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
vacuumInducedDipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Vacuum induced dipoles
vacuumInducedDipoleCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
vacuumRanges - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
val() - Method in record class ffx.utilities.ObjectPair: Returns the value of the val record component.
VAL - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
valence - Variable in class ffx.potential.parameters.AtomType: Valence number for this type.
validate(int) - Method in class ffx.numerics.fft.TornadoDFT: Validate the Discrete Fourier Transform on the default TornadoDevice.
validate(TornadoDevice) - Method in class ffx.numerics.fft.TornadoDFT: Validate the Discrete Fourier Transform on a TornadoDevice.
validateDEE(Residue[]) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
validateLambda(double) - Method in class ffx.algorithms.mc.LambdaMove: Validate lambda is in the range [0 .. 1].
validOutsideBounds() - Method in class ffx.numerics.switching.BellCurveSwitch: Remains in the range 0-1 outside the bounds.
validOutsideBounds() - Method in class ffx.numerics.switching.CompositeSwitch
validOutsideBounds() - Method in class ffx.numerics.switching.ConstantSwitch: Remains in the range 0-1 outside the bounds.
validOutsideBounds() - Method in class ffx.numerics.switching.LinearDerivativeSwitch: Remains in the range 0-1 outside the bounds.
validOutsideBounds() - Method in class ffx.numerics.switching.MultiplicativeSwitch: Remains in the range 0-1 outside the bounds.
validOutsideBounds() - Method in class ffx.numerics.switching.PowerSwitch: Remains in the range 0-1 outside the bounds.
validOutsideBounds() - Method in class ffx.numerics.switching.SquaredTrigSwitch: Remains in the range 0-1 outside the bounds.
validOutsideBounds() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: Remains in the range 0-1 outside the bounds.
validParameters(double, double, double, double, double, double) - Method in enum class ffx.crystal.LatticeSystem: Check that the lattice parameters satisfy the restrictions of the lattice systems.
VALINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
value - Variable in class ffx.potential.bonded.BondedTerm: Value of the term (e.g. bond length, angle, dihedral angle, etc).
value() - Element in annotation interface ffx.utilities.FFXProperties: An array of FFXProperty annotations.
valueAt(double) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
valueAt(double) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction: Value at a point
valueAt(double) - Method in class ffx.numerics.switching.BellCurveSwitch: Value at a point
valueAt(double) - Method in class ffx.numerics.switching.CompositeSwitch
valueAt(double) - Method in class ffx.numerics.switching.ConstantSwitch: Value at a point
valueAt(double) - Method in class ffx.numerics.switching.LinearDerivativeSwitch: Value at a point
valueAt(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: Value at a point
valueAt(double) - Method in class ffx.numerics.switching.PowerSwitch: Value at a point
valueAt(double) - Method in class ffx.numerics.switching.SquaredTrigSwitch: Value at a point
valueChanged(TreeSelectionEvent) - Method in class ffx.ui.Hierarchy
valueOf(String) - Static method in enum class edu.rit.http.HttpResponse.Status: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class edu.rit.pj.cluster.BackendInfo.State: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class edu.rit.pj.cluster.JobInfo.State: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class edu.rit.pj.cluster.ProcessInfo.State: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.dynamics.MDEngine: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.dynamics.MDVerbosity: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.dynamics.MDWriteAction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.dynamics.thermostats.ThermostatEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.Direction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.DistanceMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.crystal.ASULimit: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.crystal.CrystalSystem: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.crystal.LatticeSystem: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.crystal.LaueSystem: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.estimator.Zwanzig.Directionality: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.fft.DataLayout1D: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.fft.DataLayout2D: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.fft.DataLayout3D: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationSide: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.multipole.CoordinateSystem: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.multipole.GKMultipoleOrder: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.multipole.GKTensorMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.multipole.Operator: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.Potential.STATE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.numerics.Potential.VARIABLE_TYPE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AA: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AIB: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ALA: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ARG: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASD: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASH: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASN: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASP: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.CYD: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.CYS: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.CYX: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLD: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLH: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLN: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLU: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLY: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.HID: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.HIE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.HIS: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ILE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.LEU: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.LYD: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.LYS: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.MET: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ORN: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.PCA: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.PHE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.PRO: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.SER: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.THR: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.TRP: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.TYD: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.TYR: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.AminoAcidUtils.VAL: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.Atom.Descriptions: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.Atom.ElementSymbol: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.Atom.Resolution: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.NamingUtils.HetAtoms: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.NucleicAcidUtils.NA: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.RendererCache.ColorModel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.RendererCache.ViewModel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.Residue.ResidueType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.Residue.SSType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.ROLSP.PARALLELMETHOD: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.RotamerLibrary.NucleicAcidLibrary: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.ForceFieldEnergy.RestrainMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.MolecularAssembly.FractionalMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.pme.AlchemicalParameters.AlchemicalMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.pme.LambdaMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.pme.Polarization: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.pme.SCFAlgorithm: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.pme.SCFPredictor: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.ReciprocalSpace.GridMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.AngleType.AngleFunction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.AngleType.AngleMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.BondType.BondFunction: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.ForceField.ELEC_FORM: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.ForceField.ForceFieldName: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.ForceField.ForceFieldType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TitrationUtils.CysStates: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TitrationUtils.HisStates: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TitrationUtils.LysStates: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TitrationUtils.Titration: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.TorsionType.TorsionMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.VDWType.EPSILON_RULE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.VDWType.RADIUS_RULE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.VDWType.RADIUS_SIZE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.VDWType.RADIUS_TYPE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.VDWType.VDW_TYPE: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parameters.VDWType.VDWMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parsers.PDBFilter.PDBFileStandard: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.parsers.SystemFilter.Versioning: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.Platform: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.Utilities.FileType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.potential.Utilities.PolymerType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.ui.GraphicsCanvas.ImageFormat: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.ui.GraphicsCanvas.LeftButtonMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.ui.GraphicsCanvas.MouseMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.ui.GraphicsPicking.PickLevel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.ui.KeywordComponent.SwingRepresentation: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.utilities.PropertyGroup: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.xray.CrystalReciprocalSpace.GridMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class ffx.xray.RefinementMinimize.RefinementMode: Returns the enum constant of this class with the specified name.
values() - Static method in enum class edu.rit.http.HttpResponse.Status: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class edu.rit.pj.cluster.BackendInfo.State: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class edu.rit.pj.cluster.JobInfo.State: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class edu.rit.pj.cluster.ProcessInfo.State: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.dynamics.MDEngine: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.dynamics.MDVerbosity: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.dynamics.MDWriteAction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.dynamics.thermostats.ThermostatEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.Direction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.DistanceMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.crystal.ASULimit: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.crystal.CrystalSystem: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.crystal.LatticeSystem: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.crystal.LaueSystem: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.estimator.Zwanzig.Directionality: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.fft.DataLayout1D: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.fft.DataLayout2D: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.fft.DataLayout3D: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationSide: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.multipole.CoordinateSystem: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.multipole.GKMultipoleOrder: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.multipole.GKTensorMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.multipole.Operator: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.Potential.STATE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.numerics.Potential.VARIABLE_TYPE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AA: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AIB: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ALA: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ARG: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASD: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASH: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASN: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ASP: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.CYD: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.CYS: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.CYX: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLD: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLH: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLN: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLU: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GLY: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.HID: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.HIE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.HIS: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ILE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.LEU: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.LYD: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.LYS: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.MET: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ORN: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.PCA: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.PHE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.PRO: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.SER: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.THR: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.TRP: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.TYD: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.TYR: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.AminoAcidUtils.VAL: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.Atom.Descriptions: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.Atom.ElementSymbol: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.Atom.Resolution: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.NamingUtils.HetAtoms: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.NucleicAcidUtils.NA: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.RendererCache.ColorModel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.RendererCache.ViewModel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.Residue.ResidueType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.Residue.SSType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.ROLSP.PARALLELMETHOD: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.RotamerLibrary.NucleicAcidLibrary: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.ForceFieldEnergy.RestrainMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.MolecularAssembly.FractionalMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.pme.AlchemicalParameters.AlchemicalMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.pme.LambdaMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.pme.Polarization: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.pme.SCFAlgorithm: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.pme.SCFPredictor: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.ReciprocalSpace.GridMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.AngleType.AngleFunction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.AngleType.AngleMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.BondType.BondFunction: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.ForceField.ELEC_FORM: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.ForceField.ForceFieldName: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.ForceField.ForceFieldType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TitrationUtils.CysStates: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TitrationUtils.HisStates: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TitrationUtils.LysStates: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TitrationUtils.Titration: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.TorsionType.TorsionMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.VDWType.EPSILON_RULE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.VDWType.RADIUS_RULE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.VDWType.RADIUS_SIZE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.VDWType.RADIUS_TYPE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.VDWType.VDW_TYPE: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parameters.VDWType.VDWMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parsers.PDBFilter.PDBFileStandard: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.parsers.SystemFilter.Versioning: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.Platform: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.Utilities.FileType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.potential.Utilities.PolymerType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.ui.GraphicsCanvas.ImageFormat: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.ui.GraphicsCanvas.LeftButtonMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.ui.GraphicsCanvas.MouseMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.ui.GraphicsPicking.PickLevel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.ui.KeywordComponent.SwingRepresentation: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.utilities.PropertyGroup: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.xray.CrystalReciprocalSpace.GridMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class ffx.xray.RefinementMinimize.RefinementMode: Returns an array containing the constants of this enum class, in the order they are declared.
VanDerWaals - Class in ffx.potential.nonbonded: The Van der Waals class computes Van der Waals interaction in parallel using a NeighborList for any Crystal.
VanDerWaals() - Constructor for class ffx.potential.nonbonded.VanDerWaals
VanDerWaals(Atom[], int[], boolean[], Crystal, ForceField, ParallelTeam, double, double) - Constructor for class ffx.potential.nonbonded.VanDerWaals: The VanDerWaals class constructor.
VanDerWaals.LambdaFactors - Class in ffx.potential.nonbonded: The trick: The setFactors(i,k) method is called every time through the inner VdW loop, avoiding an "if (esv)" branch statement.
VanDerWaals.LambdaFactorsOST - Class in ffx.potential.nonbonded
VanDerWaalsForm - Class in ffx.potential.nonbonded: This class contains fields and methods for maintaining details of the van der Waals functional form.
VanDerWaalsForm(ForceField) - Constructor for class ffx.potential.nonbonded.VanDerWaalsForm: Constructor for VanDerWaalsForm.
VanDerWaalsFunctionalForm - Enum constant in enum class ffx.utilities.PropertyGroup: Van der Waals functional form.
VanDerWaalsTornado - Class in ffx.potential.nonbonded: The Van der Waals class computes Van der Waals interaction in parallel using a NeighborList for P1 (no symmetry) Crystal systems.
VanDerWaalsTornado(Atom[], Crystal, ForceField, double) - Constructor for class ffx.potential.nonbonded.VanDerWaalsTornado: The VanDerWaalsTornado class constructor.
VAPOR - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
vaporCrystal - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Boundary conditions for the vapor end of the alchemical path.
vaporEwaldSchedule - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
vaporLists - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
vaporPermanentSchedule - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
var - Variable in class ffx.numerics.math.BootStrapStatistics: The variance.
var - Variable in class ffx.numerics.math.SummaryStatistics: Sample variance.
VariableLangevinIntegrator - Class in ffx.openmm: This class implements a Langevin integrator with variable time stepping.
VariableLangevinIntegrator(double, double, double) - Constructor for class ffx.openmm.VariableLangevinIntegrator: Create a VariableLangevinIntegrator.
VariableVerletIntegrator - Class in ffx.openmm: This class implements a Verlet integrator with variable time stepping.
VariableVerletIntegrator(double) - Constructor for class ffx.openmm.VariableVerletIntegrator: Create a VariableVerletIntegrator.
varPopulation - Variable in class ffx.numerics.math.BootStrapStatistics: The population variance.
varPopulation - Variable in class ffx.numerics.math.SummaryStatistics: Population variance.
VCoord - Record Class in ffx.numerics.clustering.visualization: Immutable Virtual coordinate.
VCoord(double, double) - Constructor for record class ffx.numerics.clustering.visualization.VCoord: Constructs an immutable virtual coordinate with the given X and Y values.
VDW - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
VDW - Enum constant in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE
VDW14 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
VDW14 - Enum constant in enum class ffx.potential.parameters.VDWType.VDWMode
VdwForce - Class in ffx.openmm.amoeba: This class models van der Waals forces in the AMOEBA force field.
VdwForce() - Constructor for class ffx.openmm.amoeba.VdwForce: Create an Amoeba VdwForce.
vdwH - Variable in class ffx.potential.parsers.SystemFilter: True if atoms are to be printed to their van der Waals centers instead of nuclear centers (applies primarily to hydrogen).
VDWPAIR - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
VDWPairType - Class in ffx.potential.parameters: The VDWPairType class defines a van der Waals Pair type.
VDWPairType(int[], double, double) - Constructor for class ffx.potential.parameters.VDWPairType: van der Waals constructor.
VDWPR - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
vdwType - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: van der Waals functional form.
VDWType - Class in ffx.potential.parameters: The VDWType class defines van der Waals type for a normal interaction or a special 1-4 interaction.
VDWType(int, double, double, double) - Constructor for class ffx.potential.parameters.VDWType: van der Waals constructor.
VDWType(int, double, double, double, VDWType.VDWMode) - Constructor for class ffx.potential.parameters.VDWType: van der Waals constructor.
VDWType.EPSILON_RULE - Enum Class in ffx.potential.parameters: Epsilon combining rule.
VDWType.RADIUS_RULE - Enum Class in ffx.potential.parameters: Radius combining rule.
VDWType.RADIUS_SIZE - Enum Class in ffx.potential.parameters: Radius size in the parameter file (radius or diameter).
VDWType.RADIUS_TYPE - Enum Class in ffx.potential.parameters: Radius type in the parameter file (R-Min or Sigma).
VDWType.VDW_TYPE - Enum Class in ffx.potential.parameters: VDW Type.
VDWType.VDWMode - Enum Class in ffx.potential.parameters: Torsion modes include Normal or In-Plane
Vec3Array - Class in ffx.openmm: Vec3 Array.
Vec3Array(int) - Constructor for class ffx.openmm.Vec3Array: OpenMM Vec3 Array constructor.
Vec3Array(PointerByReference) - Constructor for class ffx.openmm.Vec3Array: OpenMM Vec3 Array constructor.
vec3Mat3(double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath: Vector times a matrix.
vec3Mat3(double[], double[][], double[]) - Static method in class ffx.numerics.math.MatrixMath: vec3mat3
Vector3d - Class in ffx.numerics.quickhull: A three-element vector.
Vector3d() - Constructor for class ffx.numerics.quickhull.Vector3d: Creates a 3-vector and initializes its elements to 0.
Vector3d(double, double, double) - Constructor for class ffx.numerics.quickhull.Vector3d: Creates a 3-vector with the supplied element values.
Vector3d(Vector3d) - Constructor for class ffx.numerics.quickhull.Vector3d: Creates a 3-vector by copying an existing one.
velocity - Variable in class ffx.ui.commands.SimulationUpdate
VELOCITY - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
VELOCITY_VERLET - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
VelocityVerlet - Class in ffx.algorithms.dynamics.integrators: Integrate Newton's equations of motion using a Velocity Verlet multistep recursion formula.
VelocityVerlet(SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.VelocityVerlet: Constructor for VelocityVerlet.
verbose - Variable in class ffx.algorithms.commands.Thermodynamics: -v or --verbose Log additional information (primarily for MC-OST).
VERBOSE - Enum constant in enum class ffx.algorithms.dynamics.MDVerbosity
VERBOSE - Static variable in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
VERLET - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
VerletIntegrator - Class in ffx.openmm: Verlet Integrator.
VerletIntegrator(double) - Constructor for class ffx.openmm.VerletIntegrator: Constructor.
version - Static variable in class ffx.ui.MainPanel: Constant version="1.0.0"
version - Variable in class ffx.utilities.FFXCommand: -V or --version Prints the FFX version and exits.
version(File) - Static method in class ffx.potential.parsers.SystemFilter: Use setVersioning() to choose between prefix/postfix.
version(File) - Static method in class ffx.utilities.TinkerUtils: This follows the TINKER file versioning scheme.
Version - Class in edu.rit.pj: Class Version defines version information for the Parallel Java Library.
VERSION2_3 - Enum constant in enum class ffx.potential.parsers.PDBFilter.PDBFileStandard
VERSION3_0 - Enum constant in enum class ffx.potential.parsers.PDBFilter.PDBFileStandard
VERSION3_1 - Enum constant in enum class ffx.potential.parsers.PDBFilter.PDBFileStandard
VERSION3_2 - Enum constant in enum class ffx.potential.parsers.PDBFilter.PDBFileStandard
VERSION3_3 - Enum constant in enum class ffx.potential.parsers.PDBFilter.PDBFileStandard
versionFile(File) - Method in interface ffx.potential.utils.PotentialsFunctions: Versions a file, attempting to find an unused filename in the set filename, and filename_1 to filename_999.
versionFile(String) - Method in interface ffx.potential.utils.PotentialsFunctions: Versions a file, attempting to find an unused filename in the set filename, and filename_1 to filename_999.
vertex - Variable in class ffx.numerics.quickhull.HalfEdge: The vertex associated with the head of this half-edge.
Vertex - Class in ffx.numerics.quickhull: Represents vertices of the hull, as well as the points from which it is formed.
Vertex() - Constructor for class ffx.numerics.quickhull.Vertex: Constructs a vertex and sets its coordinates to 0.
Vertex(double, double, double, int) - Constructor for class ffx.numerics.quickhull.Vertex: Constructs a vertex with the specified coordinates and index.
vertexPointIndices - Variable in class ffx.numerics.quickhull.QuickHull3D
ViewerTG - Variable in class ffx.ui.behaviors.MouseBehavior
viewModelHash - Static variable in class ffx.potential.bonded.RendererCache: Constant viewModelHash
viewWait(String) - Method in class ffx.ui.GraphicsCanvas: viewWait
VirtualSite - Class in ffx.openmm: A VirtualSite describes the rules for computing a particle's position based on other particles.
VirtualSite(PointerByReference) - Constructor for class ffx.openmm.VirtualSite: Create a VirtualSite from an existing pointer.
VISIBLE - Static variable in class ffx.numerics.quickhull.Face
volume - Variable in class ffx.crystal.Crystal: The crystal unit cell volume.
Volume - Class in ffx.potential.commands: Calculate the surface area and volume using the GaussVol (default) or Connolly algorithm.
Volume() - Constructor for class ffx.potential.commands.Volume
Volume(FFXBinding) - Constructor for class ffx.potential.commands.Volume
Volume(String[]) - Constructor for class ffx.potential.commands.Volume
VolumeArc - Class in ffx.potential.commands: Calculate the surface area and volume using the GaussVol (default) or Connolly algorithm for each snapshot in an ARC file.
VolumeArc() - Constructor for class ffx.potential.commands.VolumeArc
VolumeArc(FFXBinding) - Constructor for class ffx.potential.commands.VolumeArc
VolumeArc(String[]) - Constructor for class ffx.potential.commands.VolumeArc

W

W - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
W - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
W - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
W_H - Enum constant in enum class ffx.potential.parameters.VDWType.EPSILON_RULE
wA - Variable in class ffx.xray.cli.DataRefinementOptions: --wA or --dataWeight The weight of the data (wA).
WAIT - Static variable in class edu.rit.pj.BarrierAction: Do a barrier wait, without executing any code in a single thread.
waitForCommence() - Method in class edu.rit.pj.cluster.JobBackend: Wait until this job commences.
waitForFinish() - Method in class edu.rit.mp.IORequest: Wait until the send or receive operation corresponding to this I/O request has finished.
waitForFinish() - Method in class edu.rit.pj.CommRequest: Wait for the message passing operation associated with this CommRequest object to finish.
WAITING - Enum constant in enum class edu.rit.pj.cluster.JobInfo.State: The job is waiting to run.
wakeup() - Method in class ffx.ui.behaviors.MouseBehavior: Manually wake up the behavior.
wakeUp - Variable in class ffx.ui.behaviors.MouseBehavior
wakeupCondition - Variable in class ffx.ui.behaviors.PickMouseBehavior
warning(SAXParseException) - Method in class ffx.potential.parsers.PDBMLFilter
wasHistogramRead() - Method in class ffx.algorithms.thermodynamics.HistogramData
wasLambdaRead() - Method in class ffx.algorithms.thermodynamics.LambdaData
WAT - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
WBMP - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
WcaDispersionForce - Class in ffx.openmm.amoeba: This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model.
WcaDispersionForce() - Constructor for class ffx.openmm.amoeba.WcaDispersionForce: Create an AmoebaWcaDispersionForce.
weakCompareAndSet(boolean, boolean) - Method in class edu.rit.pj.reduction.SharedBoolean: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(byte, byte) - Method in class edu.rit.pj.reduction.SharedByte: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(char, char) - Method in class edu.rit.pj.reduction.SharedCharacter: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(double, double) - Method in class edu.rit.pj.reduction.SharedDouble: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(float, float) - Method in class edu.rit.pj.reduction.SharedFloat: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, boolean, boolean) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, byte, byte) - Method in class edu.rit.pj.reduction.SharedByteArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, char, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, double, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, float, float) - Method in class edu.rit.pj.reduction.SharedFloatArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, int) - Method in class edu.rit.pj.reduction.SharedInteger: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Atomically set this matrix reduction variable at the given row and column to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, int, long, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Atomically set this matrix reduction variable at the given row and column to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, long, long) - Method in class edu.rit.pj.reduction.SharedLongArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, short, short) - Method in class edu.rit.pj.reduction.SharedShortArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(int, T, T) - Method in class edu.rit.pj.reduction.SharedObjectArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
weakCompareAndSet(long, long) - Method in class edu.rit.pj.reduction.SharedLong: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(short, short) - Method in class edu.rit.pj.reduction.SharedShort: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
weakCompareAndSet(T, T) - Method in class edu.rit.pj.reduction.SharedObject: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
WEB_PORT - Static variable in class edu.rit.pj.cluster.Constants: The default port number for the Job Scheduler's web interface (8080).
WeightedEnsemble - Class in ffx.algorithms.commands.test: WeightedEnsemble
Usage: Accelerated Sampling with Weighted Ensemble
ffxc test.WeightedEnsemble [options] <filename> [file2
WeightedEnsemble() - Constructor for class ffx.algorithms.commands.test.WeightedEnsemble: Constructor.
WeightedEnsemble(FFXBinding) - Constructor for class ffx.algorithms.commands.test.WeightedEnsemble: Constructor.
WeightedEnsemble(String[]) - Constructor for class ffx.algorithms.commands.test.WeightedEnsemble: WeightedEnsemble constructor that sets the command line arguments.
WeightedEnsembleManager - Class in ffx.algorithms.dynamics: This class implements the Weighted Ensemble algorithm.
WeightedEnsembleManager(WeightedEnsembleManager.OneDimMetric, int, MolecularDynamics, File, boolean) - Constructor for class ffx.algorithms.dynamics.WeightedEnsembleManager
WeightedEnsembleManager.OneDimMetric - Enum Class in ffx.algorithms.dynamics
WeightedLinkageStrategy - Class in ffx.numerics.clustering: Linkage strategy that computes a weighted average of pairwise distances using the associated weights of cluster members.
WeightedLinkageStrategy() - Constructor for class ffx.numerics.clustering.WeightedLinkageStrategy
weightMultipoleTypes(MultipoleType[], double[], int[]) - Static method in class ffx.potential.parameters.MultipoleType: Create a new multipole representing a weighted average.
wellDepth - Variable in class ffx.potential.parameters.VDWPairType: The minimum energy of the vdw function (kcal/mol).
wellDepth - Variable in class ffx.potential.parameters.VDWType: The minimum energy of the vdw function (kcal/mol).
WideAngle - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult: Angle between gradient and search direction is too wide.
WINDOW - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
windowLength(int) - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule: Get the relative size of a window (normalized to the number of MD steps in a "regular" window).
windowLength(int) - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
windowLength(int) - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
windowLength(int) - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
WIREFRAME - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
withoutReplacement(Random, int, int) - Static method in class edu.rit.util.RandomSample: Create an iterator that generates a random sample of ints without replacement.
withoutReplacement(Random, int, int, int[]) - Static method in class edu.rit.util.RandomSample: Generate a random sample of ints without replacement.
withoutReplacement(Random, int, long) - Static method in class edu.rit.util.RandomSample: Create an iterator that generates a random sample of longs without replacement.
withoutReplacement(Random, int, long, long[]) - Static method in class edu.rit.util.RandomSample: Generate a random sample of longs without replacement.
WOLFENDEN - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
work - Variable in class ffx.numerics.multipole.MultipoleTensor: Store the work array to avoid memory consumption.
work - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: A work array with auxiliary terms for the recursion.
work3D - Variable in class ffx.numerics.fft.Complex3DParallel: Work array used for transforms along the Z-axis.
WorkerConstruct - Class in edu.rit.pj: Class WorkerConstruct is the common base class for all worker constructs that are executed by a WorkerTeam.
WorkerConstruct() - Constructor for class edu.rit.pj.WorkerConstruct: Construct a new worker construct.
WorkerForLoop - Class in edu.rit.pj: Class WorkerForLoop is the abstract base class for a worker for loop that is executed inside a WorkerRegion.
WorkerForLoop() - Constructor for class edu.rit.pj.WorkerForLoop: Construct a new worker for loop.
WorkerIntegerForLoop - Class in edu.rit.pj: Class WorkerIntegerForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.
WorkerIntegerForLoop() - Constructor for class edu.rit.pj.WorkerIntegerForLoop: Construct a new worker for loop.
WorkerIntegerStrideForLoop - Class in edu.rit.pj: Class WorkerIntegerStrideForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.
WorkerIntegerStrideForLoop() - Constructor for class edu.rit.pj.WorkerIntegerStrideForLoop: Construct a new worker for loop.
WorkerIteration<T> - Class in edu.rit.pj: Class WorkerIteration is the abstract base class for a worker iteration that is executed inside a WorkerRegion.
WorkerIteration() - Constructor for class edu.rit.pj.WorkerIteration: Construct a new worker iteration.
WorkerLongForLoop - Class in edu.rit.pj: Class WorkerLongForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.
WorkerLongForLoop() - Constructor for class edu.rit.pj.WorkerLongForLoop: Construct a new worker for loop.
WorkerLongStrideForLoop - Class in edu.rit.pj: Class WorkerLongStrideForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.
WorkerLongStrideForLoop() - Constructor for class edu.rit.pj.WorkerLongStrideForLoop: Construct a new worker for loop.
workerRank(int) - Method in class edu.rit.pj.HybridTeam: Determine the rank of the process that contains the worker thread with the given index.
workerRank(int) - Method in class edu.rit.pj.WorkerTeam: Determine the rank of the process that contains the worker thread with the given index.
WorkerRegion - Class in edu.rit.pj: Class WorkerRegion is the abstract base class for a worker region that is executed by a WorkerTeam of threads distributed across the processes of a cluster parallel program.
WorkerRegion() - Constructor for class edu.rit.pj.WorkerRegion: Construct a new worker region.
WorkerTeam - Class in edu.rit.pj: Class WorkerTeam provides a team of threads, distributed across the processes of a cluster parallel program, for executing a WorkerRegion in parallel.
WorkerTeam() - Constructor for class edu.rit.pj.WorkerTeam: Construct a new worker team with one thread per process and using the world communicator for message passing.
WorkerTeam(Comm) - Constructor for class edu.rit.pj.WorkerTeam: Construct a new worker team with one thread per process and using the given communicator for message passing.
world - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram: Parallel Java world communicator.
world - Variable in class ffx.algorithms.thermodynamics.SendSynchronous: Parallel Java world communicator.
world() - Static method in class edu.rit.pj.Comm: Obtain a reference to the world communicator.
worldAddress - Variable in class edu.rit.pj.cluster.ProcessInfo: Host/port to which the job backend process is listening for the world communicator.
write() - Method in class edu.rit.io.DoubleMatrixFile.Writer: Write all rows and columns of the matrix to the output stream.
write() - Method in class ffx.xray.parsers.MTZWriter: write
write(byte[]) - Method in class edu.rit.io.LineBufferedOutputStream: Write the given byte array to this line buffered output stream.
write(byte[]) - Method in class edu.rit.pj.cluster.BackendFileOutputStream: Write the given byte array to this output stream.
write(byte[], int, int) - Method in class edu.rit.io.LineBufferedOutputStream: Write a portion of the given byte array to this line buffered output stream.
write(byte[], int, int) - Method in class edu.rit.pj.cluster.BackendFileOutputStream: Write a portion of the given byte array to this output stream.
write(double[]) - Method in class ffx.xray.parsers.CCP4MapWriter: Write data to file (does not normalize).
write(double[]) - Method in class ffx.xray.parsers.CNSMapWriter: write
write(double[], boolean) - Method in class ffx.xray.parsers.CCP4MapWriter: write data to file, does not normalize
write(int) - Method in class edu.rit.io.LineBufferedOutputStream: Write the given byte to this line buffered output stream.
write(int) - Method in class edu.rit.pj.cluster.BackendFileOutputStream: Write the given byte to this output stream.
write(DataOutput) - Method in class edu.rit.util.ByteSequence: Write this byte sequence's contents to the given data output stream.
write(OutputStream) - Method in class edu.rit.util.ByteSequence: Write this byte sequence's contents to the given output stream.
writeAdditionalRestartInfo(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
writeAdditionalRestartInfo(boolean) - Method in interface ffx.numerics.Potential: Writes additional restart information, if any (e.g.
writeAtomRanges(int[]) - Static method in class ffx.utilities.StringUtils: Write atoms ranges for a list of atom indices.
writeBoolean(boolean) - Method in class edu.rit.io.DataOutputStream: Write the given Boolean value to this data output stream.
writeColSlice(Range) - Method in class edu.rit.io.DoubleMatrixFile.Writer: Write the given column slice of the matrix to the output stream.
writeData(String) - Method in class ffx.xray.DiffractionData: write current datasets to MTZ files
writeData(String, int) - Method in class ffx.xray.DiffractionData: write dataset i to MTZ file
writeDistanceMatrix(String, List<double[]>) - Static method in class ffx.potential.parsers.DistanceMatrixFilter: Write the distance matrix to a file.
writeDistanceMatrixRow(String, double[], int) - Static method in class ffx.potential.parsers.DistanceMatrixFilter: Write the distance matrix to a file.
writeDouble(double) - Method in class edu.rit.io.DataOutputStream: Write the given double value to this data output stream.
writeDYN(File, Crystal, double[], double[], double[], double[]) - Method in class ffx.potential.parsers.DYNFilter: writeDYN
writeEnergyRestart - Variable in class ffx.algorithms.optimize.RotamerOptimization: If true, write out an energy restart file.
writeESV(File, double[], double[], double[], List<Residue>, int[][][], double) - Method in class ffx.potential.parsers.ESVFilter: Write the extended system variables to a file.
writeESVInfoTo(File) - Method in class ffx.potential.extended.ExtendedSystem: Writes out the current state of the extended system to the specified file without setting the file to that location.
writeExternal(ObjectOutput) - Method in class edu.rit.pj.cluster.JobBackendMessage: Write this job backend message to the given object output stream.
writeExternal(ObjectOutput) - Method in class edu.rit.pj.cluster.JobFrontendMessage: Write this job frontend message to the given object output stream.
writeExternal(ObjectOutput) - Method in class edu.rit.pj.cluster.JobSchedulerMessage: Write this job scheduler message to the given object output stream.
writeExternal(ObjectOutput) - Method in class edu.rit.pj.job.Job: Write this job to the given object output stream.
writeExternal(ObjectOutput) - Method in class edu.rit.util.LongRange: Write this range to the given object output stream.
writeExternal(ObjectOutput) - Method in class edu.rit.util.Range: Write this range to the given object output stream.
writeFile(double[][], File, double) - Method in class ffx.numerics.estimator.MBARFilter: Write the energies to a file.
writeFile(double[][], File, double) - Static method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
writeFile(File, boolean) - Method in class ffx.potential.parsers.CIFFilter: Save a CIF file for the given molecular assembly.
writeFile(File, boolean) - Method in class ffx.potential.parsers.PDBFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean) - Method in class ffx.potential.parsers.SystemFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean, boolean) - Method in class ffx.potential.parsers.PDBFilter: Writes out the atomic information in PDB format.
writeFile(File, boolean, boolean, boolean) - Method in class ffx.potential.parsers.PDBFilter: writeFile
writeFile(File, boolean, String[]) - Method in class ffx.potential.parsers.CIFFilter: Save a CIF file for the given molecular assembly.
writeFile(File, boolean, String[]) - Method in class ffx.potential.parsers.INTFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean, String[]) - Method in class ffx.potential.parsers.MergeFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean, String[]) - Method in class ffx.potential.parsers.PDBFilter
writeFile(File, boolean, String[]) - Method in class ffx.potential.parsers.SystemFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean, String[]) - Method in class ffx.potential.parsers.XPHFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean, String[]) - Method in class ffx.potential.parsers.XYZFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean, String[]) - Method in class ffx.ui.commands.SimulationFilter: This method is different for each subclass and must be overridden.
writeFile(File, boolean, Set<Atom>, boolean, boolean) - Method in class ffx.potential.parsers.PDBFilter: writeFile
writeFile(File, boolean, Set<Atom>, boolean, boolean, String[]) - Method in class ffx.potential.parsers.PDBFilter: writeFile
writeFile(String, boolean) - Method in class ffx.potential.parsers.BARFilter: Write TINKER bar files
writeFile(String, boolean, boolean) - Method in class ffx.potential.parsers.BARFilter: Write TINKER bar files
writeFileAsP1(File) - Method in class ffx.potential.parsers.PDBFilter: Expand the current system to P1 during the save operation.
writeFileAsP1(File, boolean, Crystal) - Method in class ffx.potential.parsers.XPHFilter: writeFileAsP1
writeFileAsP1(File, boolean, Crystal) - Method in class ffx.potential.parsers.XYZFilter: writeFileAsP1
writeFileAsP1(File, boolean, Crystal, int[], String[]) - Method in class ffx.potential.parsers.XYZFilter: Write file as a P1 system in XYZ format.
writeFileAsP1(File, boolean, Crystal, String[]) - Method in class ffx.potential.parsers.XPHFilter: writeFileAsP1
writeFileAsP1(File, boolean, Crystal, String[]) - Method in class ffx.potential.parsers.XYZFilter: writeFileAsP1
writeFiles() - Method in class ffx.potential.parsers.CIFFilter: Write CIF files for multiple File objects.
writeFiles(File, double[][][], double[]) - Method in class ffx.numerics.estimator.MBARFilter: Write the energies to files.
writeFilesForStep(long, boolean, boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Write restart and trajectory files if the provided step matches the frequency and that file type is requested.
writeFilesForStep(long, boolean, boolean) - Method in class ffx.algorithms.mc.MDMove: Write restart and trajectory files if the provided step matches the frequency.
writeFilesForStep(long, boolean, boolean, String[]) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Write restart and trajectory files if the provided step matches the frequency and that file type is requested.
writeFileWithHeader(File, String) - Method in class ffx.potential.parsers.PDBFilter: writeFileWithHeader.
writeFileWithHeader(File, StringBuilder) - Method in class ffx.potential.parsers.PDBFilter: writeFileWithHeader.
writeFileWithHeader(File, String, boolean) - Method in class ffx.potential.parsers.PDBFilter: writeFileWithHeader.
writeFloat(float) - Method in class edu.rit.io.DataOutputStream: Write the given float value to this data output stream.
writeHistogram() - Method in class ffx.algorithms.thermodynamics.HistogramData: Marshall this histogram data to a file.
writeHistogram(HistogramData, File) - Static method in class ffx.algorithms.thermodynamics.HistogramData: Marshall the histogram data to a file.
writeInt(int) - Method in class edu.rit.io.DataOutputStream: Write the given integer value to this data output stream.
writeLambdaData() - Method in class ffx.algorithms.thermodynamics.LambdaData: Marshall the lambda data to a file.
writeLambdaData(LambdaData, File) - Static method in class ffx.algorithms.thermodynamics.LambdaData: Marshall the lambda data to a file.
writeLambdaHistogram(boolean) - Method in class ffx.potential.extended.ExtendedSystem: Execute writeLambdaHistogrm from esvFilter that is contained within ExtendedSystem Prints the ESV histogram for each titrating residue
writeLong(long) - Method in class edu.rit.io.DataOutputStream: Write the given long value to this data output stream.
writeMaps(String) - Method in class ffx.xray.DiffractionData: write 2Fo-Fc and Fo-Fc maps for all datasets
writeModel(String) - Method in class ffx.xray.DiffractionData: Write current model to PDB file.
writeModel(String, Set<Atom>, double) - Method in class ffx.xray.DiffractionData: Write current model to PDB file.
writeoutOptions - Variable in class ffx.algorithms.commands.Thermodynamics
WriteoutOptions - Class in ffx.potential.cli: Represents command line options for scripts that periodically write out structures.
WriteoutOptions() - Constructor for class ffx.potential.cli.WriteoutOptions
writeOutputFile(MolecularAssembly) - Method in class ffx.potential.parsers.CIFFilter: Write an output file.
writePatch(Range, Range) - Method in class edu.rit.io.DoubleMatrixFile.Writer: Write the given patch of the matrix to the output stream.
writePDBBackbone(double[][], double[][], double[][], int, int, MolecularAssembly, int, boolean) - Method in class ffx.potential.bonded.SturmMethod: Write out loop coordinates and determine oxygen placement.
writePropertiesFile(String, String, String, List<MSNode>) - Method in class ffx.potential.parsers.CIFFilter: Write a properties file.
writeRestart() - Method in class ffx.algorithms.dynamics.MolecularDynamics: Write out a restart file.
writeRestart() - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
writeRestart() - Method in class ffx.potential.extended.ExtendedSystem: Execute writeESV from esvFilter that is contained within ExtendedSystem
WriteRestraints - Class in ffx.potential.commands: WriteRestraints logs "restrain-position" properties for a PDB/XYZ file.
WriteRestraints() - Constructor for class ffx.potential.commands.WriteRestraints
WriteRestraints(FFXBinding) - Constructor for class ffx.potential.commands.WriteRestraints
WriteRestraints(String[]) - Constructor for class ffx.potential.commands.WriteRestraints
writeRowSlice(Range) - Method in class edu.rit.io.DoubleMatrixFile.Writer: Write the given row slice of the matrix to the output stream.
writeSolventMask(String) - Method in class ffx.xray.DiffractionData: Write bulk solvent mask for all datasets to a CCP4 map file.
writeSolventMaskCNS(String) - Method in class ffx.xray.DiffractionData: Write bulk solvent mask for all datasets to a CNS map file.
writeString(String) - Method in class edu.rit.io.DataOutputStream: Write the given string value to this data output stream.
writeStructuresToXYZ(File) - Method in class ffx.algorithms.optimize.ConformationScan
writeUnsignedInt(int) - Method in class edu.rit.io.DataOutputStream: Write the given unsigned integer value to this data output stream.
writeUnsignedLong(long) - Method in class edu.rit.io.DataOutputStream: Write the given unsigned long value to this data output stream.

X

x - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
x - Variable in class ffx.algorithms.optimize.Minimize: Current value of each variable.
x - Variable in class ffx.algorithms.optimize.PhMinimize: Current value of each variable.
x - Variable in class ffx.numerics.integrate.FunctionDataCurve: Input points.
x - Variable in class ffx.numerics.math.SSETest: A vector of double values.
x - Variable in class ffx.numerics.multipole.MultipoleTensor: Xk - Xi.
x - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Xk - Xi.
x - Variable in class ffx.numerics.quickhull.Vector3d: First element
x - Variable in class ffx.potential.SystemState: Coordinates.
x - Variable in class ffx.ui.behaviors.MouseBehavior
x() - Method in record class ffx.numerics.clustering.visualization.VCoord: Returns the X coordinate value in model space.
x() - Method in class ffx.numerics.math.Double3: Get the value x.
x() - Method in class ffx.numerics.math.Float3: Get the value x.
x() - Method in class ffx.potential.SystemState: Get a reference to the internal coordinates array.
x() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the x record component.
X - Enum constant in enum class ffx.numerics.Potential.VARIABLE_TYPE: X-coordinate.
X - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
X - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
X(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the cross-product between two vectors
X(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the cross-product between two vectors
X(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the cross-product between two vectors.
X(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the cross-product between two vectors.
X(Double3) - Method in class ffx.numerics.math.Double3: Cross product of this Double3 with b.
X(Float3) - Method in class ffx.numerics.math.Float3: Cross product of this Float3 with b.
Xe - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
XI(Double3) - Method in class ffx.numerics.math.Double3: In-place Cross product of this Double3 with b.
XI(Float3) - Method in class ffx.numerics.math.Float3: In-place Cross product of this Float3 with b.
xLast - Variable in class ffx.ui.behaviors.MouseBehavior
XOR - Static variable in class edu.rit.pj.reduction.BooleanOp: The Boolean logical "exclusive or" binary operation.
XOR - Static variable in class edu.rit.pj.reduction.ByteOp: The byte bitwise "exclusive or" binary operation.
XOR - Static variable in class edu.rit.pj.reduction.CharacterOp: The character bitwise "exclusive or" binary operation.
XOR - Static variable in class edu.rit.pj.reduction.IntegerOp: The integer bitwise "exclusive or" binary operation.
XOR - Static variable in class edu.rit.pj.reduction.LongOp: The long bitwise "exclusive or" binary operation.
XOR - Static variable in class edu.rit.pj.reduction.ShortOp: The short bitwise "exclusive or" binary operation.
XPH - Enum constant in enum class ffx.potential.Utilities.FileType
XPHFileFilter - Class in ffx.potential.parsers: The XPHFileFilter class is used to choose a XPH Coordinate (*.XPH) file.
XPHFileFilter() - Constructor for class ffx.potential.parsers.XPHFileFilter: Public Constructor.
XPHFilter - Class in ffx.potential.parsers: The XYZFilter class parses TINKER Cartesian coordinate (*.XYZ) files.
XPHFilter(SystemFilter, ExtendedSystem) - Constructor for class ffx.potential.parsers.XPHFilter
XPHFilter(File, MolecularAssembly, ForceField, CompositeConfiguration, ExtendedSystem) - Constructor for class ffx.potential.parsers.XPHFilter: Constructor for XPHFilter.
XRayEnergy - Class in ffx.xray: Combine the X-ray target and chemical potential energy.
XRayEnergy(DiffractionData, int, int, int, RefinementMinimize.RefinementMode) - Constructor for class ffx.xray.XRayEnergy: Diffraction data energy target
XRayFormFactor - Class in ffx.xray: This implementation uses the coefficients from Su and Coppens and 3 coefficient parameters derived from CCTBX.
XRayFormFactor(Atom) - Constructor for class ffx.xray.XRayFormFactor: Constructor for XRayFormFactor.
XRayFormFactor(Atom, boolean) - Constructor for class ffx.xray.XRayFormFactor: Constructor for XRayFormFactor.
XRayFormFactor(Atom, boolean, double) - Constructor for class ffx.xray.XRayFormFactor: Constructor for XRayFormFactor.
XRayFormFactor(Atom, boolean, double, double[]) - Constructor for class ffx.xray.XRayFormFactor: Constructor for XRayFormFactor.
XrayOptions - Class in ffx.xray.cli: Represents command line options for scripts that utilize X-ray data with a maximum likelihood target.
XrayOptions() - Constructor for class ffx.xray.cli.XrayOptions
XtalEnergy - Class in ffx.potential: This class computes the energy and Cartesian coordinate gradient, plus finite difference derivatives of lattice parameters.
XtalEnergy(ForceFieldEnergy, MolecularAssembly) - Constructor for class ffx.potential.XtalEnergy: Constructor for XtalEnergy.
XtalEnergy(ForceFieldEnergy, MolecularAssembly, boolean) - Constructor for class ffx.potential.XtalEnergy: Constructor for XtalEnergy.
XYZ - Enum constant in enum class ffx.potential.Utilities.FileType
XYZFileFilter - Class in ffx.potential.parsers: The XYZFileFilter class is used to choose a TINKER Cartesian Coordinate (*.XYZ) file.
XYZFileFilter() - Constructor for class ffx.potential.parsers.XYZFileFilter: Public Constructor.
XYZFilter - Class in ffx.potential.parsers: The XYZFilter class parses TINKER Cartesian coordinate (*.XYZ) files.
XYZFilter(File, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.XYZFilter: Constructor for XYZFilter.
XYZFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.XYZFilter: Constructor for XYZFilter.
XyzIndex_Name - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
XYZIndexComparator - Static variable in class ffx.potential.bonded.Atom: Compare two atoms (implementation of the Comparator interface).

Y

y - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
y - Variable in class ffx.numerics.multipole.MultipoleTensor: Yk - Yi.
y - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Yk - Yi.
y - Variable in class ffx.numerics.quickhull.Vector3d: Second element
y - Variable in class ffx.ui.behaviors.MouseBehavior
y() - Method in record class ffx.numerics.clustering.visualization.VCoord: Returns the Y coordinate value in model space.
y() - Method in class ffx.numerics.math.Double3: Get the value of y.
y() - Method in class ffx.numerics.math.Float3: Get the value of y.
Y - Enum constant in enum class ffx.numerics.Potential.VARIABLE_TYPE: Y-coordinate.
Y - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
Y - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Yb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
yFromRowIndex(int) - Method in class ffx.potential.nonbonded.RowRegion: yFromRowIndex.
yLast - Variable in class ffx.ui.behaviors.MouseBehavior
YYG - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3

Z

z - Variable in class ffx.numerics.multipole.MultipoleTensor: Zk - Zi.
z - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD: Zk - Zi.
z - Variable in class ffx.numerics.quickhull.Vector3d: Third element
z - Variable in class ffx.potential.nonbonded.NeighborList.AtomIndex
z() - Method in class ffx.numerics.math.Double3: Get the value of z.
z() - Method in class ffx.numerics.math.Float3: Get the value of z.
Z - Enum constant in enum class ffx.numerics.Potential.VARIABLE_TYPE: Z-coordinate.
Z - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
Z - Variable in class ffx.numerics.multipole.PolarizableMultipole
ZERO_ROTATION - Static variable in class ffx.crystal.SymOp: Constant ZERO_ROTATION = {{1.0, 0.0, 0.0}, {0.0, 1.0, 0.0}, {0.0, 0.0, 1.0}}
zeroD - Static variable in class ffx.potential.parameters.MultipoleType: Constant zeroD
zeroM - Static variable in class ffx.potential.parameters.MultipoleType: Constant zeroM
zeroQ - Static variable in class ffx.potential.parameters.MultipoleType: Constant zeroD
ZEROS - Enum constant in enum class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType
zFromRowIndex(int) - Method in class ffx.potential.nonbonded.RowRegion: zFromRowIndex.
Zn - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ZN - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
ZN2 - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
ZONLY - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
zoom - Variable in class ffx.ui.behaviors.PickZoomBehavior
ZOOM - Enum constant in enum class ffx.ui.GraphicsCanvas.LeftButtonMode
ZOOM - Static variable in interface ffx.ui.behaviors.MouseBehaviorCallback: Constant ZOOM=2
ZOOM - Static variable in interface ffx.ui.behaviors.PickingCallback: Constant ZOOM=2
Zr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ZTHENBISECTOR - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
ZTHENX - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
Zwanzig - Class in ffx.numerics.estimator: The Zwanzig class implements exponential averaging/free energy perturbation using the Zwanzig relationship, in either the forwards or backwards direction (not both).
Zwanzig(double[], double[][], double[][], double[][], double[], Zwanzig.Directionality) - Constructor for class ffx.numerics.estimator.Zwanzig: Estimates a free energy using the Zwanzig relationship.
ZWANZIG - Enum constant in enum class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType
Zwanzig.Directionality - Enum Class in ffx.numerics.estimator: Directionality of the Zwanzig estimation (forwards perturbation or backwards perturbation).

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