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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
A matrix of double values.
A00 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A01 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A02 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A10 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A11 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A12 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A20 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A21 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
A22 - Variable in class ffx.crystal.Crystal
Entry in the A matrix.
AA - Enum constant in enum class ffx.potential.bonded.Residue.ResidueType
 
AA_C - Static variable in class ffx.potential.bonded.AminoAcidUtils
Constant AA_C
AA_CA - Static variable in class ffx.potential.bonded.AminoAcidUtils
Constant AA_CA
AA_CB - Static variable in class ffx.potential.bonded.AminoAcidUtils
Constant AA_CB
AA_HA - Static variable in class ffx.potential.bonded.AminoAcidUtils
Constant AA_HA
AA_HN - Static variable in class ffx.potential.bonded.AminoAcidUtils
Constant AA_HN
AA_N - Static variable in class ffx.potential.bonded.AminoAcidUtils
Biotype keys for amino acid backbone atom types.
AA_O - Static variable in class ffx.potential.bonded.AminoAcidUtils
Constant AA_O
AA1toAA3 - Static variable in class ffx.potential.bonded.AminoAcidUtils
Constant AA1toAA3
AAPATTERN - Static variable in class ffx.potential.bonded.AminoAcidUtils
Repeating atomic numbers of an amino acid chain.
about() - Method in class ffx.ui.MainPanel
about
aboutString - Static variable in class ffx.ui.MainPanel
 
abs() - Method in class ffx.numerics.math.ComplexNumber
abs
ABSOLUTE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
Ac - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
acceleration - Variable in class ffx.ui.commands.SimulationUpdate
 
ACCELERATION - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
accept(File) - Method in class ffx.potential.parsers.ARCFileFilter
accept(File) - Method in class ffx.potential.parsers.CoordinateFileFilter
accept(File) - Method in class ffx.potential.parsers.DistanceMatrixFileFilter
accept(File) - Method in class ffx.potential.parsers.DYNFileFilter
accept(File) - Method in class ffx.potential.parsers.ESVFileFilter
accept(File) - Method in class ffx.potential.parsers.FFXFileFilter
accept(File) - Method in class ffx.potential.parsers.ForceFieldFileFilter
accept(File) - Method in class ffx.potential.parsers.InducedFileFilter
accept(File) - Method in class ffx.potential.parsers.INTFileFilter
accept(File) - Method in class ffx.potential.parsers.KeyFileFilter
accept(File) - Method in class ffx.potential.parsers.PDBFileFilter
accept(File) - Method in class ffx.potential.parsers.PDBMLFileFilter
accept(File) - Method in class ffx.potential.parsers.XPHFileFilter
accept(File) - Method in class ffx.potential.parsers.XYZFileFilter
accept(File) - Method in class ffx.xray.parsers.MTZFileFilter
acceptChance(double, double, double) - Static method in class ffx.algorithms.mc.BoltzmannMC
Boltzmann-weighted acceptance probability
acceptDeep(File) - Method in class ffx.potential.parsers.CoordinateFileFilter
acceptDeep
acceptDeep(File) - Method in class ffx.potential.parsers.INTFileFilter
acceptDeep
acceptDeep(File) - Method in class ffx.potential.parsers.PDBFileFilter
acceptDeep Accepts a PDB file if it finds at least one parseable ATOM line.
acceptDeep(File) - Method in class ffx.potential.parsers.XYZFileFilter
acceptDeep
acceptDeep(File) - Method in class ffx.xray.parsers.MTZFileFilter
acceptDeep
ACE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
action(Timer) - Method in interface edu.rit.util.TimerTask
Perform this timer task's timed actions.
actionPerformed(ActionEvent) - Method in class ffx.ui.GraphicsCanvas
actionPerformed(ActionEvent) - Method in class ffx.ui.GraphicsPrefs
actionPerformed(ActionEvent) - Method in class ffx.ui.KeywordComponent
actionPerformed(ActionEvent) - Method in class ffx.ui.KeywordPanel
Handles input from KeywordPanel ToolBar buttons.
actionPerformed(ActionEvent) - Method in class ffx.ui.MainPanel
actionPerformed(ActionEvent) - Method in class ffx.ui.ModelingPanel
actionPerformed(ActionEvent) - Method in class ffx.ui.SimulationLoader
actionPerformed(ActionEvent) - Method in class ffx.ui.Trajectory
activeAssembly - Variable in class ffx.algorithms.cli.AlgorithmsScript
An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
activeAssembly - Variable in class ffx.potential.cli.PotentialCommand
An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
activeAssembly - Variable in class ffx.potential.cli.PotentialScript
An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
ACTIVESYSTEM - Enum constant in enum class ffx.ui.GraphicsCanvas.MouseMode
 
actOnAtoms(MolecularAssembly, String, BiConsumer<Atom, Boolean>, String) - Static method in class ffx.potential.cli.AtomSelectionOptions
 
actualCount - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
actualWork - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
Number of octant work cells with at least one atom (actualWork is less than or equal to nWork).
add(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
sum
add(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
sum
add(float[], float[]) - Static method in class ffx.numerics.math.FloatMath
sum
add(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath
sum
add(int) - Method in class ffx.potential.parameters.PolarizeType
Add an atom type to the polarization group.
add(int, int) - 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
A java.util.concurrent.atomic.DoubleAdder implementation.
AdderDoubleArray - Class in ffx.numerics.atomic
AdderDoubleArray implements the AtomicDoubleArray interface using an array of java.util.concurrent.atomic.DoubleAdder.
AdderDoubleArray(int) - Constructor for class ffx.numerics.atomic.AdderDoubleArray
Construct an AdderDoubleArray.
addExclusion(int, int) - Method in class ffx.openmm.CustomNonbondedForce
Add an exclusion.
addForce(Force) - Method in class ffx.openmm.System
Add a force to the system.
addForceFieldType(T) - Method in class ffx.potential.parameters.ForceField
Add an instance of a force field type.
addForces() - Method in class ffx.potential.openmm.OpenMMSystem
Add forces to the system.
addGlobalParameter(String, double) - Method in class ffx.openmm.CustomBondForce
Add a global parameter to the CustomBondForce.
addGlobalParameter(String, double) - Method in class ffx.openmm.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
Allowed is used for centric reflections.
allReduce(int, Buf, Op) - Method in class edu.rit.pj.Comm
Perform an all-reduce on all processes in this communicator using the given message tag.
allReduce(Buf, Op) - Method in class edu.rit.pj.Comm
Perform an all-reduce on all processes in this communicator.
allToAll(int, Buf[], Buf[]) - Method in class edu.rit.pj.Comm
Do an all-to-all among all processes in this communicator using the given message tag.
allToAll(Buf[], Buf[]) - Method in class edu.rit.pj.Comm
Do an all-to-all among all processes in this communicator.
alpha - Variable in class ffx.crystal.Crystal
The interaxial lattice angle between b and c.
Am - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
AMBER_1994 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
AMBER_1996 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
AMBER_1998 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
AMBER_1999 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
AMBER_1999_SB - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
AMINOACID - Enum constant in enum class ffx.potential.Utilities.PolymerType
 
aminoAcid1List - Static variable in class ffx.potential.bonded.AminoAcidUtils
List of values from the AminoAcid1 enum.
aminoAcid3 - Variable in class ffx.potential.bonded.Rotamer
The A.A.
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
 
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.
applyMasks(DoubleVector, DoubleVector) - Method in class ffx.numerics.multipole.PolarizableMultipoleSIMD
Compute the scaled and averaged induced dipole.
applyMatrixTranspose(double[], double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath
Multiply coordinates by the transpose of a matrix.
applyProperties(CompositeConfiguration) - Method in class ffx.algorithms.thermodynamics.HistogramData
 
applyRandomDensity(double) - Method in class ffx.potential.MolecularAssembly
Applies a randomly drawn density to a molecular system's crystal.
applyRandomSymOp(double) - Method in class ffx.potential.MolecularAssembly
Randomizes position in the unit cell of each molecule by applying a Cartesian SymOp with a random translation.
applyRotamer(Residue, Rotamer) - Static method in class ffx.potential.bonded.RotamerLibrary
Applies a Rotamer to a Residue by calling applyAARotamer or applyNARotamer.
applyRotamer(Residue, Rotamer, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary
Version of applyRotamer which allows for chain context-independent drawing of nucleic acid Rotamers.
applyRotation(double[], double[][]) - Static method in class ffx.potential.utils.Superpose
Apply a rotation matrix to a set of coordinates.
applySoluteRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
Apply solute radii definitions used to calculate Born radii.
applySugarPucker(Residue, RotamerLibrary.NucleicSugarPucker, boolean, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary
If place is true, builds C2', C3', and O3' based on delta(i) and returns an empty double[]; if place is false, returns a double[] filled with the coordinates at which O3' would be placed by the specified pucker.
applySymOp(double[], double[], SymOp) - Method in class ffx.crystal.Crystal
Apply a fractional symmetry operator to one set of cartesian coordinates.
applySymOp(int, double[], double[], double[], double[], double[], double[], SymOp) - Method in class ffx.crystal.Crystal
Apply a fractional symmetry operator to an array of Cartesian coordinates.
applySymOp(int, int, int, int[], SymOp, int, int, int) - Static method in class ffx.crystal.SymOp
Apply a symmetry operator to one set of coordinates.
applySymRot(double[], double[], SymOp) - Method in class ffx.crystal.Crystal
Apply a fractional symmetry operator to one set of cartesian coordinates.
applySymRot(HKL, HKL, SymOp) - Static method in class ffx.crystal.SymOp
Apply a symmetry operator to one HKL.
applyTranslation(double[], double[]) - Static method in class ffx.potential.utils.Superpose
Apply a translation matrix [dx,dy,dz] to a molecular system.
applyTransSymRot(int, double[], double[], double[], double[], double[], double[], SymOp, double[][]) - Method in class ffx.crystal.Crystal
Apply the transpose of a symmetry rotation to an array of Cartesian coordinates.
applyTransSymRot(HKL, HKL, SymOp) - Static method in class ffx.crystal.SymOp
Apply a transpose rotation symmetry operator to one HKL.
APPLYUSERCOLOR - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
 
approxEquals(double, double) - Static method in class ffx.numerics.integrate.FunctionDataCurve
Checks for equality to +/- 10 ulp.
approxEquals(double, double, double) - Static method in class ffx.numerics.integrate.FunctionDataCurve
Compare two doubles to machine precision.
aPrevious - Variable in class ffx.potential.SystemState
Previous accelerations.
aPrevious() - Method in class ffx.potential.SystemState
Get a reference to the internal previous accelerations array.
aPrevious() - Method in record class ffx.potential.UnmodifiableState
Returns the value of the aPrevious record component.
Ar - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
ARC - Enum constant in enum class ffx.potential.Utilities.FileType
 
ARCFileFilter - Class in ffx.potential.parsers
The ARCFileFilter class is used to choose a TINKER Archive (*.ARC).
ARCFileFilter() - Constructor for class ffx.potential.parsers.ARCFileFilter
Default Constructor
ARG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
ARGININE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
args - Variable in class ffx.utilities.FFXCommand
The array of args passed into the Script.
args - Variable in class ffx.utilities.FFXScript
The array of args passed into the Script.
ARITHMETIC - Enum constant in enum class ffx.potential.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
 
ASH1toASH2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
 
ASHtoASP - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
 
askToInterruptScript() - Method in class ffx.ui.ModelingShell
If at exit time, a script is running, the user is given an option to interrupt it first
askToSaveFile() - Method in class ffx.ui.ModelingShell
asMatrix() - Method in class ffx.crystal.SymOp
Return the SymOp as a 4x4 matrix.
asMatrixString(SymOp) - Static method in class ffx.crystal.SymOp
Print a Sym Op matrix as a continued line string.
ASN - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
ASP - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
ASPARAGINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
ASPARTATE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
 
ASPC - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
 
ASPC - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
 
aspcPredictor(LambdaMode, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters
Always-stable predictor-corrector for the mutual induced dipoles.
assembleMolecularDynamics(MolecularAssembly[], CrystalPotential, DynamicsOptions, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions
Assembles a MolecularDynamics wrapped around a Potential.
assemblePotential(MolecularAssembly[], int, StringBuilder) - Method in class ffx.potential.cli.TopologyOptions
Performs the bulk of the work of setting up a multi-topology system.
AssemblyState - Class in ffx.potential
The AssemblyState class stores the chemical and coordinate state of a Molecular Assembly.
AssemblyState(MolecularAssembly) - Constructor for class ffx.potential.AssemblyState
Construct a snapshot of a MolecularAssembly.
assertXIntegrity() - Method in class ffx.numerics.integrate.FunctionDataCurve
Used to check that x array is composed of equally-spaced points from lb to ub.
assignAminoAcidAtomTypes(Residue, Residue, Residue, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils
assignAminoAcidAtomTypes.
assignAminoAcidAtomTypes(List<Residue>, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils
Assign atom types to an amino acid polymer.
assignAtomsToCells() - Method in class ffx.potential.nonbonded.SpatialDensityRegion
Assign asymmetric and symmetry mate atoms to cells.
assignAtomTypes(MolecularAssembly, PDBFilter.PDBFileStandard) - Static method in class ffx.potential.bonded.PolymerUtils
Assign force field atoms types to common chemistries using "biotype" records.
assignAxisAtoms(Atom) - Static method in class ffx.potential.parameters.MultipoleType
Assign local multipole frame defining atoms.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.JobFrontend
Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage
Construct a new "assign backend" message.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy
Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef
Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Assign a backend process to the job.
assignBondedTerms(ForceField) - Method in class ffx.potential.bonded.MSGroup
assignBondedTerms
assignBondedTerms(ForceField) - Method in class ffx.potential.bonded.MultiResidue
assignBondedTerms
assigned(int[], boolean, boolean) - Method in class ffx.potential.parameters.ImproperTorsionType
Returns true if the atoms can be assigned this improperTorsionType.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontend
Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage
Construct a new "assign job number" message.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy
Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef
Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Assign a job number to the job.
assignMultipole(ForceField.ELEC_FORM, Atom, ForceField, double[], int, int[][], MultipoleType.MultipoleFrameDefinition[]) - Static method in class ffx.potential.parameters.MultipoleType
Assign the multipole type.
assignNucleicAcidAtomTypes(List<Residue>, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.NucleicAcidUtils
Assign atom types for a nucleic acid polymer.
assignPolarizationGroups() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
AssignPolarizationGroups.
assignPolarizationGroups(Atom[], int[][], int[][], int[][]) - Static method in class ffx.potential.parameters.PolarizeType
assignPolarizationGroups.
ASULimit - Enum Class in ffx.crystal
Enumeration of the different asymmetric unit limit operators.
asuLimitOperators - Variable in class ffx.crystal.SpaceGroup
Real space ASU limit operators.
At - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
ATM_TO_BAR - Static variable in class ffx.utilities.Constants
Constant ATM_TO_BAR=1.01325
atom - Variable in exception class ffx.potential.bonded.BondedUtils.MissingAtomTypeException
 
Atom - Class in ffx.potential.bonded
The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
Atom(int, Atom, double[], int, char, String) - Constructor for class ffx.potential.bonded.Atom
Creates a new Atom similar to an existing Atom (e.g.
Atom(int, String, AtomType, double[]) - Constructor for class ffx.potential.bonded.Atom
Constructor used when parsing XYZ files.
Atom(int, String, Character, double[], String, int, Character, double, double, String) - Constructor for class ffx.potential.bonded.Atom
Constructor used when parsing PDB files.
Atom(int, String, Character, double[], String, int, Character, double, double, String, boolean) - Constructor for class ffx.potential.bonded.Atom
Constructor for Atom.
Atom(String) - Constructor for class ffx.potential.bonded.Atom
Default constructor.
ATOM - Enum constant in enum class ffx.potential.MolecularAssembly.FractionalMode
 
ATOM - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
ATOM_DISTANCE - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
 
Atom.Descriptions - Enum Class in ffx.potential.bonded
 
Atom.ElementSymbol - Enum Class in ffx.potential.bonded
Element symbols for the first 109 elements.
Atom.Resolution - Enum Class in ffx.potential.bonded
 
atomAttachedToAtom(Atom, Atom) - Static method in class ffx.potential.bonded.BondedUtils
Checks if atom a1 is bonded to atom a2.
atomClass - Variable in class ffx.potential.parameters.AtomType
Atom class.
atomClass - Variable in class ffx.potential.parameters.VDWType
The atom class that uses this van der Waals parameter.
atomClasses - Variable in class ffx.potential.parameters.AngleTorsionType
Atom classes for this stretch-torsion type.
atomClasses - Variable in class ffx.potential.parameters.AngleType
Atom classes that for this Angle type.
atomClasses - Variable in class ffx.potential.parameters.BondType
Atom classes that form this bond stretch.
atomClasses - Variable in class ffx.potential.parameters.ImproperTorsionType
Atom classes that for this Improper Torsion angle.
atomClasses - Variable in class ffx.potential.parameters.OutOfPlaneBendType
Atom classes for this out-of-plane angle bending type.
atomClasses - Variable in class ffx.potential.parameters.PiOrbitalTorsionType
Atom classes that form this Pi-Torsion.
atomClasses - Variable in class ffx.potential.parameters.StretchBendType
Atom class for this stretch-bend type.
atomClasses - Variable in class ffx.potential.parameters.StretchTorsionType
Atom classes for this stretch-torsion type.
atomClasses - Variable in class ffx.potential.parameters.TorsionTorsionType
Atom classes that form this Torsion-Torsion type.
atomClasses - Variable in class ffx.potential.parameters.TorsionType
Atom classes that for this Torsion angle.
atomClasses - Variable in class ffx.potential.parameters.UreyBradleyType
Atom classes that form this Urey-Bradley cross term.
atomClasses - Variable in class ffx.potential.parameters.VDWPairType
Atom classes that form this bond stretch.
AtomColor - Static variable in class ffx.potential.bonded.Atom
Constant AtomColor
atomic - Variable in class ffx.ui.commands.SimulationDefinition
 
AtomicDoubleArray - Interface in ffx.numerics.atomic
This interface abstracts away the implementation of maintaining a 1D double array that is operated on by multiple threads.
AtomicDoubleArray.AtomicDoubleArrayImpl - Enum Class in ffx.numerics.atomic
AtomicDoubleArray implementations (ADDER, MULTI, PJ).
AtomicDoubleArray3D - Class in ffx.numerics.atomic
Implementation of maintaining a 3D double array that is operated on by multiple threads.
AtomicDoubleArray3D(AtomicDoubleArray.AtomicDoubleArrayImpl, int) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D
Construct an atomic 3D double array of the specified size using the specified implementation.
AtomicDoubleArray3D(AtomicDoubleArray.AtomicDoubleArrayImpl, int, int) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D
Construct an atomic 3D double array of the specified size, using the specified implementation, and the requested number of threads.
AtomicDoubleArray3D(AtomicDoubleArray, AtomicDoubleArray, AtomicDoubleArray) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D
Construct an atomic 3D double array using the specified AtomicDoubleArray instances.
atomicDoubleArrayFactory(AtomicDoubleArray.AtomicDoubleArrayImpl, int, int) - Static method in interface ffx.numerics.atomic.AtomicDoubleArray
Factory method to create an AtomicDoubleArray instance.
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
Backwards perturbation.
BadIntpln - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult
Bad interpolation.
BALLANDSTICK - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
 
BAR - Enum constant in enum class ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType
 
BARFilter - Class in ffx.potential.parsers
The BARFilter class parses TINKER bar(*.BAR) files.
BARFilter(File) - Constructor for class ffx.potential.parsers.BARFilter
BARFilter constructor
BARFilter(File, double[], double[], double[], double[], double[], double[], double) - Constructor for class ffx.potential.parsers.BARFilter
BARFilter constructor
BARFilter(File, int, int) - Constructor for class ffx.potential.parsers.BARFilter
BARFilter constructor
barostat - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Reference to the Barostat in use; if present this must be turned off during optimization.
Barostat - Class in ffx.algorithms.dynamics
The Barostat class maintains constant pressure using random trial moves in lattice parameters, which are consistent with the space group.
Barostat(MolecularAssembly, CrystalPotential) - Constructor for class ffx.algorithms.dynamics.Barostat
Initialize the Barostat.
Barostat(MolecularAssembly, CrystalPotential, double) - Constructor for class ffx.algorithms.dynamics.Barostat
Initialize the Barostat.
BarostatOptions - Class in ffx.algorithms.cli
Represents command line options for scripts that use a barostat/NPT.
BarostatOptions() - Constructor for class ffx.algorithms.cli.BarostatOptions
 
barrier() - Method in class edu.rit.pj.Comm
Cause all processes in this communicator to wait at a barrier.
barrier() - Method in class edu.rit.pj.ParallelRegion
Perform a barrier.
barrier(int) - Method in class edu.rit.pj.Comm
Cause all processes in this communicator to wait at a barrier, using the given message tag.
barrier(BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Perform a barrier, with a barrier action.
BarrierAction - Class in edu.rit.pj
Class BarrierAction is the abstract base class for an object containing code that is executed as part of a barrier wait.
BarrierAction() - Constructor for class edu.rit.pj.BarrierAction
Construct a new barrier action.
baseDir - Variable in class ffx.algorithms.cli.AlgorithmsScript
The directory in which to place output files.
baseDir - Variable in class ffx.potential.cli.PotentialCommand
A temporary directory that contains script artifacts.
baseDir - Variable in class ffx.potential.cli.PotentialScript
A temporary directory that contains script artifacts.
BaseType - Class in ffx.potential.parameters
All force field types should extend the BaseType class.
BaseType(ForceField.ForceFieldType, int[]) - Constructor for class ffx.potential.parameters.BaseType
Public constructor.
BaseType(ForceField.ForceFieldType, String) - Constructor for class ffx.potential.parameters.BaseType
Public constructor.
Be - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
BEEMAN - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
 
before() - Method in class ffx.ui.ModelingShell
before
beforeClass() - Static method in class ffx.algorithms.misc.AlgorithmsTest
Initialize the PJ communication layer.
beforeClass() - Static method in class ffx.utilities.FFXTest
beforeClass.
beforeTest() - Method in class ffx.algorithms.misc.AlgorithmsTest
 
beforeTest() - Method in class ffx.potential.utils.PotentialTest
 
beforeTest() - Method in class ffx.utilities.FFXTest
beforeTest.
beginMCOST(MonteCarloOST, DynamicsOptions, ThermodynamicsOptions) - Method in class ffx.algorithms.cli.OSTOptions
Runs MC-OST.
beginMDOST(OrthogonalSpaceTempering, MolecularAssembly[], CrystalPotential, DynamicsOptions, WriteoutOptions, ThermodynamicsOptions, File, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions
Begins MD-OST sampling from an assembled OST.
BellCurveSwitch - Class in ffx.numerics.switching
Implements a bell-shaped switching function by stitching together a pair of MultiplicativeSwitches.
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
The bin number of this reflection, which is used for resolution dependent R/Rfree.
BINARY - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel
The classic binary (0, 1) model.
binding - Variable in class ffx.algorithms.misc.AlgorithmsTest
 
binding - Variable in class ffx.potential.utils.PotentialTest
 
binomial(long, long) - Static method in class ffx.numerics.math.ScalarMath
binomial
binWidth() - Method in interface ffx.numerics.integrate.DataSet
Separation between points along x; should be uniform.
binWidth() - Method in class ffx.numerics.integrate.DoublesDataSet
Separation between points along x; should be uniform.
binWidth() - Method in class ffx.numerics.integrate.FunctionDataCurve
Separation between points along x; should be uniform.
biochemistry(MolecularAssembly, List<Atom>) - Static method in class ffx.potential.Utilities
This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.
BioType - Class in ffx.potential.parameters
The BioType class maps PDB identifiers to atom types.
BioType(int, String, String, int, String[]) - Constructor for class ffx.potential.parameters.BioType
BioType Constructor.
BIOTYPE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
BISECTOR - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
 
Bk - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
BLACK - Static variable in class ffx.potential.bonded.RendererCache
Constant BLACK
BMP - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
 
bn - Variable in class ffx.numerics.multipole.GKSource
Chain rule terms from differentiating zeroth order born radii auxiliary functions (bn0) with respect to Ai or Aj.
bn - Variable in class ffx.numerics.multipole.GKSourceSIMD
Chain rule terms from differentiating zeroth order born radii auxiliary functions (bn0) with respect to Ai or Aj.
bn(int) - Method in class ffx.numerics.multipole.GKSource
Compute the function b, which are chain rule terms from differentiating zeroth order auxiliary functions (an0) with respect to Ai or Aj.
bn(int) - Method in class ffx.numerics.multipole.GKSourceSIMD
Compute the function b, which are chain rule terms from differentiating zeroth order auxiliary functions (an0) with respect to Ai or Aj.
BOHR - Static variable in class ffx.utilities.Constants
Conversion from Bohr to Angstroms.
BOHR2 - Static variable in class ffx.utilities.Constants
Conversion from Bohr^2 to Angstroms^2.
BOLTZMANN_SI - Static variable in class ffx.utilities.Constants
Boltzmann's constant in J/K, defining the Kelvin.
BoltzmannMC - Class in ffx.algorithms.mc
The BoltzmannMC abstract class is a skeleton for Boltzmann-weighted Metropolis Monte Carlo simulations.
BoltzmannMC() - Constructor for class ffx.algorithms.mc.BoltzmannMC
 
Bond - Class in ffx.potential.bonded
The Bond class represents a covalent bond formed between two atoms.
Bond(Atom, Atom) - Constructor for class ffx.potential.bonded.Bond
Bond constructor.
Bond(String) - Constructor for class ffx.potential.bonded.Bond
Simple Bond constructor that is intended to be used with the equals method.
BOND - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
 
bond0Eq - Variable in class ffx.potential.bonded.StretchBend
First equilibrium bond distance.
bond1Eq - Variable in class ffx.potential.bonded.StretchBend
Second equilibrium bond distance.
bondAngle(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Finds the angle formed by three atoms.
bondAngle(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Finds the angle formed by three atoms
BondArray - Class in ffx.openmm
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.RestrainDistance
 
BondType - Class in ffx.potential.parameters
The BondType class defines one harmonic bond stretch energy term.
BondType(int[], double, double) - Constructor for class ffx.potential.parameters.BondType
The default BondType constructor defines use of the Quartic BondFunction.
BondType(int[], double, double, BondType.BondFunction) - Constructor for class ffx.potential.parameters.BondType
BondType constructor.
BondType(int[], double, double, BondType.BondFunction, double) - Constructor for class ffx.potential.parameters.BondType
BondType constructor.
BondType.BondFunction - Enum Class in ffx.potential.parameters
Describes the function used by the bond.
bondType1 - Variable in class ffx.potential.bonded.StretchTorsion
First bond force field type.
bondType2 - Variable in class ffx.potential.bonded.StretchTorsion
Second bond force field type.
bondType3 - Variable in class ffx.potential.bonded.StretchTorsion
Third bond force field type.
bondUnit - Variable in class ffx.potential.parameters.BondType
Convert bond stretch energy to kcal/mole.
bondwidth - Static variable in class ffx.potential.bonded.RendererCache
Constant bondwidth=3
BOOLE - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType
Boole's Five Point Integration, requiring 5 points.
BooleanArrayBuf - Class in edu.rit.mp.buf
Class BooleanArrayBuf provides a buffer for an array of Boolean items sent or received using the Message Protocol (MP).
BooleanArrayBuf(boolean[], Range) - Constructor for class edu.rit.mp.buf.BooleanArrayBuf
Construct a new Boolean array buffer.
BooleanArrayBuf_1 - Class in edu.rit.mp.buf
Class BooleanArrayBuf_1 provides a buffer for an array of Boolean items sent or received using the Message Protocol (MP).
BooleanArrayBuf_1(boolean[], Range) - Constructor for class edu.rit.mp.buf.BooleanArrayBuf_1
Construct a new Boolean array buffer.
BooleanBuf - Class in edu.rit.mp
Class BooleanBuf is the abstract base class for a buffer of Boolean items sent or received using the Message Protocol (MP).
BooleanBuf(int) - Constructor for class edu.rit.mp.BooleanBuf
Construct a new Boolean buffer.
BooleanItemBuf - Class in edu.rit.mp.buf
Class BooleanItemBuf provides a buffer for a single Boolean item sent or received using the Message Protocol (MP).
BooleanItemBuf() - Constructor for class edu.rit.mp.buf.BooleanItemBuf
Construct a new Boolean item buffer.
BooleanItemBuf(boolean) - Constructor for class edu.rit.mp.buf.BooleanItemBuf
Construct a new Boolean item buffer with the given initial value.
BooleanMatrixBuf - Class in edu.rit.mp.buf
Class BooleanMatrixBuf provides a buffer for a matrix of Boolean items sent or received using the Message Protocol (MP).
BooleanMatrixBuf(boolean[][], Range, Range) - Constructor for class edu.rit.mp.buf.BooleanMatrixBuf
Construct a new Boolean matrix buffer.
BooleanMatrixBuf_1 - Class in edu.rit.mp.buf
Class BooleanMatrixBuf_1 provides a buffer for a matrix of Boolean items sent or received using the Message Protocol (MP).
BooleanMatrixBuf_1(boolean[][], Range, Range) - Constructor for class edu.rit.mp.buf.BooleanMatrixBuf_1
Construct a new Boolean matrix buffer.
BooleanOp - Class in edu.rit.pj.reduction
Class BooleanOp is the abstract base class for a binary operation on Boolean values, used to do reduction in a parallel program.
BooleanOp() - Constructor for class edu.rit.pj.reduction.BooleanOp
Construct a new Boolean binary operation.
booles(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set using Boole's rule.
booles(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set, in bounds lb-ub inclusive, using Boole's rule.
boolesParallel(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set using Boole's rule.
boolesParallel(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric
Numerically integrates a data set, in bounds lb-ub inclusive, using Boole's rule.
bootstrap(long) - Method in class ffx.numerics.estimator.EstimateBootstrapper
Perform bootstrap analysis.
bootstrap(long, long) - Method in class ffx.numerics.estimator.EstimateBootstrapper
Perform bootstrap analysis.
BootstrappableEstimator - Interface in ffx.numerics.estimator
The BootstrappableEstimator interface describes a StatisticalEstimator which can use bootstrap sampling as an additional method of calculating free energy and uncertainty.
BootStrapStatistics - Class in ffx.numerics.math
The BootStrapStatistics class uses bootstrapping to estimate statistics from a given population.
BootStrapStatistics(double[]) - Constructor for class ffx.numerics.math.BootStrapStatistics
Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], double[], int, int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics
Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int) - Constructor for class ffx.numerics.math.BootStrapStatistics
Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics
Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int, int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics
Constructs a static summary of a statistic from provided values.
border - Static variable in class ffx.ui.MainPanel
Constant
BORN - Enum constant in enum class ffx.numerics.multipole.GKTensorMode
The tensor is for the GK Born-chain rule.
BORN_CAV_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
 
BORN_SOLV - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
 
BornGradRegion - Class in ffx.potential.nonbonded.implicit
Parallel computation of Born radii chain rule terms via the Grycuk method.
BornGradRegion(int, boolean, boolean, boolean) - Constructor for class ffx.potential.nonbonded.implicit.BornGradRegion
Compute the gradient due to changes in Born radii.
BornRadiiRegion - Class in ffx.potential.nonbonded.implicit
Parallel computation of Born radii via the Grycuk method.
BornRadiiRegion(int, int, ForceField, boolean, boolean, boolean) - Constructor for class ffx.potential.nonbonded.implicit.BornRadiiRegion
BornRadiiRegion Constructor.
bornRadiiTotal - Variable in class ffx.potential.nonbonded.pme.PMETimings
 
BornTanhRescaling - Class in ffx.potential.nonbonded.implicit
Rescale the Born radius integral to account for interstitial spaces.
BornTanhRescaling() - Constructor for class ffx.potential.nonbonded.implicit.BornTanhRescaling
 
BOTH - Enum constant in enum class ffx.numerics.Potential.STATE
Include both FAST and SLOW varying energy terms.
BOX - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
 
Br - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
BR - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
 
broadcast(int, int, Buf) - Method in class edu.rit.pj.Comm
Broadcast a message to all processes in this communicator using the given message tag.
broadcast(int, Buf) - Method in class edu.rit.pj.Comm
Broadcast a message to all processes in this communicator.
broadcastPattern(int, int, int) - Static method in class edu.rit.pj.cluster.CommPattern
Calculate the communication pattern for a parallel broadcast tree.
BRUTE_FORCE - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
 
bSpline(double, int, double[]) - Static method in class ffx.numerics.spline.UniformBSpline
Generate uniform b-Spline coefficients.
bSplineDerivatives(double, int, int, double[][], double[][]) - Static method in class ffx.numerics.spline.UniformBSpline
Generate uniform b-Spline coefficients and their derivatives.
Buf - Class in edu.rit.mp
Class Buf is the abstract base class for a buffer of items sent or received using the Message Protocol (MP).
buff - Variable in class ffx.potential.nonbonded.NonbondedCutoff
A buffer added to the cut-off distance off to define neighbors included when collecting Verlet lists.
buff - Variable in class ffx.potential.nonbonded.RowRegion
 
buff - Variable in class ffx.potential.nonbonded.SliceRegion
 
buffer() - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for a Boolean item.
buffer() - Static method in class edu.rit.mp.ByteBuf
Create a buffer for a byte item.
buffer() - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for a character item.
buffer() - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for a double item.
buffer() - Static method in class edu.rit.mp.FloatBuf
Create a buffer for a float item.
buffer() - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.LongBuf
Create a buffer for a long item.
buffer() - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for an object item.
buffer() - Static method in class edu.rit.mp.ShortBuf
Create a buffer for a short item.
buffer() - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for an integer item.
buffer() - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for an integer item.
buffer(boolean) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for a Boolean item with the given initial value.
buffer(boolean[]) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for the entire given Boolean array.
buffer(boolean[][]) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for the entire given Boolean matrix.
buffer(byte) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for a byte item with the given initial value.
buffer(byte[]) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for the entire given byte array.
buffer(byte[][]) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for the entire given byte matrix.
buffer(char) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for a character item with the given initial value.
buffer(char[]) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for the entire given character array.
buffer(char[][]) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for the entire given character matrix.
buffer(double) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for a double item with the given initial value.
buffer(double[]) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for the entire given double array.
buffer(double[][]) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for the entire given double matrix.
buffer(float) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for a float item with the given initial value.
buffer(float[]) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for the entire given float array.
buffer(float[][]) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for the entire given float matrix.
buffer(int) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for an integer item with the given initial value.
buffer(int) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for an integer item with the given initial value.
buffer(int[]) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for the entire given integer array.
buffer(int[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for the entire given integer array.
buffer(int[][]) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for the entire given integer matrix.
buffer(int[][]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for the entire given integer matrix.
buffer(long) - Static method in class edu.rit.mp.LongBuf
Create a buffer for a long item with the given initial value.
buffer(long[]) - Static method in class edu.rit.mp.LongBuf
Create a buffer for the entire given long array.
buffer(long[][]) - Static method in class edu.rit.mp.LongBuf
Create a buffer for the entire given long matrix.
buffer(short) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for a short item with the given initial value.
buffer(short[]) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for the entire given short array.
buffer(short[][]) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for the entire given short matrix.
buffer(SharedBoolean) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for a shared Boolean item.
buffer(SharedBooleanArray) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for the entire given shared Boolean array.
buffer(SharedByte) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for a shared byte item.
buffer(SharedByteArray) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for the entire given shared byte array.
buffer(SharedCharacter) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for a shared character item.
buffer(SharedCharacterArray) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for the entire given shared character array.
buffer(SharedDouble) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for a shared double item.
buffer(SharedDoubleArray) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for the entire given shared double array.
buffer(SharedFloat) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for a shared float item.
buffer(SharedFloatArray) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for the entire given shared float array.
buffer(SharedInteger) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for a shared integer item.
buffer(SharedInteger) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for a shared integer item.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for the entire given shared integer array.
buffer(SharedIntegerArray) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for the entire given shared integer array.
buffer(SharedLong) - Static method in class edu.rit.mp.LongBuf
Create a buffer for a shared long item.
buffer(SharedLongArray) - Static method in class edu.rit.mp.LongBuf
Create a buffer for the entire given shared long array.
buffer(SharedObject<T>) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for a shared object item.
buffer(SharedObjectArray<T>) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for the entire given shared object array.
buffer(SharedShort) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for a shared short item.
buffer(SharedShortArray) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for the entire given shared short array.
buffer(T) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for an object item with the given initial value.
buffer(T[]) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for the entire given object array.
buffer(T[][]) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for the entire given object matrix.
BUFFERED_14_7 - Enum constant in enum class ffx.potential.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
Is this reflection 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.
chargeIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
Compute the field components due to site I charge at site K.
chargeIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD
Compute the field components due to site I charge at site K.
chargeIPotentialAtK(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD
Compute the field components due to site I charge at site K.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI
Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor
Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
Compute the field components due to site K charge at site I.
chargeKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD
Compute the field components due to site K charge at site I.
chargeKPotentialAtI(PolarizableMultipoleSIMD, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD
Compute the field components due to site K charge at site I.
ChargeType - Class in ffx.potential.parameters
The ChargeType class defines a partial atomic charge type.
ChargeType(int, double) - Constructor for class ffx.potential.parameters.ChargeType
ChargeType constructor.
CHARMM_22 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
CHARMM_22_CMAP - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
 
CHEAP - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
 
check(double, double) - Method in enum class ffx.crystal.ASULimit
Check the given point is within the asymmetric unit limit.
check(double, double) - Static method in enum class ffx.crystal.LatticeSystem
If the two passed values are the same, within the tolerance, return true.
check(int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Check for eliminated rotamer; true if eliminated.
check(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Check for eliminated rotamer pair; true if eliminated.
checkAtomicNumberAndMass(int, double) - Static method in class ffx.potential.parameters.AtomType
Check if the supplied atomic mass is within 0.1 AMU of the IUPAC value for the given atomic number.
checkAtomicNumberAndMass(int, double, double) - Static method in class ffx.potential.parameters.AtomType
Check if the supplied atomic mass is within the supplied tolerance (in AMU) of the IUPAC value for the given atomic number.
CHECKBOX - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
 
CHECKBOXES - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
 
checkDistMatrix(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Gets the raw distance between two rotamers using lazy loading of the distance matrix.
checkHydrogenAtomNames(Residue, PDBFilter.PDBFileStandard) - Static method in class ffx.potential.bonded.NamingUtils
Ensures proper naming of hydrogen according to latest PDB format.
checkList(int[][][], int) - Method in class ffx.potential.nonbonded.RowLoop
checkList.
checkList(int[][], int) - Method in class ffx.potential.nonbonded.SliceLoop
checkList.
checkMultipoleChirality(MultipoleType.MultipoleFrameDefinition, double[], double[][]) - Static method in class ffx.potential.parameters.MultipoleType
checkMultipoleChirality.
checkNeighboringPair(int, int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Checks if residue i is considered to be interacting with residue j, and thus has non-null elements in the pair energies matrix.
checkNeighboringTriple(int, int, int) - Method in class ffx.algorithms.optimize.RotamerOptimization
Checks if residue i is considered to be interacting with residue j, that residue k is interacting with either i or j, and thus i-j-k has non-null elements in the triple energy matrix.
checkNPT(MolecularAssembly, CrystalPotential) - Method in class ffx.algorithms.cli.BarostatOptions
If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.
checkPairDistThreshold(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Checks if the i,ri,j,rj pair exceeds the pair distance thresholds.
checkProperties(CompositeConfiguration) - Static method in class ffx.crystal.Crystal
checkProperties
checkProperties(CompositeConfiguration) - Static method in class ffx.crystal.Resolution
checkProperties
checkPrunedPairs(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Check for pruned rotamer pair; true if eliminated.
checkPrunedSingles(int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Check for pruned rotamer; true if eliminated.
checkPucker(double, boolean) - Static method in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker
Returns the sugar pucker associated with a delta torsion.
checkQuadDistThreshold(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Checks if the i,ri,j,rj,k,rk,l,rl quad exceeds the 3-body threshold, or if any component exceeds the pair/triple distance thresholds.
checkRestrictions(int, int, int) - Method in enum class ffx.crystal.LaueSystem
Check the given HKL is valid given the Laue system.
checkThole(double) - Method in class ffx.numerics.multipole.TholeTensorGlobal
Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(double) - Method in class ffx.numerics.multipole.TholeTensorQI
Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(double, double, double) - Static method in class ffx.numerics.multipole.TholeTensorGlobal
Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(DoubleVector) - Method in class ffx.numerics.multipole.TholeTensorGlobalSIMD
Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(DoubleVector) - Method in class ffx.numerics.multipole.TholeTensorQISIMD
Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(DoubleVector, DoubleVector, DoubleVector) - Static method in class ffx.numerics.multipole.TholeTensorGlobalSIMD
Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkToJ(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Checks to see if any eliminations with j,rj have occurred; assumes i,ri self has already been checked.
checkToK(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Checks to see if any eliminations with k,rk have occurred; assumes i,ri,j,rj 2-Body has already been checked.
checkToL(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Checks to see if any eliminations with l,rl have occurred; assumes i,ri,j,rj,k,rk 3-Body has already been checked.
checkTriDistThreshold(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix
Checks if the i,ri,j,rj,k,rk triple exceeds the 3-body threshold, or if any component exceeds the pair distance threshold.
checkValidMove(int, int, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization
Checks the pair elimination array to see if this permutation has been eliminated.
chi1 - Variable in class ffx.potential.bonded.Rotamer
Torsions chi 1-4 are used for amino acids and nucleic acids.
chi2 - Variable in class ffx.potential.bonded.Rotamer
 
chi3 - Variable in class ffx.potential.bonded.Rotamer
 
chi4 - Variable in class ffx.potential.bonded.Rotamer
 
chi5 - Variable in class ffx.potential.bonded.Rotamer
Torsions chi 5-7 are only currently used for nucleic acids.
chunk(int, int) - Method in class edu.rit.util.Range
Slice off a chunk of this range and return the chunk.
chunk(long, long) - Method in class edu.rit.util.LongRange
Slice off a chunk of this range and return the chunk.
CIF - Enum constant in enum class ffx.potential.Utilities.FileType
 
CIFFilter - Class in ffx.potential.parsers
The CIFFilter class parses CIF coordinate (*.CIF) files.
CIFFilter - Class in ffx.xray.parsers
CIF file reader
CIFFilter() - Constructor for class ffx.xray.parsers.CIFFilter
Constructor.
CIFFilter(File, MolecularAssembly, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter
Constructor for CIFFilter on a single file and a single assembly.
CIFFilter(File, List<MolecularAssembly>, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter
Constructor for CIFFilter on a single file and multiple assemblies.
CIFFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter
Constructor for CIFFilter on a multiple files and a single assembly.
cifForID(String) - Static method in class ffx.utilities.StringUtils
cifForID
Cl - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
CL - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
 
classpath - Variable in class edu.rit.pj.cluster.BackendInfo
The Java class path for the Parallel Java Library on the backend.
clazz() - Element in annotation interface ffx.utilities.FFXProperty
The Class used to represent the value of this FFXProperty.
clear() - Method in class ffx.potential.nonbonded.NeighborList.Cell
Clear the list of atoms in the cell.
clear() - Method in class ffx.ui.GraphicsPicking
Clear currently selected nodes
clear() - Method in class ffx.utilities.Keyword
clear
clearContext() - Method in class ffx.ui.ModelingShell
 
clearContext(EventObject) - Method in class ffx.ui.ModelingShell
 
clearForceFieldType(ForceField.ForceFieldType) - Method in class ffx.potential.parameters.ForceField
Clear all force field types of a given type.
clearInducedDipoles() - Method in class ffx.numerics.multipole.PolarizableMultipole
Clear the induced dipoles.
clearOutput() - Method in class ffx.ui.ModelingShell
clearOutput(EventObject) - Method in class ffx.ui.ModelingShell
 
clearProperty(String) - Method in class ffx.potential.parameters.ForceField
Clear a property from the force field instance.
clearSegIDs() - Method in class ffx.potential.parsers.PDBFilter
clearSegIDs
close() - Method in class edu.rit.http.HttpResponse
Close this HTTP response.
close() - Method in class edu.rit.http.HttpServer
Close this HTTP server.
close() - Method in class edu.rit.io.DoubleMatrixFile.Reader
Close the input stream.
close() - Method in class edu.rit.io.DoubleMatrixFile.Writer
Close the output stream.
close() - Method in class edu.rit.io.LineBufferedOutputStream
Close this line buffered output stream.
close() - Method in class edu.rit.mp.Channel
Close this channel.
close() - Method in class edu.rit.mp.ChannelGroup
Close this channel group.
close() - Method in class edu.rit.pj.cluster.BackendFileInputStream
Close this input stream.
close() - Method in class edu.rit.pj.cluster.BackendFileOutputStream
Close this output stream.
close() - Method in class edu.rit.pj.cluster.JobBackend
Close communication with this Job Backend.
close() - Method in interface edu.rit.pj.cluster.JobBackendRef
Close communication with this Job Backend.
close() - Method in class edu.rit.pj.cluster.JobFrontend
Close communication with this Job Frontend.
close() - Method in interface edu.rit.pj.cluster.JobFrontendRef
Close communication with this Job Frontend.
close() - Method in class edu.rit.pj.cluster.JobScheduler
Close communication with this Job Scheduler.
close() - Method in interface edu.rit.pj.cluster.JobSchedulerRef
Close communication with this Job Scheduler.
close() - Method in class edu.rit.pj.cluster.NonPjJobFrontend
Close communication with this Job Frontend.
close() - Method in class edu.rit.pj.cluster.Proxy
Close communication with this proxy's far end process.
close() - Method in class ffx.ui.LogHandler
close() - Method in class ffx.ui.MainPanel
Detach the active FSystem's BranchGroup from the Scene and clear that FSystem's data
close() - Method in class ffx.utilities.StringOutputStream
close.
close(MolecularAssembly) - Method in interface ffx.potential.utils.PotentialsFunctions
Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
close(MolecularAssembly) - Method in class ffx.potential.utils.PotentialsUtils
Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
close(MolecularAssembly) - Method in class ffx.ui.UIUtils
 
close(FFXSystem) - Method in class ffx.ui.MainPanel
close
closeAll(MolecularAssembly[]) - Method in interface ffx.potential.utils.PotentialsFunctions
Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
closeAll(MolecularAssembly[]) - Method in class ffx.potential.utils.PotentialsUtils
Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.
closeAll(MolecularAssembly[]) - Method in class ffx.ui.UIUtils
 
closeReader() - Method in class ffx.potential.parsers.CIFFilter
Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.INTFilter
Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.MergeFilter
Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.PDBFilter
Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.SystemFilter
Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.XPHFilter
Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.potential.parsers.XYZFilter
Attempts to close any open resources associated with the underlying file; primarily to be used when finished reading a trajectory.
closeReader() - Method in class ffx.ui.commands.SimulationFilter
 
CLOSING - Static variable in class ffx.ui.commands.SimulationMessage
Constant CLOSING=2
Clustering - Class in ffx.potential.utils
Cluster contains methods utilized in the Cluster.groovy file.
Clustering() - Constructor for class ffx.potential.utils.Clustering
 
Clustering.Conformation - Class in ffx.potential.utils
Class for cluster objects.
Cm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
CMMotionRemover - Class in ffx.openmm
Center of Mass Motion Remover.
CMMotionRemover(int) - Constructor for class ffx.openmm.CMMotionRemover
OpenMM CMMotionRemover constructor.
cn(int, double, double) - Static method in class ffx.numerics.multipole.GKSource
Compute the Kirkwood dielectric function for a multipole of order n.
CNSFilter - Class in ffx.xray.parsers
CNSFilter class.
CNSFilter() - Constructor for class ffx.xray.parsers.CNSFilter
Constructor for CNSFilter.
CNSMapWriter - Class in ffx.xray.parsers
The CNSMapWriter class writes an output map that covers the unit cell (not the asymmetric unit).
CNSMapWriter(int, int, int, Crystal, String) - Constructor for class ffx.xray.parsers.CNSMapWriter
Constructor for CNSMapWriter.
Co - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
codePotentialMultipoleI(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor
Collect the potential its partial derivatives at K due to multipole moments at the origin.
codePotentialMultipoleISIMD(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor
Collect the potential its partial derivatives at K due to multipole moments at the origin using SIMD instructions.
codePotentialMultipoleK(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor
Collect the potential its partial derivatives at the origin due to multipole moments at site K.
codePotentialMultipoleKSIMD(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor
Collect the potential its partial derivatives at the origin due to multipole moments at site K using SIMD instructions.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
This function is a driver to collect elements of the Cartesian multipole tensor.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI
This function is a driver to collect elements of the Cartesian multipole tensor.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
This function is a driver to collect elements of the Cartesian multipole tensor.
codeVectorTensorRecursion() - Method in class ffx.numerics.multipole.CoulombTensorGlobal
Emit code to calculate the Cartesian multipole tensor using SIMD vectorization.
codeVectorTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI
This function is a driver to collect elements of the Cartesian multipole tensor.
COH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
 
collectAtoms(Atom, ArrayList<Atom>) - Static method in class ffx.potential.parsers.CIFFilter
Finds all atoms that are bonded to one another.
collectResidues(MolecularAssembly) - Method in class ffx.algorithms.cli.ManyBodyOptions
Collect residues based on residue selection flags.
colLength(boolean[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given Boolean matrix.
colLength(byte[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given byte matrix.
colLength(char[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given character matrix.
colLength(double[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given double matrix.
colLength(float[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given float matrix.
colLength(int[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given integer matrix.
colLength(long[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given long matrix.
colLength(short[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given short matrix.
colLength(T[][], int) - Static method in class edu.rit.util.Arrays
Determine the number of columns in the given row of the given object matrix.
color - Variable in class ffx.utilities.FFXCommand
Unix shells are able to evaluate PicoCLI ANSI color codes, but right now the FFX GUI Shell does not.
color - Variable in class ffx.utilities.FFXScript
Unix shells are able to evaluate PicoCLI ANSI color codes, but right now the FFX GUI Shell does not.
colorModelHash - Static variable in class ffx.potential.bonded.RendererCache
Constant colorModelHash
colorWait(String) - Method in class ffx.ui.GraphicsCanvas
colorWait
cols() - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Returns the number of columns in this matrix reduction variable.
cols() - Method in class edu.rit.pj.reduction.SharedLongMatrix
Returns the number of columns in this matrix reduction variable.
colSliceBuffer(boolean[][], Range) - Static method in class edu.rit.mp.BooleanBuf
Create a buffer for one column slice of the given Boolean matrix.
colSliceBuffer(byte[][], Range) - Static method in class edu.rit.mp.ByteBuf
Create a buffer for one column slice of the given byte matrix.
colSliceBuffer(char[][], Range) - Static method in class edu.rit.mp.CharacterBuf
Create a buffer for one column slice of the given character matrix.
colSliceBuffer(double[][], Range) - Static method in class edu.rit.mp.DoubleBuf
Create a buffer for one column slice of the given double matrix.
colSliceBuffer(float[][], Range) - Static method in class edu.rit.mp.FloatBuf
Create a buffer for one column slice of the given float matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.IntegerBuf
Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(long[][], Range) - Static method in class edu.rit.mp.LongBuf
Create a buffer for one column slice of the given long matrix.
colSliceBuffer(short[][], Range) - Static method in class edu.rit.mp.ShortBuf
Create a buffer for one column slice of the given short matrix.
colSliceBuffer(T[][], Range) - Static method in class edu.rit.mp.ObjectBuf
Create a buffer for one column slice of the given object matrix.
colSliceBuffers(boolean[][], Range[]) - Static method in class edu.rit.mp.BooleanBuf
Create an array of buffers for multiple column slices of the given Boolean matrix.
colSliceBuffers(byte[][], Range[]) - Static method in class edu.rit.mp.ByteBuf
Create an array of buffers for multiple column slices of the given byte matrix.
colSliceBuffers(char[][], Range[]) - Static method in class edu.rit.mp.CharacterBuf
Create an array of buffers for multiple column slices of the given character matrix.
colSliceBuffers(double[][], Range[]) - Static method in class edu.rit.mp.DoubleBuf
Create an array of buffers for multiple column slices of the given double matrix.
colSliceBuffers(float[][], Range[]) - Static method in class edu.rit.mp.FloatBuf
Create an array of buffers for multiple column slices of the given float matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.IntegerBuf
Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(long[][], Range[]) - Static method in class edu.rit.mp.LongBuf
Create an array of buffers for multiple column slices of the given long matrix.
colSliceBuffers(short[][], Range[]) - Static method in class edu.rit.mp.ShortBuf
Create an array of buffers for multiple column slices of the given short matrix.
colSliceBuffers(T[][], Range[]) - Static method in class edu.rit.mp.ObjectBuf
Create an array of buffers for multiple column slices of the given object matrix.
COM_DISTANCE - Enum constant in enum class ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
 
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
Compute the Discrete Fourier Transform.
computeElasticityTensor(boolean) - Method in class ffx.algorithms.optimize.CrystalMinimize
computeStressTensor.
computeEnergy(Residue[], int[], boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization
Uses existing backbone, self, 2-Body, and 3-body energies from rotamerEnergies() to calculate an approximate energy for a rotamer permutation.
computeFractionalCoordinates() - Method in class ffx.potential.MolecularAssembly
Compute fractional coordinates.
computeInducedGKField() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
computeInducedGKField
computeInduceDipoleField() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
 
computeInducedPhi(double[][], double[][], double[][], double[][]) - Method in class ffx.potential.nonbonded.ReciprocalSpace
computeInducedPhi
computeKineticEnergy() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat
Compute the current temperature and kinetic energy of the system.
computeMoments(Atom[], boolean) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Compute multipole moments for an array of atoms.
computePermanentGKField() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood
computePermanentGKField
computePermanentPhi(double[][], double[][]) - Method in class ffx.potential.nonbonded.ReciprocalSpace
Compute the potential Phi and its derivatives for all atoms.
computeSelfEnergy(Residue[], int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
Computes a self energy, defined as energy with all side-chains but one turned off, minus the backbone energy.
computeSolventDensity(double[][]) - Method in class ffx.xray.CrystalReciprocalSpace
parallelized computation of bulk solvent structure factors
computeVolumeAndSA(double[][]) - Method in class ffx.potential.nonbonded.implicit.GaussVol
Compute molecular volume and surface area.
COMRestraint - Class in ffx.potential.nonbonded
Restrain molecules to their center of mass.
COMRestraint(MolecularAssembly) - Constructor for class ffx.potential.nonbonded.COMRestraint
This COMRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
CONDENSED - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
 
CONDENSED_NO_LIGAND - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
 
conditions - Variable in class ffx.ui.behaviors.PickMouseBehavior
 
coneFactory(Appearance, int) - Static method in class ffx.potential.bonded.RendererCache
coneFactory
confidenceInterval() - Method in class ffx.numerics.math.BootStrapStatistics
Computes a 95% confidence interval based on a Student's T-distribution.
confidenceInterval() - Method in class ffx.numerics.math.SummaryStatistics
Computes a 95% confidence interval based on a Student's T-distribution.
confidenceInterval(double) - Method in class ffx.numerics.math.BootStrapStatistics
Computes a confidence interval based on a Student's T-distribution.
confidenceInterval(double) - Method in class ffx.numerics.math.SummaryStatistics
Computes a confidence interval based on a Student's T-distribution.
Configuration - Class in edu.rit.pj.cluster
Class Configuration provides configuration information about a parallel computer running Parallel Java.
Configuration(String) - Constructor for class edu.rit.pj.cluster.Configuration
Construct a new configuration.
ConformationScan - Class in ffx.algorithms.optimize
This class is for a configuration optimization of two small systems.
ConformationScan(MolecularAssembly, Molecule[], Molecule[], double, int, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.ConformationScan
 
conjugate() - Method in class ffx.numerics.math.ComplexNumber
Return a new Complex object whose value is the conjugate of this.
conjugateIP() - Method in class ffx.numerics.math.ComplexNumber
conjugateIP
connect() - Method in class ffx.ui.commands.FFXClient
Attempts to connect to a Tinker FServer.
connect(InetSocketAddress) - Method in class edu.rit.mp.ChannelGroup
Create a new channel connected to the given far end host and port.
connectivity - Variable in class ffx.ui.commands.SimulationDefinition
 
ConnectListener - Interface in edu.rit.mp
Interface ConnectListener specifies the interface for an object that is notified whenever a Channel is connected in a ChannelGroup.
ConnollyRegion - Class in ffx.potential.nonbonded.implicit
ConnollyRegion uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the analytical molecular surface area and volume of a collection of spherical atoms; thus it implements Fred Richards' molecular surface definition as a set of analytically defined spherical and toroidal polygons.
ConnollyRegion(Atom[], double[], int) - Constructor for class ffx.potential.nonbonded.implicit.ConnollyRegion
ConnollyRegion constructor.
consecutiveInts(int[]) - Static method in class ffx.utilities.StringUtils
Finds consecutive subranges in an array of ints, and returns their mins and maxes.
CONSENSUS - Enum constant in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE
 
constantOutsideBounds() - Method in class ffx.numerics.switching.BellCurveSwitch
Remains 0 below the lower bound, and 1 above the upper bound (i.e.
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.numerics.multipole.MultipoleTensorSIMD
The coordinate system in use (global or QI).
coordinates - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Dimensions of [nsymm][xyz][nAtoms].
coordinates - Variable in class ffx.potential.nonbonded.RowRegion
 
coordinates - Variable in class ffx.potential.nonbonded.SliceRegion
 
coordinates - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
coordinates - Variable in class ffx.ui.commands.SimulationDefinition
 
coordinates - Variable in class ffx.ui.commands.SimulationUpdate
 
COORDINATES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode
refine coordinates only
COORDINATES_AND_BFACTORS - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode
refine coordinates and B factors (if anisotropic, refined as such)
COORDINATES_AND_BFACTORS_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode
refine all
COORDINATES_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode
refine coordinates and occupancies
CoordinateSystem - Enum Class in ffx.numerics.multipole
Global and Quasi-Internal (QI) coordinate systems are supported.
copy() - Method in class ffx.numerics.math.Double3
Returns a new copy of this Double3.
copy() - Method in class ffx.numerics.math.Float3
Returns a new copy of this Float3.
copy(boolean[][], Range, Range, boolean[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one Boolean matrix to a range of elements in another Boolean matrix.
copy(boolean[], Range, boolean[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one Boolean array to a range of elements in another Boolean array.
copy(byte[]) - Method in class edu.rit.util.ByteSequence
Copy this byte sequence's contents into the given byte array.
copy(byte[][], Range, Range, byte[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one byte matrix to a range of elements in another byte matrix.
copy(byte[], int, int) - Method in class edu.rit.util.ByteSequence
Copy this byte sequence's contents into a portion of the given byte array.
copy(byte[], Range, byte[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one byte array to a range of elements in another byte array.
copy(char[][], Range, Range, char[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one character matrix to a range of elements in another character matrix.
copy(char[], Range, char[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one character array to a range of elements in another character array.
copy(double[][], Range, Range, double[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one double matrix to a range of elements in another double matrix.
copy(double[], Range, double[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one double array to a range of elements in another double array.
copy(float[][], Range, Range, float[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one float matrix to a range of elements in another float matrix.
copy(float[], Range, float[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one float array to a range of elements in another float array.
copy(int[][], Range, Range, int[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one integer matrix to a range of elements in another integer matrix.
copy(int[], Range, int[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one integer array to a range of elements in another integer array.
copy(long[][], Range, Range, long[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one long matrix to a range of elements in another long matrix.
copy(long[], Range, long[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one long array to a range of elements in another long array.
copy(short[][], Range, Range, short[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one short matrix to a range of elements in another short matrix.
copy(short[], Range, short[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one short array to a range of elements in another short array.
copy(Buf) - Method in class edu.rit.mp.BooleanBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.BooleanArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.BooleanMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ByteArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ByteMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.CharacterArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.CharacterMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Buf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.DoubleArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.DoubleMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyBooleanBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyByteBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyCharacterBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyDoubleBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyFloatBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyLongBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyObjectBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyShortBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptySigned16BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptySigned8BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.FloatArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.FloatMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.IntegerArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.IntegerMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.LongArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.LongMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ObjectArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ObjectMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ShortArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.ShortMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed16BitIntegerArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed16BitIntegerMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed8BitIntegerArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Signed8BitIntegerMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.ByteBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.CharacterBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.DoubleBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.FloatBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.IntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.LongBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.ObjectBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.ShortBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Signed16BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Signed8BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(Buf) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf
Copy items from the given buffer to this buffer.
copy(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber
copy
copy(ST[][], Range, Range, DT[][], Range, Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one object matrix to a range of elements in another object matrix.
copy(ST[], Range, DT[], Range) - Static method in class edu.rit.util.Arrays
Copy a range of elements from one object array to a range of elements in another object array.
copyAccelerationsToPrevious() - Method in class ffx.potential.SystemState
Copy the current accelerations to the previous accelerations.
copyAccelerationToPrevious() - Method in class ffx.algorithms.dynamics.integrators.Integrator
Copy acceleration to previous acceleration.
copyEstimator() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Return a copy of this Estimator.
copyEstimator() - Method in interface ffx.numerics.estimator.BootstrappableEstimator
Return a copy of this Estimator.
copyEstimator() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
 
copyEstimator() - Method in class ffx.numerics.estimator.Zwanzig
Return a copy of this Estimator.
copyESVHistogramTo(int[][]) - Method in class ffx.potential.extended.ExtendedSystem
Changes this ESV's histogram to equal the one passed
copyInputStreamToTmpFile(InputStream, String, String, String) - Static method in class ffx.utilities.FileUtils
Returns the file name of a temporary copy of input content.
copyResidue(Residue, Residue) - Static method in class ffx.potential.bonded.AminoAcidUtils
copyResidue.
copyState(AssemblyState) - Static method in class ffx.potential.AssemblyState
Copies an AssemblyState.
cos - Variable in class ffx.potential.parameters.ImproperTorsionType
Value of cos(toRadians(phase)).
cos() - Method in class ffx.numerics.math.ComplexNumber
Return a new Complex object whose value is the complex cosine of this.
cosDiameter - Variable in class ffx.potential.parameters.SoluteType
Solute atomic diameter for ddCOSMO.
cosine - Variable in class ffx.potential.parameters.TorsionType
Cosine of the phase angle.
CosineWave - Class in ffx.numerics.integrate
A CosineWave describes points along a sine wave of f(x) = a*sin(jx).
CosineWave(double[], boolean, double, double) - Constructor for class ffx.numerics.integrate.CosineWave
Constructs f(x) = a*cos(nx).
CosineWave(double[], double, double) - Constructor for class ffx.numerics.integrate.CosineWave
Constructs f(x) = a*cos(nx).
COULOMB - Enum constant in enum class ffx.numerics.multipole.Operator
Coulomb operator.
coulombSource - Variable in class ffx.numerics.multipole.MultipoleTensor
These are the "source" terms for the recursion for the Coulomb operator (1/R).
coulombSource - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
These are the "source" terms for the recursion for the Coulomb operator (1/R).
CoulombTensorGlobal - Class in ffx.numerics.multipole
The CoulombTensorGlobal class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame.
CoulombTensorGlobal(int) - Constructor for class ffx.numerics.multipole.CoulombTensorGlobal
Constructor for CoulombTensorGlobal.
CoulombTensorGlobalSIMD - Class in ffx.numerics.multipole
The CoulombTensorGlobal class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame using SIMD instructions.
CoulombTensorGlobalSIMD(int) - Constructor for class ffx.numerics.multipole.CoulombTensorGlobalSIMD
Constructor for CoulombTensorGlobalSIMD.
CoulombTensorQI - Class in ffx.numerics.multipole
The CoulombTensorQI class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
CoulombTensorQI(int) - Constructor for class ffx.numerics.multipole.CoulombTensorQI
Create a new CoulombTensorQI object.
CoulombTensorQISIMD - Class in ffx.numerics.multipole
The CoulombTensorQISIMD class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame using SIMD instructions.
CoulombTensorQISIMD(int) - Constructor for class ffx.numerics.multipole.CoulombTensorQISIMD
Create a new CoulombTensorQI object.
count - Variable in class edu.rit.pj.cluster.JobInfo
The number of processes that have been assigned to the job so far.
count - Variable in class ffx.numerics.math.BootStrapStatistics
The number of entries.
count - Variable in class ffx.numerics.math.SummaryStatistics
Count of observations.
countNumModels() - Method in class ffx.potential.parsers.PDBFilter
 
countNumModels() - Method in class ffx.potential.parsers.SystemFilter
 
countNumModels() - Method in class ffx.potential.parsers.XPHFilter
 
countNumModels() - Method in class ffx.potential.parsers.XYZFilter
 
counts - Variable in class ffx.algorithms.thermodynamics.HistogramData
The number of hills added to the recursion kernel.
CPK - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
 
cpus - Variable in class edu.rit.pj.cluster.JobInfo
Number of CPUs assigned to each process in the job in rank order.
Cr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
createAnnealer(DynamicsOptions, MolecularAssembly, Potential, AlgorithmListener) - Method in class ffx.algorithms.cli.AnnealOptions
Creates a SimulatedAnnealing object.
createAnnealer(DynamicsOptions, MolecularAssembly, Potential, AlgorithmListener, File) - Method in class ffx.algorithms.cli.AnnealOptions
Creates a SimulatedAnnealing object.
createBarostat(MolecularAssembly, CrystalPotential) - Method in class ffx.algorithms.cli.BarostatOptions
Creates a Barostat around a CrystalPotential.
createBox() - Method in class ffx.potential.MolecularAssembly
createBox
createComm(boolean) - Method in class edu.rit.pj.Comm
Create a new communicator.
createComm(boolean, int) - Method in class edu.rit.pj.Comm
Create a new communicator.
createCustomMTSIntegrator(double, OpenMMSystem) - Static method in class ffx.potential.openmm.OpenMMIntegrator
Create a Custom MTS Integrator.
createCustomMTSLangevinIntegrator(double, double, OpenMMSystem) - Static method in class ffx.potential.openmm.OpenMMIntegrator
Create a Custom MTS Langevin integrator.
createExceptionsFromBonds(BondArray, double, double) - Method in class ffx.openmm.NonbondedForce
Create exceptions from bonds.
createGzipReader(File) - Static method in class ffx.utilities.StringUtils
Creates a reader from a Gzip file to text.
createGzipReader(File, Charset) - Static method in class ffx.utilities.StringUtils
Creates a reader from a Gzip file to text.
createGzipWriter(File) - Static method in class ffx.utilities.StringUtils
Creates a writer for text to a Gzip file.
createGzipWriter(File, Charset) - Static method in class ffx.utilities.StringUtils
Creates a writer for text to a Gzip file.
createIntegrator(String, double, double, OpenMMSystem) - Static method in class ffx.potential.openmm.OpenMMIntegrator
Create a integrator.
createJob(int) - Method in class edu.rit.pj.job.JobGenerator
Create the job with the given job number.
createJoint(Bond, MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MSGroup
Create a joint between two chemical groups.
createJoint(Bond, MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MultiResidue
Create a joint between two chemical groups.
createJoint(MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MSGroup
Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
createJoint(MSGroup, MSGroup, ForceField) - Method in class ffx.potential.bonded.MultiResidue
Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
createJoint(Residue, Residue, ForceField) - Method in class ffx.potential.bonded.Polymer
createLangevinIntegrator(double, double, ForceField) - Static method in class ffx.potential.openmm.OpenMMIntegrator
Create a Langevin integrator.
createMTSLangevinSubStep(int, int[], int[], StringBuilder) - Method in class ffx.potential.openmm.CustomMTSLangevinIntegrator
Create substeps for the MTS Langevin CustomIntegrator.
createMTSSubStep(int, int[], int[]) - Method in class ffx.potential.openmm.CustomMTSIntegrator
Create substeps for the MTS CustomIntegrator.
createTimer(TimerTask) - Method in class edu.rit.util.TimerThread
Create a new timer associated with the given timer task and under the control of this timer thread.
createVerletIntegrator(double) - Static method in class ffx.potential.openmm.OpenMMIntegrator
Create a Verlet integrator.
critical(Lock, ParallelSection) - Method in class edu.rit.pj.ParallelRegion
Perform a section of code in a critical region with exclusive locking using the given lock.
critical(ParallelSection) - Method in class edu.rit.pj.ParallelRegion
Perform a section of code in a critical region with exclusive locking.
criticalNonexclusive(Lock, ParallelSection) - Method in class edu.rit.pj.ParallelRegion
Perform a section of code in a critical region with nonexclusive locking using the given lock.
criticalNonexclusive(ParallelSection) - Method in class edu.rit.pj.ParallelRegion
Perform a section of code in a critical region with nonexclusive locking.
crystal - Variable in class ffx.crystal.ReflectionList
The Crystal instance.
crystal - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
 
Crystal - Class in ffx.crystal
The Crystal class encapsulates the lattice parameters and space group that describe the geometry and symmetry of a crystal.
Crystal(double, double, double, double, double, double, int) - Constructor for class ffx.crystal.Crystal
The Crystal class encapsulates the lattice parameters and space group.
Crystal(double, double, double, double, double, double, String) - Constructor for class ffx.crystal.Crystal
The Crystal class encapsulates the lattice parameters and space group.
CrystalMinimize - Class in ffx.algorithms.optimize
Minimize the energy of a system to an RMS gradient per atom convergence criteria.
CrystalMinimize(MolecularAssembly, XtalEnergy, AlgorithmListener) - Constructor for class ffx.algorithms.optimize.CrystalMinimize
Constructor for CrystalMinimize.
CrystalPotential - Interface in ffx.crystal
The CrystalPotential interface extends Potential to provide methods that change the periodic boundary conditions and symmetry via a Crystal instance.
CrystalReciprocalSpace - Class in ffx.xray
Structure factor calculation (including bulk solvent structure factors)
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam) - Constructor for class ffx.xray.CrystalReciprocalSpace
Crystal Reciprocal Space constructor, assumes this is not a bulk solvent mask and is not a neutron data set
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam, boolean) - Constructor for class ffx.xray.CrystalReciprocalSpace
Crystal Reciprocal Space constructor, assumes this is not a neutron data set and implements a polynomial bulk solvent mask if needed
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam, boolean, boolean) - Constructor for class ffx.xray.CrystalReciprocalSpace
Crystal Reciprocal Space constructor, assumes a polynomial bulk solvent mask if needed
CrystalReciprocalSpace(ReflectionList, Atom[], ParallelTeam, ParallelTeam, boolean, boolean, CrystalReciprocalSpace.SolventModel, CrystalReciprocalSpace.GridMethod) - Constructor for class ffx.xray.CrystalReciprocalSpace
Crystal Reciprocal Space constructor, all parameters provided
CrystalReciprocalSpace.GridMethod - Enum Class in ffx.xray
 
CrystalReciprocalSpace.SolventModel - Enum Class in ffx.xray
The possible solvent model methods
CrystalStats - Class in ffx.xray
Crystal statistics output/logger
crystalSystem - Variable in class ffx.crystal.SpaceGroup
Crystal system.
CrystalSystem - Enum Class in ffx.crystal
Enumeration of the 7 crystal systems.
Cs - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
csdPercent - Static variable in class ffx.crystal.SpaceGroupInfo
Space group frequency ranking for the 1,231,510 CSD structures for which the space group is fully defined.
CTRL_ALL - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
 
Cu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
cubic - Variable in class ffx.potential.parameters.AngleType
Cubic coefficient in angle bending potential.
cubic - Variable in class ffx.potential.parameters.BondType
Cubic coefficient in bond stretch potential.
cubic - Variable in class ffx.potential.parameters.OutOfPlaneBendType
Cubic coefficient in out-of-plane angle bending potential.
cubic - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
 
cubic - Variable in class ffx.potential.parameters.UreyBradleyType
Cubic coefficient in bond stretch potential.
CUBIC - Enum constant in enum class ffx.crystal.CrystalSystem
Cubic crystal system.
CUBIC_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem
Cubic lattice system.
CUBIC_MEAN - Enum constant in enum class ffx.potential.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="June 2024"
Db - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
DCY - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
 
ddgunToNPChange(List<String>) - Method in class ffx.potential.utils.GetProteinFeatures
Use the ddgun output file to get the amino acid changes
ddp - Variable in class ffx.potential.parameters.PolarizeType
Direct polarization damping.
deallocate(boolean[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given Boolean matrix.
deallocate(boolean[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given Boolean matrix.
deallocate(byte[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given byte matrix.
deallocate(byte[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given byte matrix.
deallocate(char[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given character matrix.
deallocate(char[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given character matrix.
deallocate(double[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given double matrix.
deallocate(double[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given double matrix.
deallocate(float[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given float matrix.
deallocate(float[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given float matrix.
deallocate(int[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given integer matrix.
deallocate(int[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given integer matrix.
deallocate(long[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given long matrix.
deallocate(long[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given long matrix.
deallocate(short[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given short matrix.
deallocate(short[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given short matrix.
deallocate(T[]) - Static method in class edu.rit.util.Arrays
Deallocate all elements in the given object array.
deallocate(T[][]) - Static method in class edu.rit.util.Arrays
Deallocate the elements in the given object matrix.
deallocate(T[][], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row index range in the given object matrix.
deallocate(T[][], Range, Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given row and column index ranges in the given object matrix.
deallocate(T[], Range) - Static method in class edu.rit.util.Arrays
Deallocate the elements within the given index range in the given object array.
decode(int, String) - Static method in class ffx.utilities.Hybrid36
Hybrid-36 decoder: converts string s to integer result.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedByte
Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedCharacter
Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedDouble
Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedFloat
Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedInteger
Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedLong
Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedShort
Subtract one from this reduction variable and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedByteArray
Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray
Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray
Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedFloatArray
Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray
Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedLongArray
Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedShortArray
Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix
Subtract one from this matrix reduction variable at the given row and column and return the new value.
decrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix
Subtract one from this matrix reduction variable at the given row and column and return the new value.
dEdLSign - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
 
dEdLZeroAtEnds() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in interface ffx.potential.bonded.LambdaInterface
Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.DualTopologyEnergy
Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.ForceFieldEnergy
Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.QuadTopologyEnergy
Returns true if dUdL is guaranteed to be zero at 0 and 1.
Default - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
 
DEFAULT_ANGLE_CUBIC - Static variable in class ffx.potential.parameters.AngleType
Default cubic coefficient in angle bending potential.
DEFAULT_ANGLE_PENTIC - Static variable in class ffx.potential.parameters.AngleType
Default pentic coefficient in angle bending potential.
DEFAULT_ANGLE_QUARTIC - Static variable in class ffx.potential.parameters.AngleType
Default quartic coefficient in angle bending potential.
DEFAULT_ANGLE_SEXTIC - Static variable in class ffx.potential.parameters.AngleType
Default quintic coefficient in angle bending potential.
DEFAULT_ANGLE_UNIT - Static variable in class ffx.potential.parameters.AngleType
Default convert angle bending energy to kcal/mole.
DEFAULT_ANGLEMAX - Static variable in class ffx.numerics.optimization.LBFGS
The default maximum angle between search direction and gradient.
DEFAULT_ANGTOR_UNIT - Static variable in class ffx.potential.parameters.AngleTorsionType
 
DEFAULT_BAROSTAT_INTERVAL - Static variable in class ffx.algorithms.cli.BarostatOptions
Default mean number of MD steps (Poisson distribution) between barostat move proposals.
DEFAULT_BAROSTAT_PRINT_INTERVAL - Static variable in class ffx.algorithms.cli.BarostatOptions
Default number of Barostat moves between print statements.
DEFAULT_BOND_CUBIC - Static variable in class ffx.potential.parameters.BondType
Default cubic coefficient in bond stretch potential.
DEFAULT_BOND_QUARTIC - Static variable in class ffx.potential.parameters.BondType
Default quartic coefficient in bond stretch potential.
DEFAULT_BOND_UNIT - Static variable in class ffx.potential.parameters.BondType
 
DEFAULT_CAPPA - Static variable in class ffx.numerics.optimization.LBFGS
Controls the accuracy of the line search.
DEFAULT_CAVDISP_SURFACE_TENSION - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood
Default surface tension for apolar models with an explicit dispersion term.
DEFAULT_CCMA_NONZERO_CUTOFF - Static variable in class ffx.potential.constraint.CcmaConstraint
 
DEFAULT_CG_PRECONDITIONER_CUTOFF - Static variable in class ffx.potential.nonbonded.pme.PCGSolver
A preconditioner cut-off of 3 to 4 Angstroms generally works well.
DEFAULT_CG_PRECONDITIONER_EWALD - Static variable in class ffx.potential.nonbonded.pme.PCGSolver
An Ewald coefficient of 0 indicates use of Coulomb's law with no damping.
DEFAULT_CG_PRECONDITIONER_SCALE - Static variable in class ffx.potential.nonbonded.pme.PCGSolver
The scale factor is applied to the diagonal terms of the preconditioner.
DEFAULT_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.RestrainDistance
 
DEFAULT_RB_LAM_START - Static variable in class ffx.potential.bonded.RestrainDistance
 
DEFAULT_SLOPEMAX - Static variable in class ffx.numerics.optimization.LBFGS
The default projected gradient above which step size is reduced.
DEFAULT_SNECK - Variable in class ffx.potential.parameters.SoluteType
 
DEFAULT_SOLUTE_OFFSET - Static variable in class ffx.potential.nonbonded.implicit.DispersionRegion
Each solute atom blocks dispersion interactions with solvent: Rmin + SOLUTE_OFFSET
DEFAULT_SOLVENT_PRESSURE - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood
Default solvent pressure for apolar models with an explicit volume term.
DEFAULT_STEPMAX - Static variable in class ffx.numerics.optimization.LBFGS
This specifies the default upper bound for the step in the line search.
DEFAULT_STEPMIN - Static variable in class ffx.numerics.optimization.LBFGS
This specifies the default lower bound for the step in the line search.
DEFAULT_STRBND_UNIT - Static variable in class ffx.potential.parameters.StretchBendType
Constant units=PI / 180.0
DEFAULT_STRTOR_UNIT - Static variable in class ffx.potential.parameters.StretchTorsionType
 
DEFAULT_TANH_BETA0 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood
Default value of beta0 for tanh scaling
DEFAULT_TANH_BETA1 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood
Default value of beta1 for tanh scaling
DEFAULT_TANH_BETA2 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood
Default value of beta2 for tanh scaling
DEFAULT_TORSION_UNIT - Static variable in class ffx.potential.parameters.TorsionType
 
DEFAULT_TORTOR_UNIT - Static variable in class ffx.potential.parameters.TorsionTorsionType
Default units to convert Torsion-Torsion energy to kcal/mole.
DEFAULT_UREY_CUBIC - Static variable in class ffx.potential.parameters.UreyBradleyType
Default cubic coefficient in Urey-Bradley stretch potential.
DEFAULT_UREY_QUARTIC - Static variable in class ffx.potential.parameters.UreyBradleyType
Default quartic coefficient in Urey-Bradley stretch potential.
DEFAULT_UREY_UNIT - Static variable in class ffx.potential.parameters.UreyBradleyType
Default conversion Urey-Bradley stretch energy to kcal/mole.
DEFAULT_VDW_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.GKMultipoleOrder
Dipole potential.
dipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal
Permanent multipole energy and gradient using the GK dipole tensor.
dipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI
Permanent multipole energy and gradient using the GK dipole tensor.
dipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD
Permanent multipole energy and gradient using the GK dipole tensor.
dipoleEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector[], DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD
Permanent multipole energy and gradient using the GK dipole tensor.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorQI
Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.MultipoleTensor
Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD
Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD
Compute the induced dipole field components due to site I at site K.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal
Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorQI
Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.MultipoleTensor
Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobalSIMD
Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.CoulombTensorQISIMD
Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(DoubleVector, DoubleVector, DoubleVector, int) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD
Compute the induced dipole field components due to site K at site I.
dipolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal
Dipole Polarization Energy and Gradient.
dipolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI
Dipole Polarization Energy and Gradient.
dipolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorGlobalSIMD
Dipole Polarization Energy and Gradient.
dipolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD, PolarizableMultipoleSIMD, DoubleVector, DoubleVector[], DoubleVector[], DoubleVector[]) - Method in class ffx.numerics.multipole.GKTensorQISIMD
Dipole Polarization Energy and Gradient.
dipoleTorque(PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor
Compute the torque on a permanent dipole.
dipoleTorque(PolarizableMultipoleSIMD, DoubleVector[]) - Method in class ffx.numerics.multipole.MultipoleTensorSIMD
Compute the torque on a permanent dipole.
DIRECT - Enum constant in enum class ffx.potential.nonbonded.pme.Polarization
 
directDipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Direct induced dipoles.
directDipole - Variable in class ffx.potential.nonbonded.pme.DirectRegion
Direct induced dipoles.
directDipole - Variable in class ffx.potential.nonbonded.pme.SORRegion
Direct induced dipoles.
directDipoleCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
directDipoleCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
 
directDipoleCR - Variable in class ffx.potential.nonbonded.pme.SORRegion
 
directField - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
directField - Variable in class ffx.potential.nonbonded.pme.DirectRegion
 
directFieldCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
 
directFieldCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
 
directionality - Variable in class ffx.numerics.estimator.Zwanzig
Directionality of the Zwanzig estimation (forwards perturbation or backwards perturbation).
DirectoryUtils - Class in ffx.utilities
DirectoryUtils class.
DirectRegion - Class in ffx.potential.nonbonded.pme
Parallel computation of induced dipoles due to the direct field.
DirectRegion(int) - Constructor for class ffx.potential.nonbonded.pme.DirectRegion
 
directSum() - Method in class ffx.potential.nonbonded.octree.Octree
Direct summation.
disableResetStatistics() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
 
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
The number of degrees of freedom.
dof - Variable in class ffx.numerics.math.SummaryStatistics
Degrees of freedom.
dOffset - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion
Dielectric offset from:
doLigandGKElec - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
Intramolecular electrostatics for the ligand in done in GK implicit solvent.
doLigandVaporElec - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
Intramolecular electrostatics for the ligand in vapor is included by default.
done - Variable in class ffx.algorithms.dynamics.MolecularDynamics
Flag to indicate a run has finished.
done - Variable in class ffx.algorithms.optimize.Minimize
A flag to indicate the algorithm is done.
done - Variable in class ffx.algorithms.optimize.PhMinimize
A flag to indicate the algorithm is done.
doNoLigandCondensedSCF - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
Condensed phase SCF without the ligand present is included by default.
doPermanentRealSpace - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
 
doPolarization - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
 
dot(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath
Finds the dot product between two vectors.
dot(float[], float[]) - Static method in class ffx.numerics.math.FloatMath
Finds the dot product between two vectors.
dot(Double3) - Method in class ffx.numerics.math.Double3
Finds the dot product between two vectors.
dot(Float3) - Method in class ffx.numerics.math.Float3
Finds the dot product between two vectors.
dotVec(DoubleVector[], DoubleVector[]) - Static method in class ffx.numerics.multipole.QIFrameSIMD
Compute the dot product of two vectors.
Double() - Constructor for class edu.rit.util.Searching.Double
 
Double() - Constructor for class edu.rit.util.Sorting.Double
 
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.
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.numerics.multipole.PolarizableMultipoleSIMD
Dipole x-component.
dx - Variable in class ffx.potential.parameters.TorsionTorsionType
First derivative along x.
dxy - Variable in class ffx.potential.parameters.TorsionTorsionType
Second derivatives.
dy - Variable in class ffx.numerics.multipole.PolarizableMultipole
Dipole y-component.
dy - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD
Dipole y-component.
dy - Variable in class ffx.potential.parameters.TorsionTorsionType
First derivative along y.
Dy - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
dynamic() - Static method in class edu.rit.pj.IntegerSchedule
Returns a dynamic schedule object with a chunk size of 1.
dynamic() - Static method in class edu.rit.pj.LongSchedule
Returns a dynamic schedule object with a chunk size of 1.
dynamic(int) - Static method in class edu.rit.pj.IntegerSchedule
Returns a dynamic schedule object with the given chunk size.
dynamic(long) - Static method in class edu.rit.pj.LongSchedule
Returns a dynamic schedule object with the given chunk size.
dynamic(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Blocking molecular dynamics.
dynamic(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM
Blocking molecular dynamics.
dynamic(long, double, double, double, double, boolean, String, double, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics
Blocking molecular dynamics.
dynamicsFactory(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum) - Static method in class ffx.algorithms.dynamics.MolecularDynamics
Method that determines whether a dynamics is done by the java implementation native to ffx or the OpenMM implementation
dynamicsFactory(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum, MDEngine) - Static method in class ffx.algorithms.dynamics.MolecularDynamics
dynamicsFactory.
DynamicsOptions - Class in ffx.algorithms.cli
Represents command line options for scripts that run molecular dynamics.
DynamicsOptions() - Constructor for class ffx.algorithms.cli.DynamicsOptions
 
DYNFileFilter - Class in ffx.potential.parsers
The DYNFileFilter class is used to choose a TINKER Restart (*.DYN) file.
DYNFileFilter() - Constructor for class ffx.potential.parsers.DYNFileFilter
Default Constructor.
DYNFilter - Class in ffx.potential.parsers
The DYNFilter class parses TINKER Restart (*.DYN) files.
DYNFilter(String) - Constructor for class ffx.potential.parsers.DYNFilter
Constructor for DYNFilter.
dz - Variable in class ffx.numerics.multipole.PolarizableMultipole
Dipole z-component.
dz - Variable in class ffx.numerics.multipole.PolarizableMultipoleSIMD
Dipole z-component.

E

e - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
E - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
 
E000 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E001 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E002 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E003 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E010 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E011 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E012 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E020 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E021 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E030 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E100 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E101 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E102 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E110 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E111 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E120 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E200 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E201 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E210 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
E300 - Variable in class ffx.numerics.multipole.MultipoleTensorSIMD
 
eAll - Variable in class ffx.numerics.estimator.SequentialEstimator
 
eAllFlat - Variable in class ffx.numerics.estimator.SequentialEstimator
 
eAt - Variable in class ffx.numerics.estimator.SequentialEstimator
 
EDITCOMBOBOX - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
 
edu.rit.http - package edu.rit.http
The HTTP package provides a lightweight HTTP/1.0 server.
edu.rit.io - package edu.rit.io
The IO package provides the DataOutputStream and DataInputStream classes to read/write primitive data types and strings in binary form.
edu.rit.mp - package edu.rit.mp
The MP package provides low-level support for Message Passing.
edu.rit.mp.buf - package edu.rit.mp.buf
The BUF package provides data buffers for Message Passing.
edu.rit.pj - package edu.rit.pj
The PJ package (Parallel Java) support shared memory, message passing and hybrid shared memory/message passing parallelization in pure Java.
edu.rit.pj.cluster - package edu.rit.pj.cluster
The Cluster package contains the Parallel Java cluster middleware and the main program for the PJ Job Scheduler Daemon process for a parallel computer.
edu.rit.pj.io - package edu.rit.pj.io
The IO package represents a file that resides in the user's account in the job frontend process of a PJ cluster parallel program.
edu.rit.pj.job - package edu.rit.pj.job
The Job package encapsulates a job and its attributes.
edu.rit.pj.reduction - package edu.rit.pj.reduction
The Reduction package provides a variety of reduction variables.
edu.rit.pj.replica - package edu.rit.pj.replica
The Replica package provides replicated, shared reduction variables.
edu.rit.util - package edu.rit.util
The Util package contains utilities that support the PJ API.
eHigh - Variable in class ffx.numerics.estimator.SequentialEstimator
 
ELEC_ANG_TO_DEBYE - Static variable in class ffx.utilities.Constants
Conversion from electron-Angstroms to Debye.
ELEC_ANG2_TO_BUCKINGHAMS - Static variable in class ffx.utilities.Constants
Conversion from electron-Angstroms^2 to Buckinghams.
electric - Variable in class ffx.potential.nonbonded.GeneralizedKirkwood
Conversion from electron**2/Ang to kcal/mole.
electric - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion
Conversion from electron**2/Ang to kcal/mole.
electric - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
Coulomb constant in units of kcal*Ang/(mol*electron^2)
ELECTRIC_CODATA_2018 - Static variable in class ffx.utilities.Constants
Coulomb constant in units of kcal*Ang/(mol*electron^2), as derived from CODATA 2018 permittivity of free space measured at 8.8541878128*10^-12 F/m ELECTRIC_CODATA_2018=332.063713299
ElectrostaticsFunctionalForm - Enum constant in enum class ffx.utilities.PropertyGroup
Electrostatics functional form.
ELEMENTARY_CHARGE_SI - Static variable in class ffx.utilities.Constants
Elementary charge in Coulombs, defining the Coulomb.
eliminatedPairs - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Eliminated rotamer pairs.
EliminatedRotamers - Class in ffx.algorithms.optimize.manybody
 
EliminatedRotamers(RotamerOptimization, DistanceMatrix, List<Residue>, int, double, double, double, double, double, double, boolean, boolean, boolean, Residue[]) - Constructor for class ffx.algorithms.optimize.manybody.EliminatedRotamers
 
eliminatedSingles - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Eliminated rotamers.
eliminateRotamer(Residue[], int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
Safe method to eliminate a rotamer: will not eliminate if there are no alternate rotamers for residue i, or if i-ri is already eliminated.
eliminateRotamerPair(Residue[], int, int, int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
 
eliminateRotamerPairs(Residue[], int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
 
eLow - Variable in class ffx.numerics.estimator.SequentialEstimator
 
EmptyBooleanBuf - Class in edu.rit.mp.buf
Class EmptyBooleanBuf provides a Boolean buffer that contains no items for messages using the Message Protocol (MP).
EmptyBooleanBuf() - Constructor for class edu.rit.mp.buf.EmptyBooleanBuf
Construct a new empty Boolean buffer.
emptyBuffer() - Static method in class edu.rit.mp.BooleanBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ByteBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.CharacterBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.DoubleBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.FloatBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.IntegerBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.LongBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ObjectBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ShortBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Signed16BitIntegerBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Signed8BitIntegerBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf
Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf
Create an empty buffer.
EmptyByteBuf - Class in edu.rit.mp.buf
Class EmptyByteBuf provides a byte buffer that contains no items for messages using the Message Protocol (MP).
EmptyByteBuf() - Constructor for class edu.rit.mp.buf.EmptyByteBuf
Construct a new empty byte buffer.
EmptyCharacterBuf - Class in edu.rit.mp.buf
Class EmptyCharacterBuf provides a character buffer that contains no items for messages using the Message Protocol (MP).
EmptyCharacterBuf() - Constructor for class edu.rit.mp.buf.EmptyCharacterBuf
Construct a new empty character buffer.
EmptyDoubleBuf - Class in edu.rit.mp.buf
Class EmptyDoubleBuf provides a double buffer that contains no items for messages using the Message Protocol (MP).
EmptyDoubleBuf() - Constructor for class edu.rit.mp.buf.EmptyDoubleBuf
Construct a new empty double buffer.
EmptyFloatBuf - Class in edu.rit.mp.buf
Class EmptyFloatBuf provides a float buffer that contains no items for messages using the Message Protocol (MP).
EmptyFloatBuf() - Constructor for class edu.rit.mp.buf.EmptyFloatBuf
Construct a new empty float buffer.
EmptyIntegerBuf - Class in edu.rit.mp.buf
Class EmptyIntegerBuf provides an integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyIntegerBuf
Construct a new empty integer buffer.
EmptyLongBuf - Class in edu.rit.mp.buf
Class EmptyLongBuf provides a long buffer that contains no items for messages using the Message Protocol (MP).
EmptyLongBuf() - Constructor for class edu.rit.mp.buf.EmptyLongBuf
Construct a new empty long buffer.
EmptyObjectBuf - Class in edu.rit.mp.buf
Class EmptyObjectBuf provides an object buffer that contains no items for messages using the Message Protocol (MP).
EmptyObjectBuf() - Constructor for class edu.rit.mp.buf.EmptyObjectBuf
Construct a new empty object buffer.
EmptyShortBuf - Class in edu.rit.mp.buf
Class EmptyShortBuf provides a short buffer that contains no items for messages using the Message Protocol (MP).
EmptyShortBuf() - Constructor for class edu.rit.mp.buf.EmptyShortBuf
Construct a new empty short buffer.
EmptySigned16BitIntegerBuf - Class in edu.rit.mp.buf
Class EmptySigned16BitIntegerBuf provides a signed 16-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptySigned16BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptySigned16BitIntegerBuf
Construct a new empty signed 16-bit integer buffer.
EmptySigned8BitIntegerBuf - Class in edu.rit.mp.buf
Class EmptySigned8BitIntegerBuf provides a signed 8-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptySigned8BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptySigned8BitIntegerBuf
Construct a new empty signed 8-bit integer buffer.
EmptyUnsigned16BitIntegerBuf - Class in edu.rit.mp.buf
Class EmptyUnsigned16BitIntegerBuf provides an unsigned 16-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyUnsigned16BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf
Construct a new empty unsigned 16-bit integer buffer.
EmptyUnsigned8BitIntegerBuf - Class in edu.rit.mp.buf
Class EmptyUnsigned8BitIntegerBuf provides an unsigned 8-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyUnsigned8BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf
Construct a new empty unsigned 8-bit integer buffer.
encode(int, int) - Static method in class ffx.utilities.Hybrid36
Hybrid-36 encoder: converts integer value to string result.
energy - Variable in class ffx.algorithms.optimize.Minimize
The final potential energy.
energy - Variable in class ffx.algorithms.optimize.PhMinimize
The final potential energy.
energy - Variable in class ffx.potential.bonded.BondedTerm
Energy of the term (kcal/mol).
energy - Variable in class ffx.potential.commands.Energy
 
energy - Variable in class ffx.potential.parameters.TorsionTorsionType
Energy values.
energy - Variable in class ffx.ui.commands.SimulationUpdate
 
energy() - Method in class ffx.potential.ForceFieldEnergy
energy.
energy() - Method in class ffx.ui.ModelingShell
energy
energy(boolean) - Method in interface ffx.potential.bonded.BondedEnergy
energy.
energy(boolean) - Method in class ffx.potential.nonbonded.RestrainGroups
Compute energy and derivatives for group distance restraint terms.
energy(boolean, boolean) - Method in class ffx.potential.ANIEnergy
Compute the ANI energy and gradint.
energy(boolean, boolean) - Method in class ffx.potential.ForceFieldEnergy
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.ParticleMeshEwald
Calculate the PME electrostatic energy.
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.VanDerWaals
The energy routine may be called repeatedly.
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.VanDerWaalsTornado
The energy routine may be called repeatedly.
energy(boolean, int, AtomicDoubleArray3D) - Method in interface ffx.potential.bonded.BondedEnergy
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Angle
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.AngleTorsion
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Bond
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in interface ffx.potential.bonded.BondedEnergy
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.ImproperTorsion
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.OutOfPlaneBend
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.PiOrbitalTorsion
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.RestrainDistance
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.RestraintTorsion
 
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.StretchBend
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.StretchTorsion
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Torsion
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.TorsionTorsion
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.UreyBradley
energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.RestrainPosition
Calculates energy and gradients for this coordinate restraint.
energy(double[]) - Method in class ffx.algorithms.dynamics.Barostat
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
Compute the force field + bias energy.
energy(double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
MBAR objective function evaluation at a given free energy estimate for L-BFGS optimization.
energy(double[]) - Method in interface ffx.numerics.OptimizationInterface
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.ANIEnergy
 
energy(double[]) - Method in class ffx.potential.DualTopologyEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
energy(double[]) - Method in class ffx.potential.ForceFieldEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.QuadTopologyEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.potential.XtalEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.realspace.RealSpaceEnergy
The parameters passed in are only for "active" atoms.
energy(double[]) - Method in class ffx.xray.RefinementEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.ScaleBulkEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.SigmaAEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.SplineEnergy
This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.xray.XRayEnergy
This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in interface ffx.numerics.OptimizationInterface
This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.DualTopologyEnergy
This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.ForceFieldEnergy
This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy
This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.potential.QuadTopologyEnergy
This method is called repeatedly to compute the function energy.
energy(double[], boolean) - Method in class ffx.xray.RefinementEnergy
This method is called repeatedly to compute the function energy.
energy(MolecularAssembly) - Method in interface ffx.potential.utils.PotentialsFunctions
Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.
energy(MolecularAssembly) - Method in class ffx.potential.utils.PotentialsUtils
Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.
energy(MolecularAssembly) - Method in class ffx.ui.UIUtils
 
energy(MolecularAssembly[]) - Method in interface ffx.potential.utils.PotentialsFunctions
Evaluates the energy of each MolecularAssembly and returns their ForceFieldEnergy instances.
energy(MolecularAssembly[]) - Method in class ffx.potential.utils.PotentialsUtils
Evaluates the energy of each MolecularAssembly and returns their ForceFieldEnergy instances.
Energy - Class in ffx.potential.commands
The Energy script evaluates the energy of a system.
Energy() - Constructor for class ffx.potential.commands.Energy
Energy constructor.
Energy(FFXContext) - Constructor for class ffx.potential.commands.Energy
Energy constructor.
energyAndGradient(double[][], AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
Compute molecular volume and surface area.
energyAndGradient(double[], double[]) - Method in class ffx.algorithms.dynamics.Barostat
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
MBAR objective function evaluation and gradient at a given free energy estimate for L-BFGS optimization.
energyAndGradient(double[], double[]) - Method in interface ffx.numerics.OptimizationInterface
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.ANIEnergy
 
energyAndGradient(double[], double[]) - Method in class ffx.potential.DualTopologyEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.extended.ExtendedSystem
 
energyAndGradient(double[], double[]) - Method in class ffx.potential.ForceFieldEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.openmm.OpenMMEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.QuadTopologyEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.potential.XtalEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.realspace.RealSpaceEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.RefinementEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.ScaleBulkEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.SigmaAEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.SplineEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[]) - Method in class ffx.xray.XRayEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in interface ffx.numerics.OptimizationInterface
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.DualTopologyEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.ForceFieldEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.potential.QuadTopologyEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradient(double[], double[], boolean) - Method in class ffx.xray.RefinementEnergy
This method is called repeatedly to compute the function energy and gradient.
energyAndGradientConnolly(AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
Compute the cavitation energy.
energyAndGradientFFX(double[], double[]) - Method in class ffx.potential.openmm.OpenMMEnergy
Compute the energy and gradient using the pure Java code path.
energyAndGradientFFX(double[], double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy
Compute the energy and gradient using the pure Java code path.
energyAndGradientGausVol(double[][], AtomicDoubleArray3D) - Method in class ffx.potential.nonbonded.implicit.ChandlerCavitation
Compute molecular volume and surface area.
EnergyException - Exception Class in ffx.potential.utils
This Exception class indicates an error in calculating energy or gradients.
EnergyException() - Constructor for exception class ffx.potential.utils.EnergyException
Constructor for EnergyException.
EnergyException(String) - Constructor for exception class ffx.potential.utils.EnergyException
Constructor for EnergyException.
EnergyException(String, boolean) - Constructor for exception class ffx.potential.utils.EnergyException
Constructor for EnergyException.
EnergyException(String, boolean, double) - Constructor for exception class ffx.potential.utils.EnergyException
Constructor for EnergyException.
EnergyExpansion - Class in ffx.algorithms.optimize.manybody
 
EnergyExpansion(RotamerOptimization, DistanceMatrix, EliminatedRotamers, MolecularAssembly, Potential, AlgorithmListener, List<Residue>, int[][], boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.manybody.EnergyExpansion
 
energyFactory(MolecularAssembly) - Static method in class ffx.potential.ForceFieldEnergy
Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.
energyFactory(MolecularAssembly, int) - Static method in class ffx.potential.ForceFieldEnergy
Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.
energyFFX(double[]) - Method in class ffx.potential.openmm.OpenMMEnergy
Compute the energy using the pure Java code path.
energyFFX(double[], boolean) - Method in class ffx.potential.openmm.OpenMMEnergy
Compute the energy using the pure Java code path.
EnergyRegion - Class in ffx.algorithms.optimize.manybody
 
EnergyRegion(int) - Constructor for class ffx.algorithms.optimize.manybody.EnergyRegion
 
EnergyUnitConversion - Enum constant in enum class ffx.utilities.PropertyGroup
Energy unit conversion factors.
environment - Variable in class ffx.potential.parameters.AtomType
Description of the atom's bonding environment.
epsilon - Variable in class ffx.crystal.HKL
The epsilon value of the reflection, which is used for systematic absences.
epsilonc() - Method in class ffx.crystal.HKL
epsilonc
epsilonRule - Variable in class ffx.potential.nonbonded.VanDerWaalsForm
Epsilon combining rule.
EPT - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
 
equals(Object) - Method in class edu.rit.pj.io.StreamFile
Determine if this stream file is equal to the given object.
equals(Object) - Method in class edu.rit.util.LongRange
Determine if this range is equal to the given object.
equals(Object) - Method in class edu.rit.util.Range
Determine if this range is equal to the given object.
equals(Object) - Method in class ffx.crystal.Crystal
Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.HKL
equals(Object) - Method in class ffx.crystal.NCSCrystal
Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.ReplicatesCrystal
Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.potential.bonded.Atom
equals(Object) - Method in class ffx.potential.bonded.BondedTerm
equals(Object) - Method in class ffx.potential.bonded.Molecule
 
equals(Object) - Method in class ffx.potential.bonded.MSNode
equals(Object) - Method in class ffx.potential.bonded.MSRoot
equals(Object) - Method in class ffx.potential.bonded.MultiResidue
equals(Object) - Method in class ffx.potential.bonded.Polymer
equals(Object) - Method in class ffx.potential.bonded.Residue
equals(Object) - Method in class ffx.potential.bonded.ROLSP
equals(Object) - Method in class ffx.potential.parameters.AngleTorsionType
equals(Object) - Method in class ffx.potential.parameters.AngleType
equals(Object) - Method in class ffx.potential.parameters.AtomType
equals(Object) - Method in class ffx.potential.parameters.BioType
equals(Object) - Method in class ffx.potential.parameters.BondType
equals(Object) - Method in class ffx.potential.parameters.ImproperTorsionType
equals(Object) - Method in class ffx.potential.parameters.MultipoleType
equals(Object) - Method in class ffx.potential.parameters.OutOfPlaneBendType
equals(Object) - Method in class ffx.potential.parameters.PiOrbitalTorsionType
equals(Object) - Method in class ffx.potential.parameters.PolarizeType
equals(Object) - Method in class ffx.potential.parameters.RelativeSolvationType
equals(Object) - Method in class ffx.potential.parameters.SoluteType
equals(Object) - Method in class ffx.potential.parameters.StretchBendType
equals(Object) - Method in class ffx.potential.parameters.StretchTorsionType
equals(Object) - Method in class ffx.potential.parameters.TorsionTorsionType
equals(Object) - Method in class ffx.potential.parameters.TorsionType
equals(Object) - Method in class ffx.potential.parameters.UreyBradleyType
equals(Object) - Method in class ffx.potential.parameters.VDWPairType
equals(Object) - Method in class ffx.potential.parameters.VDWType
equals(Object) - Method in record class ffx.potential.UnmodifiableState
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ffx.ui.KeywordComponent
equals(Object) - Method in record class ffx.utilities.DoubleIndexPair
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ffx.utilities.IndexIndexPair
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ffx.utilities.ObjectPair
Indicates whether some other object is "equal to" this one.
Er - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
erf(double) - Static method in class ffx.numerics.special.Erf
Evaluates erf(x) for a real argument x.
Erf - Class in ffx.numerics.special
Static methods to evaluate erf(x) and erfc(x) for a real argument x.
erfc(double) - Static method in class ffx.numerics.special.Erf
Evaluate erfc(x) for a real argument x.
err - Variable in class edu.rit.pj.cluster.BackendFileWriter
Print stream for printing on the job frontend's standard error.
err() - Static method in class edu.rit.io.Stdio
Get the standard error stream for the calling thread.
err(PrintStream) - Static method in class edu.rit.io.Stdio
Set the standard error stream for the calling thread.
error(SAXParseException) - Method in class ffx.potential.parsers.PDBMLFilter
Es - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
EstimateBootstrapper - Class in ffx.numerics.estimator
Bootstrap Free Energy Estimate.
EstimateBootstrapper(BootstrappableEstimator) - Constructor for class ffx.numerics.estimator.EstimateBootstrapper
Constructor.
estimateDG() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Main driver for estimation of delta-G.
estimateDG() - Method in interface ffx.numerics.estimator.BootstrappableEstimator
Re-calculates free energy and enthalpy without bootstrapping.
estimateDG() - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
Get the MBAR free-energy estimates at each lambda value.
estimateDG() - Method in class ffx.numerics.estimator.Zwanzig
Re-calculates free energy and enthalpy without bootstrapping.
estimateDG(boolean) - Method in class ffx.numerics.estimator.BennettAcceptanceRatio
Main driver for estimation of delta-G.
estimateDG(boolean) - Method in interface ffx.numerics.estimator.BootstrappableEstimator
Re-calculates free energy and enthalpy.
estimateDG(boolean) - Method in class ffx.numerics.estimator.MultistateBennettAcceptanceRatio
MBAR solved with self-consistent iteration and Newton/L-BFGS optimization.
estimateDG(boolean) - Method in class ffx.numerics.estimator.Zwanzig
Re-calculates free energy and enthalpy.
ESVFileFilter - Class in ffx.potential.parsers
The ESVFileFilter class is used to choose a Extended System Restart (*.ESV) file.
ESVFileFilter() - Constructor for class ffx.potential.parsers.ESVFileFilter
Default Constructor.
ESVFilter - Class in ffx.potential.parsers
The ESVFilter class parses Extended System Restart (*.ESV) files.
ESVFilter(String) - Constructor for class ffx.potential.parsers.ESVFilter
Constructor for ESVFilter.
esvSystem - Variable in class ffx.algorithms.optimize.PhMinimize
The extended system that contains the fictitious particle
Eu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
evalPotnetial() - Method in class ffx.potential.nonbonded.octree.Octree
Evaluate potential at all target points
evaluate2DOSTBias(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
evaluate2DOSTBias.
evaluateMove(double, double) - Method in class ffx.algorithms.mc.BoltzmannMC
Returns true if the move from e1 to e2 is accepted.
evaluateMove(double, double) - Method in interface ffx.algorithms.mc.MetropolisMC
Returns true if the move from e1 to e2 is accepted.
evaluateMove(Random, double, double, double) - Static method in class ffx.algorithms.mc.BoltzmannMC
Boltzmann-weighted acceptance probability
evaluateTotalOSTBias(boolean) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
evaluateTotalBias.
ewaldCutoff(double, double, double) - Static method in class ffx.potential.nonbonded.pme.EwaldParameters
Determine the Ewald real space cutoff given the Ewald coefficient and a target precision.
EwaldParameters - Class in ffx.potential.nonbonded.pme
Mutable Particle Mesh Ewald constants.
EwaldParameters(double, double) - Constructor for class ffx.potential.nonbonded.pme.EwaldParameters
 
EwaldTensorGlobal - Class in ffx.numerics.multipole
The EwaldMultipoleTensorGlobal class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame.
EwaldTensorGlobal(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorGlobal
Constructor for EwaldMultipoleTensorGlobal.
EwaldTensorGlobalSIMD - Class in ffx.numerics.multipole
The EwaldMultipoleTensorGlobal class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame.
EwaldTensorGlobalSIMD(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorGlobalSIMD
Constructor for EwaldMultipoleTensorGlobal.
EwaldTensorQI - Class in ffx.numerics.multipole
The EwaldTensorQI class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
EwaldTensorQI(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorQI
Constructor for EwaldTensorQI.
EwaldTensorQISIMD - Class in ffx.numerics.multipole
The EwaldTensorQI class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
EwaldTensorQISIMD(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorQISIMD
Constructor for EwaldTensorQI.
excludeExcessAtoms(Set<Atom>, int[], List<Residue>) - Method in class ffx.algorithms.optimize.TitrationManyBody
 
exclusiveScan(int, Buf, Op, Object) - Method in class edu.rit.pj.Comm
Perform an exclusive scan on all processes in this communicator using the given message tag.
exclusiveScan(Buf, Op, Object) - Method in class edu.rit.pj.Comm
Perform an exclusive scan on all processes in this communicator.
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 the Discrete Fourier Transform on the default TornadoDevice.
execute(int, int, int, IntegerStrideForLoop) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(int, int, int, IntegerStrideForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(int, int, int, WorkerIntegerStrideForLoop) - Method in class edu.rit.pj.WorkerRegion
Execute a worker for loop within this worker region.
execute(int, int, IntegerForLoop) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(int, int, IntegerForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(int, int, WorkerIntegerForLoop) - Method in class edu.rit.pj.WorkerRegion
Execute a worker for loop within this worker region.
execute(long, long, long, LongStrideForLoop) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(long, long, long, LongStrideForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(long, long, long, WorkerLongStrideForLoop) - Method in class edu.rit.pj.WorkerRegion
Execute a worker for loop within this worker region.
execute(long, long, LongForLoop) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(long, long, LongForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel for loop within this parallel region.
execute(long, long, WorkerLongForLoop) - Method in class edu.rit.pj.WorkerRegion
Execute a worker for loop within this worker region.
execute(ParallelRegion) - Method in class edu.rit.pj.ParallelTeam
Execute the given parallel region.
execute(ParallelSection) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel section within this parallel region.
execute(ParallelSection[]) - Method in class edu.rit.pj.ParallelRegion
Execute a group of parallel sections concurrently within this parallel region.
execute(ParallelSection[], BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a group of parallel sections concurrently within this parallel region.
execute(ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel section within this parallel region.
execute(ParallelSection, ParallelSection) - Method in class edu.rit.pj.ParallelRegion
Execute a group of two parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a group of two parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, ParallelSection) - Method in class edu.rit.pj.ParallelRegion
Execute a group of three parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a group of three parallel sections concurrently within this parallel region.
execute(WorkerRegion) - Method in class edu.rit.pj.WorkerTeam
Execute the given worker region.
execute(Iterable<T>, ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel iteration within this parallel region.
execute(Iterable<T>, ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel iteration within this parallel region.
execute(Iterable<T>, WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion
Execute a worker iteration within this worker region.
execute(Iterator<T>, ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel iteration within this parallel region.
execute(Iterator<T>, ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel iteration within this parallel region.
execute(Iterator<T>, WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion
Execute a worker iteration within this worker region.
execute(T[], ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel iteration within this parallel region.
execute(T[], ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion
Execute a parallel iteration within this parallel region.
execute(T[], WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion
Execute a worker iteration within this worker region.
execute(TornadoDevice) - Method in class ffx.numerics.fft.TornadoDFT
Execute the Discrete Fourier Transform on a TornadoDevice.
executeCommand() - Method in class ffx.ui.ModelingPanel
Launch the TINKER command specified by the ModelingPanel
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.implicit.BornGradRegion
Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.implicit.InitializationRegion
Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.DirectRegion
Execute the DirectRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
Execute the ExpandInducedDipolesRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
Execute the InducedDipoleFieldReduceRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
Execute the InducedDipoleFieldRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InitializationRegion
Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
Execute the RealSpaceEnergyRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
Execute the ReciprocalEnergyRegion with the passed ParallelTeam.
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
Include FAST varying energy terms.
fatalError(SAXParseException) - Method in class ffx.potential.parsers.PDBMLFilter
fc - Variable in class ffx.xray.DiffractionRefinementData
Calculated atomic structure factors.
fcF(int) - Method in class ffx.xray.DiffractionRefinementData
get the amplitude of a complex Fc
FCONLY - Static variable in interface ffx.xray.parsers.MTZWriter.MTZType
Output unscaled Fcs only (still requires data to be read in).
fcPhi(int) - Method in class ffx.xray.DiffractionRefinementData
get the phase of a complex Fc
FCTOESQ - Static variable in interface ffx.xray.SplineEnergy.Type
 
fcTotF(int) - Method in class ffx.xray.DiffractionRefinementData
fcTotF
fcTotPhi(int) - Method in class ffx.xray.DiffractionRefinementData
fcTotPhi
Fe - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
 
fermiFunction(double) - Static method in class ffx.numerics.math.ScalarMath
Compute 1.0 / (1.0 + exp(x)).
fft(double[]) - Method in class ffx.numerics.fft.Complex3D
Compute the 3D FFT.
fft(double[]) - Method in class ffx.numerics.fft.Complex3DParallel
Compute the 3D FFT in parallel.
fft(double[]) - Method in class ffx.numerics.fft.Real3D
Compute the 3D FFT.
fft(double[]) - Method in class ffx.numerics.fft.Real3DParallel
Compute the 3D FFT.
fft(double[], int) - Method in class ffx.numerics.fft.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
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
 
fillEwaldSource(int, double, double[], double, double[]) - Static method in class ffx.numerics.multipole.EwaldTensorGlobal
Fill the Ewald source terms.
fillEwaldSource(int, double, double[], DoubleVector, DoubleVector[], double[]) - Static method in class ffx.numerics.multipole.EwaldTensorGlobalSIMD
Fill the Ewald source terms.
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Molecule
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MSGroup
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MultiResidue
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Polymer
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Residue
Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.MolecularAssembly
Abstract method that should specify how to finalize a MSGroup
findAtom(Atom) - Method in class ffx.potential.MolecularAssembly
findAtom
findAtomsOfElement(Residue, int) - Static method in class ffx.potential.bonded.BondedUtils
Finds all Atoms belonging to a Residue of a given atomic number.
findAtomType(int, ForceField) - Static method in class ffx.potential.bonded.BondedUtils
findAtomType.
findBondedAtoms(Atom, int) - Static method in class ffx.potential.bonded.BondedUtils
Finds Atoms bonded to a given Atom that match a certain atomic number.
findBondedAtoms(Atom, Atom, int) - Static method in class ffx.potential.bonded.BondedUtils
Finds Atoms bonded to a given Atom that match a certain atomic number that do not match an excluded atom.
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