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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
 
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) - Method in class ffx.potential.nonbonded.NeighborList.Cell
Add an atom to the cell.
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, 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.CentroidBondForce
Add a bond between two groups 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.
addEnergyTerm(String, int) - Method in class ffx.openmm.CustomGBForce
Add an energy term.
ADDER - Enum constant in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl
 
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.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.CentroidBondForce
Add a atoms of atoms to the force.
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.CentroidBondForce
Add a per bond parameters
addPerBondParameter(String) - Method in class ffx.openmm.CustomBondForce
Add a per-bond parameter to the CustomBondForce.
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
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.
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
 
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.
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
 
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.
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_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
 
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
 
analyticalVariances() - 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.
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
 
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.
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.nonbonded.VanDerWaalsForm.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
 
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.
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.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
 
atomicDoubleArrayFactory(AtomicDoubleArray.AtomicDoubleArrayImpl, int, int) - Static method in interface ffx.numerics.atomic.AtomicDoubleArray
Factory method to create an AtomicDoubleArray instance.
atomicNumber - Variable in class ffx.potential.parameters.AtomType
Atomic Number.
atomicWeight - Variable in class ffx.potential.parameters.AtomType
Atomic weight.
AtomIndex(int, int) - 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
 
BadIntpln - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult
 
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.
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.
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
 
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
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(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.
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
Bond Array.
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.RestraintBond
 
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
 
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.GKSource.GK_TENSOR_MODE
 
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
 
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.nonbonded.VanDerWaalsForm.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.
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
centric
CentroidBondForce - Class in ffx.openmm
Custom Centroid Bond Force.
CentroidBondForce(int, String) - Constructor for class ffx.openmm.CentroidBondForce
OpenMM CustomCentroidBondForce constructor.
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.
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.
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).
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.
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.
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.
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.
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(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, 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 data of length n.
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.
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.
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
computeDft(float[], float[], float[], float[]) - Static method in class ffx.numerics.fft.TornadoDFT
 
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.
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.
constantOutsideBounds() - Method in class ffx.numerics.switching.LinearDerivativeSwitch
Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.MultiplicativeSwitch
Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.PowerSwitch
Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.SquaredTrigSwitch
Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction
Remains 0 below the lower bound, and 1 above the upper bound (i.e.
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 it equals the argument, that MSNode is returned.
contains(String) - Method in class edu.rit.pj.cluster.ResourceCache
Determine if this resource cache contains resource information for the given resource name.
containsContent(String) - Method in class edu.rit.pj.cluster.ResourceCache
Determine if this resource cache contains the resource content for the given resource name.
containsHydrogen() - Method in class ffx.potential.bonded.BondedTerm
containsHydrogen
containsResolution(Atom.Resolution) - Method in class ffx.potential.bonded.BondedTerm
Checks if at least one atom in this BondedTerm is of the given resolution.
Context - Class in ffx.openmm
A Context stores the complete state of a simulation.
Context() - Constructor for class ffx.openmm.Context
Constructor.
Context(System, Integrator, Platform) - Constructor for class ffx.openmm.Context
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.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
coordinatesToHilbertIndex(int, int, long[]) - Static method in class ffx.numerics.math.HilbertCurveTransforms
 
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.
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.MultipoleTensor.OPERATOR
 
coulombSource - Variable in class ffx.numerics.multipole.MultipoleTensor
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.
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
 
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
 
count - Variable in class ffx.numerics.math.SummaryStatistics
 
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_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem
 
CUBIC_MEAN - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.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.
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
 
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.
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="February 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_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.
DEFAULT_DIELECTRIC_OFFSET - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood
Default dielectric offset
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_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_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_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_RB_LAM_END - Static variable in class ffx.potential.bonded.RestraintBond
 
DEFAULT_RB_LAM_START - Static variable in class ffx.potential.bonded.RestraintBond
 
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_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_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.CentroidBondForce
Destroy the OpenMM CustomCentroidBondForce.
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.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.LangevinIntegrator
Destroy the integrator.
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.
DGU - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
 
DIAMETER - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.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.
DIPOLE - Enum constant in enum class ffx.numerics.multipole.GKSource.GK_MULTIPOLE_ORDER
 
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.
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.
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.
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.
dipoleTorque(PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
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
 
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
 
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, boolean) - Constructor for class ffx.algorithms.optimize.manybody.DistanceMatrix
 
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.
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.
dLpdLi - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Derivative of lambdaProduct w.r.t.
dLpdLk - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Derivative of lambdaProduct w.r.t.
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
 
dof - Variable in class ffx.numerics.math.SummaryStatistics
 
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.
Double() - Constructor for class edu.rit.util.Searching.Double
 
Double() - Constructor for class edu.rit.util.Sorting.Double
 
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!! Precondition: n .GE.
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.
DoubleMath() - Constructor for class ffx.numerics.math.DoubleMath
 
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
 
downloadPDB(String) - Static method in class ffx.utilities.DownloadUtils
Download a PDB file.
DownloadUtils - Class in ffx.utilities
Download utilities.
DownloadUtils() - Constructor for class ffx.utilities.DownloadUtils
 
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.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.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.

E

e - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
E - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
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.RestraintBond
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(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
 
epsilonc() - Method in class ffx.crystal.HKL
epsilonc
epsilonRule - Variable in class ffx.potential.nonbonded.VanDerWaalsForm
Epsilon combining rule.
EPT - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
 
equals(Object) - Method in class edu.rit.pj.io.StreamFile
Determine if this stream file is equal to the given object.
equals(Object) - Method in class edu.rit.util.LongRange
Determine if this range is equal to the given object.
equals(Object) - Method in class edu.rit.util.Range
Determine if this range is equal to the given object.
equals(Object) - Method in class ffx.crystal.Crystal
Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.HKL
equals(Object) - Method in class ffx.crystal.NCSCrystal
Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.ReplicatesCrystal
Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.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
 
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
Implementation of MBAR solved with self-consistent iteration and 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.
evenlySpacedOscillators(int, int, double, double, double, double, Long) - Static method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
 
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.
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.
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.
excuteWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ReduceRegion
Execute the ReduceRegion with the passed ParallelTeam.
execute() - Method in class ffx.numerics.fft.TornadoDFT
 
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
 
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.
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
 
factorial(long) - Static method in class ffx.numerics.math.ScalarMath
Returns n!
Precondition: n .GE.
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
 
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.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.
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
 
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 package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.cli - package ffx.potential.cli
The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands - package ffx.potential.commands
 
ffx.potential.constraint - package ffx.potential.constraint
 
ffx.potential.extended - package ffx.potential.extended
The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e.
ffx.potential.nonbonded - package ffx.potential.nonbonded
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.implicit - package ffx.potential.nonbonded.implicit
 
ffx.potential.nonbonded.octree - package ffx.potential.nonbonded.octree
 
ffx.potential.nonbonded.pme - package ffx.potential.nonbonded.pme
 
ffx.potential.openmm - package ffx.potential.openmm
 
ffx.potential.parameters - package ffx.potential.parameters
The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.potential.parsers - package ffx.potential.parsers
The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.utils - package ffx.potential.utils
The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.realspace - package ffx.realspace
The Real Space package implements real space structure refinement.
ffx.realspace.cli - package ffx.realspace.cli
The Real Space CLI package defines options for PicoCLI command line scripts.
ffx.realspace.parsers - package ffx.realspace.parsers
The Parsers package reads and writes CCP4 map files.
ffx.ui - package ffx.ui
The UI package provides views and controllers for manipulating molecular systems.
ffx.ui.behaviors - package ffx.ui.behaviors
The Behaviors package contains Java3D Behaviors that turn user actions into scenegraph changes.
ffx.ui.commands - package ffx.ui.commands
The Commands package implements a Client/Server interface between Force Field X and simulations.
ffx.ui.properties - package ffx.ui.properties
The Properties package will eventually encapsulate internationalization features.
ffx.utilities - package ffx.utilities
The Utilities package implements a variety of useful Directory, File, Port, String, etc functionality.
ffx.xray - package ffx.xray
The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.cli - package ffx.xray.cli
The X-ray CLI package defines options for PicoCLI command line scripts.
ffx.xray.parsers - package ffx.xray.parsers
The Parsers package reads CNS files and reads/writes MTZ files.
ffxCI - Static variable in class ffx.utilities.FFXTest
Constant ffxCI=System.getProperty("ffx.ci", "false").equalsIgnoreCase("true")
FFXClient - Class in ffx.ui.commands
The FFXClient class encapsulates a socket connection to an FFXServer started by an executing FFX instance.
FFXClient() - Constructor for class ffx.ui.commands.FFXClient
Constructor for FFXClient.
FFXClient(int) - Constructor for class ffx.ui.commands.FFXClient
Constructor for FFXClient.
FFXClient(InetSocketAddress) - Constructor for class ffx.ui.commands.FFXClient
Constructor for FFXClient.
FFXCommand - Class in ffx.utilities
Base Command class.
FFXCommand(FFXContext) - Constructor for class ffx.utilities.FFXCommand
Default constructor for an FFX Script.
FFXContext - Class in ffx.utilities
This represents the context of an FFX MolecularAssembly.
FFXContext() - Constructor for class ffx.utilities.FFXContext
Constructor for FFXContext.
FFXContext(String[]) - Constructor for class ffx.utilities.FFXContext
A helper constructor used in main(String[]) method calls
FFXContext(Map<String, Object>) - Constructor for class ffx.utilities.FFXContext
Constructor for FFXContext.
FFXExec - Class in ffx.ui
FFXExec encapsulates a native replacement for the JDK System.exec() method.
FFXExec(FFXSystem, String, String, String, MainPanel, File, boolean) - Constructor for class ffx.ui.FFXExec
Constructor
FFXFileFilter - Class in ffx.potential.parsers
The FFXFileFilter class is used to choose Force Field X script (*.FFX) files.
FFXFileFilter() - Constructor for class ffx.potential.parsers.FFXFileFilter
Default Constructor.
FFXLocale - Class in ffx.ui.properties
The FFXLocale class will encapsulate internationalization features.
FFXLocale() - Constructor for class ffx.ui.properties.FFXLocale
Constructor for FFXLocale.
FFXLocale(String, String) - Constructor for class ffx.ui.properties.FFXLocale
Constructor for FFXLocale.
ffxOpenMM - Static variable in class ffx.utilities.FFXTest
Constant ffxOpenMM=System.getProperty("ffx.openMM", "false").equalsIgnoreCase("true")
FFXProperties - Annotation Interface in ffx.utilities
The FFXProperty Annotation can be applied multiple times to some classes.
FFXProperty - Annotation Interface in ffx.utilities
The FFXProperty Annotation should be used to document fields that are set using property files, keyword files, force field parameter files and the Java property system.
ffxScript(String[]) - Static method in class ffx.Main
A main entry point that runs a script and return a refernce to the result.
FFXScript - Class in ffx.utilities
BaseScript class.
FFXScript(Binding) - Constructor for class ffx.utilities.FFXScript
Default constructor for an FFX Script.
FFXServer - Class in ffx.ui.commands
The FFXServer is launched by an FFX instance to allow Force Field X Clients to connect.
FFXServer(SimulationDefinition) - Constructor for class ffx.ui.commands.FFXServer
Constructor for FFXServer.
FFXSystem - Class in ffx.ui
The FFXSystem class contains extensions to the generic MolecularAssembly class.
FFXSystem(File, String, CompositeConfiguration) - Constructor for class ffx.ui.FFXSystem
Constructor.
FFXTest - Class in ffx.utilities
The FFXTest configures the context for FFX tests.
FFXTest() - Constructor for class ffx.utilities.FFXTest
FFXTest constructor.
FFXTornado - Class in ffx.numerics.tornado
Utility Routines to use the TornadoVM
FFXTornado() - Constructor for class ffx.numerics.tornado.FFXTornado
 
file - Variable in class ffx.ui.commands.SimulationDefinition
 
FILE_READ_DATA - Static variable in class edu.rit.pj.cluster.Message
The message tag for a message containing data read from a file.
FILE_WRITE_DATA - Static variable in class edu.rit.pj.cluster.Message
The message tag for a message containing data to write to a file.
fileAppend(File, String) - Static method in class edu.rit.io.Files
Append the given suffix to the given file.
fileForRank(File, int) - Static method in class edu.rit.io.Files
Append the given rank to the given file.
fileNameAppend(String, String) - Static method in class edu.rit.io.Files
Append the given suffix to the given file name.
fileNameForRank(String, int) - Static method in class edu.rit.io.Files
Append the given rank to the given file name.
fileNamePrepend(String, String) - Static method in class edu.rit.io.Files
Prepend the given prefix to the given file name.
fileNewWindow() - Method in class ffx.ui.ModelingShell
 
fileNewWindow(EventObject) - Method in class ffx.ui.ModelingShell
 
FileOpener - Interface in ffx.potential.parsers
The FileOpener interface specifies Runnable objects which can return one or more MolecularAssemblies.
filePrepend(File, String) - Static method in class edu.rit.io.Files
Prepend the given prefix to the given file.
fileRead - Variable in class ffx.potential.parsers.SystemFilter
True after the file has been read successfully.
fileRead() - Method in class ffx.potential.parsers.SystemFilter
Returns true if the read was successful
files - Variable in class ffx.potential.parsers.SystemFilter
Append multiple files into one MolecularAssembly.
Files - Class in edu.rit.io
Class Files provides static methods for various file related operations.
fileType - Variable in class ffx.algorithms.dynamics.MolecularDynamics
File type to use when saving files.
fileType - Variable in class ffx.potential.cli.WriteoutOptions
-F or --fileFormat Choose the file type to write [PDB/XYZ].
fileType - Variable in class ffx.potential.parsers.SystemFilter
The file format being handled.
FileUtils - Class in ffx.utilities
FileUtils class.
fill(Object) - Method in class edu.rit.mp.BooleanBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Buf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ByteBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.CharacterBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.DoubleBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.FloatBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.IntegerBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.LongBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ObjectBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ShortBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Signed16BitIntegerBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Signed8BitIntegerBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf
Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf
Fill this buffer with the given item.
FILL - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Molecule
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MSGroup
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MultiResidue
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Polymer
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Residue
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.MolecularAssembly
Abstract method that should specify how to finalize a MSGroup
findAtom(Atom) - Method in class ffx.potential.MolecularAssembly
findAtom
findAtomsOfElement(Residue, int) - Static method in class ffx.potential.bonded.BondedUtils
Finds all Atoms belonging to a Residue of a given atomic number.
findAtomType(int, ForceField) - Static method in class ffx.potential.bonded.BondedUtils
findAtomType.
findBondedAtoms(Atom, int) - Static method in class ffx.potential.bonded.BondedUtils
Finds Atoms bonded to a given Atom that match a certain atomic number.
findBondedAtoms(Atom, Atom, int) - Static method in class ffx.potential.bonded.BondedUtils
Finds Atoms bonded to a given Atom that match a certain atomic number that do not match an excluded atom.
findChainBreaks(List<Residue>, double) - Static method in class ffx.potential.bonded.PolymerUtils
 
findClass(String) - Method in class edu.rit.pj.cluster.BackendClassLoader
Find the class with the given name.
findDangelingAtoms() - Method in class ffx.potential.bonded.MSGroup
This method constructs a List of atoms which are under-constrained.
findDangelingAtoms() - Method in class ffx.potential.bonded.MultiResidue
This method constructs a List of atoms which are under-constrained.
findMaxLessIndex(ArrayList<ArrayList<Atom>>, int) - Method in class ffx.potential.parsers.CIFFilter
Find the maximum index that is less than those contained in current model.
findNitrogenAtom(Residue) - Static method in class ffx.potential.bonded.BondedUtils
Finds the backbone nitrogen of a residue.
findNucleotideO4s(Residue) - Static method in class ffx.potential.bonded.BondedUtils
Find the O4' of a nucleic acid Residue.
findResource(String) - Method in class edu.rit.pj.cluster.BackendClassLoader
Find the resource with the given name.
findSeed(Atom, Atom) - Static method in class ffx.potential.Utilities
Returns an atom bonded to the "end" atom, which is not equal to "other".
findSymHKL(int, int, int, HKL) - Method in class ffx.crystal.ReflectionList
findSymHKL
findSymHKL(int, int, int, HKL, boolean) - Method in class ffx.crystal.ReflectionList
findSymHKL
findSymHKL(HKL, HKL) - Method in class ffx.crystal.ReflectionList
findSymHKL
finish() - Method in class edu.rit.pj.IntegerForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.IntegerStrideForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.LongForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.LongStrideForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.ParallelIteration
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.ParallelRegion
Perform finalization actions after parallel execution ends.
finish() - Method in class edu.rit.pj.WorkerIntegerForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerIteration
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerLongForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerLongStrideForLoop
Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerRegion
Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
 
finish() - Method in class ffx.algorithms.optimize.manybody.SelfEnergyRegion
 
finish() - Method in class ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
 
finish() - Method in class ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
 
finish() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
 
finish() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
finish() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
 
finish() - Method in class ffx.potential.nonbonded.NeighborList
Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
 
finish() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
finish() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
finish() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
 
finish() - Method in class ffx.potential.nonbonded.RowRegion
Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.potential.nonbonded.SliceRegion
Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.xray.BulkSolventList
Perform finalization actions after parallel execution ends.
finished() - Method in class ffx.ui.SwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
FINISHED - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State
The job backend process has finished.
FIRST_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
 
firstDerivative(double) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
 
firstDerivative(double) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction
First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.BellCurveSwitch
First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.CompositeSwitch
 
firstDerivative(double) - Method in class ffx.numerics.switching.ConstantSwitch
First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.LinearDerivativeSwitch
First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch
First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.PowerSwitch
First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.SquaredTrigSwitch
First derivative at a point.
fixed() - Static method in class edu.rit.pj.IntegerSchedule
Returns a fixed schedule object.
fixed() - Static method in class edu.rit.pj.LongSchedule
Returns a fixed schedule object.
FIXED - Enum constant in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm
 
FIXED_CHARGE - Enum constant in enum class ffx.potential.parameters.ForceField.ELEC_FORM
 
FIXEDCHARGE - Enum constant in enum class ffx.potential.bonded.Atom.Resolution
 
FixedChargeAlchemicalForces - Class in ffx.potential.openmm
Fixed Charge Alchemical Forces.
FixedChargeAlchemicalForces(OpenMMEnergy, FixedChargeNonbondedForce) - Constructor for class ffx.potential.openmm.FixedChargeAlchemicalForces
 
FixedChargeGBForce - Class in ffx.potential.openmm
FixedChargeGBForce.
FixedChargeGBForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.FixedChargeGBForce
FixedChargeGBForce constructor.
FixedChargeNonbondedForce - Class in ffx.potential.openmm
Define a fixed charge non-bonded force.
FixedChargeNonbondedForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.FixedChargeNonbondedForce
 
fixParameters(double, double, double, double, double, double) - Method in enum class ffx.crystal.LatticeSystem
Change the lattice parameters to satisfy the restrictions of the lattice system.
flags - Variable in class ffx.ui.behaviors.MouseBehavior
 
FLAT_BOTTOM_HARMONIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
 
FLAT_BOTTOM_QUARTIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
 
flatBottomRadius - Variable in class ffx.potential.parameters.BondType
Radius of a flat bottom where energy and force is 0; typically used for restraints.
FlatEndAnnealSchedule - Class in ffx.algorithms.optimize.anneal
Composite annealing schedule with flat ends (i.e.
FlatEndAnnealSchedule(AnnealingSchedule, double, double, double, double) - Constructor for class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
Creates a flat-ended annealing schedule based on a provided schedule for the middle, which is flat for some number of steps at the ends.
Float() - Constructor for class edu.rit.util.Searching.Float
 
Float() - Constructor for class edu.rit.util.Sorting.Float
 
Float3 - Class in ffx.numerics.math
Convenience class for working with 3D float vectors.
Float3() - Constructor for class ffx.numerics.math.Float3
Construct a Float3 at (0.0, 0.0, 0.0).
Float3(float[]) - Constructor for class ffx.numerics.math.Float3
Construct a Float3 at a.
Float3(float, float, float) - Constructor for class ffx.numerics.math.Float3
Construct a Float3 at (x, y, z).
FloatArrayBuf - Class in edu.rit.mp.buf
Class FloatArrayBuf provides a buffer for an array of float items sent or received using the Message Protocol (MP).
FloatArrayBuf(float[], Range) - Constructor for class edu.rit.mp.buf.FloatArrayBuf
Construct a new float array buffer.
FloatArrayBuf_1 - Class in edu.rit.mp.buf
Class FloatArrayBuf_1 provides a buffer for an array of float items sent or received using the Message Protocol (MP).
FloatArrayBuf_1(float[], Range) - Constructor for class edu.rit.mp.buf.FloatArrayBuf_1
Construct a new float array buffer.
FloatBuf - Class in edu.rit.mp
Class FloatBuf is the abstract base class for a buffer of float items sent or received using the Message Protocol (MP).
FloatBuf(int) - Constructor for class edu.rit.mp.FloatBuf
Construct a new float buffer.
FloatItemBuf - Class in edu.rit.mp.buf
Class FloatItemBuf provides a buffer for a single float item sent or received using the Message Protocol (MP).
FloatItemBuf() - Constructor for class edu.rit.mp.buf.FloatItemBuf
Construct a new float item buffer.
FloatItemBuf(float) - Constructor for class edu.rit.mp.buf.FloatItemBuf
Construct a new float item buffer with the given initial value.
FloatMath - Class in ffx.numerics.math
The FloatMath class is a simple math library that operates on 3-coordinate float arrays.
FloatMath() - Constructor for class ffx.numerics.math.FloatMath
 
FloatMatrixBuf - Class in edu.rit.mp.buf
Class FloatMatrixBuf provides a buffer for a matrix of float items sent or received using the Message Protocol (MP).
FloatMatrixBuf(float[][], Range, Range) - Constructor for class edu.rit.mp.buf.FloatMatrixBuf
Construct a new float matrix buffer.
FloatMatrixBuf_1 - Class in edu.rit.mp.buf
Class FloatMatrixBuf_1 provides a buffer for a matrix of float items sent or received using the Message Protocol (MP).
FloatMatrixBuf_1(float[][], Range, Range) - Constructor for class edu.rit.mp.buf.FloatMatrixBuf_1
Construct a new float matrix buffer.
FloatOp - Class in edu.rit.pj.reduction
Class FloatOp is the abstract base class for a binary operation on float values, used to do reduction in a parallel program.
FloatOp() - Constructor for class edu.rit.pj.reduction.FloatOp
Construct a new float binary operation.
floatValue() - Method in class edu.rit.pj.reduction.SharedByte
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedCharacter
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedDouble
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedFloat
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedInteger
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedLong
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedShort
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedByte
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedDouble
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedFloat
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedInteger
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedLong
Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedShort
Returns this reduction variable's current value converted to type float.
floodReceive(Buf) - Method in class edu.rit.pj.Comm
Flood-receive a message from any process in this communicator.
floodReceive(Buf, CommRequest) - Method in class edu.rit.pj.Comm
Flood-receive a message from any process in this communicator (non-blocking).
floodReceive(Integer, Buf) - Method in class edu.rit.pj.Comm
Flood-receive a message from any process in this communicator with the given message tag.
floodReceive(Integer, Buf, CommRequest) - Method in class edu.rit.pj.Comm
Flood-receive a message from any process in this communicator with the given message tag (non-blocking).
floodSend(int, Buf) - Method in class edu.rit.pj.Comm
Flood-send a message to all processes in this communicator with the given message tag.
floodSend(int, Buf, CommRequest) - Method in class edu.rit.pj.Comm
Flood-send a message to all processes in this communicator with the given message tag (non-blocking).
floodSend(Buf) - Method in class edu.rit.pj.Comm
Flood-send a message to all processes in this communicator.
floodSend(Buf, CommRequest) - Method in class edu.rit.pj.Comm
Flood-send a message to all processes in this communicator (non-blocking).
flush() - Method in class edu.rit.io.LineBufferedOutputStream
Flush this line buffered output stream.
flush() - Method in class edu.rit.pj.cluster.BackendFileOutputStream
Flush this output stream.
flush() - Method in class ffx.ui.LogHandler
Fm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
fma(double[], double, double[]) - Static method in class ffx.numerics.math.DoubleMath
Compute a * b + c and return the result in a new array.
fma(double[], double, double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Compute a * b + c.
fma(double, Double3) - Method in class ffx.numerics.math.Double3
Compute this * b + c and return the result in a new Double3.
fma(float[], float, float[]) - Static method in class ffx.numerics.math.FloatMath
Compute a * b + c and return the result in a new array.
fma(float[], float, float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Compute a * b + c.
fma(float, Float3) - Method in class ffx.numerics.math.Float3
Compute a * b + c and return the result in a new Float3.
fmaI(double, Double3) - Method in class ffx.numerics.math.Double3
Compute this * b + c and return the result in a new Double3.
fmaI(float, Float3) - Method in class ffx.numerics.math.Float3
Compute a * b + c and return the result in a new Float3.
fN(HKL, int) - Method in class ffx.xray.XRayFormFactor
f_n
FOFC - Static variable in interface ffx.xray.SplineEnergy.Type
 
foFc1 - Variable in class ffx.xray.DiffractionRefinementData
mFo - DFc coefficients.
foFc1F(int) - Method in class ffx.xray.DiffractionRefinementData
foFc1F
foFc1Phi(int) - Method in class ffx.xray.DiffractionRefinementData
foFc1Phi
FoFc2F(int) - Method in class ffx.xray.DiffractionRefinementData
FoFc2F
FoFc2Phi(int) - Method in class ffx.xray.DiffractionRefinementData
FoFc2Phi
fomPhi - Variable in class ffx.xray.DiffractionRefinementData
Figure of merit and phase.
FOR - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
Force - Class in ffx.openmm
Force objects apply forces to the particles in a System, or alter their behavior in other ways.
Force() - Constructor for class ffx.openmm.Force
 
FORCE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
force0 - Variable in class ffx.potential.bonded.StretchBend
Force constant.
force1 - Variable in class ffx.potential.bonded.StretchBend
Force constant.
forceConstant - Variable in class ffx.potential.parameters.AngleType
Force constant (Kcal/mole/radian^2).
forceConstant - Variable in class ffx.potential.parameters.BondType
Force constant (Kcal/mol).
forceConstant - Variable in class ffx.potential.parameters.OutOfPlaneBendType
Force constant (Kcal/mol/Angstrom).
forceConstant - Variable in class ffx.potential.parameters.PiOrbitalTorsionType
Force constant.
forceConstant - Variable in class ffx.potential.parameters.UreyBradleyType
Force constant (Kcal/mole/angstroms^2).
forceConstants - Variable in class ffx.potential.parameters.AngleTorsionType
Force constants.
forceConstants - Variable in class ffx.potential.parameters.StretchBendType
Force constants (Kcal/mole/Angstrom-Degrees).
forceConstants - Variable in class ffx.potential.parameters.StretchTorsionType
Force constants.
forcefield - Variable in class ffx.ui.commands.SimulationDefinition
 
forceField - Variable in class ffx.potential.MolecularAssembly
 
forceField - Variable in class ffx.potential.parsers.SystemFilter
The molecular mechanics force field being used.
ForceField - Class in ffx.potential.parameters
The ForceField class organizes parameters for a molecular mechanics force field.
ForceField(CompositeConfiguration) - Constructor for class ffx.potential.parameters.ForceField
ForceField Constructor.
ForceField.ELEC_FORM - Enum Class in ffx.potential.parameters
 
ForceField.ForceFieldName - Enum Class in ffx.potential.parameters
Available force fields.
ForceField.ForceFieldType - Enum Class in ffx.potential.parameters
 
forceFieldEnergy - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Force Field Potential Energy (i.e.
forceFieldEnergy - Variable in class ffx.potential.commands.Energy
 
ForceFieldEnergy - Class in ffx.potential
Compute the potential energy and derivatives of a molecular system described by a force field.
ForceFieldEnergy(MolecularAssembly) - Constructor for class ffx.potential.ForceFieldEnergy
Constructor for ForceFieldEnergy.
ForceFieldEnergy(MolecularAssembly, int) - Constructor for class ffx.potential.ForceFieldEnergy
Constructor for ForceFieldEnergy.
ForceFieldFileFilter - Class in ffx.potential.parsers
The ForceFieldFileFilter class is used to choose a TINKER Parameter file (*.PRM).
ForceFieldFileFilter() - Constructor for class ffx.potential.parsers.ForceFieldFileFilter
Default Constructor
ForceFieldFilter - Class in ffx.potential.parsers
The ForceFieldFilter Class is used to parse and store molecular mechanics data from keyword/property and parameter (*.PRM) files.
ForceFieldFilter(CompositeConfiguration) - Constructor for class ffx.potential.parsers.ForceFieldFilter
Constructor for ForceFieldFilter.
forceFieldURL - Variable in class ffx.potential.parameters.ForceField
URL to the force field parameter file.
format(LogRecord) - Method in class ffx.ui.LogFormatter
formatEnergy(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Utility method for formatting energies, using 16 spaces with 8 digits of precision.
FormFactor - Interface in ffx.xray
FormFactor interface.
FORWARD - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Direction
 
FORWARDS - Enum constant in enum class ffx.numerics.estimator.Zwanzig.Directionality
 
FOTOESQ - Static variable in interface ffx.xray.SplineEnergy.Type
 
FourBodyEnergyRegion - Class in ffx.algorithms.optimize.manybody
Compute 4-Body energies.
FourBodyEnergyRegion(RotamerOptimization, DistanceMatrix, EnergyExpansion, EliminatedRotamers, Residue[], List<Residue>, double) - Constructor for class ffx.algorithms.optimize.manybody.FourBodyEnergyRegion
 
Fr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
fractionalCount() - Method in class ffx.potential.MolecularAssembly
Count the number of fractional coordinate entities in the system.
fractionalMultipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Fractional multipoles in the global frame with dimensions of [nsymm][nAtoms][10]
frame() - Method in class ffx.ui.MainPanel
frame
frameAtomTypes - Variable in class ffx.potential.parameters.MultipoleType
Atom types that define the local frame of this multipole.
frameDefinition - Variable in class ffx.potential.parameters.MultipoleType
Local frame definition method.
free() - Method in class ffx.potential.openmm.OpenMMContext
Free OpenMM memory for the current Context and Integrator.
free() - Method in class ffx.potential.openmm.OpenMMSystem
Destroy the system.
freeEnergyDiff - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
 
freeR - Variable in class ffx.xray.DiffractionRefinementData
Array of R free flags;
FROM_JOB_BACKEND - Static variable in class edu.rit.pj.cluster.Message
The message tag for a message from a job backend process.
FROM_JOB_FRONTEND - Static variable in class edu.rit.pj.cluster.Message
The message tag for a message from a job frontend process.
FROM_JOB_LAUNCHER - Static variable in class edu.rit.pj.cluster.Message
The message tag for a message from a job launcher process.
FROM_JOB_SCHEDULER - Static variable in class edu.rit.pj.cluster.Message
The message tag for a message from a job scheduler process.
fromRank - Variable in class edu.rit.pj.CommStatus
The rank of the source process that sent the message.
frontend - Variable in class edu.rit.pj.cluster.JobInfo
Reference to the job frontend process.
frontendAddress - Variable in class edu.rit.pj.cluster.ProcessInfo
Host/port to which the job backend process is listening for the frontend communicator, or null if the frontend communicator does not exist.
FrontendFileReader - Class in edu.rit.pj.cluster
Class FrontendFileReader provides an object that reads sequential files in the job frontend process.
FrontendFileReader(JobFrontend) - Constructor for class edu.rit.pj.cluster.FrontendFileReader
Construct a new frontend file reader.
FrontendFileWriter - Class in edu.rit.pj.cluster
Class FrontendFileWriter provides an object that writes sequential files in the job frontend process.
FrontendFileWriter(JobFrontend) - Constructor for class edu.rit.pj.cluster.FrontendFileWriter
Construct a new frontend file writer.
fs - Variable in class ffx.xray.DiffractionRefinementData
Calculated bulk solvent structure factors.
FSEC_TO_PSEC - Static variable in class ffx.utilities.Constants
Constant FSEC_TO_PSEC=0.001
fsF(int) - Method in class ffx.xray.DiffractionRefinementData
fsF
fSigFCutoff - Variable in class ffx.xray.DiffractionRefinementData
 
fsPhi(int) - Method in class ffx.xray.DiffractionRefinementData
fsPhi
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic
The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Berendsen
The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Bussi
The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
The full-step temperature correction.
FunctionDataCurve - Class in ffx.numerics.integrate
A FunctionDataCurve represents a set of points along a 1-dimensional, analytically integrable function.
FunctionDataCurve() - Constructor for class ffx.numerics.integrate.FunctionDataCurve
 
fwDec(double, int, int) - Static method in class ffx.utilities.StringUtils
Prints a fixed-width decimal, similar to String.format(%width.precf, val), but ensuring the resulting string is never longer than width.
fwFpDec(double, int, int) - Static method in class ffx.utilities.StringUtils
Prints a fixed-width decimal using String.format conventions, throwing an error if the value cannot be formatted within that space.
fwFpTrunc(double, int, int) - Static method in class ffx.utilities.StringUtils
Prints a fixed-width decimal using String.format conventions, reducing the value if necessary to fit within the width.
fX(double) - Method in class ffx.numerics.integrate.CompositeCurve
Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.CosineWave
Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.FunctionDataCurve
Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.PolynomialCurve
Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.SinWave
Evaluates the function at x.

G

G - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
G - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
 
G - Variable in class ffx.crystal.Crystal
The direct space metric matrix.
Ga - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
gamma - Variable in class ffx.crystal.Crystal
The interaxial lattice angle between a and b.
gamma - Variable in class ffx.potential.nonbonded.VanDerWaalsForm
First constant suggested by Halgren for the Buffered-14-7 potential.
gather(int, int, Buf, Buf[]) - Method in class edu.rit.pj.Comm
Gather messages from all processes in this communicator using the given message tag.
gather(int, Buf, Buf[]) - Method in class edu.rit.pj.Comm
Gather messages from all processes in this communicator.
GAUSS_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
 
GAUSSIAN - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel
Smooth the boundary of the classic model using Gaussians.
GaussVol - Class in ffx.potential.nonbonded.implicit
GaussVol implements a description molecular volume and surface area described by overlapping Gaussian spheres.
GaussVol(Atom[], ForceField, ParallelTeam) - Constructor for class ffx.potential.nonbonded.implicit.GaussVol
Creates/Initializes a GaussVol instance.
Gd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
Ge - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
GeneralizedKirkwood - Class in ffx.potential.nonbonded
This Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a NeighborList.
GeneralizedKirkwood(ForceField, Atom[], ParticleMeshEwald, Crystal, ParallelTeam, double) - Constructor for class ffx.potential.nonbonded.GeneralizedKirkwood
Constructor for GeneralizedKirkwood.
GeneralizedKirkwood.NonPolarModel - Enum Class in ffx.potential.nonbonded
 
GeneralizedKirkwoodForce - Class in ffx.openmm.amoeba
Amoeba Generalized Kirkwood Force.
GeneralizedKirkwoodForce() - Constructor for class ffx.openmm.amoeba.GeneralizedKirkwoodForce
 
generate(int, double, double) - Method in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules
Creates an AnnealingSchedule corresponding to this enum and provided values.
generateFsigFfromAnomalousFsigF(double[][]) - Method in class ffx.xray.DiffractionRefinementData
Generate average F/sigF from anomalous F/sigF.
generateLoops(int, int) - Method in class ffx.potential.utils.Loop
generateLoops.
generateLoops(int, int, double[]) - Method in class ffx.potential.utils.Loop
generateLoops.
generateRFree() - Method in class ffx.xray.DiffractionRefinementData
Mark 5% of reflections for cross validation (R free flags).
GenerateRotamers - Class in ffx.algorithms.misc
The GenerateRotamers class helps generate a rotamer library (particularly for nonstandard amino acids) for a Residue.
GenerateRotamers(MolecularAssembly, Potential, Residue, File, int, AlgorithmListener) - Constructor for class ffx.algorithms.misc.GenerateRotamers
Intended to create rotamer sets for nonstandard amino acids.
GenerateRotamers(MolecularAssembly, Potential, Residue, File, int, AlgorithmListener, RotamerLibrary) - Constructor for class ffx.algorithms.misc.GenerateRotamers
Intended to create rotamer sets for nonstandard amino acids.
generateSource(GKSource.GK_TENSOR_MODE, GKSource.GK_MULTIPOLE_ORDER, double, double, double) - Method in class ffx.numerics.multipole.GKSource
Generate source terms for the Kirkwood version of the Challacombe et al.
generateTensor() - Method in class ffx.numerics.multipole.MultipoleTensor
Generate the tensor using hard-coded methods or via recursion.
generateTensor(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
For the MultipoleTensorTest class and testing.
generateTestData_v1() - Static method in class ffx.numerics.integrate.Integration
generateTestData_v1.
generateXPoints(double, double, int, boolean) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Generates a set of points along x.
GEOMETRIC - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.EPSILON_RULE
 
GEOMETRIC - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.RADIUS_RULE
 
get() - Method in class edu.rit.pj.reduction.SharedBoolean
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedByte
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedCharacter
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedDouble
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedFloat
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedInteger
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedLong
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedObject
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedShort
Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedBoolean
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedByte
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedCharacter
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedDouble
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedFloat
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedInteger
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedLong
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedObject
Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedShort
Returns this replicated, shared reduction variable's current value.
get() - Method in class ffx.numerics.math.Double3
Returns a reference to the internal double array that stores this Double3.
get() - Method in class ffx.numerics.math.Float3
Returns a reference to the internal float array that stores this Float3.
get() - Method in class ffx.ui.SwingWorker
Return the value created by the construct method.
get(int) - Method in class edu.rit.mp.BooleanBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.BooleanMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ByteMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.CharacterMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.DoubleMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyBooleanBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyByteBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyCharacterBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyDoubleBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyFloatBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyLongBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyObjectBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyShortBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.FloatMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.IntegerMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.LongMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ObjectMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedBooleanBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedByteArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedByteBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedCharacterBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedDoubleBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedFloatBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedLongArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedLongBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedObjectBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedShortArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedShortBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.ShortMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.ByteBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.CharacterBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.DoubleBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.FloatBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.IntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.LongBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.ObjectBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.ShortBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Signed16BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Signed8BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf
Obtain the given item from this buffer.
get(int) - Method in class edu.rit.pj.reduction.SharedBooleanArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedByteArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedFloatArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedLongArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedObjectArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class edu.rit.pj.reduction.SharedShortArray
Returns this array reduction variable's current value at the given index.
get(int) - Method in class ffx.numerics.atomic.AdderDoubleArray
Get the value of the array at the specified index.
get(int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray
Get the value of the array at the specified index.
get(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Get the Double3 at the specified index.
get(int) - Method in class ffx.numerics.atomic.MultiDoubleArray
Get the value of the array at the specified index.
get(int) - Method in class ffx.numerics.atomic.PJDoubleArray
Get the value of the array at the specified index.
get(int) - Method in class ffx.numerics.math.Double3
Returns the coordinate at position i.
get(int) - Method in class ffx.numerics.math.Float3
Returns the coordinate at position i.
get(int) - Method in class ffx.openmm.DoubleArray
Get a value from the array.
get(int) - Method in class ffx.openmm.IntArray
Get a value from the array.
get(int) - Method in class ffx.openmm.StringArray
Return the String at index i.
get(int) - Method in class ffx.openmm.Vec3Array
Get a Vec3 from the Vec3Array.
get(int) - Method in class ffx.potential.nonbonded.NeighborList.Cell
 
get(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Returns this matrix reduction variable's current value at the given row and column.
get(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Returns this matrix reduction variable's current value at the given row and column.
get(int, int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Get the value of the array at the specified index after calling the reduce method.
get(int, IntByReference, IntByReference) - Method in class ffx.openmm.BondArray
Get the bond at index.
get(int, IntBuffer, IntBuffer) - Method in class ffx.openmm.BondArray
Get the bond at index.
get(String) - Method in class edu.rit.pj.cluster.ResourceCache
Obtain the resource content for the given resource name from this resource cache (blocking).
GET_METHOD - Static variable in class edu.rit.http.HttpRequest
The GET method string, "GET".
get1_2(Atom) - Method in class ffx.potential.bonded.Bond
Find the other Atom in this Bond.
get1_2(Atom) - Method in class ffx.potential.bonded.RestraintBond
Find the other Atom in this Bond.
get1_3(Atom) - Method in class ffx.potential.bonded.Angle
If the specified atom is not the central atom of this angle, the atom of the opposite leg is returned.
get1_4(Atom) - Method in class ffx.potential.bonded.AngleTorsion
If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
get1_4(Atom) - Method in class ffx.potential.bonded.StretchTorsion
If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
get1_4(Atom) - Method in class ffx.potential.bonded.Torsion
If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
get12List() - Method in class ffx.potential.bonded.Atom
Get the list of 1-2 atoms ordered by XYZ index.
get13List() - Method in class ffx.potential.bonded.Atom
Get the list of 1-3 atoms ordered by XYZ index.
get14List() - Method in class ffx.potential.bonded.Atom
Get the list of 1-4 atoms ordered by XYZ index.
get15List() - Method in class ffx.potential.bonded.Atom
Get the list of 1-5 atoms ordered by XYZ index.
get2Body(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Return a previously computed 2-body energy.
get2BodyDistance(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Checks the distance matrix, finding the shortest distance between two residues' rotamers or any rotamers from two residues under any symmetry operator; will evaluate this if distance matrix not already filled.
get3Body(Residue[], int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Return a previously computed 3-body energy.
get3BodyResidueDistance(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Returns the RMS separation distance for the closest rotamers of three residues' 2-body distances.
get4BodyResidueDistance(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Returns the RMS separation distance for the closest rotamers of 6 2-body distances from four residues.
getABCIndices() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell
Returns the a, b, and c axis indices of this cell.
getAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat
getAcceleration.
getAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
getAcceleration.
getAcceleration(double[]) - Method in interface ffx.numerics.Potential
getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
 
getAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field acceleration.
getAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy
getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
getAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy
getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy
getAcceleration.
getAcceleration(double[]) - Method in class ffx.potential.XtalEnergy
getAcceleration.
getAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy
getAcceleration.
getAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy
getAcceleration.
getAcceleration(double[]) - Method in class ffx.xray.XRayEnergy
getAcceleration.
getAccelerations(double[]) - Method in class ffx.potential.openmm.OpenMMState
The force array contains the OpenMM force information for all atoms.
getAccept() - Method in class ffx.algorithms.mc.BoltzmannMC
If last step taken was a success.
getAccept() - Method in interface ffx.algorithms.mc.MetropolisMC
If last step taken was a success.
getAcceptanceRate() - Method in class ffx.algorithms.mc.MCLoop
Get the current MC acceptance rate.
getActive() - Method in class ffx.potential.bonded.MultiResidue
getActive.
getActive() - Method in class ffx.ui.Hierarchy
Returns the active FSystem.
getActiveAssemblies(String) - Method in class ffx.algorithms.cli.AlgorithmsScript
If a filename is supplied, open it and return the MolecularAssemblies.
getActiveAssemblies(String) - Method in class ffx.potential.cli.PotentialCommand
If a filename is supplied, open it and return the MolecularAssemblies.
getActiveAssemblies(String) - Method in class ffx.potential.cli.PotentialScript
If a filename is supplied, open it and return the MolecularAssemblies.
getActiveAssembly() - Method in interface ffx.potential.utils.PotentialsFunctions
Returns either the active assembly from the overlying UI, or the "active" molecular assembly from the last used SystemFilter.
getActiveAssembly() - Method in class ffx.ui.UIUtils
 
getActiveAssembly(String) - Method in class ffx.algorithms.cli.AlgorithmsScript
If a filename is supplied, open it and return the MolecularAssembly.
getActiveAssembly(String) - Method in class ffx.potential.cli.PotentialCommand
If a filename is supplied, open it and return the MolecularAssembly.
getActiveAssembly(String) - Method in class ffx.potential.cli.PotentialScript
If a filename is supplied, open it and return the MolecularAssembly.
getActiveAtomArray() - Method in class ffx.potential.MolecularAssembly
getActiveAtomArray
getActiveAtomArray() - Method in class ffx.realspace.RealSpaceData
getActiveAtomArray
getActiveAtomArray() - Method in interface ffx.xray.DataContainer
getActiveAtomArray
getActiveAtomArray() - Method in class ffx.xray.DiffractionData
getActiveAtomArray.
getActiveAtomArray() - Method in class ffx.xray.RefinementModel
Getter for the field activeAtomArray.
getActiveAtomList() - Method in class ffx.xray.RefinementModel
Getter for the field activeAtomList.
getActiveAtoms() - Method in class ffx.potential.cli.AtomSelectionOptions
--aa or --activeAtoms Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].
getActiveAtoms() - Method in class ffx.xray.RefinementEnergy
getActiveAtoms.
getActiveMolecularSystem() - Method in class ffx.potential.parsers.SystemFilter
Return the MolecularSystem that has been read in
getActiveNode() - Method in class ffx.ui.Hierarchy
Getter for the field activeNode.
getAddress() - Method in class edu.rit.http.HttpServer
Obtain the host and port to which this HTTP server is listening for connections.
getAlchemicalAlchemicalStericsForce() - Method in class ffx.potential.openmm.FixedChargeAlchemicalForces
 
getAlchemicalAtoms() - Method in class ffx.potential.cli.AlchemicalOptions
--ac or --alchemicalAtoms Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N]."
getAlchemicalAtoms2() - Method in class ffx.potential.cli.TopologyOptions
--ac2 or --alchemicalAtoms2 Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N].
getAlgorithm() - Method in class ffx.algorithms.cli.ThermodynamicsOptions
Return the selected Thermodynamics algorithm as an enumerated type.
getAlgorithm(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
Returns the user selected algorithm or one chosen based on number of residues.
getAlgorithm(int) - Static method in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
 
getAllAssemblies() - Method in interface ffx.potential.parsers.FileOpener
getAllAssemblies.
getAllAssemblies() - Method in class ffx.potential.utils.PotentialsFileOpener
getAllAssemblies.
getAllAssemblies() - Method in class ffx.ui.UIFileOpener
Returns all MolecularAssemblys in the user interface hierarchy.
getAllBondedEntities() - Method in class ffx.potential.MolecularAssembly
Gets all bonded entities in this MolecularAssembly, where an entity can be a polymer, molecule, monoatomic ion, or monoatomic gas (i.e.
getAllFxPoints() - Method in interface ffx.numerics.integrate.DataSet
Returns copy of the array of points f(x) to integrate (y-axis).
getAllFxPoints() - Method in class ffx.numerics.integrate.DoublesDataSet
Returns copy of the array of points f(x) to integrate (y-axis).
getAllFxPoints() - Method in class ffx.numerics.integrate.FunctionDataCurve
Returns copy of the array of points f(x) to integrate (y-axis).
getAllHistograms() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
 
getAllowed() - Method in class ffx.crystal.HKL
getAllowed
getAllProperties() - Method in interface ffx.potential.parsers.FileOpener
getAllProperties.
getAllProperties() - Method in class ffx.potential.utils.PotentialsFileOpener
getAllProperties.
getAllProperties() - Method in class ffx.ui.UIFileOpener
Returns the properties of all FFXSystems in the hierarchy.
getAlpha() - Method in class ffx.potential.nonbonded.VanDerWaals
getAlpha.
getAlphaCarbon(Residue, Atom) - Static method in class ffx.potential.bonded.BondedUtils
Finds the alpha carbon of a residue, and handles any C-terminal ACE caps while at it.
getAlternateLocation() - Method in class ffx.potential.MolecularAssembly
Get the alternate location.
getAltLoc() - Method in class ffx.potential.bonded.Atom
Getter for the field altLoc.
getAltLocs() - Method in class ffx.potential.parsers.PDBFilter
Get the list of alternate locations encountered.
getAltMolecules() - Method in class ffx.realspace.RealSpaceData
getAltMolecules
getAltMolecules() - Method in interface ffx.xray.DataContainer
getAltMolecules
getAltMolecules() - Method in class ffx.xray.DiffractionData
getAltMolecules
getAltMolecules() - Method in class ffx.xray.RefinementModel
Getter for the field altMolecules.
getAltResidues() - Method in class ffx.realspace.RealSpaceData
getAltResidues
getAltResidues() - Method in interface ffx.xray.DataContainer
getAltResidues
getAltResidues() - Method in class ffx.xray.DiffractionData
getAltResidues
getAltResidues() - Method in class ffx.xray.RefinementModel
Getter for the field altResidues.
getAminoAcid(String) - Static method in class ffx.potential.bonded.AminoAcidUtils
getAminoAcid.
getAminoAcid3() - Method in class ffx.potential.bonded.MultiResidue
getAminoAcid3.
getAminoAcid3() - Method in class ffx.potential.bonded.Residue
getAminoAcid3.
getAminoAcid3From1(String) - Static method in class ffx.potential.bonded.AminoAcidUtils
This method takes a one letter amino acid code and converts it to a three letter amino acid code.
getAminoAcidNumber(String) - Static method in class ffx.potential.bonded.AminoAcidUtils
getAminoAcidNumber.
getAndAdd(byte) - Method in class edu.rit.pj.reduction.SharedByte
Add the given value to this reduction variable and return the previous value.
getAndAdd(char) - Method in class edu.rit.pj.reduction.SharedCharacter
Add the given value to this reduction variable and return the previous value.
getAndAdd(double) - Method in class edu.rit.pj.reduction.SharedDouble
Add the given value to this reduction variable and return the previous value.
getAndAdd(float) - Method in class edu.rit.pj.reduction.SharedFloat
Add the given value to this reduction variable and return the previous value.
getAndAdd(int) - Method in class edu.rit.pj.reduction.SharedInteger
Add the given value to this reduction variable and return the previous value.
getAndAdd(int, byte) - Method in class edu.rit.pj.reduction.SharedByteArray
Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, float) - Method in class edu.rit.pj.reduction.SharedFloatArray
Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Add the given value to this matrix reduction variable at the given row and column and return the previous value.
getAndAdd(int, int, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Add the given value to this matrix reduction variable at the given row and column and return the previous value.
getAndAdd(int, long) - Method in class edu.rit.pj.reduction.SharedLongArray
Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(int, short) - Method in class edu.rit.pj.reduction.SharedShortArray
Add the given value to this array reduction variable at the given index and return the previous value.
getAndAdd(long) - Method in class edu.rit.pj.reduction.SharedLong
Add the given value to this reduction variable and return the previous value.
getAndAdd(short) - Method in class edu.rit.pj.reduction.SharedShort
Add the given value to this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedByte
Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedCharacter
Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedDouble
Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedFloat
Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedInteger
Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedLong
Subtract one from this reduction variable and return the previous value.
getAndDecrement() - Method in class edu.rit.pj.reduction.SharedShort
Subtract one from this reduction variable and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedByteArray
Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedFloatArray
Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedLongArray
Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int) - Method in class edu.rit.pj.reduction.SharedShortArray
Subtract one from this array reduction variable at the given index and return the previous value.
getAndDecrement(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Subtract one from this matrix reduction variable at the given row and column and return the previous value.
getAndDecrement(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Subtract one from this matrix reduction variable at the given row and column and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedByte
Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedCharacter
Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedDouble
Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedFloat
Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedInteger
Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedLong
Add one to this reduction variable and return the previous value.
getAndIncrement() - Method in class edu.rit.pj.reduction.SharedShort
Add one to this reduction variable and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedByteArray
Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedFloatArray
Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedLongArray
Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int) - Method in class edu.rit.pj.reduction.SharedShortArray
Add one to this array reduction variable at the given index and return the previous value.
getAndIncrement(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Add one to this matrix reduction variable at the given row and column and return the previous value.
getAndIncrement(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Add one to this matrix reduction variable at the given row and column and return the previous value.
getAndSet(boolean) - Method in class edu.rit.pj.reduction.SharedBoolean
Set this reduction variable to the given value and return the previous value.
getAndSet(byte) - Method in class edu.rit.pj.reduction.SharedByte
Set this reduction variable to the given value and return the previous value.
getAndSet(char) - Method in class edu.rit.pj.reduction.SharedCharacter
Set this reduction variable to the given value and return the previous value.
getAndSet(double) - Method in class edu.rit.pj.reduction.SharedDouble
Set this reduction variable to the given value and return the previous value.
getAndSet(float) - Method in class edu.rit.pj.reduction.SharedFloat
Set this reduction variable to the given value and return the previous value.
getAndSet(int) - Method in class edu.rit.pj.reduction.SharedInteger
Set this reduction variable to the given value and return the previous value.
getAndSet(int, boolean) - Method in class edu.rit.pj.reduction.SharedBooleanArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, byte) - Method in class edu.rit.pj.reduction.SharedByteArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, float) - Method in class edu.rit.pj.reduction.SharedFloatArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Set this matrix reduction variable at the given row and column to the given value and return the previous value.
getAndSet(int, int, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Set this matrix reduction variable at the given row and column to the given value and return the previous value.
getAndSet(int, long) - Method in class edu.rit.pj.reduction.SharedLongArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, short) - Method in class edu.rit.pj.reduction.SharedShortArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(int, T) - Method in class edu.rit.pj.reduction.SharedObjectArray
Set this array reduction variable at the given index to the given value and return the previous value.
getAndSet(long) - Method in class edu.rit.pj.reduction.SharedLong
Set this reduction variable to the given value and return the previous value.
getAndSet(short) - Method in class edu.rit.pj.reduction.SharedShort
Set this reduction variable to the given value and return the previous value.
getAndSet(T) - Method in class edu.rit.pj.reduction.SharedObject
Set this reduction variable to the given value and return the previous value.
getAngle(Atom, Atom) - Method in class ffx.potential.bonded.Atom
getAngle.
getAngleEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field angleEnergy.
getAngleEnergyString() - Method in class ffx.potential.ForceFieldEnergy
 
getAngleList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Angles below the present MSNode.
getAngleMode() - Method in class ffx.potential.bonded.Angle
Getter for the field angleMode.
getAngles() - Method in class ffx.potential.bonded.Atom
Getter for the field angles.
getAngles() - Method in class ffx.potential.bonded.MSGroup
Returns the MultiScaleGroup's angles FNode.
getAngles() - Method in class ffx.potential.bonded.MultiResidue
Returns the MultiScaleGroup's angles FNode.
getAngles() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field angles.
getAngles(AngleType.AngleMode) - Method in class ffx.potential.ForceFieldEnergy
Getter for the field angles with only AngleMode angles.
getAngleTorsionEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field angleTorsionEnergy.
getAngleTorsionList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all AngleTorsions below the present MSNode.
getAngleTorsions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field angleTorsions.
getAngleTorsionType(String) - Method in class ffx.potential.parameters.ForceField
getAngleTorsionType
getAngleType() - Method in class ffx.potential.bonded.Angle
Get the AngleType for this angle.
getAngleType(AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField
getAngleType
getAngleType(String) - Method in class ffx.potential.parameters.ForceField
getAngleType
getAnisou(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field anisou.
getAnisouAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field anisouAcceleration.
getAnisouGradient(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field anisouGradient.
getAnisouPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field anisouPreviousAcceleration.
getAnisouVelocity(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field anisouVelocity.
getApproxBoxLength() - Method in class ffx.algorithms.cli.ManyBodyOptions
Approximate side lengths of boxes to be constructed (over-rides numXYZBoxes).
getApproximate() - Method in class ffx.algorithms.cli.ManyBodyOptions
 
getApproximate() - Method in class ffx.algorithms.optimize.RotamerOptimization
 
getaRadBuff() - Method in class ffx.xray.DiffractionData
Getter for the field aRadBuff.
getArchiveFile() - Method in class ffx.potential.MolecularAssembly
Getter for the field archiveFile.
getArea() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
 
getArgs() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's command line arguments.
getArguments() - Method in interface ffx.potential.utils.PotentialsFunctions
If available, returns CLI arguments; default implementation does not have access to CLI arguments, and throws UnsupportedOperationException.
getArguments() - Method in class ffx.ui.UIUtils
 
getArray() - Method in class ffx.openmm.Vec3Array
Convert the Vec3Array to a double array.
getArrayIndex() - Method in class ffx.potential.bonded.Atom
getArrayIndex.
getAssembly() - Method in interface ffx.potential.parsers.FileOpener
getAssembly.
getAssembly() - Method in class ffx.potential.utils.PotentialsFileOpener
getAssembly.
getAssembly() - Method in class ffx.ui.UIFileOpener
Returns the active MolecularAssembly from the user interface hierarchy.
getAssembly() - Method in class ffx.xray.DiffractionData
Getter for the field assembly.
getAssemblyArray() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Returns the MolecularAssembly array.
getAtom(int) - Method in class ffx.potential.bonded.BondedTerm
Get the constituent Atom specified by index.
getAtom(int) - Method in class ffx.potential.bonded.RestraintTorsion
 
getAtom(String) - Method in class ffx.potential.bonded.Molecule
getAtom
getAtom4() - Method in class ffx.potential.bonded.Angle
Getter for the field atom4.
getAtomArray() - Method in class ffx.potential.bonded.BondedTerm
Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
getAtomArray() - Method in class ffx.potential.MolecularAssembly
Return an Array of all atoms in the System.
getAtomArray() - Method in class ffx.realspace.RealSpaceData
getAtomArray
getAtomArray() - Method in interface ffx.xray.DataContainer
getAtomArray
getAtomArray() - Method in class ffx.xray.DiffractionData
getAtomArray
getAtomArray(boolean) - Method in class ffx.potential.bonded.BondedTerm
Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
getAtomByName(String, boolean) - Method in class ffx.potential.bonded.MSGroup
getAtomByName.
getAtomElement(Atom) - Static method in class ffx.potential.parsers.CIFFilter
Parse atom name to determine atomic element.
getAtomFromWireVertex(int) - Method in class ffx.potential.MolecularAssembly
getAtomFromWireVertex
getAtomicNumber() - Method in class ffx.potential.bonded.Atom
Gets the Atomic Number
getAtomList() - Method in class ffx.potential.bonded.Atom
Returns a List of all Atoms below the present MSNode.
getAtomList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Atoms below the present MSNode.
getAtomList() - Method in class ffx.potential.parsers.SystemFilter
Getter for the field atomList.
getAtomList(boolean) - Method in class ffx.potential.bonded.MSNode
getAtomList.
getAtomNode() - Method in class ffx.potential.bonded.MSGroup
Returns the AtomNode.
getAtomNode() - Method in class ffx.potential.bonded.MultiResidue
Returns the AtomNode.
getAtomNode(int) - Method in class ffx.potential.bonded.MSGroup
Returns the MSNode at the given index.
getAtomNode(int) - Method in class ffx.potential.bonded.MultiResidue
Returns the MSNode at the given index.
getAtomNode(String) - Method in class ffx.potential.bonded.MSGroup
Returns the AtomNode specified by the String n.
getAtomNode(String) - Method in class ffx.potential.bonded.MultiResidue
Returns the AtomNode specified by the String n.
getAtomNodeList() - Method in class ffx.potential.bonded.MSGroup
Returns a List of the AtomNode's children.
getAtomNodeList() - Method in class ffx.potential.bonded.MultiResidue
Returns a List of the AtomNode's children.
getAtoms() - Method in class ffx.potential.bonded.BondedTerm
Returns a reference to the Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
getAtoms() - Method in class ffx.potential.bonded.ResidueState
Getter for the field atoms.
getAtoms() - Method in class ffx.potential.bonded.RestraintTorsion
 
getAtoms() - Method in class ffx.potential.nonbonded.RestrainPosition
Returns a copy of the atoms array.
getAtomSelectionOptions() - Method in class ffx.potential.commands.Energy
 
getAtomType() - Method in class ffx.potential.bonded.Atom
Getter for the field atomType.
getAtomType(String) - Method in class ffx.potential.parameters.ForceField
getAtomType
getAtomType(String, String) - Method in class ffx.potential.parameters.ForceField
getAtomType
getAtomTypes(String) - Method in class ffx.potential.parameters.ForceField
Getter for the field atomTypes.
getAvailableCommands() - Method in class ffx.ui.ModelingPanel
getAvailableCommands
getAverageEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
 
getAverageEnergyNoOutlier() - Method in class ffx.algorithms.optimize.ConformationScan
 
getAxisAtomIndices() - Method in class ffx.potential.bonded.Atom
Getter for the field axisAtomIndices.
getAxisAtoms() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getBackboneAtoms() - Method in class ffx.potential.bonded.Residue
Returns a list of backbone atoms; for our purposes, nucleic acid backbone atoms are those of the nucleobase.
getBackBoneAtoms() - Method in class ffx.potential.MolecularAssembly
getBackBoneAtoms
getBackboneEnergy() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
getBackboneEnergy() - Method in class ffx.algorithms.optimize.RotamerOptimization
 
getBackendCount() - Method in class edu.rit.pj.cluster.Configuration
Returns the number of backend processors.
getBackendHost() - Method in class edu.rit.pj.cluster.JobBackend
Obtain the backend host name on which this job is running.
getBackendInfo(int) - Method in class edu.rit.pj.cluster.Configuration
Returns information about the given backend processor.
getBackendInfoList() - Method in class edu.rit.pj.cluster.Configuration
Returns information about all backend processors.
getBackendNames() - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Obtain a list of the backend names assigned to this Non-PJ Job Frontend.
getBAR() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getBarInt() - Method in class ffx.algorithms.cli.BarostatOptions
The mean number of MD steps (Poisson distribution) between barostat move proposals.
getBaseDirString(String) - Method in class ffx.potential.cli.PotentialCommand
Check that we can write into the current base directory.
getBaseDirString(String) - Method in class ffx.potential.cli.PotentialScript
Check that we can write into the current base directory.
getBaseRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getBaseRadii.
getBeta() - Method in class ffx.potential.nonbonded.VanDerWaals
getBeta.
getBeta0() - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
 
getBeta1() - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
 
getBeta2() - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
 
getBiasDecomposition() - Method in class ffx.potential.extended.ExtendedSystem
getBiasDecomposition.
getBiasEnergy() - Method in class ffx.potential.extended.ExtendedSystem
Sum up total bias (Ubias = UpH + Udiscr - Umod)
getBiasMag() - Method in class ffx.algorithms.cli.OSTOptions
Sets the initial Gaussian bias magnitude in kcal/mol.
getBiasMag() - Method in class ffx.algorithms.thermodynamics.HistogramData
Gets the Gaussian bias magnitude in kcal/mol.
getBin() - Method in class ffx.crystal.HKL
getBin
getBinEnergies() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Gets the free energy change per bin/window.
getBinEnergies() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getBinEnergies() - Method in interface ffx.numerics.estimator.StatisticalEstimator
Gets the free energy change per bin/window.
getBinEnergies() - Method in class ffx.numerics.estimator.Zwanzig
Gets the free energy change per bin/window.
getBinEnthalpies() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Gets the enthalpy per bin/window.
getBinEnthalpies() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getBinEnthalpies() - Method in interface ffx.numerics.estimator.StatisticalEstimator
Gets the enthalpy per bin/window.
getBinEnthalpies() - Method in class ffx.numerics.estimator.Zwanzig
Gets the enthalpy per bin/window.
getBinUncertainties() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Gets the uncertainty in free energy associated with each bin/window.
getBinUncertainties() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getBinUncertainties() - Method in interface ffx.numerics.estimator.StatisticalEstimator
Gets the uncertainty in free energy associated with each bin/window.
getBinUncertainties() - Method in class ffx.numerics.estimator.Zwanzig
Gets the uncertainty in free energy associated with each bin/window.
getBioType(String) - Method in class ffx.potential.parameters.ForceField
getBioType
getBioType(String, String) - Method in class ffx.potential.parameters.ForceField
getBioType.
getBioTypeMap() - Method in class ffx.potential.parameters.ForceField
getBioTypeMap.
getBond(int) - Method in class ffx.potential.bonded.BondedTerm
Get the constituent Bond specified by index.
getBond(int) - Method in class ffx.potential.bonded.MSGroup
Returns the Bond at the supplied index.
getBond(int) - Method in class ffx.potential.bonded.MultiResidue
Returns the Bond at the supplied index.
getBond(Atom) - Method in class ffx.potential.bonded.Atom
getBond
getBond(String) - Method in class ffx.potential.bonded.MSGroup
Returns the Bond with the given id.
getBond(String) - Method in class ffx.potential.bonded.MultiResidue
Returns the Bond with the given id.
getBondEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field bondEnergy.
getBondEnergyString() - Method in class ffx.potential.ForceFieldEnergy
 
getBondList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Bonds below the present MSNode.
getBonds() - Method in class ffx.potential.bonded.Atom
Gets the list of the Bonds this Atom helps to form
getBonds() - Method in class ffx.potential.bonded.MSGroup
Returns the MultiScaleGroup's bonds FNode.
getBonds() - Method in class ffx.potential.bonded.MultiResidue
Returns the MultiScaleGroup's bonds FNode.
getBonds() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field bonds.
getBonds(String, String) - Method in class ffx.potential.parameters.ForceField
getBonds
getBondType() - Method in class ffx.potential.bonded.Bond
Return the BondType for this Bond.
getBondType() - Method in class ffx.potential.bonded.RestraintBond
Getter for the field bondType.
getBondType(AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField
getBondType
getBondType(String) - Method in class ffx.potential.parameters.ForceField
getBondType
getBoolean(String) - Method in class ffx.potential.parameters.ForceField
getBoolean
getBoolean(String, boolean) - Method in class ffx.potential.parameters.ForceField
getBoolean
getBootstrapEnthalpyResults() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get Bootstrap Free Energy results for each window.
getBootstrapIndices(int) - Static method in class ffx.numerics.estimator.EstimateBootstrapper
Gets randomized bootstrap indices; ensures there are at least two distinct indices.
getBootstrapIndices(int, Random) - Static method in class ffx.numerics.estimator.EstimateBootstrapper
Gets randomized bootstrap indices; ensures there are at least two distinct indices.
getBootstrapIndices(int, Random, int) - Static method in class ffx.numerics.estimator.EstimateBootstrapper
Gets randomized bootstrap indices; ensures there are at least a few distinct indices.
getBorn() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getBorn() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
 
getBoxBorderSize() - Method in class ffx.algorithms.cli.ManyBodyOptions
Extent of overlap between optimization boxes (default: 0.0 A).
getBoxInclusionCriterion() - Method in class ffx.algorithms.cli.ManyBodyOptions
Criterion to use for adding residues to boxes.
getBranchGroup() - Method in class ffx.potential.MolecularAssembly
Getter for the field branchGroup.
getBuffer() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the buffer size.
getBuilt() - Method in class ffx.potential.bonded.Atom
If true, this atom was built during PDB file parsing.
getCavitationEnergy() - Method in class ffx.potential.ForceFieldEnergy
getCavitationEnergy.
getCavitationEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the cavitation component of the solvation energy.
getCavitationEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getCCDCPercent(int) - Static method in class ffx.crystal.SpaceGroupInfo
Return the given space group representation in the CCDC.
getCellIndex() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell
Returns the linear index of this Box.
getCellParametersFromVectors(double[][]) - Method in class ffx.crystal.Crystal
 
getCensusSoluteType(int) - Static method in class ffx.potential.parameters.SoluteType
 
getCenter() - Method in class ffx.potential.bonded.MSGroup
Returns the MultiScaleGroup's center as a double[3].
getCenter() - Method in class ffx.potential.bonded.MultiResidue
Returns the MultiScaleGroup's center as a double[3].
getCenter(boolean) - Method in class ffx.potential.bonded.MSNode
getCenter
getCenter(boolean) - Method in interface ffx.potential.bonded.ROLS
getCenter
getCentralAtom() - Method in class ffx.potential.bonded.Angle
getCentralAtom.
getChain() - Method in class ffx.algorithms.cli.ManyBodyOptions
Single character chain ID of the residues to optimize.
getChain(String) - Method in class ffx.potential.MolecularAssembly
getChain
getChainID() - Method in class ffx.potential.bonded.Atom
Get the chain name
getChainID() - Method in class ffx.potential.bonded.Molecule
Getter for the field chainID.
getChainID() - Method in class ffx.potential.bonded.Polymer
Getter for the field chainID.
getChainID() - Method in class ffx.potential.bonded.Residue
Returns this Residues Parent Polymer name.
getChainID(int) - Static method in class ffx.potential.Utilities
Determine chainID for a given polymer number.
getChainNames() - Method in class ffx.potential.MolecularAssembly
getChainNames
getChains() - Method in class ffx.potential.MolecularAssembly
getChains
getChandlerCavitation() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Return the Chandler Cavitation instance.
getChannelGroup() - Method in class edu.rit.mp.Channel
Obtain the channel group that created this channel.
getChannelGroupId() - Method in class edu.rit.mp.ChannelGroup
Obtain this channel group's channel group ID.
getCharge() - Method in class ffx.potential.bonded.Atom
Gets the partial atomic charge
getCharge() - Method in class ffx.potential.nonbonded.octree.OctreeParticle
 
getCharge() - Method in class ffx.potential.parameters.MultipoleType
Getter for the field charge.
getCharge(boolean) - Method in class ffx.potential.MolecularAssembly
Sums up charge of the system, checking nonstandard residues for non-unitary charges.
getCharge(ForceField) - Method in class ffx.potential.bonded.Atom
Gets the partial atomic charge.
getCheckpoint() - Method in class ffx.algorithms.cli.DynamicsOptions
The restart save frequency in picoseconds (1.0 psec default).
getCheckpointFrequency(int) - Method in class ffx.algorithms.cli.DynamicsOptions
The checkpoint frequency in steps.
getCheckRestrictions() - Method in class ffx.crystal.Crystal
 
getCheckRestrictions() - Method in class ffx.crystal.ReplicatesCrystal
getChildAtIndex(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
getChildList() - Method in class ffx.potential.bonded.MSNode
Returns a List of the MSNode's Children (instead of using an Enumeration).
getChiralAtom() - Method in class ffx.potential.bonded.TorsionTorsion
getChiralAtom.
getClashThreshold() - Method in class ffx.algorithms.cli.ManyBodyOptions
The threshold for pruning clashes.
getClassLoader() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's backend class loader.
getClusterName() - Method in class edu.rit.pj.cluster.Configuration
Returns the cluster name.
getColCount() - Method in class edu.rit.io.DoubleMatrixFile
Returns the number of columns in this matrix file.
getColRange() - Method in class edu.rit.io.DoubleMatrixFile.Reader
Obtain the column range of the next matrix element segment in the input stream.
getCombinedEps(double, double, double, double, VanDerWaalsForm.EPSILON_RULE) - Static method in class ffx.potential.nonbonded.VanDerWaalsForm
Get the combined EPS value.
getCombinedEps(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm
Return the combined well depth (kcal/mol)
getCombinedEps14(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm
Return the combined well depth (kcal/mol) for special 1-4 interactions
getCombinedInverseRmin(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm
Return the combined inverse Rmin value (1/Rmin).
getCombinedInverseRmin14(int, int) - Method in class ffx.potential.nonbonded.VanDerWaalsForm
Return the combined inverse Rmin value (1/Rmin) for special 1-4 interactions.
getCombinedRadius(double, double, VanDerWaalsForm.RADIUS_RULE) - Static method in class ffx.potential.nonbonded.VanDerWaalsForm
Get the combined radius value.
getCommand() - Method in class ffx.ui.ModelingPanel
 
getCommand(String) - Static method in class ffx.utilities.FFXCommand
Use the System ClassLoader to find the requested command.
getConfidenceScore(Residue) - Method in class ffx.potential.utils.GetProteinFeatures
Get the alphafold confidence score or b-factor from an X-ray model.
getConnollyRegion() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
getConsideredResidues() - Method in class ffx.potential.bonded.MultiResidue
Returns a copy of this MultiResidue's consideredResidues array.
getConstantPh() - Method in class ffx.potential.extended.ExtendedSystem
getConstantPh.
getConstants() - Method in class ffx.potential.bonded.AngleTorsion
Returns the array of stretch-torsion constants, in units of kcal/mol/degree.
getConstants() - Method in class ffx.potential.bonded.StretchTorsion
Returns the array of stretch-torsion constants, in units of kcal/mol/A.
getConstraints() - Method in class ffx.algorithms.dynamics.integrators.Integrator
Returns a copy of the list of Constraints.
getConstraints() - Method in interface ffx.numerics.Potential
Returns the list of Constraints associated with this Potential.
getConstraints() - Method in class ffx.potential.extended.ExtendedSystem
 
getConstraints() - Method in class ffx.potential.ForceFieldEnergy
Returns a copy of the list of constraints this ForceFieldEnergy has.
getContext() - Method in class ffx.potential.openmm.OpenMMEnergy
Returns the Context instance.
getCoordinates() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Get the coordinates.
getCoordinates() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getCoordinates(double[]) - Method in class ffx.algorithms.dynamics.Barostat
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getCoordinates(double[]) - Method in interface ffx.numerics.OptimizationInterface
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.ANIEnergy
 
getCoordinates(double[]) - Method in class ffx.potential.DualTopologyEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
getCoordinates(double[]) - Method in class ffx.potential.ForceFieldEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.QuadTopologyEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.potential.XtalEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.realspace.RealSpaceEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.RefinementEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.ScaleBulkEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.ScaleBulkMinimize
getCoordinates.
getCoordinates(double[]) - Method in class ffx.xray.SigmaAEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.SigmaAMinimize
getCoordinates.
getCoordinates(double[]) - Method in class ffx.xray.SplineEnergy
Load the current value of the parameters.
getCoordinates(double[]) - Method in class ffx.xray.SplineMinimize
getCoordinates.
getCoordinates(double[]) - Method in class ffx.xray.XRayEnergy
Load the current value of the parameters.
getCoordinatesCopy() - Method in class ffx.potential.SystemState
Get a copy of the internal coordinate array.
getCount() - Method in class ffx.numerics.math.RunningStatistics
Get the count.
getCount() - Method in class ffx.potential.nonbonded.NeighborList.Cell
 
getCount(int) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
getCountInterval() - Method in class ffx.algorithms.cli.OSTOptions
Sets the number of time steps between OST counts.
getCreatedFileNames() - Method in class ffx.potential.parsers.CIFFilter
Obtain a list of output files written from the conversion.
getCrossOver() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
getCrystal() - Method in class ffx.algorithms.dynamics.Barostat
getCrystal() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
getCrystal() - Method in interface ffx.crystal.CrystalPotential
 
getCrystal() - Method in class ffx.potential.DualTopologyEnergy
getCrystal() - Method in class ffx.potential.ForceFieldEnergy
getCrystal() - Method in class ffx.potential.MolecularAssembly
getCrystal
getCrystal() - Method in class ffx.potential.QuadTopologyEnergy
getCrystal() - Method in class ffx.realspace.RealSpaceData
Getter for the field crystal.
getCrystal() - Method in class ffx.realspace.RealSpaceEnergy
getCrystal() - Method in class ffx.xray.DiffractionData
Getter for the field crystal.
getCrystal() - Method in class ffx.xray.RefinementEnergy
getCrystal() - Method in class ffx.xray.XRayEnergy
getCrystal(String, CompositeConfiguration) - Method in class ffx.realspace.parsers.CCP4MapFilter
getCrystal
getCrystal(String, CompositeConfiguration) - Method in interface ffx.realspace.parsers.RealSpaceFileFilter
getCrystal
getCrystalReciprocalSpacesFc() - Method in class ffx.xray.DiffractionData
Getter for the field crs_fc.
getCrystalReciprocalSpacesFs() - Method in class ffx.xray.DiffractionData
Getter for the field crs_fs.
getCrystalStats() - Method in class ffx.xray.DiffractionData
Getter for the field crystalStats.
getCurrentCycle() - Method in class ffx.potential.MolecularAssembly
Getter for the field currentCycle.
getCurrentDistance() - Method in class ffx.potential.bonded.Bond
Gets the current distance between the two Atoms in this Bond.
getCurrentTemperature() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Get the current temperature.
getCutoff() - Method in class ffx.algorithms.cli.ManyBodyOptions
The sliding window and box cutoff radius (Angstroms).
getCutoff() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Getter for the field cutoff.
getCutoff() - Method in class ffx.potential.nonbonded.NeighborList
Returns the cutoff distance used internally by NeighborList.
getCutoffPlusBuffer() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field cutoffPlusBuffer.
getCycles() - Method in class ffx.potential.MolecularAssembly
Getter for the field cycles.
getd2EdL2() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.ANIEnergy
 
getd2EdL2() - Method in class ffx.potential.bonded.AngleTorsion
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in interface ffx.potential.bonded.LambdaInterface
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.PiOrbitalTorsion
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.RestraintBond
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.RestraintTorsion
 
getd2EdL2() - Method in class ffx.potential.bonded.StretchTorsion
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.Torsion
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.bonded.TorsionTorsion
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.DualTopologyEnergy
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.ForceFieldEnergy
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.COMRestraint
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.NCSRestraint
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.RestrainPosition
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.openmm.OpenMMEnergy
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.potential.QuadTopologyEnergy
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.realspace.RealSpaceEnergy
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.xray.RefinementEnergy
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdL2() - Method in class ffx.xray.XRayEnergy
Get the 2nd partial derivative of the energy with respect to lambda.
getd2EdZ2() - Method in class ffx.numerics.multipole.CoulombTensorGlobal
getd2EdZ2.
getd2EdZ2() - Method in class ffx.numerics.multipole.MultipoleTensor
getd2EdZ2.
getDanglingAtoms() - Method in class ffx.potential.bonded.MSGroup
Returns the MultiScaleGroup's dangling Atoms list.
getDanglingAtoms() - Method in class ffx.potential.bonded.MultiResidue
Returns the MultiScaleGroup's dangling Atoms list.
getData() - Method in class ffx.realspace.RealSpaceRefinementData
Getter for the field data.
getDataEnergy() - Method in class ffx.xray.RefinementEnergy
Getter for the field dataEnergy.
getDataFiles() - Method in class ffx.xray.DiffractionData
Getter for the field dataFiles.
getDataTypes() - Method in class ffx.openmm.State
Get the data types.
getDataTypes() - Method in class ffx.potential.openmm.OpenMMState
Get the mask of information contained in the state.
getDDGunValues(List<String>) - Method in class ffx.potential.utils.GetProteinFeatures
Get ddgun values from ddgun file
getdEdL() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.ANIEnergy
 
getdEdL() - Method in class ffx.potential.bonded.AngleTorsion
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in interface ffx.potential.bonded.LambdaInterface
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.PiOrbitalTorsion
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.RestraintBond
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.RestraintTorsion
 
getdEdL() - Method in class ffx.potential.bonded.StretchTorsion
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.Torsion
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.bonded.TorsionTorsion
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.DualTopologyEnergy
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.ForceFieldEnergy
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.COMRestraint
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.NCSRestraint
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.RestrainPosition
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.openmm.OpenMMEnergy
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.potential.QuadTopologyEnergy
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.realspace.RealSpaceEnergy
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.xray.RefinementEnergy
Get the partial derivative of the energy with respect to lambda.
getdEdL() - Method in class ffx.xray.XRayEnergy
Get the partial derivative of the energy with respect to lambda.
getdEdXdL(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.ANIEnergy
 
getdEdXdL(double[]) - Method in class ffx.potential.bonded.AngleTorsion
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in interface ffx.potential.bonded.LambdaInterface
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.PiOrbitalTorsion
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.RestraintBond
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.RestraintTorsion
 
getdEdXdL(double[]) - Method in class ffx.potential.bonded.StretchTorsion
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.Torsion
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.bonded.TorsionTorsion
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.DualTopologyEnergy
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.ForceFieldEnergy
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.COMRestraint
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.NCSRestraint
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.RestrainPosition
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.nonbonded.VanDerWaals
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.potential.QuadTopologyEnergy
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.realspace.RealSpaceEnergy
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.xray.RefinementEnergy
Get the gradient of dEdL with respect to each parameter.
getdEdXdL(double[]) - Method in class ffx.xray.XRayEnergy
Get the gradient of dEdL with respect to each parameter.
getdEdZ() - Method in class ffx.numerics.multipole.CoulombTensorGlobal
getdEdZ.
getdEdZ() - Method in class ffx.numerics.multipole.MultipoleTensor
getdEdZ.
getDefault() - Static method in class edu.rit.util.TimerThread
Get the default timer thread, a single shared instance of class TimerThread.
getDefaultAlpha() - Method in enum class ffx.crystal.LatticeSystem
Returns the default alpha for the lattice system.
getDefaultBAxis(double) - Method in enum class ffx.crystal.LatticeSystem
Returns the default b-axis for the lattice system.
getDefaultBeta() - Method in enum class ffx.crystal.LatticeSystem
Returns the default beta for the lattice system.
getDefaultCAxis(double, double) - Method in enum class ffx.crystal.LatticeSystem
Returns the default c-axis for the lattice system.
getDefaultDevice(CompositeConfiguration) - Static method in class ffx.potential.openmm.OpenMMEnergy
Gets the default coprocessor device, ignoring any CUDA_DEVICE over-ride.
getDefaultGamma() - Method in enum class ffx.crystal.LatticeSystem
Returns the default gamma for the lattice system.
getDefaultLibrary() - Static method in class ffx.potential.bonded.RotamerLibrary
getDefaultLibrary.
getDefaultListener() - Method in interface ffx.algorithms.AlgorithmFunctions
Returns a default Listener if available (null by default).
getDefaultListener() - Method in class ffx.ui.UIUtils
 
getDefaultPressure() - Method in class ffx.openmm.MonteCarloBarostat
Get the default pressure.
getDefaultTemperature() - Method in class ffx.openmm.MonteCarloBarostat
Get the default temperature.
getDefaultThreadCount() - Static method in class edu.rit.pj.HybridTeam
Determine the default number of threads per process for a hybrid team.
getDefaultThreadCount() - Static method in class edu.rit.pj.ParallelTeam
Determine the default number of threads for a parallel team.
getDegreesOfFreedom() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Return the number of degrees of freedom.
getDensity(double) - Method in class ffx.crystal.Crystal
Compute the density of the system.
getDensity(double) - Method in class ffx.crystal.ReplicatesCrystal
Return the density of the ReplicatesCrystal.
getDensityGrid() - Method in class ffx.xray.CrystalReciprocalSpace
Getter for the field densityGrid.
getDerivatives() - Method in class ffx.potential.extended.ExtendedSystem
get array of dU/dL for each titrating residue
getDescreenOffset() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Return the descreening dielectric offset.
getDescreenRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getDescreenRadii.
getDescription() - Method in class edu.rit.pj.job.Job
Returns this job's description.
getDescription() - Method in class ffx.potential.parsers.ARCFileFilter
getDescription() - Method in class ffx.potential.parsers.CoordinateFileFilter
getDescription() - Method in class ffx.potential.parsers.DistanceMatrixFileFilter
getDescription() - Method in class ffx.potential.parsers.DYNFileFilter
getDescription() - Method in class ffx.potential.parsers.ESVFileFilter
getDescription() - Method in class ffx.potential.parsers.FFXFileFilter
getDescription() - Method in class ffx.potential.parsers.ForceFieldFileFilter
getDescription() - Method in class ffx.potential.parsers.InducedFileFilter
getDescription() - Method in class ffx.potential.parsers.INTFileFilter
getDescription() - Method in class ffx.potential.parsers.KeyFileFilter
getDescription() - Method in class ffx.potential.parsers.PDBFileFilter
getDescription() - Method in class ffx.potential.parsers.PDBMLFileFilter
getDescription() - Method in class ffx.potential.parsers.XPHFileFilter
getDescription() - Method in class ffx.potential.parsers.XYZFileFilter
getDescription() - Method in class ffx.xray.parsers.MTZFileFilter
getDevice() - Static method in class ffx.numerics.tornado.FFXTornado
Get the default Tornado Device.
getDevice(int) - Static method in class ffx.numerics.tornado.FFXTornado
Get the specified Tornado Device.
getDevice(int, int) - Static method in class ffx.numerics.tornado.FFXTornado
Get the Tornado Device using specified driver and device index.
getDielecOffset() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the dielectric offset (in Angstroms).
getDiffMatrix() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getDiffractionData(List<String>, MolecularAssembly[], CompositeConfiguration) - Method in class ffx.xray.cli.XrayOptions
Process input from opened molecular assemblies to a DiffractionData.
getDiffractionfilter() - Method in class ffx.xray.parsers.DiffractionFile
getDiffractionfilter.
getDipole() - Method in class ffx.potential.parameters.MultipoleType
Getter for the field dipole.
getDispersionEnergy() - Method in class ffx.potential.ForceFieldEnergy
getDispersionEnergy.
getDispersionEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the dispersion component of the solvation energy.
getDispersionEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getDispersionOffset() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
The dispersion integral begins offset from the vdW radius.
getDispersionOverlapFactor() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
 
getDispersionRegion() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getDistributeWalkersString() - Method in class ffx.algorithms.cli.MultiDynamicsOptions
Allows walkers to start from multiple conformations; AUTO picks up per-walker conformations as filename.pdb_(walker number), and specifying a residue starts a rotamer optimization to generate side-chain configurations to start from.
getDOF() - Method in class ffx.numerics.math.RunningStatistics
Get the DOF.
getDoLongRangeCorrection() - Method in class ffx.potential.nonbonded.VanDerWaals
Return use of the long-range vdW correction.
getDouble(String) - Method in class ffx.potential.parameters.ForceField
getDouble
getDouble(String, Double) - Method in class ffx.potential.parameters.ForceField
getDouble
getDt() - Method in class ffx.algorithms.cli.DynamicsOptions
The time step in femtoseconds (default of 1.0).
getDtPsec() - Method in class ffx.algorithms.cli.DynamicsOptions
 
getDualTopA() - Method in class ffx.potential.QuadTopologyEnergy
Returns the first component DualTopologyEnergy.
getDualTopB() - Method in class ffx.potential.QuadTopologyEnergy
Returns the second component DualTopologyEnergy.
getDUDLBins() - Method in class ffx.algorithms.thermodynamics.HistogramData
 
getDx() - Method in class ffx.potential.cli.GradientOptions
-d or --dx Finite-difference step size.
getDynamics(WriteoutOptions, Potential, MolecularAssembly, AlgorithmListener) - Method in class ffx.algorithms.cli.DynamicsOptions
Initialize a MolecularDynamics from the parsed options.
getDynamics(WriteoutOptions, Potential, MolecularAssembly, AlgorithmListener, MDEngine) - Method in class ffx.algorithms.cli.DynamicsOptions
Initialize a MolecularDynamics from the parsed options.
getDynFile() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Returns the associated dynamics file.
getE1() - Method in class ffx.algorithms.mc.BoltzmannMC
Return starting energy from last attempted step.
getE1() - Method in interface ffx.algorithms.mc.MetropolisMC
Return starting energy from last attempted step.
getE1l1() - Method in class ffx.potential.parsers.BARFilter
 
getE1l2() - Method in class ffx.potential.parsers.BARFilter
 
getE2() - Method in class ffx.algorithms.mc.BoltzmannMC
Return trial energy from last attempted step.
getE2() - Method in interface ffx.algorithms.mc.MetropolisMC
Return trial energy from last attempted step.
getE2l1() - Method in class ffx.potential.parsers.BARFilter
 
getE2l2() - Method in class ffx.potential.parsers.BARFilter
 
getEffectiveRadius() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
getElecForm() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Returns the ELEC_FORM.
getElectrostaticEnergy() - Method in class ffx.potential.ForceFieldEnergy
getElectrostaticEnergy.
getElectrostatics() - Method in class ffx.potential.bonded.Atom
Getter for the field electrostatics.
getEliminatedRotamers() - Method in class ffx.algorithms.optimize.RotamerOptimization
 
getEnd() - Method in class ffx.algorithms.optimize.TorsionSearch
 
getEnergies() - Method in class ffx.algorithms.optimize.ConformationScan
 
getEnergies() - Method in class ffx.algorithms.optimize.TorsionSearch
List of energies for each state in order of lowest to highest energy.
getEnergiesWithinEnergy(double) - Method in class ffx.algorithms.optimize.ConformationScan
 
getEnergy() - Method in class ffx.algorithms.optimize.Minimize
Getter for the field energy.
getEnergy() - Method in class ffx.algorithms.optimize.PhMinimize
Getter for the field energy.
getEnergy() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
getEnergy() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
 
getEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
getEnergy() - Method in class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
 
getEnergy() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
 
getEnergy() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the total Van der Waals potential energy.
getEnergy() - Method in class ffx.potential.nonbonded.VanDerWaalsTornado
Get the total Van der Waals potential energy.
getEnergy() - Method in exception class ffx.potential.utils.EnergyException
Return the reported Energy.
getEnergyChange() - Method in class ffx.algorithms.mc.MDMove
Get the total energy change for the current move.
getEnergyCount() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Returns the number of energy evaluations performed by this OST, including those picked up in the lambda file.
getEnergyExpansion() - Method in class ffx.algorithms.optimize.RotamerOptimization
 
getEnergyRestart() - Method in class ffx.algorithms.cli.ManyBodyOptions
Energy restart file from a previous run (requires that all parameters are the same).
getEnergyTermState() - Method in class ffx.algorithms.dynamics.Barostat
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in interface ffx.numerics.Potential
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.ANIEnergy
 
getEnergyTermState() - Method in class ffx.potential.DualTopologyEnergy
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.extended.ExtendedSystem
 
getEnergyTermState() - Method in class ffx.potential.ForceFieldEnergy
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.QuadTopologyEnergy
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.potential.XtalEnergy
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.realspace.RealSpaceEnergy
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.xray.RefinementEnergy
Get the Potential Energy terms that is active.
getEnergyTermState() - Method in class ffx.xray.XRayEnergy
Get the Potential Energy terms that is active.
getEngineString() - Method in class ffx.algorithms.cli.DynamicsOptions
The default engine choice for integrating the equations of motion
getEnsemble() - Method in class ffx.algorithms.optimize.RotamerOptimization
getEnsemble.
getEnthalpy() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get bootstrap enthalpy estimate for each window.
getEnthalpyUncertainty() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the enthalpy standard deviation estimate from bootstrap analysis for each window.
getEnthalpyVariance() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the enthalpy variance estimate from bootstrap analysis for each window.
getEntries() - Method in class ffx.utilities.Keyword
getEntries
getEntry(int) - Method in class ffx.utilities.Keyword
getEntry
getEps() - Method in class ffx.algorithms.cli.MinimizeOptions
Convergence criteria.
getEps() - Method in class ffx.potential.nonbonded.pme.SORRegion
 
getEps() - Method in class ffx.potential.nonbonded.VanDerWaalsForm
Return the eps value for each class.
getEps() - Method in class ffx.xray.RefinementMinimize
Getter for the field eps.
getEpsilon() - Method in class ffx.crystal.HKL
getEpsilon
getEpsilon() - Method in class ffx.potential.bonded.Atom
Gets the Epsilon value
getEquilibrationSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions
The number of equilibration steps prior to production OST counts begin.
getEquilibriumCoordinates() - Method in class ffx.potential.nonbonded.RestrainPosition
Returns the original coordinates of this restraint, indexed by atoms then x,y,z.
getEquilSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions
getEquilSteps.
getEsvBiasEnergy() - Method in class ffx.potential.ForceFieldEnergy
getEsvBiasEnergy.
getESVHistogram(int[][]) - Method in class ffx.potential.extended.ExtendedSystem
Overwrites the histogram passed into it and returns the new one out ~output never used?~
getEwaldCoefficient() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getEwaldCutoff() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getExceptionMap() - Method in exception class edu.rit.pj.MultipleParallelException
Obtain this multiple parallel exception's exception map.
getExceptionParameters(int, IntByReference, IntByReference, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.NonbondedForce
Get the exception parameters.
getExclude() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
getExponent() - Method in class ffx.algorithms.cli.RepExOptions
 
getExponent() - Method in class ffx.numerics.switching.PowerSwitch
Gets the value of beta in f(x) = (a*x)^beta
getExtendedAtoms() - Method in class ffx.potential.extended.ExtendedSystem
All atoms of the fully-protonated system (not just those affected by this system).
getExtendedLambdas() - Method in class ffx.potential.extended.ExtendedSystem
Gets a copy of the array of doubles that matches the nESVs correspoding to each titration and tautomer lambda
getExtendedMolecule() - Method in class ffx.potential.extended.ExtendedSystem
Companion to getExtendedAtoms() for vdw::setAtoms and pme::setAtoms.
getExtendedResidueList() - Method in class ffx.potential.extended.ExtendedSystem
Return the List of Extended Residues which = TitratingResidueList + TautomerizingResidueList
getExtendedSystem() - Method in class ffx.potential.ForceFieldEnergy
getExtendedSystem.
getExtendedSystem() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the ExtendedSystem instance.
getExtendedSystem() - Method in class ffx.potential.parsers.XPHFilter
 
getExtent() - Method in class ffx.potential.bonded.MSNode
getExtent
getExtent() - Method in class ffx.potential.MolecularAssembly
getExtent
getF(int) - Method in class ffx.xray.DiffractionRefinementData
getF
getFactor() - Method in class ffx.ui.behaviors.MouseZoom
Return the y-axis movement multipler.
getFactors() - Method in class ffx.numerics.fft.Complex
Getter for the field factors.
getFcTot(int) - Method in class ffx.xray.DiffractionRefinementData
getFcTot
getFE() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get bootstrap free energy estimate for each window.
getFfxContext() - Method in class ffx.utilities.FFXCommand
Obtain the Context for this command.
getFieldGK() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getFieldGKCR() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getFile() - Method in class edu.rit.pj.io.StreamFile
Obtain the file in the frontend processor to which this stream file refers.
getFile() - Method in class ffx.potential.MolecularAssembly
Getter for the field file.
getFile() - Method in class ffx.potential.parsers.SystemFilter
getFile
getFilename() - Method in class ffx.realspace.parsers.RealSpaceFile
Getter for the field filename.
getFilename() - Method in class ffx.xray.parsers.DiffractionFile
getFilename.
getFileReader() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's backend file reader.
getFiles() - Method in class ffx.potential.parsers.SystemFilter
Getter for the field files.
getFileType() - Method in class ffx.potential.cli.WriteoutOptions
Getter for the field fileType.
getFileWriter() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's backend file writer.
getFilter() - Method in class ffx.potential.utils.PotentialsFileOpener
Getter for the field filter.
getFilter() - Method in interface ffx.potential.utils.PotentialsFunctions
Returns the last SystemFilter created by this (can be null).
getFilter() - Method in class ffx.potential.utils.PotentialsUtils
Returns the last SystemFilter created by this (can be null).
getFilter() - Method in class ffx.ui.MainPanel
Return the active SystemFilter.
getFilter() - Method in class ffx.ui.UIUtils
 
getFinish() - Method in class ffx.algorithms.cli.ManyBodyOptions
Final residue to perform the optimization on (-1 exits).
getFirstAngleAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend
Get the first atom of the Angle.
getFirstDir() - Method in class ffx.algorithms.cli.MultiDynamicsOptions
 
getFirstResidue() - Method in class ffx.potential.bonded.Polymer
getFirstResidue
getFitSoluteType(ForceField, int) - Static method in class ffx.potential.parameters.SoluteType
 
getFixedChargeSoftcoreForce() - Method in class ffx.potential.openmm.FixedChargeAlchemicalForces
 
getFoFc1(int) - Method in class ffx.xray.DiffractionRefinementData
getFoFc1
getFoFc1IP(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData
getFoFc1IP
getFoFc2(int) - Method in class ffx.xray.DiffractionRefinementData
getFoFc2
getFoFc2IP(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData
getFoFc2IP
getForceConstant() - Method in class ffx.potential.nonbonded.RestrainPosition
Returns the force constant in kcal/mol/Angstrom^2.
getForceConstants() - Method in class ffx.potential.nonbonded.RestrainGroups
Force constant for each restraint.
getForceField() - Method in class ffx.potential.MolecularAssembly
Getter for the field forceField.
getForceField() - Method in class ffx.potential.openmm.OpenMMSystem
Get the ForceField in use.
getForceFieldEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Getter for the field forceFieldEnergy.
getForceFieldTypeCount(ForceField.ForceFieldType) - Method in class ffx.potential.parameters.ForceField
getForceFieldTypeCount
getForceFieldURL(ForceField.ForceFieldName) - Static method in class ffx.potential.parameters.ForceField
Get for the URL for the named force field.
getForceGroup() - Method in class ffx.openmm.Force
Get the force group.
getForceIndex() - Method in class ffx.openmm.Force
Get the force index.
getForces() - Method in class ffx.openmm.State
Get the forces.
getFormFactorA(String) - Static method in class ffx.xray.NeutronFormFactor
getFormFactorA
getFormFactorA(String) - Static method in class ffx.xray.XRayFormFactor
getFormFactorA
getFormFactorB(String) - Static method in class ffx.xray.XRayFormFactor
getFormFactorB
getFormFactorIndex() - Method in class ffx.potential.bonded.Atom
Getter for the field formFactorIndex.
getFormFactorIndex(String) - Static method in class ffx.xray.NeutronFormFactor
getFormFactorIndex
getFormFactorIndex(String) - Static method in class ffx.xray.XRayFormFactor
getFormFactorIndex
getFormFactorWidth() - Method in class ffx.potential.bonded.Atom
Getter for the field formFactorWidth.
getFormFactorWidth2() - Method in class ffx.potential.bonded.Atom
Getter for the field formFactorWidth.
getFourBodyEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
getFourthAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend
The atom of this out-of-plane bend that was not part of the Angle.
getFourthAtomOfTrigonalCenter() - Method in class ffx.potential.bonded.Angle
If the central atom of the angle is trigonal, the 4th member of the trigonal center (that is not a part of the angle) will be returned.
getFractionalMode() - Method in class ffx.potential.MolecularAssembly
Getter for the field fractionalMode.
getFrame() - Method in class ffx.ui.MainPanel
Getter for the field frame.
getFrame() - Method in class ffx.ui.Trajectory
getFrame
getFreeEnergy() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Returns the estimated free energy (usually in kcal/mol).
getFreeEnergy() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getFreeEnergy() - Method in interface ffx.numerics.estimator.StatisticalEstimator
Returns the estimated free energy (usually in kcal/mol).
getFreeEnergy() - Method in class ffx.numerics.estimator.Zwanzig
Returns the estimated free energy (usually in kcal/mol).
getFreeR(int) - Method in class ffx.xray.DiffractionRefinementData
getFreeR
getFrequency() - Method in class ffx.openmm.MonteCarloBarostat
Get the frequency.
getFrontendAddress() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's array of hosts/ports for the frontend communicator.
getFrontendChannelGroup() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's frontend communicator channel group.
getFrontendHost() - Method in class edu.rit.pj.cluster.Configuration
Returns the host name of the cluster's frontend processor.
getFs(int) - Method in class ffx.xray.DiffractionRefinementData
getFs
getFSigF(int) - Method in class ffx.xray.DiffractionRefinementData
getFSigF
getFsigfCutoff() - Method in class ffx.xray.DiffractionData
Getter for the field fsigfCutoff.
getFSystem() - Method in class ffx.ui.Trajectory
getFSystem
getFxPoint(int) - Method in interface ffx.numerics.integrate.DataSet
Point f(x) at index.
getFxPoint(int) - Method in class ffx.numerics.integrate.DoublesDataSet
Point f(x) at index.
getFxPoint(int) - Method in class ffx.numerics.integrate.FunctionDataCurve
Point f(x) at index.
getGaussVol() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
getGeneralizedKirkwoordEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the GK component of the solvation energy.
getGeneralizedKirkwoordPermanentEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the GK component of the solvation energy.
getGeneralizedKirkwoordPolariztionEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the GK component of the solvation energy.
getGK() - Method in class ffx.potential.ForceFieldEnergy
getGK.
getGK() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getGKEnergy() - Method in class ffx.potential.ForceFieldEnergy
getGKEnergy.
getGKEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getGeneralizedKirkwoodEnergy.
getGKInteractions() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getGKInteractions
getGrad() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getGradient(double[]) - Method in class ffx.potential.ForceFieldEnergy
getGradient
getGradient(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy
Re-compute the gradient using OpenMM and return it.
getGradient(double[]) - Method in class ffx.potential.openmm.OpenMMState
The force array contains the OpenMM force information for all atoms.
getGradientAtoms() - Method in class ffx.potential.cli.GradientOptions
--ga or --gradientAtoms Ranges of atoms to test [ALL, NONE, Range(s): 1-3,6-N].
getGrid() - Method in class ffx.potential.nonbonded.RowRegion
Getter for the field grid.
getGrid() - Method in class ffx.potential.nonbonded.SliceRegion
Getter for the field grid.
getGrid() - Method in class ffx.potential.nonbonded.SpatialDensityRegion
Getter for the field grid.
getGroup1() - Method in class ffx.potential.nonbonded.RestrainGroups
Group 1 for each restraint.
getGroup2() - Method in class ffx.potential.nonbonded.RestrainGroups
Group 2 for each restraint.
getGroupMembers(int) - Method in class ffx.potential.nonbonded.RestrainGroups
Get group members.
getH() - Method in class ffx.crystal.HKL
h
getHalfStepEnergy() - Method in class ffx.algorithms.dynamics.integrators.Respa
Get the potential energy of the fast degrees of freedom.
getHeader(String) - Method in class edu.rit.http.HttpRequest
Obtain the value of the given header in this HTTP request.
getHeaderLines() - Method in class ffx.potential.MolecularAssembly
Gets the header lines associated with this MolecularAssembly (particularly for PDB)
getHeaders() - Method in class edu.rit.http.HttpRequest
Obtain a collection of all the headers in this HTTP request.
getHierarchy() - Method in class ffx.ui.MainPanel
Getter for the field hierarchy.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.BellCurveSwitch
The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.CompositeSwitch
 
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.ConstantSwitch
The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.LinearDerivativeSwitch
The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.MultiplicativeSwitch
The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.PowerSwitch
The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in class ffx.numerics.switching.SquaredTrigSwitch
The highest-order derivative that is zero at the bounds.
getHighestOrderZeroDerivative() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction
The highest-order derivative that is zero at the bounds.
getHighlighting() - Method in class ffx.ui.MainMenu
getHighlighting
getHighTemp() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule
Gets the starting temperature.
getHighTemp() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
 
getHighTemp() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
 
getHighTemp() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
 
getHilbertIndices() - Method in class ffx.algorithms.optimize.TorsionSearch
List of hilbert indices for each state in order of lowest to highest energy.
getHistogram() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Return the current 2D Histogram of counts.
getHistogramFile() - Method in class ffx.algorithms.thermodynamics.HistogramData
 
getHistogramFileName() - Method in class ffx.algorithms.thermodynamics.HistogramData
 
getHistogramIndex() - Method in class ffx.algorithms.thermodynamics.SendSynchronous
 
getHKL(int, int, int) - Method in class ffx.crystal.ReflectionList
getHKL
getHKL(HKL) - Method in class ffx.crystal.ReflectionList
getHKL
getHttpVersion() - Method in class edu.rit.http.HttpRequest
Obtain this HTTP request's version.
getHybridization() - Method in class ffx.potential.bonded.Atom
Gets the Atomic Hybridization
getID() - Method in class ffx.potential.bonded.BondedTerm
Get the Term's id.
getIdent() - Method in class ffx.potential.bonded.Atom
Gets the atom ID
getImproperTorsionEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field improperTorsionEnergy.
getImproperTorsionList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all ImproperTorsions below the present MSNode.
getImproperTorsions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field improperTorsions.
getImproperType(String) - Method in class ffx.potential.parameters.ForceField
getImproperType
getImproperTypes() - Method in class ffx.potential.parameters.ForceField
getImproperType
getInactive() - Method in class ffx.potential.bonded.MultiResidue
Returns a list of this MultiResidue's inactive residues.
getInactiveAtoms() - Method in class ffx.potential.cli.AtomSelectionOptions
--ia or --inactiveAtoms Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].
getIncrement() - Method in class ffx.algorithms.cli.ManyBodyOptions
Sliding window increment (default = 3).
getIndependentWalkers() - Method in class ffx.algorithms.cli.OSTOptions
Checks if independent walkers has been specified.
getIndependentWalkers() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
For MPI parallel jobs, returns true if the walkers are independent (i.e.
getIndex() - Method in class ffx.crystal.HKL
index
getIndex() - Method in class ffx.potential.bonded.Atom
Getter for the field index.
getIndRealEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getIndRealEnergy.
getIndRecipEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getIndRecipEnergy.
getIndSelfEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getIndSelfEnergy.
getInducedDipoleReciprocalEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
getInducedDipoleSelfEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
getInitialBackwardsGuess() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Returns the backwards Zwanzig estimator used to seed BAR.
getInitialForwardsGuess() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Returns the forwards Zwanzig estimator used to seed BAR.
getInitialKinetic() - Method in class ffx.algorithms.mc.MDMove
 
getInitialKineticEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Gets the kinetic energy at the start of the last dynamics run.
getInitialLambda() - Method in class ffx.potential.cli.AlchemicalOptions
-l or --lambda sets the initial lambda value.
getInitialLambda(boolean) - Method in class ffx.potential.cli.AlchemicalOptions
Gets the initial value of lambda.
getInitialLambda(int, int) - Method in class ffx.potential.cli.AlchemicalOptions
Gets the initial value of lambda.
getInitialLambda(int, int, boolean) - Method in class ffx.potential.cli.AlchemicalOptions
Gets the initial value of lambda.
getInitialPotential() - Method in class ffx.algorithms.mc.MDMove
 
getInitialPotentialEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Gets the potential energy at the start of the last dynamics run.
getInitialTemperature() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Gets the temperature at the start of the last dynamics run.
getInitialTotal() - Method in class ffx.algorithms.mc.MDMove
 
getInitialTotalEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Gets the total energy at the start of the last dynamics run.
getInPlaneAngleEnergyString() - Method in class ffx.potential.ForceFieldEnergy
 
getInputAngles(double[], double[], double[], double[]) - Method in class ffx.potential.utils.LoopClosure
Get the input angles.
getInputStream() - Method in class edu.rit.pj.io.StreamFile
Open an input stream for reading this stream file.
getInstance(long) - Static method in class edu.rit.util.Random
Construct a new PRNG with the given seed using the default algorithm.
getInstance(long, String) - Static method in class edu.rit.util.Random
Construct a new PRNG with the given seed using the given algorithm.
getInteger(String) - Method in class ffx.potential.parameters.ForceField
getInteger
getInteger(String, Integer) - Method in class ffx.potential.parameters.ForceField
getInteger
getIntegratorString() - Method in class ffx.algorithms.cli.DynamicsOptions
The integrator: current choices are Beeman, RESPA, Stochastic (Langevin) or Verlet.
getInteractions() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getInteractions
getInteractions() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
getInteractions() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Getter for the field interactions.
getInteractions() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
getInteractions() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the number of interacting pairs.
getInteractions() - Method in class ffx.potential.nonbonded.VanDerWaalsTornado
Get the number of interacting pairs.
getIntervalSteps() - Method in class ffx.algorithms.dynamics.MolecularDynamics
getIntervalSteps.
getIntervalSteps() - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
getIntervalSteps.
getIonNames() - Static method in class ffx.utilities.StringUtils
Returns a Map from recognized ion names to standard ion names.
getIons() - Method in class ffx.potential.MolecularAssembly
Getter for the field ions.
getIterations() - Method in class ffx.algorithms.cli.MinimizeOptions
Number of minimization steps.
getIterations() - Method in class ffx.algorithms.optimize.Minimize
Getter for the number of iterations completed this minimization.
getIterations() - Method in class ffx.potential.cli.TimerOptions
Getter for the field iterations.
getJobBackend() - Static method in class edu.rit.pj.cluster.JobBackend
Obtain the Job Backend object.
getJobNumber() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's job number.
getJobNumber() - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Obtain the job number assigned to this Non-PJ Job Frontend.
getJobNumber() - Method in class edu.rit.pj.job.Job
Returns this job's number.
getJobTime() - Method in class edu.rit.pj.cluster.Configuration
Returns the maximum job time.
getK() - Method in class edu.rit.pj.cluster.JobBackend
Obtain the number of backend processes in this job.
getK() - Method in class ffx.crystal.HKL
k
getKey() - Method in class ffx.potential.bonded.Atom
Gets the atom Key
getKey() - Method in class ffx.potential.bonded.Molecule
 
getKey() - Method in class ffx.potential.parameters.BaseType
Get the key for this Type.
getKey(String) - Method in class ffx.ui.properties.FFXLocale
getKey
getKeyFile() - Method in class ffx.ui.FFXSystem
Getter for the field keyFile.
getKeyword() - Method in class ffx.ui.KeywordComponent
Getter for the field keyword.
getKeyword() - Method in class ffx.utilities.Keyword
Getter for the field keyword.
getKeyword(String) - Method in class ffx.ui.FFXSystem
getKeyword
getKeyword(String) - Method in class ffx.ui.KeywordPanel
getKeyword
getKeywordDescription(String) - Method in class ffx.ui.KeywordPanel
getKeywordDescription
getKeywords() - Method in class ffx.ui.FFXSystem
Getter for the field keywords.
getKeywordValue(String) - Method in class ffx.ui.KeywordPanel
getKeywordValue
getKineticEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Get the system kinetic energy.
getKineticEnergy() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Get the current kinetic energy.
getKineticEnergy() - Method in class ffx.algorithms.mc.MDMove
getKineticEnergy.
getKineticEnergy() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
getKineticEnergy.
getKineticEnergy() - Method in class ffx.openmm.State
Get the kinetic energy.
getKineticEnergy() - Method in class ffx.potential.openmm.OpenMMState
Get the kinetic energy.
getKineticEnergy() - Method in class ffx.potential.SystemState
Get the kinetic energy.
getKTScale() - Method in class ffx.xray.RefinementEnergy
get the current kT scaling weight
getL() - Method in class ffx.crystal.HKL
l
getL() - Method in class ffx.crystal.ReplicatesCrystal
The number of replicates along the a-axis.
getLambda() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
Returns the current value of lambda
getLambda() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Getter for the field lambda.
getLambda() - Method in class ffx.potential.ANIEnergy
 
getLambda() - Method in class ffx.potential.bonded.AngleTorsion
Get the current value of the state variable.
getLambda() - Method in interface ffx.potential.bonded.LambdaInterface
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.PiOrbitalTorsion
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.RestraintBond
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.RestraintTorsion
 
getLambda() - Method in class ffx.potential.bonded.StretchTorsion
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.Torsion
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.bonded.TorsionTorsion
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.DualTopologyEnergy
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.ForceFieldEnergy
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.COMRestraint
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.NCSRestraint
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.RestrainPosition
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the current value of the state variable.
getLambda() - Method in class ffx.potential.QuadTopologyEnergy
Get the current value of the state variable.
getLambda() - Method in class ffx.realspace.RealSpaceData
Getter for the field lambda.
getLambda() - Method in class ffx.realspace.RealSpaceEnergy
Get the current value of the state variable.
getLambda() - Method in class ffx.xray.RefinementEnergy
Get the current value of the state variable.
getLambda() - Method in class ffx.xray.XRayEnergy
Get the current value of the state variable.
getLambdaBins() - Method in class ffx.algorithms.thermodynamics.HistogramData
 
getLambdaBinWidth() - Method in class ffx.algorithms.thermodynamics.HistogramData
 
getLambdaElec() - Method in class ffx.potential.openmm.OpenMMSystem
 
getLambdaFile() - Method in class ffx.algorithms.thermodynamics.LambdaData
 
getLambdaFileName() - Method in class ffx.algorithms.thermodynamics.LambdaData
 
getLambdaFriction() - Method in class ffx.algorithms.cli.LambdaParticleOptions
Friction on the lambda particle.
getLambdaFunction() - Method in class ffx.potential.cli.TopologyOptions
-sf or --switchingFunction
getLambdaHistogram(List<Residue>, int[][][], double) - Method in class ffx.potential.parsers.ESVFilter
 
getLambdaList() - Method in class ffx.potential.extended.ExtendedSystem
getLambdaList.
getLambdaMass() - Method in class ffx.algorithms.cli.LambdaParticleOptions
The mass of the lambda particle.
getLambdaResetValue() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
 
getLambdaStart() - Method in class ffx.potential.openmm.OpenMMEnergy
 
getLambdaTerm() - Method in class ffx.potential.openmm.OpenMMEnergy
Get the lambdaTerm flag.
getLambdaWriteOut() - Method in class ffx.algorithms.cli.OSTOptions
Only write out snapshots if lambda is greater than the value specified.
getLambdaXYZGradient(double[]) - Method in class ffx.potential.bonded.Atom
getLambdaXYZGradient
getLargerDistance() - Method in class ffx.potential.nonbonded.RestrainGroups
Larger distance for each restraint.
getLastAngleAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend
Get the first atom of the Angle.
getLastReadLambda() - Method in class ffx.potential.parsers.PDBFilter
Gets the last read lambda value read by the filter, if any.
getLastReadLambda() - Method in class ffx.potential.parsers.SystemFilter
Gets the last read lambda value read by the filter, if any.
getLastReadLambda() - Method in class ffx.potential.parsers.XPHFilter
Gets the last read lambda value read by the filter, if any.
getLastReadLambda() - Method in class ffx.potential.parsers.XYZFilter
Gets the last read lambda value read by the filter, if any.
getLeavesValueAtIndex(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
getLibrary() - Method in class ffx.algorithms.cli.ManyBodyOptions
Ponder and Richards (1) or Richardson (2) rotamer library.
getLibrary() - Method in class ffx.potential.bonded.RotamerLibrary
Get the protein rotamer library.
getLink() - Method in class ffx.potential.bonded.Polymer
Getter for the field link.
getList(Class<T>) - Method in class ffx.potential.bonded.MSNode
getList(Class<T>, List<T>) - Method in class ffx.potential.bonded.MSNode
getList
getList(Class<T>, List<T>) - Method in interface ffx.potential.bonded.ROLS
getList
getListResidues() - Method in class ffx.algorithms.cli.ManyBodyOptions
Choose a list of individual residues to optimize (e.g.
getLogFile() - Method in class edu.rit.pj.cluster.Configuration
Returns the Job Scheduler's log file name.
getLogFile() - Method in class ffx.ui.FFXSystem
Getter for the field logFile.
getLow() - Method in class ffx.algorithms.cli.AnnealOptions
Low temperature limit in degrees Kelvin.
getLowerBounds() - Method in class ffx.xray.GradientSchedule
Getter for the field lowerBounds.
getLowTemp() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule
Gets the final temperature.
getLowTemp() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
 
getLowTemp() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
 
getLowTemp() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
 
getM() - Method in class ffx.crystal.ReplicatesCrystal
The number of replicates along the b-axis.
getM1MinEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
 
getM2MinEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
 
getMainClassName() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's main class name.
getMainMenu() - Method in class ffx.ui.MainPanel
Getter for the field mainMenu.
getMask12() - Method in class ffx.potential.nonbonded.VanDerWaals
Getter for the field bondMask.
getMask13() - Method in class ffx.potential.nonbonded.VanDerWaals
Getter for the field angleMask.
getMask14() - Method in class ffx.potential.nonbonded.VanDerWaals
Getter for the field torsionMask.
getMass() - Method in class ffx.algorithms.dynamics.Barostat
Get the mass of each degree of freedom.
getMass() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the mass of each degree of freedom.
getMass() - Method in interface ffx.numerics.Potential
Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.ANIEnergy
 
getMass() - Method in class ffx.potential.bonded.Atom
Gets the Atomic Mass.
getMass() - Method in class ffx.potential.DualTopologyEnergy
Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.extended.ExtendedSystem
 
getMass() - Method in class ffx.potential.ForceFieldEnergy
Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.MolecularAssembly
getMass.
getMass() - Method in class ffx.potential.QuadTopologyEnergy
Get the mass of each degree of freedom.
getMass() - Method in class ffx.potential.SystemState
Get a reference to the internal mass array.
getMass() - Method in class ffx.potential.XtalEnergy
Get the mass of each degree of freedom.
getMass() - Method in class ffx.realspace.RealSpaceEnergy
Get the mass of each degree of freedom.
getMass() - Method in class ffx.xray.RefinementEnergy
Get the mass of each degree of freedom.
getMass() - Method in class ffx.xray.XRayEnergy
Get the mass of each degree of freedom.
getMatrix() - Method in class edu.rit.io.DoubleMatrixFile
Obtain this matrix file's underlying matrix.
getMax() - Method in class ffx.numerics.math.RunningStatistics
Get the max.
getMaxAM() - Method in class ffx.algorithms.cli.BarostatOptions
The width of proposed crystal angle moves (uniformly distributed) in degrees.
getMaxD() - Method in class ffx.algorithms.cli.BarostatOptions
The maximum density accepted by the MC Barostat (g/cc).
getMaximumDepth() - Method in class ffx.potential.nonbonded.implicit.GaussVol
Returns the maximum depth of the overlap tree
getMaxResolution() - Method in class ffx.crystal.ReflectionList
Get the maximum resolution.
getMaxV() - Method in class ffx.algorithms.cli.BarostatOptions
The volume of a proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
getMBAR(MultistateBennettAcceptanceRatio.SeedType) - Method in class ffx.potential.parsers.MBARFilter
 
getMBAR(MultistateBennettAcceptanceRatio.SeedType, double) - Method in class ffx.potential.parsers.MBARFilter
 
getMBARFreeEnergies() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getMcLambdaStdDev() - Method in class ffx.algorithms.cli.OSTOptions
The standard deviation for lambda moves.
getMcMDSteps() - Method in class ffx.algorithms.cli.OSTOptions
The number of steps to take for each MD trajectory for MC-OST.
getMD() - Method in class ffx.algorithms.mc.MDMove
 
getMD() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
 
getMean() - Method in class ffx.numerics.math.BootStrapStatistics
The mean.
getMean() - Method in class ffx.numerics.math.RunningStatistics
Gets the mean as of the last value added.
getMean() - Method in class ffx.numerics.math.SummaryStatistics
The mean.
getMeanBarostatInterval() - Method in class ffx.algorithms.dynamics.Barostat
Returns the mean number of steps between barostat applications.
getMessage() - Method in class ffx.ui.commands.SimulationMessage
Getter for the field message.
getMethod() - Method in class edu.rit.http.HttpRequest
Obtain this HTTP request's method.
getMiddleBond() - Method in class ffx.potential.bonded.PiOrbitalTorsion
Get the middle bond that the Pi-Orbital Torsion is formed around.
getMin() - Method in class ffx.numerics.math.RunningStatistics
Get the min.
getMinD() - Method in class ffx.algorithms.cli.BarostatOptions
The minimum density accepted by the MC Barostat (g/cc).
getMinimumEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
 
getMinResolution() - Method in class ffx.crystal.ReflectionList
Get the minimum resolution.
getMissedResidues() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
 
getMode() - Method in class ffx.algorithms.mc.RosenbluthChiAllMove
Getter for the field mode.
getModelingJobs() - Method in class ffx.ui.ModelingPanel
Get an ArrayList of executing jobs
getModelingShell() - Method in class ffx.ui.MainPanel
Getter for the field modelingShell.
getModelName() - Method in class ffx.xray.DiffractionData
Getter for the field modelName.
getMolecularAssemblies() - Method in class ffx.realspace.RealSpaceData
getMolecularAssemblies
getMolecularAssemblies() - Method in interface ffx.xray.DataContainer
getMolecularAssemblies
getMolecularAssemblies() - Method in class ffx.xray.DiffractionData
getMolecularAssemblies
getMolecularAssembly() - Method in class ffx.algorithms.mc.MolecularMC
Returns the associated MolecularAssembly.
getMolecularAssembly() - Method in class ffx.potential.AssemblyState
Returns the MolecularAssembly associated with this AssemblyState.
getMolecularAssembly() - Method in class ffx.potential.openmm.OpenMMEnergy
Returns the MolecularAssembly instance.
getMolecularAssemblyArray() - Method in class ffx.potential.parsers.SystemFilter
Get the MolecularAssembly array.
getMoleculeArray() - Method in class ffx.potential.MolecularAssembly
 
getMoleculeNumber() - Method in class ffx.potential.bonded.Atom
Getter for the field moleculeNumber.
getMoleculeNumbers() - Method in class ffx.potential.MolecularAssembly
This method assigns a unique integer to every molecule in the MolecularAssembly beginning at 0.
getMolecules() - Method in class ffx.potential.MolecularAssembly
Getter for the field molecules.
getMonteCarlo() - Method in class ffx.algorithms.cli.ManyBodyOptions
Follow elimination criteria with 'n' Monte Carlo steps, or enumerate all remaining conformations, whichever is smaller.
getMonteCarlo() - Method in class ffx.algorithms.cli.RepExOptions
 
getMouseMode() - Method in class ffx.ui.MainMenu
getMouseMode
getMoveSize() - Method in class ffx.algorithms.mc.LambdaMove
Get the Lambda move size, which is a standard deviation for continuous moves or step size for discrete moves.
getMSCount(Class<T>, long) - Method in class ffx.potential.bonded.MSNode
getMSCount
getMSCount(Class<T>, long) - Method in interface ffx.potential.bonded.ROLS
getMSCount
getMSNode(Class<T>) - Method in class ffx.potential.bonded.MSNode
getMSNode
getMSNode(Class<T>) - Method in interface ffx.potential.bonded.ROLS
getMSNode
getMultiplier() - Method in class ffx.numerics.switching.PowerSwitch
Gets the value of a in f(x) = (a*x)^beta.
getMultipole() - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
getMultipole() - Method in class ffx.potential.parameters.MultipoleType
Getter for the field multipole.
getMultipole(Atom, double, double, double[]) - Method in class ffx.potential.parameters.TitrationUtils
 
getMultipoleTautomerDeriv(Atom, double, double, double[]) - Method in class ffx.potential.parameters.TitrationUtils
 
getMultipoleTitrationDeriv(Atom, double, double, double[]) - Method in class ffx.potential.parameters.TitrationUtils
 
getMultipoleType() - Method in class ffx.potential.bonded.Atom
Getter for the field multipoleType.
getMultipoleType(int) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Get the MultipoleType for Atom i.
getMultipoleType(String) - Method in class ffx.potential.parameters.ForceField
getMultipoleType
getMultipoleTypeBeginsWith(String) - Method in class ffx.potential.parameters.ForceField
Find the MultipoleType whose key begins with the supplied String.
getMultipoleTypes(String) - Method in class ffx.potential.parameters.ForceField
Find each MultipoleType whose key begins with the supplied String.
getMultiScaleCenter(boolean) - Method in class ffx.potential.bonded.MSGroup
This method finds the Geometrical center of this MultiScaleGroup, or the atomicWeight-weighted center if w is set to true, and returns it as a double[3].
getMultiScaleCenter(boolean) - Method in class ffx.potential.bonded.MultiResidue
This method finds the Geometrical center of this MultiScaleGroup, or the atomicWeight-weighted center if w is set to true, and returns it as a double[3].
getMW() - Method in class ffx.potential.bonded.MSNode
getMW
getMW() - Method in interface ffx.potential.bonded.ROLS
getMW
getN() - Method in class ffx.crystal.ReplicatesCrystal
The number of replicates along the c-axis.
getN() - Method in class ffx.xray.DiffractionData
Getter for the field n.
getNaLibraryName() - Method in class ffx.algorithms.cli.ManyBodyOptions
Nucleic acid library: currently only Richardson available.
getName() - Method in class ffx.openmm.Force
Get the name of the force.
getName() - Method in class ffx.openmm.Platform
Get the name of the OpenMM Platform.
getName() - Method in class ffx.potential.bonded.MSNode
Returns the name of this MSNode.
getName() - Method in class ffx.potential.bonded.MultiResidue
Returns the name of this MSNode.
getName() - Method in class ffx.potential.bonded.Rotamer
 
getNames(Class<? extends Enum<?>>) - Static method in class ffx.potential.bonded.AminoAcidUtils
Turn an Enum into String array.
getNativeEnvironmentApproximation() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Checks whether GK uses the Native Environment Approximation.
getNatoms() - Method in class ffx.potential.nonbonded.RowRegion
getNatoms.
getNatoms() - Method in class ffx.potential.nonbonded.SliceRegion
getNatoms.
getNavigation() - Method in class ffx.ui.GraphicsCanvas
getNavigation
getNB() - Method in class ffx.xray.RefinementMinimize
get the number of B factor parameters being fit
getNB() - Method in class ffx.xray.XRayEnergy
get the number of B factor parameters being fit
getNBFGS() - Method in class ffx.algorithms.cli.MinimizeOptions
The number of corrections used in the BFGS update.
getnChild() - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
getNeckConstants(double, double) - Static method in class ffx.potential.nonbonded.implicit.NeckIntegral
 
getNeckScale() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Getter for the field neckScale.
getNeighborList() - Method in class ffx.potential.nonbonded.NeighborList
Return the Verlet list.
getNeighborList() - Method in class ffx.potential.nonbonded.VanDerWaals
Allow sharing the of the VanDerWaals NeighborList with ParticleMeshEwald.
getNeighborLists() - Method in class ffx.potential.nonbonded.VanDerWaals
Getter for the field neighborLists.
getNeuralNetworkIdentity() - Method in class ffx.potential.MolecularAssembly
Construct a boolean orray of flags to indicate atoms treated by a neural network.
getNeutralNetworkEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field nnEnergy.
getNextResidue() - Method in class ffx.potential.bonded.Residue
Returns the Residue bonded to this Residue at this Residue's 3' or C-terminal end.
getNi() - Method in class ffx.realspace.RealSpaceRefinementData
Getter for the field ni.
getNOcc() - Method in class ffx.xray.RefinementMinimize
get the number of occupancy parameters being fit
getNOcc() - Method in class ffx.xray.XRayEnergy
get the number of occupancy parameters being fit
getNodeList() - Method in class ffx.potential.MolecularAssembly
getNodeList
getNoGradient() - Method in class ffx.potential.cli.TimerOptions
Getter for the field noGradient.
getNonAlchemicalAlchemicalStericsForce() - Method in class ffx.potential.openmm.FixedChargeAlchemicalForces
 
getNonbondedCutoff() - Method in class ffx.potential.nonbonded.VanDerWaals
Get details of the non-bonded cutoff.
getNonPolarModel() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
getNonPolarModel.
getNonPolarModel(String) - Static method in class ffx.potential.nonbonded.GeneralizedKirkwood
getNonPolarModel.
getNoWait(String) - Method in class edu.rit.pj.cluster.ResourceCache
Obtain the resource content for the given resource name from this resource cache (non-blocking).
getNPar() - Method in class ffx.potential.cli.TopologyOptions
-np or --nParallel sets the number of topologies to evaluate in parallel; currently 1, 2, or 4.
getNsymm() - Method in class ffx.potential.nonbonded.RowRegion
getNsymm.
getNsymm() - Method in class ffx.potential.nonbonded.SliceRegion
getNsymm.
getNsymm() - Method in class ffx.potential.nonbonded.SpatialDensityRegion
getNsymm
getNucleicAcid3() - Method in class ffx.potential.bonded.Residue
getNucleicAcid3.
getNucleicAcid3(boolean) - Method in class ffx.potential.bonded.Residue
Returns the NucleicAcid3 corresponding to this Residue, with additional robust checking for 1- or 2-letter names.
getNumAngles() - Method in class ffx.potential.bonded.Atom
getNumAngles
getNumAtoms() - Method in class ffx.potential.nonbonded.RestrainPosition
getNumAtoms.
getNumberofAngles() - Method in class ffx.potential.ForceFieldEnergy
getNumberofAngles.
getNumberofAngleTorsions() - Method in class ffx.potential.ForceFieldEnergy
getNumberofAngleTorsions.
getNumberOfBondedHydrogen() - Method in class ffx.potential.bonded.Atom
Count the number of bonded hydrogen.
getNumberofBonds() - Method in class ffx.potential.ForceFieldEnergy
getNumberofBonds.
getNumberOfDevices() - Static method in class ffx.numerics.tornado.FFXTornado
Get all TornadoDevice instances.
getNumberOfGroups() - Method in class ffx.potential.nonbonded.RestrainGroups
Get the number of groups.
getNumberofImproperTorsions() - Method in class ffx.potential.ForceFieldEnergy
getNumberofImproperTorsions.
getNumberofOutOfPlaneBends() - Method in class ffx.potential.ForceFieldEnergy
getNumberofOutOfPlaneBends.
getNumberofPiOrbitalTorsions() - Method in class ffx.potential.ForceFieldEnergy
getNumberofPiOrbitalTorsions.
getNumberOfRestraints() - Method in class ffx.potential.nonbonded.RestrainGroups
Get the number of group restraints.
getNumberofStretchBends() - Method in class ffx.potential.ForceFieldEnergy
getNumberofStretchBends.
getNumberofStretchTorsions() - Method in class ffx.potential.ForceFieldEnergy
getNumberofStretchTorsions.
getNumberOfSymOps() - Method in class ffx.crystal.SpaceGroup
Return the number of symmetry operators.
getNumberofTorsions() - Method in class ffx.potential.ForceFieldEnergy
getNumberofTorsions.
getNumberofTorsionTorsions() - Method in class ffx.potential.ForceFieldEnergy
getNumberofTorsionTorsions.
getNumberofUreyBradleys() - Method in class ffx.potential.ForceFieldEnergy
getNumberofUreyBradleys.
getNumberOfVariables() - Method in class ffx.algorithms.dynamics.Barostat
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getNumberOfVariables() - Method in interface ffx.numerics.OptimizationInterface
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.ANIEnergy
 
getNumberOfVariables() - Method in class ffx.potential.DualTopologyEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.extended.ExtendedSystem
 
getNumberOfVariables() - Method in class ffx.potential.ForceFieldEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.QuadTopologyEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.potential.SystemState
Get the number of variables.
getNumberOfVariables() - Method in class ffx.potential.XtalEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.realspace.RealSpaceEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.RefinementEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.ScaleBulkEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.ScaleBulkMinimize
getNumberOfVariables.
getNumberOfVariables() - Method in class ffx.xray.SigmaAEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.SigmaAMinimize
getNumberOfVariables.
getNumberOfVariables() - Method in class ffx.xray.SplineEnergy
Get the number of variables being operated on.
getNumberOfVariables() - Method in class ffx.xray.SplineMinimize
getNumberOfVariables.
getNumberOfVariables() - Method in class ffx.xray.XRayEnergy
Get the number of variables being operated on.
getNumBonds() - Method in class ffx.potential.bonded.Atom
Gets the number of atoms bonded to this Atom
getNumBoxes() - Method in class ffx.algorithms.cli.ManyBodyOptions
The number of boxes along X, Y, and Z (default: '3,3,3').
getNumConstraints() - Method in class ffx.openmm.System
Get the number of constraints in the system.
getNumDegreesFrozen() - Method in interface ffx.numerics.Constraint
Returns the number of degrees of freedom this Constraint constrains.
getNumDegreesFrozen() - Method in class ffx.potential.constraint.CcmaConstraint
Returns the number of degrees of freedom this Constraint constrains.
getNumDegreesFrozen() - Method in class ffx.potential.constraint.SettleConstraint
 
getNumDegreesFrozen() - Method in class ffx.potential.constraint.ShakeChargeConstraint
 
getNumDihedrals() - Method in class ffx.potential.bonded.Atom
getNumDihedrals
getNumExceptions() - Method in class ffx.openmm.NonbondedForce
Get the number of exceptions.
getNumLeaves() - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
getNumParallel(int, int) - Method in class ffx.potential.cli.TopologyOptions
The number of topologies to run in parallel.
getNumPlatforms() - Static method in class ffx.openmm.Platform
Get the number of OpenMM Platforms.
getNumSharedVariables() - Method in class ffx.potential.DualTopologyEnergy
Returns the number of shared variables (3 * number of shared atoms).
getNumSharedVariables() - Method in class ffx.potential.QuadTopologyEnergy
Returns number of shared variables.
getNumSteps() - Method in class ffx.algorithms.cli.DynamicsOptions
 
getNumSymOps() - Method in class ffx.crystal.Crystal
Return the number of symmetry operators for this crystal.
getNumWindows() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule
Gets the number of annealing windows (including repeat windows).
getNumWindows() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
 
getNumWindows() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
 
getNumWindows() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
 
getNXYZ() - Method in class ffx.xray.RefinementMinimize
get the number of xyz parameters being fit
getNXYZ() - Method in class ffx.xray.XRayEnergy
Get the number of xyz parameters being fit.
getOccupancy() - Method in class ffx.potential.bonded.Atom
Getter for the field occupancy.
getOccupancyAcceleration() - Method in class ffx.potential.bonded.Atom
Getter for the field occupancyAccelerationy.
getOccupancyGradient() - Method in class ffx.potential.bonded.Atom
Getter for the field occupancyGradient.
getOccupancyPreviousAcceleration() - Method in class ffx.potential.bonded.Atom
Getter for the field occupancyPreviousAccelerationy.
getOccupancyVelocity() - Method in class ffx.potential.bonded.Atom
Getter for the field occupancyVelocity.
getOffset() - Method in class ffx.potential.MolecularAssembly
Getter for the field offset.
getOffsetCYS(TitrationUtils.CysStates) - Method in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
 
getOffsetHIS(TitrationUtils.HisStates) - Method in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
 
getOffsetLYS(TitrationUtils.LysStates) - Method in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
 
getOmega(Residue) - Method in class ffx.potential.utils.GetProteinFeatures
Get the omega angle of a residue
getOneBound() - Method in class ffx.numerics.switching.BellCurveSwitch
Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.CompositeSwitch
 
getOneBound() - Method in class ffx.numerics.switching.ConstantSwitch
Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.LinearDerivativeSwitch
Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.MultiplicativeSwitch
Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.PowerSwitch
Gets the one bound, where f(x) becomes one.
getOneBound() - Method in class ffx.numerics.switching.SquaredTrigSwitch
Gets the one bound, where f(x) becomes one.
getOneBound() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction
Gets the one bound, where f(x) becomes one.
getOpenMMState(int) - Method in class ffx.potential.openmm.OpenMMContext
Get an OpenMM State from the Context.
getOpenMMState(int) - Method in class ffx.potential.openmm.OpenMMEnergy
Create an immutable OpenMM State.
getOpenMMVersion() - Static method in class ffx.openmm.Platform
Get the OpenMM version.
getOptimizationParameters() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Return the OST optimization information.
getOptimize() - Method in class ffx.algorithms.cli.DynamicsOptions
Getter for the field optimize.
getOptimumCoordinates() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters
getOptimumCoordinates.
getOptimumEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters
getOptimumEnergy.
getOptimumRotamers() - Method in class ffx.algorithms.optimize.RotamerOptimization
Return an integer array of optimized rotamers following rotamer optimization.
getOrder() - Method in enum class ffx.numerics.multipole.GKSource.GK_MULTIPOLE_ORDER
 
getOrigin() - Method in class ffx.realspace.RealSpaceRefinementData
Getter for the field origin.
getOriginToRot() - Method in class ffx.potential.MolecularAssembly
Getter for the field originToRot.
getOscillate() - Method in class ffx.ui.Trajectory
Getter for the field oscillate.
getOST() - Method in class ffx.algorithms.thermodynamics.RepExOST
 
getOutOfPlaneBendEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field outOfPlaneBendEnergy.
getOutOfPlaneBendList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Out-of-Plane Bends below the present MSNode.
getOutOfPlaneBends() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field outOfPlaneBends.
getOutOfPlaneBendType(AtomType, AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField
getOutOfPlaneBendType
getOutOfPlaneBendType(String) - Method in class ffx.potential.parameters.ForceField
getOutOfPlaneBendType
getOutOfPlaneEnergyString() - Method in class ffx.potential.ForceFieldEnergy
 
getOutputStream() - Method in class edu.rit.pj.io.StreamFile
Open an output stream for writing this stream file.
getOutputStream(boolean) - Method in class edu.rit.pj.io.StreamFile
Open an output stream for writing this stream file.
getOverlapScale() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Getter for the field overlapScale.
getPairClashThreshold() - Method in class ffx.algorithms.cli.ManyBodyOptions
The threshold for pruning clashes.
getPairwiseSchedule() - Method in class ffx.potential.nonbonded.NeighborList
Getter for the field pairwiseSchedule.
getParallelTeam() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field parallelTeam.
getParallelTeam() - Method in class ffx.potential.MolecularAssembly
getParallelTeam.
getParallelTeam() - Method in class ffx.xray.DiffractionData
Getter for the field parallelTeam.
getParamPath(String) - Method in class ffx.ui.KeywordPanel
getParamPath
getParent() - Method in class ffx.potential.bonded.ResidueState
Getter for the field parent.
getParentIndex() - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
getParticleParameters(int, DoubleByReference, DoubleByReference, DoubleByReference) - Method in class ffx.openmm.NonbondedForce
Get the particle parameters.
getPDBHeaderString() - Method in class ffx.potential.ForceFieldEnergy
getPDBHeaderString
getPDBRank(SpaceGroup) - Static method in class ffx.crystal.SpaceGroupInfo
PDB space group ranking (as of Feb.
getPerfectRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Return perfect Born radii read in as keywords, or base radii if perfect radii are not available.
getPerfectRadii() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
Return perfect Born radii read in as keywords, or base radii if perfect radii are not available.
getPeriod() - Method in class ffx.numerics.switching.SquaredTrigSwitch
Get the repeating period of this switch.
getPeriodicBoxVectors() - Method in class ffx.openmm.State
Get the periodic box vectors.
getPeriodicBoxVectors() - Method in class ffx.potential.openmm.OpenMMState
Read the periodic lattice vectors from a state.
getPeriodicBoxVolume() - Method in class ffx.openmm.State
Get the periodic box volume.
getPeriodicBoxVolume() - Method in class ffx.potential.openmm.OpenMMState
Get the periodic box volume.
getPermanentEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
getPermanentEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPermanentEnergy() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
getPermanentInteractions() - Method in class ffx.potential.ForceFieldEnergy
getPermanentInteractions.
getPermanentMultipoleEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field permanentMultipoleEnergy.
getPermanentRealSpaceEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field permanentRealSpaceEnergy.
getPermanentReciprocalEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
getPermanentReciprocalMpoleEnergy() - Method in class ffx.potential.ForceFieldEnergy
getPermanentReciprocalMpoleEnergy.
getPermanentReciprocalSelfEnergy() - Method in class ffx.potential.ForceFieldEnergy
getPermanentReciprocalSelfEnergy.
getPermanentSelfEnergy() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
getPermRealEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPermRecipEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPermSelfEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getPermSelfEnergy.
getPhi(Residue) - Method in class ffx.potential.utils.GetProteinFeatures
Get the phi angle of a residue
getPhiPsiList() - Method in class ffx.potential.bonded.Polymer
Get lists of the phi and psi torsions.
getPicking() - Method in class ffx.ui.GraphicsPicking
Getter for the field picking.
getPicking() - Method in class ffx.ui.MainMenu
getPicking
getPickMode() - Method in class ffx.ui.behaviors.PickOrbitBehavior
Return the pickMode component of this PickTranslateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickPropertiesBehavior
getPickMode
getPickMode() - Method in class ffx.ui.behaviors.PickRotateBehavior
Return the pickMode component of this PickRotateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickSelectionBehavior
Return the pickMode component of this PickRotateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickTranslateBehavior
Return the pickMode component of this PickTranslateBehavior.
getPickMode() - Method in class ffx.ui.behaviors.PickZoomBehavior
Return the pickMode component of this PickTranslateBehavior.
getPiOrbitalTorsionEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field piOrbitalTorsionEnergy.
getPiOrbitalTorsionEnergyString() - Method in class ffx.potential.ForceFieldEnergy
 
getPiOrbitalTorsionList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Pi-Orbital Torsions below the present MSNode.
getPiOrbitalTorsions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field piOrbitalTorsions.
getPiOrbitalTorsionType(AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField
getPiOrbitalTorsionType
getPiOrbitalTorsionType(String) - Method in class ffx.potential.parameters.ForceField
getPiOrbitalTorsionType
getPjHost() - Static method in class edu.rit.pj.PJProperties
Determine the host name of the Job Scheduler Daemon to use when running a cluster parallel program.
getPjJobTime() - Static method in class edu.rit.pj.PJProperties
Determine the maximum amount of time (seconds) the job is allowed to run when running a cluster parallel program.
getPjJvmFlags() - Static method in class edu.rit.pj.PJProperties
Determine the JVM flags to include on the Java command line when running a backend process in a cluster parallel program.
getPjNn() - Static method in class edu.rit.pj.PJProperties
Determine the number of backend nodes in a parallel program.
getPjNp() - Static method in class edu.rit.pj.PJProperties
Determine the number of processes in a parallel program.
getPjNt() - Static method in class edu.rit.pj.PJProperties
Determine the number of CPUs per process in a parallel program.
getPjPort() - Static method in class edu.rit.pj.PJProperties
Determine the port number of the Job Scheduler Daemon to use when running a cluster parallel program.
getPjPrng() - Static method in class edu.rit.pj.PJProperties
Determine the fully-qualified class name of the default pseudorandom number generator (PRNG) class.
getPjSchedule() - Static method in class edu.rit.pj.PJProperties
Determine the schedule for a parallel loop in an SMP parallel program.
getPlatform() - Method in class ffx.potential.ForceFieldEnergy
Gets the Platform associated with this force field energy.
getPlatform() - Method in class ffx.potential.openmm.OpenMMContext
 
getPlatform() - Method in class ffx.potential.openmm.OpenMMEnergy
Gets the Platform associated with this force field energy.
getPluginLoadFailures() - Static method in class ffx.openmm.Platform
Get the plugin load failures.
getPmeNode() - Method in class ffx.potential.ForceFieldEnergy
getPmeNode.
getPoint() - Method in class ffx.potential.utils.Clustering.Conformation
 
getPointer() - Method in class ffx.openmm.BondArray
Get the pointer to the bond array.
getPointer() - Method in class ffx.openmm.Context
Get the pointer to the context.
getPointer() - Method in class ffx.openmm.DoubleArray
Get the pointer to the array.
getPointer() - Method in class ffx.openmm.DoubleArray3D
Get the pointer to the array.
getPointer() - Method in class ffx.openmm.Force
Get the pointer to the OpenMM Force.
getPointer() - Method in class ffx.openmm.IntArray
Get the pointer to the array.
getPointer() - Method in class ffx.openmm.Integrator
Get the OpenMM Integrator pointer.
getPointer() - Method in class ffx.openmm.IntSet
Get the pointer to the set.
getPointer() - Method in class ffx.openmm.Platform
Get the OpenMM Platform pointer.
getPointer() - Method in class ffx.openmm.State
Get the pointer to the state.
getPointer() - Method in class ffx.openmm.System
Get the pointer to the system.
getPointer() - Method in class ffx.openmm.Vec3Array
Get the pointer to the vec3 array pointer.
getPolarEps() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPolarGeom(int) - Static method in class ffx.potential.bonded.RendererCache
getPolarGeom
getPolarityAndAcidityChange(List<String>, boolean, boolean) - Method in class ffx.potential.utils.GetProteinFeatures
Get the polarity and acidity changes
getPolarizability(Atom, double, double, double) - Method in class ffx.potential.parameters.TitrationUtils
 
getPolarizabilityTautomerDeriv(Atom, double, double) - Method in class ffx.potential.parameters.TitrationUtils
 
getPolarizabilityTitrationDeriv(Atom, double, double) - Method in class ffx.potential.parameters.TitrationUtils
 
getPolarization11() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPolarization12() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPolarization13() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPolarizationEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field polarizationEnergy.
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Getter for the field polarizationEnergy.
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
Return the final polarization energy.
getPolarizationEnergy() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
getPolarizationType() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getPolarizeType() - Method in class ffx.potential.bonded.Atom
Getter for the field polarizeType.
getPolarizeType(int) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Get the PolarizeType for Atom i.
getPolarizeType(String) - Method in class ffx.potential.parameters.ForceField
getPolarizeType
getPolyCoeff(double[]) - Method in class ffx.potential.utils.LoopClosure
Get Polynomial Coefficient.
getPolymer(Character, String, boolean) - Method in class ffx.potential.MolecularAssembly
getPolymer
getPopulationStandardDeviation() - Method in class ffx.numerics.math.RunningStatistics
Get the population standard deviations.
getPopulationVariance() - Method in class ffx.numerics.math.RunningStatistics
Get the population variance.
getPositions() - Method in class ffx.openmm.State
Get the positions.
getPositions(double[]) - Method in class ffx.potential.openmm.OpenMMState
The positions array contains the OpenMM atomic position information for all atoms.
getPotential() - Method in class ffx.algorithms.mc.MolecularMC
Returns the associated Potential.
getPotentialEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Get the system potential energy.
getPotentialEnergy() - Method in class ffx.algorithms.mc.MDMove
getPotentialEnergy.
getPotentialEnergy() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
getPotentialEnergy.
getPotentialEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
getPotentialEnergy.
getPotentialEnergy() - Method in class ffx.openmm.State
Get the potential energy.
getPotentialEnergy() - Method in class ffx.potential.MolecularAssembly
Getter for the field potentialEnergy.
getPotentialEnergy() - Method in class ffx.potential.openmm.OpenMMState
Get the potential energy.
getPotentialEnergy() - Method in class ffx.potential.SystemState
Get the potential energy.
getPotentials() - Method in class ffx.algorithms.cli.AlgorithmsScript
Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.potential.cli.PotentialCommand
Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.potential.cli.PotentialScript
Returns a List of all Potential objects associated with this script.
getPotentials() - Method in class ffx.potential.commands.Energy
 
getPreconditionerCounts() - Method in class ffx.potential.nonbonded.pme.PCGSolver
Number of neighbors when applying the preconditioner.
getPreconditionerCutoff() - Method in class ffx.potential.nonbonded.pme.PCGSolver
Get the preconditioner cutoff.
getPreconditionerEwald() - Method in class ffx.potential.nonbonded.pme.PCGSolver
Get the preconditioner Ewald coefficient.
getPreconditionerLists() - Method in class ffx.potential.nonbonded.pme.PCGSolver
Neighbor lists when applying the preconditioner.
getPreconditionerMode() - Method in class ffx.potential.nonbonded.pme.PCGSolver
Get the preconditioner mode.
getPreconditionerScale() - Method in class ffx.potential.nonbonded.pme.PCGSolver
Get the preconditioner matrix diagonal scale factor.
getPressure() - Method in class ffx.algorithms.cli.BarostatOptions
-p or --npt Specify use of a Monte Carlo Barostat at the given pressure (default 0 = constant volume).
getPressure() - Method in class ffx.algorithms.dynamics.Barostat
Gets the pressure of this Barostat in atm.
getPreviousAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in interface ffx.numerics.Potential
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
 
getPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field previousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
getPreviousAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.potential.XtalEnergy
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy
getPreviousAcceleration.
getPreviousAcceleration(double[]) - Method in class ffx.xray.XRayEnergy
getPreviousAcceleration.
getPreviousResidue() - Method in class ffx.potential.bonded.Residue
Returns the Residue bonded to this Residue at this Residue's 5' or N-terminal end.
getPrintInt() - Method in class ffx.algorithms.cli.BarostatOptions
--bpi or --barostatPrintInterval Sets the number of Barostat MC cycles between print statements.
getPrintOnFailure() - Method in class ffx.xray.RefinementEnergy
Getter for the field printOnFailure.
getPrintWriter() - Method in class edu.rit.http.HttpResponse
Obtain the print writer for writing the entity body to this HTTP response.
getProbe() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
getProbeRadius() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the probe radius (typically 1.4 Angstroms).
getPropagateLambda() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
If true, the Lambda extended system particle is propagated using Langevin dynamics.
getProperties() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's Java system properties.
getProperties() - Method in class ffx.potential.MolecularAssembly
Getter for the field properties.
getProperties() - Method in class ffx.potential.parameters.ForceField
Getter for the field properties.
getProperties() - Method in interface ffx.potential.parsers.FileOpener
getProperties.
getProperties() - Method in class ffx.potential.utils.PotentialsFileOpener
getProperties.
getProperties() - Method in class ffx.ui.FFXSystem
Getter for the field properties.
getProperties() - Method in class ffx.ui.UIFileOpener
Returns the properties of the hierarchy's active FFXSystem.
GetProteinFeatures - Class in ffx.potential.utils
 
GetProteinFeatures() - Constructor for class ffx.potential.utils.GetProteinFeatures
 
getProteinLibrary(String) - Static method in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary
Parses a String input to a ProteinLibrary.
getProtonatedAssemblies() - Method in class ffx.algorithms.optimize.TitrationManyBody
 
getProtonatedAssembly() - Method in class ffx.algorithms.optimize.TitrationManyBody
 
getPrune() - Method in class ffx.algorithms.cli.ManyBodyOptions
Prune no clashes (0), only single clashes (1), or all clashes (2).
getPsi(Residue) - Method in class ffx.potential.utils.GetProteinFeatures
Get the psi angle of a residue
getQuadrupole() - Method in class ffx.potential.parameters.MultipoleType
Getter for the field quadrupole.
getR() - Method in class ffx.potential.nonbonded.octree.OctreeCell
Returns cell radius
getR() - Method in class ffx.xray.CrystalStats
Simply return the current R value.
getr_o() - Method in class ffx.potential.bonded.SturmMethod
Used only in JUnit testing.
getRA() - Method in class ffx.potential.utils.Loop
getRA.
getRadii() - Method in class ffx.potential.nonbonded.implicit.GaussVol
Get the radii.
getRandomCartTranslation() - Method in class ffx.crystal.Crystal
Create a random Cartesian translation vector.
getRandomNumberSeed() - Method in class ffx.openmm.MonteCarloBarostat
Get the random number seed.
getRandomSymOp() - Method in class ffx.algorithms.cli.RandomUnitCellOptions
A random SymOp with translation range -X/2 ..
getRandomUnitCell() - Method in class ffx.algorithms.cli.RandomUnitCellOptions
Random unit cell parameters will be used achieve the specified density (g/cc) (no default density).
getRank() - Method in class edu.rit.pj.cluster.JobBackend
Obtain the rank of this backend process in this job.
getRank() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
For MPI parallel jobs, return the rank of this process.
getRate() - Method in class ffx.ui.Trajectory
getRate
getRawNBodyDistance(int...) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Returns the RMS distance between an arbitrary set of rotamers.
getRC() - Method in class ffx.potential.utils.Loop
getRC.
getRCrystalStat() - Method in class ffx.xray.DiffractionData
Return R value for OST x-ray minimization.
getRealSpaceFileFilter() - Method in class ffx.realspace.parsers.RealSpaceFile
Getter for the field realSpaceFileFilter.
getRealSpaceGradient(double[]) - Method in class ffx.realspace.RealSpaceData
Getter for the field realSpaceGradient.
getRealSpacePermTotal() - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
 
getRealSpaceSCFTotal() - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
 
getReciprocalSpace() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.BooleanMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ByteMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.CharacterMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.DoubleMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyBooleanBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyByteBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyCharacterBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyDoubleBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyFloatBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyLongBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyObjectBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyShortBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.FloatMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.Buf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.IntegerMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.LongMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ObjectMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedBooleanBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedByteArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedByteBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedCharacterBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedDoubleBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedFloatBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedLongArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedLongBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedObjectArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedObjectBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedShortArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedShortBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.ShortMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1
Create a buffer for performing parallel reduction using the given binary operation.
getReductionBuf(Op) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf
Create a buffer for performing parallel reduction using the given binary operation.
getReductionIndex() - Method in class ffx.potential.nonbonded.VanDerWaals
Get the reduction index.
getRedX() - Method in class ffx.potential.bonded.Atom
Gets the reduced x coordinate (van der Waals center).
getRedXYZ() - Method in class ffx.potential.bonded.Atom
getRedXYZ
getRedXYZ(double[]) - Method in class ffx.potential.bonded.Atom
getRedXYZ
getRedY() - Method in class ffx.potential.bonded.Atom
Gets the reduced y coordinate (van der Waals center).
getRedZ() - Method in class ffx.potential.bonded.Atom
Gets the reduced z coordinate (van der Waals center).
getReferenceAtom() - Method in class ffx.potential.bonded.Residue
Returns a reference Atom for a Residue, primarily intended for rough distance calculations.
getRefinementData() - Method in class ffx.realspace.RealSpaceData
Getter for the field refinementData.
getRefinementData() - Method in class ffx.xray.DiffractionData
Getter for the field refinementData.
getRefinementMode() - Method in class ffx.realspace.RealSpaceEnergy
Getter for the field refinementMode.
getRefinementMode() - Method in class ffx.xray.XRayEnergy
Getter for the field refinementMode.
getRefinementModel() - Method in class ffx.realspace.RealSpaceData
getRefinementModel
getRefinementModel() - Method in interface ffx.xray.DataContainer
getRefinementModel
getRefinementModel() - Method in class ffx.xray.DiffractionData
getRefinementModel
getReflectionList() - Method in class ffx.xray.DiffractionData
Getter for the field reflectionList.
getReflectionList(File) - Method in class ffx.xray.parsers.CIFFilter
Get reflection information from a reflection file.
getReflectionList(File) - Method in class ffx.xray.parsers.CNSFilter
Get reflection information from a reflection file.
getReflectionList(File) - Method in interface ffx.xray.parsers.DiffractionFileFilter
Get reflection information from a reflection file.
getReflectionList(File) - Method in class ffx.xray.parsers.MTZFilter
Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in class ffx.xray.parsers.CIFFilter
Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in class ffx.xray.parsers.CNSFilter
Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in interface ffx.xray.parsers.DiffractionFileFilter
Get reflection information from a reflection file.
getReflectionList(File, CompositeConfiguration) - Method in class ffx.xray.parsers.MTZFilter
Get reflection information from a reflection file.
getRelativeSolvationEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field relativeSolvationEnergy.
getRelativeSolvationTypes() - Method in class ffx.potential.parameters.ForceField
Getter for the field relativeSolvationTypes.
getRemarkLines() - Method in class ffx.potential.parsers.PDBFilter
Returns all the remark lines found by the last readFile call.
getRemarkLines() - Method in class ffx.potential.parsers.SystemFilter
Gets all remark lines read by the last readFile or readNext call.
getRemarkLines() - Method in class ffx.potential.parsers.XPHFilter
 
getRemarkLines() - Method in class ffx.potential.parsers.XYZFilter
 
getRemoveCenterOfMassMotion() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Getter for the field removeCenterOfMassMotion.
getRepEx() - Method in class ffx.algorithms.cli.RepExOptions
 
getRepexFrequency() - Method in class ffx.algorithms.cli.RepexOSTOptions
The interval (in psec) between replica exchange attempts.
getReplicaSteps() - Method in class ffx.algorithms.cli.RepExOptions
 
getReport() - Method in class ffx.algorithms.cli.DynamicsOptions
The thermodynamics reporting frequency in picoseconds (0.1 psec default).
getReportFrequency(int) - Method in class ffx.algorithms.cli.DynamicsOptions
The molecular dynamics reporting frequency in steps.
getResetNumSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions
Getter for the field resetNumSteps.
getResetStatistics() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
 
getResidue() - Method in class ffx.potential.bonded.RotamerLibrary.RotamerGuess
 
getResidue(int) - Method in class ffx.potential.bonded.Polymer
getResidue
getResidue(String, int, boolean) - Method in class ffx.potential.bonded.Polymer
getResidue
getResidue(String, int, boolean, Residue.ResidueType) - Method in class ffx.potential.bonded.Polymer
getResidue
getResidueCount() - Method in class ffx.potential.bonded.MultiResidue
getResidueCount.
getResidueDistance(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Checks the distance matrix, finding the shortest distance between the closest rotamers of two residues.
getResidueList() - Method in class ffx.potential.MolecularAssembly
getResidueList
getResidueName() - Method in class ffx.potential.bonded.Atom
Get the residue name
getResidueName() - Method in class ffx.potential.bonded.Molecule
Getter for the field residueName.
getResidueNumber() - Method in class ffx.potential.bonded.Atom
getResidueNumber
getResidueNumber() - Method in class ffx.potential.bonded.Molecule
getResidueNumber
getResidueNumber() - Method in class ffx.potential.bonded.Residue
Returns this Residue's sequence number.
getResidues() - Method in class ffx.algorithms.optimize.RotamerOptimization
Return the residue list.
getResidues() - Method in class ffx.potential.bonded.Polymer
getResidues
getResiduesAsList() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell
Returns a copy of the ArrayList of residues.
getResidueSurfaceArea(Residue) - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
 
getResidueType() - Method in class ffx.potential.bonded.Residue
Getter for the field residueType.
getResName() - Method in class ffx.potential.parameters.RelativeSolvationType
Getter for the field resName.
getResolution() - Method in class ffx.potential.bonded.Atom
Getter for the field resolution.
getResolution() - Method in class ffx.xray.DiffractionData
Getter for the field resolution.
getResolution(File, Crystal) - Method in class ffx.xray.parsers.CIFFilter
Attempt to determine resolution of reflection file.
getResolution(File, Crystal) - Method in class ffx.xray.parsers.CNSFilter
Attempt to determine resolution of reflection file.
getResolution(File, Crystal) - Method in interface ffx.xray.parsers.DiffractionFileFilter
Attempt to determine resolution of reflection file.
getResolution(File, Crystal) - Method in class ffx.xray.parsers.MTZFilter
Attempt to determine resolution of reflection file.
getResourceFile(String) - Method in class ffx.algorithms.misc.AlgorithmsTest
Get a resource file from the classpath.
getResourceFile(String) - Method in class ffx.potential.utils.PotentialTest
Get a resource file from the classpath.
getResourcePath(String) - Method in class ffx.algorithms.misc.AlgorithmsTest
Get a resource file from the classpath.
getResourcePath(String) - Method in class ffx.potential.utils.PotentialTest
Get a resource file from the classpath.
getRestartColumn() - Method in class ffx.potential.parsers.DistanceMatrixFilter
Get the number of columns in the last row that was read in.
getRestartFile() - Method in class ffx.algorithms.cli.ManyBodyOptions
Gets the restart file created during rotamer optimization.
getRestartFile() - Method in class ffx.algorithms.optimize.RotamerOptimization
Returns the restart file.
getRestartRow() - Method in class ffx.potential.parsers.DistanceMatrixFilter
Get the number of rows read in.
getRestrainGroups() - Method in class ffx.potential.ForceFieldEnergy
Getter for the RestrainGroup field.
getRestrainPositions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field coordRestraints.
getRestraintBonds(BondType.BondFunction) - Method in class ffx.potential.ForceFieldEnergy
Getter for the field restraintBonds.
getRestraintTorsions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field restraintBonds.
getReturnValue() - Method in class ffx.ui.FFXExec
Getter for the field returnValue.
getRmin() - Method in class ffx.potential.nonbonded.VanDerWaalsForm
Return the Rmin value for each class.
getRMSD() - Method in class ffx.potential.bonded.RotamerLibrary.RotamerGuess
 
getRMSGradient() - Method in class ffx.algorithms.optimize.Minimize
getRMSGradient.
getRMSGradient() - Method in class ffx.algorithms.optimize.PhMinimize
getRMSGradient.
getRN() - Method in class ffx.potential.utils.Loop
getRN.
getRotamer() - Method in class ffx.potential.bonded.Residue
Get the current rotamer.
getRotamer() - Method in class ffx.potential.bonded.RotamerLibrary.RotamerGuess
 
getRotamerLibrary(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
getRotamerPhBias() - Method in class ffx.potential.bonded.Rotamer
 
getRotamerPhBias(AminoAcidUtils.AminoAcid3) - Method in class ffx.potential.parameters.TitrationUtils
 
getRotamers() - Method in class ffx.potential.bonded.MultiResidue
Return all currently set rotamers.
getRotamers() - Method in class ffx.potential.bonded.Residue
Return all currently set rotamers.
getRotamers(AminoAcidUtils.AminoAcid3) - Method in class ffx.potential.bonded.RotamerLibrary
Return an array of Rotamers for the given amino acid.
getRotamers(AminoAcidUtils.AminoAcid3, TitrationUtils) - Method in class ffx.potential.bonded.RotamerLibrary
Return an array of Rotamers for the given amino acid.
getRotamers(NucleicAcidUtils.NucleicAcid3) - Method in class ffx.potential.bonded.RotamerLibrary
Return an array of Rotamers for the given nucleic acid.
getRotationMatrix(MultipoleType.MultipoleFrameDefinition, double[], double[][]) - Static method in class ffx.potential.parameters.MultipoleType
Return the rotation matrix for the local to lab frame.
getRotationMatrix(MultipoleType.MultipoleFrameDefinition, double[], double[][], double[][]) - Static method in class ffx.potential.parameters.MultipoleType
Return the rotation matrix for the local to lab frame.
getRowCount() - Method in class edu.rit.io.DoubleMatrixFile
Returns the number of rows in this matrix file.
getRowRange() - Method in class edu.rit.io.DoubleMatrixFile.Reader
Obtain the row range of the next matrix element segment in the input stream.
getScale14() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
getScale14() - Method in class ffx.potential.nonbonded.VanDerWaalsForm
Getter for the field scale14.
getScaleBulkMinimize() - Method in class ffx.xray.DiffractionData
Getter for the field scaleBulkMinimize.
getScaled() - Method in class ffx.xray.DiffractionData
Getter for the field scaled.
getScaling() - Method in class ffx.algorithms.dynamics.Barostat
Get the problem scaling.
getScaling() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the problem scaling.
getScaling() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getScaling() - Method in interface ffx.numerics.OptimizationInterface
Get the problem scaling.
getScaling() - Method in class ffx.potential.ANIEnergy
 
getScaling() - Method in class ffx.potential.DualTopologyEnergy
Get the problem scaling.
getScaling() - Method in class ffx.potential.extended.ExtendedSystem
 
getScaling() - Method in class ffx.potential.ForceFieldEnergy
Get the problem scaling.
getScaling() - Method in class ffx.potential.QuadTopologyEnergy
Get the problem scaling.
getScaling() - Method in class ffx.potential.XtalEnergy
Get the problem scaling.
getScaling() - Method in class ffx.realspace.RealSpaceEnergy
Get the problem scaling.
getScaling() - Method in class ffx.xray.RefinementEnergy
Get the problem scaling.
getScaling() - Method in class ffx.xray.ScaleBulkEnergy
Get the problem scaling.
getScaling() - Method in class ffx.xray.SigmaAEnergy
Get the problem scaling.
getScaling() - Method in class ffx.xray.SplineEnergy
Get the problem scaling.
getScaling() - Method in class ffx.xray.XRayEnergy
Get the problem scaling.
getSchedule() - Method in class ffx.algorithms.cli.AnnealOptions
Constructs an AnnealingSchedule.
getSchedulerHost() - Method in class edu.rit.pj.cluster.Configuration
Returns the Job Scheduler's channel group host name.
getSchedulerPort() - Method in class edu.rit.pj.cluster.Configuration
Returns the Job Scheduler's channel group port number.
getScript(String) - Static method in class ffx.utilities.FFXScript
Use the System ClassLoader to find the requested script.
getSd() - Method in class ffx.numerics.math.BootStrapStatistics
The standard deviation.
getSd() - Method in class ffx.numerics.math.SummaryStatistics
The standard deviation.
getSecondaryStructure() - Method in class ffx.potential.utils.GetProteinFeatures
Get the secondary structure annotation from the ramachandran angle map
getSegID() - Method in class ffx.potential.bonded.Atom
Getter for the field segID.
getSegID() - Method in class ffx.potential.bonded.Molecule
Getter for the field segID.
getSegID() - Method in class ffx.potential.bonded.Residue
Getter for the field segID.
getSelf() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
 
getSelf(int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Return a previously computed self-energy.
getSelf(int, int, Rotamer, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Return a previously computed self-energy.
getSelfEnergy() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getSelfEnergy() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
getSelfEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
getSelfVolumeFractions() - Method in class ffx.potential.nonbonded.implicit.GaussVol
Return the self volume fraction for each atom.
getSideChainAtoms() - Method in class ffx.potential.bonded.MultiResidue
Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
getSideChainAtoms() - Method in class ffx.potential.bonded.Residue
Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
getSigF(int) - Method in class ffx.xray.DiffractionRefinementData
getSigF
getSigma() - Method in class ffx.potential.bonded.Atom
Gets the Sigma value
getSigmaA() - Method in class ffx.xray.CrystalStats
Simply return the current sigmaA value.
getSigmaAMinimize() - Method in class ffx.xray.DiffractionData
Getter for the field sigmaAMinimize.
getSigmaATol() - Method in class ffx.xray.DiffractionData
Getter for the field sigmaATol.
getSimilarAtomTypes(AtomType) - Method in class ffx.potential.parameters.ForceField
Getter for the field atomTypes.
getSize() - Method in class ffx.openmm.BondArray
Get the size of the bond array.
getSize() - Method in class ffx.openmm.DoubleArray
Get the size of the array.
getSize() - Method in class ffx.openmm.IntArray
Get the size of the array.
getSize() - Method in class ffx.openmm.IntSet
Get the size of the set.
getSize() - Method in class ffx.openmm.StringArray
Get the number of strings in the String Array.
getSize() - Method in class ffx.openmm.Vec3Array
Get the size of the Vec3Array.
getSmallerDistance() - Method in class ffx.potential.nonbonded.RestrainGroups
Smaller distance for each restraint.
getSnaps() - Method in class ffx.potential.parsers.BARFilter
 
getSnapshot() - Method in class ffx.potential.parsers.PDBFilter
 
getSnapshot() - Method in class ffx.potential.parsers.SystemFilter
Return snapshot number.
getSnapshot() - Method in class ffx.potential.parsers.XPHFilter
 
getSnapshot() - Method in class ffx.potential.parsers.XYZFilter
 
getSnapshotInterval() - Method in class ffx.algorithms.cli.DynamicsOptions
Write/snapshot appending interval.
getSoluteOffset() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
 
getSolutePermittivity() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the solvent relative permittivity (typically 1.0).
getSoluteType() - Method in class ffx.potential.bonded.Atom
getSoluteType
getSoluteType(Atom, ForceField, SoluteType.SOLUTE_RADII_TYPE) - Static method in class ffx.potential.parameters.SoluteType
 
getSoluteType(String) - Method in class ffx.potential.parameters.ForceField
Get a SoluteType.
getSoluteTypes() - Method in class ffx.potential.parameters.ForceField
 
getSolvationEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field solvationEnergy.
getSolvationEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
getGKEnergy
getSolvationEnergy(Residue, boolean) - Method in class ffx.potential.bonded.RelativeSolvation
Gets the solvation energy (de-solvation penalty) for a given residue, allowing for sequence optimization to include an estimate of energy relative to the unfolded state.
getSolvationInteractions() - Method in class ffx.potential.ForceFieldEnergy
getSolvationInteractions.
getSolvEnergy() - Method in class ffx.potential.parameters.RelativeSolvationType
Getter for the field solvEnergy.
getSolventModel() - Method in class ffx.xray.DiffractionData
Getter for the field solventModel.
getSolventPermittivity() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Returns the solvent relative permittivity (typically 78.3).
getSolventPressure() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
getSOR() - Method in class ffx.potential.nonbonded.pme.SORRegion
 
getSpecialPositionCutoff() - Method in class ffx.crystal.Crystal
Getter for the field specialPositionCutoff.
getSpecialPositionCutoff2() - Method in class ffx.crystal.Crystal
Getter for the field specialPositionCutoff2.
getSpecialResidueList() - Method in class ffx.potential.extended.ExtendedSystem
 
getSpeed() - Method in class ffx.openmm.Platform
Get an estimate of how fast this Platform class is.
getSplineMinimize() - Method in class ffx.xray.DiffractionData
Getter for the field splineMinimize.
getStandardDeviation() - Method in class ffx.numerics.math.RunningStatistics
Get the standard deviation.
getStart() - Method in class ffx.algorithms.cli.ManyBodyOptions
Starting residue to perform the optimization on (-1 exits).
getState() - Method in class ffx.potential.extended.ExtendedSystem
 
getState(int, int) - Method in class ffx.openmm.Context
Get the state of the context.
getStates() - Method in class ffx.algorithms.optimize.ConformationScan
 
getStates() - Method in class ffx.algorithms.optimize.TorsionSearch
List of states in order of lowest to highest energy.
getStatesAroundAverage(double, double) - Method in class ffx.algorithms.optimize.ConformationScan
 
getStatesFilteredByRMSD(double) - Method in class ffx.algorithms.optimize.ConformationScan
 
getStatesWithinEnergy(double) - Method in class ffx.algorithms.optimize.ConformationScan
 
getStatus() - Method in class ffx.algorithms.optimize.Minimize
Getter for the field status.
getStatus() - Method in class ffx.algorithms.optimize.PhMinimize
Getter for the field status.
getStdOfEnergies() - Method in class ffx.algorithms.optimize.ConformationScan
 
getStdOfEnergiesNoOutlier() - Method in class ffx.algorithms.optimize.ConformationScan
 
getStep() - Method in class ffx.ui.commands.SimulationMessage
Getter for the field step.
getSteps() - Method in class ffx.algorithms.cli.DynamicsOptions
The number of molecular dynamics steps (default is 1,000,000).
getStrenchBendEnergy() - Method in class ffx.potential.ForceFieldEnergy
getStrenchBendEnergy.
getStretchBendEnergyString() - Method in class ffx.potential.ForceFieldEnergy
 
getStretchBendList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Stretch-Bends below the present MSNode.
getStretchBends() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field stretchBends.
getStretchBendType(AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField
getStretchBendType
getStretchBendType(String) - Method in class ffx.potential.parameters.ForceField
getStretchBendType
getStretchTorsionEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field stretchTorsionEnergy.
getStretchTorsionList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all StretchTorsions below the present MSNode.
getStretchTorsions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field stretchTorsions.
getStretchTorsionType(String) - Method in class ffx.potential.parameters.ForceField
getStretchTorsionType
getString(String) - Method in class ffx.potential.parameters.ForceField
getBoolean
getString(String, String) - Method in class ffx.potential.parameters.ForceField
getBoolean
getSubCurves() - Method in class ffx.numerics.integrate.CompositeCurve
Gets the component FunctionDataCurves of this CompositeCurve.
getSum() - Method in class ffx.numerics.math.RunningStatistics
Get the sum.
getSumOverK() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
 
getSupportedPlatforms() - Method in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine
Gets the set of Platforms supported by this DynamicsEngine
getSurfaceArea() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
Return Surface Area (A^2).
getSurfaceArea() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
getSurfaceArea() - Method in class ffx.potential.nonbonded.implicit.GaussVol
Return Surface Area (A^2).
getSurfaceAreaEnergy() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
Return Surface Area based cavitation energy.
getSurfaceAreaGradient() - Method in class ffx.potential.nonbonded.implicit.GaussVol
 
getSurfaceAreaRegion() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getSurfaceTension() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Getter for the field surfaceTension.
getSurfaceTension() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
getSwitch() - Method in class ffx.potential.DualTopologyEnergy
Returns the switching function used by this DualTopologyEnergy; presently, switching functions are immutable, and cannot be changed once a DualTopologyEnergy is constructed.
getSwitchEnd() - Method in class ffx.numerics.switching.MultiplicativeSwitch
Get the value where the switch starts.
getSwitchingFunction() - Method in class ffx.potential.cli.TopologyOptions
Return the switching function between topology energies.
getSwitchStart() - Method in class ffx.numerics.switching.MultiplicativeSwitch
Get the value where the switch starts.
getSymOp(int) - Method in class ffx.crystal.SpaceGroup
Return the ith symmetry operator.
getSymOpAtoms(int, int[]) - Method in class ffx.potential.nonbonded.NeighborList.Cell
Return the number of atoms in the cell for a given symmetry operator.
getSynchronousSend() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
Return the SynchronousSend associated with this Histogram, if any.
getSystem() - Method in class ffx.potential.openmm.OpenMMEnergy
Get a reference to the System instance.
getSystem() - Method in class ffx.ui.commands.FFXClient
Getter for the field system.
getSystems() - Method in class ffx.ui.Hierarchy
getSystems
getTag() - Method in class edu.rit.pj.cluster.Message
Get the message tag to use when sending this message.
getTanhBetas() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getTanhCorrection() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getTargetTemperature() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Get the target temperature.
getTau() - Method in class ffx.algorithms.dynamics.thermostats.Berendsen
Getter for the field tau.
getTau() - Method in class ffx.algorithms.dynamics.thermostats.Bussi
Getter for the field tau.
getTautomerESVIndex(int) - Method in class ffx.potential.extended.ExtendedSystem
 
getTautomerizingResidueList() - Method in class ffx.potential.extended.ExtendedSystem
Return the List of Tautomerizing Residues
getTautomerLambda(int) - Method in class ffx.potential.extended.ExtendedSystem
get Tautomer Lambda for an extended atom
getTautomerLambda(Residue) - Method in class ffx.potential.extended.ExtendedSystem
Gets the tautomer lambda for the input residue if the residue is tautomerizing
getTemperAfter() - Method in class ffx.algorithms.cli.AnnealOptions
Sets the number of annealing windows to hold flat at the low temperature (in addition to normal windows).
getTemperature() - Method in class ffx.algorithms.cli.DynamicsOptions
The simulation temperature (Kelvin).
getTemperature() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Get the current temperature of the system
getTemperature() - Method in class ffx.algorithms.mc.BoltzmannMC
Returns temperature of the Monte Carlo criterion.
getTemperature() - Method in interface ffx.algorithms.mc.MetropolisMC
Returns temperature of the Monte Carlo criterion.
getTemperature() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
getTemperature.
getTemperature() - Method in class ffx.potential.SystemState
Get the temperature.
getTemperature(double) - Method in class ffx.potential.openmm.OpenMMSystem
 
getTemperature(int) - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule
Get the temperature for annealing step i.
getTemperature(int) - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
 
getTemperature(int) - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
 
getTemperature(int) - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
 
getTemperatures() - Method in interface ffx.algorithms.optimize.anneal.AnnealingSchedule
Get all temperatures this schedule specifies.
getTemperatures() - Method in class ffx.algorithms.optimize.anneal.ExpAnnealSchedule
 
getTemperatures() - Method in class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
 
getTemperatures() - Method in class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
 
getTemperBefore() - Method in class ffx.algorithms.cli.AnnealOptions
Sets the number of annealing windows to hold flat at the high temperature (in addition to normal windows).
getTemperingOffset() - Method in class ffx.algorithms.thermodynamics.HistogramData
Gets the tempering offset.
getTemperingRate() - Method in class ffx.algorithms.cli.OSTOptions
The Dama et al.
getTemperingThreshold() - Method in class ffx.algorithms.cli.OSTOptions
The tempering threshold/offset in kcal/mol.
getTemperString() - Method in class ffx.algorithms.cli.AnnealOptions
Sets the schedule to be used.
getTempFactor() - Method in class ffx.potential.bonded.Atom
Getter for the field tempFactor.
getTempFactorAcceleration() - Method in class ffx.potential.bonded.Atom
Getter for the field tempFactorAcceleration.
getTempFactorGradient() - Method in class ffx.potential.bonded.Atom
Getter for the field tempFactorGradient.
getTempFactorPreviousAcceleration() - Method in class ffx.potential.bonded.Atom
Getter for the field tempFactorPreviousAcceleration.
getTempFactorVelocity() - Method in class ffx.potential.bonded.Atom
Getter for the field tempFactorVelocity.
getTemporaryBuf() - Method in class edu.rit.mp.BooleanBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Buf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.ByteBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.CharacterBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.DoubleBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.FloatBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.IntegerBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.LongBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.ObjectBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.ShortBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Signed16BitIntegerBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Signed8BitIntegerBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTemporaryBuf() - Method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a temporary buffer with the same type of items and the same length as this buffer.
getTensor(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
Load the tensor components.
getTermNode() - Method in class ffx.potential.bonded.MSGroup
Returns the MultiScaleGroup's terms FNode.
getTermNode() - Method in class ffx.potential.bonded.MultiResidue
Returns the MultiScaleGroup's terms FNode.
getThermoAlgoString() - Method in class ffx.algorithms.cli.ThermodynamicsOptions
The algorithm to be used (e.g.
getThermostat() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Getter for the field thermostat.
getThermostat() - Method in class ffx.xray.RefinementEnergy
Getter for the field thermostat.
getThermostatString() - Method in class ffx.algorithms.cli.DynamicsOptions
The desired thermostat: current choices are Adiabatic, Berendsen, or Bussi.
getThetaAccel() - Method in class ffx.potential.extended.ExtendedSystem
 
getThetaFriction() - Method in class ffx.potential.extended.ExtendedSystem
 
getThetaMass() - Method in class ffx.potential.extended.ExtendedSystem
 
getThetaMassArray() - Method in class ffx.potential.extended.ExtendedSystem
 
getThetaPosition() - Method in class ffx.potential.extended.ExtendedSystem
 
getThetaVelocity() - Method in class ffx.potential.extended.ExtendedSystem
 
getThreadCount() - Method in class edu.rit.pj.ParallelConstruct
Determine the number of threads in the parallel team executing this parallel construct.
getThreadCount() - Method in class edu.rit.pj.ParallelTeam
Determine the number of threads in this parallel team.
getThreadCount() - Method in class edu.rit.pj.WorkerConstruct
Determine the number of worker threads in the current process in the worker team executing this worker construct.
getThreadCount() - Method in class edu.rit.pj.WorkerTeam
Determine the number of worker threads in this worker team in this process.
getThreadIndex() - Method in class edu.rit.pj.ParallelConstruct
Determine the index of the calling thread in the parallel team executing this parallel construct.
getThreadIndex() - Method in class edu.rit.pj.WorkerConstruct
Determine the index of the calling thread in the worker team executing this worker construct.
getThreads() - Method in class ffx.potential.cli.TimerOptions
Getter for the field threads.
getThreadWeights() - Method in class ffx.xray.GradientSchedule
getThreadWeights.
getThreeBody() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
 
getThreeBodyCutoff() - Method in class ffx.algorithms.cli.ManyBodyOptions
Cutoff distance for three-body interactions.
getThreeBodyEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
getTime() - Method in class ffx.openmm.State
Get the time.
getTime() - Method in class ffx.ui.commands.SimulationMessage
Getter for the field time.
getTimeout() - Method in class edu.rit.util.Timer
Determine the time when this timer is or was scheduled to time out.
getTimerTask() - Method in class edu.rit.util.Timer
Returns this timer's timer task.
getTimeStep() - Method in class ffx.algorithms.dynamics.integrators.Integrator
Get the time step.
getTimeStep() - Method in class ffx.algorithms.dynamics.MolecularDynamics
getTimeStep.
getTimeStep() - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
getTimeStep.
getTimings() - Method in class ffx.numerics.fft.Complex3DParallel
 
getTitratingHydrogenDirection(AminoAcidUtils.AminoAcid3, Atom) - Static method in class ffx.potential.parameters.TitrationUtils
 
getTitratingResidueList() - Method in class ffx.potential.extended.ExtendedSystem
Return the List of Titrating Residues
getTitrationESVIndex(int) - Method in class ffx.potential.extended.ExtendedSystem
get the index of the extended residue list that corresponds to this atom
getTitrationLambda(int) - Method in class ffx.potential.extended.ExtendedSystem
get Titration Lambda for an extended atom
getTitrationLambda(Residue) - Method in class ffx.potential.extended.ExtendedSystem
Gets the titration lambda for the input residue if the residue is titrating
getTitrationPH() - Method in class ffx.algorithms.cli.ManyBodyOptions
 
getTitrationUtils() - Method in class ffx.potential.bonded.Residue
 
getTitrationUtils() - Method in class ffx.potential.extended.ExtendedSystem
 
getTolerance() - Method in class ffx.potential.cli.GradientOptions
--tol or --tolerance Gradient error tolerance (kcal/mol/Ã…).
getTopology(MolecularAssembly[], UnivariateSwitchingFunction, List<Integer>, List<Integer>, int, StringBuilder) - Method in class ffx.potential.cli.TopologyOptions
Configure a Dual-, Quad- or Oct- Topology.
getTorque() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
getTorsion(Atom, Atom, Atom) - Method in class ffx.potential.bonded.Atom
Finds a Torsion which contains this atom, and atoms 2, 3, and 4.
getTorsionEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field torsionEnergy.
getTorsionList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Torsions below the present MSNode.
getTorsions() - Method in class ffx.potential.bonded.Atom
Getter for the field torsions.
getTorsions() - Method in class ffx.potential.bonded.MSGroup
Returns the MultiScaleGroup's Torsion MSNode.
getTorsions() - Method in class ffx.potential.bonded.MultiResidue
Returns the MultiScaleGroup's Torsion MSNode.
getTorsions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field torsions.
getTorsionScale() - Method in class ffx.potential.bonded.Torsion
Get the torsion scale up factor.
getTorsionTorsionEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field torsionTorsionEnergy.
getTorsionTorsionList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Torsion-Torsions below the present MSNode.
getTorsionTorsions() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field torsionTorsions.
getTorsionTorsionType(String) - Method in class ffx.potential.parameters.ForceField
getTorsionTorsionType
getTorsionType(AtomType, AtomType, AtomType, AtomType) - Method in class ffx.potential.parameters.ForceField
getTorsionType
getTorsionType(String) - Method in class ffx.potential.parameters.ForceField
getTorsionType
getTotalAtomArray() - Method in class ffx.xray.RefinementModel
Getter for the field totalAtomArray.
getTotaldEdLambda() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
getTotaldEdLambda.
getTotalElectrostaticEnergy() - Method in class ffx.potential.ForceFieldEnergy
getTotalElectrostaticEnergy.
getTotalEnergy() - Method in class ffx.algorithms.dynamics.Barostat
Get the total energy of the system
getTotalEnergy() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Get the total system energy (kinetic plus potential).
getTotalEnergy() - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
getTotalEnergy.
getTotalEnergy() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the total energy of the system
getTotalEnergy() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getTotalEnergy() - Method in interface ffx.numerics.OptimizationInterface
Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.ANIEnergy
 
getTotalEnergy() - Method in class ffx.potential.DualTopologyEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.extended.ExtendedSystem
 
getTotalEnergy() - Method in class ffx.potential.ForceFieldEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.openmm.OpenMMState
Get the total energy.
getTotalEnergy() - Method in class ffx.potential.QuadTopologyEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.potential.SystemState
Get the total energy as the sum of the kinetic and potential energies.
getTotalEnergy() - Method in record class ffx.potential.UnmodifiableState
 
getTotalEnergy() - Method in class ffx.potential.XtalEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.realspace.RealSpaceEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.RefinementEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.ScaleBulkEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.SigmaAEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.SplineEnergy
Get the total energy of the system
getTotalEnergy() - Method in class ffx.xray.XRayEnergy
Get the total energy of the system
getTotalEnthalpy() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total enthalpy estimate from bootstrap analysis.
getTotalEnthalpy(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total enthalpy estimate from per window bootstrap analysis.
getTotalEnthalpyUncertainty() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total enthalpy variance estimate from bootstrap analysis.
getTotalEnthalpyUncertainty(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total enthalpy estimate from per window bootstrap analysis.
getTotalFE() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total free energy difference estimate from bootstrap analysis.
getTotalFE(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total free energy difference estimate from per window bootstrap analysis.
getTotalMass() - Method in class ffx.potential.bonded.MSNode
Returns the total mass of all atoms in the MolecularAssembly, calculating the mass if it has not already been done, defaulting to simple addition.
getTotalMonomerMinimizedEnergy() - Method in class ffx.algorithms.optimize.ConformationScan
 
getTotalMultipoleEnergy() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Getter for the field totalMultipoleEnergy.
getTotalNumberOfOverlaps() - Method in class ffx.potential.nonbonded.implicit.GaussVol
Return the total number of overlaps in the tree
getTotalRotamerPhBias(Rotamer[]) - Method in class ffx.potential.parameters.TitrationUtils
 
getTotalRotamerPhBias(List<Residue>, int[]) - Static method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Compute the total rotamer Ph bias for an array of residues.
getTotalSurfaceArea() - Method in class ffx.potential.utils.GetProteinFeatures
Get the total surface area for the protein
getTotalThreadCount() - Method in class edu.rit.pj.WorkerConstruct
Determine the total number of worker threads in all processes in the worker team executing this worker construct.
getTotalThreadCount() - Method in class edu.rit.pj.WorkerTeam
Determine the total number of worker threads in this worker team in all processes.
getTotalUncertainty() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total free energy difference variance estimate from bootstrap analysis.
getTotalUncertainty(double[]) - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the total free energy difference estimate from per window bootstrap analysis.
getTrajectory() - Method in class ffx.ui.FFXSystem
Getter for the field trajectory.
getTrajectoryCoords(int) - Method in class ffx.potential.bonded.Atom
getTrajectoryCoords
getTrajectoryLength() - Method in class ffx.potential.bonded.Atom
getTrajectoryLength
getTrajSteps() - Method in class ffx.algorithms.cli.DynamicsOptions
Number of steps for each OpenMM MD cycle.
getTransformationOperator(SymOp, double[][]) - Method in class ffx.crystal.Crystal
Compute the total transformation operator R = ToCart * Rot * ToFrac.
getTransformGroup() - Method in class ffx.potential.MolecularAssembly
getTransformGroup
getTrigonalAtom() - Method in class ffx.potential.bonded.OutOfPlaneBend
Get the trigonal atom of this out-of-plane bend (central atom of the Angle).
getTwoBody() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
 
getTwoBodyCutoff() - Method in class ffx.algorithms.cli.ManyBodyOptions
Cutoff distance for two-body interactions.
getTwoBodyEnergyMap() - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.AIB
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ALA
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ARG
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASD
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASH
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASN
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ASP
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.CYD
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.CYS
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.CYX
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLD
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLH
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLN
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.GLU
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.HID
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.HIE
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.HIS
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ILE
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.LEU
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.LYD
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.LYS
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.MET
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.ORN
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.PCA
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.PHE
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.PRO
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.SER
Returns Biotype of this atom.
getType() - Method in interface ffx.potential.bonded.AminoAcidUtils.SideChainType
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.THR
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.TRP
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.TYD
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.TYR
Returns Biotype of this atom.
getType() - Method in enum class ffx.potential.bonded.AminoAcidUtils.VAL
Returns Biotype of this atom.
getType() - Method in class ffx.potential.bonded.Atom
getType
getType() - Method in class ffx.potential.parsers.SystemFilter
getType
getType() - Method in class ffx.ui.commands.SimulationMessage
Getter for the field type.
getTypes(ForceField.ForceFieldType) - Method in class ffx.potential.parameters.ForceField
Return all force field types of a given type.
getUIAlgorithmUtils() - Method in class ffx.ui.ModelingShell
 
getUIPotentialsUtils() - Method in class ffx.ui.ModelingShell
 
getUncertainty() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Returns the uncertainty in the free energy estimate.
getUncertainty() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the free energy difference standard deviation estimate from bootstrap analysis for each window.
getUncertainty() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
getUncertainty() - Method in interface ffx.numerics.estimator.StatisticalEstimator
Returns the uncertainty in the free energy estimate.
getUncertainty() - Method in class ffx.numerics.estimator.Zwanzig
Returns the uncertainty in the free energy estimate.
getUnchargedAtoms() - Method in class ffx.potential.cli.AlchemicalOptions
--uc or --unchargedAtoms Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].
getUnchargedAtoms2() - Method in class ffx.potential.cli.TopologyOptions
--uc2 or --unchargedAtoms2 Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].
getUnderlyingPotentials() - Method in class ffx.algorithms.dynamics.Barostat
 
getUnderlyingPotentials() - Method in interface ffx.numerics.OptimizationInterface
Returns a List of Potentials this Potential depends on with a recursive search, excluding the top level of this call.
getUnderlyingPotentials() - Method in class ffx.potential.DualTopologyEnergy
 
getUnderlyingPotentials() - Method in class ffx.potential.QuadTopologyEnergy
 
getUnderlyingPotentials() - Method in class ffx.xray.RefinementEnergy
 
getUniqueAtoms(MolecularAssembly, String, String) - Static method in class ffx.potential.cli.TopologyOptions
Collect unique atoms for a dual-topology.
getUniqueAtomsA(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions
Collect unique atoms for the A dual-topology.
getUniqueAtomsB(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions
Collect unique atoms for the B dual-topology.
getUnitCell() - Method in class ffx.crystal.Crystal
The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
getUnitCell() - Method in class ffx.crystal.NCSCrystal
The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
getUnitCell() - Method in class ffx.crystal.ReplicatesCrystal
The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
getUnmodifiableState() - Method in class ffx.potential.SystemState
Get an unmodifiable view of the current state.
getUnscaledBornIntegral() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
 
getUnsharedA() - Method in class ffx.potential.cli.TopologyOptions
--uaA or --unsharedA sets atoms unique to the A dual-topology, as period-separated hyphenated ranges or singletons.
getUnsharedB() - Method in class ffx.potential.cli.TopologyOptions
--uaB or --unsharedB sets atoms unique to the A dual-topology, as period-separated hyphenated ranges or singletons.
getUpdate() - Method in class ffx.ui.commands.FFXClient
Getter for the field update.
getUpper() - Method in class ffx.algorithms.cli.AnnealOptions
Upper temperature limit in degrees Kelvin.
getUreyBradleyEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field ureyBradleyEnergy.
getUreyBradleyList() - Method in class ffx.potential.bonded.MSNode
Returns a List of all Urey-Bradleys below the present MSNode.
getUreyBradleys() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field ureyBradleys.
getUreyBradleyType(String) - Method in class ffx.potential.parameters.ForceField
getUreyBradleyType
getUri() - Method in class edu.rit.http.HttpRequest
Obtain this HTTP request's URI.
getUse() - Method in class ffx.potential.bonded.Atom
If true, this atom should be used in potential energy functions.
getUse() - Method in class ffx.potential.bonded.BondedTerm
This method returns true if any atom is being used.
getUsePerfectRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
GK is using perfect radii where available.
getUserName() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's user name.
getUsingOrigCoordsRotamer() - Method in class ffx.potential.bonded.RotamerLibrary
getUsingOrigCoordsRotamer.
getUsingOriginalCoordinates() - Method in class ffx.algorithms.cli.ManyBodyOptions
 
getV3D(Vector3d) - Method in class ffx.potential.bonded.Atom
Gets the Atom's Cartesian Coordinates return The Cartesian Coordinates
getValue() - Method in class ffx.potential.bonded.BondedTerm
Get the Term's value.
getValue() - Method in class ffx.ui.SwingWorker
Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValue(String) - Method in class ffx.ui.properties.FFXLocale
getValue
getVanDerWaalsEnergy() - Method in class ffx.potential.ForceFieldEnergy
Getter for the field vanDerWaalsEnergy.
getVanDerWaalsInteractions() - Method in class ffx.potential.ForceFieldEnergy
getVanDerWaalsInteractions.
getVar() - Method in class ffx.numerics.math.BootStrapStatistics
The variance.
getVar() - Method in class ffx.numerics.math.SummaryStatistics
The variance.
getVariable(String) - Method in class ffx.utilities.FFXContext
getVariable.
getVariableAtoms() - Method in class ffx.potential.bonded.MultiResidue
Returns a list of atoms liable to change during dead-end elimination repacking.
getVariableAtoms() - Method in class ffx.potential.bonded.Residue
Returns a list of atoms liable to change during dead-end elimination repacking.
getVariables() - Method in class ffx.utilities.FFXContext
Get the Map of all variables.
getVariableTypes() - Method in class ffx.algorithms.dynamics.Barostat
Get the type of all variables.
getVariableTypes() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Get the type of all variables.
getVariableTypes() - Method in interface ffx.numerics.Potential
Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.ANIEnergy
 
getVariableTypes() - Method in class ffx.potential.DualTopologyEnergy
Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.extended.ExtendedSystem
 
getVariableTypes() - Method in class ffx.potential.ForceFieldEnergy
Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.QuadTopologyEnergy
Get the type of all variables.
getVariableTypes() - Method in class ffx.potential.XtalEnergy
Get the type of all variables.
getVariableTypes() - Method in class ffx.realspace.RealSpaceEnergy
Get the type of all variables.
getVariableTypes() - Method in class ffx.xray.RefinementEnergy
Get the type of all variables.
getVariableTypes() - Method in class ffx.xray.XRayEnergy
Get the type of all variables.
getVariance() - Method in class ffx.numerics.estimator.EstimateBootstrapper
Get the free energy difference variance estimate from bootstrap analysis for each window.
getVariance() - Method in class ffx.numerics.math.RunningStatistics
Get the variance.
getVDW14Type(String) - Method in class ffx.potential.parameters.ForceField
getVDW14Type
getVDW14Types() - Method in class ffx.potential.parameters.ForceField
getVDW14Types
getVDWForm() - Method in class ffx.potential.nonbonded.VanDerWaals
getVDWForm.
getVdwLambdaTerm() - Method in class ffx.potential.openmm.OpenMMSystem
Get the value of the vdW lambda term flag.
getVdwNode() - Method in class ffx.potential.ForceFieldEnergy
getVdwNode.
getVDWPairType(String) - Method in class ffx.potential.parameters.ForceField
getVDWPairType
getVDWPairTypes() - Method in class ffx.potential.parameters.ForceField
getVDWPairTypes
getVdwPrefactor(int, double[]) - Method in class ffx.potential.extended.ExtendedSystem
Calculate prefactor for scaling the van der Waals based on titration/tautomer state if titrating proton
getVDWR() - Method in class ffx.potential.bonded.Atom
Gets the van der Waals radius.
getVdWSoftcoreAlpha() - Method in class ffx.potential.openmm.OpenMMSystem
Set the vdW softcore alpha value.
getVdwSoftcorePower() - Method in class ffx.potential.openmm.OpenMMSystem
Set the vdW softcore power.
getVDWSoluteType(VDWType) - Static method in class ffx.potential.parameters.SoluteType
 
getVDWType() - Method in class ffx.potential.bonded.Atom
getVDWType
getVDWType(String) - Method in class ffx.potential.parameters.ForceField
getVDWType
getVDWTypes() - Method in class ffx.potential.parameters.ForceField
getVDWTypes
getVelocities() - Method in class ffx.openmm.State
Get the velocities.
getVelocities(double[]) - Method in class ffx.potential.openmm.OpenMMState
The positions array contains the OpenMM atomic position information for all atoms.
getVelocity(double[]) - Method in class ffx.algorithms.dynamics.Barostat
getVelocity.
getVelocity(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
getVelocity.
getVelocity(double[]) - Method in interface ffx.numerics.Potential
getVelocity.
getVelocity(double[]) - Method in class ffx.potential.ANIEnergy
 
getVelocity(double[]) - Method in class ffx.potential.bonded.Atom
Getter for the field velocity.
getVelocity(double[]) - Method in class ffx.potential.DualTopologyEnergy
getVelocity.
getVelocity(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
getVelocity(double[]) - Method in class ffx.potential.ForceFieldEnergy
getVelocity.
getVelocity(double[]) - Method in class ffx.potential.QuadTopologyEnergy
getVelocity.
getVelocity(double[]) - Method in class ffx.potential.XtalEnergy
getVelocity.
getVelocity(double[]) - Method in class ffx.realspace.RealSpaceEnergy
getVelocity.
getVelocity(double[]) - Method in class ffx.xray.RefinementEnergy
getVelocity.
getVelocity(double[]) - Method in class ffx.xray.XRayEnergy
getVelocity.
getVerbose() - Method in class ffx.potential.cli.GradientOptions
-v or --verbose is a flag to print out energy at each step.
getVerbose() - Method in class ffx.potential.cli.TimerOptions
Getter for the field verbose.
getVerbosityLevel() - Method in class ffx.algorithms.dynamics.MolecularDynamics
 
getVolume() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
Return Volume (A^3).
getVolume() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
getVolume() - Method in class ffx.potential.nonbonded.implicit.GaussVol
Return Volume (A^3).
getVolume1() - Method in class ffx.potential.parsers.BARFilter
 
getVolume2() - Method in class ffx.potential.parsers.BARFilter
 
getVolumeEnergy() - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
Return Volume based cavitation energy.
getVolumeGradient() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
getVolumeGradient() - Method in class ffx.potential.nonbonded.implicit.GaussVol
 
getwA() - Method in class ffx.xray.cli.DataRefinementOptions
Getter for the field wA.
getWater() - Method in class ffx.potential.MolecularAssembly
getWater
getWaterNames() - Static method in class ffx.utilities.StringUtils
Returns a List of recognized water names (defensive copy).
getWebHost() - Method in class edu.rit.pj.cluster.Configuration
Returns the Job Scheduler's web interface host name.
getWebPort() - Method in class edu.rit.pj.cluster.Configuration
Returns the Job Scheduler's web interface port number.
getWeight() - Method in class ffx.numerics.math.RunningStatistics
Get the weight.
getWeight() - Method in class ffx.realspace.parsers.RealSpaceFile
Return the weight of this dataset.
getWeight() - Method in class ffx.realspace.RealSpaceData
getWeight
getWeight() - Method in class ffx.xray.CrystalReciprocalSpace
return dataset weight
getWeight() - Method in interface ffx.xray.DataContainer
getWeight
getWeight() - Method in class ffx.xray.DiffractionData
getWeight
getWeight() - Method in class ffx.xray.parsers.DiffractionFile
return the weight of this dataset
getWeights() - Method in class ffx.numerics.integrate.CompositeCurve
Gets the weights to the corresponding component curves.
getWindow() - Method in class ffx.algorithms.cli.ManyBodyOptions
Size of the sliding window with respect to adjacent residues (default = 7).
getWindows() - Method in class ffx.algorithms.cli.AnnealOptions
Number of annealing windows.
getWireFrame() - Method in class ffx.potential.MolecularAssembly
getWireFrame
getWn() - Method in class ffx.algorithms.mc.RosenbluthChiAllMove
getWn.
getWorldAddress() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's array of hosts/ports for the world communicator.
getWorldChannelGroup() - Method in class edu.rit.pj.cluster.JobBackend
Obtain this job's world communicator channel group.
getWrite() - Method in class ffx.algorithms.cli.DynamicsOptions
Snapshot save frequency in picoseconds (1.0 psec default).
getX() - Method in interface ffx.numerics.integrate.DataSet
Returns copy of the array of points x (x-axis).
getX() - Method in class ffx.numerics.integrate.DoublesDataSet
Returns copy of the array of points x (x-axis).
getX() - Method in class ffx.numerics.integrate.FunctionDataCurve
Returns copy of the array of points x (x-axis).
getX() - Method in class ffx.potential.bonded.Atom
Gets the x coordinate
getX() - Method in class ffx.potential.nonbonded.octree.OctreeCell
Gets x coordinate of center of cell
getX() - Method in class ffx.potential.nonbonded.octree.OctreePoint
 
getX(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Get the X-value of the array at the specified index after calling the reduce method.
getXDim() - Method in class ffx.potential.nonbonded.ReciprocalSpace
getXDim
getXDim() - Method in class ffx.xray.CrystalReciprocalSpace
getXDim
getXFactor() - Method in class ffx.ui.behaviors.MouseOrbit
Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseProperties
Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseRotate
Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseSelection
Return the x-axis movement multipler.
getXFactor() - Method in class ffx.ui.behaviors.MouseTranslate
Return the x-axis movement multipler.
getXrayScaleTol() - Method in class ffx.xray.DiffractionData
Getter for the field xrayScaleTol.
getxWeight() - Method in class ffx.xray.DiffractionData
Getter for the field xWeight.
getXWeight() - Method in class ffx.xray.RefinementEnergy
Get the current data weight (wA).
getXYZ() - Method in class ffx.potential.bonded.Atom
getXYZ
getXYZ(double[]) - Method in class ffx.potential.bonded.Atom
getXYZ
getXYZGradient(double[]) - Method in class ffx.potential.bonded.Atom
getXYZGradient
getXyzIndex() - Method in class ffx.potential.bonded.Atom
Getter for the field xyzIndex.
getY() - Method in class ffx.potential.bonded.Atom
Gets the y coordinate
getY() - Method in class ffx.potential.nonbonded.octree.OctreeCell
Gets y coordinate of center of cell
getY() - Method in class ffx.potential.nonbonded.octree.OctreePoint
 
getY(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Get the Y-value of the array at the specified index after calling the reduce method.
getYDim() - Method in class ffx.potential.nonbonded.ReciprocalSpace
getYDim
getYDim() - Method in class ffx.xray.CrystalReciprocalSpace
getYDim
getYFactor() - Method in class ffx.ui.behaviors.MouseOrbit
Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseProperties
Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseRotate
Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseSelection
Return the y-axis movement multipler.
getYFactor() - Method in class ffx.ui.behaviors.MouseTranslate
Return the y-axis movement multipler.
getZ() - Method in class ffx.potential.bonded.Atom
Gets the z coordinate
getZ() - Method in class ffx.potential.nonbonded.octree.OctreeCell
Gets z coordinate of center of cell
getZ() - Method in class ffx.potential.nonbonded.octree.OctreePoint
 
getZ(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Get the Z-value of the array at the specified index after calling the reduce method.
getZDim() - Method in class ffx.potential.nonbonded.ReciprocalSpace
getZDim
getZDim() - Method in class ffx.xray.CrystalReciprocalSpace
getZDim
getZeroBound() - Method in class ffx.numerics.switching.BellCurveSwitch
Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.CompositeSwitch
 
getZeroBound() - Method in class ffx.numerics.switching.ConstantSwitch
Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.LinearDerivativeSwitch
Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.MultiplicativeSwitch
Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.PowerSwitch
Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in class ffx.numerics.switching.SquaredTrigSwitch
Gets the zero bound, where f(x) becomes zero.
getZeroBound() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction
Gets the zero bound, where f(x) becomes zero.
GIF - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
 
GK - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
 
gkc - Variable in class ffx.potential.nonbonded.GeneralizedKirkwood
The Generalized Kirkwood cross-term parameter.
gkc - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion
Empirical constant that controls the GK cross-term.
GKCavitationForce - Class in ffx.openmm.amoeba
Implicit Solvent Cavitation Force.
GKCavitationForce() - Constructor for class ffx.openmm.amoeba.GKCavitationForce
Constructor.
gkDiameter - Variable in class ffx.potential.parameters.SoluteType
Solute atomic diameter for GK.
GKEnergyGlobal - Class in ffx.numerics.multipole
 
GKEnergyGlobal(double, double, boolean) - Constructor for class ffx.numerics.multipole.GKEnergyGlobal
Constructor for GKEnergyGlobal.
GKEnergyQI - Class in ffx.numerics.multipole
 
GKEnergyQI(double, double, double, boolean) - Constructor for class ffx.numerics.multipole.GKEnergyQI
Compute the GK Energy using a QI frame.
GKEnergyRegion - Class in ffx.potential.nonbonded.implicit
Parallel calculation of the Generalized Kirkwood reaction field energy.
GKEnergyRegion(int, Polarization, GeneralizedKirkwood.NonPolarModel, double, double, double, double, double, double, boolean) - Constructor for class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
gkEnergyTotal - Variable in class ffx.potential.nonbonded.pme.PMETimings
 
GKSource - Class in ffx.numerics.multipole
 
GKSource(int, double) - Constructor for class ffx.numerics.multipole.GKSource
 
GKSource.GK_MULTIPOLE_ORDER - Enum Class in ffx.numerics.multipole
The GK tensor can be constructed for a monopole potential (GB), a dipole potential or a quadrupole potential.
GKSource.GK_TENSOR_MODE - Enum Class in ffx.numerics.multipole
The "mode" for the tensor (either POTENTIAL or BORN).
GKTensorGlobal - Class in ffx.numerics.multipole
The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood interaction tensors.
GKTensorGlobal(GKSource.GK_MULTIPOLE_ORDER, int, GKSource, double, double) - Constructor for class ffx.numerics.multipole.GKTensorGlobal
 
GKTensorQI - Class in ffx.numerics.multipole
The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood interaction tensors.
GKTensorQI(GKSource.GK_MULTIPOLE_ORDER, int, GKSource, double, double) - Constructor for class ffx.numerics.multipole.GKTensorQI
 
GLD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
GLH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
GLHtoGLU - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
 
GLN - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
GLOBAL - Enum constant in enum class ffx.numerics.multipole.MultipoleTensor.COORDINATES
 
GlobalBehavior - Class in ffx.ui.behaviors
The GlobalBehavior class allows mouse control over camera position, adding a few functions to the OrbitBehavior class.
GlobalBehavior() - Constructor for class ffx.ui.behaviors.GlobalBehavior
Constructor for GlobalBehavior.
GlobalBehavior(Canvas3D) - Constructor for class ffx.ui.behaviors.GlobalBehavior
Constructor for GlobalBehavior.
globalMultipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Cartesian multipoles in the global frame with dimensions of [nsymm][nAtoms][10]
GLU - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
GLUTAMATE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
GLUTAMINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
GLY - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
GLYCINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
GO_PARALLEL - Static variable in class ffx.potential.bonded.ROLSP
Constant GO_PARALLEL=false
GoldsteinPairRegion - Class in ffx.algorithms.optimize.manybody
 
GoldsteinPairRegion(int) - Constructor for class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
 
goldsteinPairSumOverK(Residue[], int, int, int, int, int, int, int, int, List<Residue>, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization
 
grad - Variable in class ffx.algorithms.optimize.Minimize
The gradient.
grad - Variable in class ffx.algorithms.optimize.PhMinimize
The gradient.
gradESV - Variable in class ffx.algorithms.optimize.PhMinimize
The gradient.
gradient - Variable in class ffx.potential.SystemState
The gradient.
gradient() - Method in class ffx.potential.SystemState
Get a reference to the internal gradient array.
gradient() - Method in record class ffx.potential.UnmodifiableState
Returns the value of the gradient record component.
GradientOptions - Class in ffx.potential.cli
Represents command line options for scripts that test gradients.
GradientOptions() - Constructor for class ffx.potential.cli.GradientOptions
 
gradients - Variable in class ffx.ui.commands.SimulationUpdate
 
GradientSchedule - Class in ffx.xray
GradientSchedule class.
GradientSchedule(int, int) - Constructor for class ffx.xray.GradientSchedule
Constructor for GradientSchedule.
GradientUtils - Class in ffx.potential.utils
GradientUtils is a utility class for testing the gradient of a potential.
GradientUtils(Potential) - Constructor for class ffx.potential.utils.GradientUtils
Constructor.
GraphicsAxis - Class in ffx.ui
The GraphicsAxis class encapsulates the 3D Axis that is used to display and control rotation/translation in the global frame.
GraphicsCanvas - Class in ffx.ui
The GraphicsCanvas class provides a Canvas on which to render 3D Graphics.
GraphicsCanvas(MainPanel) - Constructor for class ffx.ui.GraphicsCanvas
Constructor for GraphicsCanvas.
GraphicsCanvas.ImageFormat - Enum Class in ffx.ui
The ImageFormat enum lists supported image formats.
GraphicsCanvas.LeftButtonMode - Enum Class in ffx.ui
The LeftButtonMode enum describes what the left mouse button does.
GraphicsCanvas.MouseMode - Enum Class in ffx.ui
The MouseMode enum describes what system is affected by mouse drags.
GraphicsEvents - Class in ffx.ui
The GraphicsEvents class listens for mouse events over the Java3D GraphicsCanvas, dispatching work to more specialized System Rotation and Translation Behaviors or to the GlobalOrbitBehavior.
GraphicsEvents(MainPanel, GraphicsCanvas, GraphicsAxis, SimpleUniverse, Bounds, BranchGroup, TransformGroup) - Constructor for class ffx.ui.GraphicsEvents
Constructor for GraphicsEvents.
GraphicsFullScreen - Class in ffx.ui
The FullScreenWindow class controls full screen graphics.
GraphicsFullScreen(Frame, GraphicsCanvas) - Constructor for class ffx.ui.GraphicsFullScreen
Constructor for GraphicsFullScreen.
GraphicsPanel - Class in ffx.ui
The GraphicsPanel class contains the 3D Canvas and its status box.
GraphicsPanel(GraphicsCanvas, JPanel) - Constructor for class ffx.ui.GraphicsPanel
Constructor for GraphicsPanel.
GraphicsPicking - Class in ffx.ui
The GraphicsPicking class is used to make selections and measurements.
GraphicsPicking(BranchGroup, Bounds, GraphicsCanvas, MainPanel) - Constructor for class ffx.ui.GraphicsPicking
Constructor
GraphicsPicking.PickLevel - Enum Class in ffx.ui
 
GraphicsPrefs - Class in ffx.ui
The GraphicsPrefs class allows users to select graphics preferences.
GraphicsSplitPane - Class in ffx.ui
The GraphicsSplitPane is an early attempt at working around issues caused by the heavyweight Canvas3D inside a lightweight Swing SplitPane.
GraphicsSplitPane() - Constructor for class ffx.ui.GraphicsSplitPane
Constructor for GraphicsSplitPane.
GraphicsSplitPane(int, boolean, Component, Component) - Constructor for class ffx.ui.GraphicsSplitPane
Constructor for GraphicsSplitPane.
gridDensity(int, int) - Method in class ffx.potential.nonbonded.SpatialDensityLoop
gridDensity
gridDensity(int, int, int, int) - Method in class ffx.potential.nonbonded.RowLoop
Apply electron density "as normal" for an atom, but check that the y and z indeces are within the supplied bounds (inclusive).
gridDensity(int, int, int, int) - Method in class ffx.potential.nonbonded.SliceLoop
Apply electron density "as normal" for an atom, but check that the z index is within the supplied bounds (inclusive).
GROUP - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
 
groupSelection(MSNode, MSNode) - Method in class ffx.ui.Hierarchy
groupSelection
growGroup(List<Integer>, Atom) - Static method in class ffx.potential.parameters.PolarizeType
A recursive method that checks all atoms bonded to the seed atom for inclusion in the polarization group.
GUA - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
 
GUANINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
 
guessRotamer(Residue) - Method in class ffx.potential.bonded.RotamerLibrary
Guess at what rotamer a residue is currently in.
guessTitrState - Variable in class ffx.potential.extended.ExtendedSystem
 
guided() - Static method in class edu.rit.pj.IntegerSchedule
Returns a self-guided schedule object with a minimum chunk size of 1.
guided() - Static method in class edu.rit.pj.LongSchedule
Returns a self-guided schedule object with a minimum chunk size of 1.
guided(int) - Static method in class edu.rit.pj.IntegerSchedule
Returns a self-guided schedule object with the given minimum chunk size.
guided(long) - Static method in class edu.rit.pj.LongSchedule
Returns a self-guided schedule object with the given minimum chunk size.

H

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

I

i - Variable in class ffx.potential.nonbonded.NeighborList.AtomIndex
 
I - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
I - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
I - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
 
i0() - Method in class ffx.crystal.ReflectionSpline
i0
i0(double) - Static method in class ffx.numerics.special.ModifiedBessel
Modified zero-order Bessel function.
i1() - Method in class ffx.crystal.ReflectionSpline
i1
i1(double) - Static method in class ffx.numerics.special.ModifiedBessel
Modified 1st-order Bessel function.
i1OverI0(double) - Static method in class ffx.numerics.special.ModifiedBessel
Compute the ratio of i1(x) to i0(x).
i2() - Method in class ffx.crystal.ReflectionSpline
i2
IAMOEBA_WATER - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
iComplex3D(int, int, int, int, int) - Static method in class ffx.numerics.fft.Complex3D
Determine the index of the complex number in the 1D array from the X, Y and Z indices.
id - Variable in class ffx.potential.bonded.BondedTerm
ID of this BondedTerm.
id - Variable in class ffx.ui.behaviors.MouseBehavior
 
identifyHullAtoms(QuickHull3D, Atom[]) - Static method in class ffx.potential.utils.ConvexHullOps
UNTESTED: Identifies atoms forming the convex hull.
IDLE - Enum constant in enum class edu.rit.pj.cluster.BackendInfo.State
The backend is available for jobs.
ifft(double[]) - Method in class ffx.numerics.fft.Complex3D
Compute the inverse 3D FFT.
ifft(double[]) - Method in class ffx.numerics.fft.Complex3DParallel
Compute the inverse 3D FFT in parallel.
ifft(double[]) - Method in class ffx.numerics.fft.Real3D
Compute the inverse 3D FFT.
ifft(double[]) - Method in class ffx.numerics.fft.Real3DParallel
Compute the inverse 3D FFT.
ifft(double[], int) - Method in class ffx.numerics.fft.Real
ifft
ifft(double[], int, int) - Method in class ffx.numerics.fft.Complex
Compute the (un-normalized) inverse FFT of data, leaving it in place.
ik - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Atom indices used only by LambdaFactorsESV::print.
il - Variable in class ffx.numerics.multipole.MultipoleTensor
Order plus one.
ILE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
im - Variable in class ffx.numerics.multipole.MultipoleTensor
im = (Order plus one)^2.
im() - Method in class ffx.numerics.math.ComplexNumber
im
im(double) - Method in class ffx.numerics.math.ComplexNumber
im
image(double[]) - Method in class ffx.crystal.Crystal
Apply the minimum image convention.
image(double[], double[]) - Method in class ffx.crystal.Crystal
Apply the minimum image convention.
image(double, double, double) - Method in class ffx.crystal.Crystal
Apply the minimum image convention.
ImplicitSolvent - Enum constant in enum class ffx.utilities.PropertyGroup
Implicit solvent functional form.
IMPROPER - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
IMPROPER - Enum constant in enum class ffx.potential.parameters.TorsionType.TorsionMode
 
ImproperTorsion - Class in ffx.potential.bonded
The ImproperTorsion class represents an Improper Torsion.
ImproperTorsionForce - Class in ffx.potential.openmm
OpenMM Improper Torsion Force.
ImproperTorsionForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.ImproperTorsionForce
Create an OpenMM Improper Torsion Force.
improperTorsionTime - Static variable in class ffx.potential.bonded.MSGroup
Constant torsionTorsionTime=0
ImproperTorsionType - Class in ffx.potential.parameters
The ImproperTorsionType class defines an improper torsion.
ImproperTorsionType(int[], double, double, int) - Constructor for class ffx.potential.parameters.ImproperTorsionType
TorsionType Constructor.
improperType - Variable in class ffx.potential.bonded.ImproperTorsion
Force field parameters to compute the ImproperTorsion energy.
IMPTORS - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
impTorUnit - Variable in class ffx.potential.parameters.ImproperTorsionType
Convert angle bending energy to kcal/mole.
in - Variable in class edu.rit.pj.cluster.BackendFileReader
Input stream for reading from the job frontend's standard input.
in - Variable in class ffx.numerics.multipole.MultipoleTensor
in = (Order plus one)^3.
in() - Static method in class edu.rit.io.Stdio
Get the standard input stream for the calling thread.
in(InputStream) - Static method in class edu.rit.io.Stdio
Set the standard input stream for the calling thread.
In - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
IN_PLANE - Enum constant in enum class ffx.potential.parameters.AngleType.AngleMode
 
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedByte
Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedCharacter
Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedDouble
Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedFloat
Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedInteger
Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedLong
Add one to this reduction variable and return the new value.
incrementAndGet() - Method in class edu.rit.pj.reduction.SharedShort
Add one to this reduction variable and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedByteArray
Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedFloatArray
Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedLongArray
Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedShortArray
Add one to this array reduction variable at the given index and return the new value.
incrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Add one to this matrix reduction variable at the given row and column and return the new value.
incrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Add one to this matrix reduction variable at the given row and column and return the new value.
incrementClasses(int) - Method in class ffx.potential.parameters.AngleTorsionType
incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.AngleType
incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.BondType
incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.ImproperTorsionType
incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.OutOfPlaneBendType
incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.PiOrbitalTorsionType
incrementClasses
incrementClasses(int) - Method in class ffx.potential.parameters.StretchBendType
Increment the atom classes by a given value.
incrementClasses(int) - Method in class ffx.potential.parameters.StretchTorsionType
Increment the atom classes by a specified amount.
incrementClasses(int) - Method in class ffx.potential.parameters.TorsionTorsionType
Increment the atom classes by a value.
incrementClasses(int) - Method in class ffx.potential.parameters.TorsionType
Increment the atom classes by a specified amount.
incrementClasses(int) - Method in class ffx.potential.parameters.UreyBradleyType
Increment the atom classes by a specified amount.
incrementClasses(int) - Method in class ffx.potential.parameters.VDWPairType
Increment the atom classes by a specified amount.
incrementType(int) - Method in class ffx.potential.parameters.ChargeType
incrementType
INDEPENDENT - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
 
independentWrite() - Method in class ffx.algorithms.thermodynamics.HistogramData
Returns the value of independentWrite.
index - Variable in class ffx.crystal.HKL
 
index - Variable in class ffx.potential.parameters.BioType
The index of this BioType.
index() - Method in record class ffx.utilities.DoubleIndexPair
Returns the value of the index record component.
index(int, int, int) - Method in class ffx.potential.nonbonded.SpatialDensityRegion
index
IndexIndexPair - Record Class in ffx.utilities
The IndexIndexPair record.
IndexIndexPair(int, int) - Constructor for record class ffx.utilities.IndexIndexPair
Creates an instance of a IndexIndexPair record class.
induced - Variable in class ffx.ui.commands.SimulationUpdate
 
inducedDipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.DirectRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.OPTRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.PermanentFieldRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.pme.SORRegion
Dimensions of [nsymm][nAtoms][3]
inducedDipole - Variable in class ffx.potential.nonbonded.ScfPredictor
Dimensions of [nsymm][nAtoms][3]
INDUCEDDIPOLE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.OPTRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.PermanentFieldRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.pme.SORRegion
 
inducedDipoleCR - Variable in class ffx.potential.nonbonded.ScfPredictor
 
InducedDipoleFieldReduceRegion - Class in ffx.potential.nonbonded.pme
Parallel summation and reduction of components of the induced dipole field at each atom.
InducedDipoleFieldReduceRegion(int) - Constructor for class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
 
InducedDipoleFieldRegion - Class in ffx.potential.nonbonded.pme
Parallel calculation of the induced dipole field.
InducedDipoleFieldRegion(ParallelTeam, ForceField, boolean) - Constructor for class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
 
InducedFileFilter - Class in ffx.potential.parsers
The InducedFileFilter class is used to choose a TINKER induced dipole (*.IND) file.
InducedFileFilter() - Constructor for class ffx.potential.parsers.InducedFileFilter
Default Constructor.
InducedFilter - Class in ffx.potential.parsers
The InducedFilter class parses TINKER Induced Dipole (*.*U) files.
InducedFilter(MolecularAssembly, File) - Constructor for class ffx.potential.parsers.InducedFilter
Constructor for InducedFilter.
InducedGKFieldRegion - Class in ffx.potential.nonbonded.implicit
Parallel calculation of the Generalized Kirkwood induced reaction field.
InducedGKFieldRegion(int, double, double, double) - Constructor for class ffx.potential.nonbonded.implicit.InducedGKFieldRegion
Compute the GK field due to induced dipoles.
inducedRealSpaceEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
inducedReciprocalEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
inducedSelfEnergy - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
info() - Method in class edu.rit.mp.Channel
Obtain this channel's information object.
info(Object) - Method in class edu.rit.mp.Channel
Set this channel's information object.
inInverseResSqRange(double) - Method in class ffx.crystal.Resolution
inInverseResSqRange
init() - Method in class ffx.algorithms.cli.AlgorithmsScript
Initialize this Script based on the specified command line arguments.
init() - Method in class ffx.algorithms.cli.DynamicsOptions
Parse the thermostat and integrator.
init() - Method in class ffx.potential.cli.PotentialCommand
Initialize this Script based on the specified command line arguments.
init() - Method in class ffx.potential.cli.PotentialScript
Initialize this Script based on the specified command line arguments.
init() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
init() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
 
init() - Method in class ffx.potential.nonbonded.pme.PMETimings
 
init() - Method in class ffx.utilities.FFXCommand
Initialize this Script based on the specified command line arguments.
init() - Method in class ffx.utilities.FFXScript
Initialize this Script based on the specified command line arguments.
init() - Method in class ffx.xray.cli.XrayOptions
Parse options.
init(boolean, boolean, Atom[], double[][][], MultipoleType.MultipoleFrameDefinition[], int[][], AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.pme.ReduceRegion
 
init(boolean, ExtendedSystem, Atom[], double[][][], Crystal, MultipoleType.MultipoleFrameDefinition[], int[][], double[][][], double[][][], double[][][], double[], double[], double[], double[], double[], boolean[], int[][][], int[][][], int[][][], AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.pme.InitializationRegion
 
init(int[][], MultipoleType.MultipoleFrameDefinition[], double[][][]) - Method in class ffx.potential.nonbonded.pme.Torque
 
init(int, Atom[], double[], double[][][], double[][][], double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, boolean, GeneralizedKirkwood, EwaldParameters, double) - Method in class ffx.potential.nonbonded.pme.OPTRegion
 
init(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics
A version of init with the original method header.
init(long, double, double, double, String, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics
init
init(long, double, double, double, String, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
init
init(DistanceMatrix, MolecularAssembly, Residue[], AlgorithmListener, double[][][][]) - Method in class ffx.algorithms.optimize.manybody.DistanceRegion
 
init(EnergyExpansion, Residue[], int[], boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
 
init(Atom[], boolean) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
Initialize this VolumeRegion instance for an energy evaluation.
init(Atom[], double[][][], double[][][], boolean, GeneralizedKirkwood, EwaldParameters, double, double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
 
init(Atom[], double[][][], double[][][], double[][][], Crystal, double[][][], int[][][], boolean[], double, double[], double[], boolean, ParallelTeam, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray) - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
init(Atom[], double[][][], double[][][], Crystal, double[][][], int[][][], boolean[], double, double[], AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.InducedGKFieldRegion
 
init(Atom[], double[][][], double[], double[], double[], boolean[], Crystal, double[][][], double[][][], double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, EwaldParameters, double, ParallelTeam, IntegerSchedule, long[]) - Method in class ffx.potential.nonbonded.pme.PCGSolver
 
init(Atom[], double[][][], Crystal, double[][][], int[][][], boolean[], double, double[], AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.PermanentGKFieldRegion
 
init(Atom[], double[], double[][][], double[][][], double[][], double[][], double[][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, boolean, GeneralizedKirkwood, EwaldParameters) - Method in class ffx.potential.nonbonded.pme.SORRegion
 
init(Atom[], double[], double[][][], double[][], double) - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
 
init(Atom[], double[], double[][][], double[][], AtomicDoubleArray3D, AtomicDoubleArray3D, boolean, GeneralizedKirkwood, EwaldParameters, double, double[][][], double[][][], double[][], double[][], double[][], double[][]) - Method in class ffx.potential.nonbonded.pme.DirectRegion
 
init(Atom[], Crystal, boolean[], int[][][], double[], double[], double[], double, boolean, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
Initialize the DispersionRegion for energy calculation.
init(Atom[], Crystal, boolean[], int[], double[], double[], double[][][], RealSpaceNeighborParameters, double[][][], double[][][], boolean, ReciprocalSpace, LambdaMode, EwaldParameters, AtomicDoubleArray3D, AtomicDoubleArray3D, PMETimings) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
 
init(Atom[], Crystal, boolean, boolean, boolean, boolean[], double[][][], double[][][], double[][][], double[][][], double[][], double[][], Polarization, double[][][], double[][][], double[][], double[][], double[][], double[][], ReciprocalSpace, AlchemicalParameters, ExtendedSystem, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, SharedDouble, SharedDouble) - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
init(Atom[], Crystal, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
 
init(Atom[], Crystal, double[][][], double[][][], double[][][], double[][][], int[][][], ScaleParameters, boolean[], int[], double[], double[], int[][], int[][], int[][], int[][], LambdaMode, boolean, ReciprocalSpace, EwaldParameters, PCGSolver, IntegerSchedule, RealSpaceNeighborParameters, AtomicDoubleArray3D, AtomicDoubleArray3D, PMETimings) - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion
 
init(Atom[], Crystal, double[][][], int[][][], double[], double[], double[], double[], double, boolean[], double, boolean, double[]) - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
 
init(Atom[], Crystal, double[][][], int[][][], double[], double[], double[], double[], double, double[], boolean[], double, boolean, double[], AtomicDoubleArray3D, AtomicDoubleArray) - Method in class ffx.potential.nonbonded.implicit.BornGradRegion
 
init(Atom[], Crystal, ExtendedSystem, boolean, double[][][], MultipoleType.MultipoleFrameDefinition[], int[][], double[][][], double[][][], double[][][], double[][][], double[][][], boolean[], int[], int[][], int[][], int[][], int[][], int[][], boolean[], double[], double[], RealSpaceNeighborParameters, boolean, boolean, boolean, LambdaMode, Polarization, EwaldParameters, ScaleParameters, AlchemicalParameters, long[], AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray3D, SharedDouble, SharedDouble) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
init(Residue[], int, int, int, int, int, int, int[][], RotamerOptimization) - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
Initializes a ParallelRegion to attempt the elimination of riA,rjC by riB,rjD.
init(GeneralizedKirkwood, Atom[], boolean, AtomicDoubleArray3D, AtomicDoubleArray3D, AtomicDoubleArray) - Method in class ffx.potential.nonbonded.implicit.InitializationRegion
 
init(ForceField) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters
 
init(String[]) - Static method in class edu.rit.pj.Comm
Initialize the PJ message passing middleware.
initBorn(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyGlobal
 
initBorn(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyQI
 
initEsvIndElec() - Method in class ffx.potential.extended.ExtendedSystem
Zero out each array element of the indElec ESV array
initEsvPermElec() - Method in class ffx.potential.extended.ExtendedSystem
Zero out each array element of the permElec ESV array
initEsvVdw() - Method in class ffx.potential.extended.ExtendedSystem
Zero out each array element of the vdW ESV array
InitializationRegion - Class in ffx.potential.nonbonded.implicit
Parallel initialization of accumulation arrays for Generalized Kirkwood.
InitializationRegion - Class in ffx.potential.nonbonded.pme
Parallel initialization of accumulation arrays, expand atomic coordinates and rotation of multipoles into the global frame.
InitializationRegion(int) - Constructor for class ffx.potential.nonbonded.implicit.InitializationRegion
 
InitializationRegion(ParticleMeshEwald, int, ForceField) - Constructor for class ffx.potential.nonbonded.pme.InitializationRegion
 
initialize() - Method in class ffx.potential.Renderer
initialize() - Method in class ffx.ui.behaviors.MouseBehavior
initialize
initialize() - Method in class ffx.ui.behaviors.MouseOrbit
initialize
initialize() - Method in class ffx.ui.behaviors.MouseProperties
initialize
initialize() - Method in class ffx.ui.behaviors.MouseRotate
initialize
initialize() - Method in class ffx.ui.behaviors.MouseSelection
initialize
initialize() - Method in class ffx.ui.behaviors.MouseTranslate
initialize
initialize() - Method in class ffx.ui.behaviors.MouseZoom
initialize
initialize() - Method in class ffx.ui.behaviors.PickMouseBehavior
initialize
initialize() - Method in class ffx.ui.GraphicsEvents
initialize
initialize() - Method in class ffx.ui.MainPanel
initialize
initializeDefaultAtomicCoordinates() - Method in class ffx.potential.bonded.Residue
Initializes this (presumably nucleic acid) Residue's C1s, O4s, C4s, O3sNorth, and O3sSouth default coordinates based on default PDB atom locations; to preserve rotamer independence, this must be called before any NA rotamers are applied.
initializeDefaultAtomicCoordinates(Polymer[]) - Static method in class ffx.potential.bonded.RotamerLibrary
Initializes default coordinates (presently PDB coordinates) for key atoms in all nucleic acid Residues.
initialState - Variable in class ffx.algorithms.dynamics.MolecularDynamics
State of the system as of the last init call (and start of the last dynamics run).
initMain(String[], List<String>) - Static method in class ffx.Main
Process the input arguments into a List, start the logging, start Parallel Java and process the input command.
initPotential(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyGlobal
 
initPotential(double[], double, double, double) - Method in class ffx.numerics.multipole.GKEnergyQI
 
initRotamerOptimization(RotamerOptimization, MolecularAssembly) - Method in class ffx.algorithms.cli.ManyBodyOptions
initRotamerOptimization.
initTiming() - Method in class ffx.numerics.fft.Complex3DParallel
 
initTimings() - Method in class ffx.potential.nonbonded.ReciprocalSpace
initTimings.
initVelocities - Variable in class ffx.algorithms.dynamics.MolecularDynamics
Flag to indicate velocities should be initialized.
InPlaneAngleForce - Class in ffx.potential.openmm
OpenMM In-Plane Angle Force.
InPlaneAngleForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.InPlaneAngleForce
Create an OpenMM Angle Force.
input - Variable in class ffx.numerics.fft.Complex3DParallel
 
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.FrontendFileReader
Close the given input file.
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontend
Close the given input file.
inputFileClose(JobBackendRef, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage
Construct a new "input file close" message.
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy
Close the given input file.
inputFileClose(JobBackendRef, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef
Close the given input file.
inputFileClose(JobBackendRef, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Close the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader
Report the result of closing the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend
Report the result of closing the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage
Construct a new "input file close result" message.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy
Report the result of closing the given input file.
inputFileCloseResult(JobFrontendRef, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef
Report the result of closing the given input file.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.FrontendFileReader
Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.JobFrontend
Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Static method in class edu.rit.pj.cluster.JobFrontendMessage
Construct a new "input file open" message.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.JobFrontendProxy
Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Method in interface edu.rit.pj.cluster.JobFrontendRef
Open the given input file for reading.
inputFileOpen(JobBackendRef, int, File) - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Open the given input file for reading.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader
Report the result of opening the given input file.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.JobBackend
Report the result of opening the given input file.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage
Construct a new "input file open result" message.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy
Report the result of opening the given input file.
inputFileOpenResult(JobFrontendRef, int, int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef
Report the result of opening the given input file.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.FrontendFileReader
Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.JobFrontend
Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage
Construct a new "input file read" message.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy
Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef
Read bytes from the given input file.
inputFileRead(JobBackendRef, int, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Read bytes from the given input file.
inputFileReadResult(JobFrontendRef, int, byte[], int, IOException) - Method in class edu.rit.pj.cluster.JobBackend
Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, byte[], int, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy
Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, byte[], int, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef
Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, int, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader
Report the result of reading the given input file.
inputFileReadResult(JobFrontendRef, int, int, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage
Construct a new "input file read result" message.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.FrontendFileReader
Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.JobFrontend
Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Static method in class edu.rit.pj.cluster.JobFrontendMessage
Construct a new "input file skip" message.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.JobFrontendProxy
Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Method in interface edu.rit.pj.cluster.JobFrontendRef
Skip bytes from the given input file.
inputFileSkip(JobBackendRef, int, long) - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Skip bytes from the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in class edu.rit.pj.cluster.BackendFileReader
Report the result of skipping the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in class edu.rit.pj.cluster.JobBackend
Report the result of skipping the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Static method in class edu.rit.pj.cluster.JobBackendMessage
Construct a new "input file skip result" message.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in class edu.rit.pj.cluster.JobBackendProxy
Report the result of skipping the given input file.
inputFileSkipResult(JobFrontendRef, int, long, IOException) - Method in interface edu.rit.pj.cluster.JobBackendRef
Report the result of skipping the given input file.
inResolutionRange(double) - Method in class ffx.crystal.Resolution
inResolutionRange
insert(int) - Method in class ffx.openmm.IntSet
Insert a value into the set.
insertUpdate(DocumentEvent) - Method in class ffx.ui.KeywordComponent
Instance - Class in edu.rit.util
Class Instance provides static methods for creating instances of classes.
INT - Enum constant in enum class ffx.potential.Utilities.FileType
 
IntArray - Class in ffx.openmm
Int Array.
IntArray(int) - Constructor for class ffx.openmm.IntArray
Constructor.
Integer() - Constructor for class edu.rit.util.Searching.Integer
 
Integer() - Constructor for class edu.rit.util.Sorting.Integer
 
IntegerArrayBuf - Class in edu.rit.mp.buf
Class IntegerArrayBuf provides a buffer for an array of integer items sent or received using the Message Protocol (MP).
IntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.IntegerArrayBuf
Construct a new integer array buffer.
IntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class IntegerArrayBuf_1 provides a buffer for an array of integer items sent or received using the Message Protocol (MP).
IntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.IntegerArrayBuf_1
Construct a new integer array buffer.
IntegerBuf - Class in edu.rit.mp
Class IntegerBuf is the abstract base class for a buffer of integer items sent or received using the Message Protocol (MP).
IntegerBuf(int) - Constructor for class edu.rit.mp.IntegerBuf
Construct a new integer buffer.
IntegerForLoop - Class in edu.rit.pj
Class IntegerForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
IntegerForLoop() - Constructor for class edu.rit.pj.IntegerForLoop
Construct a new parallel for loop.
IntegerItemBuf - Class in edu.rit.mp.buf
Class IntegerItemBuf provides a buffer for a single integer item sent or received using the Message Protocol (MP).
IntegerItemBuf() - Constructor for class edu.rit.mp.buf.IntegerItemBuf
Construct a new integer item buffer.
IntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.IntegerItemBuf
Construct a new integer item buffer with the given initial value.
IntegerMatrixBuf - Class in edu.rit.mp.buf
Class IntegerMatrixBuf provides a buffer for a matrix of integer items sent or received using the Message Protocol (MP).
IntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.IntegerMatrixBuf
Construct a new integer matrix buffer.
IntegerMatrixBuf_1 - Class in edu.rit.mp.buf
Class IntegerMatrixBuf_1 provides a buffer for a matrix of integer items sent or received using the Message Protocol (MP).
IntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.IntegerMatrixBuf_1
Construct a new integer matrix buffer.
IntegerOp - Class in edu.rit.pj.reduction
Class IntegerOp is the abstract base class for a binary operation on integer values, used to do reduction in a parallel program.
IntegerOp() - Constructor for class edu.rit.pj.reduction.IntegerOp
Construct a new integer binary operation.
IntegerSchedule - Class in edu.rit.pj
Class IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.
IntegerSchedule() - Constructor for class edu.rit.pj.IntegerSchedule
Construct a new schedule object.
IntegerStrideForLoop - Class in edu.rit.pj
Class IntegerStrideForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
IntegerStrideForLoop() - Constructor for class edu.rit.pj.IntegerStrideForLoop
Construct a new parallel for loop.
integralAt(double) - Method in class ffx.numerics.integrate.CompositeCurve
Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.CosineWave
Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.FunctionDataCurve
Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.PolynomialCurve
Analytical integral at a point.
integralAt(double) - Method in class ffx.numerics.integrate.SinWave
Analytical integral at a point.
integrate(int) - Method in class ffx.potential.openmm.OpenMMContext
Use the Context / Integrator combination to take the requested number of steps.
Integrate1DNumeric - Class in ffx.numerics.integrate
This program integrates using four methods: rectangular integration, the trapezoidal method, Simpson's Three Point Integration, and Boole's Five Point Integration.
Integrate1DNumeric() - Constructor for class ffx.numerics.integrate.Integrate1DNumeric
 
Integrate1DNumeric.IntegrationSide - Enum Class in ffx.numerics.integrate
Left vs right-hand integration; left-hand integration will start from the first available point, run right as far as possible, and then clean up any remaining points using finishIntegration, while right-hand integration will start from the last available point, run left as far as possible, and then clean up any remaining points using finishIntegration.
Integrate1DNumeric.IntegrationType - Enum Class in ffx.numerics.integrate
Enumeration of implemented integration methods, and the number of points required by them.
integrateByBins(DataSet, Integrate1DNumeric.IntegrationSide, Integrate1DNumeric.IntegrationType) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Returns the contribution of each bin to the overall integral as an array; will be most accurate at break-points for the integration type.
integrateData(DataSet, Integrate1DNumeric.IntegrationSide, Integrate1DNumeric.IntegrationType) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Generic caller for 1D integration schemes given an IntegrationType.
integrateTransforms() - Method in class ffx.ui.behaviors.GlobalBehavior
integrateTransforms
Integration - Class in ffx.numerics.integrate
This program integrates using three methods: the trapezoidal method, Simpson's Three Point Integration, and Boole's Five Point Integration
Integration() - Constructor for class ffx.numerics.integrate.Integration
 
integrator - Variable in class ffx.algorithms.cli.DynamicsOptions
Integrator.
Integrator - Class in ffx.algorithms.dynamics.integrators
The Integrator class is responsible for propagation of degrees of freedom through time.
Integrator - Class in ffx.openmm
An Integrator defines a method for simulating a System by integrating the equations of motion.
Integrator() - Constructor for class ffx.openmm.Integrator
Constructor.
Integrator(SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.Integrator
Constructor for Integrator.
IntegratorEnum - Enum Class in ffx.algorithms.dynamics.integrators
An enumeration of available integrators.
intensitiesToAmplitudes() - Method in class ffx.xray.DiffractionRefinementData
Generate amplitudes from intensities.
interfacialRadiusA - Variable in class ffx.crystal.Crystal
Interfacial radius in the direction of the A-axis.
interfacialRadiusB - Variable in class ffx.crystal.Crystal
Interfacial radius in the direction of the B-axis.
interfacialRadiusC - Variable in class ffx.crystal.Crystal
Interfacial radius in the direction of the C-axis.
intermolecular - Variable in class ffx.ui.commands.SimulationUpdate
 
interResidueDistance(double[][], double[][], SymOp) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Calculates the minimum distance between two sets of coordinates in a given symmetry operator.
interrupt() - Method in class ffx.ui.SwingWorker
A new method that interrupts the worker thread.
INTFileFilter - Class in ffx.potential.parsers
The INTFileFilter class is used to choose TINKER Internal Coordinate (*.INT) files.
INTFileFilter() - Constructor for class ffx.potential.parsers.INTFileFilter
Default Constructor.
INTFilter - Class in ffx.potential.parsers
The INTFilter class parses TINKER internal coordinate (*.INT) files.
INTFilter(File, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.INTFilter
Constructor for INTFilter.
INTFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.INTFilter
Constructor for INTFilter.
IntplnErr - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult
 
intra12Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters
An intra-12-scale factor other than 0.0 is not supported and will cause FFX to exit.
intra13Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters
An intra-13-scale factor other than 0.0 is not supported and will cause FFX to exit.
intra14Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters
Provides a multiplicative scale factor that is applied to polarization interactions between 1-4 connected atoms located in the same polarization group.
intra15Scale - Variable in class ffx.potential.nonbonded.pme.ScaleParameters
An intra-15-scale factor other than 1.0 is not supported and will cause FFX to exit.
IntSet - Class in ffx.openmm
Int Set.
IntSet() - Constructor for class ffx.openmm.IntSet
Constructor.
intToProteinLibrary(int) - Static method in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary
Converts an integer to a corresponding ProteinLibrary.
intValue() - Method in class edu.rit.pj.reduction.SharedByte
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedCharacter
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedDouble
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedFloat
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedInteger
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedLong
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.reduction.SharedShort
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedByte
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedDouble
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedFloat
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedInteger
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedLong
Returns this reduction variable's current value converted to type int.
intValue() - Method in class edu.rit.pj.replica.ReplicatedShort
Returns this reduction variable's current value converted to type int.
intxyz(Atom, Atom, double, Atom, double, Atom, double, int) - Static method in class ffx.potential.bonded.BondedUtils
This routine was derived from a similar routine in TINKER.
InvalidMatrixFileException - Exception Class in edu.rit.io
Class InvalidMatrixFileException provides an exception thrown when the contents of a matrix file are invalid.
InvalidMatrixFileException() - Constructor for exception class edu.rit.io.InvalidMatrixFileException
Construct a new invalid matrix file exception with no detail message and no cause.
InvalidMatrixFileException(String) - Constructor for exception class edu.rit.io.InvalidMatrixFileException
Construct a new invalid matrix file exception with the given detail message and no cause.
InvalidMatrixFileException(String, Throwable) - Constructor for exception class edu.rit.io.InvalidMatrixFileException
Construct a new invalid matrix file exception with the given detail message and the given cause.
InvalidMatrixFileException(Throwable) - Constructor for exception class edu.rit.io.InvalidMatrixFileException
Construct a new invalid matrix file exception with the given cause and the default detail message.
inverse(double[], int) - Method in class ffx.numerics.fft.Real
inverse
inverse(double[], int, int) - Method in class ffx.numerics.fft.Complex
Compute the normalized inverse FFT of data, leaving it in place.
inverseResSqLimit() - Method in class ffx.crystal.Resolution
inverseResSqLimit
invert - Variable in class ffx.ui.behaviors.MouseBehavior
 
INVERT_INPUT - Static variable in class ffx.ui.behaviors.MouseBehavior
Constant INVERT_INPUT=0x2
invertSymOp(SymOp) - Static method in class ffx.crystal.SymOp
Invert a symmetry operator.
INVISIBLE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
invoke(JobBackendRef, JobFrontendRef) - Method in class edu.rit.pj.cluster.JobBackendMessage
Invoke the method corresponding to this job backend message on the given Job Backend object.
invoke(JobFrontendRef, JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontendMessage
Invoke the method corresponding to this job frontend message on the given Job Frontend object.
invoke(JobFrontendRef, JobSchedulerRef) - Method in class edu.rit.pj.cluster.JobFrontendMessage
Invoke the method corresponding to this job frontend message on the given Job Frontend object.
invoke(JobSchedulerRef, JobFrontendRef) - Method in class edu.rit.pj.cluster.JobSchedulerMessage
Invoke the method corresponding to this job scheduler message on the given Job Scheduler object.
invressq(HKL) - Method in class ffx.crystal.Crystal
invressq
IORequest - Class in edu.rit.mp
Class IORequest encapsulates the state of a message being sent or received in the Message Protocol (MP).
IORequest() - Constructor for class edu.rit.mp.IORequest
Construct a new I/O request object.
ip11 - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Polarization groups.
ip11 - Variable in class ffx.potential.nonbonded.pme.PermanentFieldRegion
Polarization groups.
ip11 - Variable in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
Polarization groups.
ip12 - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
ip13 - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
Ir - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
iReal3D(int, int, int, int, int) - Static method in class ffx.numerics.fft.Real3D
Determine the index of the real number in the 1D array from the X, Y and Z indices.
is_1_3(Atom) - Method in class ffx.potential.bonded.Atom
is_1_3
is_1_4(Atom) - Method in class ffx.potential.bonded.Atom
Are these atoms 1-4 bonded?
is_1_5(Atom) - Method in class ffx.potential.bonded.Atom
Are these atoms 1-5 bonded?
is_1_6(Atom) - Method in class ffx.potential.bonded.Atom
Are these atoms 1-6 bonded?
is_1_7(Atom) - Method in class ffx.potential.bonded.Atom
Are these atoms 1-7 bonded?
is_1_8(Atom) - Method in class ffx.potential.bonded.Atom
Are these atoms 1-8 bonded?
is_12_or_13(Atom) - Method in class ffx.potential.bonded.Atom
is_12_or_13
isActive() - Method in class ffx.algorithms.dynamics.Barostat
 
isActive() - Method in class ffx.potential.bonded.Atom
If active, the coordinates of this atom can be modified.
isActive() - Method in class ffx.ui.KeywordComponent
isActive
isAlive() - Method in class ffx.ui.commands.FFXServer
isAlive
isAlive() - Method in class ffx.ui.FFXExec
isAlive
isARC(File) - Static method in class ffx.potential.parsers.ARCFileFilter
This is a static version of the accept method.
isArmed() - Method in class ffx.potential.Renderer
Check to see if a graphics operation is pending/executing
isAtomSelectionSet() - Method in class ffx.potential.cli.AtomSelectionOptions
Check if either the active or inactive atom selection is set.
isBonded(Atom) - Method in class ffx.potential.bonded.Atom
Checks to see if an Atom is bonded to this Atom
isCacheFull() - Method in class ffx.potential.Renderer
isCacheFull
isClosed() - Method in class ffx.ui.commands.FFXClient
isClosed
isClosing() - Method in class ffx.ui.FFXSystem
isClosing
isConnected() - Method in class ffx.ui.commands.FFXClient
isConnected
isConnected() - Method in class ffx.ui.SimulationLoader
isConnected
isConstantPhTautomer - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
isConstantPhTitratable - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
isConstrained() - Method in class ffx.potential.bonded.BondedTerm
Check if this BondedTerm is constrained.
isContinuous() - Method in class ffx.algorithms.mc.LambdaMove
If true, do continuous moves.
isCosine() - Method in class ffx.numerics.switching.SquaredTrigSwitch
Return true if a cos^2(ax) transform, false if a sin^2(ax) transform.
isDecompose() - Method in class ffx.algorithms.cli.ManyBodyOptions
-E or --decompose Print energy decomposition for the input structure (no optimization).
isDee() - Method in class ffx.algorithms.cli.ManyBodyOptions
Use dead-end elimination criteria instead of Goldstein criteria.
isDeuterium() - Method in class ffx.potential.bonded.Atom
isDeuterium
isDYN(File) - Static method in class ffx.potential.parsers.DYNFileFilter
This is a static version of the accept method.
isExecutingInParallel() - Method in class edu.rit.pj.ParallelConstruct
Determine if a parallel team is executing this parallel construct.
isExecutingInParallel() - Method in class edu.rit.pj.ParallelTeam
Determine if this parallel team is executing a parallel region.
isExecutingInParallel() - Method in class edu.rit.pj.WorkerConstruct
Determine if a worker team is executing this worker construct.
isExecutingInParallel() - Method in class edu.rit.pj.WorkerTeam
Determine if this worker team is executing a worker region.
isFinalized() - Method in class ffx.potential.bonded.MSGroup
Returns true if the MultiScaleGroup is finalized.
isFinalized() - Method in class ffx.potential.bonded.MultiResidue
Returns true if the MultiScaleGroup is finalized.
isFinished() - Method in class edu.rit.mp.IORequest
Determine if this I/O request has finished.
isFinished() - Method in class edu.rit.pj.CommRequest
Determine if the message passing operation associated with this CommRequest object has finished.
isFixedSchedule() - Method in class edu.rit.pj.IntegerSchedule
Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class edu.rit.pj.LongSchedule
Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.potential.nonbonded.PairwiseSchedule
Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.potential.nonbonded.SpatialDensitySchedule
Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.xray.GradientSchedule
Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.xray.RowSchedule
Determine if this schedule is a fixed schedule.
isFixedSchedule() - Method in class ffx.xray.SliceSchedule
Determine if this schedule is a fixed schedule.
isForceFieldType(String) - Static method in class ffx.potential.parameters.ForceField
Check if a keyword is a force field type.
isFreeR(int, int) - Method in class ffx.xray.DiffractionRefinementData
isFreeR
isHalogen() - Method in class ffx.potential.bonded.Atom
Check if this atom is a Halogen (F, Cl, Br, I)
isHeavy() - Method in class ffx.potential.bonded.Atom
isHeavy checks whether this Atom is a heavy (non-hydrogen) atom.
isHetero() - Method in class ffx.potential.bonded.Atom
isHetero
isHydrogen() - Method in class ffx.potential.bonded.Atom
isHydrogen
isIndependentWalkers() - Method in class ffx.algorithms.cli.OSTOptions
Enforces that each walker maintains their own histogram.
isINT(File) - Static method in class ffx.potential.parsers.INTFileFilter
This is a static version of the accept method.
isIsotropic() - Method in class ffx.algorithms.cli.BarostatOptions
Restrict the MC Barostat to isotropic moves.
isIsotropic() - Method in class ffx.algorithms.dynamics.Barostat
Restrict the MC Barostat to isotropic moves.
isKeyword(String) - Method in class ffx.ui.KeywordPanel
isKeyword
isLambdaScaled() - Method in class ffx.potential.bonded.BondedTerm
Check if this BondedTerm is lambda-sensitive (e.g., a softcore dihedral).
isLambdaScaled() - Method in class ffx.potential.bonded.RestraintBond
 
isLocal() - Method in interface ffx.potential.utils.PotentialsFunctions
True if using a local implementation (not in a user interfaces module).
isLocal() - Method in class ffx.potential.utils.PotentialsUtils
True if using a local implementation (not in a user interfaces module).
isLocal() - Method in class ffx.ui.UIUtils
 
isMasterThread() - Method in class edu.rit.pj.WorkerConstruct
Determine if the calling thread is the master thread in the worker team executing this worker construct.
isMcHardWall() - Method in class ffx.algorithms.cli.OSTOptions
The Monte Carlo scheme can use a hard wall that rejects any sample (Lambda, dU/dL) located in an empty histogram bin.
isMetaDynamics() - Method in class ffx.algorithms.cli.OSTOptions
Use a MetaDynamics style bias.
isModRes() - Method in class ffx.potential.bonded.Atom
isModRes
isMonteCarlo() - Method in class ffx.algorithms.cli.OSTOptions
Checks if the use of the Monte Carlo algorithm has been specified.
isNeuralNetwork() - Method in class ffx.potential.bonded.Atom
If true, this atom is part of a molecule whose intramolecular interactions are handled by a neural network.
isNeuralNetwork() - Method in class ffx.potential.bonded.BondedTerm
This method returns true if any atom is marked as being part of a neural network.
isNeutron() - Method in class ffx.xray.parsers.DiffractionFile
is this a neutron dataset?
isNewer(SimulationMessage) - Method in class ffx.ui.commands.SimulationUpdate
isNewer
isNoOriginal() - Method in class ffx.algorithms.cli.ManyBodyOptions
Do not include starting coordinates as their own rotamer.
ISOLEUCINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
isOptimize() - Method in class ffx.algorithms.cli.DynamicsOptions
Saves low-energy snapshots discovered (only for single topology simulations).
isPDB(File) - Static method in class ffx.potential.parsers.PDBFileFilter
This is a static version of the accept method.
isPickingActive() - Method in class ffx.ui.MainMenu
isPickingActive
isqrt(double) - Static method in class ffx.numerics.math.SquareRoot
Compute the inverse square root 1.0/sqrt(x2) of the input value x2 using a look-up table and two iterations of Newton's method for finding roots of an equation.
isQuiet() - Method in enum class ffx.algorithms.dynamics.MDVerbosity
 
isRefineMolOcc() - Method in class ffx.xray.DiffractionData
isRefineMolOcc.
isReinitVelocities() - Method in class ffx.algorithms.cli.AnnealOptions
Forces simulated annealing to re-initialize velocities to the new temperature at each annealing step, rather than letting the thermostat shift temperature downwards.
isResetNumSteps() - Method in class ffx.algorithms.cli.ThermodynamicsOptions
Ignores steps detected in .lam lambda-restart files.
isRevert() - Method in class ffx.algorithms.cli.ManyBodyOptions
Revert unfavorable changes.
isRing(Atom) - Method in class ffx.potential.bonded.Atom
Determine if atom is in a ring with second atom WARNING: Does not work for 8+ membered rings...
isSaveOutput() - Method in class ffx.algorithms.cli.ManyBodyOptions
Save eliminated singles and eliminated pairs to a text file (global and box optimization).
isSelected() - Method in class ffx.potential.bonded.MSNode
isSelected
isSohnckeGroup(int) - Static method in class ffx.crystal.SpaceGroupInfo
Sohncke groups respect chiral molecules (i.e., non-enantiogenic) and include space group numbers: 1, 3-5, 16-24, 75-80, 89-98, 143-146, 149-155, 168-173, 177-182, 195-199 and 207-214.
isSpecialPosition() - Method in class ffx.potential.bonded.Atom
If true, this atom is at a special position.
isSpecialPositionSymOp(int) - Method in class ffx.potential.bonded.Atom
If true, this atom is at a special position for the specified symmetry operation.
isStale() - Method in class ffx.potential.bonded.Atom
isStale
isStale() - Method in class ffx.ui.FFXSystem
isStale
isStarted() - Method in class edu.rit.util.Timer
Determine whether this timer is started.
isState - Variable in class ffx.potential.bonded.Rotamer
Flag to indicate the rotamer was initialized from a Residue state.
isStochastic(IntegratorEnum) - Static method in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
 
isStopped() - Method in class edu.rit.util.Timer
Determine whether this timer is stopped.
isSupported(Platform) - Method in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
Checks if this platform is supported
isSynchronous() - Method in class ffx.algorithms.cli.MultiDynamicsOptions
Synchronous walker communication.
isTautomer(Residue) - Method in class ffx.potential.extended.ExtendedSystem
Returns the tautomerizibility of a residue
isTautomerizing(int) - Method in class ffx.potential.extended.ExtendedSystem
Returns whether an atom is tautomerizing
isTcpPortAvailable(int) - Static method in class ffx.utilities.PortUtils
Check if a port is available.
isThreeBody() - Method in class ffx.algorithms.cli.ManyBodyOptions
-T or --threeBody Include 3-Body interactions in the elimination criteria.
isTitratable(Residue) - Method in class ffx.potential.extended.ExtendedSystem
Returns the titratibility of the passed residue
isTitrating - Variable in class ffx.potential.bonded.Rotamer
If this flag is set, application of a rotamer requires updating force field parameters.
isTitrating() - Method in class ffx.algorithms.cli.ManyBodyOptions
 
isTitrating(int) - Method in class ffx.potential.extended.ExtendedSystem
Returns whether an atom is titrating
isTitratingHeavy(int) - Method in class ffx.potential.extended.ExtendedSystem
Questions whether the current non-hydrogen atom's polarizability is changing in response to lambda being updated.
isTitratingHeavy(AminoAcidUtils.AminoAcid3, Atom) - Static method in class ffx.potential.parameters.TitrationUtils
Used to keep track of heavy atoms with changing polarizability.
isTitratingHydrogen(int) - Method in class ffx.potential.extended.ExtendedSystem
Questions whether the current hydrogen's polarizability is changing in response to lambda being updated.
isTitratingHydrogen(AminoAcidUtils.AminoAcid3, Atom) - Static method in class ffx.potential.parameters.TitrationUtils
 
isTriggered() - Method in class edu.rit.util.Timer
Determine whether this timer is triggered.
isTrigonal() - Method in class ffx.potential.bonded.Atom
isTrigonal
isTwoStep() - Method in class ffx.algorithms.cli.OSTOptions
Returns true if the 2-step option is enabled (not guaranteed to also mean that MC is enabled!).
isUse_3g() - Method in class ffx.xray.DiffractionData
isUse_3g.
isValid() - Method in class edu.rit.http.HttpRequest
Determine if this HTTP request is valid.
isVisible() - Method in class ffx.potential.bonded.Atom
isVisible
isVisible() - Method in class ffx.potential.MolecularAssembly
isVisible
isXYZ(File) - Static method in class ffx.potential.parsers.XYZFileFilter
This is a static version of the accept method.
iSymm - Variable in class ffx.potential.nonbonded.NeighborList.AtomIndex
 
item - Variable in class edu.rit.mp.buf.BooleanItemBuf
Boolean item to be sent or received.
item - Variable in class edu.rit.mp.buf.ByteItemBuf
Byte item to be sent or received.
item - Variable in class edu.rit.mp.buf.CharacterItemBuf
Character item to be sent or received.
item - Variable in class edu.rit.mp.buf.DoubleItemBuf
Double item to be sent or received.
item - Variable in class edu.rit.mp.buf.FloatItemBuf
Float item to be sent or received.
item - Variable in class edu.rit.mp.buf.IntegerItemBuf
Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.LongItemBuf
Long item to be sent or received.
item - Variable in class edu.rit.mp.buf.ObjectItemBuf
Object item to be sent or received.
item - Variable in class edu.rit.mp.buf.ShortItemBuf
Short item to be sent or received.
item - Variable in class edu.rit.mp.buf.Signed16BitIntegerItemBuf
Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.Signed8BitIntegerItemBuf
Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf
Integer item to be sent or received.
item - Variable in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf
Integer item to be sent or received.
iterativeClustering(List<double[]>, int, double) - Static method in class ffx.potential.utils.Clustering
Perform an iterative clustering for a specified number of clusters.
iterator() - Method in class edu.rit.pj.job.JobGenerator
Get an iterator for generating the jobs in the job group.

J

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

K

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

L

l - Variable in class ffx.crystal.HKL
 
L - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
L111 - Enum constant in enum class ffx.crystal.LaueSystem
 
L112 - Enum constant in enum class ffx.crystal.LaueSystem
 
L113 - Enum constant in enum class ffx.crystal.LaueSystem
 
L114 - Enum constant in enum class ffx.crystal.LaueSystem
 
L11T - Enum constant in enum class ffx.crystal.LaueSystem
 
L121 - Enum constant in enum class ffx.crystal.LaueSystem
 
L131 - Enum constant in enum class ffx.crystal.LaueSystem
 
L141 - Enum constant in enum class ffx.crystal.LaueSystem
 
L1T1 - Enum constant in enum class ffx.crystal.LaueSystem
 
L211 - Enum constant in enum class ffx.crystal.LaueSystem
 
L21U - Enum constant in enum class ffx.crystal.LaueSystem
 
L21V - Enum constant in enum class ffx.crystal.LaueSystem
 
L21W - Enum constant in enum class ffx.crystal.LaueSystem
 
L21X - Enum constant in enum class ffx.crystal.LaueSystem
 
L21Y - Enum constant in enum class ffx.crystal.LaueSystem
 
L21Z - Enum constant in enum class ffx.crystal.LaueSystem
 
L222 - Enum constant in enum class ffx.crystal.LaueSystem
 
L223 - Enum constant in enum class ffx.crystal.LaueSystem
 
L224 - Enum constant in enum class ffx.crystal.LaueSystem
 
L22U - Enum constant in enum class ffx.crystal.LaueSystem
 
L22V - Enum constant in enum class ffx.crystal.LaueSystem
 
L22W - Enum constant in enum class ffx.crystal.LaueSystem
 
L232 - Enum constant in enum class ffx.crystal.LaueSystem
 
L242 - Enum constant in enum class ffx.crystal.LaueSystem
 
l2Error(double[], double[]) - Method in class ffx.potential.nonbonded.octree.Octree
Compute the L2 error.
L311 - Enum constant in enum class ffx.crystal.LaueSystem
 
L31A - Enum constant in enum class ffx.crystal.LaueSystem
 
L31B - Enum constant in enum class ffx.crystal.LaueSystem
 
L31C - Enum constant in enum class ffx.crystal.LaueSystem
 
L31D - Enum constant in enum class ffx.crystal.LaueSystem
 
L322 - Enum constant in enum class ffx.crystal.LaueSystem
 
L32A - Enum constant in enum class ffx.crystal.LaueSystem
 
L32B - Enum constant in enum class ffx.crystal.LaueSystem
 
L32C - Enum constant in enum class ffx.crystal.LaueSystem
 
L32D - Enum constant in enum class ffx.crystal.LaueSystem
 
L32U - Enum constant in enum class ffx.crystal.LaueSystem
 
L32V - Enum constant in enum class ffx.crystal.LaueSystem
 
L32W - Enum constant in enum class ffx.crystal.LaueSystem
 
L32X - Enum constant in enum class ffx.crystal.LaueSystem
 
L32Y - Enum constant in enum class ffx.crystal.LaueSystem
 
L32Z - Enum constant in enum class ffx.crystal.LaueSystem
 
L411 - Enum constant in enum class ffx.crystal.LaueSystem
 
L422 - Enum constant in enum class ffx.crystal.LaueSystem
 
La - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
labelAtoms - Static variable in class ffx.potential.bonded.RendererCache
Constant labelAtoms=false
labelResidues - Static variable in class ffx.potential.bonded.RendererCache
Constant labelResidues=false
lAlpha - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
lAlpha = α*(1 - L)^2
lambda - Variable in class ffx.realspace.RealSpaceEnergy
Value of the lambda state variable.
lambda - Variable in class ffx.xray.XRayEnergy
 
lambdaBins - Variable in class ffx.algorithms.thermodynamics.HistogramData
For continuous lambda: The first Lambda bin is centered on 0.0 (-0.0025 to 0.0025).
lambdaBinWidth_2 - Variable in class ffx.algorithms.thermodynamics.HistogramData
Half the width of a lambda bin, or zero for discrete lambda values.
lambdaBondedTerms - Variable in class ffx.potential.ForceFieldEnergy
Indicates only bonded energy terms effected by Lambda should be evaluated.
LambdaData - Class in ffx.algorithms.thermodynamics
 
LambdaData() - Constructor for class ffx.algorithms.thermodynamics.LambdaData
 
LambdaDefaults - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
The defaults are effectively final, as the implementation of setFactors in the base class is always a no-op.
LambdaFactors() - Constructor for class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
 
LambdaFactors() - Constructor for class ffx.potential.nonbonded.VanDerWaals.LambdaFactors
 
LambdaFactorsESV() - Constructor for class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsESV
 
LambdaFactorsOST() - Constructor for class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsOST
 
LambdaFactorsOST() - Constructor for class ffx.potential.nonbonded.VanDerWaals.LambdaFactorsOST
 
LambdaInterface - Interface in ffx.potential.bonded
The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 ..
lambdaLadder - Variable in class ffx.algorithms.thermodynamics.HistogramData
Either the discrete lambda values used, or null (continuous lambda).
LambdaMode - Enum Class in ffx.potential.nonbonded.pme
 
LambdaMove - Class in ffx.algorithms.mc
Define an MC move to update lambda.
LambdaMove(int, OrthogonalSpaceTempering) - Constructor for class ffx.algorithms.mc.LambdaMove
Constructor for LambdaMove.
LambdaMove(OrthogonalSpaceTempering) - Constructor for class ffx.algorithms.mc.LambdaMove
Constructor for LambdaMove.
LambdaParticleOptions - Class in ffx.algorithms.cli
Represents command line options for scripts that utilize a mobile lambda particle, such as Thermodynamics.
LambdaParticleOptions() - Constructor for class ffx.algorithms.cli.LambdaParticleOptions
 
lambdaPattern - Static variable in class ffx.potential.parsers.SystemFilter
 
lambdaProd - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
lambda * esvLambda[i] * esvLambda[k]
lambdaTerm - Variable in class ffx.potential.ForceFieldEnergy
Indicates use of the Lambda state variable.
lambdaVariance - Variable in class ffx.algorithms.thermodynamics.HistogramData
The variance for the Gaussian bias in the lambda dimension.
lamValues - Variable in class ffx.numerics.estimator.SequentialEstimator
 
LANGEVIN - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
 
LANGEVIN_MTS - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
 
LangevinIntegrator - Class in ffx.openmm
Langevin Integrator.
LangevinIntegrator(double, double, double) - Constructor for class ffx.openmm.LangevinIntegrator
Constructor.
LAST_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
 
lastEnergy() - Method in class ffx.algorithms.mc.BoltzmannMC
Returns the energy as of the last step taken (not including any extra potential energy adjustments).
lastEnergy() - Method in interface ffx.algorithms.mc.MetropolisMC
Returns the energy as of the last step taken (not including any extra potential energy adjustments).
latticeSystem - Variable in class ffx.crystal.SpaceGroup
Lattice system.
LatticeSystem - Enum Class in ffx.crystal
Enumeration of the 7 lattice systems.
laueSystem - Variable in class ffx.crystal.SpaceGroup
Laue group
LaueSystem - Enum Class in ffx.crystal
Enumeration of the different Laue systems.
lb - Variable in class ffx.numerics.integrate.FunctionDataCurve
Lower bound.
lb() - Method in class edu.rit.util.LongRange
Returns this range's lower bound.
lb() - Method in class edu.rit.util.Range
Returns this range's lower bound.
LBFGS - Class in ffx.numerics.optimization
This class implements the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm for large-scale multidimensional unconstrained optimization problems.
LEASE_EXPIRE_INTERVAL - Static variable in class edu.rit.pj.cluster.Constants
The lease expiration interval (default is 150 seconds).
LEASE_RENEW_INTERVAL - Static variable in class edu.rit.pj.cluster.Constants
The lease renewal interval (default is 60 seconds).
leastSquaresOptimizer - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters
 
leastSquaresPredictor(LambdaMode, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters
The least-squares predictor with induced dipole information from 8-10 previous steps reduces the number SCF iterations by ~50%.
LEFT - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationSide
 
leftBoole(double[]) - Static method in class ffx.numerics.integrate.Integration
leftBoole.
leftRectangularMethod(double[]) - Static method in class ffx.numerics.integrate.Integration
leftRectangularMethod.
leftSimpsons(double[]) - Static method in class ffx.numerics.integrate.Integration
leftSimpsons.
leftTrapInput(double[]) - Static method in class ffx.numerics.integrate.Integration
leftTrapInput.
length - Variable in class edu.rit.mp.Status
The actual number of items in the message that was received.
length - Variable in class edu.rit.pj.CommStatus
The actual number of items in the message that was received.
length - Variable in class ffx.potential.bonded.Rotamer
Number of chi/sigma values.
length() - Method in class edu.rit.mp.Buf
Obtain the number of items in this buffer.
length() - Method in class edu.rit.pj.reduction.SharedBooleanArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedByteArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedCharacterArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedDoubleArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedFloatArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedIntegerArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedLongArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedObjectArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.pj.reduction.SharedShortArray
Returns this array reduction variable's length.
length() - Method in class edu.rit.util.ByteSequence
Obtain the length of this byte sequence.
length() - Method in class edu.rit.util.LongRange
Returns this range's length.
length() - Method in class edu.rit.util.Range
Returns this range's length.
length() - Method in class ffx.numerics.math.Double3
Finds the length of this Double3.
length() - Method in class ffx.numerics.math.Float3
Finds the length of this Float3.
length(boolean[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given Boolean array.
length(byte[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given byte array.
length(char[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given character array.
length(double[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given double array.
length(double[]) - Static method in class ffx.numerics.math.DoubleMath
Finds the length of a vector.
length(float[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given float array.
length(float[]) - Static method in class ffx.numerics.math.FloatMath
Finds the length of a vector.
length(int[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given integer array.
length(long[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given long array.
length(short[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given short array.
length(T[]) - Static method in class edu.rit.util.Arrays
Determine the number of elements in the given object array.
length2() - Method in class ffx.numerics.math.Double3
Finds the length of this Double3 squared.
length2() - Method in class ffx.numerics.math.Float3
Finds the length of this Float3 squared.
length2(double[]) - Static method in class ffx.numerics.math.DoubleMath
Finds the length^2 of a vector.
length2(float[]) - Static method in class ffx.numerics.math.FloatMath
Finds the length of a vector squared.
LENNARD_JONES - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.VDW_TYPE
 
LEU - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
LEUCINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
lfAlpha - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Interatomic buffer distance: alpha*(1-lambda)*(1-lambda).
lfPowPerm - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Lambda to its permanent exponent.
lfPowPol - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Lambda to its polarization exponent.
Li - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
library - Variable in class ffx.algorithms.optimize.RotamerOptimization
RotamerLibrary instance.
likelihoodFree() - Method in class ffx.xray.DiffractionRefinementData
return the current likelihood
likelihoodWork() - Method in class ffx.xray.DiffractionRefinementData
return the current likelihood
linear - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
 
LINEAR - Enum constant in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules
 
LinearAnnealSchedule - Class in ffx.algorithms.optimize.anneal
Linear temperature schedule for simulated annealing
LinearAnnealSchedule(int, double, double) - Constructor for class ffx.algorithms.optimize.anneal.LinearAnnealSchedule
Creates an exponential annealing schedule that decays as tHigh-(n*(tHigh-tLow)).
LinearDerivativeSwitch - Class in ffx.numerics.switching
A LinearDerivativeSwitch interpolates between 0 and 1 vi f(x) = 2*x - x^2.
LinearDerivativeSwitch() - Constructor for class ffx.numerics.switching.LinearDerivativeSwitch
Constructor for the LinearDerivativeSwitch.
LineBufferedOutputStream - Class in edu.rit.io
Class LineBufferedOutputStream provides a line buffer layered on top of an underlying output stream.
LineBufferedOutputStream(OutputStream) - Constructor for class edu.rit.io.LineBufferedOutputStream
Construct a new line buffered output stream.
LINES - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
LineSearch - Class in ffx.numerics.optimization
This class implements an algorithm for uni-dimensional line search.
LineSearch.LineSearchResult - Enum Class in ffx.numerics.optimization
The six possible line search results:
list() - Method in class ffx.ui.properties.FFXLocale
list
listCommands(boolean, boolean) - Static method in class ffx.utilities.FFXCommand
List the embedded FFX Groovy Scripts.
listen(InetSocketAddress) - Method in class edu.rit.mp.ChannelGroup
Listen for connection requests on the given host and port.
listen(ServerSocketChannel) - Method in class edu.rit.mp.ChannelGroup
Listen for connection requests using the given server socket channel.
listenAddress() - Method in class edu.rit.mp.ChannelGroup
Obtain this channel group's listen address.
listGroovyScripts(boolean, boolean) - Static method in class ffx.utilities.FFXScript
List the embedded FFX Groovy Scripts.
LITERS_PER_CUBIC_ANGSTROM - Static variable in class ffx.utilities.Constants
Constant LITERS_PER_CUBIC_ANGSTROM=1E-30
LM3B - Enum constant in enum class ffx.crystal.LaueSystem
 
LM3M - Enum constant in enum class ffx.crystal.LaueSystem
 
lnI0(double) - Static method in class ffx.numerics.special.ModifiedBessel
Compute the natural log(i0(x)).
loadEnergyRestart(File, Residue[]) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
loadEnergyRestart(File, Residue[], int, int[]) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
loadPluginsFromDirectory(String) - Static method in class ffx.openmm.Platform
Load plugins from a directory.
loadProperties(File) - Static method in class ffx.utilities.Keyword
This method sets up configuration properties in the following precedence * order:
loadUpdate(SimulationUpdate) - Method in class ffx.ui.commands.FFXServer
loadUpdate
loadVRML() - Method in class ffx.potential.MolecularAssembly
loadVRML
LocalGeometryFunctionalForm - Enum constant in enum class ffx.utilities.PropertyGroup
Local geometry functional form.
locateDisulfideBonds(List<String>, MolecularAssembly, Map<String, String>) - Static method in class ffx.potential.bonded.PolymerUtils
Locate disulfide bonds based on SSBOND records.
Lock - Class in edu.rit.pj
Class Lock provides an object used for synchronizing parallel team threads in a critical region.
Lock() - Constructor for class edu.rit.pj.Lock
Construct a new lock.
log() - Method in class ffx.numerics.math.Double3
Log this Double3.
log() - Method in class ffx.numerics.math.Float3
Log this Float3.
log() - Method in class ffx.potential.bonded.Angle
Log details for this Angle energy term.
log() - Method in class ffx.potential.bonded.AngleTorsion
Log details for this Angle-Torsion energy term.
log() - Method in class ffx.potential.bonded.Bond
Log details for this Bond energy term.
log() - Method in class ffx.potential.bonded.ImproperTorsion
Log details for this Improper Torsion energy term.
log() - Method in class ffx.potential.bonded.OutOfPlaneBend
Log details for this Out-of-Plane Bend energy term.
log() - Method in class ffx.potential.bonded.PiOrbitalTorsion
Log details for this Pi-Orbital Torsion energy term.
log() - Method in class ffx.potential.bonded.RestraintBond
Log details for this Bond energy term.
log() - Method in class ffx.potential.bonded.StretchBend
log
log() - Method in class ffx.potential.bonded.StretchTorsion
Log details for this Stretch-Torsional Angle energy term.
log() - Method in class ffx.potential.bonded.Torsion
Log details for this Torsional Angle energy term.
log() - Method in class ffx.potential.bonded.TorsionTorsion
Log details for this Torsion-Torsion energy term.
log() - Method in class ffx.potential.bonded.UreyBradley
log
log() - Method in class ffx.potential.parameters.BaseType
Log this type.
log() - Method in class ffx.potential.parameters.ForceField
log
log(double[]) - Static method in class ffx.numerics.math.DoubleMath
logVector
log(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
log.
log(double[], String) - Static method in class ffx.numerics.math.DoubleMath
logVector.
log(float[]) - Static method in class ffx.numerics.math.FloatMath
logVector
log(float[], String) - Static method in class ffx.numerics.math.FloatMath
logVector.
log(long, String) - Method in interface edu.rit.util.Logger
Log the given date and message.
log(long, String) - Method in class edu.rit.util.PrintStreamLogger
Log the given date and message.
log(long, String, Throwable) - Method in interface edu.rit.util.Logger
Log the given date, message, and exception.
log(long, String, Throwable) - Method in class edu.rit.util.PrintStreamLogger
Log the given date, message, and exception.
log(long, Throwable) - Method in interface edu.rit.util.Logger
Log the given date and exception.
log(long, Throwable) - Method in class edu.rit.util.PrintStreamLogger
Log the given date and exception.
log(String) - Method in interface edu.rit.util.Logger
Log the given message.
log(String) - Method in class edu.rit.util.PrintStreamLogger
Log the given message.
log(String) - Method in class ffx.potential.parameters.ForceField
Prints any force field keyword to Standard.out.
log(String, Throwable) - Method in interface edu.rit.util.Logger
Log the given message and exception.
log(String, Throwable) - Method in class edu.rit.util.PrintStreamLogger
Log the given message and exception.
log(Throwable) - Method in interface edu.rit.util.Logger
Log the given exception.
log(Throwable) - Method in class edu.rit.util.PrintStreamLogger
Log the given exception.
log(Level) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Log the target temperature and current number of kT per degree of freedom (should be 0.5 kT at equilibrium).
logAllEnergyInformation() - Method in class ffx.algorithms.optimize.ConformationScan
 
logBindingEnergyCalculation(ConformationScan, ConformationScan, ConformationScan) - Static method in class ffx.algorithms.optimize.ConformationScan
 
logBondedTerms() - Method in class ffx.potential.ForceFieldEnergy
Log out all bonded energy terms.
logDevice(TornadoDevice) - Static method in class ffx.numerics.tornado.FFXTornado
List details about the passed TornadoDevice instance.
LogFormatter - Class in ffx.ui
A minor extension to the SimpleFormatter to reduce verbosity if debugging is not turned on.
logFrequency - Variable in class ffx.algorithms.dynamics.MolecularDynamics
Time steps between logging information to the screen.
logger - Static variable in class ffx.potential.cli.AlchemicalOptions
The logger for this class.
logger - Static variable in class ffx.potential.cli.TopologyOptions
The logger for this class.
logger - Static variable in class ffx.potential.nonbonded.SpatialDensityRegion
Constant logger
logger - Static variable in interface ffx.potential.utils.PotentialsFunctions
Constant logger
logger - Static variable in class ffx.utilities.FFXCommand
The logger for this class.
logger - Static variable in class ffx.utilities.FFXScript
The logger for this class.
logger - Static variable in class ffx.utilities.FFXTest
Constant logger
logger - Static variable in class ffx.utilities.HistogramXmlAdapter
The logger for this class.
logger - Static variable in class ffx.xray.BulkSolventRowRegion
Constant logger
logger - Static variable in class ffx.xray.BulkSolventSliceRegion
Constant logger
Logger - Interface in edu.rit.util
Interface Logger specifies the interface for an object that logs messages.
LogHandler - Class in ffx.ui
The default ConsoleHanlder publishes logging to System.err.
LogHandler() - Constructor for class ffx.ui.LogHandler
Construct the Force Field X Log Handler.
logIfRank0(String) - Method in class ffx.algorithms.optimize.RotamerOptimization
 
logIfRank0(String, Level) - Method in class ffx.algorithms.optimize.RotamerOptimization
 
logNoAngleType(Atom, Atom, Atom, ForceField) - Static method in class ffx.potential.bonded.Angle
Log that no AngleType exists.
logNoBondType(Atom, Atom, ForceField) - Static method in class ffx.potential.bonded.Bond
Log that no BondType exists.
logNoTorsionType(Atom, Atom, Atom, Atom, ForceField) - Static method in class ffx.potential.bonded.Torsion
Log that no TorsionType exists.
logOutputFiles(int) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
 
logResources() - Static method in class ffx.utilities.Resources
Log resources.
logTemp() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
 
logThermoForTime(long, long) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Checks if thermodynamics must be logged.
Long() - Constructor for class edu.rit.util.Searching.Long
 
Long() - Constructor for class edu.rit.util.Sorting.Long
 
LongArrayBuf - Class in edu.rit.mp.buf
Class LongArrayBuf provides a buffer for an array of long items sent or received using the Message Protocol (MP).
LongArrayBuf(long[], Range) - Constructor for class edu.rit.mp.buf.LongArrayBuf
Construct a new long array buffer.
LongArrayBuf_1 - Class in edu.rit.mp.buf
Class LongArrayBuf_1 provides a buffer for an array of long items sent or received using the Message Protocol (MP).
LongArrayBuf_1(long[], Range) - Constructor for class edu.rit.mp.buf.LongArrayBuf_1
Construct a new long array buffer.
LongBuf - Class in edu.rit.mp
Class LongBuf is the abstract base class for a buffer of long items sent or received using the Message Protocol (MP).
LongBuf(int) - Constructor for class edu.rit.mp.LongBuf
Construct a new long buffer.
LongForLoop - Class in edu.rit.pj
Class LongForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
LongForLoop() - Constructor for class edu.rit.pj.LongForLoop
Construct a new parallel for loop.
LongItemBuf - Class in edu.rit.mp.buf
Class LongItemBuf provides a buffer for a single long item sent or received using the Message Protocol (MP).
LongItemBuf() - Constructor for class edu.rit.mp.buf.LongItemBuf
Construct a new long item buffer.
LongItemBuf(long) - Constructor for class edu.rit.mp.buf.LongItemBuf
Construct a new long item buffer with the given initial value.
LongMatrixBuf - Class in edu.rit.mp.buf
Class LongMatrixBuf provides a buffer for a matrix of long items sent or received using the Message Protocol (MP).
LongMatrixBuf(long[][], Range, Range) - Constructor for class edu.rit.mp.buf.LongMatrixBuf
Construct a new long matrix buffer.
LongMatrixBuf_1 - Class in edu.rit.mp.buf
Class LongMatrixBuf_1 provides a buffer for a matrix of long items sent or received using the Message Protocol (MP).
LongMatrixBuf_1(long[][], Range, Range) - Constructor for class edu.rit.mp.buf.LongMatrixBuf_1
Construct a new long matrix buffer.
LongOp - Class in edu.rit.pj.reduction
Class LongOp is the abstract base class for a binary operation on long values, used to do reduction in a parallel program.
LongOp() - Constructor for class edu.rit.pj.reduction.LongOp
Construct a new long binary operation.
LongRange - Class in edu.rit.util
Class LongRange provides a range of type long.
LongRange() - Constructor for class edu.rit.util.LongRange
Construct a new range object representing an empty range.
LongRange(long, long) - Constructor for class edu.rit.util.LongRange
Construct a new range object with the given lower bound and upper bound.
LongRange(long, long, long) - Constructor for class edu.rit.util.LongRange
Construct a new range object with the given lower bound, upper bound, and stride.
LongRange(LongRange) - Constructor for class edu.rit.util.LongRange
Construct a new range object that is a copy of the given range object.
LongSchedule - Class in edu.rit.pj
Class LongSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.
LongSchedule() - Constructor for class edu.rit.pj.LongSchedule
Construct a new schedule object.
LongStrideForLoop - Class in edu.rit.pj
Class LongStrideForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.
LongStrideForLoop() - Constructor for class edu.rit.pj.LongStrideForLoop
Construct a new parallel for loop.
longValue() - Method in class edu.rit.pj.reduction.SharedByte
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedCharacter
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedDouble
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedFloat
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedInteger
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedLong
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.reduction.SharedShort
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedByte
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedDouble
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedFloat
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedInteger
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedLong
Returns this reduction variable's current value converted to type long.
longValue() - Method in class edu.rit.pj.replica.ReplicatedShort
Returns this reduction variable's current value converted to type long.
looksLikeIon(String) - Static method in class ffx.utilities.StringUtils
Checks if a String matches a known monoatomic ion name.
looksLikeWater(String) - Static method in class ffx.utilities.StringUtils
Checks if a String matches a known water name.
Loop - Class in ffx.potential.utils
Loop class.
Loop(MolecularAssembly) - Constructor for class ffx.potential.utils.Loop
Constructor for Loop.
Loop(MolecularAssembly, int, int) - Constructor for class ffx.potential.utils.Loop
Constructor for Loop.
loopbackChannel() - Method in class edu.rit.mp.ChannelGroup
Obtain this channel group's loopback channel.
LoopClosure - Class in ffx.potential.utils
LoopClosure class.
LoopClosure() - Constructor for class ffx.potential.utils.LoopClosure
 
lowerBound() - Method in interface ffx.numerics.integrate.DataSet
Lower bound of the points along x.
lowerBound() - Method in class ffx.numerics.integrate.DoublesDataSet
Lower bound of the points along x.
lowerBound() - Method in class ffx.numerics.integrate.FunctionDataCurve
Lower bound of the points along x.
lowestPairEnergy(Residue[], int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Return the lowest pair-energy for residue (i,ri) with residue j.
lowestSelfEnergy(Residue[], int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Return the lowest self-energy for residue i.
lPowPerm - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
lPowPerm = L^permanentLambdaExponent
lPowPol - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
lPowPol = L^polarizationLambdaExponent
Lr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
LS - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
 
LS - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
 
LT - Enum constant in enum class ffx.crystal.ASULimit
 
LT11 - Enum constant in enum class ffx.crystal.LaueSystem
 
LTE - Enum constant in enum class ffx.crystal.ASULimit
 
Lu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
LYD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
LYD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysStates
 
LYS - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
LYS - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysStates
 
LYSINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
LYStoLYD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
 

M

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

N

n - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
n - Variable in class ffx.algorithms.optimize.Minimize
Number of variables.
n - Variable in class ffx.algorithms.optimize.PhMinimize
Number of variables.
n - Variable in class ffx.xray.DiffractionRefinementData
Number of reflections in the data set.
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
 
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
 
N - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms
 
N - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
nA - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
The number of divisions along the A-axis.
Na - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
NA - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
 
NA - Enum constant in enum class ffx.potential.bonded.Residue.ResidueType
 
NA_C1 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_C1
NA_C2 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_C2
NA_C3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_C3
NA_C4 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_C4
NA_C5 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_C5
NA_H1 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_H1
NA_H21 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_H21
NA_H22 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_H22
NA_H3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_H3
NA_H4 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_H4
NA_H51 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_H51
NA_H52 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_H52
NA_HO3T - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Should be NA_HO3' (' replaced by T in the name).
NA_HO5T - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Should be NA_HO5' (' replaced by T in the name).
NA_O2 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_O2
NA_O3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_O3
NA_O4 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_O4
NA_O5 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Biotype keys for nucleic acid backbone atom types.
NA_OP - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_OP
NA_P - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA_P
NA1toNA3 - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant NA1toNA3
name - Variable in class edu.rit.pj.cluster.BackendInfo
The backend's name.
name - Variable in class edu.rit.pj.cluster.ProcessInfo
The job backend node's name.
name - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat
The identity of this Thermostat.
name - Variable in class ffx.potential.parameters.AtomType
Short name (ie CH3/CH2 etc).
name - Variable in class ffx.ui.commands.SimulationDefinition
 
name() - Method in interface ffx.potential.bonded.AminoAcidUtils.SideChainType
This is already implemented by all enum instances.
name() - Element in annotation interface ffx.utilities.FFXProperty
The name of this FFXProperty.
nameAcetylCap(Residue, Atom) - Static method in class ffx.potential.bonded.NamingUtils
Names the atoms in an N-terminal acetyl ACE capping group.
NamingUtils - Class in ffx.potential.bonded
Utilities for importing atoms from PDB files and checking their names.
NamingUtils() - Constructor for class ffx.potential.bonded.NamingUtils
 
NamingUtils.HetAtoms - Enum Class in ffx.potential.bonded
Common HETATOM labels for water and ions.
NAPATTERN - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Repeating atomic numbers of a nucleic acid chain.
nAtoms - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
The number of atoms in the system.
nAtoms - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
nB - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
The number of divisions along the B-axis.
Nb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
nBins - Variable in class ffx.crystal.ReflectionList
For binning reflections based on resolution
nC - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
The number of divisions along the C-Axis.
NCSCrystal - Class in ffx.crystal
The NCSCrystal class extends Crystal to support non-crystallographic symmetry (NCS).
NCSCrystalFactory(Crystal, List<SymOp>) - Static method in class ffx.crystal.NCSCrystal
Returns an NCSCrystal by expanding the orignal unit cell with the symmetry operators provided by the BIOMT records in the PDB files.
NCSRestraint - Class in ffx.potential.nonbonded
Given unit cell parameters and symmetry operators, NCS copies are restrained to the asymmetric unit atoms.
NCSRestraint(Atom[], ForceField, Crystal) - Constructor for class ffx.potential.nonbonded.NCSRestraint
This NCSRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
Nd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
ND1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
 
ND1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
 
ND1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
 
ND1 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
 
ND2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
 
Ne - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
NE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
 
NE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
 
NE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
 
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
 
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
 
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
 
NE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
 
NE2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
 
nearEndAddress() - Method in class edu.rit.mp.Channel
Obtain this channel's near end address.
nearEndChannelGroupId() - Method in class edu.rit.mp.Channel
Obtain the channel group ID of this channel's near end channel group.
nearEndConnected(ChannelGroup, Channel) - Method in interface edu.rit.mp.ConnectListener
Report that a channel was connected in the given channel group, initiated by the near end.
NeckIntegral - Class in ffx.potential.nonbonded.implicit
This class is used to compute interstitial space integrals of the form 1/r^6.
NeckIntegral() - Constructor for class ffx.potential.nonbonded.implicit.NeckIntegral
 
needUpdate() - Method in class ffx.ui.commands.FFXServer
needUpdate
neg() - Method in class ffx.crystal.HKL
neg
NeighborList - Class in ffx.potential.nonbonded
The NeighborList class builds Verlet lists in parallel via a spatial decomposition.
NeighborList(MaskingInterface, Crystal, Atom[], double, double, ParallelTeam) - Constructor for class ffx.potential.nonbonded.NeighborList
Constructor for the NeighborList class.
NeighborList.AtomIndex - Class in ffx.potential.nonbonded
Hold the atom index and its symmetry operator.
NeighborList.Cell - Class in ffx.potential.nonbonded
Hold the atoms in each cell.
neighborLists - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Neighbor lists, including atoms beyond the real space cutoff.
nESV - Variable in class ffx.algorithms.optimize.PhMinimize
Number of Extended System variables.
NeutronFormFactor - Class in ffx.xray
This implementation uses the coefficients from International Tables, Vol.
NeutronFormFactor(Atom) - Constructor for class ffx.xray.NeutronFormFactor
Constructor for NeutronFormFactor.
NeutronFormFactor(Atom, double) - Constructor for class ffx.xray.NeutronFormFactor
Constructor for NeutronFormFactor.
NeutronFormFactor(Atom, double, double[]) - Constructor for class ffx.xray.NeutronFormFactor
Constructor for NeutronFormFactor.
newInstance(String) - Static method in class edu.rit.util.Instance
Create a new instance of a class as specified by the given string.
next() - Method in class edu.rit.util.DefaultRandom
Return the next 64-bit pseudorandom value in this PRNG's sequence.
next() - Method in class edu.rit.util.Mcg1Random
Return the next 64-bit pseudorandom value in this PRNG's sequence.
next() - Method in class edu.rit.util.Random
Return the next 64-bit pseudorandom value in this PRNG's sequence.
next() - Method in class edu.rit.util.RandomSubset
Returns the next integer in the random subset.
next(int) - Method in class edu.rit.pj.IntegerSchedule
Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class edu.rit.pj.LongSchedule
Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.potential.nonbonded.PairwiseSchedule
Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.potential.nonbonded.SpatialDensitySchedule
Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.xray.GradientSchedule
Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.xray.RowSchedule
Obtain the next chunk of iterations for the given thread index.
next(int) - Method in class ffx.xray.SliceSchedule
Obtain the next chunk of iterations for the given thread index.
next(long) - Method in class edu.rit.util.DefaultRandom
Return the 64-bit pseudorandom value the given number of positions ahead in this PRNG's sequence.
next(long) - Method in class edu.rit.util.Mcg1Random
Return the 64-bit pseudorandom value the given number of positions ahead in this PRNG's sequence.
next(long) - Method in class edu.rit.util.Random
Return the 64-bit pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextBoolean() - Method in class edu.rit.util.Random
Return the Boolean value from the next pseudorandom value in this PRNG's sequence.
nextBoolean(long) - Method in class edu.rit.util.Random
Return the Boolean value from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextByte() - Method in class edu.rit.util.Random
Return the byte value from the next pseudorandom value in this PRNG's sequence.
nextByte(long) - Method in class edu.rit.util.Random
Return the byte value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextCharacter() - Method in class edu.rit.util.Random
Return the character value from the next pseudorandom value in this PRNG's sequence.
nextCharacter(long) - Method in class edu.rit.util.Random
Return the character value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextDouble() - Method in class edu.rit.util.Random
Return the double precision floating point value from the next pseudorandom value in this PRNG's sequence.
nextDouble(long) - Method in class edu.rit.util.Random
Return the double precision floating point value from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextFloat() - Method in class edu.rit.util.Random
Return the single precision floating point value from the next pseudorandom value in this PRNG's sequence.
nextFloat(long) - Method in class edu.rit.util.Random
Return the single precision floating point value from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextInt(int) - Method in class edu.rit.util.Random
Return the integer value in the given range from the next pseudorandom value in this PRNG's sequence.
nextInt(int, long) - Method in class edu.rit.util.Random
Return the integer value in the given range from the pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextInteger() - Method in class edu.rit.util.Random
Return the integer value from the next pseudorandom value in this PRNG's sequence.
nextInteger(long) - Method in class edu.rit.util.Random
Return the integer value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextLong() - Method in class edu.rit.util.Random
Return the long value from the next pseudorandom value in this PRNG's sequence.
nextLong(long) - Method in class edu.rit.util.Random
Return the long value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextShort() - Method in class edu.rit.util.Random
Return the short value from the next pseudorandom value in this PRNG's sequence.
nextShort(long) - Method in class edu.rit.util.Random
Return the short value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextUnsignedByte() - Method in class edu.rit.util.Random
Return the unsigned byte value from the next pseudorandom value in this PRNG's sequence.
nextUnsignedByte(long) - Method in class edu.rit.util.Random
Return the unsigned byte value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nextUnsignedShort() - Method in class edu.rit.util.Random
Return the unsigned short value from the next pseudorandom value in this PRNG's sequence.
nextUnsignedShort(long) - Method in class edu.rit.util.Random
Return the unsigned short value from the next pseudorandom value the given number of positions ahead in this PRNG's sequence.
nh - Variable in class ffx.potential.bonded.Angle
Number of hydrogen on the central atom that are not part of this Angle.
NH1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
 
NH2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
NH2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
 
Ni - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
NME - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
Nn - Variable in class edu.rit.pj.cluster.JobInfo
The number of backend nodes in the job.
No - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
NO_PICK - Static variable in interface ffx.ui.behaviors.PickingCallback
The user made a selection but nothing was actually picked
NO_WAIT - Static variable in class edu.rit.pj.BarrierAction
Do not do a barrier wait.
noCutoffFactory() - Static method in class ffx.potential.nonbonded.NonbondedCutoff
Returns a NonbondedCutoff that does not cut off anything.
nodeCount - Variable in class edu.rit.pj.cluster.JobInfo
The number of nodes that have been assigned to the job so far.
NonbondedCutoff - Class in ffx.potential.nonbonded
This class contains fields and methods for maintaining details of non-bonded cutoffs.
NonbondedCutoff(double, double, double) - Constructor for class ffx.potential.nonbonded.NonbondedCutoff
Non-bonded Cutoff constructor.
NonBondedCutoff - Enum constant in enum class ffx.utilities.PropertyGroup
Non-bonded cutoff.
NonbondedForce - Class in ffx.openmm
Nonbonded Force.
NonbondedForce() - Constructor for class ffx.openmm.NonbondedForce
 
None - Enum constant in enum class ffx.potential.bonded.RotamerLibrary.ProteinLibrary
 
NONE - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
 
NONE - Enum constant in enum class ffx.potential.bonded.Residue.SSType
 
NONE - Enum constant in enum class ffx.potential.bonded.ROLSP.PARALLELMETHOD
 
NONE - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
 
NONE - Enum constant in enum class ffx.potential.nonbonded.pme.Polarization
 
NONE - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
 
NONE - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
 
NONE - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
 
NONE - Enum constant in enum class ffx.potential.parsers.SystemFilter.Versioning
 
NONE - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel
Do not model solvent scattering.
NONE - Static variable in class ffx.ui.commands.SimulationUpdate
Constant NONE=0
NonPjJobFrontend - Class in edu.rit.pj.cluster
Class NonPjJobFrontend provides the message handler for a job frontend process that communicates with the Job Scheduler to allocate backend nodes but does not run a PJ program.
NonPjJobFrontend(String, int) - Constructor for class edu.rit.pj.cluster.NonPjJobFrontend
Construct a new non-PJ job frontend object.
nonPolarModel - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
nonStandardProtonation - Variable in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
NORMAL - Enum constant in enum class ffx.potential.parameters.AngleType.AngleMode
 
NORMAL - Enum constant in enum class ffx.potential.parameters.TorsionType.TorsionMode
 
NORMAL - Enum constant in enum class ffx.potential.parameters.VDWType.VDWMode
 
normalize() - Method in class ffx.numerics.math.Double3
Normalize this Double3.
normalize() - Method in class ffx.numerics.math.Float3
Normalize this Float3.
normalize(double[]) - Static method in class ffx.numerics.math.DoubleMath
Normalizes a vector.
normalize(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Normalizes a vector.
normalize(float[]) - Static method in class ffx.numerics.math.FloatMath
Normalizes a vector.
normalize(float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Normalizes a vector.
normalizeI() - Method in class ffx.numerics.math.Double3
Normalize this Double3 in place.
normalizeI() - Method in class ffx.numerics.math.Float3
Normalize this Float3 in place.
noStorageRecursion(double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI
This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI
This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
noStorageRecursion(double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
This method is a driver to collect elements of the Cartesian multipole tensor given the recursion relationships implemented by the method "Tlmnj", which can be called directly to get a single tensor element.
NOT_STARTED - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State
The job backend process has not started yet.
noZeroClasses() - Method in class ffx.potential.parameters.ImproperTorsionType
Check if this Improper Torsion Type is defined by 1 or more atom classes equal to zero.
Np - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
Np - Variable in class edu.rit.pj.cluster.JobInfo
The number of processes in the job.
NS2SEC - Static variable in class ffx.utilities.Constants
Convert nanoseconds to seconds.
nSteps - Variable in class ffx.algorithms.optimize.Minimize
The number of optimization steps taken.
nSteps - Variable in class ffx.algorithms.optimize.PhMinimize
The number of optimization steps taken.
nSymm - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
Nt - Variable in class edu.rit.pj.cluster.JobInfo
The number of CPUs per process in the job.
Nt - Variable in class edu.rit.pj.cluster.ProcessInfo
Number of CPUs assigned to the job backend process.
nthDerivative(double, int) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
 
nthDerivative(double, int) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction
N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.BellCurveSwitch
N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.CompositeSwitch
 
nthDerivative(double, int) - Method in class ffx.numerics.switching.ConstantSwitch
N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.LinearDerivativeSwitch
N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.MultiplicativeSwitch
N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.PowerSwitch
N'th order derivative at a point.
nthDerivative(double, int) - Method in class ffx.numerics.switching.SquaredTrigSwitch
N'th order derivative at a point.
nThreads - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
nTrajectories - Variable in class ffx.numerics.estimator.SequentialEstimator
 
NUCLEICACID - Enum constant in enum class ffx.potential.Utilities.PolymerType
 
nucleicAcid3 - Variable in class ffx.potential.bonded.Rotamer
The N.A.
nucleicAcidList - Static variable in class ffx.potential.bonded.NucleicAcidUtils
Constant nucleicAcidList
NucleicAcidUtils - Class in ffx.potential.bonded
Utilities for creating Nucleic Acid residues.
NucleicAcidUtils() - Constructor for class ffx.potential.bonded.NucleicAcidUtils
 
NucleicAcidUtils.NA - Enum Class in ffx.potential.bonded
The 4 RNA bases, 4 DNA bases, and mono- di- and triphosphate.
NucleicAcidUtils.NucleicAcid1 - Enum Class in ffx.potential.bonded
 
NucleicAcidUtils.NucleicAcid3 - Enum Class in ffx.potential.bonded
Since enumeration values must start with a letter, an 'M' is added to modified bases whose IUPAC name starts with an integer.
numatoms - Variable in class ffx.ui.commands.SimulationDefinition
 
numatoms - Variable in class ffx.ui.commands.SimulationUpdate
 
number - Variable in class ffx.crystal.SpaceGroup
Space group number.
numberAtoms(MolecularAssembly) - Static method in class ffx.potential.bonded.BondedUtils
Re-number atoms, especially if missing atoms were created.
numberOfBins() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute free energy.
numberOfBins() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
numberOfBins() - Method in interface ffx.numerics.estimator.StatisticalEstimator
Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute free energy.
numberOfBins() - Method in class ffx.numerics.estimator.Zwanzig
Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute free energy.
numberOfVariables - Variable in class ffx.potential.SystemState
Number of dynamics variables.
numkeys - Variable in class ffx.ui.commands.SimulationDefinition
 
numPoints() - Method in interface ffx.numerics.integrate.DataSet
Number of points along x.
numPoints() - Method in class ffx.numerics.integrate.DoublesDataSet
Number of points along x.
numPoints() - Method in class ffx.numerics.integrate.FunctionDataCurve
Number of points along x.
numPrimitiveSymEquiv - Variable in class ffx.crystal.SpaceGroup
Number of primitive symmetry equivalents.
numThreads - Variable in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters
 
nVariables - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Number of variables.
nx - Variable in class ffx.potential.parameters.TorsionTorsionType
Number of points along x.
ny - Variable in class ffx.potential.parameters.TorsionTorsionType
Number of point along y.
NZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
 
NZ - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
 
NZ - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
 

O

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

P

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

Q

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

R

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

S

S - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
S - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
sample(int[], String, Long) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
Sample from harmonic oscillator w/ gaussian invalid input: '&' std
sample(int, long, double, double, double) - Method in class ffx.algorithms.dynamics.ReplicaExchange
Sample.
sample(int, long, double, double, double, int) - Method in class ffx.algorithms.dynamics.PhReplicaExchange
Sample.
sample(int, long, long, double, double, double, int) - Method in class ffx.algorithms.dynamics.PhReplicaExchange
 
sampleOneStep() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
The goal is to sample lambda and coordinates (X) simultaneously to converge the ensemble average dU/dL for every state (lambda) along the thermodynamic path.
sampleTwoStep() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
The goal is to sample lambda and coordinates (X) separately to converge the ensemble average dU/dL for every state (lambda) along the thermodynamic path.
sampling - Variable in class ffx.crystal.Resolution
 
samplingLimit() - Method in class ffx.crystal.Resolution
samplingLimit
save(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions
Saves the current state of a MolecularAssembly to an XYZ file.
save(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils
Saves the current state of a MolecularAssembly to an XYZ file.
save(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
 
saveAsPDB(MolecularAssembly[], File) - Method in interface ffx.potential.utils.PotentialsFunctions
Saves the current state of an array of MolecularAssembly instances to a PDB file.
saveAsPDB(MolecularAssembly[], File) - Method in class ffx.potential.utils.PotentialsUtils
Saves the current state of an array of MolecularAssembly instances to a PDB file.
saveAsPDB(MolecularAssembly[], File) - Method in class ffx.ui.UIUtils
 
saveAsPDB(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions
Saves the current state of a MolecularAssembly to a PDB file.
saveAsPDB(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils
Saves the current state of a MolecularAssembly to a PDB file.
saveAsPDB(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
 
saveAsPDB(MolecularAssembly, File, boolean, boolean) - Method in interface ffx.potential.utils.PotentialsFunctions
 
saveAsPDB(MolecularAssembly, File, boolean, boolean) - Method in class ffx.potential.utils.PotentialsUtils
saveAsPDB(MolecularAssembly, File, boolean, boolean) - Method in class ffx.ui.UIUtils
 
saveAsPDBinP1(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions
Saves the symmetry mates of a MolecularAssembly to PDB files.
saveAsPDBinP1(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils
Saves the symmetry mates of a MolecularAssembly to PDB files.
saveAsPDBinP1(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
 
saveAsPDBinP1(MolecularAssembly, File, int[]) - Method in class ffx.potential.utils.PotentialsUtils
 
saveAsXYZ(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions
Saves the current state of a MolecularAssembly to an XYZ file.
saveAsXYZ(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils
Saves the current state of a MolecularAssembly to an XYZ file.
saveAsXYZ(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
 
saveAsXYZasReplicates(MolecularAssembly, File, int[]) - Method in interface ffx.potential.utils.PotentialsFunctions
Saves the current state of a MolecularAssembly to an XYZ file as a replicates crystal.
saveAsXYZasReplicates(MolecularAssembly, File, int[]) - Method in class ffx.potential.utils.PotentialsUtils
Saves the current state of a MolecularAssembly to an XYZ file as a replicates crystal.
saveAsXYZinP1(MolecularAssembly, File) - Method in interface ffx.potential.utils.PotentialsFunctions
Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.
saveAsXYZinP1(MolecularAssembly, File) - Method in class ffx.potential.utils.PotentialsUtils
Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.
saveAsXYZinP1(MolecularAssembly, File) - Method in class ffx.ui.UIUtils
 
saveDirFile(File) - Method in class ffx.algorithms.cli.AlgorithmsScript
Return a File in the base directory with the same name as the input file.
saveFeatures(Residue, double, boolean, boolean) - Method in class ffx.potential.utils.GetProteinFeatures
Make a string array of surface area and additional selected features (phi,psi,omega,and structure annotations)
saveFile(String, PotentialsFunctions, MolecularAssembly) - Method in class ffx.potential.cli.WriteoutOptions
Saves a single-snapshot file to either .xyz or .pdb, depending on the value of fileType.
saveKeywordFile(File) - Method in class ffx.ui.MainPanel
 
saveMutualInducedDipoles(double[][][], double[][][], double[][], double[][]) - Method in class ffx.potential.nonbonded.ScfPredictor
Save the current converged mutual induced dipoles.
saveMutualInducedDipoles(LambdaMode, double[][][], double[][][], double[][], double[][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters
Save the current converged mutual induced dipoles.
SaveOptions - Class in ffx.potential.cli
Represents command line options for scripts that save a structure to disc.
SaveOptions() - Constructor for class ffx.potential.cli.SaveOptions
 
saveZValues(int[][]) - Method in class ffx.potential.nonbonded.SliceLoop
saveZValues.
saveZYValues(int[][][]) - Method in class ffx.potential.nonbonded.RowLoop
saveZYValues.
Sb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
Sc - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
scalarMat3Mat3(double, double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath
scalar times a matrix times a matrix.
scalarMat3Mat3(double, double[][], double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath
scalarMat3mat3
ScalarMath - Class in ffx.numerics.math
The ScalarMath class is a simple math library that operates on single variables
ScalarMath() - Constructor for class ffx.numerics.math.ScalarMath
 
scale(double) - Method in class ffx.numerics.math.Double3
Scales a Double3.
scale(double[], double) - Static method in class ffx.numerics.math.DoubleMath
Scales a vector.
scale(double[], double[]) - Static method in class ffx.potential.parameters.MultipoleType
scale.
scale(double[], double, double[]) - Static method in class ffx.numerics.math.DoubleMath
Scales a vector.
scale(float) - Method in class ffx.numerics.math.Float3
Scales a Float3.
scale(float[], float) - Static method in class ffx.numerics.math.FloatMath
Scales a vector.
scale(float[], float, float[]) - Static method in class ffx.numerics.math.FloatMath
Scales a vector.
scale(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray
Scale the double array at the specified index by the given value.
scale(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray
Scale the double array at the specified index by the given value.
scale(int, int, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Scale the double arrays at the specified index to the given values.
scale(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray
Scale the double array at the specified index by the given value.
scale(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray
Scale the double array at the specified index by the given value.
scale(MultipoleType, double[]) - Static method in class ffx.potential.parameters.MultipoleType
scale.
scale12 - Variable in class ffx.potential.nonbonded.VanDerWaalsForm
Define scale factors between 1-2 atoms.
scale13 - Variable in class ffx.potential.nonbonded.VanDerWaalsForm
Define scale factors between 1-3 atoms.
scale14 - Variable in class ffx.potential.nonbonded.VanDerWaalsForm
Define scale factors between 1-4 atoms.
scaleB - Variable in class ffx.crystal.Crystal
Anisotropic bulk solvent B-factor scaling (0 or 1 for each component).
ScaleBulkEnergy - Class in ffx.xray
Fit bulk solvent and aniso B scaling terms to correct calculated structure factors against data
scaleBulkFit() - Method in class ffx.xray.DiffractionData
Scale model and fit bulk solvent to all data.
scaleBulkFit(int) - Method in class ffx.xray.DiffractionData
Scale model and fit bulk solvent to dataset i of n.
ScaleBulkMinimize - Class in ffx.xray
ScaleBulkMinimize class.
ScaleBulkMinimize(ReflectionList, DiffractionRefinementData, CrystalReciprocalSpace, ParallelTeam) - Constructor for class ffx.xray.ScaleBulkMinimize
Constructor for ScaleBulkMinimize.
scaleCoordinates(double[]) - Method in interface ffx.numerics.OptimizationInterface
Default method to scale coordinates.
scaleCoordinatesAndGradient(double[], double[]) - Method in interface ffx.numerics.OptimizationInterface
Default method to unscale coordinates.
scaleFactor - Variable in class ffx.potential.bonded.ImproperTorsion
Scale factor.
scaleI(double) - Method in class ffx.numerics.math.Double3
Scales a Double3 in place.
scaleI(float) - Method in class ffx.numerics.math.Float3
Scales a Float3 in place.
scaleN - Variable in class ffx.crystal.Crystal
Number of bulk solvent B-factor components.
ScaleParameters - Class in ffx.potential.nonbonded.pme
Scale factors and masking rules for electrostatics.
ScaleParameters(ForceField.ELEC_FORM, ForceField) - Constructor for class ffx.potential.nonbonded.pme.ScaleParameters
 
ScaleStep - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult
 
scaling - Variable in class ffx.algorithms.optimize.Minimize
Scaling applied to each variable.
scaling - Variable in class ffx.algorithms.optimize.PhMinimize
Scaling applied to each variable.
scan() - Method in class ffx.algorithms.optimize.ConformationScan
 
scan(int, Buf, Op) - Method in class edu.rit.pj.Comm
Perform a scan on all processes in this communicator using the given message tag.
scan(Buf, Op) - Method in class edu.rit.pj.Comm
Perform a scan on all processes in this communicator.
scatter(int, int, Buf[], Buf) - Method in class edu.rit.pj.Comm
Scatter messages to all processes in this communicator using the given message tag.
scatter(int, Buf[], Buf) - Method in class edu.rit.pj.Comm
Scatter messages to all processes in this communicator.
sceneGraphChange(List<BranchGroup>) - Method in class ffx.potential.MolecularAssembly
sceneGraphChange
scfAlgorithm - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
SCFAlgorithm - Enum Class in ffx.potential.nonbonded.pme
Describes available SCF algorithms, and whether they are supported by the FFX and/or CUDA implementations.
scfByPCG(boolean, long, ParticleMeshEwald) - Method in class ffx.potential.nonbonded.pme.PCGSolver
 
scfPredictor - Variable in class ffx.potential.nonbonded.pme.SCFPredictorParameters
 
ScfPredictor - Class in ffx.potential.nonbonded
Predict Mutual Induced Dipoles based on previous steps.
ScfPredictor(ScfPredictor.PredictorMode, int, ForceField) - Constructor for class ffx.potential.nonbonded.ScfPredictor
Constructor for ScfPredictor.
SCFPredictor - Enum Class in ffx.potential.nonbonded.pme
 
ScfPredictor.PredictorMode - Enum Class in ffx.potential.nonbonded
 
SCFPredictorParameters - Class in ffx.potential.nonbonded.pme
 
SCFPredictorParameters(SCFPredictor, int) - Constructor for class ffx.potential.nonbonded.pme.SCFPredictorParameters
 
schedule() - Method in class edu.rit.pj.IntegerForLoop
Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.IntegerStrideForLoop
Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.LongForLoop
Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.LongStrideForLoop
Determine this parallel for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerIntegerForLoop
Determine this worker for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop
Determine this worker for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerLongForLoop
Determine this worker for loop's schedule.
schedule() - Method in class edu.rit.pj.WorkerLongStrideForLoop
Determine this worker for loop's schedule.
schedule() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
 
schedule() - Method in class ffx.potential.nonbonded.SpatialDensityLoop
Determine this parallel for loop's schedule.
Schedule - Class in edu.rit.pj
Class Schedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.
SCREENED_COULOMB - Enum constant in enum class ffx.numerics.multipole.MultipoleTensor.OPERATOR
 
sd - Variable in class ffx.numerics.math.BootStrapStatistics
 
sd - Variable in class ffx.numerics.math.SummaryStatistics
 
SD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
 
sdPopulation - Variable in class ffx.numerics.math.BootStrapStatistics
 
sdPopulation - Variable in class ffx.numerics.math.SummaryStatistics
 
Se - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
search(int, double[], double, double[], double[], double[], double, LineSearch.LineSearchResult[], int[], OptimizationInterface) - Method in class ffx.numerics.optimization.LineSearch
Minimize a function along a search direction.
Searching - Class in edu.rit.util
Class Searching provides static methods for searching arrays of primitive types and object types.
Searching.Byte - Class in edu.rit.util
Class Searching.Byte is the base class for a helper object used to search an array of type byte[].
Searching.Character - Class in edu.rit.util
Class Searching.Character is the base class for a helper object used to search an array of type char[].
Searching.Double - Class in edu.rit.util
Class Searching.Double is the base class for a helper object used to search an array of type double[].
Searching.Float - Class in edu.rit.util
Class Searching.Float is the base class for a helper object used to search an array of type float[].
Searching.Integer - Class in edu.rit.util
Class Searching.Integer is the base class for a helper object used to search an array of type int[].
Searching.Long - Class in edu.rit.util
Class Searching.Long is the base class for a helper object used to search an array of type long[].
Searching.Object<T> - Class in edu.rit.util
Class Searching.Object is the base class for a helper object used to search an array of type T[].
Searching.Short - Class in edu.rit.util
Class Searching.Short is the base class for a helper object used to search an array of type short[].
searchSorted(byte[], byte, Searching.Byte) - Static method in class edu.rit.util.Searching
Search the given ordered array of type byte[] for the given element.
searchSorted(char[], char, Searching.Character) - Static method in class edu.rit.util.Searching
Search the given ordered array of type char[] for the given element.
searchSorted(double[], double, Searching.Double) - Static method in class edu.rit.util.Searching
Search the given ordered array of type double[] for the given element.
searchSorted(float[], float, Searching.Float) - Static method in class edu.rit.util.Searching
Search the given ordered array of type float[] for the given element.
searchSorted(int[], int, Searching.Integer) - Static method in class edu.rit.util.Searching
Search the given ordered array of type int[] for the given element.
searchSorted(long[], long, Searching.Long) - Static method in class edu.rit.util.Searching
Search the given ordered array of type long[] for the given element.
searchSorted(short[], short, Searching.Short) - Static method in class edu.rit.util.Searching
Search the given ordered array of type short[] for the given element.
searchSorted(T[], T) - Static method in class edu.rit.util.Searching
Search the given ordered array of type T[] for the given element.
searchSorted(T[], T, Searching.Object<T>) - Static method in class edu.rit.util.Searching
Search the given ordered array of type T[] for the given element.
searchSorted(T[], T, Comparator<T>) - Static method in class edu.rit.util.Searching
Search the given ordered array of type T[] for the given element.
searchUnsorted(byte[], byte, Searching.Byte) - Static method in class edu.rit.util.Searching
Search the given unordered array of type byte[] for the given element.
searchUnsorted(char[], char, Searching.Character) - Static method in class edu.rit.util.Searching
Search the given unordered array of type char[] for the given element.
searchUnsorted(double[], double, Searching.Double) - Static method in class edu.rit.util.Searching
Search the given unordered array of type double[] for the given element.
searchUnsorted(float[], float, Searching.Float) - Static method in class edu.rit.util.Searching
Search the given unordered array of type float[] for the given element.
searchUnsorted(int[], int, Searching.Integer) - Static method in class edu.rit.util.Searching
Search the given unordered array of type int[] for the given element.
searchUnsorted(long[], long, Searching.Long) - Static method in class edu.rit.util.Searching
Search the given unordered array of type long[] for the given element.
searchUnsorted(short[], short, Searching.Short) - Static method in class edu.rit.util.Searching
Search the given unordered array of type short[] for the given element.
searchUnsorted(T[], T) - Static method in class edu.rit.util.Searching
Search the given unordered array of type T[] for the given element.
searchUnsorted(T[], T, Searching.Object<T>) - Static method in class edu.rit.util.Searching
Search the given unordered array of type T[] for the given element.
searchUnsorted(T[], T, Comparator<T>) - Static method in class edu.rit.util.Searching
Search the given unordered array of type T[] for the given element.
SEC_TO_PSEC - Static variable in class ffx.utilities.Constants
Constant SEC_TO_PSEC=1E12
secondDerivative(double) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
 
secondDerivative(double) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction
Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.BellCurveSwitch
Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.CompositeSwitch
 
secondDerivative(double) - Method in class ffx.numerics.switching.ConstantSwitch
Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.LinearDerivativeSwitch
Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch
Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.PowerSwitch
Second derivative at a point.
secondDerivative(double) - Method in class ffx.numerics.switching.SquaredTrigSwitch
Second derivative at a point.
select - Variable in class ffx.potential.nonbonded.RowRegion
 
select - Variable in class ffx.potential.nonbonded.SliceRegion
 
select - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
select(MSNode) - Method in class ffx.ui.ModelingShell
select
select(MSNode, Class<? extends Object>, String) - Static method in class ffx.ui.Selection
select
select(MSNode, String, String) - Static method in class ffx.ui.Selection
select
SELECT - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
 
selectAtoms() - Method in class ffx.potential.nonbonded.RowRegion
Select atoms that should be included.
selectAtoms() - Method in class ffx.potential.nonbonded.SliceRegion
Select atoms that should be included.
selectAtoms() - Method in class ffx.potential.nonbonded.SpatialDensityRegion
Select atoms that should be assigned to cells.
selectAtoms() - Method in class ffx.xray.BulkSolventDensityRegion
Select atoms that should be assigned to cells.
selectAtoms() - Method in class ffx.xray.BulkSolventRowRegion
Select atoms that should be included.
selectAtoms() - Method in class ffx.xray.BulkSolventSliceRegion
Select atoms that should be included.
selected - Variable in class ffx.potential.bonded.MSNode
True if this node is selected.
selected() - Method in class ffx.ui.GraphicsCanvas
selected
selected() - Method in class ffx.ui.KeywordPanel
selected
selected() - Method in class ffx.ui.ModelingPanel
Selected.
Selection - Class in ffx.ui
The Selection class will be used to make recursive multiscale selections, however its implementation is not yet complete.
SELECTION - Static variable in interface ffx.ui.behaviors.MouseBehaviorCallback
Constant SELECTION=4
SELECTION - Static variable in interface ffx.ui.behaviors.PickingCallback
Constant SELECTION=4
selectionColor - Static variable in class ffx.potential.bonded.RendererCache
Constant selectionColor
selfEnergy(PolarizableMultipole, double, double, double) - Static method in class ffx.numerics.multipole.GKSource
 
SelfEnergyRegion - Class in ffx.algorithms.optimize.manybody
Compute residue self-energy values in parallel across nodes.
SelfEnergyRegion(RotamerOptimization, EnergyExpansion, EliminatedRotamers, Residue[], BufferedWriter, Comm, int, boolean, boolean, int, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.manybody.SelfEnergyRegion
 
send(double, double, double) - Method in class ffx.algorithms.thermodynamics.SendSynchronous
Send an OST count to all other processes while also receiving an OST count from all other processes.
send(int, int, Buf) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator with the given message tag.
send(int, int, Buf, CommRequest) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator with the given message tag (non-blocking).
send(int, Buf) - Method in class edu.rit.pj.cluster.Proxy
Send a message with the given tag and items to this proxy's far end process.
send(int, Buf) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator.
send(int, Buf, CommRequest) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator (non-blocking).
send(Channel, int, Buf) - Method in class edu.rit.mp.ChannelGroup
Send a message to the given channel with the given tag.
send(Channel, Buf) - Method in class edu.rit.mp.ChannelGroup
Send a message to the given channel.
send(Message) - Method in class edu.rit.pj.cluster.Proxy
Send the given message to this proxy's far end process.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.BooleanMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ByteMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.CharacterMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.DoubleMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyBooleanBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyByteBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyCharacterBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyDoubleBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyFloatBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyLongBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyShortBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.FloatMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.IntegerMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.LongMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.Buf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedBooleanBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedByteBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedCharacterBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedDoubleBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedFloatBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedLongBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedShortBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned16BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedSigned8BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.ShortMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerItemBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf
Send as many items as possible from this buffer to the given byte buffer.
sendItems(int, ByteBuffer) - Method in class edu.rit.mp.ObjectBuf
Send as many items as possible from this buffer to the given byte buffer.
sendNoWait(Channel, int, Buf, IORequest) - Method in class edu.rit.mp.ChannelGroup
Send (non-blocking) a message to the given channel with the given tag.
sendNoWait(Channel, Buf, IORequest) - Method in class edu.rit.mp.ChannelGroup
Send (non-blocking) a message to the given channel.
sendReceive(int, int, Buf, int, int, Buf) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator with the given message tag, and receive a message from the process at the given rank in this communicator with the given message tag.
sendReceive(int, int, Buf, int, int, Buf, CommRequest) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator with the given message tag, and receive a message from the process at the given rank in this communicator with the given message tag (non-blocking).
sendReceive(int, Buf, int, Buf) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator, and receive a message from the process at the given rank in this communicator.
sendReceive(int, Buf, int, Buf, CommRequest) - Method in class edu.rit.pj.Comm
Send a message to the process at the given rank in this communicator, and receive a message from the process at the given rank in this communicator (non-blocking).
SendSynchronous - Class in ffx.algorithms.thermodynamics
Synchronous (blocking) communication of OST counts.
SendSynchronous(OrthogonalSpaceTempering.Histogram[], int[]) - Constructor for class ffx.algorithms.thermodynamics.SendSynchronous
Synchronous Communication Constructor.
sendTaskInput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongForLoop
Send additional input data associated with a task.
sendTaskInput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongStrideForLoop
Send additional input data associated with a task.
sendTaskInput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerForLoop
Send additional input data associated with a task.
sendTaskInput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerStrideForLoop
Send additional input data associated with a task.
sendTaskInput(T, Comm, int, int) - Method in class edu.rit.pj.WorkerIteration
Send additional input data associated with a task.
sendTaskOutput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongForLoop
Send additional output data associated with a task.
sendTaskOutput(LongRange, Comm, int, int) - Method in class edu.rit.pj.WorkerLongStrideForLoop
Send additional output data associated with a task.
sendTaskOutput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerForLoop
Send additional output data associated with a task.
sendTaskOutput(Range, Comm, int, int) - Method in class edu.rit.pj.WorkerIntegerStrideForLoop
Send additional output data associated with a task.
sendTaskOutput(T, Comm, int, int) - Method in class edu.rit.pj.WorkerIteration
Send additional output data associated with a task.
SequentialEstimator - Class in ffx.numerics.estimator
The SequentialEstimator abstract class defines a statistical estimator based on perturbative potential energy differences between adjacent windows (e.g.
SequentialEstimator(double[], double[][][], double[]) - Constructor for class ffx.numerics.estimator.SequentialEstimator
The SequentialEstimator constructor largely just copies its parameters into local variables.
SequentialEstimator(double[], double[][], double[][], double[][], double[]) - Constructor for class ffx.numerics.estimator.SequentialEstimator
The SequentialEstimator constructor largely just copies its parameters into local variables.
SER - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
SERINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
set(boolean) - Method in class edu.rit.pj.reduction.SharedBoolean
Set this reduction variable to the given value.
set(byte) - Method in class edu.rit.pj.reduction.SharedByte
Set this reduction variable to the given value.
set(char) - Method in class edu.rit.pj.reduction.SharedCharacter
Set this reduction variable to the given value.
set(double) - Method in class edu.rit.pj.reduction.SharedDouble
Set this reduction variable to the given value.
set(double[]) - Method in class ffx.numerics.math.Double3
Set the value of this Double3.
set(double[], double[], double[]) - Method in class ffx.numerics.multipole.PolarizableMultipole
Set the permanent multipole.
set(double, double, double) - Method in class ffx.numerics.math.Double3
Set the value of this Double3.
set(float) - Method in class edu.rit.pj.reduction.SharedFloat
Set this reduction variable to the given value.
set(float[]) - Method in class ffx.numerics.math.Float3
Set the value of this Float3.
set(float, float, float) - Method in class ffx.numerics.math.Float3
Set the value of this Float3.
set(int) - Method in class edu.rit.pj.reduction.SharedInteger
Set this reduction variable to the given value.
set(int, boolean) - Method in class edu.rit.pj.reduction.SharedBooleanArray
Set this array reduction variable at the given index to the given value.
set(int, byte) - Method in class edu.rit.pj.reduction.SharedByteArray
Set this array reduction variable at the given index to the given value.
set(int, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Set this array reduction variable at the given index to the given value.
set(int, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Set this array reduction variable at the given index to the given value.
set(int, double) - Method in class ffx.openmm.DoubleArray
Set a value in the array.
set(int, float) - Method in class edu.rit.pj.reduction.SharedFloatArray
Set this array reduction variable at the given index to the given value.
set(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Set this array reduction variable at the given index to the given value.
set(int, int) - Method in class ffx.openmm.IntArray
Set a value in the array.
set(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray
Set the double array at the specified index to the given value.
set(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray
Set the double array at the specified index to the given value.
set(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray
Set the double array at the specified index to the given value.
set(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray
Set the double array at the specified index to the given value.
set(int, int, double, double, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Set the double arrays at the specified index to the given values.
set(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Set this matrix reduction variable at the given row and column to the given value.
set(int, int, int) - Method in class ffx.openmm.BondArray
Set the bond at index to i1 and i2.
set(int, int, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Set this matrix reduction variable at the given row and column to the given value.
set(int, int, Double3) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Set the double arrays at the specified index to the given Double3.
set(int, int, DoubleArray) - Method in class ffx.openmm.DoubleArray3D
Set the value of the array at the given index.
set(int, long) - Method in class edu.rit.pj.reduction.SharedLongArray
Set this array reduction variable at the given index to the given value.
set(int, short) - Method in class edu.rit.pj.reduction.SharedShortArray
Set this array reduction variable at the given index to the given value.
set(int, OpenMM_Vec3.ByValue) - Method in class ffx.openmm.Vec3Array
Set a Vec3 in the Vec3Array.
set(int, String) - Method in class ffx.openmm.StringArray
Set the String at index i.
set(int, T) - Method in class edu.rit.pj.reduction.SharedObjectArray
Set this array reduction variable at the given index to the given value.
set(long) - Method in class edu.rit.pj.reduction.SharedLong
Set this reduction variable to the given value.
set(short) - Method in class edu.rit.pj.reduction.SharedShort
Set this reduction variable to the given value.
set(Double3) - Method in class ffx.numerics.math.Double3
Set the value of this Double3.
set(Float3) - Method in class ffx.numerics.math.Float3
Set the value of this Float3.
set(T) - Method in class edu.rit.pj.reduction.SharedObject
Set this reduction variable to the given value.
set2Body(int, int, int, int, double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
set2Body(int, int, int, int, double, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Store a pair energy in the pairs energy matrix.
set3Body(Residue[], int, int, int, int, int, int, double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
set3Body.
set3Body(Residue[], int, int, int, int, int, int, double, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Stores a triple energy in the triples energy matrix.
setAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat
setAcceleration.
setAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
setAcceleration.
setAcceleration(double[]) - Method in interface ffx.numerics.Potential
setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
 
setAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field acceleration.
setAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy
setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
setAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy
setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy
setAcceleration.
setAcceleration(double[]) - Method in class ffx.potential.XtalEnergy
setAcceleration.
setAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy
setAcceleration.
setAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy
setAcceleration.
setAcceleration(double[]) - Method in class ffx.xray.XRayEnergy
setAcceleration.
setAcceleration(double, double, double) - Method in class ffx.potential.bonded.Atom
Setter for the field acceleration.
setAccelerations(double[]) - Method in class ffx.potential.SystemState
Set the accelerations via a copy of the passed array into the internal array.
setActive(boolean) - Method in class ffx.algorithms.dynamics.Barostat
Setter for the field active.
setActive(boolean) - Method in class ffx.potential.bonded.Atom
If active, the coordinates of this atom can be modified.
setActive(int) - Method in class ffx.ui.Hierarchy
setActive
setActive(FFXSystem) - Method in class ffx.ui.Hierarchy
Sets the FFXSystem s to be active.
setActiveAssembly(MolecularAssembly) - Method in class ffx.algorithms.cli.AlgorithmsScript
Set the Active Assembly.
setActiveAssembly(MolecularAssembly) - Method in class ffx.potential.cli.PotentialCommand
Set the Active Assembly.
setActiveAssembly(MolecularAssembly) - Method in class ffx.potential.cli.PotentialScript
Set the Active Assembly.
setActiveAtoms() - Method in class ffx.potential.openmm.OpenMMEnergy
Update active atoms.
setActiveAtoms(MolecularAssembly) - Method in class ffx.potential.cli.AtomSelectionOptions
Set active atoms for a MolecularAssembly.
setActiveResidue(int) - Method in class ffx.potential.bonded.MultiResidue
Request the ith residue be set active.
setActiveResidue(AminoAcidUtils.AminoAcid3) - Method in class ffx.potential.bonded.MultiResidue
Method may be redundant with requestSetActiveResidue.
setActiveResidue(Residue) - Method in class ffx.potential.bonded.MultiResidue
Setter for the field activeResidue.
setAEwald(double) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the Ewald coefficient for the multipole force.
setAlchemicalAtoms(MolecularAssembly, String) - Static method in class ffx.potential.cli.AlchemicalOptions
Sets the alchemical atoms for a MolecularAssembly.
setAlchemicalMethod(int) - Method in class ffx.openmm.amoeba.VdwForce
Set the alchemical method.
setAlgorithm(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setAllowed(int) - Method in class ffx.crystal.HKL
setAllowed
setAlternateClassLoader(ClassLoader) - Method in class edu.rit.mp.ChannelGroup
Specify an alternate class loader for this channel group.
setAlternateLocation(Character) - Method in class ffx.potential.MolecularAssembly
Set the alternate location.
setAltID(MolecularAssembly, Character) - Method in class ffx.potential.parsers.PDBFilter
Specify the alternate location.
setAltLoc(Character) - Method in class ffx.potential.bonded.Atom
Setter for the field altLoc.
setAndRotate(double[], PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.QIFrame
Update the QIFrame rotation matrix and rotate the multipoles.
setAndRotate(double, double, double, PolarizableMultipole, PolarizableMultipole) - Method in class ffx.numerics.multipole.QIFrame
Update the QIFrame rotation matrix and rotate the multipoles.
setAngle(Angle) - Method in class ffx.potential.bonded.Atom
setAngle
setAngleFunction(AngleType.AngleFunction) - Method in class ffx.potential.parameters.AngleType
Set the AngleFunction.
setAngleFunction(AngleType.AngleFunction) - Method in class ffx.potential.parameters.ForceField
The AngleFunction in use by this ForceField.
setAngleParameters(int, int, int, int, DoubleArray) - Method in class ffx.openmm.CustomAngleForce
Set the parameters for one angle in the OpenMM System.
setAngles(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the Angles node to t.
setAngles(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the Angles node to t.
setAngleTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the MultiScaleGroup's angle-torsion node to t.
setAngleType(AngleType) - Method in class ffx.potential.bonded.Angle
Set a reference to the force field parameters for this Angle.
setAnisou(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field anisou.
setAnisouAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field anisouAcceleration.
setAnisouGradient(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field anisouGradient.
setAnisouPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field anisouPreviousAcceleration.
setAnisouVelocity(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field anisouVelocity.
setAperiodic(boolean) - Method in class ffx.crystal.Crystal
Is this a finite system without periodic boundary conditions.
setApplyLambda(boolean) - Method in class ffx.potential.bonded.Atom
setApplyLambda
setApproxBoxLength(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setApproxBoxLength(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the approximate dimensions of boxes, over-riding numXYZBoxes in determining box size.
setArchiveFile(File) - Method in class ffx.potential.MolecularAssembly
Set the File for writing out an archive.
setArchiveFiles(File[]) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Set the archive file for each MolecularAssembly.
setArgList(List<String>) - Method in class ffx.ui.ModelingShell
setArgList
setAsynchronous(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
setAtomNode(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the Moieties node to t.
setAtomNode(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the Moieties node to t.
setAtoms(int) - Method in class ffx.potential.nonbonded.PairwiseSchedule
setAtoms.
setAtoms(Atom[]) - Method in class ffx.potential.bonded.BondedTerm
Add a constituent Atom to the Term.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.NeighborList
The NeighborList will be re-configured, if necessary, for the supplied atom list.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace
Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.RowRegion
Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.SliceRegion
Setter for the field atoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.SpatialDensityRegion
setAtoms.
setAtoms(Atom[]) - Method in class ffx.potential.nonbonded.VanDerWaalsTornado
Setter for the field atoms.
setAtoms(Atom[], int[]) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
setAtoms(Atom[], int[], boolean[]) - Method in class ffx.potential.nonbonded.VanDerWaals
Setter for the field atoms.
setAtomSelectionOptions(AtomSelectionOptions) - Method in class ffx.potential.commands.Energy
 
setAtomType(AtomType) - Method in class ffx.potential.bonded.Atom
Setter for the field atomType.
setAtomTypes(AtomTypeFactory, IAtom) - Static method in class ffx.potential.parsers.CIFFilter
Specify the atom types for atoms created by factory.
setAutomaticWriteouts(boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Enable or disable automatic writeout of trajectory snapshots and restart files.
setAutomaticWriteouts(boolean) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
 
setAwater(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the water density parameter.
setAxisAtoms(Atom...) - Method in class ffx.potential.bonded.Atom
Setter for the field axisAtoms.
setAxisShowing(boolean) - Method in class ffx.ui.MainMenu
setAxisShowing
setBackboneEnergy(double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
setBarInt(int) - Method in class ffx.algorithms.cli.BarostatOptions
 
setBarostatPrintFrequency(int) - Method in class ffx.algorithms.dynamics.Barostat
Set the Barostat print frequency.
setBaseDir(File) - Method in class ffx.algorithms.cli.AlgorithmsScript
Sets the directory this script should save files to.
setBaselineAARes(AminoAcidUtils.AminoAcid3) - Method in class ffx.algorithms.misc.GenerateRotamers
Sets a standard amino acid to be the baseline for rotamer generation.
setBeta0(double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
 
setBeta1(double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
 
setBeta2(double) - Static method in class ffx.potential.nonbonded.implicit.BornTanhRescaling
 
setBiasMag(double) - Method in class ffx.algorithms.thermodynamics.HistogramData
Set the bias magnitude.
setBiasMag(double[]) - Method in class ffx.algorithms.cli.OSTOptions
 
setBin(int) - Method in class ffx.crystal.HKL
setBin
setBond(Bond) - Method in class ffx.potential.bonded.Atom
Specify that this Atom is part of a Bond
setBondFunction(BondType.BondFunction) - Method in class ffx.potential.parameters.BondType
 
setBondFunction(BondType.BondFunction) - Method in class ffx.potential.parameters.ForceField
The BondFunction in use by this ForceField.
setBondParameters(int, int, int, double, double) - Method in class ffx.openmm.HarmonicBondForce
Set the bond parameters.
setBondParameters(int, int, int, DoubleArray) - Method in class ffx.openmm.CustomBondForce
Set the parameters for one bond in the OpenMM System.
setBondParameters(int, IntArray, DoubleArray) - Method in class ffx.openmm.CustomCompoundBondForce
Set the parameters for a Custom Compound Bond.
setBonds(Bond[]) - Method in class ffx.potential.bonded.BondedTerm
Add constituent Bonds to the Term.
setBonds(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the Bonds node to t.
setBonds(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the Bonds node to t.
setBondTolerance(double) - Method in class ffx.potential.parsers.CIFFilter
Set buffer value when bonding atoms together.
setBondType(BondType) - Method in class ffx.potential.bonded.Bond
Set a reference to the force field parameters.
setBondType(BondType) - Method in class ffx.potential.bonded.RestraintBond
Set a reference to the force field parameters.
setBoxBorderSize(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setBoxBorderSize(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the amount of overlap between adjacent boxes for box optimization.
setBoxEnd(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the ending box index.
setBoxInclusionCriterion(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setBoxInclusionCriterion(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets behavior for how Residues are added to boxOptCells; 1 uses just reference atom (C alpha for protein, N1/9 for nucleic acids), 2 uses any atom, 3 uses any atom in any rotamer.
setBoxStart(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the starting box index.
setBuilt(boolean) - Method in class ffx.potential.bonded.Atom
Setter for the field built.
setCaptures(boolean) - Method in class ffx.ui.GraphicsCanvas
setCaptures
setCellVectors(double[][]) - Method in class ffx.crystal.Crystal
Set the unit cell vectors.
setCellVectors(double[][]) - Method in class ffx.crystal.ReplicatesCrystal
Change the cell vectors for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
setCellVectorsAndVolume(double[][], double) - Method in class ffx.crystal.Crystal
Set the unit cell vectors.
setCellVectorsAndVolume(double[][], double) - Method in class ffx.crystal.ReplicatesCrystal
Change the cell vectors and volume for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
setCenter(double[]) - Method in class ffx.potential.bonded.MSGroup
Set the value of Center to d.
setCenter(double[]) - Method in class ffx.potential.bonded.MultiResidue
Set the value of Center to d.
setChain(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setChainID(Character) - Method in class ffx.potential.bonded.Atom
Set the chain name.
setChainID(Character) - Method in class ffx.potential.bonded.Molecule
Setter for the field chainID.
setChainID(Character) - Method in class ffx.potential.bonded.Polymer
Set the Polymer chainID.
setChainID(Character) - Method in class ffx.potential.bonded.Residue
Setter for the field chainID.
setChainIDAndRenumberMolecules(Character) - Method in class ffx.potential.MolecularAssembly
This method sets all HETATM molecules, including water and ions, to use the given chainID and then renumbers the molecules.
setChannelGroupId(int) - Method in class edu.rit.mp.ChannelGroup
Set this channel group's channel group ID.
setCharge(double) - Method in class ffx.potential.nonbonded.octree.OctreeParticle
 
setCharset(Charset) - Method in class edu.rit.http.HttpResponse
Set this HTTP response's character set.
setCheckpoint(double) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setCheckRestrictions(boolean) - Method in class ffx.crystal.Crystal
 
setCheckRestrictions(boolean) - Method in class ffx.crystal.ReplicatesCrystal
setChildren(int, int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
setClashThreshold(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setClosing(boolean) - Method in class ffx.ui.FFXSystem
Setter for the field closing.
setColor(Atom) - Method in class ffx.potential.bonded.Bond
Set the color of this Bond's Java3D shapes based on the passed Atom.
setColor(RendererCache.ColorModel) - Method in class ffx.potential.bonded.Joint
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.Atom
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.BondedTerm
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.MSGroup
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.MSNode
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.MultiResidue
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.Polymer
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.bonded.Residue
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in interface ffx.potential.bonded.ROLS
setColor
setColor(RendererCache.ColorModel, Color3f, Material) - Method in class ffx.potential.MolecularAssembly
setColor
setColor(String) - Method in class ffx.ui.GraphicsCanvas
setColor
setColorModel(String, MSNode) - Method in class ffx.ui.GraphicsCanvas
Operates on the passed node.
setCommand(String) - Method in class ffx.ui.ModelingPanel
setCommand
setCommandDescription(String) - Method in class ffx.ui.FFXSystem
Setter for the field commandDescription.
setComment(String) - Method in class edu.rit.pj.cluster.JobBackend
Set the comment string for this job backend process.
setConnectListener(ConnectListener) - Method in class edu.rit.mp.ChannelGroup
Register the given connect listener with this channel group.
setConstantPh(double) - Method in class ffx.potential.extended.ExtendedSystem
setConstantPh.
setConstantPH(boolean) - Method in class ffx.potential.parsers.PDBFilter
 
setConstraint(Constraint) - Method in class ffx.potential.bonded.Angle
 
setConstraint(Constraint) - Method in class ffx.potential.bonded.BondedTerm
Sets the Constraint on this bond (clearing it if null).
setConstraintTolerance(double) - Method in class ffx.openmm.Integrator
Set the tolerance within which constraints must be satisfied during the simulation.
setContentLength(int) - Method in class edu.rit.http.HttpResponse
Set this HTTP response's content length.
setContentType(String) - Method in class edu.rit.http.HttpResponse
Set this HTTP response's content type.
setContinuous(boolean) - Method in class ffx.algorithms.mc.LambdaMove
If true, do continuous moves.
setCoordinates(double[]) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Set the coordinates.
setCoordinates(double[]) - Method in class ffx.potential.ForceFieldEnergy
The coordinate array should only contain active atoms.
setCoordinates(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy
Set FFX and OpenMM coordinates for active atoms.
setCoordinates(double[]) - Method in class ffx.potential.SystemState
Set the coordinates via a copy of the passed array into the internal array.
setCoordinates(double[]) - Method in class ffx.realspace.RealSpaceEnergy
Set atomic coordinates positions.
setCoordinates(double[]) - Method in class ffx.xray.CrystalReciprocalSpace
Set atomic coordinates.
setCoordinates(double[]) - Method in class ffx.xray.XRayEnergy
set atomic xyz coordinates based on current position
setCoordinatesToEnsemble(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
setCoordinatesToEnsemble.
setCountInterval(int) - Method in class ffx.algorithms.cli.OSTOptions
 
setCountInterval(int) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
setCovalentMap(int, int, IntArray) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the covalent map.
setCrossOver(double) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
setCrystal(Crystal) - Method in class ffx.algorithms.dynamics.Barostat
setCrystal(Crystal) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
setCrystal(Crystal) - Method in interface ffx.crystal.CrystalPotential
 
setCrystal(Crystal) - Method in class ffx.potential.DualTopologyEnergy
setCrystal(Crystal) - Method in class ffx.potential.ForceFieldEnergy
setCrystal(Crystal) - Method in class ffx.potential.MolecularAssembly
Set the Crystal for the Potential of this MolecularAssembly.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Setter for the field crystal.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.NeighborList
The NeighborList will be re-configured, if necessary, for the supplied Crystal.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.ReciprocalSpace
Setter for the field crystal.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.VanDerWaals
If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated.
setCrystal(Crystal) - Method in class ffx.potential.nonbonded.VanDerWaalsTornado
If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated.
setCrystal(Crystal) - Method in class ffx.potential.openmm.OpenMMEnergy
setCrystal(Crystal) - Method in class ffx.potential.QuadTopologyEnergy
setCrystal(Crystal) - Method in class ffx.realspace.RealSpaceEnergy
setCrystal(Crystal) - Method in class ffx.xray.RefinementEnergy
setCrystal(Crystal) - Method in class ffx.xray.XRayEnergy
setCrystal(Crystal[]) - Method in class ffx.realspace.RealSpaceData
Setter for the field crystal.
setCrystal(Crystal, boolean) - Method in class ffx.potential.ForceFieldEnergy
Set the boundary conditions for this calculation.
setCrystal(Crystal, int, int, int) - Method in class ffx.potential.nonbonded.RowRegion
Setter for the field crystal.
setCrystal(Crystal, int, int, int) - Method in class ffx.potential.nonbonded.SliceRegion
Setter for the field crystal.
setCrystal(Crystal, int, int, int) - Method in class ffx.potential.nonbonded.SpatialDensityRegion
Setter for the field crystal.
setCurrentCycle(int) - Method in class ffx.potential.bonded.Atom
setCurrentCycle
setCurrentCycle(int) - Method in class ffx.potential.MolecularAssembly
Setter for the field currentCycle.
setCutoff(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setCutoff(double) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Setter for the field cutoff.
setCutoffDistance(double) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the cutoff distance for the multipole force.
setCutoffDistance(double) - Method in class ffx.openmm.amoeba.VdwForce
Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.CustomGBForce
Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.CustomNonbondedForce
Set the cutoff distance.
setCutoffDistance(double) - Method in class ffx.openmm.NonbondedForce
Set the cutoff distance.
setCycles(int) - Method in class ffx.potential.MolecularAssembly
Setter for the field cycles.
setDanglingAtoms(List<Atom>) - Method in class ffx.potential.bonded.MSGroup
Sets the MultiScaleGroup's danglingAtoms member to a.
setDanglingAtoms(List<Atom>) - Method in class ffx.potential.bonded.MultiResidue
Sets the MultiScaleGroup's danglingAtoms member to a.
setData(double[]) - Method in class ffx.realspace.RealSpaceRefinementData
Setter for the field data.
setDecompose(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setDecomposeOriginal(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the decompose-original flag.
setDee(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setDefaultCollisionFrequency(double) - Method in class ffx.openmm.AndersenThermostat
Set the default collision frequency.
setDefaultPeriodicBoxVectors(OpenMM_Vec3, OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.System
Set the default periodic box vectors.
setDefaultPressure(double) - Method in class ffx.openmm.MonteCarloBarostat
Set the default pressure.
setDefaultTemperature(double) - Method in class ffx.openmm.AndersenThermostat
Set the default temperature.
setDefaultTemperature(double) - Method in class ffx.openmm.MonteCarloBarostat
Set the default temperature.
setDensity(double) - Method in class ffx.algorithms.dynamics.Barostat
setDensity.
setDensity(double, double) - Method in class ffx.crystal.Crystal
 
setDensity(double, double) - Method in class ffx.crystal.ReplicatesCrystal
Update the ReplicatesCrystal dimensions to the target density.
setDensityLoop(RowLoop[]) - Method in class ffx.potential.nonbonded.RowRegion
setDensityLoop.
setDensityLoop(SliceLoop[]) - Method in class ffx.potential.nonbonded.SliceRegion
setDensityLoop.
setDensityLoop(SpatialDensityLoop[]) - Method in class ffx.potential.nonbonded.SpatialDensityRegion
setDensityLoop
setDepth(int, int) - Method in class ffx.algorithms.misc.GenerateRotamers
Set which torsions to work on.
setDielectricOffset(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the dielectric offset.
setDirection(RotamerOptimization.Direction) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the optimization direction to forward or backward.
setDisableUpdates(boolean) - Method in class ffx.potential.nonbonded.NeighborList
If disableUpdates true, disable updating the neighbor list upon motion.
setDiscreteLambda(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
setDispersionOffest(double) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
The dispersion integral begins offset from the vdW radius.
setDispersionOverlapFactor(double) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
Set the dispersion overlap HCT scale factor.
setDispoff(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the dispersion offset.
setDistanceCutoff(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the cut-off distance for inclusion of residues in sliding box and window methods.
setDistributeWalkersString(String) - Method in class ffx.algorithms.cli.MultiDynamicsOptions
 
setDomain(double) - Method in class ffx.potential.nonbonded.octree.OctreeParticle
 
setDomain(double) - Method in class ffx.potential.nonbonded.octree.OctreePoint
 
setDt(double) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setElectrostatics(boolean) - Method in class ffx.potential.bonded.Atom
Setter for the field electrostatics.
setElectrostatics(String) - Method in class ffx.algorithms.misc.GenerateRotamers
Inactivates electrostatics for atom sets defined by 'start-end,start-end,...'.
setElementHCTScaleFactors(HashMap<Integer, Double>) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Setter for element-specific HCT overlap scale factors
setEnable(boolean) - Method in class ffx.ui.behaviors.GlobalBehavior
setEnergyExpansion(EnergyExpansion) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
 
setEnergyRestart(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setEnergyRestartFile(File) - Method in class ffx.algorithms.optimize.RotamerOptimization
Setter for the field energyRestartFile.
setEnergyTermState(Potential.STATE) - Method in class ffx.algorithms.dynamics.Barostat
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in interface ffx.numerics.Potential
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.ANIEnergy
 
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.DualTopologyEnergy
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.extended.ExtendedSystem
 
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.ForceFieldEnergy
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.QuadTopologyEnergy
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.potential.XtalEnergy
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.realspace.RealSpaceEnergy
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.xray.RefinementEnergy
Set the Potential Energy terms that should be active.
setEnergyTermState(Potential.STATE) - Method in class ffx.xray.XRayEnergy
Set the Potential Energy terms that should be active.
setEngineString(String) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setEnsemble(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
setEnsemble.
setEnsemble(int, double) - Method in class ffx.algorithms.optimize.RotamerOptimization
setEnsemble.
setEps(double) - Method in class ffx.algorithms.cli.MinimizeOptions
 
setEpsh(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the water hydrogen epsilon parameter.
setEpsilon(int) - Method in class ffx.crystal.HKL
setEpsilon
setEpso(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the water oxygen epsilon parameter.
setEquilibration(boolean) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
Sets the value of the boolean equilibration variables to true or false to either allow an equilibration step or skip it.
setEquilibrationSteps(long) - Method in class ffx.algorithms.cli.ThermodynamicsOptions
 
setEvenSpacePhLadder(double, double, int) - Static method in class ffx.algorithms.dynamics.PhReplicaExchange
Sets an even pH ladder based on the pH gap.
setEwaldErrorTolerance(double) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the Ewald error tolerance for the multipole force.
setEwaldParameters(double, double) - Method in class ffx.potential.nonbonded.pme.EwaldParameters
Determine the real space Ewald parameters and permanent multipole self energy.
setExceptionParameters(int, int, int, double, double, double) - Method in class ffx.openmm.NonbondedForce
Set the exception parameters.
setExclude(double) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
setExponent(double) - Method in class ffx.algorithms.cli.RepExOptions
 
setExponentialTemperatureLadder(double, double) - Method in class ffx.algorithms.dynamics.ReplicaExchange
setExponentialTemperatureLadder.
setExtendedSystem(ExtendedSystem) - Method in class ffx.potential.parsers.XPHFilter
 
setExtent(int, int, int) - Method in class ffx.realspace.RealSpaceRefinementData
Setter for the field extent.
setExtrapolationCoefficients(DoubleArray) - Method in class ffx.openmm.amoeba.MultipoleForce
Set extrapolation coefficients.
setF(int, double) - Method in class ffx.xray.DiffractionRefinementData
Set amplitude (F).
setFactor(double) - Method in class ffx.ui.behaviors.MouseOrbit
Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseProperties
Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseRotate
Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseSelection
Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseTranslate
Set the x-axis amd y-axis movement multipler with factor.
setFactor(double) - Method in class ffx.ui.behaviors.MouseZoom
Set the y-axis movement multipler with factor.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseOrbit
Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseProperties
Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseRotate
Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseSelection
Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactor(double, double) - Method in class ffx.ui.behaviors.MouseTranslate
Set the x-axis amd y-axis movement multipler with xFactor and yFactor respectively.
setFactors() - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Overriden by the OST version which updates only during setLambda().
setFactors() - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsOST
 
setFactors() - Method in class ffx.potential.nonbonded.VanDerWaals.LambdaFactors
Overriden by the OST version which updates only during setLambda().
setFactors() - Method in class ffx.potential.nonbonded.VanDerWaals.LambdaFactorsOST
 
setFactors(int, int, LambdaMode) - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
Overriden by the ESV version which updates with every softcore interaction.
setFactors(int, int, LambdaMode) - Method in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsESV
 
setFallbackDynFile(File) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Sets the "fallback" .dyn file to write to if none is passed to the dynamic method.
setFc(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData
set complex Fc
setFcTot(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData
setFcTot
setFile(File) - Method in class ffx.potential.MolecularAssembly
Setter for the field file.
setFile(File) - Method in class ffx.potential.parsers.SystemFilter
setFile
setFileRead(boolean) - Method in class ffx.potential.parsers.SystemFilter
Setter for the field fileRead.
setFiles(List<File>) - Method in class ffx.potential.parsers.SystemFilter
Setter for the field files.
setFileType(String) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Method to set file type from groovy scripts.
setFileType(String) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
Method to set file type from groovy scripts.
setFinalized(boolean) - Method in class ffx.potential.bonded.MSGroup
Specifies whether the MultiScaleGroup has been finalized.
setFinalized(boolean) - Method in class ffx.potential.bonded.MultiResidue
Specifies whether the MultiScaleGroup has been finalized.
setFinish(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setFirstDir(int) - Method in class ffx.algorithms.cli.MultiDynamicsOptions
 
setFirstSystemAlchemistry(MolecularAssembly) - Method in class ffx.potential.cli.AlchemicalOptions
Set the alchemical atoms for this molecularAssembly.
setFirstSystemUnchargedAtoms(MolecularAssembly) - Method in class ffx.potential.cli.AlchemicalOptions
Set uncharged atoms for this molecularAssembly.
setFixedTautomerState(boolean) - Method in class ffx.potential.extended.ExtendedSystem
Does not allow for changes to the tautomer states of tautomerizing residues
setFixedTitrationState(boolean) - Method in class ffx.potential.extended.ExtendedSystem
Does not allow for changes to the tautomer states of titrating residues
setFixLattice(boolean) - Method in class ffx.potential.parsers.CIFFilter
Determine whether lattice parameters can be manipulated to follow lattice system constraints.
setFoFc1(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData
setFoFc1
setFoFc2(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData
setFoFc2
setForceField(ForceField) - Method in class ffx.potential.MolecularAssembly
Setter for the field forceField.
setForceField(ForceField) - Method in class ffx.potential.parsers.SystemFilter
Setter for the field forceField.
setForceGroup(int) - Method in class ffx.openmm.Force
Set the force group.
setForceIndex(int) - Method in class ffx.openmm.Force
Set the force index.
setFormFactorIndex(int) - Method in class ffx.potential.bonded.Atom
Setter for the field formFactorIndex.
setFormFactorWidth(double) - Method in class ffx.potential.bonded.Atom
Setter for the field formFactorWidth.
setFractionalCoordinateMode(MolecularAssembly.FractionalMode) - Method in class ffx.potential.XtalEnergy
setFractionalCoordinateMode.
setFractionalMode(MolecularAssembly.FractionalMode) - Method in class ffx.potential.MolecularAssembly
Setter for the field fractionalMode.
setFrame(int) - Method in class ffx.ui.Trajectory
setFrame
setFreeR(int, int) - Method in class ffx.xray.DiffractionRefinementData
Set FreeR value flag of a reflection.
setFreeRFlag(int) - Method in class ffx.xray.DiffractionRefinementData
Set FreeR value flag.
setFrequency(int) - Method in class ffx.openmm.MonteCarloBarostat
Set the frequency.
setFs(int, ComplexNumber) - Method in class ffx.xray.DiffractionRefinementData
setFs
setFSigF(int, double, double) - Method in class ffx.xray.DiffractionRefinementData
Set amplitude and sigF.
setGlobalCenter(double[]) - Method in class ffx.ui.GraphicsEvents
setGlobalCenter
setGradient(boolean) - Method in class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
 
setH(int) - Method in class ffx.crystal.HKL
h
setHardWallConstraint(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
If this flag is true, (lambda, dU/dL) Monte Carlo samples that have no weight in the Histogram are rejected.
setHeader(String, String) - Method in class edu.rit.http.HttpResponse
Set the given header in this HTTP response.
setHetero(boolean) - Method in class ffx.potential.bonded.Atom
setHetero
setHistogramFile(File) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
setHistogramIndex(int) - Method in class ffx.algorithms.thermodynamics.LambdaData
 
setHistogramRead(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
setHistograms(OrthogonalSpaceTempering.Histogram[], int[]) - Method in class ffx.algorithms.thermodynamics.SendSynchronous
Update the synchronous communication histograms.
setID(String) - Method in class ffx.potential.bonded.BondedTerm
Sets the Term's id.
setID_Key(boolean) - Method in class ffx.potential.bonded.BondedTerm
setID_Key
setImproperTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the ImproperTorsion node to t.
setInactiveAtoms(String) - Method in class ffx.algorithms.misc.GenerateRotamers
Inactivates atom sets defined by 'start-end,start-end,...'.
setIncludeCavityTerm(int) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the include cavity term.
setIncrement(double) - Method in class ffx.algorithms.misc.GenerateRotamers
Sets the angle to change torsions by.
setIncrement(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setIncrement(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the residue increment for sliding window.
setIndependentWalkers(boolean) - Method in class ffx.algorithms.cli.OSTOptions
 
setIndependentWalkers(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
Sets the value of independentWalkers; if true, it also sets writeIndependent to true.
setIndex(int) - Method in class ffx.crystal.HKL
index
setInducedDipole(double[], double[]) - Method in class ffx.numerics.multipole.PolarizableMultipole
Set the induced dipole.
setInducedDipoleReferences(double[][][], double[][][], boolean) - Method in class ffx.potential.nonbonded.ScfPredictor
To be called upon initialization and update of inducedDipole arrays in parent.
setInitValue(double) - Method in class ffx.potential.nonbonded.RowRegion
Setter for the field initValue.
setInitValue(double) - Method in class ffx.potential.nonbonded.SliceRegion
Setter for the field initValue.
setInitValue(double) - Method in class ffx.potential.nonbonded.SpatialDensityRegion
Setter for the field initValue.
setInnerTimeSteps(int) - Method in class ffx.algorithms.dynamics.integrators.Respa
Set inner Respa number of time steps.
setIntegrator(IntegratorEnum) - Method in class ffx.algorithms.cli.DynamicsOptions
Set the integrator.
setIntegratorString(String) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setIntermolecular(boolean) - Method in class ffx.potential.nonbonded.NeighborList
Setter for the field intermolecular.
setIntervalSteps(int) - Method in class ffx.algorithms.dynamics.MolecularDynamics
No-op; FFX does not need to occasionally return information from FFX.
setIntervalSteps(int) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
Setter for the field intervalSteps.
setIsotropic(boolean) - Method in class ffx.algorithms.cli.BarostatOptions
 
setIsotropic(boolean) - Method in class ffx.algorithms.dynamics.Barostat
Restrict the MC Barostat to isotropic moves.
setIterations(int) - Method in class ffx.algorithms.cli.MinimizeOptions
 
setIterations(int) - Method in class ffx.algorithms.mc.MCLoop
Setter for the field iterations.
setK(int) - Method in class ffx.crystal.HKL
k
setKey(int[]) - Method in class ffx.potential.parameters.BaseType
Setter for the field key.
setKey(String) - Method in class ffx.potential.parameters.BaseType
Setter for the field key.
setKeyFile(File) - Method in class ffx.ui.FFXSystem
Setter for the field keyFile.
setKeywordGroup(String) - Method in class ffx.ui.KeywordPanel
Make the passed Keyword Group active in the editor.
setKeywords(Hashtable<String, Keyword>) - Method in class ffx.ui.FFXSystem
Setter for the field keywords.
setKeywordValue(String, String) - Method in class ffx.ui.KeywordPanel
Load a value into a KeywordComponent.
setKineticEnergy(double) - Method in class ffx.potential.SystemState
Set the kinetic energy.
setKTScale(double) - Method in class ffx.xray.RefinementEnergy
set the current kT scaling weight
setL(int) - Method in class ffx.crystal.HKL
l
setLambda(double) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
Calls on the OST method set lambda to update lambda to the current value in this class
setLambda(double) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Setter for the field lambda.
setLambda(double) - Method in class ffx.potential.ANIEnergy
 
setLambda(double) - Method in class ffx.potential.bonded.AngleTorsion
Set the current value of the state variable.
setLambda(double) - Method in interface ffx.potential.bonded.LambdaInterface
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.PiOrbitalTorsion
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.RestraintBond
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.RestraintTorsion
 
setLambda(double) - Method in class ffx.potential.bonded.StretchTorsion
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.Torsion
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.bonded.TorsionTorsion
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.DualTopologyEnergy
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.ForceFieldEnergy
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.COMRestraint
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.NCSRestraint
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.RestrainPosition
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.nonbonded.VanDerWaals
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.openmm.OpenMMEnergy
Set the current value of the state variable.
setLambda(double) - Method in class ffx.potential.openmm.OpenMMSystem
Set the overall lambda value for the system.
setLambda(double) - Method in class ffx.potential.QuadTopologyEnergy
Set the current value of the state variable.
setLambda(double) - Method in class ffx.realspace.RealSpaceData
Set the current value of the state variable.
setLambda(double) - Method in class ffx.realspace.RealSpaceEnergy
Set the current value of the state variable.
setLambda(double) - Method in class ffx.xray.RefinementEnergy
Set the current value of the state variable.
setLambda(double) - Method in class ffx.xray.XRayEnergy
Set the current value of the state variable.
setLambdaBinWidth(double) - Method in class ffx.algorithms.thermodynamics.HistogramData
Sets lambdaBinWidth; if an invalid value is provided (not 0-1), resets it to default 0.005.
setLambdaFile(File) - Method in class ffx.algorithms.thermodynamics.LambdaData
 
setLambdaFriction(double) - Method in class ffx.algorithms.cli.LambdaParticleOptions
 
setLambdaMass(double) - Method in class ffx.algorithms.cli.LambdaParticleOptions
 
setLambdaRead(boolean) - Method in class ffx.algorithms.thermodynamics.LambdaData
 
setLambdaStart(double) - Method in class ffx.potential.openmm.OpenMMEnergy
 
setLambdaStdDev(double) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
Calls on LambdaMove class method setLambdaStdDev to update the lambda standard deviation to the current value in this class
setLambdaTerm(boolean) - Method in class ffx.potential.nonbonded.COMRestraint
Setter for the field lambdaTerm.
setLambdaTerm(boolean) - Method in class ffx.potential.openmm.OpenMMEnergy
Set the lambdaTerm flag.
setLambdaTorsion(double) - Method in class ffx.potential.openmm.ImproperTorsionForce
Set the lambda torsion scale factor.
setLambdaTorsion(double) - Method in class ffx.potential.openmm.TorsionForce
Set the lambda torsion scale factor.
setLambdaWriteOut(double) - Method in class ffx.algorithms.cli.OSTOptions
 
setLambdaXYZGradient(double, double, double) - Method in class ffx.potential.bonded.Atom
setLambdaXYZGradient
setLastReceiveddUdL(double) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
 
setLastReceivedLambda(double) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
 
setLeaf(int, int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
setLibrary(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setLink(boolean) - Method in class ffx.potential.bonded.Polymer
Setter for the field link.
setListResidues(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setLMN(int[]) - Method in class ffx.potential.parsers.PDBFilter
 
setLocale(String, String) - Method in class ffx.ui.properties.FFXLocale
setLocale
setLogFile(File) - Method in class ffx.ui.FFXSystem
Setter for the field logFile.
setLogMode(String) - Method in class ffx.ui.ModelingPanel
 
setLogWrites(boolean) - Method in class ffx.potential.parsers.PDBFilter
Sets whether this PDBFilter should log each time it saves to a file.
setLow(double) - Method in class ffx.algorithms.cli.AnnealOptions
 
setMainPanel(MainPanel) - Method in class ffx.ui.LogHandler
A reference to the Force Field X MainPanel container to shut down if we encounter a fatal (SEVERE) exception.
setMass(double) - Method in class ffx.potential.bonded.Atom
Set the Atomic Mass.
setMass(double[]) - Method in class ffx.potential.SystemState
Set the mass of each degree of freedom.
setMatrix(int, int, double[][]) - Method in class edu.rit.io.DoubleMatrixFile
Set this matrix file's number of rows, number of columns, and underlying matrix.
setMaxAM(double) - Method in class ffx.algorithms.cli.BarostatOptions
 
setMaxAngleMove(double) - Method in class ffx.algorithms.dynamics.Barostat
Setter for the field maxAngleMove.
setMaxD(double) - Method in class ffx.algorithms.cli.BarostatOptions
 
setMaxDensity(double) - Method in class ffx.algorithms.dynamics.Barostat
Setter for the field maxDensity.
setMaxRotCheckDepth(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Control the depth of self-consistency checking with a rotamer is eliminated.
setMaxV(double) - Method in class ffx.algorithms.cli.BarostatOptions
 
setMaxVolumeMove(double) - Method in class ffx.algorithms.dynamics.Barostat
Setter for the field maxVolumeMove.
setMcHardWall(boolean) - Method in class ffx.algorithms.cli.OSTOptions
 
setMcLambdaStdDev(double) - Method in class ffx.algorithms.cli.OSTOptions
 
setMcMDSteps(int) - Method in class ffx.algorithms.cli.OSTOptions
 
setMDIntervalSteps(int) - Method in class ffx.algorithms.mc.MDMove
 
setMeanBarostatInterval(int) - Method in class ffx.algorithms.dynamics.Barostat
Setter for the field meanBarostatInterval.
setMessage(int) - Method in class ffx.ui.commands.SimulationMessage
Setter for the field message.
setMetaDynamics(boolean) - Method in class ffx.algorithms.cli.OSTOptions
 
setMetaDynamics(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
setMinD(double) - Method in class ffx.algorithms.cli.BarostatOptions
 
setMinDensity(double) - Method in class ffx.algorithms.dynamics.Barostat
Setter for the field minDensity.
setMinimumNumberAcceptedNARotamers(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the minimum number of accepted nucleic acid rotamers.
setModelNumbering(int) - Method in class ffx.potential.parsers.PDBFilter
setModelNumbering.
setModRes(boolean) - Method in class ffx.potential.bonded.Atom
setModRes
setMolecularAssembly(MolecularAssembly) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
 
setMoleculeNumber(int) - Method in class ffx.potential.bonded.Atom
Setter for the field moleculeNumber.
setMonteCarlo(boolean) - Method in class ffx.algorithms.cli.OSTOptions
 
setMonteCarlo(boolean) - Method in class ffx.algorithms.cli.RepExOptions
 
setMonteCarlo(boolean, int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the option to use a number of Monte Carlo steps for final optimization.
setMonteCarlo(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setMonteCarloTesting(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the monteCarloTesting boolean in RotamerOptimization.java to true or false.
setMouseButton(int) - Method in class ffx.ui.behaviors.MouseTranslate
Setter for the field mouseButton.
setMouseButton(int) - Method in class ffx.ui.behaviors.MouseZoom
Setter for the field mouseButton.
setMoveSize(double) - Method in class ffx.algorithms.mc.LambdaMove
Get the Lambda move size, which is a standard deviation for continuous moves or step size for discrete moves.
setMultipoleParameters(int, double, DoubleArray, DoubleArray, int, int, int, int, double, double, double) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the multipole parameters.
setMultipoleType(MultipoleType) - Method in class ffx.potential.bonded.Atom
Setter for the field multipoleType.
setMutualInducedMaxIterations(int) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the mutual induced target maximum number of iterations.
setMutualInducedTargetEpsilon(double) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the mutual induced target epsilon.
setNaLibraryName(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setName(String) - Method in class ffx.openmm.Force
Set the name of the force.
setName(String) - Method in class ffx.potential.bonded.Molecule
Sets the name of this NodeObject to n.
setName(String) - Method in class ffx.potential.bonded.MSNode
Sets the name of this NodeObject to n.
setName(String) - Method in class ffx.potential.bonded.Residue
 
setNB(int) - Method in class ffx.xray.XRayEnergy
set the number of B factor parameters
setNBFGS(int) - Method in class ffx.algorithms.cli.MinimizeOptions
 
setnChild(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
setnCritical(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
setNeighborList(int[][][]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
setNeighborList.
setNeuralNetwork(boolean) - Method in class ffx.potential.bonded.Atom
If true, this atom is part of a molecule whose intramolecular interactions are handled by a neural network.
setNI(int, int, int) - Method in class ffx.realspace.RealSpaceRefinementData
setNI.
setNOcc(int) - Method in class ffx.xray.XRayEnergy
set the number of occupancy parameters
setNonbondedMethod(int) - Method in class ffx.openmm.amoeba.GKCavitationForce
Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the nonbonded method for the multipole force.
setNonbondedMethod(int) - Method in class ffx.openmm.amoeba.VdwForce
Set the non-bonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.CustomNonbondedForce
Set the nonbonded method.
setNonbondedMethod(int) - Method in class ffx.openmm.NonbondedForce
Set the nonbonded method.
setNoOriginal(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setNsymm(int) - Method in class ffx.potential.nonbonded.RowLoop
setNsymm
setNsymm(int) - Method in class ffx.potential.nonbonded.SliceLoop
setNsymm
setNsymm(int) - Method in class ffx.potential.nonbonded.SpatialDensityLoop
setNsymm
setNucleicCorrectionThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
The nucleic acid correction threshold.
setNucleicPruningFactor(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Also sets derivative pruning factors.
setNumber(int) - Method in class ffx.potential.bonded.Residue
setNumber
setNumBoxes(String) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setNumLeaves(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
setNumXYZBoxes(int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the number of boxes in the x, y, and z axes if the box optimization is to be carried out.
setNXYZ(int) - Method in class ffx.xray.XRayEnergy
set the number of xyz parameters
setObtainVelAcc(boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Not meaningful for FFX dynamics (no need to obtain velocities/accelerations from a different program, especially one running on a GPU).
setObtainVelAcc(boolean) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
Sets whether to obtain all variables (velocities, gradients) from OpenMM, or just positions and energies.
setOccupancies(double[]) - Method in class ffx.xray.XRayEnergy
set atom occupancies based on current position
setOccupancy(double) - Method in class ffx.potential.bonded.Atom
Setter for the field occupancy.
setOccupancyAcceleration(double) - Method in class ffx.potential.bonded.Atom
Setter for the field occupancyAcceleration.
setOccupancyGradient(double) - Method in class ffx.potential.bonded.Atom
Setter for the field occupancyGradient.
setOccupancyPreviousAcceleration(double) - Method in class ffx.potential.bonded.Atom
Setter for the field occupancyPreviousAcceleration.
setOccupancyVelocity(double) - Method in class ffx.potential.bonded.Atom
Setter for the field occupancyVelocity.
setOctant(int) - Method in class ffx.potential.nonbonded.SpatialDensityLoop
Setter for the field octant.
setOffset(Vector3d) - Method in class ffx.potential.MolecularAssembly
Setter for the field offset.
setOptimization(boolean, MolecularAssembly) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters
setOptimization.
setOptimize(boolean) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setOrigin(int, int, int) - Method in class ffx.realspace.RealSpaceRefinementData
Setter for the field origin.
setOriginalCoordinates(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setOSXProperties() - Static method in class ffx.ui.OSXAdapter
Set Mac OS X Systems Properties to promote native integration.
setOutOfPlaneBends(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the Out-of-Plane Bend node to t.
setOutOfPlaneBends(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the Out-of-Plane Bend node to t.
setOutOfPlaneBendType(OutOfPlaneBendType) - Method in class ffx.potential.bonded.OutOfPlaneBend
Set a reference to the force field parameters for this Angle.
setPairClashThreshold(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setPairClashThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Setter for the field pairClashThreshold.
setParallel(boolean) - Method in class ffx.potential.DualTopologyEnergy
setParallel.
setParallel(boolean) - Method in class ffx.potential.QuadTopologyEnergy
setParallel.
setParameter(String, double) - Method in class ffx.openmm.Context
Set a parameter value.
setParentIndex(int) - Method in class ffx.potential.nonbonded.octree.OctreeCell
 
setParticleExclusions(int, IntArray) - Method in class ffx.openmm.amoeba.VdwForce
Set the particle exclusions.
setParticleMass(int, double) - Method in class ffx.openmm.System
Set the mass of a particle.
setParticleParameters(int, double, double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the parameters for a particle.
setParticleParameters(int, double, double, double) - Method in class ffx.openmm.NonbondedForce
Set the particle parameters.
setParticleParameters(int, double, double, int) - Method in class ffx.openmm.amoeba.GKCavitationForce
Set the parameters for an atom in the Cavitation force.
setParticleParameters(int, int, double, double, double, int, int, double) - Method in class ffx.openmm.amoeba.VdwForce
Set the particle parameters.
setParticleParameters(int, DoubleArray) - Method in class ffx.openmm.CustomGBForce
Set the particle parameters.
setParticleParameters_1(int, double, double, double, double, double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the particle parameters.
setPeriodicBoxVectors(OpenMM_Vec3, OpenMM_Vec3, OpenMM_Vec3) - Method in class ffx.openmm.Context
Set the periodic box vectors.
setPeriodicBoxVectors(Crystal) - Method in class ffx.potential.openmm.OpenMMContext
Set the periodic box vectors for a context based on the crystal instance.
setPermanentMultipole(double[]) - Method in class ffx.numerics.multipole.PolarizableMultipole
Set the permanent multipole.
setPicking(boolean) - Method in class ffx.ui.GraphicsPicking
Setter for the field picking.
setPickMode(int) - Method in class ffx.ui.behaviors.PickOrbitBehavior
Sets the pickMode component of this PickTranslateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickPropertiesBehavior
setPickMode
setPickMode(int) - Method in class ffx.ui.behaviors.PickRotateBehavior
Sets the pickMode component of this PickRotateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickSelectionBehavior
Sets the pickMode component of this PickRotateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickTranslateBehavior
Sets the pickMode component of this PickTranslateBehavior to the value of the passed pickMode.
setPickMode(int) - Method in class ffx.ui.behaviors.PickZoomBehavior
Sets the pickMode component of this PickTranslateBehavior to the value of the passed pickMode.
setPiOrbitalTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.
setPiOrbitalTorsions(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.
setPiOrbitalTorsionType(PiOrbitalTorsionType) - Method in class ffx.potential.bonded.PiOrbitalTorsion
Set the PiOrbitalTorsionType.
setPmeGridDimensions(IntArray) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the PME grid dimensions for the multipole force.
setPMEParameters(double, int, int, int) - Method in class ffx.openmm.NonbondedForce
Set the PME parameters.
setPointer(PointerByReference) - Method in class ffx.openmm.Integrator
Set the OpenMM Integrator pointer.
setPolarization(Polarization) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Setter for the field polarization.
setPolarizationEnergy(double) - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
Set the current polarization energy.
setPolarizationType(int) - Method in class ffx.openmm.amoeba.MultipoleForce
Set the polarization method.
setPolarizeType(PolarizeType) - Method in class ffx.potential.bonded.Atom
Setter for the field polarizeType.
setPosition() - Method in class ffx.ui.GraphicsCanvas
setPosition
setPosition(MSNode) - Method in class ffx.ui.GraphicsCanvas
setPosition
setPositions(double[]) - Method in class ffx.openmm.Context
Set the atomic positions.
setPositions(double[]) - Method in class ffx.potential.openmm.OpenMMContext
The array x contains atomic coordinates only for active atoms.
setPotential(ForceFieldEnergy) - Method in class ffx.potential.MolecularAssembly
setPotential
setPotentialEnergy(double) - Method in class ffx.potential.SystemState
Set the potential energy.
setPressure(double) - Method in class ffx.algorithms.cli.BarostatOptions
 
setPressure(double) - Method in class ffx.algorithms.dynamics.Barostat
Setter for the field pressure.
setPreviousAcceleration(double[]) - Method in class ffx.algorithms.dynamics.Barostat
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in interface ffx.numerics.Potential
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.ANIEnergy
 
setPreviousAcceleration(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field previousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.DualTopologyEnergy
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
setPreviousAcceleration(double[]) - Method in class ffx.potential.ForceFieldEnergy
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.QuadTopologyEnergy
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.potential.XtalEnergy
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.realspace.RealSpaceEnergy
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.xray.RefinementEnergy
setPreviousAcceleration.
setPreviousAcceleration(double[]) - Method in class ffx.xray.XRayEnergy
setPreviousAcceleration.
setPreviousAccelerations(double[]) - Method in class ffx.potential.SystemState
Set the previous accelerations via a copy of the passed array into the internal array.
setPrint(boolean) - Method in class ffx.algorithms.mc.BoltzmannMC
Sets whether the implementation prints its own messages.
setPrint(boolean) - Method in interface ffx.algorithms.mc.MetropolisMC
Sets whether the implementation prints its own messages.
setPrint(boolean) - Method in class ffx.algorithms.misc.GenerateRotamers
Sets algorithm to log all torsions/energies (not just to file).
setPrintFiles(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets whether rotamer optimization should print out any files, or act solely to optimize a structure in memory.
setPrintInt(int) - Method in class ffx.algorithms.cli.BarostatOptions
 
setPrintInterval(double) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
Setter for the field printInterval.
setPrintOnFailure(boolean, boolean) - Method in class ffx.potential.DualTopologyEnergy
Sets the printOnFailure flag; if override is true, over-rides any existing property.
setPrintOnFailure(boolean, boolean) - Method in class ffx.potential.ForceFieldEnergy
Sets the printOnFailure flag; if override is true, over-rides any existing property.
setPrintOnFailure(boolean, boolean) - Method in class ffx.potential.QuadTopologyEnergy
Sets the printOnFailure flag; if override is true, over-rides any existing property.
setPrintOnFailure(boolean, boolean) - Method in class ffx.xray.RefinementEnergy
Sets the printOnFailure flag; if override is true, over-rides any existing property.
setProbe(double) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
setProbeRadius(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the probe radius.
setPropagateLambda(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Indicate if the Lambda extended system particle should be propagated using Langevin dynamics.
setProperties(CompositeConfiguration) - Method in class ffx.potential.parsers.SystemFilter
Setter for the field properties.
setProperties(CommandLine.ParseResult, CompositeConfiguration) - Method in class ffx.xray.cli.XrayOptions
setProperties.
setPropertyDefaultValue(String, String) - Method in class ffx.openmm.Platform
Set an OpenMM Platform property.
setPrune(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setPruning(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets level of pruning: 0 for fully off, 1 for only singles, 2 for single and pair pruning.
setQIVector(double[]) - Method in class ffx.numerics.multipole.QIFrame
Update the QIFrame rotation matrix.
setQIVector(double, double, double) - Method in class ffx.numerics.multipole.QIFrame
Update the QIFrame rotation matrix.
setQuiet(boolean) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Setter for the field quiet.
setR(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell
Sets cell radius
setR(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
Set the separation vector.
setR(double, double, double) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
Set the separation vector.
setR(double, double, double) - Method in class ffx.numerics.multipole.CoulombTensorQI
Set the separation vector.
setR(double, double, double) - Method in class ffx.numerics.multipole.MultipoleTensor
Set the separation vector.
setRandomNumberSeed(int) - Method in class ffx.openmm.LangevinIntegrator
Set the random number seed.
setRandomNumberSeed(int) - Method in class ffx.openmm.MonteCarloBarostat
Set the random number seed.
setRandomSeed(int) - Method in class ffx.algorithms.mc.BoltzmannMC
Set the random seed.
setRandomSeed(long) - Method in class ffx.algorithms.dynamics.integrators.Stochastic
Initialize the Random number generator used to apply random forces to the particles.
setRandomSeed(long) - Method in class ffx.algorithms.dynamics.thermostats.Bussi
The setRandomSeed method is used to initialize the Random number generator to the same starting state, such that separate runs produce the same Maxwell-Boltzmann initial velocities.
setRandomSeed(long) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
The setRandomSeed method is used to initialize the Random number generator to the same starting state, such that separate runs produce the same Maxwell-Boltzmann initial velocities.
setRandomSymOp(double) - Method in class ffx.algorithms.cli.RandomUnitCellOptions
 
setRandomUnitCell(double) - Method in class ffx.algorithms.cli.RandomUnitCellOptions
 
setRate(int) - Method in class ffx.ui.Trajectory
setRate
setRecip(double[]) - Method in class ffx.numerics.fft.Complex3D
Setter for the field recip.
setRecip(double[]) - Method in class ffx.numerics.fft.Complex3DParallel
Setter for the field recip.
setRecip(double[]) - Method in class ffx.numerics.fft.Real3D
Setter for the field recip.
setRecip(double[]) - Method in class ffx.numerics.fft.Real3DParallel
Setter for the field recip.
setRedXYZ(double[]) - Method in class ffx.potential.bonded.Atom
setXYZ
setRefinementData(RealSpaceRefinementData[]) - Method in class ffx.realspace.RealSpaceData
Setter for the field refinementData.
setRefinementMode(RefinementMinimize.RefinementMode) - Method in class ffx.realspace.RealSpaceEnergy
Setter for the field refinementMode.
setRefinementMode(RefinementMinimize.RefinementMode) - Method in class ffx.xray.XRayEnergy
Setter for the field refinementMode.
setRegion(SpatialDensityRegion) - Method in class ffx.potential.nonbonded.SpatialDensityLoop
setRegion.
setReinitVelocities(boolean) - Method in class ffx.algorithms.cli.AnnealOptions
 
setRemoveCenterOfMassMotion(boolean) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
If center of mass motion is being removed, then the mean kinetic energy of the system will be 3 kT/2 less than if center of mass motion is allowed.
setRepEx(boolean) - Method in class ffx.algorithms.cli.RepExOptions
 
setRepexFrequency(double) - Method in class ffx.algorithms.cli.RepexOSTOptions
 
setReplicaSteps(int) - Method in class ffx.algorithms.cli.RepExOptions
 
setReport(double) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setResetHistogramAtLambda(double) - Method in class ffx.algorithms.thermodynamics.HistogramData
Set the lambda value at which to reset the histogram.
setResetNumSteps(boolean) - Method in class ffx.algorithms.cli.ThermodynamicsOptions
 
setResidueNum(int) - Method in class ffx.potential.bonded.Molecule
Setter for the field residueNum.
setResidueNumber(int) - Method in class ffx.potential.bonded.Atom
setResidueNumber
setResidues(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the residue list.
setResiduesIgnoreNull(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization
Accepts a list of residues but throws out null residues.
setResName(String) - Method in class ffx.potential.bonded.Atom
Setter for the field resName.
setResolution(Atom.Resolution) - Method in class ffx.potential.bonded.Atom
Setter for the field resolution.
setRestartFile(File) - Method in class ffx.potential.extended.ExtendedSystem
Sets the restartFile field of this extended system to the passed file.
setRestartFrequency(double) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Method to set the Restart Frequency.
setRestartFrequency(double) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
Method to set the Restart Frequency.
setRevert(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setRevert(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization
Set the algorithm to revert to starting coordinates if the energy increases.
setRigidScale(double) - Method in class ffx.potential.bonded.Angle
Setter for the field rigidScale.
setRigidScale(double) - Method in class ffx.potential.bonded.Bond
Setter for the field rigidScale.
setRigidScale(double) - Method in class ffx.potential.bonded.StretchBend
Setter for the field rigidScale.
setRigidScale(double) - Method in class ffx.potential.bonded.UreyBradley
Setter for the field rigidScale.
setRminh(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the water hydrogen radius parameter.
setRmino(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the water oxygen radius parameter.
setRotamer(Rotamer) - Method in class ffx.potential.bonded.Residue
Set the current rotamer.
setRotamerLibrary(RotamerLibrary) - Method in class ffx.algorithms.optimize.RotamerOptimization
 
setRotamerPhBias(double, double) - Method in class ffx.potential.parameters.TitrationUtils
 
setRotamers(RotamerLibrary) - Method in class ffx.potential.bonded.MultiResidue
Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.
setRotamers(RotamerLibrary) - Method in class ffx.potential.bonded.Residue
Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.
setRotamerTitration(boolean) - Method in class ffx.potential.parsers.PDBFilter
 
setSaveFrequency(double) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
Sets the frequency of writing to the trajectory file.
setSaveOutput(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setScaling(double[]) - Method in class ffx.algorithms.dynamics.Barostat
Scale the problem.
setScaling(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Scale the problem.
setScaling(double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
setScaling(double[]) - Method in interface ffx.numerics.OptimizationInterface
Scale the problem.
setScaling(double[]) - Method in class ffx.potential.ANIEnergy
 
setScaling(double[]) - Method in class ffx.potential.DualTopologyEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
setScaling(double[]) - Method in class ffx.potential.ForceFieldEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.potential.QuadTopologyEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.potential.XtalEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.realspace.RealSpaceEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.xray.RefinementEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.xray.ScaleBulkEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.xray.SigmaAEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.xray.SplineEnergy
Scale the problem.
setScaling(double[]) - Method in class ffx.xray.XRayEnergy
Scale the problem.
setSearchWidth(double) - Method in class ffx.algorithms.misc.GenerateRotamers
Sets the width around each torsion to search (+/-, so 10 degree width will search a 20 degree arc).
setSecondSystemAlchemistry(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions
Set the alchemical atoms for this topology.
setSecondSystemUnchargedAtoms(MolecularAssembly) - Method in class ffx.potential.cli.TopologyOptions
Set uncharged atoms for this topology.
setSeed(long) - Method in class edu.rit.util.DefaultRandom
Set this PRNG's seed.
setSeed(long) - Method in class edu.rit.util.Mcg1Random
Set this PRNG's seed.
setSeed(long) - Method in class edu.rit.util.Random
Set this PRNG's seed.
setSegID(String) - Method in class ffx.potential.bonded.Atom
Set this atom's seg ID.
setSegID(String) - Method in class ffx.potential.bonded.Polymer
Set the Polymer segID.
setSegID(String) - Method in class ffx.potential.bonded.Residue
Setter for the field segID.
setSelected(boolean) - Method in class ffx.potential.bonded.Atom
Setter for the field selected.
setSelected(boolean) - Method in class ffx.potential.bonded.BondedTerm
Setter for the field selected.
setSelected(boolean) - Method in class ffx.potential.bonded.MSNode
Setter for the field selected.
setSelf(int, int, double) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
 
setSelf(int, int, double, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Stores a self energy in the self energy matrix.
setSgName(String) - Method in class ffx.potential.parsers.CIFFilter
Override the space group of a CIF conversion based on space group name.
setSgNum(int) - Method in class ffx.potential.parsers.CIFFilter
Override the space group of a CIF conversion based on space group number.
setShctd(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the overlap factor.
setSigF(int, double) - Method in class ffx.xray.DiffractionRefinementData
Set amplitude sigma (sigF).
setSingletonClashThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
setSingletonClashThreshold.
setSlevy(double) - Method in class ffx.openmm.amoeba.WcaDispersionForce
Set the Levy parameter.
setSneck(double) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
setSoftcoreAlpha(double) - Method in class ffx.openmm.amoeba.VdwForce
Set the softcore power.
setSoftcorePower(int) - Method in class ffx.openmm.amoeba.VdwForce
Set the softcore power.
setSoluteDielectric(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the solute dielectric constant.
setSoluteOffset(double) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
 
setSoluteRadii(ForceField, Atom[], SoluteType.SOLUTE_RADII_TYPE) - Static method in class ffx.potential.parameters.SoluteType
 
setSoluteType(SoluteType) - Method in class ffx.potential.bonded.Atom
setSoluteType
setSolventAB(double, double) - Method in class ffx.xray.DiffractionData
set the bulk solvent parameters for a given bulk solvent model
setSolventDielectric(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the solvent dielectric constant.
setSolventPressure(double) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
setSpecialPositionCutoff(double) - Method in class ffx.crystal.Crystal
Setter for the field specialPositionCutoff.
setSpecialPositionSymOps(List<Integer>) - Method in class ffx.potential.bonded.Atom
Set the symmetry operations that leave this atom's molecule at a special position.
setStart(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setStatusCode(HttpResponse.Status) - Method in class edu.rit.http.HttpResponse
Set this HTTP response's status code.
setStep(int) - Method in class ffx.ui.commands.SimulationMessage
Setter for the field step.
setSteps(long) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setStepsTaken(int) - Method in class ffx.algorithms.thermodynamics.LambdaData
 
setStretchBends(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the Stretch-Bends node to t.
setStretchBends(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the Stretch-Bends node to t.
setStretchBendType(StretchBendType) - Method in class ffx.potential.bonded.StretchBend
Setter for the field stretchBendType.
setStretchTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the MultiScaleGroup's stretch-torsion node to t.
setStride(int) - Method in class ffx.xray.parsers.CCP4MapWriter
Set the stepping across the array (e.g.
setSuperpositionThreshold(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Setter for the field superpositionThreshold.
setSurfaceAreaFactor(double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the surface area factor.
setSurfaceTension(double) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
 
setSurfaceTension(double) - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
 
setSwitchingDistance(double) - Method in class ffx.openmm.CustomNonbondedForce
Set the switching distance.
setSwitchingDistance(double) - Method in class ffx.openmm.NonbondedForce
Set the switching distance.
setSymOp(int) - Method in class ffx.potential.parsers.PDBFilter
setSymOp.
setSynchronous(boolean) - Method in class ffx.algorithms.cli.MultiDynamicsOptions
 
setTanhBetas(double[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
 
setTanhParameters(double, double, double) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the tanh parameters.
setTanhRescaling(int) - Method in class ffx.openmm.amoeba.GeneralizedKirkwoodForce
Set the tanh rescaling.
setTargetTemperature(double) - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic
Set the target temperature.
setTargetTemperature(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Set the target temperature.
setTau(double) - Method in class ffx.algorithms.dynamics.thermostats.Berendsen
Setter for the field tau.
setTau(double) - Method in class ffx.algorithms.dynamics.thermostats.Bussi
Setter for the field tau.
setTautomerLambda(Residue, double) - Method in class ffx.potential.extended.ExtendedSystem
Set the tautomer lambda of a residue and update corresponding theta
setTautomerLambda(Residue, double, boolean) - Method in class ffx.potential.extended.ExtendedSystem
Set the tautomer lambda of a residue and update corresponding theta if desired
setTemperAfter(int) - Method in class ffx.algorithms.cli.AnnealOptions
 
setTemperature(double) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setTemperature(double) - Method in class ffx.algorithms.dynamics.Barostat
Set the Metropolis Monte Carlo temperature.
setTemperature(double) - Method in class ffx.algorithms.dynamics.integrators.Stochastic
Setter for the field temperature.
setTemperature(double) - Method in class ffx.algorithms.mc.BoltzmannMC
Sets temperature of Monte Carlo criterion.
setTemperature(double) - Method in interface ffx.algorithms.mc.MetropolisMC
Sets temperature of Monte Carlo criterion.
setTemperature(double) - Method in class ffx.potential.extended.ExtendedSystem
setTemperature.
setTemperature(double) - Method in class ffx.potential.SystemState
Set the temperature.
setTemperatures(double[]) - Method in class ffx.algorithms.dynamics.ReplicaExchange
Setter for the field temperatures.
setTemperBefore(int) - Method in class ffx.algorithms.cli.AnnealOptions
 
setTemperingFactor(double) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
setTemperingOffset(double) - Method in class ffx.algorithms.thermodynamics.HistogramData
Sets an explicit tempering offset in kcal/mol.
setTemperingRate(double[]) - Method in class ffx.algorithms.cli.OSTOptions
 
setTemperingThreshold(double[]) - Method in class ffx.algorithms.cli.OSTOptions
 
setTemperString(String) - Method in class ffx.algorithms.cli.AnnealOptions
 
setTempFactor(double) - Method in class ffx.potential.bonded.Atom
Setter for the field tempFactor.
setTempFactorAcceleration(double) - Method in class ffx.potential.bonded.Atom
Setter for the field tempFactorAcceleration.
setTempFactorGradient(double) - Method in class ffx.potential.bonded.Atom
Setter for the field tempFactorGradient.
setTempFactorPreviousAcceleration(double) - Method in class ffx.potential.bonded.Atom
Setter for the field tempFactorPreviousAcceleration.
setTempFactorVelocity(double) - Method in class ffx.potential.bonded.Atom
Setter for the field tempFactorVelocity.
setTensor(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
Set the tensor components.
setTerms(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the MultiScaleGroup's terms node to t.
setTerms(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the MultiScaleGroup's terms node to t.
setThermoAlgoString(String) - Method in class ffx.algorithms.cli.ThermodynamicsOptions
 
setThermostat(Thermostat) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Setter for the field thermostat.
setThermostat(Thermostat) - Method in class ffx.xray.RefinementEnergy
Setter for the field thermostat.
setThermostat(ThermostatEnum) - Method in class ffx.algorithms.cli.DynamicsOptions
Set the thermostat.
setThermostatString(String) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setThole(double, double) - Method in class ffx.numerics.multipole.TholeTensorGlobal
Set Thole damping parameters
setThole(double, double) - Method in class ffx.numerics.multipole.TholeTensorQI
Set Thole damping parameters
setThreeBody(boolean) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setThreeBodyCutoff(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setThreeBodyCutoff(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the threeBodyCutoffDist.
setThreeBodyEnergy(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization
Flag to control use of 3-body energy terms.
setTime(double) - Method in class ffx.ui.commands.SimulationMessage
Setter for the field time.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.BetterBeeman
Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.Integrator
Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.Respa
Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.Stochastic
Set the time step.
setTimeStep(double) - Method in class ffx.algorithms.dynamics.integrators.VelocityVerlet
Set the time step.
setTitrationLambda(Residue, double) - Method in class ffx.potential.extended.ExtendedSystem
Set the titration lambda of a residue and update corresponding theta
setTitrationLambda(Residue, double, boolean) - Method in class ffx.potential.extended.ExtendedSystem
Set the titration lambda of a residue and update corresponding theta if desired
setTitrationPH(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setTitrationUtils(TitrationUtils) - Method in class ffx.potential.bonded.Residue
 
SettleConstraint - Class in ffx.potential.constraint
SETTLE triatomic distance constraints, intended for rigid water models.
settleFactory(Angle) - Static method in class ffx.potential.constraint.SettleConstraint
Constructs a SETTLE constraint from an angle and its two bonds.
setTolerance(float) - Method in class ffx.ui.behaviors.PickMouseBehavior
setTolerance
setTorsion(Torsion) - Method in class ffx.potential.bonded.Atom
setTorsion
setTorsionParameters(int, int, int, int, int, int, double, double) - Method in class ffx.openmm.PeriodicTorsionForce
Set the parameters for a torsion.
setTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the MultiScaleGroup's torsion node to t.
setTorsions(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the MultiScaleGroup's torsion node to t.
setTorsionScale(double) - Method in class ffx.potential.bonded.Torsion
Set the torsion scale up factor.
setTorsionTorsionGrid(int, PointerByReference) - Method in class ffx.openmm.amoeba.TorsionTorsionForce
Set the grid for a torsion-torsion.
setTorsionTorsions(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the MultiScaleGroup's Torsion-Torsion node to t.
setTorsionTorsions(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the MultiScaleGroup's Torsion-Torsion node to t.
setTorsionType(TorsionType) - Method in class ffx.potential.bonded.Torsion
Set the torsion type.
setTotalSteps(long) - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
Sets the next number of steps MC-OST should run.
setTrajectory(Trajectory) - Method in class ffx.ui.FFXSystem
Setter for the field trajectory.
setTrajectorySteps(int) - Method in class ffx.algorithms.optimize.anneal.SimulatedAnnealing
Sets the number of steps to use per OpenMM cycle.
setTrajSteps(int) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setTransformGroup(TransformGroup) - Method in class ffx.ui.behaviors.MouseBehavior
Setter for the field transformGroup.
setTransformGroups(TransformGroup, TransformGroup) - Method in class ffx.ui.behaviors.MouseOrbit
setTransformGroups
setTransformGroups(TransformGroup, TransformGroup) - Method in class ffx.ui.behaviors.PickOrbitBehavior
setTransformGroups
setTwoBodyCutoff(double) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setTwoBodyCutoff(double) - Method in class ffx.algorithms.optimize.RotamerOptimization
Sets the twoBodyCutoffDist.
setTwoSidedFiniteDifference(boolean) - Method in class ffx.potential.openmm.OpenMMEnergy
 
setTwoStep(boolean) - Method in class ffx.algorithms.cli.OSTOptions
 
setType(int) - Method in class ffx.ui.commands.SimulationMessage
Setter for the field type.
setType(Utilities.FileType) - Method in class ffx.potential.parsers.SystemFilter
setType
setUnchargedAtoms(MolecularAssembly, String) - Static method in class ffx.potential.cli.AlchemicalOptions
Sets the uncharged atoms for a MolecularAssembly.
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseOrbit
The transformChanged method in the callback class will be called every time the transform is updated
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseProperties
The transformChanged method in the callback class will be called every time the transform is updated
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseRotate
setupCallback
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseSelection
The transformChanged method in the callback class will be called every time the transform is updated
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseTranslate
The transformChanged method in the callback class will be called every time the transform is updated.
setupCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.MouseZoom
The transformChanged method in the callback class will be called every time the transform is updated.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickOrbitBehavior
Register the class @param callback to be called each time the picked object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickPropertiesBehavior
Register the class @param callback to be called each time the picked object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickRotateBehavior
Register the class @param callback to be called each time the picked object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickSelectionBehavior
Register the class @param callback to be called each time the picked * object moves.
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickTranslateBehavior
Register the class @param callback to be called each time the picked object moves
setupCallback(PickingCallback) - Method in class ffx.ui.behaviors.PickZoomBehavior
Register the class @param callback to be called each time the picked object moves.
setUpCallback(MouseBehaviorCallback) - Method in class ffx.ui.behaviors.GlobalBehavior
setUpCallback
setUpdateBondedTerms(boolean) - Method in class ffx.potential.openmm.OpenMMSystem
 
setUpdated() - Method in class ffx.ui.commands.FFXServer
setUpdated
setupMCOST(OrthogonalSpaceTempering, MolecularAssembly[], DynamicsOptions, ThermodynamicsOptions, boolean, File, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions
setupMCOST.
setUpper(double) - Method in class ffx.algorithms.cli.AnnealOptions
 
setUreyBradleys(MSNode) - Method in class ffx.potential.bonded.MSGroup
Sets the Urey-Bradley node to t.
setUreyBradleys(MSNode) - Method in class ffx.potential.bonded.MultiResidue
Sets the Urey-Bradley node to t.
setUse(boolean) - Method in class ffx.potential.bonded.Atom
If true, this atom should be used in potential energy functions.
setUse(boolean[]) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Setter for the field use.
setUseDispersionCorrection(int) - Method in class ffx.openmm.amoeba.VdwForce
Set the vdW force to use a long-range dispersion correction.
setUseDispersionCorrection(int) - Method in class ffx.openmm.NonbondedForce
Set if a dispersion correction will be used.
setUseGoldstein(boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization
Specify use of Goldstein optimization.
setUseOrigCoordsRotamer(boolean) - Method in class ffx.potential.bonded.RotamerLibrary
Setter for the field useOrigCoordsRotamer.
setUsesPeriodicBoundaryConditions(int) - Method in class ffx.openmm.CentroidBondForce
Set whether to use periodic boundary conditions.
setUseSwitchingFunction(int) - Method in class ffx.openmm.CustomNonbondedForce
Flag to contol use of a switching function.
setUseSwitchingFunction(int) - Method in class ffx.openmm.NonbondedForce
Set if a switching function will be used.
setValue(double) - Method in class ffx.potential.bonded.BondedTerm
Sets the Term's value.
setVariable(String, Object) - Method in class ffx.utilities.FFXContext
Sets the value of the given variable
setVariables(Map<String, Object>) - Method in class ffx.utilities.FFXContext
Set the Map of all variables.
setVDWType(VDWType) - Method in class ffx.potential.bonded.Atom
setVDWType
setVelocities(double[]) - Method in class ffx.openmm.Context
Set the atomic velocities.
setVelocities(double[]) - Method in class ffx.potential.openmm.OpenMMContext
The array v contains velocity values for active atomic coordinates.
setVelocities(double[]) - Method in class ffx.potential.SystemState
Set the velocities via a copy of the passed array into the internal array.
setVelocity(double[]) - Method in class ffx.algorithms.dynamics.Barostat
setVelocity.
setVelocity(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
setVelocity.
setVelocity(double[]) - Method in interface ffx.numerics.Potential
setVelocity.
setVelocity(double[]) - Method in class ffx.potential.ANIEnergy
 
setVelocity(double[]) - Method in class ffx.potential.bonded.Atom
Setter for the field velocity.
setVelocity(double[]) - Method in class ffx.potential.DualTopologyEnergy
setVelocity.
setVelocity(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
setVelocity(double[]) - Method in class ffx.potential.ForceFieldEnergy
setVelocity.
setVelocity(double[]) - Method in class ffx.potential.QuadTopologyEnergy
setVelocity.
setVelocity(double[]) - Method in class ffx.potential.XtalEnergy
setVelocity.
setVelocity(double[]) - Method in class ffx.realspace.RealSpaceEnergy
setVelocity.
setVelocity(double[]) - Method in class ffx.xray.RefinementEnergy
setVelocity.
setVelocity(double[]) - Method in class ffx.xray.XRayEnergy
setVelocity.
setVelocity(double, double, double) - Method in class ffx.potential.bonded.Atom
Setter for the field velocity.
setVerbosityLevel(MDVerbosity) - Method in class ffx.algorithms.dynamics.MolecularDynamics
 
setVersioning(SystemFilter.Versioning) - Static method in class ffx.potential.parsers.SystemFilter
Negative: prefix a version number; Positive: postfix; Zero: TINKER-style.
setVideo(String) - Method in class ffx.algorithms.misc.GenerateRotamers
Null file indicates to not write a video.
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Atom
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Bond
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.BondedTerm
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Joint
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.MSGroup
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.MSNode
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.MultiResidue
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.Polymer
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in interface ffx.potential.bonded.ROLS
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.bonded.ROLSP
setView
setView(RendererCache.ViewModel, List<BranchGroup>) - Method in class ffx.potential.MolecularAssembly
setView
setView(String) - Method in class ffx.ui.GraphicsCanvas
 
SETVIEW - Enum constant in enum class ffx.potential.bonded.ROLSP.PARALLELMETHOD
 
setViewModel(String, MSNode) - Method in class ffx.ui.GraphicsCanvas
Operates on the supplied node.
setVisible(boolean) - Method in class ffx.ui.GraphicsPanel
setWeight(double) - Method in class ffx.realspace.RealSpaceData
setWeight
setWeight(double) - Method in class ffx.xray.CrystalReciprocalSpace
set the dataset weight
setWeight(double) - Method in interface ffx.xray.DataContainer
setWeight
setWeight(double) - Method in class ffx.xray.DiffractionData
setWeight
setWiggle(double) - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
Apply a random perturbation to the atomic coordinates to avoid numerical instabilities for various linear, planar and symmetric structures.
setWindow(int) - Method in class ffx.algorithms.cli.ManyBodyOptions
 
setWindows(int) - Method in class ffx.algorithms.cli.AnnealOptions
 
setWindowSize(int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Setter for the field windowSize.
setWire(LineArray, int) - Method in class ffx.potential.bonded.Bond
setWire
setWireWidth(float) - Method in class ffx.potential.MolecularAssembly
setWireWidth
setWrite(double) - Method in class ffx.algorithms.cli.DynamicsOptions
 
setWriteIndependent(boolean) - Method in class ffx.algorithms.thermodynamics.HistogramData
Sets the value of writeIndependent.
setX(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell
Sets x coordinate of center of cell
setXYZ(double[]) - Method in class ffx.potential.bonded.Atom
setXYZ
setXYZGradient(double, double, double) - Method in class ffx.potential.bonded.Atom
setXYZGradient
setXyzIndex(int) - Method in class ffx.potential.bonded.Atom
Setter for the field xyzIndex.
setY(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell
Sets y coordinate of center of cell
setZ(double) - Method in class ffx.potential.nonbonded.octree.OctreeCell
Sets z coordinate of center of cell
setZprime(int) - Method in class ffx.potential.parsers.CIFFilter
Override the number of copies in the asymmetric unit (Z').
SEV_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
 
sextic - Variable in class ffx.potential.parameters.AngleType
Sextic coefficient in angle bending potential.
sextic - Variable in class ffx.potential.parameters.OutOfPlaneBendType
Sextic coefficient in out-of-plane angle bending potential.
SEXTIC - Enum constant in enum class ffx.potential.parameters.AngleType.AngleFunction
 
Sg - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
SG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYD
 
SG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYS
 
SG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYX
 
SG - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
 
ShakeChargeConstraint - Class in ffx.potential.constraint
 
ShakeChargeConstraint(int, int, double) - Constructor for class ffx.potential.constraint.ShakeChargeConstraint
 
SharedBoolean - Class in edu.rit.pj.reduction
Class SharedBoolean provides a reduction variable for a value of type boolean.
SharedBoolean() - Constructor for class edu.rit.pj.reduction.SharedBoolean
Construct a new Boolean reduction variable with the initial value false.
SharedBoolean(boolean) - Constructor for class edu.rit.pj.reduction.SharedBoolean
Construct a new Boolean reduction variable with the given initial value.
SharedBooleanArray - Class in edu.rit.pj.reduction
Class SharedBooleanArray provides an array reduction variable with elements of type boolean.
SharedBooleanArray(boolean[]) - Constructor for class edu.rit.pj.reduction.SharedBooleanArray
Construct a new Boolean array reduction variable whose elements are copied from the given array.
SharedBooleanArray(int) - Constructor for class edu.rit.pj.reduction.SharedBooleanArray
Construct a new Boolean array reduction variable with the given length.
SharedBooleanArrayBuf - Class in edu.rit.mp.buf
Class SharedBooleanArrayBuf provides a buffer for a multiple thread safe array of Boolean items sent or received using the Message Protocol (MP).
SharedBooleanArrayBuf(SharedBooleanArray, Range) - Constructor for class edu.rit.mp.buf.SharedBooleanArrayBuf
Construct a new shared Boolean array buffer.
SharedBooleanArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedBooleanArrayBuf_1 provides a buffer for a multiple thread safe array of Boolean items sent or received using the Message Protocol (MP).
SharedBooleanArrayBuf_1(SharedBooleanArray, Range) - Constructor for class edu.rit.mp.buf.SharedBooleanArrayBuf_1
Construct a new shared Boolean array buffer.
SharedBooleanBuf - Class in edu.rit.mp.buf
Class SharedBooleanBuf provides a buffer for a multiple thread safe Boolean item sent or received using the Message Protocol (MP).
SharedBooleanBuf(SharedBoolean) - Constructor for class edu.rit.mp.buf.SharedBooleanBuf
Construct a new shared Boolean buffer.
SharedByte - Class in edu.rit.pj.reduction
Class SharedByte provides a reduction variable for a value of type byte.
SharedByte() - Constructor for class edu.rit.pj.reduction.SharedByte
Construct a new byte reduction variable with the initial value 0.
SharedByte(byte) - Constructor for class edu.rit.pj.reduction.SharedByte
Construct a new byte reduction variable with the given initial value.
SharedByteArray - Class in edu.rit.pj.reduction
Class SharedByteArray provides an array reduction variable with elements of type byte.
SharedByteArray(byte[]) - Constructor for class edu.rit.pj.reduction.SharedByteArray
Construct a new byte array reduction variable whose elements are copied from the given array.
SharedByteArray(int) - Constructor for class edu.rit.pj.reduction.SharedByteArray
Construct a new byte array reduction variable with the given length.
SharedByteArrayBuf - Class in edu.rit.mp.buf
Class SharedByteArrayBuf provides a buffer for a multiple thread safe array of byte items sent or received using the Message Protocol (MP).
SharedByteArrayBuf(SharedByteArray, Range) - Constructor for class edu.rit.mp.buf.SharedByteArrayBuf
Construct a new shared byte array buffer.
SharedByteArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedByteArrayBuf_1 provides a buffer for a multiple thread safe array of byte items sent or received using the Message Protocol (MP).
SharedByteArrayBuf_1(SharedByteArray, Range) - Constructor for class edu.rit.mp.buf.SharedByteArrayBuf_1
Construct a new shared byte array buffer.
SharedByteBuf - Class in edu.rit.mp.buf
Class SharedByteBuf provides a buffer for a multiple thread safe byte item sent or received using the Message Protocol (MP).
SharedByteBuf(SharedByte) - Constructor for class edu.rit.mp.buf.SharedByteBuf
Construct a new shared byte buffer.
SharedCharacter - Class in edu.rit.pj.reduction
Class SharedCharacter provides a reduction variable for a value of type char.
SharedCharacter() - Constructor for class edu.rit.pj.reduction.SharedCharacter
Construct a new character reduction variable with the initial value 0.
SharedCharacter(char) - Constructor for class edu.rit.pj.reduction.SharedCharacter
Construct a new character reduction variable with the given initial value.
SharedCharacterArray - Class in edu.rit.pj.reduction
Class SharedCharacterArray provides an array reduction variable with elements of type char.
SharedCharacterArray(char[]) - Constructor for class edu.rit.pj.reduction.SharedCharacterArray
Construct a new character array reduction variable whose elements are copied from the given array.
SharedCharacterArray(int) - Constructor for class edu.rit.pj.reduction.SharedCharacterArray
Construct a new character array reduction variable with the given length.
SharedCharacterArrayBuf - Class in edu.rit.mp.buf
Class SharedCharacterArrayBuf provides a buffer for a multiple thread safe array of character items sent or received using the Message Protocol (MP).
SharedCharacterArrayBuf(SharedCharacterArray, Range) - Constructor for class edu.rit.mp.buf.SharedCharacterArrayBuf
Construct a new shared character array buffer.
SharedCharacterArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedCharacterArrayBuf_1 provides a buffer for a multiple thread safe array of character items sent or received using the Message Protocol (MP).
SharedCharacterArrayBuf_1(SharedCharacterArray, Range) - Constructor for class edu.rit.mp.buf.SharedCharacterArrayBuf_1
Construct a new shared character array buffer.
SharedCharacterBuf - Class in edu.rit.mp.buf
Class SharedCharacterBuf provides a buffer for a shared character item sent or received using the Message Protocol (MP).
SharedCharacterBuf(SharedCharacter) - Constructor for class edu.rit.mp.buf.SharedCharacterBuf
Construct a new shared character buffer.
SharedDouble - Class in edu.rit.pj.reduction
Class SharedDouble provides a reduction variable for a value of type double.
SharedDouble() - Constructor for class edu.rit.pj.reduction.SharedDouble
Construct a new double reduction variable with the initial value 0.
SharedDouble(double) - Constructor for class edu.rit.pj.reduction.SharedDouble
Construct a new double reduction variable with the given initial value.
SharedDoubleArray - Class in edu.rit.pj.reduction
Class SharedDoubleArray provides an array reduction variable with elements of type double.
SharedDoubleArray(double[]) - Constructor for class edu.rit.pj.reduction.SharedDoubleArray
Construct a new double array reduction variable whose elements are copied from the given array.
SharedDoubleArray(int) - Constructor for class edu.rit.pj.reduction.SharedDoubleArray
Construct a new double array reduction variable with the given length.
SharedDoubleArrayBuf - Class in edu.rit.mp.buf
Class SharedDoubleArrayBuf provides a buffer for a multiple thread safe array of double items sent or received using the Message Protocol (MP).
SharedDoubleArrayBuf(SharedDoubleArray, Range) - Constructor for class edu.rit.mp.buf.SharedDoubleArrayBuf
Construct a new shared double array buffer.
SharedDoubleArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedDoubleArrayBuf_1 provides a buffer for a multiple thread safe array of double items sent or received using the Message Protocol (MP).
SharedDoubleArrayBuf_1(SharedDoubleArray, Range) - Constructor for class edu.rit.mp.buf.SharedDoubleArrayBuf_1
Construct a new shared double array buffer.
SharedDoubleBuf - Class in edu.rit.mp.buf
Class SharedDoubleBuf provides a buffer for a shared double item sent or received using the Message Protocol (MP).
SharedDoubleBuf(SharedDouble) - Constructor for class edu.rit.mp.buf.SharedDoubleBuf
Construct a new shared double buffer.
SharedFloat - Class in edu.rit.pj.reduction
Class SharedFloat provides a reduction variable for a value of type float.
SharedFloat() - Constructor for class edu.rit.pj.reduction.SharedFloat
Construct a new float reduction variable with the initial value 0.
SharedFloat(float) - Constructor for class edu.rit.pj.reduction.SharedFloat
Construct a new float reduction variable with the given initial value.
SharedFloatArray - Class in edu.rit.pj.reduction
Class SharedFloatArray provides an array reduction variable with elements of type float.
SharedFloatArray(float[]) - Constructor for class edu.rit.pj.reduction.SharedFloatArray
Construct a new float array reduction variable whose elements are copied from the given array.
SharedFloatArray(int) - Constructor for class edu.rit.pj.reduction.SharedFloatArray
Construct a new float array reduction variable with the given length.
SharedFloatArrayBuf - Class in edu.rit.mp.buf
Class SharedFloatArrayBuf provides a buffer for a multiple thread safe array of float items sent or received using the Message Protocol (MP).
SharedFloatArrayBuf(SharedFloatArray, Range) - Constructor for class edu.rit.mp.buf.SharedFloatArrayBuf
Construct a new shared float array buffer.
SharedFloatArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedFloatArrayBuf_1 provides a buffer for a multiple thread safe array of float items sent or received using the Message Protocol (MP).
SharedFloatArrayBuf_1(SharedFloatArray, Range) - Constructor for class edu.rit.mp.buf.SharedFloatArrayBuf_1
Construct a new shared float array buffer.
SharedFloatBuf - Class in edu.rit.mp.buf
Class SharedFloatBuf provides a buffer for a shared float item sent or received using the Message Protocol (MP).
SharedFloatBuf(SharedFloat) - Constructor for class edu.rit.mp.buf.SharedFloatBuf
Construct a new shared float buffer.
SharedInteger - Class in edu.rit.pj.reduction
Class SharedInteger provides a reduction variable for a value of type int.
SharedInteger() - Constructor for class edu.rit.pj.reduction.SharedInteger
Construct a new integer reduction variable with the initial value 0.
SharedInteger(int) - Constructor for class edu.rit.pj.reduction.SharedInteger
Construct a new integer reduction variable with the given initial value.
SharedIntegerArray - Class in edu.rit.pj.reduction
Class SharedIntegerArray provides an array reduction variable with elements of type int.
SharedIntegerArray(int) - Constructor for class edu.rit.pj.reduction.SharedIntegerArray
Construct a new integer array reduction variable with the given length.
SharedIntegerArray(int[]) - Constructor for class edu.rit.pj.reduction.SharedIntegerArray
Construct a new integer array reduction variable whose elements are copied from the given array.
SharedIntegerArrayBuf - Class in edu.rit.mp.buf
Class SharedIntegerArrayBuf provides a buffer for a multiple thread safe array of integer items sent or received using the Message Protocol (MP).
SharedIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedIntegerArrayBuf
Construct a new shared integer array buffer.
SharedIntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of integer items sent or received using the Message Protocol (MP).
SharedIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedIntegerArrayBuf_1
Construct a new shared integer array buffer.
SharedIntegerBuf - Class in edu.rit.mp.buf
Class SharedIntegerBuf provides a buffer for a shared integer item sent or received using the Message Protocol (MP).
SharedIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedIntegerBuf
Construct a new shared integer buffer.
SharedIntegerMatrix - Class in edu.rit.pj.reduction
Class SharedIntegerMatrix provides a matrix reduction variable with elements of type int.
SharedIntegerMatrix(int[][]) - Constructor for class edu.rit.pj.reduction.SharedIntegerMatrix
Construct a new integer matrix reduction variable whose elements are copied from the given matrix.
SharedIntegerMatrix(int, int) - Constructor for class edu.rit.pj.reduction.SharedIntegerMatrix
Construct a new integer matrix reduction variable with the given number of rows and columns.
SharedLong - Class in edu.rit.pj.reduction
Class SharedLong provides a reduction variable for a value of type long.
SharedLong() - Constructor for class edu.rit.pj.reduction.SharedLong
Construct a new long reduction variable with the initial value 0.
SharedLong(long) - Constructor for class edu.rit.pj.reduction.SharedLong
Construct a new long reduction variable with the given initial value.
SharedLongArray - Class in edu.rit.pj.reduction
Class SharedLongArray provides an array reduction variable with elements of type long.
SharedLongArray(int) - Constructor for class edu.rit.pj.reduction.SharedLongArray
Construct a new long array reduction variable with the given length.
SharedLongArray(long[]) - Constructor for class edu.rit.pj.reduction.SharedLongArray
Construct a new long array reduction variable whose elements are copied from the given array.
SharedLongArrayBuf - Class in edu.rit.mp.buf
Class SharedLongArrayBuf provides a buffer for a multiple thread safe array of long items sent or received using the Message Protocol (MP).
SharedLongArrayBuf(SharedLongArray, Range) - Constructor for class edu.rit.mp.buf.SharedLongArrayBuf
Construct a new shared long array buffer.
SharedLongArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedLongArrayBuf_1 provides a buffer for a multiple thread safe array of long items sent or received using the Message Protocol (MP).
SharedLongArrayBuf_1(SharedLongArray, Range) - Constructor for class edu.rit.mp.buf.SharedLongArrayBuf_1
Construct a new shared long array buffer.
SharedLongBuf - Class in edu.rit.mp.buf
Class SharedLongBuf provides a buffer for a shared long item sent or received using the Message Protocol (MP).
SharedLongBuf(SharedLong) - Constructor for class edu.rit.mp.buf.SharedLongBuf
Construct a new shared long buffer.
SharedLongMatrix - Class in edu.rit.pj.reduction
Class SharedLongMatrix provides a matrix reduction variable with elements of type long.
SharedLongMatrix(int, int) - Constructor for class edu.rit.pj.reduction.SharedLongMatrix
Construct a new long matrix reduction variable with the given number of rows and columns.
SharedLongMatrix(long[][]) - Constructor for class edu.rit.pj.reduction.SharedLongMatrix
Construct a new long matrix reduction variable whose elements are copied from the given matrix.
SharedObject<T> - Class in edu.rit.pj.reduction
Class SharedObject provides a reduction variable for a value of an object type.
SharedObject() - Constructor for class edu.rit.pj.reduction.SharedObject
Construct a new object reduction variable with the initial value null.
SharedObject(T) - Constructor for class edu.rit.pj.reduction.SharedObject
Construct a new object reduction variable with the given initial value.
SharedObjectArray<T> - Class in edu.rit.pj.reduction
Class SharedObjectArray provides an array reduction variable with elements of an object type.
SharedObjectArray(int) - Constructor for class edu.rit.pj.reduction.SharedObjectArray
Construct a new object array reduction variable with the given length.
SharedObjectArray(T[]) - Constructor for class edu.rit.pj.reduction.SharedObjectArray
Construct a new object array reduction variable whose elements are copied from the given array.
SharedObjectArrayBuf<T> - Class in edu.rit.mp.buf
Class SharedObjectArrayBuf provides a buffer for a multiple thread safe array of object items sent or received using the Message Protocol (MP).
SharedObjectArrayBuf(SharedObjectArray<T>, Range) - Constructor for class edu.rit.mp.buf.SharedObjectArrayBuf
Construct a new shared object array buffer.
SharedObjectArrayBuf_1<T> - Class in edu.rit.mp.buf
Class SharedObjectArrayBuf_1 provides a buffer for a multiple thread safe array of object items sent or received using the Message Protocol (MP).
SharedObjectArrayBuf_1(SharedObjectArray<T>, Range) - Constructor for class edu.rit.mp.buf.SharedObjectArrayBuf_1
Construct a new shared object array buffer.
SharedObjectBuf<T> - Class in edu.rit.mp.buf
Class SharedObjectBuf provides a buffer for a shared object item sent or received using the Message Protocol (MP).
SharedObjectBuf(SharedObject<T>) - Constructor for class edu.rit.mp.buf.SharedObjectBuf
Construct a new shared object buffer.
SharedShort - Class in edu.rit.pj.reduction
Class SharedShort provides a reduction variable for a value of type short.
SharedShort() - Constructor for class edu.rit.pj.reduction.SharedShort
Construct a new short reduction variable with the initial value 0.
SharedShort(short) - Constructor for class edu.rit.pj.reduction.SharedShort
Construct a new short reduction variable with the given initial value.
SharedShortArray - Class in edu.rit.pj.reduction
Class SharedShortArray provides an array reduction variable with elements of type short.
SharedShortArray(int) - Constructor for class edu.rit.pj.reduction.SharedShortArray
Construct a new short array reduction variable with the given length.
SharedShortArray(short[]) - Constructor for class edu.rit.pj.reduction.SharedShortArray
Construct a new short array reduction variable whose elements are copied from the given array.
SharedShortArrayBuf - Class in edu.rit.mp.buf
Class SharedShortArrayBuf provides a buffer for a multiple thread safe array of short items sent or received using the Message Protocol (MP).
SharedShortArrayBuf(SharedShortArray, Range) - Constructor for class edu.rit.mp.buf.SharedShortArrayBuf
Construct a new shared short array buffer.
SharedShortArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedShortArrayBuf_1 provides a buffer for a multiple thread safe array of short items sent or received using the Message Protocol (MP).
SharedShortArrayBuf_1(SharedShortArray, Range) - Constructor for class edu.rit.mp.buf.SharedShortArrayBuf_1
Construct a new shared short array buffer.
SharedShortBuf - Class in edu.rit.mp.buf
Class SharedShortBuf provides a buffer for a shared short item sent or received using the Message Protocol (MP).
SharedShortBuf(SharedShort) - Constructor for class edu.rit.mp.buf.SharedShortBuf
Construct a new shared short buffer.
SharedSigned16BitIntegerArrayBuf - Class in edu.rit.mp.buf
Class SharedSigned16BitIntegerArrayBuf provides a buffer for a multiple thread safe array of signed 16-bit integer items sent or received using the Message Protocol (MP).
SharedSigned16BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf
Construct a new shared signed 16-bit integer array buffer.
SharedSigned16BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedSigned16BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of signed 16-bit integer items sent or received using the Message Protocol (MP).
SharedSigned16BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1
Construct a new shared signed 16-bit integer array buffer.
SharedSigned16BitIntegerBuf - Class in edu.rit.mp.buf
Class SharedSigned16BitIntegerBuf provides a buffer for a single signed 16-bit integer item sent or received using the Message Protocol (MP).
SharedSigned16BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedSigned16BitIntegerBuf
Construct a new shared signed 16-bit integer buffer.
SharedSigned8BitIntegerArrayBuf - Class in edu.rit.mp.buf
Class SharedSigned8BitIntegerArrayBuf provides a buffer for a multiple thread safe array of signed 8-bit integer items sent or received using the Message Protocol (MP).
SharedSigned8BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf
Construct a new shared signed 8-bit integer array buffer.
SharedSigned8BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedSigned8BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of signed 8-bit integer items sent or received using the Message Protocol (MP).
SharedSigned8BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1
Construct a new shared signed 8-bit integer array buffer.
SharedSigned8BitIntegerBuf - Class in edu.rit.mp.buf
Class SharedSigned8BitIntegerBuf provides a buffer for a shared signed 8-bit integer item sent or received using the Message Protocol (MP).
SharedSigned8BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedSigned8BitIntegerBuf
Construct a new shared signed 8-bit integer buffer.
SharedUnsigned16BitIntegerArrayBuf - Class in edu.rit.mp.buf
Class SharedUnsigned16BitIntegerArrayBuf provides a buffer for a multiple thread safe array of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned16BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf
Construct a new shared unsigned 16-bit integer array buffer.
SharedUnsigned16BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedUnsigned16BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of unsigned 16-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned16BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1
Construct a new shared unsigned 16-bit integer array buffer.
SharedUnsigned16BitIntegerBuf - Class in edu.rit.mp.buf
Class SharedUnsigned16BitIntegerBuf provides a buffer for a shared unsigned 16-bit integer item sent or received using the Message Protocol (MP).
SharedUnsigned16BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf
Construct a new shared unsigned 16-bit integer buffer.
SharedUnsigned8BitIntegerArrayBuf - Class in edu.rit.mp.buf
Class SharedUnsigned8BitIntegerArrayBuf provides a buffer for a multiple thread safe array of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned8BitIntegerArrayBuf(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf
Construct a new shared unsigned 8-bit integer array buffer.
SharedUnsigned8BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class SharedUnsigned8BitIntegerArrayBuf_1 provides a buffer for a multiple thread safe array of unsigned 8-bit integer items sent or received using the Message Protocol (MP).
SharedUnsigned8BitIntegerArrayBuf_1(SharedIntegerArray, Range) - Constructor for class edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1
Construct a new shared unsigned 8-bit integer array buffer.
SharedUnsigned8BitIntegerBuf - Class in edu.rit.mp.buf
Class SharedUnsigned8BitIntegerBuf provides a buffer for a single unsigned 8-bit integer item sent or received using the Message Protocol (MP).
SharedUnsigned8BitIntegerBuf(SharedInteger) - Constructor for class edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf
Construct a new shared unsigned 8-bit integer buffer.
SHEET - Enum constant in enum class ffx.potential.bonded.Residue.SSType
 
shellCommand - Variable in class edu.rit.pj.cluster.BackendInfo
Shell command string on the backend.
shiftButton - Variable in class ffx.ui.behaviors.PickMouseBehavior
 
Short() - Constructor for class edu.rit.util.Searching.Short
 
Short() - Constructor for class edu.rit.util.Sorting.Short
 
ShortArrayBuf - Class in edu.rit.mp.buf
Class ShortArrayBuf provides a buffer for an array of short items sent or received using the Message Protocol (MP).
ShortArrayBuf(short[], Range) - Constructor for class edu.rit.mp.buf.ShortArrayBuf
Construct a new short array buffer.
ShortArrayBuf_1 - Class in edu.rit.mp.buf
Class ShortArrayBuf_1 provides a buffer for an array of short items sent or received using the Message Protocol (MP).
ShortArrayBuf_1(short[], Range) - Constructor for class edu.rit.mp.buf.ShortArrayBuf_1
Construct a new short array buffer.
ShortBuf - Class in edu.rit.mp
Class ShortBuf is the abstract base class for a buffer of short items sent or received using the Message Protocol (MP).
ShortBuf(int) - Constructor for class edu.rit.mp.ShortBuf
Construct a new short buffer.
ShortItemBuf - Class in edu.rit.mp.buf
Class ShortItemBuf provides a buffer for a single short item sent or received using the Message Protocol (MP).
ShortItemBuf() - Constructor for class edu.rit.mp.buf.ShortItemBuf
Construct a new short item buffer.
ShortItemBuf(short) - Constructor for class edu.rit.mp.buf.ShortItemBuf
Construct a new short item buffer with the given initial value.
ShortMatrixBuf - Class in edu.rit.mp.buf
Class ShortMatrixBuf provides a buffer for a matrix of short items sent or received using the Message Protocol (MP).
ShortMatrixBuf(short[][], Range, Range) - Constructor for class edu.rit.mp.buf.ShortMatrixBuf
Construct a new short matrix buffer.
ShortMatrixBuf_1 - Class in edu.rit.mp.buf
Class ShortMatrixBuf_1 provides a buffer for a matrix of short items sent or received using the Message Protocol (MP).
ShortMatrixBuf_1(short[][], Range, Range) - Constructor for class edu.rit.mp.buf.ShortMatrixBuf_1
Construct a new short matrix buffer.
shortName - Variable in class ffx.crystal.SpaceGroup
Space group name.
ShortOp - Class in edu.rit.pj.reduction
Class ShortOp is the abstract base class for a binary operation on short values, used to do reduction in a parallel program.
ShortOp() - Constructor for class edu.rit.pj.reduction.ShortOp
Construct a new short binary operation.
showAbout() - Method in class ffx.ui.ModelingShell
 
showAbout(EventObject) - Method in class ffx.ui.ModelingShell
 
SHOWHYDROGEN - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
SHOWVRML - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
shutdown() - Method in class edu.rit.pj.ParallelTeam
Kills the team's threads run() methods so that they are no longer GC roots.
shutdown() - Method in class edu.rit.util.TimerThread
Shut down this timer thread.
Si - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
sidechainStoichiometry - Static variable in class ffx.potential.bonded.AminoAcidUtils
Stoichiometry of side chains can be used for identification, accept for a couple cases:
SIGMA - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.RADIUS_TYPE
 
sigmaA - Variable in class ffx.xray.DiffractionRefinementData
SigmaA coefficient - s.
SigmaAEnergy - Class in ffx.xray
Optimize SigmaA coefficients (using spline coefficients) and structure factor derivatives using a likelihood target function.
SigmaAMinimize - Class in ffx.xray
SigmaAMinimize class.
sigmas - Variable in class ffx.potential.bonded.Rotamer
An array of sigmas for each chi angle.
sigmaW - Variable in class ffx.xray.DiffractionRefinementData
SigmaA coefficient - w.
Signed16BitIntegerArrayBuf - Class in edu.rit.mp.buf
Class Signed16BitIntegerArrayBuf provides a buffer for an array of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerArrayBuf
Construct a new signed 16-bit integer array buffer.
Signed16BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class Signed16BitIntegerArrayBuf_1 provides a buffer for an array of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1
Construct a new signed 16-bit integer array buffer.
Signed16BitIntegerBuf - Class in edu.rit.mp
Class Signed16BitIntegerBuf is the abstract base class for a buffer of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerBuf(int) - Constructor for class edu.rit.mp.Signed16BitIntegerBuf
Construct a new signed 16-bit integer buffer.
Signed16BitIntegerItemBuf - Class in edu.rit.mp.buf
Class Signed16BitIntegerItemBuf provides a buffer for a single signed 16-bit integer item sent or received using the Message Protocol (MP).
Signed16BitIntegerItemBuf() - Constructor for class edu.rit.mp.buf.Signed16BitIntegerItemBuf
Construct a new signed 16-bit integer item buffer.
Signed16BitIntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerItemBuf
Construct a new signed 16-bit integer item buffer with the given initial value.
Signed16BitIntegerMatrixBuf - Class in edu.rit.mp.buf
Class Signed16BitIntegerMatrixBuf provides a buffer for a matrix of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf
Construct a new signed 16-bit integer matrix buffer.
Signed16BitIntegerMatrixBuf_1 - Class in edu.rit.mp.buf
Class Signed16BitIntegerMatrixBuf_1 provides a buffer for a matrix of signed 16-bit integer items sent or received using the Message Protocol (MP).
Signed16BitIntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1
Construct a new signed 16-bit integer matrix buffer.
Signed8BitIntegerArrayBuf - Class in edu.rit.mp.buf
Class Signed8BitIntegerArrayBuf provides a buffer for an array of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerArrayBuf(int[], Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerArrayBuf
Construct a new signed 8-bit integer array buffer.
Signed8BitIntegerArrayBuf_1 - Class in edu.rit.mp.buf
Class Signed8BitIntegerArrayBuf_1 provides a buffer for an array of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerArrayBuf_1(int[], Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1
Construct a new signed 8-bit integer array buffer.
Signed8BitIntegerBuf - Class in edu.rit.mp
Class Signed8BitIntegerBuf is the abstract base class for a buffer of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerBuf(int) - Constructor for class edu.rit.mp.Signed8BitIntegerBuf
Construct a new signed 8-bit integer buffer.
Signed8BitIntegerItemBuf - Class in edu.rit.mp.buf
Class Signed8BitIntegerItemBuf provides a buffer for a single signed 8-bit integer item sent or received using the Message Protocol (MP).
Signed8BitIntegerItemBuf() - Constructor for class edu.rit.mp.buf.Signed8BitIntegerItemBuf
Construct a new signed 8-bit integer item buffer.
Signed8BitIntegerItemBuf(int) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerItemBuf
Construct a new signed 8-bit integer item buffer with the given initial value.
Signed8BitIntegerMatrixBuf - Class in edu.rit.mp.buf
Class Signed8BitIntegerMatrixBuf provides a buffer for a matrix of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerMatrixBuf(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf
Construct a new signed 8-bit integer matrix buffer.
Signed8BitIntegerMatrixBuf_1 - Class in edu.rit.mp.buf
Class Signed8BitIntegerMatrixBuf_1 provides a buffer for a matrix of signed 8-bit integer items sent or received using the Message Protocol (MP).
Signed8BitIntegerMatrixBuf_1(int[][], Range, Range) - Constructor for class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1
Construct a new signed 8-bit integer matrix buffer.
SILENT - Enum constant in enum class ffx.algorithms.dynamics.MDVerbosity
 
SIM - Enum constant in enum class ffx.potential.Utilities.FileType
 
simpsons(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set using Simpson's rule.
simpsons(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set, in bounds lb-ub inclusive, using Simpson's rule.
SIMPSONS - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType
 
simpsonsParallel(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set using Boole's rule.
simpsonsParallel(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set, in bounds lb-ub inclusive, using Simpson's rule.
SimulatedAnnealing - Class in ffx.algorithms.optimize.anneal
Run NVT molecular dynamics at a series of temperatures to optimize a structure.
SimulatedAnnealing(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum, AnnealingSchedule, long, double, boolean, File) - Constructor for class ffx.algorithms.optimize.anneal.SimulatedAnnealing
Constructor for SimulatedAnnealing.
SimulatedAnnealing.Schedules - Enum Class in ffx.algorithms.optimize.anneal
Represents non-composite AnnealingSchedules known (i.e.
SIMULATION - Static variable in class ffx.ui.commands.SimulationUpdate
Constant SIMULATION=1
SimulationDefinition - Class in ffx.ui.commands
The SimulationDefinition class is a serializable wrapper that specifies an FFX simulation.
SimulationDefinition(int, int) - Constructor for class ffx.ui.commands.SimulationDefinition
Constructor that allocates space for a simulation definition.
SimulationFilter - Class in ffx.ui.commands
The SimulationFilter class parses system data sent by FFXServer to FFXClient.
SimulationFilter(SimulationDefinition, MolecularAssembly) - Constructor for class ffx.ui.commands.SimulationFilter
Constructor for SimulationFilter.
SimulationLoader - Class in ffx.ui
This SimulationLoader class oversees loading information from an executing FFX instance program this instance of Force Field X.
SimulationLoader(FFXSystem, Thread, MainPanel, InetSocketAddress) - Constructor for class ffx.ui.SimulationLoader
Constructor for SimulationLoader.
SimulationMessage - Class in ffx.ui.commands
The SimulationMessage class is used to pass simple messages between an FFXServer and its FFXClient(s).
SimulationMessage(int) - Constructor for class ffx.ui.commands.SimulationMessage
Constructor for SimulationMessage.
SimulationUpdate - Class in ffx.ui.commands
The SimulationUpdate class is a serializable wrapper for FFX simulation data that changes during a simulation.
SimulationUpdate(int, int, boolean) - Constructor for class ffx.ui.commands.SimulationUpdate
Constructor for SimulationUpdate.
sin - Variable in class ffx.potential.parameters.ImproperTorsionType
Value of sin(toRadians(phase)).
sin() - Method in class ffx.numerics.math.ComplexNumber
Return a new Complex object whose value is the complex sine of this.
sine - Variable in class ffx.potential.parameters.TorsionType
Sine of the phase angle.
SINGLE_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
 
SinWave - Class in ffx.numerics.integrate
A SinWave describes points along a sine wave of f(x) = a*sin(jx).
SinWave(double[], boolean, double, double) - Constructor for class ffx.numerics.integrate.SinWave
Constructs f(x) = a*sin(nx).
SinWave(double[], double, double) - Constructor for class ffx.numerics.integrate.SinWave
Constructs f(x) = a*sin(nx).
size - Variable in class ffx.numerics.multipole.MultipoleTensor
Size = (order + 1) * (order + 2) * (order + 3) / 6;
size() - Method in class edu.rit.pj.Comm
Obtain the number of processes in this communicator.
size() - Method in class ffx.numerics.atomic.AdderDoubleArray
Get the size of the array.
size() - Method in interface ffx.numerics.atomic.AtomicDoubleArray
Get the size of the array.
size() - Method in class ffx.numerics.atomic.MultiDoubleArray
Get the size of the array.
size() - Method in class ffx.numerics.atomic.PJDoubleArray
Get the size of the array.
skip() - Method in class edu.rit.util.Random
Skip one position ahead in this PRNG's sequence.
skip(long) - Method in class edu.rit.pj.cluster.BackendFileInputStream
Skip the given number of bytes from this input stream.
skip(long) - Method in class edu.rit.util.Random
Skip the given number of positions ahead in this PRNG's sequence.
SLICE - Enum constant in enum class ffx.potential.nonbonded.ReciprocalSpace.GridMethod
 
SLICE - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.GridMethod
 
sliceBuffer(boolean[], Range) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for one slice of the given Boolean array.
sliceBuffer(byte[], Range) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for one slice of the given byte array.
sliceBuffer(char[], Range) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for one slice of the given character array.
sliceBuffer(double[], Range) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for one slice of the given double array.
sliceBuffer(float[], Range) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for one slice of the given float array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for one slice of the given integer array.
sliceBuffer(int[], Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for one slice of the given integer array.
sliceBuffer(long[], Range) - Static method in class edu.rit.mp.LongBuf
Create a buffer for one slice of the given long array.
sliceBuffer(short[], Range) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for one slice of the given short array.
sliceBuffer(SharedBooleanArray, Range) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for one slice of the given shared Boolean array.
sliceBuffer(SharedByteArray, Range) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for one slice of the given shared byte array.
sliceBuffer(SharedCharacterArray, Range) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for one slice of the given shared character array.
sliceBuffer(SharedDoubleArray, Range) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for one slice of the given shared double array.
sliceBuffer(SharedFloatArray, Range) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for one slice of the given shared float array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedIntegerArray, Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for one slice of the given shared integer array.
sliceBuffer(SharedLongArray, Range) - Static method in class edu.rit.mp.LongBuf
Create a buffer for one slice of the given shared long array.
sliceBuffer(SharedObjectArray<T>, Range) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for one slice of the given shared object array.
sliceBuffer(SharedShortArray, Range) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for one slice of the given shared short array.
sliceBuffer(T[], Range) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for one slice of the given object array.
sliceBuffers(boolean[], Range[]) - Static method in class edu.rit.mp.BooleanBuf
Create an array of buffers for multiple slices of the given Boolean array.
sliceBuffers(byte[], Range[]) - Static method in class edu.rit.mp.ByteBuf
Create an array of buffers for multiple slices of the given byte array.
sliceBuffers(char[], Range[]) - Static method in class edu.rit.mp.CharacterBuf
Create an array of buffers for multiple slices of the given character array.
sliceBuffers(double[], Range[]) - Static method in class edu.rit.mp.DoubleBuf
Create an array of buffers for multiple slices of the given double array.
sliceBuffers(float[], Range[]) - Static method in class edu.rit.mp.FloatBuf
Create an array of buffers for multiple slices of the given float array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.IntegerBuf
Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(int[], Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create an array of buffers for multiple slices of the given integer array.
sliceBuffers(long[], Range[]) - Static method in class edu.rit.mp.LongBuf
Create an array of buffers for multiple slices of the given long array.
sliceBuffers(short[], Range[]) - Static method in class edu.rit.mp.ShortBuf
Create an array of buffers for multiple slices of the given short array.
sliceBuffers(SharedBooleanArray, Range[]) - Static method in class edu.rit.mp.BooleanBuf
Create an array of buffers for multiple slices of the given shared Boolean array.
sliceBuffers(SharedByteArray, Range[]) - Static method in class edu.rit.mp.ByteBuf
Create an array of buffers for multiple slices of the given shared byte array.
sliceBuffers(SharedCharacterArray, Range[]) - Static method in class edu.rit.mp.CharacterBuf
Create an array of buffers for multiple slices of the given shared character array.
sliceBuffers(SharedDoubleArray, Range[]) - Static method in class edu.rit.mp.DoubleBuf
Create an array of buffers for multiple slices of the given shared double array.
sliceBuffers(SharedFloatArray, Range[]) - Static method in class edu.rit.mp.FloatBuf
Create an array of buffers for multiple slices of the given shared float array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.IntegerBuf
Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedIntegerArray, Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create an array of buffers for multiple slices of the given shared integer array.
sliceBuffers(SharedLongArray, Range[]) - Static method in class edu.rit.mp.LongBuf
Create an array of buffers for multiple slices of the given shared long array.
sliceBuffers(SharedObjectArray<T>, Range[]) - Static method in class edu.rit.mp.ObjectBuf
Create an array of buffers for multiple slices of the given shared object array.
sliceBuffers(SharedShortArray, Range[]) - Static method in class edu.rit.mp.ShortBuf
Create an array of buffers for multiple slices of the given shared short array.
sliceBuffers(T[], Range[]) - Static method in class edu.rit.mp.ObjectBuf
Create an array of buffers for multiple slices of the given object array.
sliceLoop - Variable in class ffx.potential.nonbonded.SliceRegion
 
SliceLoop - Class in ffx.potential.nonbonded
The SliceLoop class is used to parallelize placing onto a 3D grid
SliceLoop(int, int, SliceRegion) - Constructor for class ffx.potential.nonbonded.SliceLoop
Constructor for SliceLoop.
sliceRegion - Variable in class ffx.potential.nonbonded.SliceLoop
 
SliceRegion - Class in ffx.potential.nonbonded
The SliceLoop class is used to parallelize placing onto a 3D grid
SliceRegion(int, int, int, double[], int, int, Atom[], double[][][]) - Constructor for class ffx.potential.nonbonded.SliceRegion
Constructor for SliceRegion.
SliceSchedule - Class in ffx.xray
SliceSchedule class.
SliceSchedule(int, int) - Constructor for class ffx.xray.SliceSchedule
Constructor for SliceSchedule.
SLOW - Enum constant in enum class ffx.numerics.Potential.STATE
 
Sm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
Sn - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
SNAPSHOT - Enum constant in enum class ffx.algorithms.dynamics.MDWriteAction
 
sneck - Variable in class ffx.potential.parameters.SoluteType
Sneck scaling factor to use with interstitial space corrections
SOLUTE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
SOLUTE - Enum constant in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE
 
soluteDielectric - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
The requested permittivity for the solute.
SoluteType - Class in ffx.potential.parameters
The SoluteType class defines one implicit solvent radius.
SoluteType(int, double) - Constructor for class ffx.potential.parameters.SoluteType
Constructor for SoluteType.
SoluteType(int, double, double, double) - Constructor for class ffx.potential.parameters.SoluteType
Constructor for SoluteType.
SoluteType(int, double, double, double, double) - Constructor for class ffx.potential.parameters.SoluteType
Constructor for SoluteType.
SoluteType(int, String, double, double, double) - Constructor for class ffx.potential.parameters.SoluteType
Constructor for SoluteType.
SoluteType.SOLUTE_RADII_TYPE - Enum Class in ffx.potential.parameters
 
solvationEnergy(boolean, boolean) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
solvationEnergy
solvationEnergy(double, boolean, boolean) - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
solvationEnergy
solve3PepPoly(double[], double[], double[], double[], double[][][], double[][][], double[][][]) - Method in class ffx.potential.utils.LoopClosure
Close a 3-residue loop by filling in the backbone atom coordinates and return the possible solution set.
SolventBinaryFormFactor - Class in ffx.xray
SolventBinaryFormFactor class.
SolventBinaryFormFactor(Atom, double) - Constructor for class ffx.xray.SolventBinaryFormFactor
Constructor for SolventBinaryFormFactor.
SolventBinaryFormFactor(Atom, double, double[]) - Constructor for class ffx.xray.SolventBinaryFormFactor
Constructor for SolventBinaryFormFactor.
SolventGaussFormFactor - Class in ffx.xray
SolventGaussFormFactor class.
SolventGaussFormFactor(Atom, double) - Constructor for class ffx.xray.SolventGaussFormFactor
Constructor for SolventGaussFormFactor.
SolventGaussFormFactor(Atom, double, double[]) - Constructor for class ffx.xray.SolventGaussFormFactor
Constructor for SolventGaussFormFactor.
solventModel - Variable in class ffx.xray.cli.XrayOptions
The SolventModel to use.
solventModel - Variable in class ffx.xray.CrystalReciprocalSpace
 
SolventPolyFormFactor - Class in ffx.xray
SolventPolyFormFactor class.
SolventPolyFormFactor(Atom, double, double) - Constructor for class ffx.xray.SolventPolyFormFactor
Constructor for SolventPolyFormFactor.
SolventPolyFormFactor(Atom, double, double, double[]) - Constructor for class ffx.xray.SolventPolyFormFactor
Constructor for SolventPolyFormFactor.
solveSturm(int, double[], double[]) - Method in class ffx.potential.bonded.SturmMethod
Solve using the Sturm method.
SOR - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
 
SORRegion - Class in ffx.potential.nonbonded.pme
Parallel successive over-relaxation (SOR) solver for the self-consistent field.
SORRegion(int, ForceField) - Constructor for class ffx.potential.nonbonded.pme.SORRegion
 
sort(byte[], Sorting.Byte) - Static method in class edu.rit.util.Sorting
Sort the given array of type byte[].
sort(char[], Sorting.Character) - Static method in class edu.rit.util.Sorting
Sort the given array of type char[].
sort(double[], Sorting.Double) - Static method in class edu.rit.util.Sorting
Sort the given array of type double[].
sort(float[], Sorting.Float) - Static method in class edu.rit.util.Sorting
Sort the given array of type float[].
sort(int[], Sorting.Integer) - Static method in class edu.rit.util.Sorting
Sort the given array of type int[].
sort(long[], Sorting.Long) - Static method in class edu.rit.util.Sorting
Sort the given array of type long[].
sort(short[], Sorting.Short) - Static method in class edu.rit.util.Sorting
Sort the given array of type short[].
sort(T[], Sorting.Object<T>) - Static method in class edu.rit.util.Sorting
Sort the given object array of type T[].
sortAndReturn(List<ObjectPair<U, V>>) - Static method in record class ffx.utilities.ObjectPair
sortAndReturn.
sortAtomsByDistance(Atom, Atom[]) - Static method in class ffx.potential.bonded.BondedUtils
In-place sorts toCompare by distance to the reference Atom.
sortAtomsByDistance(Atom, List<Atom>) - Static method in class ffx.potential.bonded.BondedUtils
Sorts toCompare by distance to the reference Atom, returning a sorted array.
sortCellResidues() - Method in class ffx.algorithms.optimize.manybody.ManyBodyCell
Sorts residues in the box.
sortedIndex() - Method in record class ffx.utilities.IndexIndexPair
Returns the value of the sortedIndex record component.
Sorting - Class in edu.rit.util
Class Sorting provides static methods for sorting arrays of primitive types and object types.
Sorting.Byte - Class in edu.rit.util
Class Sorting.Byte is the base class for a helper object used to sort an array of type byte[].
Sorting.Character - Class in edu.rit.util
Class Sorting.Character is the base class for a helper object used to sort an array of type char[].
Sorting.Double - Class in edu.rit.util
Class Sorting.Double is the base class for a helper object used to sort an array of type double[].
Sorting.Float - Class in edu.rit.util
Class Sorting.Float is the base class for a helper object used to sort an array of type float[].
Sorting.Integer - Class in edu.rit.util
Class Sorting.Integer is the base class for a helper object used to sort an array of type int[].
Sorting.Long - Class in edu.rit.util
Class Sorting.Long is the base class for a helper object used to sort an array of type long[].
Sorting.Object<T> - Class in edu.rit.util
Class Sorting.Object is the abstract base class for a helper object used to sort an array of objects of type T[].
Sorting.Short - Class in edu.rit.util
Class Sorting.Short is the base class for a helper object used to sort an array of type short[].
sortKey(int[]) - Static method in class ffx.potential.parameters.AngleTorsionType
This method sorts the atom classes for the angle-torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.AngleType
This method sorts the atom classes as: min, c[1], max
sortKey(int[]) - Static method in class ffx.potential.parameters.BondType
This method sorts the atom classes as: min, max
sortKey(int[]) - Static method in class ffx.potential.parameters.ImproperTorsionType
This method sorts the atom classes for the improper torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.OutOfPlaneBendType
This method sorts the atom classes for the out-of-plane angle bending type.
sortKey(int[]) - Static method in class ffx.potential.parameters.PiOrbitalTorsionType
This method sorts the atom classes as: min, max
sortKey(int[]) - Static method in class ffx.potential.parameters.StretchBendType
This method sorts the atom classes as: min, c[1], max
sortKey(int[]) - Static method in class ffx.potential.parameters.StretchTorsionType
This method sorts the atom classes for the torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.TorsionTorsionType
No sorting is done for the Torsion-Torsion lookup.
sortKey(int[]) - Static method in class ffx.potential.parameters.TorsionType
This method sorts the atom classes for the torsion.
sortKey(int[]) - Static method in class ffx.potential.parameters.UreyBradleyType
This method sorts the atom classes as: min, c[1], max
sortKey(int[]) - Static method in class ffx.potential.parameters.VDWPairType
This method sorts the atom classes as: min, max
source(double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
Generate source terms for the Coulomb Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI
Generate source terms for the Coulomb Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.EwaldTensorGlobal
Generate source terms for the Ewald Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.EwaldTensorQI
Generate source terms for the Ewald Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal
Generate source terms for the Kirkwood version of the Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.GKTensorQI
Generate source terms for the Kirkwood version of the Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
Generate source terms for the Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.TholeTensorGlobal
Generate source terms for the Challacombe et al.
source(double[]) - Method in class ffx.numerics.multipole.TholeTensorQI
Generate source terms for the Challacombe et al.
source(double[], GKSource.GK_MULTIPOLE_ORDER) - Method in class ffx.numerics.multipole.GKSource
Generate source terms for the Kirkwood version of the Challacombe et al.
SPACEFILL - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
spaceGroup - Variable in class ffx.crystal.Crystal
The space group of the crystal.
spaceGroup - Variable in class ffx.crystal.ReflectionList
The space group.
SpaceGroup - Class in ffx.crystal
The Spacegroup class defines the symmetry of a crystal.
SpaceGroup(int, int, int, String, String, String, CrystalSystem, LatticeSystem, LaueSystem, ASULimit[], double[], SymOp...) - Constructor for class ffx.crystal.SpaceGroup
Immutable SpaceGroup instances are made available only through the factory method so this constructor is private.
SpaceGroupConversions - Class in ffx.crystal
This class holds the functionality to convert between equivalent space groups.
SpaceGroupConversions() - Constructor for class ffx.crystal.SpaceGroupConversions
 
SpaceGroupDefinitions - Class in ffx.crystal
The SpaceGroupDefinitions class defines the 230 distinct space groups in three dimensions.
SpaceGroupDefinitions() - Constructor for class ffx.crystal.SpaceGroupDefinitions
 
spaceGroupFactory(int) - Static method in class ffx.crystal.SpaceGroupDefinitions
Returns a SpaceGroup instance corresponding to the number parameter.
spaceGroupFactory(String) - Static method in class ffx.crystal.SpaceGroupDefinitions
Return a SpaceGroup based on its name.
SpaceGroupInfo - Class in ffx.crystal
 
SpaceGroupInfo() - Constructor for class ffx.crystal.SpaceGroupInfo
 
spaceGroupNames - Static variable in class ffx.crystal.SpaceGroupInfo
Names of the 230 three-dimensional space groups.
spaceGroupNumber(String) - Static method in class ffx.crystal.SpaceGroupDefinitions
Returns the space group number for a given space group name.
SPATIAL - Enum constant in enum class ffx.potential.nonbonded.ReciprocalSpace.GridMethod
 
SPATIAL - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.GridMethod
 
spatialDensityLoop - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
SpatialDensityLoop - Class in ffx.potential.nonbonded
Loop over a list of atoms and assign their density to a grid.
SpatialDensityLoop(SpatialDensityRegion, int, int[]) - Constructor for class ffx.potential.nonbonded.SpatialDensityLoop
Constructor for SpatialDensityLoop.
SpatialDensityRegion - Class in ffx.potential.nonbonded
This class implements a spatial decomposition based on partitioning a grid into octants.
SpatialDensityRegion(int, int, int, double[], int, int, int, int, Crystal, Atom[], double[][][]) - Constructor for class ffx.potential.nonbonded.SpatialDensityRegion
Constructor for SpatialDensityRegion.
SpatialDensitySchedule - Class in ffx.potential.nonbonded
A fixed schedule that load balances work chunks across threads.
SPEED_OF_LIGHT_SI - Static variable in class ffx.utilities.Constants
Speed of light in m/s, defining the meter.
spinTorsions() - Method in class ffx.algorithms.optimize.TorsionSearch
Scanning through nTorsionsPerBond^nTorsionsPerBond (nTorsionsPerBond x nTorsionsPerBond x nTorsionsPerBond x ...) array.
spinTorsions(long, long) - Method in class ffx.algorithms.optimize.TorsionSearch
Similar to above, but with a limited number of hilbert indices to run through with this worker alone.
spline - Variable in class ffx.xray.DiffractionRefinementData
Spine scaling coefficients.
spline(double, double, double, double[][][], double[]) - Method in class ffx.numerics.spline.TriCubicSpline
Determine the spline value at a given point.
SplineEnergy - Class in ffx.xray
Fit structure factors using spline coefficients
SplineEnergy.Type - Interface in ffx.xray
 
splineInducedDipoles(double[][][], double[][][], boolean[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace
Place the induced dipoles onto the FFT grid for the atoms in use.
SplineMinimize - Class in ffx.xray
SplineMinimize class.
SplineMinimize(ReflectionList, DiffractionRefinementData, double[], int) - Constructor for class ffx.xray.SplineMinimize
Constructor for SplineMinimize.
splinePermanentMultipoles(double[][][], double[][][], boolean[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace
Use b-Splines to place the permanent multipoles onto the FFT grid for the atoms in use.
sqrt() - Method in class ffx.numerics.math.Double3
Square roots values in Double3.
sqrt() - Method in class ffx.numerics.math.Float3
Square roots values in Float3.
sqrt(double) - Static method in class ffx.numerics.math.SquareRoot
Compute the square root of the input value x.
sqrt(int) - Static method in class edu.rit.util.Mathe
Compute the integer square root of the integer x.
sqrtI() - Method in class ffx.numerics.math.Double3
Square roots values in Double3 in place.
sqrtI() - Method in class ffx.numerics.math.Float3
Square roots values in Float3 in place.
square() - Method in class ffx.numerics.math.Double3
Squares values in Double3.
square() - Method in class ffx.numerics.math.Float3
Squares values in Float3.
square(double[]) - Static method in class ffx.numerics.math.DoubleMath
Squares values of a vector.
square(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Squares values of a vector.
square(float[]) - Static method in class ffx.numerics.math.FloatMath
Squares values of a vector.
square(float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Squares values of a vector.
SquaredTrigSwitch - Class in ffx.numerics.switching
A SquaredTrigSwitch implements a 0-1 switch of form f(x) = sin^2(ax) or of form f(x) = cos^2(ax).
SquaredTrigSwitch(boolean) - Constructor for class ffx.numerics.switching.SquaredTrigSwitch
Default constructor, creating a switch sin^2(pi*x/2), or cos^2 if flag set.
SquaredTrigSwitch(double, boolean) - Constructor for class ffx.numerics.switching.SquaredTrigSwitch
Constructor permitting a custom frequency "a" in the form sin^2(a*x) or cos^2(a*x).
squareI() - Method in class ffx.numerics.math.Double3
Squares values in Double3 in place.
squareI() - Method in class ffx.numerics.math.Float3
Squares values in Float3 in place.
squareRoot(double[]) - Static method in class ffx.numerics.math.DoubleMath
Square root values of a vector.
squareRoot(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Square root values of a vector.
squareRoot(float[]) - Static method in class ffx.numerics.math.FloatMath
Square root values of a vector.
squareRoot(float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Square root values of a vector.
SquareRoot - Class in ffx.numerics.math
Software based computation of square root and inverse square root.
Sr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
SSETest - Class in ffx.numerics.math
java -cp target/numerics-1.0.0-beta.jar -XX:+UnlockDiagnosticVMOptions -XX:+PrintAssembly -Djava.library.path=hsdis-amd64.dylib ffx.numerics.math.SSETest
stackTraceToString(Throwable) - Static method in class ffx.potential.Utilities
Gets the stack trace for an exception and converts it to a String.
STANDARD_WATER_NAME - Static variable in class ffx.utilities.StringUtils
Constant STANDARD_WATER_NAME="HOH"
standardizeAtomNames - Variable in class ffx.potential.parsers.SystemFilter
Standardize atom names to PDB standard by default.
start() - Method in class edu.rit.pj.IntegerForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.IntegerStrideForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.LongForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.LongStrideForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.ParallelIteration
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.ParallelRegion
Perform initialization actions before parallel execution begins.
start() - Method in class edu.rit.pj.WorkerIntegerForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerIteration
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerLongForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerLongStrideForLoop
Perform per-thread initialization actions before starting the loop iterations.
start() - Method in class edu.rit.pj.WorkerRegion
Perform initialization actions before parallel execution begins.
start() - Method in class ffx.algorithms.optimize.manybody.EnergyRegion
 
start() - Method in class ffx.algorithms.optimize.manybody.FourBodyEnergyRegion
 
start() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
 
start() - Method in class ffx.algorithms.optimize.manybody.SelfEnergyRegion
 
start() - Method in class ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
 
start() - Method in class ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
 
start() - Method in class ffx.potential.nonbonded.implicit.BornGradRegion
 
start() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
 
start() - Method in class ffx.potential.nonbonded.implicit.ConnollyRegion
 
start() - Method in class ffx.potential.nonbonded.implicit.DispersionRegion
Perform initialization actions before parallel execution begins.
start() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
 
start() - Method in class ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
 
start() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
 
start() - Method in class ffx.potential.nonbonded.NeighborList
Perform initialization actions before parallel execution begins.
start() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
 
start() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
 
start() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
 
start() - Method in class ffx.potential.nonbonded.pme.SORRegion
 
start() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
 
start() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion
 
start() - Method in class ffx.potential.nonbonded.RowRegion
Perform initialization actions before parallel execution begins.
start() - Method in class ffx.potential.nonbonded.SliceRegion
Perform initialization actions before parallel execution begins.
start() - Method in class ffx.ui.commands.FFXServer
start
start() - Method in class ffx.ui.SwingWorker
Start the worker thread.
start() - Method in class ffx.ui.Trajectory
start
start() - Method in class ffx.xray.BulkSolventList
Perform initialization actions before parallel execution begins.
start(int, LongRange) - Method in class edu.rit.pj.LongSchedule
Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class edu.rit.pj.IntegerSchedule
Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.potential.nonbonded.PairwiseSchedule
Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.potential.nonbonded.SpatialDensitySchedule
Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.xray.GradientSchedule
Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.xray.RowSchedule
Start generating chunks of iterations for a parallel for loop using this schedule.
start(int, Range) - Method in class ffx.xray.SliceSchedule
Start generating chunks of iterations for a parallel for loop using this schedule.
start(long) - Method in class edu.rit.util.Timer
Start this timer with a one-shot timeout at the given interval from now.
start(long, long) - Method in class edu.rit.util.Timer
Start this timer with a periodic fixed-rate timeout starting at the given interval from now.
start(Date) - Method in class edu.rit.util.Timer
Start this timer with a one-shot timeout at the given absolute time.
start(Date, long) - Method in class edu.rit.util.Timer
Start this timer with a periodic fixed-rate timeout starting at the given absolute time.
startFixedIntervalTimeout(long, long) - Method in class edu.rit.util.Timer
Start this timer with a periodic fixed-interval timeout starting at the given interval from now.
startFixedIntervalTimeout(Date, long) - Method in class edu.rit.util.Timer
Start this timer with a periodic fixed-interval timeout starting at the given absolute time.
startListening() - Method in class edu.rit.mp.ChannelGroup
Start actively listening for connection requests.
state - Variable in class edu.rit.pj.cluster.BackendInfo
The backend's state.
state - Variable in class edu.rit.pj.cluster.JobInfo
The job's state.
state - Variable in class edu.rit.pj.cluster.ProcessInfo
The job backend process's state.
state - Variable in class ffx.algorithms.dynamics.integrators.Integrator
The MDState class contains the current state of the Molecular Dynamics simulation.
state - Variable in class ffx.algorithms.dynamics.MolecularDynamics
Stores the current molecular dynamics state.
state - Variable in class ffx.algorithms.dynamics.thermostats.Thermostat
The molecular dynamics state to be used.
state - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Are FAST varying energy terms being computed, SLOW varying energy terms, or BOTH.
State - Class in ffx.openmm
A State object records a snapshot of the current state of a simulation at a point in time.
State(PointerByReference) - Constructor for class ffx.openmm.State
Constructor.
stateChanged(ChangeEvent) - Method in class ffx.ui.KeywordComponent
stateChanged(ChangeEvent) - Method in class ffx.ui.MainPanel
stateTime - Variable in class edu.rit.pj.cluster.BackendInfo
The time when the backend entered its current state (milliseconds since midnight 01-Jan-1970 GMT).
stateTime - Variable in class edu.rit.pj.cluster.JobInfo
The time when the job entered its current state (milliseconds since midnight 01-Jan-1970 GMT).
staticAnalysis(int, double) - Method in class ffx.algorithms.optimize.TorsionSearch
Static analysis of torsional bonds.
StatisticalEstimator - Interface in ffx.numerics.estimator
The StatisticalEstimator interface defines a free energy estimator in the most generic sense.
status - Variable in class ffx.algorithms.optimize.Minimize
The return status of the optimization.
status - Variable in class ffx.algorithms.optimize.PhMinimize
The return status of the optimization.
Status - Class in edu.rit.mp
Class Status provides the result of receiving a message in the Message Protocol (MP).
STATUS_200_OK - Enum constant in enum class edu.rit.http.HttpResponse.Status
The request has succeeded.
STATUS_201_CREATED - Enum constant in enum class edu.rit.http.HttpResponse.Status
The request has been fulfilled and resulted in a new resource being created.
STATUS_202_ACCEPTED - Enum constant in enum class edu.rit.http.HttpResponse.Status
The request has been accepted for processing, but the processing has not been completed.
STATUS_204_NO_CONTENT - Enum constant in enum class edu.rit.http.HttpResponse.Status
The server has fulfilled the request but there is no new information to send back.
STATUS_301_MOVED_PERMANENTLY - Enum constant in enum class edu.rit.http.HttpResponse.Status
The requested resource has been assigned a new permanent URL and any future references to this resource should be done using that URL.
STATUS_302_MOVED_TEMPORARILY - Enum constant in enum class edu.rit.http.HttpResponse.Status
The requested resource resides temporarily under a different URL.
STATUS_304_NOT_MODIFIED - Enum constant in enum class edu.rit.http.HttpResponse.Status
If the client has performed a conditional GET request and access is allowed, but the document has not been modified since the date and time specified in the If-Modified-Since field, the server must respond with this status code and not send an Entity-Body to the client.
STATUS_400_BAD_REQUEST - Enum constant in enum class edu.rit.http.HttpResponse.Status
The request could not be understood by the server due to malformed syntax.
STATUS_401_UNAUTHORIZED - Enum constant in enum class edu.rit.http.HttpResponse.Status
The request requires user authentication.
STATUS_403_FORBIDDEN - Enum constant in enum class edu.rit.http.HttpResponse.Status
The server understood the request, but is refusing to fulfill it.
STATUS_404_NOT_FOUND - Enum constant in enum class edu.rit.http.HttpResponse.Status
The server has not found anything matching the Request-URI.
STATUS_500_INTERNAL_SERVER_ERROR - Enum constant in enum class edu.rit.http.HttpResponse.Status
The server encountered an unexpected condition which prevented it from fulfilling the request.
STATUS_501_NOT_IMPLEMENTED - Enum constant in enum class edu.rit.http.HttpResponse.Status
The server does not support the functionality required to fulfill the request.
STATUS_502_BAD_GATEWAY - Enum constant in enum class edu.rit.http.HttpResponse.Status
The server, while acting as a gateway or proxy, received an invalid response from the upstream server it accessed in attempting to fulfill the request.
STATUS_503_SERVICE_UNAVAILABLE - Enum constant in enum class edu.rit.http.HttpResponse.Status
The server is currently unable to handle the request due to a temporary overloading or maintenance of the server.
stderrAppendToFile(File) - Method in class edu.rit.pj.job.Job
Append this job's standard error to the end of the given file.
stderrToFile(File) - Method in class edu.rit.pj.job.Job
Store this job's standard error in the given file.
stderrToStdout() - Method in class edu.rit.pj.job.Job
Redirect this job's standard error to the same place as this job's standard output.
stdinFromFile(File) - Method in class edu.rit.pj.job.Job
Read this job's standard input from the given file.
Stdio - Class in edu.rit.io
Class Stdio provides standard I/O streams that can be redirected on a per-thread basis.
stdoutAppendToFile(File) - Method in class edu.rit.pj.job.Job
Append this job's standard output to the end of the given file.
stdoutToFile(File) - Method in class edu.rit.pj.job.Job
Store this job's standard output in the given file.
step - Variable in class ffx.ui.commands.SimulationUpdate
 
step(int) - Method in class ffx.openmm.Integrator
Integrate the system forward in time by the specified number of time steps.
step(int) - Method in class ffx.openmm.LangevinIntegrator
Step the integrator.
step(int) - Method in class ffx.openmm.VerletIntegrator
Step the integrator.
Stochastic - Class in ffx.algorithms.dynamics.integrators
Stochastic dynamics time step via a velocity Verlet integration algorithm.
Stochastic(double, SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.Stochastic
Constructor for Stochastic Dynamics.
STOCHASTIC - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
 
STOCHASTIC_MTS - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
 
stop() - Method in class edu.rit.util.Timer
Stop this timer.
stop() - Method in class ffx.ui.commands.FFXServer
stop
stop() - Method in class ffx.ui.MainPanel
stop
stop() - Method in class ffx.ui.Trajectory
stop
stopLoop() - Method in class edu.rit.pj.IntegerForLoop
Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.IntegerStrideForLoop
Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.LongForLoop
Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.LongStrideForLoop
Stop this parallel for loop.
stopLoop() - Method in class edu.rit.pj.ParallelIteration
Stop this parallel iteration.
store(FFXSystem) - Method in class ffx.ui.KeywordPanel
Store the KeywordPanel's current keyword content into sys.
storeAllCoordinates(Residue[]) - Static method in class ffx.potential.bonded.ResidueState
storeAllCoordinates.
storeAllCoordinates(List<Residue>) - Static method in class ffx.potential.bonded.ResidueState
storeAllCoordinates.
storeAtomicCoordinates(Atom[]) - Static method in class ffx.potential.bonded.ResidueState
Returns a new double[nAtoms][3] with the coordinates of an array of atoms.
storeCoordinateArray() - Method in class ffx.potential.bonded.Residue
storeCoordinateArray.
storeState() - Method in class ffx.algorithms.dynamics.MolecularDynamics
Store the current state of the molecular dynamics simulation in a MDState record.
storeState() - Method in class ffx.algorithms.mc.BoltzmannMC
Store the state for reverting a move.
storeState() - Method in class ffx.algorithms.mc.MolecularMC
Store the state for reverting a move.
storeState() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMC
 
storeState() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST
Store the state for reverting a move.
storeState() - Method in class ffx.potential.bonded.MultiResidue
storeState.
storeState() - Method in class ffx.potential.bonded.Residue
storeState.
story - Variable in class ffx.ui.commands.SimulationDefinition
 
STRBND - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
strbndunit - Variable in class ffx.potential.parameters.StretchBendType
 
StreamFile - Class in edu.rit.pj.io
Class StreamFile represents a file that resides in the user's account in the job frontend process of a PJ cluster parallel program.
StreamFile(File) - Constructor for class edu.rit.pj.io.StreamFile
Construct a new stream file that refers to the given file in the frontend processor.
StretchBend - Class in ffx.potential.bonded
The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.
StretchBend(Angle) - Constructor for class ffx.potential.bonded.StretchBend
Constructor for the Stretch-Bend class.
StretchBendForce - Class in ffx.potential.openmm
OpenMM Stretch-Bend Force.
StretchBendForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.StretchBendForce
Create an OpenMM Stretch-Bend Force.
stretchBendTime - Static variable in class ffx.potential.bonded.MSGroup
Constant stretchBendTime=0
StretchBendType - Class in ffx.potential.parameters
The StretchBendType class defines one out-of-plane angle bending energy type.
StretchBendType(int[], double[]) - Constructor for class ffx.potential.parameters.StretchBendType
StretchBendType Constructor.
StretchTorsion - Class in ffx.potential.bonded
The StretchTorsion class represents a coupling between a torsional angle and the three bonds contained in the torsion, as defined in the 2017 AMOEBA nucleic acid force field.
stretchTorsionFactory(Torsion, ForceField) - Static method in class ffx.potential.bonded.StretchTorsion
Attempt to create a new StretchTorsion based on the supplied torsion.
StretchTorsionForce - Class in ffx.potential.openmm
OpenMM Stretch-Torsion Force.
StretchTorsionForce(OpenMMEnergy) - Constructor for class ffx.potential.openmm.StretchTorsionForce
Create an OpenMM Stretch-Torsion Force.
stretchTorsionForm() - Static method in class ffx.potential.bonded.StretchTorsion
Returns the mathematical form of a stretch-torsion as an OpenMM-parsable String.
stretchTorsionTime - Static variable in class ffx.potential.bonded.MSGroup
Constant stretchTorsionTime=0
StretchTorsionType - Class in ffx.potential.parameters
The StretchTorsionType class defines one stretch-torsion energy type.
StretchTorsionType(int[], double[]) - Constructor for class ffx.potential.parameters.StretchTorsionType
StretchTorsionType Constructor.
stride() - Method in class edu.rit.util.LongRange
Returns this range's stride.
stride() - Method in class edu.rit.util.Range
Returns this range's stride.
StringArray - Class in ffx.openmm
String Array.
StringArray(int) - Constructor for class ffx.openmm.StringArray
OpenMM String Array constructor.
StringArray(PointerByReference) - Constructor for class ffx.openmm.StringArray
OpenMM String Array constructor.
StringOutputStream - Class in ffx.utilities
StringOutputStream class.
StringOutputStream(ByteArrayOutputStream) - Constructor for class ffx.utilities.StringOutputStream
Constructor for StringOutputStream.
StringOutputStream(ByteArrayOutputStream, Charset) - Constructor for class ffx.utilities.StringOutputStream
Constructor for StringOutputStream.
StringUtils - Class in ffx.utilities
StringUtils class.
STRTORS - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
strTorUnit - Variable in class ffx.potential.parameters.StretchTorsionType
Unit conversion.
StructuralRefinement - Enum constant in enum class ffx.utilities.PropertyGroup
Refinement parameters.
STRUCTURE - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
 
StructureMetrics - Class in ffx.potential.utils
Structure Metrics contains functionality to calculate characteristics of coordinate systems.
StructureMetrics() - Constructor for class ffx.potential.utils.StructureMetrics
 
SturmMethod - Class in ffx.potential.bonded
SturmMethod class.
SturmMethod() - Constructor for class ffx.potential.bonded.SturmMethod
SturmMethod constructor with termination criteria for polynomial solver.
sub(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Finds the difference between two vectors.
sub(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Finds the difference between two vectors.
sub(float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Finds the difference between two vectors.
sub(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Finds the difference between two vectors
sub(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray
Subtract value to the double array at the specified index.
sub(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray
Subtract value to the double array at the specified index.
sub(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray
Subtract value to the double array at the specified index.
sub(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray
Subtract value to the double array at the specified index.
sub(int, int, double, double, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Subtracts from the double arrays at the specified index the given values.
sub(int, int, Double3) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D
Subtracts from the double arrays at the specified index the given Double3.
sub(Double3) - Method in class ffx.numerics.math.Double3
Finds the difference between two vectors.
sub(Float3) - Method in class ffx.numerics.math.Float3
Finds the difference between two vectors.
subI(Double3) - Method in class ffx.numerics.math.Double3
Finds the difference between two vectors.
subI(Float3) - Method in class ffx.numerics.math.Float3
Finds the difference between two vectors.
subrange(int, int) - Method in class edu.rit.util.LongRange
Partition this range and return one subrange.
subrange(int, int) - Method in class edu.rit.util.Range
Partition this range and return one subrange.
subranges(int) - Method in class edu.rit.util.LongRange
Partition this range and return all the subranges.
subranges(int) - Method in class edu.rit.util.Range
Partition this range and return all the subranges.
Success - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult
 
sum - Variable in class ffx.numerics.math.BootStrapStatistics
 
sum - Variable in class ffx.numerics.math.SummaryStatistics
 
SUM - Static variable in class edu.rit.pj.reduction.ByteOp
The byte sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.DoubleOp
The double sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.FloatOp
The float sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.IntegerOp
The integer sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.LongOp
The long sum binary operation.
SUM - Static variable in class edu.rit.pj.reduction.ShortOp
The short sum binary operation.
sumBootstrapEnthalpyUncertainty(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator
Obtains bootstrap enthalpy uncertainty.
sumBootstrapResults(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator
Obtains bootstrap free energy.
sumBootstrapUncertainty(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator
Obtains bootstrap uncertainty.
sumEnthalpyBootstrapResults(double[]) - Method in interface ffx.numerics.estimator.BootstrappableEstimator
Obtains bootstrap enthalpy.
SummaryStatistics - Class in ffx.numerics.math
The SummaryStatistics class uses online, stable algorithms to calculate summary statistics from double arrays/lists, including mean, variance, standard deviation, max, min, sum, and count.
SummaryStatistics(double[]) - Constructor for class ffx.numerics.math.SummaryStatistics
Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], double[], int, int, int) - Constructor for class ffx.numerics.math.SummaryStatistics
Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], int) - Constructor for class ffx.numerics.math.SummaryStatistics
Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], int, int) - Constructor for class ffx.numerics.math.SummaryStatistics
Constructs a static summary of a statistic from provided values.
SummaryStatistics(double[], int, int, int) - Constructor for class ffx.numerics.math.SummaryStatistics
Constructs a static summary of a statistic from provided values.
SummaryStatistics(RunningStatistics) - Constructor for class ffx.numerics.math.SummaryStatistics
Builds a static view of a running statistic.
sumWeights - Variable in class ffx.numerics.math.BootStrapStatistics
 
sumWeights - Variable in class ffx.numerics.math.SummaryStatistics
 
superpose(double[], double[], double[]) - Static method in class ffx.potential.utils.Superpose
This method completes the following superposition operations and returns an RMSD: 1) translates the x1 coordinates to the origin.
Superpose - Class in ffx.potential.utils
 
Superpose(SystemFilter, SystemFilter, boolean) - Constructor for class ffx.potential.utils.Superpose
 
supportsPlatform(Platform) - Method in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine
Checks if this energy Platform is supported by this DynamicsEngine
SurfaceAreaRegion - Class in ffx.potential.nonbonded.implicit
SurfaceAreaRegion performs an analytical computation of the weighted solvent accessible surface area of each atom and the first derivatives of the area with respect to Cartesian coordinates
SurfaceAreaRegion(Atom[], double[], double[], double[], boolean[], int[][][], AtomicDoubleArray3D, int, double, double) - Constructor for class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
This class is a port of the Cavitation code in TINKER.
surfaceTension - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion
Cavitation surface tension coefficient (kcal/mol/A^2).
swap(byte[], int, int) - Method in class edu.rit.util.Sorting.Byte
Swap two elements in the given array.
swap(char[], int, int) - Method in class edu.rit.util.Sorting.Character
Swap two elements in the given array.
swap(double) - Static method in class ffx.utilities.ByteSwap
Byte swap a single double value.
swap(double[]) - Static method in class ffx.utilities.ByteSwap
Byte swap an array of doubles.
swap(double[], int, int) - Method in class edu.rit.util.Sorting.Double
Swap two elements in the given array.
swap(float) - Static method in class ffx.utilities.ByteSwap
Byte swap a single float value.
swap(float[]) - Static method in class ffx.utilities.ByteSwap
Byte swap an array of floats.
swap(float[], int, int) - Method in class edu.rit.util.Sorting.Float
Swap two elements in the given array.
swap(int) - Static method in class ffx.utilities.ByteSwap
Byte swap a single int value.
swap(int[]) - Static method in class ffx.utilities.ByteSwap
Byte swap an array of ints.
swap(int[], int, int) - Method in class edu.rit.util.Sorting.Integer
Swap two elements in the given array.
swap(long) - Static method in class ffx.utilities.ByteSwap
Byte swap a single long value.
swap(long[]) - Static method in class ffx.utilities.ByteSwap
Byte swap an array of longs.
swap(long[], int, int) - Method in class edu.rit.util.Sorting.Long
Swap two elements in the given array.
swap(short) - Static method in class ffx.utilities.ByteSwap
Byte swap a single short value.
swap(short[]) - Static method in class ffx.utilities.ByteSwap
Byte swap an array of shorts.
swap(short[], int, int) - Method in class edu.rit.util.Sorting.Short
Swap two elements in the given array.
swap(T[], int, int) - Method in class edu.rit.util.Sorting.Object
Swap two elements in the given array.
SwingWorker - Class in ffx.ui
This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class ffx.ui.SwingWorker
Start a thread that will call the construct method and then exit.
switchHistogram(int) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Switch to an alternate Histogram.
sx - Variable in class ffx.numerics.multipole.PolarizableMultipole
Averaged induced dipole + induced dipole chain-rule x-component: sx = 0.5 * (ux + px).
sy - Variable in class ffx.numerics.multipole.PolarizableMultipole
Averaged induced dipole + induced dipole chain-rule y-component: sy = 0.5 * (uy + py).
symmetricToUnity() - Method in class ffx.numerics.switching.BellCurveSwitch
True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.CompositeSwitch
 
symmetricToUnity() - Method in class ffx.numerics.switching.ConstantSwitch
True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.LinearDerivativeSwitch
True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.MultiplicativeSwitch
True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.PowerSwitch
True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in class ffx.numerics.switching.SquaredTrigSwitch
True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
symmetricToUnity() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction
True if f(lb + delta) + f(ub - delta) = 1 for all delta between 0 and (ub - lb).
SymOp - Class in ffx.crystal
The SymOp class defines the rotation and translation of a single symmetry operator.
SymOp(double[][]) - Constructor for class ffx.crystal.SymOp
The SymOp constructor using a 4x4 matrix.
SymOp(double[][], double[]) - Constructor for class ffx.crystal.SymOp
The SymOp constructor using a rotation matrix and translation vector.
SymOp(double[][], double[], int[]) - Constructor for class ffx.crystal.SymOp
The SymOp constructor using a rotation matrix and translation vector.
symOps - Variable in class ffx.crystal.SpaceGroup
A List of SymOp instances.
symPhaseShift(double[]) - Method in class ffx.crystal.SymOp
symPhaseShift
symPhaseShift(HKL) - Method in class ffx.crystal.SymOp
symPhaseShift
symVec6Mat3(double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath
vector representation of a symmetric 3x3 matrix times a matrix
symVec6Mat3(double[], double[][], double[][]) - Static method in class ffx.numerics.math.MatrixMath
symVec6mat3
sysAbs() - Method in class ffx.crystal.HKL
sysAbs
System - Class in ffx.openmm
This class represents a molecular system.
System() - Constructor for class ffx.openmm.System
Constructor.
SYSTEM - Static variable in class ffx.ui.commands.SimulationMessage
Constant SYSTEM=0
SYSTEMBELOWMOUSE - Enum constant in enum class ffx.ui.GraphicsCanvas.MouseMode
 
SystemFilter - Class in ffx.potential.parsers
The SystemFilter class is the base class for most Force Field X file parsers.
SystemFilter(File, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.SystemFilter
Constructor for SystemFilter.
SystemFilter(File, List<MolecularAssembly>, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.SystemFilter
Constructor for SystemFilter.
SystemFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration) - Constructor for class ffx.potential.parsers.SystemFilter
Constructor for SystemFilter.
SystemFilter.Versioning - Enum Class in ffx.potential.parsers
 
systems - Variable in class ffx.potential.parsers.SystemFilter
All MolecularAssembly instances defined.
SystemState - Class in ffx.potential
The current state of the molecular dynamics simulation.
SystemState(int) - Constructor for class ffx.potential.SystemState
Constructor for MDState.
sz - Variable in class ffx.numerics.multipole.PolarizableMultipole
Averaged induced dipole + induced dipole chain-rule z-component: sz = 0.5 * (uz + pz).

T

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

U

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

V

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

W

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

X

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

Y

y - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
y - Variable in class ffx.numerics.multipole.MultipoleTensor
Yk - Yi.
y - Variable in class ffx.ui.behaviors.MouseBehavior
 
y() - Method in class ffx.numerics.math.Double3
Get the value of y.
y() - Method in class ffx.numerics.math.Float3
Get the value of y.
Y - Enum constant in enum class ffx.numerics.Potential.VARIABLE_TYPE
 
Y - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
Y - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
Yb - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
yFromRowIndex(int) - Method in class ffx.potential.nonbonded.RowRegion
yFromRowIndex.
yLast - Variable in class ffx.ui.behaviors.MouseBehavior
 
YYG - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
 

Z

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