Index
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
-
Matrix to convert from Cartesian to fractional coordinates.
- A - Variable in class ffx.numerics.math.SSETest
-
A matrix of double values.
- A00 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A01 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A02 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A10 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A11 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A12 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A20 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A21 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- A22 - Variable in class ffx.crystal.Crystal
-
Entry in the A matrix.
- 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.AlgorithmsScript
-
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.
- activeAssembly - Variable in class ffx.potential.cli.PotentialScript
-
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
- 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 value to the double array at the specified index.
- add(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray
-
Add value to the double array at the specified index.
- add(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray
-
Add value to the double array at the specified index.
- add(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray
-
Add 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(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.
- 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.
- addAngle(int, int, int, DoubleArray) - Method in class ffx.openmm.CustomAngleForce
-
Add an angle force to the OpenMM System.
- 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.
- addBond(int, int, double, double) - Method in class ffx.openmm.HarmonicBondForce
-
Add a Harmonic Bond.
- addBond(int, int, DoubleArray) - Method in class ffx.openmm.CustomBondForce
-
Add a bond to the OpenMM System.
- 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 Custom Compound Bond to the OpenMM System.
- addChild(int, int) - Method in class ffx.potential.nonbonded.octree.Octree
-
Add a child.
- addCOMMRemoverForce() - Method in class ffx.potential.openmm.OpenMMSystem
-
Adds a force that removes center-of-mass motion.
- addComputedValue(String, String, int) - Method in class ffx.openmm.CustomGBForce
-
Add a computed value.
- addComputePerDof(String, String) - Method in class ffx.openmm.CustomIntegrator
-
Add a per-DOF computation to this Integrator.
- 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.
- addEnergyParameterDerivative(String) - Method in class ffx.openmm.CustomCentroidBondForce
-
Request that this Force compute the derivative of its energy with respect to a global parameter.
- addEnergyTerm(String, int) - Method in class ffx.openmm.CustomGBForce
-
Add an energy term.
- 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.
- addExclusion(int, int) - Method in class ffx.openmm.CustomNonbondedForce
-
Add an exclusion.
- 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.OpenMMSystem
-
Add forces to the system.
- addGlobalParameter(String, double) - Method in class ffx.openmm.CustomBondForce
-
Add a global parameter to the CustomBondForce.
- 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.
- addGlobalParameter(String, double) - Method in class ffx.openmm.CustomGBForce
-
Add a global parameter.
- addGlobalParameter(String, double) - Method in class ffx.openmm.CustomNonbondedForce
-
Add a global parameter.
- 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.
- 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.
- 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.
- addInteractionGroup(IntSet, IntSet) - Method in class ffx.openmm.CustomNonbondedForce
-
Add an interaction group.
- addKeyword(Keyword) - Method in class ffx.ui.FFXSystem
-
addKeyword
- 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 a multipole.
- addMultiResidue(MultiResidue) - Method in class ffx.potential.bonded.Polymer
-
addMultiResidue.
- 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 term.
- addParticle(double, double, double) - Method in class ffx.openmm.NonbondedForce
-
Add a particle.
- addParticle(double, double, int) - Method in class ffx.openmm.amoeba.GKCavitationForce
-
Add an atom to the Cavitation force.
- addParticle(int, DoubleArray) - Method in class ffx.openmm.CustomExternalForce
-
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.
- addParticle_1(double, double, double, double, double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
-
Add a particle to the force.
- addParticle_1(int, int, double, int, double) - Method in class ffx.openmm.amoeba.VdwForce
-
Add a particle to the vdW Force.
- addParticleType(double, double) - Method in class ffx.openmm.amoeba.VdwForce
-
Add a particle type to the vdW Force.
- addPerAngleParameter(String) - Method in class ffx.openmm.CustomAngleForce
-
Add a per-angle parameter to the OpenMM System.
- addPerBondParameter(String) - Method in class ffx.openmm.CustomBondForce
-
Add a per-bond parameter to the CustomBondForce.
- 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 to the OpenMM System.
- addPerDofVariable(String, double) - Method in class ffx.openmm.CustomIntegrator
-
Add a per-DOF variable to this Integrator.
- 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(String) - Method in class ffx.openmm.CustomExternalForce
-
Add per particle parameter.
- addPerParticleParameter(String) - Method in class ffx.openmm.CustomGBForce
-
Add per particle parameter.
- addPerParticleParameter(String) - Method in class ffx.openmm.CustomNonbondedForce
-
Add a per particle parameter.
- 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.
- 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.
- addSelections(ArrayList<MSNode>) - Method in class ffx.ui.Hierarchy
-
addSelections
- 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.
- 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
- addTorsion(int, int, int, int, int, double, double) - Method in class ffx.openmm.PeriodicTorsionForce
-
Add a torsion to the PeriodicTorsionForce.
- addTorsionTorsion(int, int, int, int, int, int, int) - Method in class ffx.openmm.amoeba.TorsionTorsionForce
-
Add a torsion to the TorsionTorsionForce.
- 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 to the vdW Force.
- addUpdateContextState() - Method in class ffx.openmm.CustomIntegrator
-
Add an update context state to this Integrator.
- 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.
- 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
- Ai - Variable in class ffx.crystal.Crystal
-
Matrix to convert from fractional to Cartesian coordinates.
- Ai00 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai01 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai02 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai10 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai11 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai12 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai20 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai21 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- Ai22 - Variable in class ffx.crystal.Crystal
-
Entry in the Ai matrix.
- 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
- 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.AlgorithmsScript
-
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.AlgorithmsScript
-
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.
- algorithmsScript - Variable in class ffx.algorithms.misc.AlgorithmsTest
- AlgorithmsScript - Class in ffx.algorithms.cli
-
Base class for scripts in the Algorithms package, providing some key functions.
- AlgorithmsScript() - Constructor for class ffx.algorithms.cli.AlgorithmsScript
- AlgorithmsScript(Binding) - Constructor for class ffx.algorithms.cli.AlgorithmsScript
- 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 is greater than or equal to size.
- alloc(int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray
-
Ensure the AtomicDoubleArray instance is greater than or equal to 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 is greater than or equal to size.
- alloc(int) - Method in class ffx.numerics.atomic.PJDoubleArray
-
Ensure the AtomicDoubleArray instance is greater than or equal to 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 - Class in ffx.potential.openmm
- AmoebaGeneralizedKirkwoodForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaGeneralizedKirkwoodForce
- AmoebaGKCavitationForce - Class in ffx.potential.openmm
-
AmoebaCavitationForce.
- AmoebaGKCavitationForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaGKCavitationForce
-
Constructor.
- AmoebaMultipoleForce - Class in ffx.potential.openmm
-
AmoebaMultipoleForce.
- AmoebaMultipoleForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaMultipoleForce
- 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 - Class in ffx.potential.openmm
-
OpenMM TorsionTorsion Force.
- AmoebaTorsionTorsionForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaTorsionTorsionForce
-
Create an OpenMM TorsionTorsion Force.
- AmoebaVdwForce - Class in ffx.potential.openmm
-
The Amoeba vdW Force.
- AmoebaVdwForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AmoebaVdwForce
-
The Amoeba vdW Force constructor.
- 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.
- 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 - Class in ffx.openmm
-
This class uses the Andersen method to maintain constant temperature.
- AndersenThermostat(double, double) - Constructor for class ffx.openmm.AndersenThermostat
-
OpenMM AndersenThermostat constructor.
- 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 - Class in ffx.potential.openmm
-
OpenMM Angle Force.
- AngleForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AngleForce
-
Create an OpenMM Angle Force.
- 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
- 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 - Class in ffx.potential.openmm
-
OpenMM Angle-Torsion Force.
- AngleTorsionForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.AngleTorsionForce
-
Create an OpenMM Angle-Torsion Force.
- angleTorsionForm() - Static method in class ffx.potential.bonded.AngleTorsion
-
Returns the mathematical form of an angle-torsion as an OpenMM-parsable String.
- 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
- 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(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
- 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[], 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
-
Apply constraints to the current positions.
- 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.RestraintTorsion
- 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.
- 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
- 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
- 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.
- args - Variable in class ffx.utilities.FFXScript
-
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[], int, 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
-
assignPolarizationGroups.
- 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
- 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.
- atomicDoubleArrayFactory(AtomicDoubleArray.AtomicDoubleArrayImpl, int, int) - Static method in interface ffx.numerics.atomic.AtomicDoubleArray
-
Factory method to create an AtomicDoubleArray instance.
- 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.
- 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
- 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.
- 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.
- average(StretchTorsionType, StretchTorsionType, int[]) - Static method in class ffx.potential.parameters.StretchTorsionType
-
average.
- average(TorsionTorsionType, TorsionTorsionType, int[]) - Static method in class ffx.potential.parameters.TorsionTorsionType
-
average.
- average(TorsionType, TorsionType, int[]) - Static method in class ffx.potential.parameters.TorsionType
-
average.
- average(UreyBradleyType, UreyBradleyType, int[]) - Static method in class ffx.potential.parameters.UreyBradleyType
-
average.
- 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.
- 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.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.
- BALLANDSTICK - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
- BAR - Enum constant in enum class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType
- 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) - 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 - 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.AlgorithmsScript
-
The directory in which to place output files.
- baseDir - Variable in class ffx.potential.cli.PotentialCommand
-
A temporary directory that contains script artifacts.
- baseDir - Variable in class ffx.potential.cli.PotentialScript
-
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.
- 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.
- 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
- 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.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 - Class in ffx.potential.openmm
-
Bond Force.
- BondForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.BondForce
-
Bond Force constructor.
- 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.
- 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.
- 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
- 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.
- 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.
- buildMxNList(int, int, double[][], int[][][], boolean[], boolean, boolean) - Method in class ffx.potential.nonbonded.NeighborList
- 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.OpenMMSystem
-
Calculate the number of degrees of freedom.
- 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.
- 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.
- 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
- 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.
- CHARMM_22 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
- CHARMM_22_CMAP - 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.
- 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.
- 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
-
checkList.
- 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
- 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.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
- 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
- Clustering - Class in ffx.potential.utils
-
Cluster contains methods utilized in the
Cluster.groovy
file. - Clustering() - Constructor for class ffx.potential.utils.Clustering
- Clustering.Conformation - Class in ffx.potential.utils
-
Class for cluster objects.
- Cm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
- CMMotionRemover - Class in ffx.openmm
-
Center of Mass Motion Remover.
- CMMotionRemover(int) - Constructor for class ffx.openmm.CMMotionRemover
-
OpenMM CMMotionRemover constructor.
- 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.
- 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.
- color - Variable in class ffx.utilities.FFXScript
-
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(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) - Method in class ffx.potential.utils.ProgressiveAlignmentOfCrystals
-
Compare the crystals within the SystemFilters that were inputted into the constructor of this class.
- 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 .
- 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
- 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.
- 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.
- computeFractionalCoordinates() - Method in class ffx.potential.MolecularAssembly
-
Compute fractional coordinates.
- 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.
- computeMoments(Atom[], boolean) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
-
Compute multipole moments for an array of atoms.
- 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
- computeVolumeAndSA(double[][]) - Method in class ffx.potential.nonbonded.implicit.GaussVol
-
Compute molecular volume and surface area.
- 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(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
-
Add a bond force to 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.RestrainBondsForce
-
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(MSNode) - Method in class ffx.potential.bonded.MSNode
-
If
this
MSNode or any MSNode below itequals
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
-
Constructor.
- 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.
- 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
- 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.
- createExceptionsFromBonds(BondArray, double, double) - Method in class ffx.openmm.NonbondedForce
-
Create exceptions from bonds.
- 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.
- 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
- 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.
- 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.
- 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.
- 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
- 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
-
Custom Angle Force.
- CustomAngleForce(String) - Constructor for class ffx.openmm.CustomAngleForce
- CustomBondForce - Class in ffx.openmm
-
Custom Bond Force.
- CustomBondForce(String) - Constructor for class ffx.openmm.CustomBondForce
-
Custom Bond Force Constructor.
- 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
-
Custom Compound Bond Force.
- CustomCompoundBondForce(int, String) - Constructor for class ffx.openmm.CustomCompoundBondForce
- CustomExternalForce - Class in ffx.openmm
-
Custom External Force.
- CustomExternalForce(String) - Constructor for class ffx.openmm.CustomExternalForce
-
OpenMM CustomExternalForce constructor.
- CustomGBForce - Class in ffx.openmm
-
Custom GB Force.
- CustomGBForce() - Constructor for class ffx.openmm.CustomGBForce
-
OpenMM CustomGBForce constructor.
- CustomIntegrator - Class in ffx.openmm
-
Custom Integrator.
- CustomIntegrator(double) - Constructor for class ffx.openmm.CustomIntegrator
-
Constructor.
- 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
-
Custom Non-bonded Force.
- CustomNonbondedForce(String) - Constructor for class ffx.openmm.CustomNonbondedForce
- 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="June 2024"
- 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.
- 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.
- deleteDirectoryTree(Path) - Static method in class ffx.utilities.DirectoryUtils
-
Recursively delete the contents of a directory.
- 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.
- density - Variable in class ffx.ui.commands.SimulationUpdate
- density() - Method in class ffx.algorithms.dynamics.Barostat
-
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.GeneralizedKirkwoodForce
-
Destroy the force.
- destroy() - Method in class ffx.openmm.amoeba.GKCavitationForce
-
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 vdW 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.BondArray
-
Destroy the bond array.
- destroy() - Method in class ffx.openmm.CMMotionRemover
-
Destroy the OpenMM CMMotionRemover.
- destroy() - Method in class ffx.openmm.Context
-
Destroy the context.
- 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
-
Clean up.
- 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.CustomNonbondedForce
-
Destroy the force.
- destroy() - Method in class ffx.openmm.DoubleArray
-
Destroy the array.
- destroy() - Method in class ffx.openmm.DoubleArray3D
-
Destroy the array.
- 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.MinimizationReporter
-
Destroy the reporter.
- destroy() - Method in class ffx.openmm.MonteCarloBarostat
-
Destroy the force.
- destroy() - Method in class ffx.openmm.NonbondedForce
- destroy() - Method in class ffx.openmm.PeriodicTorsionForce
- destroy() - Method in class ffx.openmm.Platform
-
Destroy the OpenMM Platform instance.
- 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.Vec3Array
-
Destroy the Vec3Array.
- destroy() - Method in class ffx.openmm.VerletIntegrator
-
Destroy the integrator.
- 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.AlgorithmsScript
-
Reclaims resources associated with all Potential objects associated with this script.
- destroyPotentials() - Method in class ffx.potential.cli.PotentialCommand
-
Reclaims resources associated with all Potential objects associated with this script.
- destroyPotentials() - Method in class ffx.potential.cli.PotentialScript
-
Reclaims resources associated with all Potential objects associated with this script.
- 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
- 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
- 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
- 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(OctreeCell) - Method in class ffx.potential.nonbonded.octree.OctreePoint
- distance(OctreePoint) - Method in class ffx.potential.nonbonded.octree.OctreePoint
- 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
- 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.
- 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
-
DoubleArray3D.
- DoubleArray3D(int, int, int) - Constructor for class ffx.openmm.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
- 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.
- 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.
- 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 - 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
- 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
- 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
- eAllFlat - Variable in class ffx.numerics.estimator.SequentialEstimator
- eAt - Variable in class ffx.numerics.estimator.SequentialEstimator
- 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.
- eHigh - Variable in class ffx.numerics.estimator.SequentialEstimator
- 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
- eLow - Variable in class ffx.numerics.estimator.SequentialEstimator
- 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.
- 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.parameters.TorsionTorsionType
-
Energy values.
- 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
- 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.RestraintTorsion
- 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(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.RestrainPosition
-
Calculates energy and gradients for this coordinate restraint.
- 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.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.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
-
The Energy script evaluates the energy of a system.
- Energy() - Constructor for class ffx.potential.commands.Energy
-
Energy constructor.
- Energy(FFXContext) - Constructor for class ffx.potential.commands.Energy
-
Energy constructor.
- 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.
- 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.OpenMMEnergy
-
Compute the energy using the pure Java code path.
- EnergyRegion - Class in ffx.algorithms.optimize.manybody
- EnergyRegion(int) - Constructor for class ffx.algorithms.optimize.manybody.EnergyRegion
- EnergyUnitConversion - Enum constant in enum class ffx.utilities.PropertyGroup
-
Energy unit conversion factors.
- 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 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 class ffx.numerics.estimator.BennettAcceptanceRatio
-
Main driver for estimation of delta-G.
- 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 delta-G.
- 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
- 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[], 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
- 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
- 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.
- 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
- 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.
- 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.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
- ffx.algorithms.optimize.manybody - package ffx.algorithms.optimize.manybody
- 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.estimator - package ffx.numerics.estimator
- 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
- 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.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
- ffx.openmm.amoeba - package ffx.openmm.amoeba
- 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 packa