Index (Force Field X 1.0.0-beta API)

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

A

a - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
a - Variable in class ffx.crystal.Crystal: Length of the cell edge in the direction of the a basis vector.
a - Variable in class ffx.potential.SystemState: Accelerations.
a() - Method in class ffx.potential.SystemState: Get a reference to the internal accelerations array.
a() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the a record component.
A - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
A - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
A - Variable in class ffx.crystal.Crystal: Matrix to convert from Cartesian to fractional coordinates.
A - Variable in class ffx.numerics.math.SSETest
A00 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A01 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A02 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A10 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A11 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A12 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A20 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A21 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
A22 - Variable in class ffx.crystal.Crystal: Entry in the A matrix.
AA - Enum constant in enum class ffx.potential.bonded.Residue.ResidueType
AA_C - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_C
AA_CA - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_CA
AA_CB - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_CB
AA_HA - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_HA
AA_HN - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_HN
AA_N - Static variable in class ffx.potential.bonded.AminoAcidUtils: Biotype keys for amino acid backbone atom types.
AA_O - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA_O
AA1toAA3 - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant AA1toAA3
AAPATTERN - Static variable in class ffx.potential.bonded.AminoAcidUtils: Repeating atomic numbers of an amino acid chain.
about() - Method in class ffx.ui.MainPanel: about
aboutString - Static variable in class ffx.ui.MainPanel
abs() - Method in class ffx.numerics.math.ComplexNumber: abs
ABSOLUTE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
Ac - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
acceleration - Variable in class ffx.ui.commands.SimulationUpdate
ACCELERATION - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
accept(File) - Method in class ffx.potential.parsers.ARCFileFilter
accept(File) - Method in class ffx.potential.parsers.CoordinateFileFilter
accept(File) - Method in class ffx.potential.parsers.DistanceMatrixFileFilter
accept(File) - Method in class ffx.potential.parsers.DYNFileFilter
accept(File) - Method in class ffx.potential.parsers.ESVFileFilter
accept(File) - Method in class ffx.potential.parsers.FFXFileFilter
accept(File) - Method in class ffx.potential.parsers.ForceFieldFileFilter
accept(File) - Method in class ffx.potential.parsers.InducedFileFilter
accept(File) - Method in class ffx.potential.parsers.INTFileFilter
accept(File) - Method in class ffx.potential.parsers.KeyFileFilter
accept(File) - Method in class ffx.potential.parsers.PDBFileFilter
accept(File) - Method in class ffx.potential.parsers.PDBMLFileFilter
accept(File) - Method in class ffx.potential.parsers.XPHFileFilter
accept(File) - Method in class ffx.potential.parsers.XYZFileFilter
accept(File) - Method in class ffx.xray.parsers.MTZFileFilter
acceptChance(double, double, double) - Static method in class ffx.algorithms.mc.BoltzmannMC: Boltzmann-weighted acceptance probability
acceptDeep(File) - Method in class ffx.potential.parsers.CoordinateFileFilter: acceptDeep
acceptDeep(File) - Method in class ffx.potential.parsers.INTFileFilter: acceptDeep
acceptDeep(File) - Method in class ffx.potential.parsers.PDBFileFilter: acceptDeep Accepts a PDB file if it finds at least one parseable ATOM line.
acceptDeep(File) - Method in class ffx.potential.parsers.XYZFileFilter: acceptDeep
acceptDeep(File) - Method in class ffx.xray.parsers.MTZFileFilter: acceptDeep
ACE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
action(Timer) - Method in interface edu.rit.util.TimerTask: Perform this timer task's timed actions.
actionPerformed(ActionEvent) - Method in class ffx.ui.GraphicsCanvas
actionPerformed(ActionEvent) - Method in class ffx.ui.GraphicsPrefs
actionPerformed(ActionEvent) - Method in class ffx.ui.KeywordComponent
actionPerformed(ActionEvent) - Method in class ffx.ui.KeywordPanel: Handles input from KeywordPanel ToolBar buttons.
actionPerformed(ActionEvent) - Method in class ffx.ui.MainPanel
actionPerformed(ActionEvent) - Method in class ffx.ui.ModelingPanel
actionPerformed(ActionEvent) - Method in class ffx.ui.SimulationLoader
actionPerformed(ActionEvent) - Method in class ffx.ui.Trajectory
activeAssembly - Variable in class ffx.algorithms.cli.AlgorithmsScript: An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
activeAssembly - Variable in class ffx.potential.cli.PotentialCommand: An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
activeAssembly - Variable in class ffx.potential.cli.PotentialScript: An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.
ACTIVESYSTEM - Enum constant in enum class ffx.ui.GraphicsCanvas.MouseMode
actOnAtoms(MolecularAssembly, String, BiConsumer<Atom, Boolean>, String) - Static method in class ffx.potential.cli.AtomSelectionOptions
actualCount - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
actualWork - Variable in class ffx.potential.nonbonded.SpatialDensityRegion: Number of octant work cells with at least one atom (actualWork is less than or equal to nWork).
add(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: sum
add(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: sum
add(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: sum
add(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: sum
add(int) - Method in class ffx.potential.parameters.PolarizeType: Add an atom type to the polarization group.
add(int, int) - Method in class ffx.potential.nonbonded.NeighborList.Cell: Add an atom to the cell.
add(int, int, double) - Method in class ffx.numerics.atomic.AdderDoubleArray: Add value to the double array at the specified index.
add(int, int, double) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Add value to the double array at the specified index.
add(int, int, double) - Method in class ffx.numerics.atomic.MultiDoubleArray: Add value to the double array at the specified index.
add(int, int, double) - Method in class ffx.numerics.atomic.PJDoubleArray: Add value to the double array at the specified index.
add(int, int, double, double, double) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Add to the double arrays at the specified index the given values.
add(int, int, Double3) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Add to the double arrays at the specified index the given Double3.
add(Double3) - Method in class ffx.numerics.math.Double3: Finds the sum of this Double3 with b.
add(Float3) - Method in class ffx.numerics.math.Float3: Finds the sum of this Float3 with b.
addAndersenThermostatForce(double) - Method in class ffx.potential.ForceFieldEnergyOpenMM.System: Add an Andersen thermostat to the system.
addAndersenThermostatForce(double, double) - Method in class ffx.potential.ForceFieldEnergyOpenMM.System: 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.
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.
addChild(int, int) - Method in class ffx.potential.nonbonded.octree.Octree: Add a child.
addCOMMRemoverForce() - Method in class ffx.potential.ForceFieldEnergyOpenMM.System: Adds a force that removes center-of-mass motion.
addConstraints(List<Constraint>) - Method in class ffx.algorithms.dynamics.integrators.Integrator: Adds a set of Constraints that this Integrator must respect.
ADDER - Enum constant in enum class ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl
AdderDoubleArray - Class in ffx.numerics.atomic: AdderDoubleArray implements the AtomicDoubleArray interface using an array of java.util.concurrent.atomic.DoubleAdder.
AdderDoubleArray(int) - Constructor for class ffx.numerics.atomic.AdderDoubleArray: Construct an AdderDoubleArray.
addForceFieldType(T) - Method in class ffx.potential.parameters.ForceField: Add an instance of a force field type.
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.
addKeyword(Keyword) - Method in class ffx.ui.FFXSystem: addKeyword
addMonteCarloBarostatForce(double, double, int) - Method in class ffx.potential.ForceFieldEnergyOpenMM.System: 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
addMultiResidue(MultiResidue) - Method in class ffx.potential.bonded.Polymer: addMultiResidue.
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.
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.BoxOptCell: 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
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)
addValue(double) - Method in class ffx.numerics.math.RunningStatistics: Add a value and update key variables.
addValue(double, double) - Method in class ffx.numerics.math.RunningStatistics: Add a value and update key variables.
addVdwDeriv(int, double, double[], double) - Method in class ffx.potential.extended.ExtendedSystem: Add van der Waals deriv to appropriate dU/dL term given the atom index and its contributions.
ADE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
ADENINE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
Adiabatic - Class in ffx.algorithms.dynamics.thermostats: The Adiabatic thermostat is for NVE simulations and does not alter particle velocities.
Adiabatic(SystemState, Potential.VARIABLE_TYPE[]) - Constructor for class ffx.algorithms.dynamics.thermostats.Adiabatic: Constructor for Adiabatic.
Adiabatic(SystemState, Potential.VARIABLE_TYPE[], List<Constraint>) - Constructor for class ffx.algorithms.dynamics.thermostats.Adiabatic
ADIABATIC - Enum constant in enum class ffx.algorithms.dynamics.thermostats.ThermostatEnum
aewald - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
aewald3 - Variable in class ffx.potential.nonbonded.pme.EwaldParameters
after() - Method in class ffx.ui.ModelingShell: after
afterClass() - Static method in class ffx.utilities.FFXTest: afterClass.
afterTest() - Method in class ffx.algorithms.misc.AlgorithmsTest
afterTest() - Method in class ffx.potential.utils.PotentialTest
afterTest() - Method in class ffx.utilities.FFXTest: afterTest.
Ag - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Ai - Variable in class ffx.crystal.Crystal: Matrix to convert from fractional to Cartesian coordinates.
Ai00 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai01 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai02 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai10 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai11 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai12 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai20 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai21 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
Ai22 - Variable in class ffx.crystal.Crystal: Entry in the Ai matrix.
AIB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
Al - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ALA - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ALANINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
AlchemicalOptions - Class in ffx.potential.cli: Represents command line options for scripts that utilize alchemistry on at least one topology.
AlchemicalOptions() - Constructor for class ffx.potential.cli.AlchemicalOptions
AlchemicalParameters - Class in ffx.potential.nonbonded.pme
AlchemicalParameters(ForceField, boolean, boolean, Polarization) - Constructor for class ffx.potential.nonbonded.pme.AlchemicalParameters
algorithmFunctions - Variable in class ffx.algorithms.cli.AlgorithmsScript: An instance of AlgorithmFunctions passed into the current context.
AlgorithmFunctions - Interface in ffx.algorithms: AlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional functionality such as molecular dynamics and L-BFGS local optimization.
algorithmListener - Variable in class ffx.algorithms.cli.AlgorithmsScript: An instance of the AlgorithmListener interface.
algorithmListener - Variable in class ffx.algorithms.dynamics.MolecularDynamics: An Algorithm Listener to send updates to the GUI.
algorithmListener - Variable in class ffx.algorithms.optimize.manybody.DistanceRegion: AlgorithmListener who should receive updates as the optimization runs.
algorithmListener - Variable in class ffx.algorithms.optimize.Minimize: The AlgorithmListener to update the UI.
algorithmListener - Variable in class ffx.algorithms.optimize.PhMinimize: The AlgorithmListener to update the UI.
algorithmListener - Variable in class ffx.algorithms.optimize.RotamerOptimization: AlgorithmListener who should receive updates as the optimization runs.
algorithmListener - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: The AlgorithmListener is called each time a count is added.
AlgorithmListener - Interface in ffx.algorithms: The AlgorithmListener will be notified at regular intervals during an algorithm.
algorithmsScript - Variable in class ffx.algorithms.misc.AlgorithmsTest
AlgorithmsScript - Class in ffx.algorithms.cli: Base class for scripts in the Algorithms package, providing some key functions.
AlgorithmsScript() - Constructor for class ffx.algorithms.cli.AlgorithmsScript
AlgorithmsScript(Binding) - Constructor for class ffx.algorithms.cli.AlgorithmsScript
AlgorithmsTest - Class in ffx.algorithms.misc: Base class for Algorithm tests.
AlgorithmsTest() - Constructor for class ffx.algorithms.misc.AlgorithmsTest
algorithmUpdate(MolecularAssembly) - Method in interface ffx.algorithms.AlgorithmListener: After a successful step or interval of an algorithm, this method of the listener will be called.
algorithmUpdate(MolecularAssembly) - Method in class ffx.ui.ModelingShell: After a successful step or interval of an algorithm, this method of the listener will be called.
algorithmUpdate(MolecularAssembly) - Method in class ffx.xray.RefinementEnergy: After a successful step or interval of an algorithm, this method of the listener will be called.
AlgorithmUtils - Class in ffx.algorithms: AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional functionality such as molecular dynamics and L-BFGS local optimization.
AlgorithmUtils() - Constructor for class ffx.algorithms.AlgorithmUtils: Constructor for AlgorithmUtils.
ALL - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
ALL - Static variable in interface ffx.xray.parsers.MTZWriter.MTZType: Everything, including fitted/scaled coefficients (e.g.
ALL_NETWORK_INTERFACES - Static variable in class edu.rit.pj.cluster.Constants: Host name referring to all network interfaces ("0.0.0.0").
allGather(int, Buf, Buf[]) - Method in class edu.rit.pj.Comm: All-gather messages from each process to all processes in this communicator using the given message tag.
allGather(Buf, Buf[]) - Method in class edu.rit.pj.Comm: All-gather messages from each process to all processes in this communicator.
alloc(int) - Method in class ffx.numerics.atomic.AdderDoubleArray: Ensure the AtomicDoubleArray instance is greater than or equal to size.
alloc(int) - Method in interface ffx.numerics.atomic.AtomicDoubleArray: Ensure the AtomicDoubleArray instance is greater than or equal to size.
alloc(int) - Method in class ffx.numerics.atomic.AtomicDoubleArray3D: Ensure the AtomicDoubleArray3D instance is greater than or equal to size.
alloc(int) - Method in class ffx.numerics.atomic.MultiDoubleArray: Ensure the AtomicDoubleArray instance is greater than or equal to size.
alloc(int) - Method in class ffx.numerics.atomic.PJDoubleArray: Ensure the AtomicDoubleArray instance is greater than or equal to size.
allocate(boolean[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given Boolean matrix.
allocate(boolean[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given Boolean matrix.
allocate(byte[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given byte matrix.
allocate(byte[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given byte matrix.
allocate(char[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given character matrix.
allocate(char[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given character matrix.
allocate(double[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given double matrix.
allocate(double[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given double matrix.
allocate(float[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given float matrix.
allocate(float[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given float matrix.
allocate(int[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given integer matrix.
allocate(int[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given integer matrix.
allocate(int, int) - Method in class ffx.potential.nonbonded.pme.RealSpaceNeighborParameters
allocate(long[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given long matrix.
allocate(long[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given long matrix.
allocate(short[][], int) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given short matrix.
allocate(short[][], Range, int) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given short matrix.
allocate(Atom[]) - Method in class ffx.potential.nonbonded.implicit.DispersionRegion: Allocate storage given the Atom array.
allocate(Atom[]) - Method in class ffx.potential.nonbonded.implicit.GaussVol
allocate(T[][], int, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements in the given object matrix.
allocate(T[][], Range, int, Range, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row and column index ranges in the given object matrix.
allocate(T[][], Range, int, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given row index range in the given object matrix.
allocate(T[], Range, Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate the elements within the given index range in the given object array.
allocate(T[], Class<ST>) - Static method in class edu.rit.util.Arrays: Allocate all elements in the given object array.
allocate2BodyJobMap(Residue[], int, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocate3BodyJobMap(Residue[], int, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocate4BodyJobMap(Residue[], int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocateLists(int, int) - Method in class ffx.potential.nonbonded.pme.PCGSolver: Allocate storage for pre-conditioner neighbor list.
allocateSelfJobMap(Residue[], int, boolean) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion
allocateVectors(int) - Method in class ffx.potential.nonbonded.pme.PCGSolver: Allocate PCG vectors.
allowed - Variable in class ffx.crystal.HKL
allReduce(int, Buf, Op) - Method in class edu.rit.pj.Comm: Perform an all-reduce on all processes in this communicator using the given message tag.
allReduce(Buf, Op) - Method in class edu.rit.pj.Comm: Perform an all-reduce on all processes in this communicator.
allToAll(int, Buf[], Buf[]) - Method in class edu.rit.pj.Comm: Do an all-to-all among all processes in this communicator using the given message tag.
allToAll(Buf[], Buf[]) - Method in class edu.rit.pj.Comm: Do an all-to-all among all processes in this communicator.
alpha - Variable in class ffx.crystal.Crystal: The interaxial lattice angle between b and c.
Am - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
AMBER_1994 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1996 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1998 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1999 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMBER_1999_SB - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMINOACID - Enum constant in enum class ffx.potential.Utilities.PolymerType
aminoAcid1List - Static variable in class ffx.potential.bonded.AminoAcidUtils: List of values from the AminoAcid1 enum.
aminoAcid3 - Variable in class ffx.potential.bonded.Rotamer: The A.A.
aminoAcidList - Static variable in class ffx.potential.bonded.AminoAcidUtils: Constant aminoAcidList
AminoAcidUtils - Class in ffx.potential.bonded: Utilities for creating Amino Acid residues.
AminoAcidUtils.AA - Enum Class in ffx.potential.bonded: The 20 standard amino acids.
AminoAcidUtils.AIB - Enum Class in ffx.potential.bonded: Constant AIB
AminoAcidUtils.ALA - Enum Class in ffx.potential.bonded: Constant ALA
AminoAcidUtils.AminoAcid1 - Enum Class in ffx.potential.bonded: Single letter amino acid codes (need to
AminoAcidUtils.AminoAcid3 - Enum Class in ffx.potential.bonded
AminoAcidUtils.AminoAcidBackboneAtoms - Enum Class in ffx.potential.bonded: Constant AminoAcidBackboneAtoms
AminoAcidUtils.ARG - Enum Class in ffx.potential.bonded: Constant ARG
AminoAcidUtils.ASD - Enum Class in ffx.potential.bonded: Constant ASD
AminoAcidUtils.ASH - Enum Class in ffx.potential.bonded: Constant ASH
AminoAcidUtils.ASN - Enum Class in ffx.potential.bonded: Constant ASN
AminoAcidUtils.ASP - Enum Class in ffx.potential.bonded: Constant ASP
AminoAcidUtils.CYD - Enum Class in ffx.potential.bonded: Constant CYD
AminoAcidUtils.CYS - Enum Class in ffx.potential.bonded: Constant CYS
AminoAcidUtils.CYX - Enum Class in ffx.potential.bonded: Constant CYS
AminoAcidUtils.GLD - Enum Class in ffx.potential.bonded: Constant GLD
AminoAcidUtils.GLH - Enum Class in ffx.potential.bonded: Constant GLH
AminoAcidUtils.GLN - Enum Class in ffx.potential.bonded: Constant GlutamineAtomNames
AminoAcidUtils.GLU - Enum Class in ffx.potential.bonded: Constant GLU
AminoAcidUtils.GLY - Enum Class in ffx.potential.bonded: Constant GLY
AminoAcidUtils.GlycineBackboneAtoms - Enum Class in ffx.potential.bonded: Constant GlycineBackboneAtoms
AminoAcidUtils.HID - Enum Class in ffx.potential.bonded: Constant HID
AminoAcidUtils.HIE - Enum Class in ffx.potential.bonded: Constant HIE
AminoAcidUtils.HIS - Enum Class in ffx.potential.bonded: Constant HistidineAtoms
AminoAcidUtils.ILE - Enum Class in ffx.potential.bonded: Constant ILE
AminoAcidUtils.LEU - Enum Class in ffx.potential.bonded: Constant LEU
AminoAcidUtils.LYD - Enum Class in ffx.potential.bonded: Constant LYD
AminoAcidUtils.LYS - Enum Class in ffx.potential.bonded: Constant LYS
AminoAcidUtils.MET - Enum Class in ffx.potential.bonded: Constant MethionineAtomNames
AminoAcidUtils.ORN - Enum Class in ffx.potential.bonded: Constant ORN
AminoAcidUtils.PCA - Enum Class in ffx.potential.bonded: Constant PCA
AminoAcidUtils.PHE - Enum Class in ffx.potential.bonded: Constant PHE
AminoAcidUtils.PRO - Enum Class in ffx.potential.bonded: Constant PRO
AminoAcidUtils.ProlineBackboneAtoms - Enum Class in ffx.potential.bonded: Constant ProlineBackboneAtoms
AminoAcidUtils.ResiduePosition - Enum Class in ffx.potential.bonded: The location of a residue within a chain.
AminoAcidUtils.SER - Enum Class in ffx.potential.bonded: Constant SER
AminoAcidUtils.SideChainType - Interface in ffx.potential.bonded: This interface is used by the "Build" routines.
AminoAcidUtils.THR - Enum Class in ffx.potential.bonded: Constant THR
AminoAcidUtils.TRP - Enum Class in ffx.potential.bonded: Constant TRP
AminoAcidUtils.TYD - Enum Class in ffx.potential.bonded: Constant TYD
AminoAcidUtils.TYR - Enum Class in ffx.potential.bonded: Constant TYR
AminoAcidUtils.VAL - Enum Class in ffx.potential.bonded: Constant VAL
amoeba - Variable in class ffx.ui.commands.SimulationUpdate
AMOEBA - Enum constant in enum class ffx.potential.bonded.Atom.Resolution
AMOEBA_2004 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_2009 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_BIO_2009 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_BIO_2018 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_BIO_2018_CPHMD - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_NUC_2017 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_PROTEIN_2004 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_PROTEIN_2013 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_WATER_2003 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
AMOEBA_WATER_2014 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
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
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.
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.
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.
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.
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.BoxOptCell: Checks if any rotamer of a Residue is inside this BoxOptCell.
aperiodic() - Method in class ffx.crystal.Crystal: aperiodic
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.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
applyConstraintToStep(double[], double[], double[], double) - Method in interface ffx.numerics.Constraint: Applies this Constraint in the context of a partially calculated MD time-step.
applyConstraintToStep(double[], double[], double[], double) - Method in class ffx.potential.constraint.CcmaConstraint: Applies this Constraint in the context of a partially calculated MD time-step.
applyConstraintToStep(double[], double[], double[], double) - Method in class ffx.potential.constraint.SettleConstraint
applyConstraintToStep(double[], double[], double[], double) - Method in class ffx.potential.constraint.ShakeChargeConstraint
applyConstraintToVelocities(double[], double[], double[], double) - Method in interface ffx.numerics.Constraint: Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions.
applyConstraintToVelocities(double[], double[], double[], double) - Method in class ffx.potential.constraint.CcmaConstraint: Applies this Constraint to velocities, ensuring relative velocities are perpendicular to constrained bonds, etc., without affecting positions.
applyConstraintToVelocities(double[], double[], double[], double) - Method in class ffx.potential.constraint.SettleConstraint
applyConstraintToVelocities(double[], double[], double[], double) - Method in class ffx.potential.constraint.ShakeChargeConstraint
applyFracSymOp(double[], double[], SymOp) - Static method in class ffx.crystal.SymOp: Apply a fractional symmetry operator to one set of coordinates.
applyLambda() - Method in class ffx.potential.bonded.Atom: applyLambda
applyLambda() - Method in class ffx.potential.bonded.BondedTerm: Check if any atom of this BondedTerm has the Lambda flag set.
applyLambda() - Method in class ffx.potential.bonded.RestraintTorsion
applyMask(int, boolean[], double[]...) - Method in interface ffx.potential.nonbonded.MaskingInterface: Interactions with atom i that should not be included in the NeighborList should be set to 0.
applyMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.pme.PermanentFieldRegion: Apply permanent field masking rules.
applyMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
applyMask(int, boolean[], double[]...) - Method in class ffx.potential.nonbonded.VanDerWaals: Interactions with atom i that should not be included in the NeighborList should be set to 0.
applyMasks(double, double) - Method in class ffx.numerics.multipole.PolarizableMultipole: Compute the scaled and averaged induced dipole.
applyMatrixTranspose(double[], double[], double[][]) - Static method in class ffx.numerics.math.MatrixMath: Multiply coordinates by the transpose of a matrix.
applyProperties(CompositeConfiguration) - Method in class ffx.algorithms.thermodynamics.HistogramData
applyRandomDensity(double) - Method in class ffx.potential.MolecularAssembly: Applies a randomly drawn density to a molecular system's crystal.
applyRandomSymOp(double) - Method in class ffx.potential.MolecularAssembly: Randomizes position in the unit cell of each molecule by applying a Cartesian SymOp with a random translation.
applyRotamer(Residue, Rotamer) - Static method in class ffx.potential.bonded.RotamerLibrary: Applies a Rotamer to a Residue by calling applyAARotamer or applyNARotamer.
applyRotamer(Residue, Rotamer, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: Version of applyRotamer which allows for chain context-independent drawing of nucleic acid Rotamers.
applyRotation(double[], double[][]) - Static method in class ffx.potential.utils.Superpose: Apply a rotation matrix to a set of coordinates.
applySoluteRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: Apply solute radii definitions used to calculate Born radii.
applySugarPucker(Residue, RotamerLibrary.NucleicSugarPucker, boolean, boolean) - Static method in class ffx.potential.bonded.RotamerLibrary: If place is true, builds C2', C3', and O3' based on delta(i) and returns an empty double[]; if place is false, returns a double[] filled with the coordinates at which O3' would be placed by the specified pucker.
applySymOp(double[], double[], SymOp) - Method in class ffx.crystal.Crystal: Apply a fractional symmetry operator to one set of cartesian coordinates.
applySymOp(int, double[], double[], double[], double[], double[], double[], SymOp) - Method in class ffx.crystal.Crystal: Apply a fractional symmetry operator to an array of Cartesian coordinates.
applySymOp(int, int, int, int[], SymOp, int, int, int) - Static method in class ffx.crystal.SymOp: Apply a symmetry operator to one set of coordinates.
applySymRot(double[], double[], SymOp) - Method in class ffx.crystal.Crystal: Apply a fractional symmetry operator to one set of cartesian coordinates.
applySymRot(HKL, HKL, SymOp) - Static method in class ffx.crystal.SymOp: Apply a symmetry operator to one HKL.
applyTranslation(double[], double[]) - Static method in class ffx.potential.utils.Superpose: Apply a translation matrix [dx,dy,dz] to a molecular system.
applyTransSymRot(int, double[], double[], double[], double[], double[], double[], SymOp, double[][]) - Method in class ffx.crystal.Crystal: Apply the transpose of a symmetry rotation to an array of Cartesian coordinates.
applyTransSymRot(HKL, HKL, SymOp) - Static method in class ffx.crystal.SymOp: Apply a transpose rotation symmetry operator to one HKL.
APPLYUSERCOLOR - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
approxEquals(double, double) - Static method in class ffx.numerics.integrate.FunctionDataCurve: Checks for equality to +/- 10 ulp.
approxEquals(double, double, double) - Static method in class ffx.numerics.integrate.FunctionDataCurve: Compare two doubles to machine precision.
aPrevious - Variable in class ffx.potential.SystemState: Previous accelerations.
aPrevious() - Method in class ffx.potential.SystemState: Get a reference to the internal previous accelerations array.
aPrevious() - Method in record class ffx.potential.UnmodifiableState: Returns the value of the aPrevious record component.
Ar - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ARC - Enum constant in enum class ffx.potential.Utilities.FileType
ARCFileFilter - Class in ffx.potential.parsers: The ARCFileFilter class is used to choose a TINKER Archive (*.ARC).
ARCFileFilter() - Constructor for class ffx.potential.parsers.ARCFileFilter: Default Constructor
ARG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ARGININE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
args - Variable in class ffx.utilities.FFXCommand: The array of args passed into the Script.
args - Variable in class ffx.utilities.FFXScript: The array of args passed into the Script.
ARITHMETIC - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.RADIUS_RULE
arm(MSNode, boolean, boolean, RendererCache.ViewModel, boolean, RendererCache.ColorModel) - Method in class ffx.potential.Renderer: arm
arm(ArrayList<MSNode>, boolean, boolean, RendererCache.ViewModel, boolean, RendererCache.ColorModel) - Method in class ffx.potential.Renderer: This node arms UpdateBehavior with a graphics operation to carry out
ArrayIndex_Name - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
Arrays - Class in edu.rit.util: Class Arrays provides static methods for various operations on arrays and matrices of primitive types and object types.
As - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ASD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASHtoASP - Enum constant in enum class ffx.potential.parameters.TitrationUtils.Titration
askToInterruptScript() - Method in class ffx.ui.ModelingShell: If at exit time, a script is running, the user is given an option to interrupt it first
askToSaveFile() - Method in class ffx.ui.ModelingShell
asMatrix() - Method in class ffx.crystal.SymOp: Return the SymOp as a 4x4 matrix.
asMatrixString(SymOp) - Static method in class ffx.crystal.SymOp: Print a Sym Op matrix as a continued line string.
ASN - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASP - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
ASPARAGINE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
ASPARTATE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AA
ASPC - Enum constant in enum class ffx.potential.nonbonded.pme.SCFPredictor
ASPC - Enum constant in enum class ffx.potential.nonbonded.ScfPredictor.PredictorMode
aspcPredictor(LambdaMode, double[][][], double[][][]) - Method in class ffx.potential.nonbonded.pme.SCFPredictorParameters: Always-stable predictor-corrector for the mutual induced dipoles.
assembleMolecularDynamics(MolecularAssembly[], CrystalPotential, DynamicsOptions, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions: Assembles a MolecularDynamics wrapped around a Potential.
assemblePotential(MolecularAssembly[], int, StringBuilder) - Method in class ffx.potential.cli.TopologyOptions: Performs the bulk of the work of setting up a multi-topology system.
AssemblyState - Class in ffx.potential: The AssemblyState class stores the chemical and coordinate state of a Molecular Assembly.
AssemblyState(MolecularAssembly) - Constructor for class ffx.potential.AssemblyState: Construct a snapshot of a MolecularAssembly.
assertXIntegrity() - Method in class ffx.numerics.integrate.FunctionDataCurve: Used to check that x array is composed of equally-spaced points from lb to ub.
assignAminoAcidAtomTypes(Residue, Residue, Residue, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: assignAminoAcidAtomTypes.
assignAminoAcidAtomTypes(List<Residue>, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.AminoAcidUtils: Assign atom types to an amino acid polymer.
assignAtomsToCells() - Method in class ffx.potential.nonbonded.SpatialDensityRegion: Assign asymmetric and symmetry mate atoms to cells.
assignAtomTypes(MolecularAssembly, PDBFilter.PDBFileStandard) - Static method in class ffx.potential.bonded.PolymerUtils: Assign force field atoms types to common chemistries using "biotype" records.
assignAxisAtoms(Atom) - Static method in class ffx.potential.parameters.MultipoleType: Assign local multipole frame defining atoms.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.JobFrontend: Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "assign backend" message.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Assign a backend process to the job.
assignBackend(JobSchedulerRef, String, String, String, String, String[], String, int) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Assign a backend process to the job.
assignBondedTerms(ForceField) - Method in class ffx.potential.bonded.MSGroup: assignBondedTerms
assignBondedTerms(ForceField) - Method in class ffx.potential.bonded.MultiResidue: assignBondedTerms
assigned(int[], boolean, boolean) - Method in class ffx.potential.parameters.ImproperTorsionType: Returns true if the atoms can be assigned this improperTorsionType.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontend: Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "assign job number" message.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Assign a job number to the job.
assignJobNumber(JobSchedulerRef, int, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Assign a job number to the job.
assignMultipole(ForceField.ELEC_FORM, Atom, ForceField, double[], int, int[][], MultipoleType.MultipoleFrameDefinition[]) - Static method in class ffx.potential.parameters.MultipoleType: Assign the multipole type.
assignNucleicAcidAtomTypes(List<Residue>, ForceField, List<Bond>) - Static method in class ffx.potential.bonded.NucleicAcidUtils: Assign atom types for a nucleic acid polymer.
assignPolarizationGroups() - Method in class ffx.potential.nonbonded.ParticleMeshEwald: AssignPolarizationGroups.
assignPolarizationGroups(Atom[], int[][], int[][], int[][]) - Static method in class ffx.potential.parameters.PolarizeType: assignPolarizationGroups.
ASULimit - Enum Class in ffx.crystal: Enumeration of the different asymmetric unit limit operators.
asuLimitOperators - Variable in class ffx.crystal.SpaceGroup: Real space ASU limit operators.
At - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
ATM_TO_BAR - Static variable in class ffx.utilities.Constants: Constant ATM_TO_BAR=1.01325
atom - Variable in exception class ffx.potential.bonded.BondedUtils.MissingAtomTypeException
Atom - Class in ffx.potential.bonded: The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
Atom(int, Atom, double[], int, char, String) - Constructor for class ffx.potential.bonded.Atom: Creates a new Atom similar to an existing Atom (e.g.
Atom(int, String, AtomType, double[]) - Constructor for class ffx.potential.bonded.Atom: Constructor used when parsing XYZ files.
Atom(int, String, Character, double[], String, int, Character, double, double, String) - Constructor for class ffx.potential.bonded.Atom: Constructor used when parsing PDB files.
Atom(int, String, Character, double[], String, int, Character, double, double, String, boolean) - Constructor for class ffx.potential.bonded.Atom: Constructor for Atom.
Atom(String) - Constructor for class ffx.potential.bonded.Atom: Default constructor.
ATOM - Enum constant in enum class ffx.potential.MolecularAssembly.FractionalMode
ATOM - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
Atom.Descriptions - Enum Class in ffx.potential.bonded
Atom.ElementSymbol - Enum Class in ffx.potential.bonded: Element symbols for the first 109 elements.
Atom.Resolution - Enum Class in ffx.potential.bonded
atomAttachedToAtom(Atom, Atom) - Static method in class ffx.potential.bonded.BondedUtils: Checks if atom a1 is bonded to atom a2.
atomClass - Variable in class ffx.potential.parameters.AtomType: Atom class.
atomClass - Variable in class ffx.potential.parameters.VDWType: The atom class that uses this van der Waals parameter.
atomClasses - Variable in class ffx.potential.parameters.AngleTorsionType: Atom classes for this stretch-torsion type.
atomClasses - Variable in class ffx.potential.parameters.AngleType: Atom classes that for this Angle type.
atomClasses - Variable in class ffx.potential.parameters.BondType: Atom classes that form this bond stretch.
atomClasses - Variable in class ffx.potential.parameters.ImproperTorsionType: Atom classes that for this Improper Torsion angle.
atomClasses - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Atom classes for this out-of-plane angle bending type.
atomClasses - Variable in class ffx.potential.parameters.PiOrbitalTorsionType: Atom classes that form this Pi-Torsion.
atomClasses - Variable in class ffx.potential.parameters.StretchBendType: Atom class for this stretch-bend type.
atomClasses - Variable in class ffx.potential.parameters.StretchTorsionType: Atom classes for this stretch-torsion type.
atomClasses - Variable in class ffx.potential.parameters.TorsionTorsionType: Atom classes that form this Torsion-Torsion type.
atomClasses - Variable in class ffx.potential.parameters.TorsionType: Atom classes that for this Torsion angle.
atomClasses - Variable in class ffx.potential.parameters.UreyBradleyType: Atom classes that form this Urey-Bradley cross term.
atomClasses - Variable in class ffx.potential.parameters.VDWPairType: Atom classes that form this bond stretch.
AtomColor - Static variable in class ffx.potential.bonded.Atom: Constant AtomColor
atomic - Variable in class ffx.ui.commands.SimulationDefinition
AtomicDoubleArray - Interface in ffx.numerics.atomic: This interface abstracts away the implementation of maintaining a 1D double array that is operated on by multiple threads.
AtomicDoubleArray.AtomicDoubleArrayImpl - Enum Class in ffx.numerics.atomic: AtomicDoubleArray implementations (ADDER, MULTI, PJ).
AtomicDoubleArray3D - Class in ffx.numerics.atomic: Implementation of maintaining a 3D double array that is operated on by multiple threads.
AtomicDoubleArray3D(AtomicDoubleArray.AtomicDoubleArrayImpl, int) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D: Construct an atomic 3D double array of the specified size using the specified implementation.
AtomicDoubleArray3D(AtomicDoubleArray.AtomicDoubleArrayImpl, int, int) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D: Construct an atomic 3D double array of the specified size, using the specified implementation, and the requested number of threads.
AtomicDoubleArray3D(AtomicDoubleArray, AtomicDoubleArray, AtomicDoubleArray) - Constructor for class ffx.numerics.atomic.AtomicDoubleArray3D
atomicDoubleArrayFactory(AtomicDoubleArray.AtomicDoubleArrayImpl, int, int) - Static method in interface ffx.numerics.atomic.AtomicDoubleArray: Factory method to create an AtomicDoubleArray instance.
atomicNumber - Variable in class ffx.potential.parameters.AtomType: Atomic Number.
atomicWeight - Variable in class ffx.potential.parameters.AtomType: Atomic weight.
AtomIndex(int, int) - Constructor for class ffx.potential.nonbonded.NeighborList.AtomIndex
atomInsideCell(Atom, Crystal, SymOp) - Method in class ffx.algorithms.optimize.manybody.BoxOptCell: 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.
atomName - Variable in exception class ffx.potential.bonded.BondedUtils.MissingHeavyAtomException
atomName - Variable in class ffx.potential.parameters.BioType: The PDB atom name for this BioType.
atoms - Variable in class ffx.potential.bonded.BondedTerm: Atoms that are used to form this term.
atoms - Variable in class ffx.potential.nonbonded.implicit.BornGradRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.BornRadiiRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.DispersionRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.InducedGKFieldRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.implicit.PermanentGKFieldRegion: An ordered array of atoms in the system.
atoms - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: An ordered array of atoms in the system.
AtomSelectionOptions - Class in ffx.potential.cli: Represents command line options for scripts that support atom selections.
AtomSelectionOptions() - Constructor for class ffx.potential.cli.AtomSelectionOptions
atomType - Variable in exception class ffx.potential.bonded.BondedUtils.MissingHeavyAtomException
atomType - Variable in class ffx.potential.parameters.BioType: The force field atom type to be used for the molecule / atom name combination.
atomType - Variable in class ffx.potential.parameters.ChargeType: The atom type that uses this charge parameter.
AtomType - Class in ffx.potential.parameters: The AtomType class represents one molecular mechanics atom type.
AtomType(int, int, String, String, int, double, int) - Constructor for class ffx.potential.parameters.AtomType: AtomType Constructor.
attachExtendedSystem(ExtendedSystem) - Method in class ffx.potential.ForceFieldEnergy: Overwrites current esvSystem if present.
attachExtendedSystem(ExtendedSystem) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Attach system with extended variable such as titrations.
attachExtendedSystem(ExtendedSystem) - Method in class ffx.potential.nonbonded.VanDerWaals: attachExtendedSystem.
attachExtendedSystem(ExtendedSystem, double) - Method in class ffx.algorithms.dynamics.MolecularDynamics: attachExtendedSystem.
Au - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
AUTO - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
automaticWriteouts - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Whether MD handles writing restart/trajectory files itself (true), or will be commanded by another class (false) to do it.
average(AngleTorsionType, AngleTorsionType, int[]) - Static method in class ffx.potential.parameters.AngleTorsionType: average.
average(AngleType, AngleType, int[]) - Static method in class ffx.potential.parameters.AngleType: Average two AngleType instances.
average(BondType, BondType, int[]) - Static method in class ffx.potential.parameters.BondType: Average two BondType instances.
average(ChargeType, ChargeType, int) - Static method in class ffx.potential.parameters.ChargeType: Average two ChargeType instances.
average(ImproperTorsionType, ImproperTorsionType, int[]) - Static method in class ffx.potential.parameters.ImproperTorsionType: Average two ImproperTorsionType instances.
average(OutOfPlaneBendType, OutOfPlaneBendType, int[]) - Static method in class ffx.potential.parameters.OutOfPlaneBendType: Average two OutOfPlaneBendType instances.
average(PiOrbitalTorsionType, PiOrbitalTorsionType, int[]) - Static method in class ffx.potential.parameters.PiOrbitalTorsionType: Average two PiTorsionType instances.
average(PolarizeType, PolarizeType, int, int[]) - Static method in class ffx.potential.parameters.PolarizeType: Average two PolarizeType instances.
average(StretchBendType, StretchBendType, int[]) - Static method in class ffx.potential.parameters.StretchBendType: average.
average(StretchTorsionType, StretchTorsionType, int[]) - Static method in class ffx.potential.parameters.StretchTorsionType: average.
average(TorsionTorsionType, TorsionTorsionType, int[]) - Static method in class ffx.potential.parameters.TorsionTorsionType: average.
average(TorsionType, TorsionType, int[]) - Static method in class ffx.potential.parameters.TorsionType: average.
average(UreyBradleyType, UreyBradleyType, int[]) - Static method in class ffx.potential.parameters.UreyBradleyType: average.
average(VDWPairType, VDWPairType, int[]) - Static method in class ffx.potential.parameters.VDWPairType: Average.
average(VDWType, VDWType, int) - Static method in class ffx.potential.parameters.VDWType: Average two VDWType objects.
AverageFc(MolecularAssembly[], int) - Method in class ffx.xray.DiffractionData: read in a different assembly to average in structure factors
averageFcs(File, File, ReflectionList, int, CompositeConfiguration) - Method in class ffx.xray.parsers.MTZFilter: Average the computed structure factors for two systems.
averageIntegral(double, double) - Static method in class ffx.numerics.integrate.Integration: averageIntegral.
averageTensor(double[][], double[][]) - Method in class ffx.crystal.Crystal: averageTensor
averageTensor(double[], double[][]) - Method in class ffx.crystal.Crystal: averageTensor
averageTypes(MultipoleType, MultipoleType, int[]) - Static method in class ffx.potential.parameters.MultipoleType: Average two MultipoleType instances.
AVOGADRO - Static variable in class ffx.utilities.Constants: Avogadro's number, defining the mol.

B

b - Variable in class ffx.crystal.Crystal: Length of the cell edge in the direction of the b basis vector.
B - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
B - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
B - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
b2u(double) - Static method in class ffx.numerics.math.ScalarMath: b2u
Ba - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
backend - Variable in class edu.rit.pj.cluster.JobInfo: Array of backend nodes for each process assigned to the job in rank order.
backend - Variable in class edu.rit.pj.cluster.ProcessInfo: Reference to the job backend process.
BackendClassLoader - Class in edu.rit.pj.cluster: Class BackendClassLoader provides a class loader for a job backend process in the PJ cluster middleware.
BackendClassLoader(JobBackendRef, JobFrontendRef, ResourceCache) - Constructor for class edu.rit.pj.cluster.BackendClassLoader: Construct a new backend class loader.
BackendClassLoader(ClassLoader, JobBackendRef, JobFrontendRef, ResourceCache) - Constructor for class edu.rit.pj.cluster.BackendClassLoader: Construct a new backend class loader.
backendFailed(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobScheduler: Report that a backend node failed.
backendFailed(JobFrontendRef, String) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "backend failed" message.
backendFailed(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Report that a backend node failed.
backendFailed(JobFrontendRef, String) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Report that a backend node failed.
BackendFileInputStream - Class in edu.rit.pj.cluster: Class BackendFileInputStream provides an object in a job backend process that reads a sequential file in the job frontend process.
BackendFileOutputStream - Class in edu.rit.pj.cluster: Class BackendFileOutputStream provides an object in a job backend process that writes a sequential file in the job frontend process.
BackendFileReader - Class in edu.rit.pj.cluster: Class BackendFileReader provides an object that reads sequential files in the job backend process.
BackendFileReader(JobFrontendRef, JobBackendRef) - Constructor for class edu.rit.pj.cluster.BackendFileReader: Construct a new backend file reader.
BackendFileWriter - Class in edu.rit.pj.cluster: Class BackendFileWriter provides an object that writes sequential files in the job backend process.
BackendFileWriter(JobFrontendRef, JobBackendRef) - Constructor for class edu.rit.pj.cluster.BackendFileWriter: Construct a new backend file writer.
backendFinished(JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontend: Report that a backend process has finished executing the job.
backendFinished(JobBackendRef) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "backend finished" message.
backendFinished(JobBackendRef) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Report that a backend process has finished executing the job.
backendFinished(JobBackendRef) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Report that a backend process has finished executing the job.
backendFinished(JobBackendRef) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Report that a backend process has finished executing the job.
BackendInfo - Class in edu.rit.pj.cluster: Class BackendInfo provides a record of information about one backend node in the PJ cluster middleware.
BackendInfo(String, int, BackendInfo.State, long, String, String, String, String[], String) - Constructor for class edu.rit.pj.cluster.BackendInfo: Construct a new backend information record.
BackendInfo.State - Enum Class in edu.rit.pj.cluster: The state of a backend node.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in class edu.rit.pj.cluster.JobFrontend: Report that a backend process is ready to commence executing the job.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "backend ready" message.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Report that a backend process is ready to commence executing the job.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Report that a backend process is ready to commence executing the job.
backendReady(JobBackendRef, int, InetSocketAddress, InetSocketAddress, InetSocketAddress) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Report that a backend process is ready to commence executing the job.
BACKWARD - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Direction
BACKWARDS - Enum constant in enum class ffx.numerics.estimator.Zwanzig.Directionality
BadIntpln - Enum constant in enum class ffx.numerics.optimization.LineSearch.LineSearchResult
BALLANDSTICK - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
BARFilter - Class in ffx.potential.parsers: The BARFilter class parses TINKER bar(*.BAR) files.
BARFilter(File) - Constructor for class ffx.potential.parsers.BARFilter: BARFilter constructor
BARFilter(File, double[], double[], double[], double[], double[], double[], double) - Constructor for class ffx.potential.parsers.BARFilter: BARFilter constructor
BARFilter(File, int, int) - Constructor for class ffx.potential.parsers.BARFilter: BARFilter constructor
barostat - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Reference to the Barostat in use; if present this must be turned off during optimization.
Barostat - Class in ffx.algorithms.dynamics: The Barostat class maintains constant pressure using random trial moves in lattice parameters, which are consistent with the space group.
Barostat(MolecularAssembly, CrystalPotential) - Constructor for class ffx.algorithms.dynamics.Barostat: Initialize the Barostat.
Barostat(MolecularAssembly, CrystalPotential, double) - Constructor for class ffx.algorithms.dynamics.Barostat: Initialize the Barostat.
BarostatOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that use a barostat/NPT.
BarostatOptions() - Constructor for class ffx.algorithms.cli.BarostatOptions
barrier() - Method in class edu.rit.pj.Comm: Cause all processes in this communicator to wait at a barrier.
barrier() - Method in class edu.rit.pj.ParallelRegion: Perform a barrier.
barrier(int) - Method in class edu.rit.pj.Comm: Cause all processes in this communicator to wait at a barrier, using the given message tag.
barrier(BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Perform a barrier, with a barrier action.
BarrierAction - Class in edu.rit.pj: Class BarrierAction is the abstract base class for an object containing code that is executed as part of a barrier wait.
BarrierAction() - Constructor for class edu.rit.pj.BarrierAction: Construct a new barrier action.
baseDir - Variable in class ffx.algorithms.cli.AlgorithmsScript: The directory in which to place output files.
baseDir - Variable in class ffx.potential.cli.PotentialCommand: A temporary directory that contains script artifacts.
baseDir - Variable in class ffx.potential.cli.PotentialScript: A temporary directory that contains script artifacts.
BaseType - Class in ffx.potential.parameters: All force field types should extend the BaseType class.
BaseType(ForceField.ForceFieldType, int[]) - Constructor for class ffx.potential.parameters.BaseType: Public constructor.
BaseType(ForceField.ForceFieldType, String) - Constructor for class ffx.potential.parameters.BaseType: Public constructor.
Be - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
BEEMAN - Enum constant in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
before() - Method in class ffx.ui.ModelingShell: before
beforeClass() - Static method in class ffx.algorithms.misc.AlgorithmsTest: Initialize the PJ communication layer.
beforeClass() - Static method in class ffx.utilities.FFXTest: beforeClass.
beforeTest() - Method in class ffx.algorithms.misc.AlgorithmsTest
beforeTest() - Method in class ffx.potential.utils.PotentialTest
beforeTest() - Method in class ffx.utilities.FFXTest: beforeTest.
beginMCOST(MonteCarloOST, DynamicsOptions, ThermodynamicsOptions) - Method in class ffx.algorithms.cli.OSTOptions: Runs MC-OST.
beginMDOST(OrthogonalSpaceTempering, MolecularAssembly[], CrystalPotential, DynamicsOptions, WriteoutOptions, ThermodynamicsOptions, File, AlgorithmListener) - Method in class ffx.algorithms.cli.OSTOptions: Begins MD-OST sampling from an assembled OST.
BellCurveSwitch - Class in ffx.numerics.switching: Implements a bell-shaped switching function by stitching together a pair of MultiplicativeSwitches.
BellCurveSwitch() - Constructor for class ffx.numerics.switching.BellCurveSwitch: Construct a bell curve (spliced 5-'th order Hermite splines) of width 1.0, midpoint 0.5.
BellCurveSwitch(double) - Constructor for class ffx.numerics.switching.BellCurveSwitch: Construct a bell curve (spliced 5-'th order Hermite splines) of width 1.0.
BellCurveSwitch(double, double) - Constructor for class ffx.numerics.switching.BellCurveSwitch: Construct a bell curve (spliced 5-'th order Hermite splines).
BennettAcceptanceRatio - Class in ffx.numerics.estimator: The Bennett Acceptance Ratio class implements the Bennett Acceptance Ratio (BAR) statistical estimator, based on the Tinker implementation.
BennettAcceptanceRatio(double[], double[][], double[][], double[][], double[]) - Constructor for class ffx.numerics.estimator.BennettAcceptanceRatio: Constructs a BAR estimator and obtains an initial free energy estimate.
BennettAcceptanceRatio(double[], double[][], double[][], double[][], double[], double) - Constructor for class ffx.numerics.estimator.BennettAcceptanceRatio: Constructs a BAR estimator and obtains an initial free energy estimate.
Berendsen - Class in ffx.algorithms.dynamics.thermostats: Thermostat a molecular dynamics trajectory to an external bath using the Berendsen weak-coupling thermostat.
Berendsen(SystemState, Potential.VARIABLE_TYPE[], double) - Constructor for class ffx.algorithms.dynamics.thermostats.Berendsen: Constructor for Berendsen.
Berendsen(SystemState, Potential.VARIABLE_TYPE[], double, double) - Constructor for class ffx.algorithms.dynamics.thermostats.Berendsen: Constructor for Berendsen.
Berendsen(SystemState, Potential.VARIABLE_TYPE[], double, double, List<Constraint>) - Constructor for class ffx.algorithms.dynamics.thermostats.Berendsen
BERENDSEN - Enum constant in enum class ffx.algorithms.dynamics.thermostats.ThermostatEnum
beta - Variable in class ffx.crystal.Crystal: The interaxial lattice angle between a and c.
BetterBeeman - Class in ffx.algorithms.dynamics.integrators: Integrate Newton's equations of motion using a Beeman multistep recursion formula; the actual coefficients are Brooks' "Better Beeman" values.
BetterBeeman(SystemState) - Constructor for class ffx.algorithms.dynamics.integrators.BetterBeeman: Constructor for BetterBeeman.
BFACTORS - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine B factors only (if anisotropic, refined as such)
BFACTORS_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine B factors and occupancies
Bh - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Bi - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
bin - Variable in class ffx.crystal.HKL
BINARY - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: The classic binary (0, 1) model.
binding - Variable in class ffx.algorithms.misc.AlgorithmsTest
binding - Variable in class ffx.potential.utils.PotentialTest
binomial(long, long) - Static method in class ffx.numerics.math.ScalarMath: binomial
binWidth() - Method in interface ffx.numerics.integrate.DataSet: Separation between points along x; should be uniform.
binWidth() - Method in class ffx.numerics.integrate.DoublesDataSet: Separation between points along x; should be uniform.
binWidth() - Method in class ffx.numerics.integrate.FunctionDataCurve: Separation between points along x; should be uniform.
biochemistry(MolecularAssembly, List<Atom>) - Static method in class ffx.potential.Utilities: This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.
BioType - Class in ffx.potential.parameters: The BioType class maps PDB identifiers to atom types.
BioType(int, String, String, int, String[]) - Constructor for class ffx.potential.parameters.BioType: BioType Constructor.
BIOTYPE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
BISECTOR - Enum constant in enum class ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
Bk - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
BLACK - Static variable in class ffx.potential.bonded.RendererCache: Constant BLACK
BMP - Enum constant in enum class ffx.ui.GraphicsCanvas.ImageFormat
bn - Variable in class ffx.numerics.multipole.GKSource: Chain rule terms from differentiating zeroth order born radii auxiliary functions (bn0) with respect to Ai or Aj.
bn(int) - Method in class ffx.numerics.multipole.GKSource: Compute the function b, which are chain rule terms from differentiating zeroth order auxiliary functions (an0) with respect to Ai or Aj.
BOHR - Static variable in class ffx.utilities.Constants: Conversion from Bohr to Angstroms.
BOHR2 - Static variable in class ffx.utilities.Constants: Conversion from Bohr^2 to Angstroms^2.
BOLTZMANN_SI - Static variable in class ffx.utilities.Constants: Boltzmann's constant in J/K, defining the Kelvin.
BoltzmannMC - Class in ffx.algorithms.mc: The BoltzmannMC abstract class is a skeleton for Boltzmann-weighted Metropolis Monte Carlo simulations.
BoltzmannMC() - Constructor for class ffx.algorithms.mc.BoltzmannMC
Bond - Class in ffx.potential.bonded: The Bond class represents a covalent bond formed between two atoms.
Bond(Atom, Atom) - Constructor for class ffx.potential.bonded.Bond: Bond constructor.
Bond(String) - Constructor for class ffx.potential.bonded.Bond: Simple Bond constructor that is intended to be used with the equals method.
BOND - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
bond0Eq - Variable in class ffx.potential.bonded.StretchBend: First equilibrium bond distance.
bond1Eq - Variable in class ffx.potential.bonded.StretchBend: Second equilibrium bond distance.
bondAngle(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the angle formed by three atoms.
bondAngle(float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the angle formed by three atoms
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.
bondFunction - Variable in class ffx.potential.parameters.BondType: The function used by the bond: harmonic or quartic with flat-bottom variants.
bondList - Variable in class ffx.potential.parsers.SystemFilter: The bondList may be filled by the filters that extend SystemFilter.
bonds - Variable in class ffx.potential.bonded.BondedTerm: Bonds that are used to form this term.
bonds - Variable in class ffx.potential.parameters.BioType: Bonds are required to listed atom names.
bondTime - Static variable in class ffx.potential.bonded.MSGroup: Constant bondTime=0
bondType - Variable in class ffx.potential.bonded.Bond: The force field BondType for this bond.
bondType - Variable in class ffx.potential.bonded.RestraintBond
BondType - Class in ffx.potential.parameters: The BondType class defines one harmonic bond stretch energy term.
BondType(int[], double, double) - Constructor for class ffx.potential.parameters.BondType: The default BondType constructor defines use of the Quartic BondFunction.
BondType(int[], double, double, BondType.BondFunction) - Constructor for class ffx.potential.parameters.BondType: BondType constructor.
BondType(int[], double, double, BondType.BondFunction, double) - Constructor for class ffx.potential.parameters.BondType: BondType constructor.
BondType.BondFunction - Enum Class in ffx.potential.parameters: Describes the function used by the bond.
bondType1 - Variable in class ffx.potential.bonded.StretchTorsion: First bond force field type.
bondType2 - Variable in class ffx.potential.bonded.StretchTorsion: Second bond force field type.
bondType3 - Variable in class ffx.potential.bonded.StretchTorsion: Third bond force field type.
bondUnit - Variable in class ffx.potential.parameters.BondType: Convert bond stretch energy to kcal/mole.
bondwidth - Static variable in class ffx.potential.bonded.RendererCache: Constant bondwidth=3
BOOLE - Enum constant in enum class ffx.numerics.integrate.Integrate1DNumeric.IntegrationType
BooleanArrayBuf - Class in edu.rit.mp.buf: Class BooleanArrayBuf provides a buffer for an array of Boolean items sent or received using the Message Protocol (MP).
BooleanArrayBuf(boolean[], Range) - Constructor for class edu.rit.mp.buf.BooleanArrayBuf: Construct a new Boolean array buffer.
BooleanArrayBuf_1 - Class in edu.rit.mp.buf: Class BooleanArrayBuf_1 provides a buffer for an array of Boolean items sent or received using the Message Protocol (MP).
BooleanArrayBuf_1(boolean[], Range) - Constructor for class edu.rit.mp.buf.BooleanArrayBuf_1: Construct a new Boolean array buffer.
BooleanBuf - Class in edu.rit.mp: Class BooleanBuf is the abstract base class for a buffer of Boolean items sent or received using the Message Protocol (MP).
BooleanBuf(int) - Constructor for class edu.rit.mp.BooleanBuf: Construct a new Boolean buffer.
BooleanItemBuf - Class in edu.rit.mp.buf: Class BooleanItemBuf provides a buffer for a single Boolean item sent or received using the Message Protocol (MP).
BooleanItemBuf() - Constructor for class edu.rit.mp.buf.BooleanItemBuf: Construct a new Boolean item buffer.
BooleanItemBuf(boolean) - Constructor for class edu.rit.mp.buf.BooleanItemBuf: Construct a new Boolean item buffer with the given initial value.
BooleanMatrixBuf - Class in edu.rit.mp.buf: Class BooleanMatrixBuf provides a buffer for a matrix of Boolean items sent or received using the Message Protocol (MP).
BooleanMatrixBuf(boolean[][], Range, Range) - Constructor for class edu.rit.mp.buf.BooleanMatrixBuf: Construct a new Boolean matrix buffer.
BooleanMatrixBuf_1 - Class in edu.rit.mp.buf: Class BooleanMatrixBuf_1 provides a buffer for a matrix of Boolean items sent or received using the Message Protocol (MP).
BooleanMatrixBuf_1(boolean[][], Range, Range) - Constructor for class edu.rit.mp.buf.BooleanMatrixBuf_1: Construct a new Boolean matrix buffer.
BooleanOp - Class in edu.rit.pj.reduction: Class BooleanOp is the abstract base class for a binary operation on Boolean values, used to do reduction in a parallel program.
BooleanOp() - Constructor for class edu.rit.pj.reduction.BooleanOp: Construct a new Boolean binary operation.
booles(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using Boole's rule.
booles(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using Boole's rule.
boolesParallel(DataSet, Integrate1DNumeric.IntegrationSide) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set using Boole's rule.
boolesParallel(DataSet, Integrate1DNumeric.IntegrationSide, int, int) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Numerically integrates a data set, in bounds lb-ub inclusive, using Boole's rule.
bootstrap(long) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Perform bootstrap analysis.
bootstrap(long, long) - Method in class ffx.numerics.estimator.EstimateBootstrapper: Perform bootstrap analysis.
BootstrappableEstimator - Interface in ffx.numerics.estimator: The BootstrappableEstimator interface describes a StatisticalEstimator which can use bootstrap sampling as an additional method of calculating free energy and uncertainty.
BootStrapStatistics - Class in ffx.numerics.math: The BootStrapStatistics class uses bootstrapping to estimate statistics from a given population.
BootStrapStatistics(double[]) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], double[], int, int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
BootStrapStatistics(double[], int, int, int) - Constructor for class ffx.numerics.math.BootStrapStatistics: Constructs a static summary of a statistic from provided values.
border - Static variable in class ffx.ui.MainPanel: Constant
BORN - Enum constant in enum class ffx.numerics.multipole.GKSource.GK_TENSOR_MODE
BORN_CAV_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
BORN_SOLV - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
BornGradRegion - Class in ffx.potential.nonbonded.implicit: Parallel computation of Born radii chain rule terms via the Grycuk method.
BornGradRegion(int, boolean, boolean, boolean) - Constructor for class ffx.potential.nonbonded.implicit.BornGradRegion: Compute the gradient due to changes in Born radii.
BornRadiiRegion - Class in ffx.potential.nonbonded.implicit: Parallel computation of Born radii via the Grycuk method.
BornRadiiRegion(int, int, ForceField, boolean, boolean, boolean) - Constructor for class ffx.potential.nonbonded.implicit.BornRadiiRegion: BornRadiiRegion Constructor.
bornRadiiTotal - Variable in class ffx.potential.nonbonded.pme.PMETimings
BornTanhRescaling - Class in ffx.potential.nonbonded.implicit: Rescale the Born radius integral to account for interstitial spaces.
BornTanhRescaling() - Constructor for class ffx.potential.nonbonded.implicit.BornTanhRescaling
BOTH - Enum constant in enum class ffx.numerics.Potential.STATE
BOX - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Algorithm
BoxOptCell - Class in ffx.algorithms.optimize.manybody: Contains a cell used for box optimization, its residues, the fractional coordinates within a crystal it takes up, its overall (linear) index, and its indices along the a, b, and c crystal axes.
BoxOptCell(double[], int[], int) - Constructor for class ffx.algorithms.optimize.manybody.BoxOptCell: Constructs a BoxOptCell object, which takes up a set of fractional coordinates within the Crystal, the Residues contained within, and the index of the cell along the crystal's a, b, and c axes.
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.ForceFieldEnergyOpenMM.System: Calculate the number of degrees of freedom.
calculateLikelihoodFree() - Method in class ffx.xray.SigmaAMinimize: calculateLikelihoodFree
calculateRMSDs(int[], boolean, boolean, boolean, boolean, boolean, boolean) - Method in class ffx.potential.utils.Superpose: This method calculates the all versus all RMSD of a multiple model pdb/arc file.
calculateRotation(double[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: Calculate a rotation to minimize RMS distance between two sets of atoms using quaternions, overlapping x2 on x1.
calculateTranslation(double[], double[]) - Static method in class ffx.potential.utils.Superpose: Calculate a translation vector [dx,dy,dz] to move the center of mass to the origin.
cancelJob(JobBackendRef, String) - Method in class edu.rit.pj.cluster.JobFrontend: Cancel the job.
cancelJob(JobBackendRef, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "cancel job" message.
cancelJob(JobBackendRef, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Cancel the job.
cancelJob(JobBackendRef, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Cancel the job.
cancelJob(JobBackendRef, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Cancel the job.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobBackend: Cancel the job.
cancelJob(JobFrontendRef, String) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "cancel job" message.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobBackendProxy: Cancel the job.
cancelJob(JobFrontendRef, String) - Method in interface edu.rit.pj.cluster.JobBackendRef: Cancel the job.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobScheduler: Cancel a job.
cancelJob(JobFrontendRef, String) - Static method in class edu.rit.pj.cluster.JobSchedulerMessage: Construct a new "cancel job" message.
cancelJob(JobFrontendRef, String) - Method in class edu.rit.pj.cluster.JobSchedulerProxy: Cancel a job.
cancelJob(JobFrontendRef, String) - Method in interface edu.rit.pj.cluster.JobSchedulerRef: Cancel a job.
cancelJob(JobSchedulerRef, String) - Method in class edu.rit.pj.cluster.JobFrontend: Cancel the job.
cancelJob(JobSchedulerRef, String) - Static method in class edu.rit.pj.cluster.JobFrontendMessage: Construct a new "cancel job" message.
cancelJob(JobSchedulerRef, String) - Method in class edu.rit.pj.cluster.JobFrontendProxy: Cancel the job.
cancelJob(JobSchedulerRef, String) - Method in interface edu.rit.pj.cluster.JobFrontendRef: Cancel the job.
cancelJob(JobSchedulerRef, String) - Method in class edu.rit.pj.cluster.NonPjJobFrontend: Cancel the job.
cartToFracInducedDipole(double[], double[], double[], double[]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: cartToFracInducedDipoles
CAV - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
CAV_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ALA
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYS
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.CYX
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.SER
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CB - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
CB - Enum constant in enum class ffx.potential.parameters.TitrationUtils.CysteineAtomNames
CB - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
CB - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CB1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
CB2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AIB
cbmcStep() - Method in class ffx.algorithms.mc.RosenbluthCBMC: cbmcStep.
CcmaConstraint - Class in ffx.potential.constraint
ccmaFactory(List<Bond>, List<Angle>, Atom[], double[], double) - Static method in class ffx.potential.constraint.CcmaConstraint: Constructs a set of bond length Constraints to be satisfied using the Constaint Constraint Matrix Approximation, a parallelizable stable numeric method.
CCP4MapFilter - Class in ffx.realspace.parsers: CCP4MapFilter class.
CCP4MapFilter() - Constructor for class ffx.realspace.parsers.CCP4MapFilter
CCP4MapWriter - Class in ffx.xray.parsers: CCP4MapWriter class.
CCP4MapWriter(int, int, int, int, int, int, int, int, int, Crystal, String) - Constructor for class ffx.xray.parsers.CCP4MapWriter: Constructor for CCP4MapWriter.
CCP4MapWriter(int, int, int, Crystal, String) - Constructor for class ffx.xray.parsers.CCP4MapWriter: construct mapwriter object
Cd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
CD - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
CD - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CD1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CD2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CD2 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
Ce - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
CE - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CE1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CE1 - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CE2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CE3 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
Cell(int, int, int) - Constructor for class ffx.potential.nonbonded.NeighborList.Cell
center() - Method in class ffx.potential.MolecularAssembly: center
center() - Method in class ffx.ui.GraphicsAxis: center
centerAt(double[]) - Method in class ffx.potential.MolecularAssembly: centerAt
centerOfMassMotion(boolean, boolean) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Compute the center of mass, linear momentum and angular momentum.
centerView(boolean, boolean) - Method in class ffx.potential.MolecularAssembly: centerView
centerView(boolean, boolean) - Method in class ffx.ui.behaviors.GlobalBehavior: centerView
centric() - Method in class ffx.crystal.HKL: centric
Cf - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ARG
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASH
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASN
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ASP
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLH
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLN
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.GLU
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HID
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIE
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.HIS
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LEU
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.LYS
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.MET
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ORN
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PCA
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PHE
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.PRO
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYD
CG - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TYR
CG - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
CG - Enum constant in enum class ffx.potential.parameters.TitrationUtils.HistidineAtomNames
CG - Enum constant in enum class ffx.potential.parameters.TitrationUtils.LysineAtomNames
CG1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CG1 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
CG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ILE
CG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.THR
CG2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.VAL
CH2 - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.TRP
CHAIN_IDS - Static variable in class ffx.potential.bonded.Polymer
ChandlerCavitation - Class in ffx.potential.nonbonded.implicit: The ChandlerCavitation class smoothly switches between a volume based dependence for small solutes to a surface area dependence for large solutes.
ChandlerCavitation(Atom[], ConnollyRegion, ForceField) - Constructor for class ffx.potential.nonbonded.implicit.ChandlerCavitation
ChandlerCavitation(Atom[], GaussVol, ForceField) - Constructor for class ffx.potential.nonbonded.implicit.ChandlerCavitation
changedUpdate(DocumentEvent) - Method in class ffx.ui.KeywordComponent
changeUnitCellParameters(double, double, double, double, double, double) - Method in class ffx.crystal.Crystal: This method should be called to update the unit cell parameters of a crystal.
changeUnitCellParameters(double, double, double, double, double, double) - Method in class ffx.crystal.NCSCrystal: Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
changeUnitCellParameters(double, double, double, double, double, double) - Method in class ffx.crystal.ReplicatesCrystal: Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
changeUnitCellParametersAndVolume(double, double, double, double, double, double, double) - Method in class ffx.crystal.Crystal: This method should be called to update the unit cell parameters of a crystal.
changeUnitCellParametersAndVolume(double, double, double, double, double, double, double) - Method in class ffx.crystal.ReplicatesCrystal: Change the cell parameters for the base unit cell, which is followed by an update of the ReplicateCrystal parameters and possibly the number of replicated cells.
channel - Variable in class edu.rit.mp.Status: The channel from which the message was received.
Channel - Class in edu.rit.mp: Class Channel provides a channel for sending and receiving messages in the Message Protocol (MP).
ChannelClosedException - Exception Class in edu.rit.mp: Class ChannelClosedException is thrown to indicate that an I/O operation failed because the channel was closed.
ChannelClosedException() - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with no detail message and no cause.
ChannelClosedException(String) - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with the given detail message and no cause.
ChannelClosedException(String, Throwable) - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with the given detail message and the given cause.
ChannelClosedException(Throwable) - Constructor for exception class edu.rit.mp.ChannelClosedException: Create a new channel closed exception with no detail message and the given cause.
ChannelGroup - Class in edu.rit.mp: Class ChannelGroup provides a group of Channels for sending and receiving messages in the Message Protocol (MP).
ChannelGroup() - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(Logger) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(InetSocketAddress) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(InetSocketAddress, Logger) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(ServerSocketChannel) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroup(ServerSocketChannel, Logger) - Constructor for class edu.rit.mp.ChannelGroup: Construct a new channel group.
ChannelGroupClosedException - Exception Class in edu.rit.mp: Class ChannelGroupClosedException is thrown to indicate that an I/O operation failed because the channel group was closed.
ChannelGroupClosedException() - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with no detail message and no cause.
ChannelGroupClosedException(String) - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with the given detail message and no cause.
ChannelGroupClosedException(String, Throwable) - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with the given detail message and the given cause.
ChannelGroupClosedException(Throwable) - Constructor for exception class edu.rit.mp.ChannelGroupClosedException: Create a new channel group closed exception with no detail message and the given cause.
Character() - Constructor for class edu.rit.util.Searching.Character
Character() - Constructor for class edu.rit.util.Sorting.Character
CharacterArrayBuf - Class in edu.rit.mp.buf: Class CharacterArrayBuf provides a buffer for an array of character items sent or received using the Message Protocol (MP).
CharacterArrayBuf(char[], Range) - Constructor for class edu.rit.mp.buf.CharacterArrayBuf: Construct a new character array buffer.
CharacterArrayBuf_1 - Class in edu.rit.mp.buf: Class CharacterArrayBuf_1 provides a buffer for an array of character items sent or received using the Message Protocol (MP).
CharacterArrayBuf_1(char[], Range) - Constructor for class edu.rit.mp.buf.CharacterArrayBuf_1: Construct a new character array buffer.
CharacterBuf - Class in edu.rit.mp: Class CharacterBuf is the abstract base class for a buffer of character items sent or received using the Message Protocol (MP).
CharacterBuf(int) - Constructor for class edu.rit.mp.CharacterBuf: Construct a new character buffer.
CharacterItemBuf - Class in edu.rit.mp.buf: Class CharacterItemBuf provides a buffer for a single character item sent or received using the Message Protocol (MP).
CharacterItemBuf() - Constructor for class edu.rit.mp.buf.CharacterItemBuf: Construct a new character item buffer.
CharacterItemBuf(char) - Constructor for class edu.rit.mp.buf.CharacterItemBuf: Construct a new character item buffer with the given initial value.
CharacterMatrixBuf - Class in edu.rit.mp.buf: Class CharacterMatrixBuf provides a buffer for a matrix of character items sent or received using the Message Protocol (MP).
CharacterMatrixBuf(char[][], Range, Range) - Constructor for class edu.rit.mp.buf.CharacterMatrixBuf: Construct a new character matrix buffer.
CharacterMatrixBuf_1 - Class in edu.rit.mp.buf: Class CharacterMatrixBuf_1 provides a buffer for a matrix of character items sent or received using the Message Protocol (MP).
CharacterMatrixBuf_1(char[][], Range, Range) - Constructor for class edu.rit.mp.buf.CharacterMatrixBuf_1: Construct a new character matrix buffer.
CharacterOp - Class in edu.rit.pj.reduction: Class CharacterOp is the abstract base class for a binary operation on character values, used to do reduction in a parallel program.
CharacterOp() - Constructor for class edu.rit.pj.reduction.CharacterOp: Construct a new character binary operation.
charge - Variable in class ffx.potential.parameters.ChargeType: Partial atomic charge in units of electrons.
charge - Variable in class ffx.potential.parameters.MultipoleType: Partial atomic charge (e).
charge - Variable in class ffx.ui.commands.SimulationDefinition
CHARGE - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldType
chargeIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to charge I at site K.
chargeIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to charge I at site K.
chargeIPotentialAtK(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to charge I at site K.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the field components due to multipole K at site I.
chargeKPotentialAtI(PolarizableMultipole, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the field components due to multipole K at site I.
ChargeType - Class in ffx.potential.parameters: The ChargeType class defines a partial atomic charge type.
ChargeType(int, double) - Constructor for class ffx.potential.parameters.ChargeType: ChargeType constructor.
CHARMM_22 - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
CHARMM_22_CMAP - Enum constant in enum class ffx.potential.parameters.ForceField.ForceFieldName
CHEAP - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
check(double, double) - Method in enum class ffx.crystal.ASULimit: Check the given point is within the asymmetric unit limit.
check(double, double) - Static method in enum class ffx.crystal.LatticeSystem: If the two passed values are the same, within the tolerance, return true.
check(int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for eliminated rotamer; true if eliminated.
check(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for eliminated rotamer pair; true if eliminated.
checkAtomicNumberAndMass(int, double) - Static method in class ffx.potential.parameters.AtomType: Check if the supplied atomic mass is within 0.1 AMU of the IUPAC value for the given atomic number.
checkAtomicNumberAndMass(int, double, double) - Static method in class ffx.potential.parameters.AtomType: Check if the supplied atomic mass is within the supplied tolerance (in AMU) of the IUPAC value for the given atomic number.
CHECKBOX - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
CHECKBOXES - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
checkDistMatrix(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Gets the raw distance between two rotamers using lazy loading of the distance matrix.
checkHydrogenAtomNames(Residue, PDBFilter.PDBFileStandard) - Static method in class ffx.potential.bonded.NamingUtils: Ensures proper naming of hydrogen according to latest PDB format.
checkList(int[][][], int) - Method in class ffx.potential.nonbonded.RowLoop: checkList.
checkList(int[][], int) - Method in class ffx.potential.nonbonded.SliceLoop: checkList.
checkMultipoleChirality(MultipoleType.MultipoleFrameDefinition, double[], double[][]) - Static method in class ffx.potential.parameters.MultipoleType: checkMultipoleChirality.
checkNeighboringPair(int, int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Checks if residue i is considered to be interacting with residue j, and thus has non-null elements in the pair energies matrix.
checkNeighboringTriple(int, int, int) - Method in class ffx.algorithms.optimize.RotamerOptimization: Checks if residue i is considered to be interacting with residue j, that residue k is interacting with either i or j, and thus i-j-k has non-null elements in the triple energy matrix.
checkNPT(MolecularAssembly, CrystalPotential) - Method in class ffx.algorithms.cli.BarostatOptions: If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.
checkPairDistThreshold(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks if the i,ri,j,rj pair exceeds the pair distance thresholds.
checkProperties(CompositeConfiguration) - Static method in class ffx.crystal.Crystal: checkProperties
checkProperties(CompositeConfiguration) - Static method in class ffx.crystal.Resolution: checkProperties
checkPrunedPairs(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for pruned rotamer pair; true if eliminated.
checkPrunedSingles(int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Check for pruned rotamer; true if eliminated.
checkPucker(double, boolean) - Static method in enum class ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker: Returns the sugar pucker associated with a delta torsion.
checkQuadDistThreshold(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks if the i,ri,j,rj,k,rk,l,rl quad exceeds the 3-body threshold, or if any component exceeds the pair/triple distance thresholds.
checkRestrictions(int, int, int) - Method in enum class ffx.crystal.LaueSystem: Check the given HKL is valid given the Laue system.
checkThole(double) - Method in class ffx.numerics.multipole.TholeTensorGlobal: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkThole(double) - Method in class ffx.numerics.multipole.TholeTensorQI: Check if the Thole damping is exponential is greater than zero (or the interaction can be neglected).
checkToJ(int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Checks to see if any eliminations with j,rj have occurred; assumes i,ri self has already been checked.
checkToK(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Checks to see if any eliminations with k,rk have occurred; assumes i,ri,j,rj 2-Body has already been checked.
checkToL(int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Checks to see if any eliminations with l,rl have occurred; assumes i,ri,j,rj,k,rk 3-Body has already been checked.
checkTriDistThreshold(int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.DistanceMatrix: Checks if the i,ri,j,rj,k,rk triple exceeds the 3-body threshold, or if any component exceeds the pair distance threshold.
checkValidMove(int, int, int[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Checks the pair elimination array to see if this permutation has been eliminated.
chi1 - Variable in class ffx.potential.bonded.Rotamer: Torsions chi 1-4 are used for amino acids and nucleic acids.
chi2 - Variable in class ffx.potential.bonded.Rotamer
chi3 - Variable in class ffx.potential.bonded.Rotamer
chi4 - Variable in class ffx.potential.bonded.Rotamer
chi5 - Variable in class ffx.potential.bonded.Rotamer: Torsions chi 5-7 are only currently used for nucleic acids.
chunk(int, int) - Method in class edu.rit.util.Range: Slice off a chunk of this range and return the chunk.
chunk(long, long) - Method in class edu.rit.util.LongRange: Slice off a chunk of this range and return the chunk.
CIF - Enum constant in enum class ffx.potential.Utilities.FileType
CIFFilter - Class in ffx.potential.parsers: The CIFFilter class parses CIF coordinate (*.CIF) files.
CIFFilter - Class in ffx.xray.parsers: CIF file reader
CIFFilter() - Constructor for class ffx.xray.parsers.CIFFilter: Constructor.
CIFFilter(File, MolecularAssembly, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter: Constructor for CIFFilter on a single file and a single assembly.
CIFFilter(File, List<MolecularAssembly>, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter: Constructor for CIFFilter on a single file and multiple assemblies.
CIFFilter(List<File>, MolecularAssembly, ForceField, CompositeConfiguration, boolean) - Constructor for class ffx.potential.parsers.CIFFilter: Constructor for CIFFilter on a multiple files and a single assembly.
cifForID(String) - Static method in class ffx.utilities.StringUtils: cifForID
Cl - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
CL - Enum constant in enum class ffx.potential.bonded.NamingUtils.HetAtoms
classpath - Variable in class edu.rit.pj.cluster.BackendInfo: The Java class path for the Parallel Java Library on the backend.
clazz() - Element in annotation interface ffx.utilities.FFXKeyword: The Class used to represent the value of this FFXKeyword.
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
cn(int, double, double) - Static method in class ffx.numerics.multipole.GKSource: Compute the Kirkwood dielectric function for a multipole of order n.
CNSFilter - Class in ffx.xray.parsers: CNSFilter class.
CNSFilter() - Constructor for class ffx.xray.parsers.CNSFilter: Constructor for CNSFilter.
CNSMapWriter - Class in ffx.xray.parsers: The CNSMapWriter class writes an output map that covers the unit cell (not the asymmetric unit).
CNSMapWriter(int, int, int, Crystal, String) - Constructor for class ffx.xray.parsers.CNSMapWriter: Constructor for CNSMapWriter.
Co - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
codePotentialMultipoleI(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor: Collect the potential its partial derivatives at K due to multipole moments at the origin.
codePotentialMultipoleK(PolarizableMultipole, double[], int, int, int, StringBuilder) - Method in class ffx.numerics.multipole.MultipoleTensor: Collect the potential its partial derivatives at the origin due to multipole moments at site K.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: This function is a driver to collect elements of the Cartesian multipole tensor.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.CoulombTensorQI: This function is a driver to collect elements of the Cartesian multipole tensor.
codeTensorRecursion(double[], double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: This function is a driver to collect elements of the Cartesian multipole tensor.
COH - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
collectAtoms(Atom, ArrayList<Atom>) - Static method in class ffx.potential.parsers.CIFFilter: Finds all atoms that are bonded to one another.
collectResidues(MolecularAssembly) - Method in class ffx.algorithms.cli.ManyBodyOptions: Collect residues based on residue selection flags.
colLength(boolean[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given Boolean matrix.
colLength(byte[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given byte matrix.
colLength(char[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given character matrix.
colLength(double[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given double matrix.
colLength(float[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given float matrix.
colLength(int[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given integer matrix.
colLength(long[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given long matrix.
colLength(short[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given short matrix.
colLength(T[][], int) - Static method in class edu.rit.util.Arrays: Determine the number of columns in the given row of the given object matrix.
color - Variable in class ffx.utilities.FFXCommand: Unix shells are able to evaluate PicoCLI ANSI color codes, but right now the FFX GUI Shell does not.
color - Variable in class ffx.utilities.FFXScript: Unix shells are able to evaluate PicoCLI ANSI color codes, but right now the FFX GUI Shell does not.
colorModelHash - Static variable in class ffx.potential.bonded.RendererCache: Constant colorModelHash
colorWait(String) - Method in class ffx.ui.GraphicsCanvas: colorWait
cols() - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Returns the number of columns in this matrix reduction variable.
cols() - Method in class edu.rit.pj.reduction.SharedLongMatrix: Returns the number of columns in this matrix reduction variable.
colSliceBuffer(boolean[][], Range) - Static method in class edu.rit.mp.BooleanBuf: Create a buffer for one column slice of the given Boolean matrix.
colSliceBuffer(byte[][], Range) - Static method in class edu.rit.mp.ByteBuf: Create a buffer for one column slice of the given byte matrix.
colSliceBuffer(char[][], Range) - Static method in class edu.rit.mp.CharacterBuf: Create a buffer for one column slice of the given character matrix.
colSliceBuffer(double[][], Range) - Static method in class edu.rit.mp.DoubleBuf: Create a buffer for one column slice of the given double matrix.
colSliceBuffer(float[][], Range) - Static method in class edu.rit.mp.FloatBuf: Create a buffer for one column slice of the given float matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.IntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(int[][], Range) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create a buffer for one column slice of the given integer matrix.
colSliceBuffer(long[][], Range) - Static method in class edu.rit.mp.LongBuf: Create a buffer for one column slice of the given long matrix.
colSliceBuffer(short[][], Range) - Static method in class edu.rit.mp.ShortBuf: Create a buffer for one column slice of the given short matrix.
colSliceBuffer(T[][], Range) - Static method in class edu.rit.mp.ObjectBuf: Create a buffer for one column slice of the given object matrix.
colSliceBuffers(boolean[][], Range[]) - Static method in class edu.rit.mp.BooleanBuf: Create an array of buffers for multiple column slices of the given Boolean matrix.
colSliceBuffers(byte[][], Range[]) - Static method in class edu.rit.mp.ByteBuf: Create an array of buffers for multiple column slices of the given byte matrix.
colSliceBuffers(char[][], Range[]) - Static method in class edu.rit.mp.CharacterBuf: Create an array of buffers for multiple column slices of the given character matrix.
colSliceBuffers(double[][], Range[]) - Static method in class edu.rit.mp.DoubleBuf: Create an array of buffers for multiple column slices of the given double matrix.
colSliceBuffers(float[][], Range[]) - Static method in class edu.rit.mp.FloatBuf: Create an array of buffers for multiple column slices of the given float matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.IntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(int[][], Range[]) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an array of buffers for multiple column slices of the given integer matrix.
colSliceBuffers(long[][], Range[]) - Static method in class edu.rit.mp.LongBuf: Create an array of buffers for multiple column slices of the given long matrix.
colSliceBuffers(short[][], Range[]) - Static method in class edu.rit.mp.ShortBuf: Create an array of buffers for multiple column slices of the given short matrix.
colSliceBuffers(T[][], Range[]) - Static method in class edu.rit.mp.ObjectBuf: Create an array of buffers for multiple column slices of the given object matrix.
combineSymOps(SymOp, SymOp) - Static method in class ffx.crystal.SymOp: Return the combined SymOp that is equivalent to first applying symOp1 and then SymOp2.
COMBOBOX - Enum constant in enum class ffx.ui.KeywordComponent.SwingRepresentation
comesBefore(byte[], int, int) - Method in class edu.rit.util.Sorting.Byte: Compare two elements in the given array.
comesBefore(char[], int, int) - Method in class edu.rit.util.Sorting.Character: Compare two elements in the given array.
comesBefore(double[], int, int) - Method in class edu.rit.util.Sorting.Double: Compare two elements in the given array.
comesBefore(float[], int, int) - Method in class edu.rit.util.Sorting.Float: Compare two elements in the given array.
comesBefore(int[], int, int) - Method in class edu.rit.util.Sorting.Integer: Compare two elements in the given array.
comesBefore(long[], int, int) - Method in class edu.rit.util.Sorting.Long: Compare two elements in the given array.
comesBefore(short[], int, int) - Method in class edu.rit.util.Sorting.Short: Compare two elements in the given array.
comesBefore(T[], int, int) - Method in class edu.rit.util.Sorting.Object: Compare two elements in the given array.
Comm - Class in edu.rit.pj: Class Comm provides a communicator for a PJ cluster parallel program.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Method in class edu.rit.pj.cluster.JobBackend: Commence the job.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Static method in class edu.rit.pj.cluster.JobBackendMessage: Construct a new "commence job" message.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Method in class edu.rit.pj.cluster.JobBackendProxy: Commence the job.
commenceJob(JobFrontendRef, InetSocketAddress[], InetSocketAddress[], InetSocketAddress[], Properties, String, String[]) - Method in interface edu.rit.pj.cluster.JobBackendRef: Commence the job.
comment - Variable in class edu.rit.pj.cluster.JobInfo: Comment for each process in the job in rank order.
CommPattern - Class in edu.rit.pj.cluster: Class CommPattern provides static methods for calculating communication patterns for collective communication operations.
CommRequest - Class in edu.rit.pj: Class CommRequest provides an object for doing a non-blocking message passing operation in a PJ cluster parallel program.
CommRequest() - Constructor for class edu.rit.pj.CommRequest: Construct a new CommRequest object.
CommStatus - Class in edu.rit.pj: Class CommStatus provides the result of receiving a message from a communicator (class Comm).
compare(byte, byte) - Method in class edu.rit.util.Searching.Byte: Compare two elements according to the desired ordering criterion.
compare(char, char) - Method in class edu.rit.util.Searching.Character: Compare two elements according to the desired ordering criterion.
compare(double, double) - Method in class edu.rit.util.Searching.Double: Compare two elements according to the desired ordering criterion.
compare(float, float) - Method in class edu.rit.util.Searching.Float: Compare two elements according to the desired ordering criterion.
compare(int, int) - Method in class edu.rit.util.Searching.Integer: Compare two elements according to the desired ordering criterion.
compare(long, long) - Method in class edu.rit.util.Searching.Long: Compare two elements according to the desired ordering criterion.
compare(short, short) - Method in class edu.rit.util.Searching.Short: Compare two elements according to the desired ordering criterion.
compare(Atom, Atom, Atom, Atom) - Method in class ffx.potential.bonded.AngleTorsion: compare
compare(Atom, Atom, Atom, Atom) - Method in class ffx.potential.bonded.StretchTorsion: compare
compare(Atom, Atom, Atom, Atom) - Method in class ffx.potential.bonded.Torsion: compare
compare(BondedTerm, BondedTerm) - Method in class ffx.potential.bonded.BondedTerm.BondedComparator: Sort using position in the naturalOrder list; fallback to alphabetical.
compare(String, String) - Method in class ffx.potential.parameters.AngleTorsionType
compare(String, String) - Method in class ffx.potential.parameters.AngleType
compare(String, String) - Method in class ffx.potential.parameters.AtomType
compare(String, String) - Method in class ffx.potential.parameters.BioType
compare(String, String) - Method in class ffx.potential.parameters.BondType
compare(String, String) - Method in class ffx.potential.parameters.ChargeType
compare(String, String) - Method in class ffx.potential.parameters.ImproperTorsionType
compare(String, String) - Method in class ffx.potential.parameters.MultipoleType
compare(String, String) - Method in class ffx.potential.parameters.OutOfPlaneBendType
compare(String, String) - Method in class ffx.potential.parameters.PiOrbitalTorsionType
compare(String, String) - Method in class ffx.potential.parameters.PolarizeType
compare(String, String) - Method in class ffx.potential.parameters.RelativeSolvationType
compare(String, String) - Method in class ffx.potential.parameters.SoluteType
compare(String, String) - Method in class ffx.potential.parameters.StretchBendType
compare(String, String) - Method in class ffx.potential.parameters.StretchTorsionType
compare(String, String) - Method in class ffx.potential.parameters.TorsionTorsionType
compare(String, String) - Method in class ffx.potential.parameters.TorsionType
compare(String, String) - Method in class ffx.potential.parameters.UreyBradleyType
compare(String, String) - Method in class ffx.potential.parameters.VDWPairType
compare(String, String) - Method in class ffx.potential.parameters.VDWType
compare(T, T) - Method in class edu.rit.util.Searching.Object: Compare two elements according to the desired ordering criterion.
compareAndSet(boolean, boolean) - Method in class edu.rit.pj.reduction.SharedBoolean: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(byte, byte) - Method in class edu.rit.pj.reduction.SharedByte: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(char, char) - Method in class edu.rit.pj.reduction.SharedCharacter: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(double, double) - Method in class edu.rit.pj.reduction.SharedDouble: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(float, float) - Method in class edu.rit.pj.reduction.SharedFloat: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(int, boolean, boolean) - Method in class edu.rit.pj.reduction.SharedBooleanArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, byte, byte) - Method in class edu.rit.pj.reduction.SharedByteArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, char, char) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, double, double) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, float, float) - Method in class edu.rit.pj.reduction.SharedFloatArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, int) - Method in class edu.rit.pj.reduction.SharedInteger: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, int, int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Atomically set this matrix reduction variable at the given row and column to the given updated value if the current value equals the expected value.
compareAndSet(int, int, long, long) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Atomically set this matrix reduction variable at the given row and column to the given updated value if the current value equals the expected value.
compareAndSet(int, long, long) - Method in class edu.rit.pj.reduction.SharedLongArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, short, short) - Method in class edu.rit.pj.reduction.SharedShortArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(int, T, T) - Method in class edu.rit.pj.reduction.SharedObjectArray: Atomically set this array reduction variable at the given index to the given updated value if the current value equals the expected value.
compareAndSet(long, long) - Method in class edu.rit.pj.reduction.SharedLong: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(short, short) - Method in class edu.rit.pj.reduction.SharedShort: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareAndSet(T, T) - Method in class edu.rit.pj.reduction.SharedObject: Atomically set this reduction variable to the given updated value if the current value equals the expected value.
compareTo(Atom) - Method in class ffx.potential.bonded.Atom
compareTo(BondedTerm) - Method in class ffx.potential.bonded.Angle
compareTo(BondedTerm) - Method in class ffx.potential.bonded.Bond
compareTo(BondedTerm) - Method in class ffx.potential.bonded.BondedTerm
compareTo(BondedTerm) - Method in class ffx.potential.bonded.ImproperTorsion
compareTo(BondedTerm) - Method in class ffx.potential.bonded.OutOfPlaneBend
compareTo(BondedTerm) - Method in class ffx.potential.bonded.StretchBend
compareTo(BondedTerm) - Method in class ffx.potential.bonded.UreyBradley
compareTo(Residue) - Method in class ffx.potential.bonded.Residue
compareTo(ResidueState) - Method in class ffx.potential.bonded.ResidueState
compareTo(DoubleIndexPair) - Method in record class ffx.utilities.DoubleIndexPair
compareTo(ObjectPair<T, S>) - Method in record class ffx.utilities.ObjectPair
compareTo(Object) - Method in record class ffx.utilities.IndexIndexPair
comparisons(int, double, double, double, int, int, String, String, boolean, boolean, boolean, int, boolean, int, boolean, boolean, boolean, boolean, boolean, int, double, boolean, String) - Method in class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Compare the crystals within the SystemFilters that were inputted into the constructor of this class.
Complex - Class in ffx.numerics.fft: Compute the FFT of complex, double precision data of arbitrary length n.
Complex(int) - Constructor for class ffx.numerics.fft.Complex: Construct a Complex instance for data of length n.
Complex3D - Class in ffx.numerics.fft: Compute the 3D FFT of complex, double precision input of arbitrary dimensions via 1D Mixed Radix FFTs.
Complex3D(int, int, int) - Constructor for class ffx.numerics.fft.Complex3D: Initialize the 3D FFT for complex 3D matrix.
Complex3DParallel - Class in ffx.numerics.fft: Compute the 3D FFT of complex, double precision input of arbitrary dimensions via 1D Mixed Radix FFTs in parallel.
Complex3DParallel(int, int, int, ParallelTeam) - Constructor for class ffx.numerics.fft.Complex3DParallel: Initialize the 3D FFT for complex 3D matrix.
Complex3DParallel(int, int, int, ParallelTeam, IntegerSchedule) - Constructor for class ffx.numerics.fft.Complex3DParallel: Initialize the 3D FFT for complex 3D matrix.
ComplexNumber - Class in ffx.numerics.math: ComplexNumber class.
ComplexNumber() - Constructor for class ffx.numerics.math.ComplexNumber: Constructor for ComplexNumber.
ComplexNumber(double, double) - Constructor for class ffx.numerics.math.ComplexNumber: Constructor for ComplexNumber.
CompositeCurve - Class in ffx.numerics.integrate: A CompositeCurve represents points along a sum of functions which also extend FunctionDataCurve.
CompositeCurve(List<FunctionDataCurve>, List<Double>) - Constructor for class ffx.numerics.integrate.CompositeCurve: Constructs a CompositeCurve that aggregates multiple FunctionDataCurves with variable weights to each component FunctionDataCurve.
CompositeSwitch - Class in ffx.numerics.switching: The CompositeSwitch uses a primary switch in the middle, and then two secondary switches at the ends of the path to smoothly switch to the primary switch.
CompositeSwitch() - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a switch that uses MultiplicativeSwitches at the ends (0-0.1, 0.9-1.0) to smoothly interpolate a linear switch between 0 and 1 with smooth 2'nd and 3'rd derivatives.
CompositeSwitch(UnivariateSwitchingFunction) - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a switch that uses MultiplicativeSwitches at the ends (0-0.1, 0.9-1.0) to smoothly interpolate a provided switch between 0 and 1 with smooth 2'nd and 3'rd derivatives.
CompositeSwitch(UnivariateSwitchingFunction, UnivariateSwitchingFunction, UnivariateSwitchingFunction, double, double) - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a composite switch in .
CompositeSwitch(UnivariateSwitchingFunction, UnivariateSwitchingFunction, UnivariateSwitchingFunction, double, double, double, double) - Constructor for class ffx.numerics.switching.CompositeSwitch: Builds a composite switch in .
compute2BodyEnergy(Residue[], int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a pair energy, defined as energy with all side-chains but two turned off, minus the sum of backbone and component self energies.
compute3BodyEnergy(Residue[], int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a 3-body energy, defined as the energy with all sidechains but three turned off, minus the sum of backbone and component self/2-Body energies.
compute4BodyEnergy(Residue[], int, int, int, int, int, int, int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a 4-body energy, defined as the energy with all sidechains but four turned off, minus the sum of backbone and component self/2-Body/3-body energies.
computeAtomicDensity() - Method in class ffx.xray.DiffractionData: Parallelized call to compute atomic density on a grid, followed by FFT to compute structure factors.
computeAtomicGradients(double[][], int[], int, RefinementMinimize.RefinementMode) - Method in class ffx.xray.CrystalReciprocalSpace: compute inverse FFT to determine atomic gradients
computeBackboneEnergy(Residue[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Computes the environment/backbone energy, defined as energy with all sidechains under consideration turned off in their 0th rotamer.
computeBornRadii() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: computeBornRadii
computeBSplines() - Method in class ffx.potential.nonbonded.ReciprocalSpace: computeBSplines
computeDft(float[], float[], float[], float[]) - Static method in class ffx.numerics.fft.TornadoDFT
computeElasticityTensor(boolean) - Method in class ffx.algorithms.optimize.CrystalMinimize: computeStressTensor.
computeEnergy(Residue[], int[], boolean) - Method in class ffx.algorithms.optimize.RotamerOptimization: Uses existing backbone, self, 2-Body, and 3-body energies from rotamerEnergies() to calculate an approximate energy for a rotamer permutation.
computeFractionalCoordinates() - Method in class ffx.potential.MolecularAssembly: Compute fractional coordinates.
computeInducedGKField() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: computeInducedGKField
computeInduceDipoleField() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
computeInducedPhi(double[][], double[][], double[][], double[][]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: computeInducedPhi
computeKineticEnergy() - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: Compute the current temperature and kinetic energy of the system.
computeMoments(Atom[], boolean) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Compute multipole moments for an array of atoms.
computePermanentGKField() - Method in class ffx.potential.nonbonded.GeneralizedKirkwood: computePermanentGKField
computePermanentPhi(double[][], double[][]) - Method in class ffx.potential.nonbonded.ReciprocalSpace: Compute the potential Phi and its derivatives for all atoms.
computeSelfEnergy(Residue[], int, int) - Method in class ffx.algorithms.optimize.manybody.EnergyExpansion: Computes a self energy, defined as energy with all side-chains but one turned off, minus the backbone energy.
computeSolventDensity(double[][]) - Method in class ffx.xray.CrystalReciprocalSpace: parallelized computation of bulk solvent structure factors
computeVolumeAndSA(double[][]) - Method in class ffx.potential.nonbonded.implicit.GaussVol: Compute molecular volume and surface area.
COMRestraint - Class in ffx.potential.nonbonded: Restrain molecules to their center of mass.
COMRestraint(MolecularAssembly) - Constructor for class ffx.potential.nonbonded.COMRestraint: This COMRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
CONDENSED - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
CONDENSED_NO_LIGAND - Enum constant in enum class ffx.potential.nonbonded.pme.LambdaMode
conditions - Variable in class ffx.ui.behaviors.PickMouseBehavior
coneFactory(Appearance, int) - Static method in class ffx.potential.bonded.RendererCache: coneFactory
confidenceInterval() - Method in class ffx.numerics.math.BootStrapStatistics: Computes a 95% confidence interval based on a Student's T-distribution.
confidenceInterval() - Method in class ffx.numerics.math.SummaryStatistics: Computes a 95% confidence interval based on a Student's T-distribution.
confidenceInterval(double) - Method in class ffx.numerics.math.BootStrapStatistics: Computes a confidence interval based on a Student's T-distribution.
confidenceInterval(double) - Method in class ffx.numerics.math.SummaryStatistics: Computes a confidence interval based on a Student's T-distribution.
Configuration - Class in edu.rit.pj.cluster: Class Configuration provides configuration information about a parallel computer running Parallel Java.
Configuration(String) - Constructor for class edu.rit.pj.cluster.Configuration: Construct a new configuration.
ConformationScan - Class in ffx.algorithms.optimize: This class is for a configuration optimization of two small systems.
ConformationScan(MolecularAssembly, Molecule[], Molecule[], double, int, boolean, boolean, boolean) - Constructor for class ffx.algorithms.optimize.ConformationScan
conjugate() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the conjugate of this.
conjugateIP() - Method in class ffx.numerics.math.ComplexNumber: conjugateIP
connect() - Method in class ffx.ui.commands.FFXClient: Attempts to connect to a Tinker FServer.
connect(InetSocketAddress) - Method in class edu.rit.mp.ChannelGroup: Create a new channel connected to the given far end host and port.
connectivity - Variable in class ffx.ui.commands.SimulationDefinition
ConnectListener - Interface in edu.rit.mp: Interface ConnectListener specifies the interface for an object that is notified whenever a Channel is connected in a ChannelGroup.
ConnollyRegion - Class in ffx.potential.nonbonded.implicit: ConnollyRegion uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the analytical molecular surface area and volume of a collection of spherical atoms; thus it implements Fred Richards' molecular surface definition as a set of analytically defined spherical and toroidal polygons.
ConnollyRegion(Atom[], double[], int) - Constructor for class ffx.potential.nonbonded.implicit.ConnollyRegion: ConnollyRegion constructor.
consecutiveInts(int[]) - Static method in class ffx.utilities.StringUtils: Finds consecutive subranges in an array of ints, and returns their mins and maxes.
CONSENSUS - Enum constant in enum class ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE
constantOutsideBounds() - Method in class ffx.numerics.switching.BellCurveSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.CompositeSwitch
constantOutsideBounds() - Method in class ffx.numerics.switching.ConstantSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.LinearDerivativeSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.MultiplicativeSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.PowerSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in class ffx.numerics.switching.SquaredTrigSwitch: Remains 0 below the lower bound, and 1 above the upper bound (i.e.
constantOutsideBounds() - Method in interface ffx.numerics.switching.UnivariateSwitchingFunction: Remains 0 below the lower bound, and 1 above the upper bound (i.e.
ConstantPhMolecularDynamics - Enum constant in enum class ffx.utilities.KeywordGroup: 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.
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.
contractMultipoleI(PolarizableMultipole, double[], int, int, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Contract multipole moments with their respective electrostatic potential derivatives.
controlButton - Variable in class ffx.ui.behaviors.PickMouseBehavior
controlStep() - Method in class ffx.algorithms.mc.RosenbluthCBMC: controlStep.
ConvexHullOps - Class in ffx.potential.utils: This ConvexHullOps class uses the QuickHull3D package by John E.
ConvexHullOps() - Constructor for class ffx.potential.utils.ConvexHullOps
convolution(double[]) - Method in class ffx.numerics.fft.Complex3D: Perform a convolution.
convolution(double[]) - Method in class ffx.numerics.fft.Complex3DParallel: Compute the 3D FFT, perform a multiplication in reciprocal space, and the inverse 3D FFT in parallel.
convolution(double[]) - Method in class ffx.numerics.fft.Real3D: convolution
convolution(double[]) - Method in class ffx.numerics.fft.Real3DParallel: Compute a convolution in parallel.
CoordinateFileFilter - Class in ffx.potential.parsers: The CoordinateFileFilter class globally determines if a file is a valid coordinate file (PDB, XYZ, INT, or ARC formats).
CoordinateFileFilter() - Constructor for class ffx.potential.parsers.CoordinateFileFilter: Public Constructor.
coordinates - Variable in class ffx.numerics.multipole.MultipoleTensor: The coordinate system in use (global or QI).
coordinates - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Dimensions of [nsymm][xyz][nAtoms].
coordinates - Variable in class ffx.potential.nonbonded.RowRegion
coordinates - Variable in class ffx.potential.nonbonded.SliceRegion
coordinates - Variable in class ffx.potential.nonbonded.SpatialDensityRegion
coordinates - Variable in class ffx.ui.commands.SimulationDefinition
coordinates - Variable in class ffx.ui.commands.SimulationUpdate
COORDINATES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine coordinates only
COORDINATES_AND_BFACTORS - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine coordinates and B factors (if anisotropic, refined as such)
COORDINATES_AND_BFACTORS_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine all
COORDINATES_AND_OCCUPANCIES - Enum constant in enum class ffx.xray.RefinementMinimize.RefinementMode: refine coordinates and occupancies
coordinatesToHilbertIndex(int, int, long[]) - Static method in class ffx.numerics.math.HilbertCurveTransforms
CoordRestraint - Class in ffx.potential.nonbonded: Restrain atoms to their initial coordinates.
CoordRestraint(Atom[], ForceField) - Constructor for class ffx.potential.nonbonded.CoordRestraint: This CoordRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
CoordRestraint(Atom[], ForceField, boolean) - Constructor for class ffx.potential.nonbonded.CoordRestraint: This CoordRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
CoordRestraint(Atom[], ForceField, boolean, double) - Constructor for class ffx.potential.nonbonded.CoordRestraint: This CoordRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
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.Zwanzig: Return a copy of this Estimator.
copyESVHistogramTo(int[][]) - Method in class ffx.potential.extended.ExtendedSystem: Changes this ESV's histogram to equal the one passed
copyInputStreamToTmpFile(InputStream, String, String, String) - Static method in class ffx.utilities.FileUtils: Returns the file name of a temporary copy of input content.
copyResidue(Residue, Residue) - Static method in class ffx.potential.bonded.AminoAcidUtils: copyResidue.
copyState(AssemblyState) - Static method in class ffx.potential.AssemblyState: Copies an AssemblyState.
cos - Variable in class ffx.potential.parameters.ImproperTorsionType: Value of cos(toRadians(phase)).
cos() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the complex cosine of this.
cosDiameter - Variable in class ffx.potential.parameters.SoluteType: Solute atomic diameter for ddCOSMO.
cosine - Variable in class ffx.potential.parameters.TorsionType: Cosine of the phase angle.
CosineWave - Class in ffx.numerics.integrate: A CosineWave describes points along a sine wave of f(x) = a*sin(jx).
CosineWave(double[], boolean, double, double) - Constructor for class ffx.numerics.integrate.CosineWave: Constructs f(x) = a*cos(nx).
CosineWave(double[], double, double) - Constructor for class ffx.numerics.integrate.CosineWave: Constructs f(x) = a*cos(nx).
COULOMB - Enum constant in enum class ffx.numerics.multipole.MultipoleTensor.OPERATOR
coulombSource - Variable in class ffx.numerics.multipole.MultipoleTensor: These are the "source" terms for the recursion for the Coulomb operator (1/R).
CoulombTensorGlobal - Class in ffx.numerics.multipole: The CoulombTensorGlobal class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in the global frame.
CoulombTensorGlobal(int) - Constructor for class ffx.numerics.multipole.CoulombTensorGlobal: Constructor for CoulombTensorGlobal.
CoulombTensorQI - Class in ffx.numerics.multipole: The CoulombTensorQI class computes derivatives of 1/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
CoulombTensorQI(int) - Constructor for class ffx.numerics.multipole.CoulombTensorQI
count - Variable in class edu.rit.pj.cluster.JobInfo: The number of processes that have been assigned to the job so far.
count - Variable in class ffx.numerics.math.BootStrapStatistics
count - Variable in class ffx.numerics.math.SummaryStatistics
countNumModels() - Method in class ffx.potential.parsers.PDBFilter
countNumModels() - Method in class ffx.potential.parsers.SystemFilter
countNumModels() - Method in class ffx.potential.parsers.XPHFilter
countNumModels() - Method in class ffx.potential.parsers.XYZFilter
counts - Variable in class ffx.algorithms.thermodynamics.HistogramData: The number of hills added to the recursion kernel.
CPK - Enum constant in enum class ffx.potential.bonded.RendererCache.ColorModel
cpus - Variable in class edu.rit.pj.cluster.JobInfo: Number of CPUs assigned to each process in the job in rank order.
Cr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
createAnnealer(DynamicsOptions, MolecularAssembly, Potential, AlgorithmListener) - Method in class ffx.algorithms.cli.AnnealOptions: Creates a SimulatedAnnealing object.
createAnnealer(DynamicsOptions, MolecularAssembly, Potential, AlgorithmListener, File) - Method in class ffx.algorithms.cli.AnnealOptions: Creates a SimulatedAnnealing object.
createBarostat(MolecularAssembly, CrystalPotential) - Method in class ffx.algorithms.cli.BarostatOptions: Creates a Barostat around a CrystalPotential.
createBox() - Method in class ffx.potential.MolecularAssembly: createBox
createComm(boolean) - Method in class edu.rit.pj.Comm: Create a new communicator.
createComm(boolean, int) - Method in class edu.rit.pj.Comm: Create a new communicator.
createContext(String, double, double, boolean) - Method in class ffx.potential.ForceFieldEnergyOpenMM: Create an OpenMM Context.
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.
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
createState(boolean, boolean, boolean, boolean) - Method in class ffx.potential.ForceFieldEnergyOpenMM: Create an immutable OpenMM State.
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.
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 807,190 CSD structures for which the space group is fully defined.
CTRL_ALL - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
Cu - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
cubic - Variable in class ffx.potential.parameters.AngleType: Cubic coefficient in angle bending potential.
cubic - Variable in class ffx.potential.parameters.BondType: Cubic coefficient in bond stretch potential.
cubic - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Cubic coefficient in out-of-plane angle bending potential.
cubic - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
cubic - Variable in class ffx.potential.parameters.UreyBradleyType: Cubic coefficient in bond stretch potential.
CUBIC - Enum constant in enum class ffx.crystal.CrystalSystem
CUBIC_LATTICE - Enum constant in enum class ffx.crystal.LatticeSystem
CUBIC_MEAN - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.RADIUS_RULE
currentEnergy() - Method in class ffx.algorithms.mc.BoltzmannMC: Must return the current energy of the system.
currentEnergy() - Method in class ffx.algorithms.mc.MolecularMC: Must return the current energy of the system.
currentEnergy() - Method in class ffx.algorithms.optimize.manybody.RotamerMatrixMC: If useFullAMOEBAEnergy is set to true, explicitly evaluates energy, else computes energy from the rotamer energy matrices.
currentEnergy() - Method in class ffx.algorithms.thermodynamics.MonteCarloOST: Must return the current energy of the system.
currentEnergy(Residue[]) - Method in class ffx.algorithms.optimize.RotamerOptimization: Calculates the energy at the current state.
currentEnergyWrapper(List<Residue>) - Method in class ffx.algorithms.optimize.RotamerOptimization: Wrapper intended for use with RotamerMatrixMC.
currentFFXPE() - Method in class ffx.algorithms.optimize.RotamerOptimization: Forces the use of a ForceFieldEnergyOpenMM's underlying ForceFieldEnergy.
currGrp - Variable in class ffx.ui.behaviors.PickMouseBehavior
currXform - Variable in class ffx.ui.behaviors.MouseBehavior
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="October 2023"
Db - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
DCY - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
ddgunToNPChange(List<String>) - Method in class ffx.potential.utils.GetProteinFeatures: Use the ddgun output file to get the amino acid changes
ddp - Variable in class ffx.potential.parameters.PolarizeType: Direct polarization damping.
deallocate(boolean[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given Boolean matrix.
deallocate(boolean[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given Boolean matrix.
deallocate(byte[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given byte matrix.
deallocate(byte[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given byte matrix.
deallocate(char[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given character matrix.
deallocate(char[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given character matrix.
deallocate(double[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given double matrix.
deallocate(double[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given double matrix.
deallocate(float[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given float matrix.
deallocate(float[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given float matrix.
deallocate(int[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given integer matrix.
deallocate(int[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given integer matrix.
deallocate(long[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given long matrix.
deallocate(long[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given long matrix.
deallocate(short[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given short matrix.
deallocate(short[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given short matrix.
deallocate(T[]) - Static method in class edu.rit.util.Arrays: Deallocate all elements in the given object array.
deallocate(T[][]) - Static method in class edu.rit.util.Arrays: Deallocate the elements in the given object matrix.
deallocate(T[][], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row index range in the given object matrix.
deallocate(T[][], Range, Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given row and column index ranges in the given object matrix.
deallocate(T[], Range) - Static method in class edu.rit.util.Arrays: Deallocate the elements within the given index range in the given object array.
decode(int, String) - Static method in class ffx.utilities.Hybrid36: Hybrid-36 decoder: converts string s to integer result.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedByte: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedCharacter: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedDouble: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedFloat: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedInteger: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedLong: Subtract one from this reduction variable and return the new value.
decrementAndGet() - Method in class edu.rit.pj.reduction.SharedShort: Subtract one from this reduction variable and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedByteArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedCharacterArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedDoubleArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedFloatArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedIntegerArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedLongArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int) - Method in class edu.rit.pj.reduction.SharedShortArray: Subtract one from this array reduction variable at the given index and return the new value.
decrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedIntegerMatrix: Subtract one from this matrix reduction variable at the given row and column and return the new value.
decrementAndGet(int, int) - Method in class edu.rit.pj.reduction.SharedLongMatrix: Subtract one from this matrix reduction variable at the given row and column and return the new value.
dEdLSign - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dEdLZeroAtEnds() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in interface ffx.potential.bonded.LambdaInterface: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.DualTopologyEnergy: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.ForceFieldEnergy: Returns true if dUdL is guaranteed to be zero at 0 and 1.
dEdLZeroAtEnds() - Method in class ffx.potential.QuadTopologyEnergy: Returns true if dUdL is guaranteed to be zero at 0 and 1.
Default - Enum constant in enum class ffx.potential.bonded.Atom.Descriptions
DEFAULT_ANGLE_CUBIC - Static variable in class ffx.potential.parameters.AngleType: Default cubic coefficient in angle bending potential.
DEFAULT_ANGLE_PENTIC - Static variable in class ffx.potential.parameters.AngleType: Default pentic coefficient in angle bending potential.
DEFAULT_ANGLE_QUARTIC - Static variable in class ffx.potential.parameters.AngleType: Default quartic coefficient in angle bending potential.
DEFAULT_ANGLE_SEXTIC - Static variable in class ffx.potential.parameters.AngleType: Default quintic coefficient in angle bending potential.
DEFAULT_ANGLE_UNIT - Static variable in class ffx.potential.parameters.AngleType: Default convert angle bending energy to kcal/mole.
DEFAULT_ANGLEMAX - Static variable in class ffx.numerics.optimization.LBFGS: The default maximum angle between search direction and gradient.
DEFAULT_ANGTOR_UNIT - Static variable in class ffx.potential.parameters.AngleTorsionType
DEFAULT_BAROSTAT_INTERVAL - Static variable in class ffx.algorithms.cli.BarostatOptions: Default mean number of MD steps (Poisson distribution) between barostat move proposals.
DEFAULT_BAROSTAT_PRINT_INTERVAL - Static variable in class ffx.algorithms.cli.BarostatOptions: Default number of Barostat moves between print statements.
DEFAULT_BOND_CUBIC - Static variable in class ffx.potential.parameters.BondType: Default cubic coefficient in bond stretch potential.
DEFAULT_BOND_QUARTIC - Static variable in class ffx.potential.parameters.BondType: Default quartic coefficient in bond stretch potential.
DEFAULT_BOND_UNIT - Static variable in class ffx.potential.parameters.BondType
DEFAULT_CAPPA - Static variable in class ffx.numerics.optimization.LBFGS: Controls the accuracy of the line search.
DEFAULT_CAVDISP_SURFACE_TENSION - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default surface tension for apolar models with an explicit dispersion term.
DEFAULT_CCMA_NONZERO_CUTOFF - Static variable in class ffx.potential.constraint.CcmaConstraint
DEFAULT_CG_PRECONDITIONER_CUTOFF - Static variable in class ffx.potential.nonbonded.pme.PCGSolver: A preconditioner cut-off of 3 to 4 Angstroms generally works well.
DEFAULT_CG_PRECONDITIONER_EWALD - Static variable in class ffx.potential.nonbonded.pme.PCGSolver: An Ewald coefficient of 0 indicates use of Coulomb's law with no damping.
DEFAULT_CG_PRECONDITIONER_SCALE - Static variable in class ffx.potential.nonbonded.pme.PCGSolver: The scale factor is applied to the diagonal terms of the preconditioner.
DEFAULT_CONSTRAINT_TOLERANCE - Static variable in class ffx.potential.ForceFieldEnergy: Default tolerance for numerical methods of solving constraints.
DEFAULT_CROSSOVER - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Using a S.P.
DEFAULT_DIELECTRIC_OFFSET - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default dielectric offset
DEFAULT_DISPERSION_OFFSET - Static variable in class ffx.potential.nonbonded.implicit.DispersionRegion: The dispersion integral begins for each atom at: Rmin_ij + DISPERSION_OFFSET
DEFAULT_ELECTRIC - Static variable in class ffx.utilities.Constants: Coulomb constant in units of kcal*Ang/(mol*electron^2)
DEFAULT_EWALD_COEFFICIENT - Static variable in class ffx.potential.nonbonded.pme.EwaldParameters: The default Ewald coefficient.
DEFAULT_EWALD_CUTOFF - Static variable in class ffx.potential.nonbonded.pme.EwaldParameters: Default cutoff values for PME under periodic boundary conditions.
DEFAULT_GAUSSVOL_RADII_OFFSET - Static variable in class ffx.potential.nonbonded.implicit.GaussVol: Default offset applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms.
DEFAULT_GAUSSVOL_RADII_SCALE - Static variable in class ffx.potential.nonbonded.implicit.GaussVol: Default scaling applied to radii for use with Gaussian Volumes to correct for not including hydrogen atoms and general underestimation of molecular volume
DEFAULT_GKC - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default constant for the Generalized Kirkwood cross-term.
DEFAULT_IMPTOR_UNIT - Static variable in class ffx.potential.parameters.ImproperTorsionType
DEFAULT_INTMAX - Static variable in class ffx.numerics.optimization.LBFGS: The default maximum number of interpolations during line search.
DEFAULT_LBFGS_VECTORS - Static variable in class ffx.algorithms.optimize.Minimize: The default number of correction vectors used by the limited-memory L-BFGS optimization routine.
DEFAULT_MAX_ANGLE_MOVE - Static variable in class ffx.algorithms.cli.BarostatOptions: Default width of proposed crystal angle moves (uniformly distributed) in degrees.
DEFAULT_MAX_DENSITY - Static variable in class ffx.algorithms.cli.BarostatOptions: Default maximum density constraint on the barostat that prevents reduction in unit cell (particularly at or near vapor states).
DEFAULT_MAX_VOLUME_MOVE - Static variable in class ffx.algorithms.cli.BarostatOptions: Default size of proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
DEFAULT_MIN_DENSITY - Static variable in class ffx.algorithms.cli.BarostatOptions: Default "tin box" constraint on the barostat that prevents expansion of the unit cell (particularly at or near vapor states).
DEFAULT_OPBEND_CUBIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default cubic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_PENTIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default pentic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_QUARTIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default quartic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_SEXTIC - Static variable in class ffx.potential.parameters.OutOfPlaneBendType: Default quintic coefficient in out-of-plane angle bending potential.
DEFAULT_OPBEND_UNIT - Static variable in class ffx.potential.parameters.OutOfPlaneBendType
DEFAULT_PITORS_UNIT - Static variable in class ffx.potential.parameters.PiOrbitalTorsionType
DEFAULT_RB_LAM_END - Static variable in class ffx.potential.bonded.RestraintBond
DEFAULT_RB_LAM_START - Static variable in class ffx.potential.bonded.RestraintBond
DEFAULT_SLOPEMAX - Static variable in class ffx.numerics.optimization.LBFGS: The default projected gradient above which step size is reduced.
DEFAULT_SNECK - Variable in class ffx.potential.parameters.SoluteType
DEFAULT_SOLUTE_OFFSET - Static variable in class ffx.potential.nonbonded.implicit.DispersionRegion: Each solute atom blocks dispersion interactions with solvent: Rmin + SOLUTE_OFFSET
DEFAULT_SOLVENT_PRESSURE - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default solvent pressure for apolar models with an explicit volume term.
DEFAULT_STEPMAX - Static variable in class ffx.numerics.optimization.LBFGS: This specifies the default upper bound for the step in the line search.
DEFAULT_STEPMIN - Static variable in class ffx.numerics.optimization.LBFGS: This specifies the default lower bound for the step in the line search.
DEFAULT_STRBND_UNIT - Static variable in class ffx.potential.parameters.StretchBendType: Constant units=PI / 180.0
DEFAULT_STRTOR_UNIT - Static variable in class ffx.potential.parameters.StretchTorsionType
DEFAULT_TANH_BETA0 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default value of beta0 for tanh scaling
DEFAULT_TANH_BETA1 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default value of beta1 for tanh scaling
DEFAULT_TANH_BETA2 - Static variable in class ffx.potential.nonbonded.GeneralizedKirkwood: Default value of beta2 for tanh scaling
DEFAULT_TORSION_UNIT - Static variable in class ffx.potential.parameters.TorsionType
DEFAULT_TORTOR_UNIT - Static variable in class ffx.potential.parameters.TorsionTorsionType: Default units to convert Torsion-Torsion energy to kcal/mole.
DEFAULT_UREY_CUBIC - Static variable in class ffx.potential.parameters.UreyBradleyType: Default cubic coefficient in Urey-Bradley stretch potential.
DEFAULT_UREY_QUARTIC - Static variable in class ffx.potential.parameters.UreyBradleyType: Default quartic coefficient in Urey-Bradley stretch potential.
DEFAULT_UREY_UNIT - Static variable in class ffx.potential.parameters.UreyBradleyType: Default conversion Urey-Bradley stretch energy to kcal/mole.
DEFAULT_VDW_CUTOFF - Static variable in class ffx.potential.nonbonded.VanDerWaalsForm: The default van der Waals cut-off radius is 12.0 Angstroms.
DEFAULT_VDW_TAPER - Static variable in class ffx.potential.nonbonded.VanDerWaalsForm: The default van der Waals taper location is at 90% of the cut-off distance.
DEFAULT_WIGGLE - Static variable in class ffx.potential.nonbonded.implicit.ConnollyRegion: Default size of a vector to randomly perturb coordinates.
defaultCopy(BooleanBuf, BooleanBuf) - Static method in class edu.rit.mp.BooleanBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(ByteBuf, ByteBuf) - Static method in class edu.rit.mp.ByteBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(CharacterBuf, CharacterBuf) - Static method in class edu.rit.mp.CharacterBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(DoubleBuf, DoubleBuf) - Static method in class edu.rit.mp.DoubleBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(FloatBuf, FloatBuf) - Static method in class edu.rit.mp.FloatBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(IntegerBuf, IntegerBuf) - Static method in class edu.rit.mp.IntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(LongBuf, LongBuf) - Static method in class edu.rit.mp.LongBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(ObjectBuf<T>, ObjectBuf<T>) - Static method in class edu.rit.mp.ObjectBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(ShortBuf, ShortBuf) - Static method in class edu.rit.mp.ShortBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Signed16BitIntegerBuf, Signed16BitIntegerBuf) - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Signed8BitIntegerBuf, Signed8BitIntegerBuf) - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Unsigned16BitIntegerBuf, Unsigned16BitIntegerBuf) - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultCopy(Unsigned8BitIntegerBuf, Unsigned8BitIntegerBuf) - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Copy items from the given source buffer to the given destination buffer.
defaultEngine(MolecularAssembly, Potential) - Static method in class ffx.algorithms.optimize.Minimize
DefaultRandom - Class in edu.rit.util: Class DefaultRandom provides a default pseudorandom number generator (PRNG) designed for use in parallel scientific programming.
DefaultRandom(long) - Constructor for class edu.rit.util.DefaultRandom: Construct a new PRNG with the given seed.
defaultRotamerFactory(Residue) - Static method in class ffx.potential.bonded.Rotamer: Factory method to construct an original-coordinates Rotamer from a residue.
defaultRotamerFactory(Residue, TitrationUtils) - Static method in class ffx.potential.bonded.Rotamer: Factory method to construct an original-coordinates Rotamer from a residue.
defaultValue() - Element in annotation interface ffx.utilities.FFXKeyword: The default value for this FFXKeyword.
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.FFXKeyword: A description of this FFXKeyword.
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.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.ForceFieldEnergyOpenMM: 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.QuadTopologyEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.potential.XtalEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.realspace.RealSpaceData: Similar to Potential.destroy(), frees up resources associated with this RealSpaceData.
destroy() - Method in class ffx.realspace.RealSpaceEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.ui.FFXSystem: destroy
destroy() - Method in class ffx.xray.DiffractionData: Similar to Potential.destroy(), frees up resources associated with this RealSpaceData.
destroy() - Method in class ffx.xray.RefinementEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.ScaleBulkEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.SigmaAEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.SplineEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
destroy() - Method in class ffx.xray.XRayEnergy: Destroys this Potential and frees up any associated resources, particularly worker Threads.
DESTROY - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
destroyPotentials() - Method in class ffx.algorithms.cli.AlgorithmsScript: Reclaims resources associated with all Potential objects associated with this script.
destroyPotentials() - Method in class ffx.potential.cli.PotentialCommand: Reclaims resources associated with all Potential objects associated with this script.
destroyPotentials() - Method in class ffx.potential.cli.PotentialScript: Reclaims resources associated with all Potential objects associated with this script.
detach() - Method in class ffx.potential.MolecularAssembly: detach
detail - Static variable in class ffx.potential.bonded.RendererCache: Constant detail=3
DETAIL - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
determinant3(double[]) - Static method in class ffx.numerics.math.MatrixMath: determinant3
determinant3(double[][]) - Static method in class ffx.numerics.math.MatrixMath: Returns the determinant for a 3x3 matrix.
determineIntxyz(double[], double, double[], double, double[], double, int) - Static method in class ffx.potential.bonded.BondedUtils: This routine was derived from a similar routine in TINKER.
deterministic - Variable in enum class ffx.algorithms.dynamics.integrators.IntegratorEnum
dfi0() - Method in class ffx.crystal.ReflectionSpline: dfi0
dfi1() - Method in class ffx.crystal.ReflectionSpline: dfi1
dfi2() - Method in class ffx.crystal.ReflectionSpline: dfi2
dft(double[], double[]) - Static method in class ffx.numerics.fft.Complex: Static DFT method used to test the FFT.
DGU - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
DIAMETER - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.RADIUS_SIZE
dieOnMissingAtom - Variable in class ffx.potential.parsers.SystemFilter: Constant dieOnMissingAtom=
DiffractionData - Class in ffx.xray: DiffractionData class.
DiffractionData(MolecularAssembly[], CompositeConfiguration) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
DiffractionData(MolecularAssembly[], CompositeConfiguration, CrystalReciprocalSpace.SolventModel, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionData(MolecularAssembly[], CompositeConfiguration, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionData(MolecularAssembly, CompositeConfiguration) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
DiffractionData(MolecularAssembly, CompositeConfiguration, CrystalReciprocalSpace.SolventModel) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
DiffractionData(MolecularAssembly, CompositeConfiguration, CrystalReciprocalSpace.SolventModel, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionData(MolecularAssembly, CompositeConfiguration, DiffractionFile...) - Constructor for class ffx.xray.DiffractionData: construct a diffraction data assembly
DiffractionFile - Class in ffx.xray.parsers: DiffractionFile class.
DiffractionFile(MolecularAssembly) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
DiffractionFile(MolecularAssembly[]) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
DiffractionFile(MolecularAssembly[], double) - Constructor for class ffx.xray.parsers.DiffractionFile: Constructor for DiffractionFile.
DiffractionFile(MolecularAssembly[], double, boolean) - Constructor for class ffx.xray.parsers.DiffractionFile: Constructor for DiffractionFile.
DiffractionFile(MolecularAssembly, double) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a neutron value of false
DiffractionFile(MolecularAssembly, double, boolean) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
DiffractionFile(String) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file, weight set to 1.0 and neutron value of false
DiffractionFile(String, double) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file, neutron value set to false
DiffractionFile(String, double, boolean) - Constructor for class ffx.xray.parsers.DiffractionFile: read in a diffraction file
DiffractionFileFilter - Interface in ffx.xray.parsers: DiffractionFileFilter interface.
DiffractionRefinementData - Class in ffx.xray: DiffractionRefinementData class.
DiffractionRefinementData(CompositeConfiguration, ReflectionList) - Constructor for class ffx.xray.DiffractionRefinementData: allocate data given a ReflectionList
dihedralAngle(double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the dihedral angle formed between 4 atoms, a, b, c, d, via position vectors AB, BC, and CD.
dihedralAngle(double[], double[], double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the dihedral angle formed between 4 atoms.
dihedralAngle(float[], float[], float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the dihedral angle formed between 4 atoms
DIPHOSPHATE - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NA
dipole - Variable in class ffx.potential.parameters.MultipoleType: Atomic dipole.
DIPOLE - Enum constant in enum class ffx.numerics.multipole.GKSource.GK_MULTIPOLE_ORDER
dipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Permanent multipole energy and gradient using the GK dipole tensor.
dipoleEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double[], double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Permanent multipole energy and gradient using the GK dipole tensor.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the induced dipole field components due to site I at site K.
dipoleIPotentialAtK(double, double, double, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the induced dipole field components due to site I at site K.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorGlobal: Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.CoulombTensorQI: Compute the induced dipole field components due to site K at site I.
dipoleKPotentialAtI(double, double, double, int) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the induced dipole field components due to site K at site I.
dipolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorGlobal: Dipole Polarization Energy and Gradient.
dipolePolarizationEnergyAndGradient(PolarizableMultipole, PolarizableMultipole, double, double[], double[], double[]) - Method in class ffx.numerics.multipole.GKTensorQI: Dipole Polarization Energy and Gradient.
dipoleTorque(PolarizableMultipole, double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: Compute the torque on a permanent dipole.
DIRECT - Enum constant in enum class ffx.potential.nonbonded.pme.Polarization
directDipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Direct induced dipoles.
directDipole - Variable in class ffx.potential.nonbonded.pme.DirectRegion: Direct induced dipoles.
directDipole - Variable in class ffx.potential.nonbonded.pme.SORRegion: Direct induced dipoles.
directDipoleCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
directDipoleCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
directDipoleCR - Variable in class ffx.potential.nonbonded.pme.SORRegion
directField - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
directField - Variable in class ffx.potential.nonbonded.pme.DirectRegion
directFieldCR - Variable in class ffx.potential.nonbonded.ParticleMeshEwald
directFieldCR - Variable in class ffx.potential.nonbonded.pme.DirectRegion
directionality - Variable in class ffx.numerics.estimator.Zwanzig
DirectoryUtils - Class in ffx.utilities: DirectoryUtils class.
DirectRegion - Class in ffx.potential.nonbonded.pme: Parallel computation of induced dipoles due to the direct field.
DirectRegion(int) - Constructor for class ffx.potential.nonbonded.pme.DirectRegion
directSum() - Method in class ffx.potential.nonbonded.octree.Octree: Direct summation.
disableResetStatistics() - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
DispersionRegion - Class in ffx.potential.nonbonded.implicit: Parallel calculation of continuum dispersion energy via pairwise descreening.
DispersionRegion(int, Atom[], ForceField) - Constructor for class ffx.potential.nonbonded.implicit.DispersionRegion: DispersionRegion constructor.
dist(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the distance between two vectors.
dist(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the distance between two vectors.
dist(Double3) - Method in class ffx.numerics.math.Double3: Finds the Euclidean distance between two positions.
dist(Float3) - Method in class ffx.numerics.math.Float3: Finds the distance between two vectors.
dist2(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the squared distance between two vectors
dist2(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the squared distance between two vectors.
dist2(Double3) - Method in class ffx.numerics.math.Double3: Finds the square of the Euclidean distance between two positions.
dist2(Float3) - Method in class ffx.numerics.math.Float3: Finds the squared distance between two vectors
distance - Variable in class ffx.potential.parameters.BondType: Equilibrium separation (Angstroms).
distance - Variable in class ffx.potential.parameters.UreyBradleyType: Equilibrium 1-3 separation (Angstroms).
distance(double[], OctreePoint) - Method in class ffx.potential.nonbonded.octree.Octree: Compute a distance between a position and the OctreePoint.
distance(OctreeCell) - Method in class ffx.potential.nonbonded.octree.OctreePoint
distance(OctreePoint) - Method in class ffx.potential.nonbonded.octree.OctreePoint
DistanceMatrix - Class in ffx.algorithms.optimize.manybody: Calculates a residue-residue distance matrix.
DistanceMatrix(MolecularAssembly, AlgorithmListener, Residue[], List<Residue>, RotamerOptimization.DistanceMethod, double, double, double, boolean) - Constructor for class ffx.algorithms.optimize.manybody.DistanceMatrix
DistanceMatrixFileFilter - Class in ffx.potential.parsers: The DistanceMatrixFileFilter class is used to choose a Distance Matrix (*.TXT) file.
DistanceMatrixFileFilter() - Constructor for class ffx.potential.parsers.DistanceMatrixFileFilter: Default Constructor.
DistanceMatrixFilter - Class in ffx.potential.parsers: The DistanceMatrixFilter class parses a Distance Matrix (*.TXT) files.
DistanceMatrixFilter() - Constructor for class ffx.potential.parsers.DistanceMatrixFilter: No public constructor for DistanceMatrixFilter.
DistanceRegion - Class in ffx.algorithms.optimize.manybody: Compute the minimum distance between each pair of residues for all rotamer permutations.
DistanceRegion(int, int, Crystal, int[][][], IntegerSchedule) - Constructor for class ffx.algorithms.optimize.manybody.DistanceRegion
distribute(MolecularAssembly[], CrystalPotential, AlgorithmFunctions, int, int) - Method in class ffx.algorithms.cli.MultiDynamicsOptions: If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
distribute(MolecularAssembly[], Potential[], CrystalPotential, AlgorithmFunctions, int, int) - Method in class ffx.algorithms.cli.MultiDynamicsOptions: If residues selected for distributing initial configurations, performs many-body optimization for this distribution.
distRow - Variable in class ffx.potential.utils.ProgressiveAlignmentOfCrystals: Row of RMSD values (length = targetSize).
divides(ComplexNumber) - Method in class ffx.numerics.math.ComplexNumber: Return a / b.
dlAlpha - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dlfAlpha - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: First lambda derivative of buffer distance.
dlfPowPerm - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: First lambda derivative of lPowPerm.
dlfPowPol - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: First lambda derivative of lPowPol.
dLpdL - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Derivative of lambdaProduct w.r.t.
dLpdLi - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Derivative of lambdaProduct w.r.t.
dLpdLk - Variable in class ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors: Derivative of lambdaProduct w.r.t.
dlPowPerm - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dlPowPol - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
doCauseSevere() - Method in exception class ffx.potential.utils.EnergyException: doCauseSevere.
dof - Variable in class ffx.numerics.math.BootStrapStatistics
dof - Variable in class ffx.numerics.math.SummaryStatistics
dOffset - Variable in class ffx.potential.nonbonded.implicit.GKEnergyRegion: Dielectric offset from:
doLigandGKElec - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Intramolecular electrostatics for the ligand in done in GK implicit solvent.
doLigandVaporElec - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Intramolecular electrostatics for the ligand in vapor is included by default.
done - Variable in class ffx.algorithms.dynamics.MolecularDynamics: Flag to indicate a run has finished.
done - Variable in class ffx.algorithms.optimize.Minimize: A flag to indicate the algorithm is done.
done - Variable in class ffx.algorithms.optimize.PhMinimize: A flag to indicate the algorithm is done.
doNoLigandCondensedSCF - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters: Condensed phase SCF without the ligand present is included by default.
doPermanentRealSpace - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
doPolarization - Variable in class ffx.potential.nonbonded.pme.AlchemicalParameters
dot(double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Finds the dot product between two vectors.
dot(float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Finds the dot product between two vectors.
dot(Double3) - Method in class ffx.numerics.math.Double3: Finds the dot product between two vectors.
dot(Float3) - Method in class ffx.numerics.math.Float3: Finds the dot product between two vectors.
Double() - Constructor for class edu.rit.util.Searching.Double
Double() - Constructor for class edu.rit.util.Sorting.Double
Double3 - Class in ffx.numerics.math: Convenience class for working with 3D double vectors.
Double3() - Constructor for class ffx.numerics.math.Double3: Construct a Double3 at (0.0, 0.0, 0.0).
Double3(double[]) - Constructor for class ffx.numerics.math.Double3: Construct a Double3 at a.
Double3(double, double, double) - Constructor for class ffx.numerics.math.Double3: Construct a Double3 at (x, y, z).
DoubleArrayBuf - Class in edu.rit.mp.buf: Class DoubleArrayBuf provides a buffer for an array of double items sent or received using the Message Protocol (MP).
DoubleArrayBuf(double[], Range) - Constructor for class edu.rit.mp.buf.DoubleArrayBuf: Construct a new double array buffer.
DoubleArrayBuf_1 - Class in edu.rit.mp.buf: Class DoubleArrayBuf_1 provides a buffer for an array of double items sent or received using the Message Protocol (MP).
DoubleArrayBuf_1(double[], Range) - Constructor for class edu.rit.mp.buf.DoubleArrayBuf_1: Construct a new double array buffer.
DoubleBuf - Class in edu.rit.mp: Class DoubleBuf is the abstract base class for a buffer of double items sent or received using the Message Protocol (MP).
DoubleBuf(int) - Constructor for class edu.rit.mp.DoubleBuf: Construct a new double buffer.
doubleFactorial(long) - Static method in class ffx.numerics.math.ScalarMath: Returns n!! Precondition: n .GE.
DoubleIndexPair - Record Class in ffx.utilities: DoubleIndexPair record.
DoubleIndexPair(int, double) - Constructor for record class ffx.utilities.DoubleIndexPair: Creates an instance of a DoubleIndexPair record class.
DoubleItemBuf - Class in edu.rit.mp.buf: Class DoubleItemBuf provides a buffer for a single double item sent or received using the Message Protocol (MP).
DoubleItemBuf() - Constructor for class edu.rit.mp.buf.DoubleItemBuf: Construct a new double item buffer.
DoubleItemBuf(double) - Constructor for class edu.rit.mp.buf.DoubleItemBuf: Construct a new double item buffer with the given initial value.
DoubleMath - Class in ffx.numerics.math: The DoubleMath class is a simple math library that operates on 3-coordinate double arrays.
DoubleMath() - Constructor for class ffx.numerics.math.DoubleMath
DoubleMatrixBuf - Class in edu.rit.mp.buf: Class DoubleMatrixBuf provides a buffer for a matrix of double items sent or received using the Message Protocol (MP).
DoubleMatrixBuf(double[][], Range, Range) - Constructor for class edu.rit.mp.buf.DoubleMatrixBuf: Construct a new double matrix buffer.
DoubleMatrixBuf_1 - Class in edu.rit.mp.buf: Class DoubleMatrixBuf_1 provides a buffer for a matrix of double items sent or received using the Message Protocol (MP).
DoubleMatrixBuf_1(double[][], Range, Range) - Constructor for class edu.rit.mp.buf.DoubleMatrixBuf_1: Construct a new double matrix buffer.
DoubleMatrixFile - Class in edu.rit.io: Class DoubleMatrixFile provides an object for reading or writing a double matrix from or to a file.
DoubleMatrixFile() - Constructor for class edu.rit.io.DoubleMatrixFile: Construct a new double matrix file object.
DoubleMatrixFile(int, int, double[][]) - Constructor for class edu.rit.io.DoubleMatrixFile: Construct a new double matrix file object with the given number of rows, number of columns, and underlying matrix.
DoubleMatrixFile.Reader - Class in edu.rit.io: Class DoubleMatrixFile.Reader provides an object with which to read a DoubleMatrixFile from an input stream.
DoubleMatrixFile.Writer - Class in edu.rit.io: Class DoubleMatrixFile.Writer provides an object with which to write a DoubleMatrixFile to an output stream.
DoubleOp - Class in edu.rit.pj.reduction: Class DoubleOp is the abstract base class for a binary operation on double values, used to do reduction in a parallel program.
DoubleOp() - Constructor for class edu.rit.pj.reduction.DoubleOp: Construct a new double binary operation.
DoublesDataSet - Class in ffx.numerics.integrate: Describes a set of x, f(x) obtained by some mechanism; intended for numerical integration.
DoublesDataSet(double[], double[]) - Constructor for class ffx.numerics.integrate.DoublesDataSet: Constructs a DataSet from actual data, with no known underlying function (or at least none with an analytically solved integral).
DoublesDataSet(double[], double[], boolean) - Constructor for class ffx.numerics.integrate.DoublesDataSet: Constructs a DataSet from actual data, with no known underlying function (or at least none with an analytically solved integral).
DoublesDataSet(DataSet) - Constructor for class ffx.numerics.integrate.DoublesDataSet: Constructs a DataSet from another DataSet, effectively masquerading a test set such as a sine wave as data from an "unknown" function.
doubleValue() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns this reduction variable's current value converted to type double.
doubleValue() - Method in record class ffx.utilities.DoubleIndexPair: Returns the value of the doubleValue record component.
DoubleXMLAdapter - Class in ffx.utilities: Convert a Double to a String and vice versa for use with JAXB.
DoubleXMLAdapter() - Constructor for class ffx.utilities.DoubleXMLAdapter
downloadPDB(String) - Static method in class ffx.utilities.DownloadUtils: Download a PDB file.
DownloadUtils - Class in ffx.utilities: Download utilities.
DownloadUtils() - Constructor for class ffx.utilities.DownloadUtils
DP2 - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
drag - Variable in class ffx.ui.behaviors.PickRotateBehavior
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in class ffx.potential.bonded.Atom: drawLabel
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in class ffx.potential.bonded.MSNode: drawLabel
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in class ffx.potential.bonded.Residue: drawLabel
drawLabel(Canvas3D, J3DGraphics2D, Node) - Method in interface ffx.potential.bonded.ROLS: drawLabel
dt - Variable in class ffx.algorithms.dynamics.integrators.Integrator: Time step (psec).
dt - Variable in class ffx.algorithms.dynamics.MolecularDynamics: The time step (picoseconds).
dtaper(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: First derivative of the switching function at r.
dtaper(double, double, double, double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: First derivative of the switching function at r.
DTDResolver - Class in ffx.ui.commands: The DTDResolver class just points the DOM DocumentBuilder to the XML Document Type Definition (DTD) files.
DTDResolver() - Constructor for class ffx.ui.commands.DTDResolver
DTY - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
DualTopologyEnergy - Class in ffx.potential: Compute the potential energy and derivatives for a dual-topology system.
DualTopologyEnergy(MolecularAssembly, MolecularAssembly, UnivariateSwitchingFunction) - Constructor for class ffx.potential.DualTopologyEnergy: Constructor for DualTopologyEnergy.
dUdLBins - Variable in class ffx.algorithms.thermodynamics.HistogramData: It is useful to have an odd number of bins, so that there is a bin from FL=-dFL/2 to dFL/2 so that as FL approaches zero its contribution to thermodynamic integration goes to zero.
dUdLBinWidth_2 - Variable in class ffx.algorithms.thermodynamics.HistogramData: Half the width of the F_lambda bin.
dUdLMaximum - Variable in class ffx.algorithms.thermodynamics.HistogramData: The maximum value of the last dUdL bin.
dUdLVariance - Variable in class ffx.algorithms.thermodynamics.HistogramData: The variance for the Gaussian bias in the dU/dL dimension.
dump(PrintStream, String) - Method in class edu.rit.mp.Channel: Dump the state of this channel on the given print stream.
dump(PrintStream, String) - Method in class edu.rit.mp.ChannelGroup: Dump the state of this channel group on the given print stream.
dump(PrintStream, String) - Method in class edu.rit.pj.Comm: Dump the state of this communicator on the given print stream.
dVdA - Variable in class ffx.crystal.Crystal: Change in the volume with respect to a.
dVdAlpha - Variable in class ffx.crystal.Crystal: Change in the volume with respect to alpha (in Radians).
dVdB - Variable in class ffx.crystal.Crystal: Change in the volume with respect to b.
dVdBeta - Variable in class ffx.crystal.Crystal: Change in the volume with respect to beta (in Radians).
dVdC - Variable in class ffx.crystal.Crystal: Change in the volume with respect to c.
dVdGamma - Variable in class ffx.crystal.Crystal: Change in the volume with respect to gamma (in Radians).
dWater - Static variable in class ffx.utilities.Constants: Permittivity of water at STP.
dx - Variable in class ffx.numerics.multipole.PolarizableMultipole: Dipole x-component.
dx - Variable in class ffx.potential.parameters.TorsionTorsionType: First derivative along x.
dxy - Variable in class ffx.potential.parameters.TorsionTorsionType: Second derivatives.
dy - Variable in class ffx.numerics.multipole.PolarizableMultipole: Dipole y-component.
dy - Variable in class ffx.potential.parameters.TorsionTorsionType: First derivative along y.
Dy - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
dynamic() - Static method in class edu.rit.pj.IntegerSchedule: Returns a dynamic schedule object with a chunk size of 1.
dynamic() - Static method in class edu.rit.pj.LongSchedule: Returns a dynamic schedule object with a chunk size of 1.
dynamic(int) - Static method in class edu.rit.pj.IntegerSchedule: Returns a dynamic schedule object with the given chunk size.
dynamic(long) - Static method in class edu.rit.pj.LongSchedule: Returns a dynamic schedule object with the given chunk size.
dynamic(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Blocking molecular dynamics.
dynamic(long, double, double, double, double, boolean, File) - Method in class ffx.algorithms.dynamics.MolecularDynamicsOpenMM: Blocking molecular dynamics.
dynamic(long, double, double, double, double, boolean, String, double, File) - Method in class ffx.algorithms.dynamics.MolecularDynamics: Blocking molecular dynamics.
dynamicsFactory(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum) - Static method in class ffx.algorithms.dynamics.MolecularDynamics: Method that determines whether a dynamics is done by the java implementation native to ffx or the OpenMM implementation
dynamicsFactory(MolecularAssembly, Potential, AlgorithmListener, ThermostatEnum, IntegratorEnum, MDEngine) - Static method in class ffx.algorithms.dynamics.MolecularDynamics: dynamicsFactory.
DynamicsOptions - Class in ffx.algorithms.cli: Represents command line options for scripts that run molecular dynamics.
DynamicsOptions() - Constructor for class ffx.algorithms.cli.DynamicsOptions
DYNFileFilter - Class in ffx.potential.parsers: The DYNFileFilter class is used to choose a TINKER Restart (*.DYN) file.
DYNFileFilter() - Constructor for class ffx.potential.parsers.DYNFileFilter: Default Constructor.
DYNFilter - Class in ffx.potential.parsers: The DYNFilter class parses TINKER Restart (*.DYN) files.
DYNFilter(String) - Constructor for class ffx.potential.parsers.DYNFilter: Constructor for DYNFilter.
dz - Variable in class ffx.numerics.multipole.PolarizableMultipole: Dipole z-component.

E

e - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
E - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
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.KeywordGroup: Electrostatics functional form.
ELEMENTARY_CHARGE_SI - Static variable in class ffx.utilities.Constants: Elementary charge in Coulombs, defining the Coulomb.
eliminatedPairs - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Eliminated rotamer pairs.
EliminatedRotamers - Class in ffx.algorithms.optimize.manybody
EliminatedRotamers(RotamerOptimization, DistanceMatrix, List<Residue>, int, double, double, double, double, double, double, boolean, boolean, boolean, Residue[]) - Constructor for class ffx.algorithms.optimize.manybody.EliminatedRotamers
eliminatedSingles - Variable in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Eliminated rotamers.
eliminateRotamer(Residue[], int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers: Safe method to eliminate a rotamer: will not eliminate if there are no alternate rotamers for residue i, or if i-ri is already eliminated.
eliminateRotamerPair(Residue[], int, int, int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
eliminateRotamerPairs(Residue[], int, int, boolean) - Method in class ffx.algorithms.optimize.manybody.EliminatedRotamers
eLow - Variable in class ffx.numerics.estimator.SequentialEstimator
EmptyBooleanBuf - Class in edu.rit.mp.buf: Class EmptyBooleanBuf provides a Boolean buffer that contains no items for messages using the Message Protocol (MP).
EmptyBooleanBuf() - Constructor for class edu.rit.mp.buf.EmptyBooleanBuf: Construct a new empty Boolean buffer.
emptyBuffer() - Static method in class edu.rit.mp.BooleanBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ByteBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.CharacterBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.DoubleBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.FloatBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.IntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.LongBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ObjectBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.ShortBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Signed16BitIntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Signed8BitIntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Unsigned16BitIntegerBuf: Create an empty buffer.
emptyBuffer() - Static method in class edu.rit.mp.Unsigned8BitIntegerBuf: Create an empty buffer.
EmptyByteBuf - Class in edu.rit.mp.buf: Class EmptyByteBuf provides a byte buffer that contains no items for messages using the Message Protocol (MP).
EmptyByteBuf() - Constructor for class edu.rit.mp.buf.EmptyByteBuf: Construct a new empty byte buffer.
EmptyCharacterBuf - Class in edu.rit.mp.buf: Class EmptyCharacterBuf provides a character buffer that contains no items for messages using the Message Protocol (MP).
EmptyCharacterBuf() - Constructor for class edu.rit.mp.buf.EmptyCharacterBuf: Construct a new empty character buffer.
EmptyDoubleBuf - Class in edu.rit.mp.buf: Class EmptyDoubleBuf provides a double buffer that contains no items for messages using the Message Protocol (MP).
EmptyDoubleBuf() - Constructor for class edu.rit.mp.buf.EmptyDoubleBuf: Construct a new empty double buffer.
EmptyFloatBuf - Class in edu.rit.mp.buf: Class EmptyFloatBuf provides a float buffer that contains no items for messages using the Message Protocol (MP).
EmptyFloatBuf() - Constructor for class edu.rit.mp.buf.EmptyFloatBuf: Construct a new empty float buffer.
EmptyIntegerBuf - Class in edu.rit.mp.buf: Class EmptyIntegerBuf provides an integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyIntegerBuf: Construct a new empty integer buffer.
EmptyLongBuf - Class in edu.rit.mp.buf: Class EmptyLongBuf provides a long buffer that contains no items for messages using the Message Protocol (MP).
EmptyLongBuf() - Constructor for class edu.rit.mp.buf.EmptyLongBuf: Construct a new empty long buffer.
EmptyObjectBuf - Class in edu.rit.mp.buf: Class EmptyObjectBuf provides an object buffer that contains no items for messages using the Message Protocol (MP).
EmptyObjectBuf() - Constructor for class edu.rit.mp.buf.EmptyObjectBuf: Construct a new empty object buffer.
EmptyShortBuf - Class in edu.rit.mp.buf: Class EmptyShortBuf provides a short buffer that contains no items for messages using the Message Protocol (MP).
EmptyShortBuf() - Constructor for class edu.rit.mp.buf.EmptyShortBuf: Construct a new empty short buffer.
EmptySigned16BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptySigned16BitIntegerBuf provides a signed 16-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptySigned16BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptySigned16BitIntegerBuf: Construct a new empty signed 16-bit integer buffer.
EmptySigned8BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptySigned8BitIntegerBuf provides a signed 8-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptySigned8BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptySigned8BitIntegerBuf: Construct a new empty signed 8-bit integer buffer.
EmptyUnsigned16BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptyUnsigned16BitIntegerBuf provides an unsigned 16-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyUnsigned16BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf: Construct a new empty unsigned 16-bit integer buffer.
EmptyUnsigned8BitIntegerBuf - Class in edu.rit.mp.buf: Class EmptyUnsigned8BitIntegerBuf provides an unsigned 8-bit integer buffer that contains no items for messages using the Message Protocol (MP).
EmptyUnsigned8BitIntegerBuf() - Constructor for class edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf: Construct a new empty unsigned 8-bit integer buffer.
encode(int, int) - Static method in class ffx.utilities.Hybrid36: Hybrid-36 encoder: converts integer value to string result.
energy - Variable in class ffx.algorithms.optimize.Minimize: The final potential energy.
energy - Variable in class ffx.algorithms.optimize.PhMinimize: The final potential energy.
energy - Variable in class ffx.potential.bonded.BondedTerm: Energy of the term (kcal/mol).
energy - Variable in class ffx.potential.commands.Energy
energy - Variable in class ffx.potential.parameters.TorsionTorsionType: Energy values.
energy - Variable in class ffx.ui.commands.SimulationUpdate
energy() - Method in class ffx.potential.ForceFieldEnergy: energy.
energy() - Method in class ffx.ui.ModelingShell: energy
energy(boolean) - Method in interface ffx.potential.bonded.BondedEnergy: energy.
energy(boolean) - Method in class ffx.potential.nonbonded.RestrainGroups: Compute energy and derivatives for group distance restraint terms.
energy(boolean, boolean) - Method in class ffx.potential.ANIEnergy: Compute the ANI energy and gradint.
energy(boolean, boolean) - Method in class ffx.potential.ForceFieldEnergy
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.ParticleMeshEwald: Calculate the PME electrostatic energy.
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.VanDerWaals: The energy routine may be called repeatedly.
energy(boolean, boolean) - Method in class ffx.potential.nonbonded.VanDerWaalsTornado: The energy routine may be called repeatedly.
energy(boolean, int, AtomicDoubleArray3D) - Method in interface ffx.potential.bonded.BondedEnergy: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Angle: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.AngleTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Bond: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in interface ffx.potential.bonded.BondedEnergy: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.ImproperTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.OutOfPlaneBend: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.PiOrbitalTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.RestraintBond: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.RestraintTorsion
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.StretchBend: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.StretchTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.Torsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.TorsionTorsion: energy.
energy(boolean, int, AtomicDoubleArray3D, AtomicDoubleArray3D) - Method in class ffx.potential.bonded.UreyBradley: energy.
energy(double[]) - Method in class ffx.algorithms.dynamics.Barostat: This method is called repeatedly to compute the function energy.
energy(double[]) - Method in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Compute the force field + bias energy.
energy(double[]) - Method in 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.ForceFieldEnergyOpenMM: 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.ForceFieldEnergyOpenMM: 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 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.ForceFieldEnergyOpenMM: 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.ForceFieldEnergyOpenMM: 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.ForceFieldEnergyOpenMM: Compute the energy and gradient using the pure Java code path.
energyAndGradientFFX(double[], double[], boolean) - Method in class ffx.potential.ForceFieldEnergyOpenMM: 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, List<CoordRestraint>) - Static method in class ffx.potential.ForceFieldEnergy: Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.
energyFactory(MolecularAssembly, List<CoordRestraint>, 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.ForceFieldEnergyOpenMM: Compute the energy using the pure Java code path.
energyFFX(double[], boolean) - Method in class ffx.potential.ForceFieldEnergyOpenMM: 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.KeywordGroup: Energy unit conversion factors.
enforcePBC - Variable in class ffx.potential.ForceFieldEnergyOpenMM: Whether to enforce periodic boundary conditions when obtaining new States.
environment - Variable in class ffx.potential.parameters.AtomType: Description of the atom's bonding environment.
epsilon - Variable in class ffx.crystal.HKL
epsilonc() - Method in class ffx.crystal.HKL: epsilonc
epsilonRule - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: Epsilon combining rule.
EPT - Enum constant in enum class ffx.potential.nonbonded.pme.SCFAlgorithm
equals(Object) - Method in class edu.rit.pj.io.StreamFile: Determine if this stream file is equal to the given object.
equals(Object) - Method in class edu.rit.util.LongRange: Determine if this range is equal to the given object.
equals(Object) - Method in class edu.rit.util.Range: Determine if this range is equal to the given object.
equals(Object) - Method in class ffx.crystal.Crystal: Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.HKL
equals(Object) - Method in class ffx.crystal.NCSCrystal: Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.crystal.ReplicatesCrystal: Two crystals are equal only if all unit cell parameters are exactly the same.
equals(Object) - Method in class ffx.potential.bonded.Atom
equals(Object) - Method in class ffx.potential.bonded.BondedTerm
equals(Object) - Method in class ffx.potential.bonded.Molecule
equals(Object) - Method in class ffx.potential.bonded.MSNode
equals(Object) - Method in class ffx.potential.bonded.MSRoot
equals(Object) - Method in class ffx.potential.bonded.MultiResidue
equals(Object) - Method in class ffx.potential.bonded.Polymer
equals(Object) - Method in class ffx.potential.bonded.Residue
equals(Object) - Method in class ffx.potential.bonded.ROLSP
equals(Object) - Method in class ffx.potential.parameters.AngleTorsionType
equals(Object) - Method in class ffx.potential.parameters.AngleType
equals(Object) - Method in class ffx.potential.parameters.AtomType
equals(Object) - Method in class ffx.potential.parameters.BioType
equals(Object) - Method in class ffx.potential.parameters.BondType
equals(Object) - Method in class ffx.potential.parameters.ImproperTorsionType
equals(Object) - Method in class ffx.potential.parameters.MultipoleType
equals(Object) - Method in class ffx.potential.parameters.OutOfPlaneBendType
equals(Object) - Method in class ffx.potential.parameters.PiOrbitalTorsionType
equals(Object) - Method in class ffx.potential.parameters.PolarizeType
equals(Object) - Method in class ffx.potential.parameters.RelativeSolvationType
equals(Object) - Method in class ffx.potential.parameters.SoluteType
equals(Object) - Method in class ffx.potential.parameters.StretchBendType
equals(Object) - Method in class ffx.potential.parameters.StretchTorsionType
equals(Object) - Method in class ffx.potential.parameters.TorsionTorsionType
equals(Object) - Method in class ffx.potential.parameters.TorsionType
equals(Object) - Method in class ffx.potential.parameters.UreyBradleyType
equals(Object) - Method in class ffx.potential.parameters.VDWPairType
equals(Object) - Method in class ffx.potential.parameters.VDWType
equals(Object) - Method in record class ffx.potential.UnmodifiableState: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class ffx.ui.KeywordComponent
equals(Object) - Method in record class ffx.utilities.DoubleIndexPair: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ffx.utilities.IndexIndexPair: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class ffx.utilities.ObjectPair: Indicates whether some other object is "equal to" this one.
Er - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
erf(double) - Static method in class ffx.numerics.special.Erf: Evaluates erf(x) for a real argument x.
Erf - Class in ffx.numerics.special: Static methods to evaluate erf(x) and erfc(x) for a real argument x.
erfc(double) - Static method in class ffx.numerics.special.Erf: Evaluate erfc(x) for a real argument x.
err - Variable in class edu.rit.pj.cluster.BackendFileWriter: Print stream for printing on the job frontend's standard error.
err() - Static method in class edu.rit.io.Stdio: Get the standard error stream for the calling thread.
err(PrintStream) - Static method in class edu.rit.io.Stdio: Set the standard error stream for the calling thread.
error(SAXParseException) - Method in class ffx.potential.parsers.PDBMLFilter
Es - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
EstimateBootstrapper - Class in ffx.numerics.estimator: Bootstrap Free Energy Estimate.
EstimateBootstrapper(BootstrappableEstimator) - Constructor for class ffx.numerics.estimator.EstimateBootstrapper
estimateDG() - Method in class ffx.numerics.estimator.BennettAcceptanceRatio: Main driver for estimation of delta-G.
estimateDG() - Method in interface ffx.numerics.estimator.BootstrappableEstimator: Re-calculates free energy and enthalpy without bootstrapping.
estimateDG() - Method in class ffx.numerics.estimator.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.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.
EwaldTensorQI - Class in ffx.numerics.multipole: The EwaldTensorQI class computes derivatives of erfc(r)/|r| via recursion to arbitrary order for Cartesian multipoles in a quasi-internal frame.
EwaldTensorQI(int, double) - Constructor for class ffx.numerics.multipole.EwaldTensorQI: Constructor for EwaldTensorQI.
excludeExcessAtoms(Set<Atom>, int[], List<Residue>) - Method in class ffx.algorithms.optimize.TitrationManyBody
exclusiveScan(int, Buf, Op, Object) - Method in class edu.rit.pj.Comm: Perform an exclusive scan on all processes in this communicator using the given message tag.
exclusiveScan(Buf, Op, Object) - Method in class edu.rit.pj.Comm: Perform an exclusive scan on all processes in this communicator.
excuteWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ReduceRegion: Execute the ReduceRegion with the passed ParallelTeam.
execute() - Method in class ffx.numerics.fft.TornadoDFT
execute(int, int, int, IntegerStrideForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, int, IntegerStrideForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, int, WorkerIntegerStrideForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(int, int, IntegerForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, IntegerForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(int, int, WorkerIntegerForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(long, long, long, LongStrideForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, long, LongStrideForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, long, WorkerLongStrideForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(long, long, LongForLoop) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, LongForLoop, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel for loop within this parallel region.
execute(long, long, WorkerLongForLoop) - Method in class edu.rit.pj.WorkerRegion: Execute a worker for loop within this worker region.
execute(ParallelRegion) - Method in class edu.rit.pj.ParallelTeam: Execute the given parallel region.
execute(ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel section within this parallel region.
execute(ParallelSection[]) - Method in class edu.rit.pj.ParallelRegion: Execute a group of parallel sections concurrently within this parallel region.
execute(ParallelSection[], BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a group of parallel sections concurrently within this parallel region.
execute(ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel section within this parallel region.
execute(ParallelSection, ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Execute a group of two parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a group of two parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, ParallelSection) - Method in class edu.rit.pj.ParallelRegion: Execute a group of three parallel sections concurrently within this parallel region.
execute(ParallelSection, ParallelSection, ParallelSection, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a group of three parallel sections concurrently within this parallel region.
execute(WorkerRegion) - Method in class edu.rit.pj.WorkerTeam: Execute the given worker region.
execute(Iterable<T>, ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterable<T>, ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterable<T>, WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion: Execute a worker iteration within this worker region.
execute(Iterator<T>, ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterator<T>, ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(Iterator<T>, WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion: Execute a worker iteration within this worker region.
execute(T[], ParallelIteration<T>) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(T[], ParallelIteration<T>, BarrierAction) - Method in class edu.rit.pj.ParallelRegion: Execute a parallel iteration within this parallel region.
execute(T[], WorkerIteration<T>) - Method in class edu.rit.pj.WorkerRegion: Execute a worker iteration within this worker region.
execute(TornadoDevice) - Method in class ffx.numerics.fft.TornadoDFT
executeCommand() - Method in class ffx.ui.ModelingPanel: Launch the TINKER command specified by the ModelingPanel
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.implicit.BornGradRegion: Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.implicit.InitializationRegion: Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.DirectRegion: Execute the DirectRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion: Execute the ExpandInducedDipolesRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion: Execute the InducedDipoleFieldReduceRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InducedDipoleFieldRegion: Execute the InducedDipoleFieldRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.InitializationRegion: Execute the InitializationRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion: Execute the RealSpaceEnergyRegion with the passed ParallelTeam.
executeWith(ParallelTeam) - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion: Execute the ReciprocalEnergyRegion with the passed ParallelTeam.
exit() - Method in class ffx.ui.MainPanel: exit with current exit code (default: 0 (ExitStatus.NORMAL))
exp() - Method in class ffx.numerics.math.ComplexNumber: Return a new Complex object whose value is the complex exponential of this.
EXP - Enum constant in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules
expandInducedDipoles() - Method in class ffx.potential.nonbonded.ParticleMeshEwald
ExpandInducedDipolesRegion - Class in ffx.potential.nonbonded.pme: Parallel expansion of the asymmetric unit induced dipoles to symmetry mates by applying symmetry operator rotation matrices.
ExpandInducedDipolesRegion(int) - Constructor for class ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
ExpAnnealSchedule - Class in ffx.algorithms.optimize.anneal: Exponential temperature schedule for simulated annealing
ExpAnnealSchedule(int, double, double) - Constructor for class ffx.algorithms.optimize.anneal.ExpAnnealSchedule: Creates an exponential annealing schedule that decays as tHigh*((tLow/tHigh)^(1/(nWindows-1)))^(n-1).
EXPENSIVE - Enum constant in enum class ffx.algorithms.mc.RosenbluthChiAllMove.MODE
expireTimer - Variable in class edu.rit.pj.cluster.JobInfo: Lease expiration timer.
expireTimer - Variable in class edu.rit.pj.cluster.ProcessInfo: Lease expiration timer.
EXPLICIT - Enum constant in enum class ffx.potential.bonded.RelativeSolvation.SolvationLibrary
ExtendedSystem - Class in ffx.potential.extended: ExtendedSystem class.
ExtendedSystem(MolecularAssembly, double, File) - Constructor for class ffx.potential.extended.ExtendedSystem: Construct extended system with the provided configuration.
extractCoordinates(int[], double[], double[]) - Static method in class ffx.potential.utils.Superpose: Extract used coordinate subset from the entire system.

F

f - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
f() - Method in class ffx.crystal.ReflectionSpline: f
f(double, double[]) - Method in class ffx.crystal.ReflectionSpline: Evaluate basis function and derivative at a given resolution
f(HKL) - Method in class ffx.xray.NeutronFormFactor: f
f(HKL) - Method in class ffx.xray.XRayFormFactor: f
F - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
F - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
F1F2 - Static variable in interface ffx.xray.SplineEnergy.Type
factorial(long) - Static method in class ffx.numerics.math.ScalarMath: Returns n!
Precondition: n .GE.
FAILED - Enum constant in enum class edu.rit.pj.cluster.BackendInfo.State: The backend has failed.
FAILED - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State: The job backend process has failed.
farEndAddress() - Method in class edu.rit.mp.Channel: Obtain this channel's far end address.
farEndChannelGroupId() - Method in class edu.rit.mp.Channel: Obtain the channel group ID of this channel's far end channel group.
farEndConnected(ChannelGroup, Channel) - Method in interface edu.rit.mp.ConnectListener: Report that a channel was connected in the given channel group, initiated by the far end.
FAST - Enum constant in enum class ffx.numerics.Potential.STATE
fatalError(SAXParseException) - Method in class ffx.potential.parsers.PDBMLFilter
fc - Variable in class ffx.xray.DiffractionRefinementData: Calculated atomic structure factors.
fcF(int) - Method in class ffx.xray.DiffractionRefinementData: get the amplitude of a complex Fc
FCONLY - Static variable in interface ffx.xray.parsers.MTZWriter.MTZType: Output unscaled Fcs only (still requires data to be read in).
fcPhi(int) - Method in class ffx.xray.DiffractionRefinementData: get the phase of a complex Fc
FCTOESQ - Static variable in interface ffx.xray.SplineEnergy.Type
fcTotF(int) - Method in class ffx.xray.DiffractionRefinementData: fcTotF
fcTotPhi(int) - Method in class ffx.xray.DiffractionRefinementData: fcTotPhi
Fe - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
fermiFunction(double) - Static method in class ffx.numerics.math.ScalarMath: Compute 1.0 / (1.0 + exp(x)).
fft(double[]) - Method in class ffx.numerics.fft.Complex3D: Compute the 3D FFT.
fft(double[]) - Method in class ffx.numerics.fft.Complex3DParallel: Compute the 3D FFT in parallel.
fft(double[]) - Method in class ffx.numerics.fft.Real3D: Compute the 3D FFT.
fft(double[]) - Method in class ffx.numerics.fft.Real3DParallel: Compute the 3D FFT.
fft(double[], int) - Method in class ffx.numerics.fft.Real: fft
fft(double[], int, int) - Method in class ffx.numerics.fft.Complex: Compute the Fast Fourier Transform of data leaving the result in data.
ffx - package ffx: Force Field X implements fixed charge and polarizable atomic multipole molecular mechanics potentials, local and global optimization, molecular dynamics, free energy differences, etc, with special support for crystal space groups.
FFX - Enum constant in enum class ffx.algorithms.dynamics.MDEngine
FFX - Enum constant in enum class ffx.algorithms.optimize.Minimize.MinimizationEngine
FFX - Enum constant in enum class ffx.potential.ForceFieldEnergy.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.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.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.
FFXKeyword - Annotation Interface in ffx.utilities: The FFXKeyword Annotation should be used to document fields that are set using property files, keyword files, force field parameter files and the Java property system.
FFXKeywords - Annotation Interface in ffx.utilities: The FFXKeyword Annotation can be applied multiple times to some classes.
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")
ffxScript(String[]) - Static method in class ffx.Main: A main entry point that runs a script and return a refernce to the result.
FFXScript - Class in ffx.utilities: BaseScript class.
FFXScript(Binding) - Constructor for class ffx.utilities.FFXScript: Default constructor for an FFX Script.
FFXServer - Class in ffx.ui.commands: The FFXServer is launched by an FFX instance to allow Force Field X Clients to connect.
FFXServer(SimulationDefinition) - Constructor for class ffx.ui.commands.FFXServer: Constructor for FFXServer.
FFXSystem - Class in ffx.ui: The FFXSystem class contains extensions to the generic MolecularAssembly class.
FFXSystem(File, String, CompositeConfiguration) - Constructor for class ffx.ui.FFXSystem: Constructor.
FFXTest - Class in ffx.utilities: The FFXTest configures the context for FFX tests.
FFXTest() - Constructor for class ffx.utilities.FFXTest: FFXTest constructor.
FFXTornado - Class in ffx.numerics.tornado: Utility Routines to use the TornadoVM
FFXTornado() - Constructor for class ffx.numerics.tornado.FFXTornado
file - Variable in class ffx.ui.commands.SimulationDefinition
FILE_READ_DATA - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message containing data read from a file.
FILE_WRITE_DATA - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message containing data to write to a file.
fileAppend(File, String) - Static method in class edu.rit.io.Files: Append the given suffix to the given file.
fileForRank(File, int) - Static method in class edu.rit.io.Files: Append the given rank to the given file.
fileNameAppend(String, String) - Static method in class edu.rit.io.Files: Append the given suffix to the given file name.
fileNameForRank(String, int) - Static method in class edu.rit.io.Files: Append the given rank to the given file name.
fileNamePrepend(String, String) - Static method in class edu.rit.io.Files: Prepend the given prefix to the given file name.
fileNewWindow() - Method in class ffx.ui.ModelingShell
fileNewWindow(EventObject) - Method in class ffx.ui.ModelingShell
FileOpener - Interface in ffx.potential.parsers: The FileOpener interface specifies Runnable objects which can return one or more MolecularAssemblies.
filePrepend(File, String) - Static method in class edu.rit.io.Files: Prepend the given prefix to the given file.
fileRead - Variable in class ffx.potential.parsers.SystemFilter: True after the file has been read successfully.
fileRead() - Method in class ffx.potential.parsers.SystemFilter: Returns true if the read was successful
files - Variable in class ffx.potential.parsers.SystemFilter: Append multiple files into one MolecularAssembly.
Files - Class in edu.rit.io: Class Files provides static methods for various file related operations.
fileType - Variable in class ffx.algorithms.dynamics.MolecularDynamics: File type to use when saving files.
fileType - Variable in class ffx.potential.cli.WriteoutOptions: -F or --fileFormat Choose the file type to write [PDB/XYZ].
fileType - Variable in class ffx.potential.parsers.SystemFilter: The file format being handled.
FileUtils - Class in ffx.utilities: FileUtils class.
fill(Object) - Method in class edu.rit.mp.BooleanBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Buf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ByteBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.CharacterBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.DoubleBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.FloatBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.IntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.LongBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ObjectBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.ShortBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Signed16BitIntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Signed8BitIntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Unsigned16BitIntegerBuf: Fill this buffer with the given item.
fill(Object) - Method in class edu.rit.mp.Unsigned8BitIntegerBuf: Fill this buffer with the given item.
FILL - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Molecule: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MSGroup: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.MultiResidue: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Polymer: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.bonded.Residue: Abstract method that should specify how to finalize a MSGroup
finalize(boolean, ForceField) - Method in class ffx.potential.MolecularAssembly: Abstract method that should specify how to finalize a MSGroup
findAtom(Atom) - Method in class ffx.potential.MolecularAssembly: findAtom
findAtomsOfElement(Residue, int) - Static method in class ffx.potential.bonded.BondedUtils: Finds all Atoms belonging to a Residue of a given atomic number.
findAtomType(int, ForceField) - Static method in class ffx.potential.bonded.BondedUtils: findAtomType.
findBondedAtoms(Atom, int) - Static method in class ffx.potential.bonded.BondedUtils: Finds Atoms bonded to a given Atom that match a certain atomic number.
findBondedAtoms(Atom, Atom, int) - Static method in class ffx.potential.bonded.BondedUtils: Finds Atoms bonded to a given Atom that match a certain atomic number that do not match an excluded atom.
findChainBreaks(List<Residue>, double) - Static method in class ffx.potential.bonded.PolymerUtils
findClass(String) - Method in class edu.rit.pj.cluster.BackendClassLoader: Find the class with the given name.
findDangelingAtoms() - Method in class ffx.potential.bonded.MSGroup: This method constructs a List of atoms which are under-constrained.
findDangelingAtoms() - Method in class ffx.potential.bonded.MultiResidue: This method constructs a List of atoms which are under-constrained.
findMaxLessIndex(ArrayList<ArrayList<Atom>>, int) - Method in class ffx.potential.parsers.CIFFilter: Find the maximum index that is less than those contained in current model.
findNitrogenAtom(Residue) - Static method in class ffx.potential.bonded.BondedUtils: Finds the backbone nitrogen of a residue.
findNucleotideO4s(Residue) - Static method in class ffx.potential.bonded.BondedUtils: Find the O4' of a nucleic acid Residue.
findResource(String) - Method in class edu.rit.pj.cluster.BackendClassLoader: Find the resource with the given name.
findSeed(Atom, Atom) - Static method in class ffx.potential.Utilities: Returns an atom bonded to the "end" atom, which is not equal to "other".
findSymHKL(int, int, int, HKL) - Method in class ffx.crystal.ReflectionList: findSymHKL
findSymHKL(int, int, int, HKL, boolean) - Method in class ffx.crystal.ReflectionList: findSymHKL
findSymHKL(HKL, HKL) - Method in class ffx.crystal.ReflectionList: findSymHKL
finish() - Method in class edu.rit.pj.IntegerForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.IntegerStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.LongForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.LongStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.ParallelIteration: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.ParallelRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class edu.rit.pj.WorkerIntegerForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerIntegerStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerIteration: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerLongForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerLongStrideForLoop: Perform per-thread finalization actions after finishing the loop iterations.
finish() - Method in class edu.rit.pj.WorkerRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.algorithms.optimize.manybody.GoldsteinPairRegion
finish() - Method in class ffx.algorithms.optimize.manybody.SelfEnergyRegion
finish() - Method in class ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
finish() - Method in class ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
finish() - Method in class ffx.potential.nonbonded.implicit.BornRadiiRegion
finish() - Method in class ffx.potential.nonbonded.implicit.GKEnergyRegion
finish() - Method in class ffx.potential.nonbonded.implicit.SurfaceAreaRegion
finish() - Method in class ffx.potential.nonbonded.NeighborList: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.potential.nonbonded.pme.PolarizationEnergyRegion
finish() - Method in class ffx.potential.nonbonded.pme.RealSpaceEnergyRegion
finish() - Method in class ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
finish() - Method in class ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
finish() - Method in class ffx.potential.nonbonded.RowRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.potential.nonbonded.SliceRegion: Perform finalization actions after parallel execution ends.
finish() - Method in class ffx.xray.BulkSolventList: Perform finalization actions after parallel execution ends.
finished() - Method in class ffx.ui.SwingWorker: Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
FINISHED - Enum constant in enum class edu.rit.pj.cluster.ProcessInfo.State: The job backend process has finished.
FIRST_RESIDUE - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.ResiduePosition
firstDerivative(double) - Method in class ffx.numerics.func1d.QuasiLinearThetaMap
firstDerivative(double) - Method in interface ffx.numerics.func1d.UnivariateDiffFunction: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.BellCurveSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.CompositeSwitch
firstDerivative(double) - Method in class ffx.numerics.switching.ConstantSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.LinearDerivativeSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.MultiplicativeSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.PowerSwitch: First derivative at a point.
firstDerivative(double) - Method in class ffx.numerics.switching.SquaredTrigSwitch: First derivative at a point.
fixed() - Static method in class edu.rit.pj.IntegerSchedule: Returns a fixed schedule object.
fixed() - Static method in class edu.rit.pj.LongSchedule: Returns a fixed schedule object.
FIXED - Enum constant in enum class ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm
FIXED_CHARGE - Enum constant in enum class ffx.potential.parameters.ForceField.ELEC_FORM
FIXEDCHARGE - Enum constant in enum class ffx.potential.bonded.Atom.Resolution
fixParameters(double, double, double, double, double, double) - Method in enum class ffx.crystal.LatticeSystem: Change the lattice parameters to satisfy the restrictions of the lattice system.
flags - Variable in class ffx.ui.behaviors.MouseBehavior
FLAT_BOTTOM_HARMONIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
FLAT_BOTTOM_QUARTIC - Enum constant in enum class ffx.potential.parameters.BondType.BondFunction
flatBottomRadius - Variable in class ffx.potential.parameters.BondType: Radius of a flat bottom where energy and force is 0; typically used for restraints.
FlatEndAnnealSchedule - Class in ffx.algorithms.optimize.anneal: Composite annealing schedule with flat ends (i.e.
FlatEndAnnealSchedule(AnnealingSchedule, double, double, double, double) - Constructor for class ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule: Creates a flat-ended annealing schedule based on a provided schedule for the middle, which is flat for some number of steps at the ends.
Float() - Constructor for class edu.rit.util.Searching.Float
Float() - Constructor for class edu.rit.util.Sorting.Float
Float3 - Class in ffx.numerics.math: Convenience class for working with 3D float vectors.
Float3() - Constructor for class ffx.numerics.math.Float3: Construct a Float3 at (0.0, 0.0, 0.0).
Float3(float[]) - Constructor for class ffx.numerics.math.Float3: Construct a Float3 at a.
Float3(float, float, float) - Constructor for class ffx.numerics.math.Float3: Construct a Float3 at (x, y, z).
FloatArrayBuf - Class in edu.rit.mp.buf: Class FloatArrayBuf provides a buffer for an array of float items sent or received using the Message Protocol (MP).
FloatArrayBuf(float[], Range) - Constructor for class edu.rit.mp.buf.FloatArrayBuf: Construct a new float array buffer.
FloatArrayBuf_1 - Class in edu.rit.mp.buf: Class FloatArrayBuf_1 provides a buffer for an array of float items sent or received using the Message Protocol (MP).
FloatArrayBuf_1(float[], Range) - Constructor for class edu.rit.mp.buf.FloatArrayBuf_1: Construct a new float array buffer.
FloatBuf - Class in edu.rit.mp: Class FloatBuf is the abstract base class for a buffer of float items sent or received using the Message Protocol (MP).
FloatBuf(int) - Constructor for class edu.rit.mp.FloatBuf: Construct a new float buffer.
FloatItemBuf - Class in edu.rit.mp.buf: Class FloatItemBuf provides a buffer for a single float item sent or received using the Message Protocol (MP).
FloatItemBuf() - Constructor for class edu.rit.mp.buf.FloatItemBuf: Construct a new float item buffer.
FloatItemBuf(float) - Constructor for class edu.rit.mp.buf.FloatItemBuf: Construct a new float item buffer with the given initial value.
FloatMath - Class in ffx.numerics.math: The FloatMath class is a simple math library that operates on 3-coordinate float arrays.
FloatMath() - Constructor for class ffx.numerics.math.FloatMath
FloatMatrixBuf - Class in edu.rit.mp.buf: Class FloatMatrixBuf provides a buffer for a matrix of float items sent or received using the Message Protocol (MP).
FloatMatrixBuf(float[][], Range, Range) - Constructor for class edu.rit.mp.buf.FloatMatrixBuf: Construct a new float matrix buffer.
FloatMatrixBuf_1 - Class in edu.rit.mp.buf: Class FloatMatrixBuf_1 provides a buffer for a matrix of float items sent or received using the Message Protocol (MP).
FloatMatrixBuf_1(float[][], Range, Range) - Constructor for class edu.rit.mp.buf.FloatMatrixBuf_1: Construct a new float matrix buffer.
FloatOp - Class in edu.rit.pj.reduction: Class FloatOp is the abstract base class for a binary operation on float values, used to do reduction in a parallel program.
FloatOp() - Constructor for class edu.rit.pj.reduction.FloatOp: Construct a new float binary operation.
floatValue() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedCharacter: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedDouble: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedFloat: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedInteger: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedLong: Returns this reduction variable's current value converted to type float.
floatValue() - Method in class edu.rit.pj.replica.ReplicatedShort: Returns this reduction variable's current value converted to type float.
floodReceive(Buf) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator.
floodReceive(Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator (non-blocking).
floodReceive(Integer, Buf) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator with the given message tag.
floodReceive(Integer, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-receive a message from any process in this communicator with the given message tag (non-blocking).
floodSend(int, Buf) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator with the given message tag.
floodSend(int, Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator with the given message tag (non-blocking).
floodSend(Buf) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator.
floodSend(Buf, CommRequest) - Method in class edu.rit.pj.Comm: Flood-send a message to all processes in this communicator (non-blocking).
flush() - Method in class edu.rit.io.LineBufferedOutputStream: Flush this line buffered output stream.
flush() - Method in class edu.rit.pj.cluster.BackendFileOutputStream: Flush this output stream.
flush() - Method in class ffx.ui.LogHandler
Fm - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
fma(double[], double, double[]) - Static method in class ffx.numerics.math.DoubleMath: Compute a * b + c and return the result in a new array.
fma(double[], double, double[], double[]) - Static method in class ffx.numerics.math.DoubleMath: Compute a * b + c.
fma(double, Double3) - Method in class ffx.numerics.math.Double3: Compute this * b + c and return the result in a new Double3.
fma(float[], float, float[]) - Static method in class ffx.numerics.math.FloatMath: Compute a * b + c and return the result in a new array.
fma(float[], float, float[], float[]) - Static method in class ffx.numerics.math.FloatMath: Compute a * b + c.
fma(float, Float3) - Method in class ffx.numerics.math.Float3: Compute a * b + c and return the result in a new Float3.
fmaI(double, Double3) - Method in class ffx.numerics.math.Double3: Compute this * b + c and return the result in a new Double3.
fmaI(float, Float3) - Method in class ffx.numerics.math.Float3: Compute a * b + c and return the result in a new Float3.
fN(HKL, int) - Method in class ffx.xray.XRayFormFactor: f_n
FOFC - Static variable in interface ffx.xray.SplineEnergy.Type
foFc1 - Variable in class ffx.xray.DiffractionRefinementData: mFo - DFc coefficients.
foFc1F(int) - Method in class ffx.xray.DiffractionRefinementData: foFc1F
foFc1Phi(int) - Method in class ffx.xray.DiffractionRefinementData: foFc1Phi
FoFc2F(int) - Method in class ffx.xray.DiffractionRefinementData: FoFc2F
FoFc2Phi(int) - Method in class ffx.xray.DiffractionRefinementData: FoFc2Phi
fomPhi - Variable in class ffx.xray.DiffractionRefinementData: Figure of merit and phase.
FOR - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid3
FORCE - Enum constant in enum class ffx.potential.bonded.RendererCache.ViewModel
force0 - Variable in class ffx.potential.bonded.StretchBend: Force constant.
force1 - Variable in class ffx.potential.bonded.StretchBend: Force constant.
forceConstant - Variable in class ffx.potential.parameters.AngleType: Force constant (Kcal/mole/radian^2).
forceConstant - Variable in class ffx.potential.parameters.BondType: Force constant (Kcal/mol).
forceConstant - Variable in class ffx.potential.parameters.OutOfPlaneBendType: Force constant (Kcal/mol/Angstrom).
forceConstant - Variable in class ffx.potential.parameters.PiOrbitalTorsionType: Force constant.
forceConstant - Variable in class ffx.potential.parameters.UreyBradleyType: Force constant (Kcal/mole/angstroms^2).
forceConstants - Variable in class ffx.potential.parameters.AngleTorsionType: Force constants.
forceConstants - Variable in class ffx.potential.parameters.StretchBendType: Force constants (Kcal/mole/Angstrom-Degrees).
forceConstants - Variable in class ffx.potential.parameters.StretchTorsionType: Force constants.
forcefield - Variable in class ffx.ui.commands.SimulationDefinition
forceField - Variable in class ffx.potential.MolecularAssembly
forceField - Variable in class ffx.potential.parsers.SystemFilter: The molecular mechanics force field being used.
ForceField - Class in ffx.potential.parameters: The ForceField class organizes parameters for a molecular mechanics force field.
ForceField(CompositeConfiguration) - Constructor for class ffx.potential.parameters.ForceField: ForceField Constructor.
ForceField.ELEC_FORM - Enum Class in ffx.potential.parameters
ForceField.ForceFieldName - Enum Class in ffx.potential.parameters: Available force fields.
ForceField.ForceFieldType - Enum Class in ffx.potential.parameters
forceFieldEnergy - Variable in class ffx.algorithms.thermodynamics.OrthogonalSpaceTempering: Force Field Potential Energy (i.e.
forceFieldEnergy - Variable in class ffx.potential.commands.Energy
ForceFieldEnergy - Class in ffx.potential: Compute the potential energy and derivatives of a molecular system described by a force field.
ForceFieldEnergy(MolecularAssembly) - Constructor for class ffx.potential.ForceFieldEnergy: Constructor for ForceFieldEnergy.
ForceFieldEnergy(MolecularAssembly, List<CoordRestraint>) - Constructor for class ffx.potential.ForceFieldEnergy: Constructor for ForceFieldEnergy.
ForceFieldEnergy(MolecularAssembly, List<CoordRestraint>, int) - Constructor for class ffx.potential.ForceFieldEnergy: Constructor for ForceFieldEnergy.
ForceFieldEnergy.Platform - Enum Class in ffx.potential: Platform describes a set of force field implementations that include a pure Java reference implementation (FFX), and two OpenMM implementations (OMM_CUDA and OMM_REF are supported)
ForceFieldEnergyOpenMM - Class in ffx.potential: Compute the potential energy and derivatives using OpenMM.
ForceFieldEnergyOpenMM(MolecularAssembly, ForceFieldEnergy.Platform, List<CoordRestraint>, int) - Constructor for class ffx.potential.ForceFieldEnergyOpenMM: ForceFieldEnergyOpenMM constructor; offloads heavy-duty computation to an OpenMM Platform while keeping track of information locally.
ForceFieldEnergyOpenMM.Context - Class in ffx.potential: Creates and manage an OpenMM Context.
ForceFieldEnergyOpenMM.State - Class in ffx.potential: Retrieve state information from an OpenMM Simulation.
ForceFieldEnergyOpenMM.System - Class in ffx.potential: Create and manage an OpenMM System.
ForceFieldFileFilter - Class in ffx.potential.parsers: The ForceFieldFileFilter class is used to choose a TINKER Parameter file (*.PRM).
ForceFieldFileFilter() - Constructor for class ffx.potential.parsers.ForceFieldFileFilter: Default Constructor
ForceFieldFilter - Class in ffx.potential.parsers: The ForceFieldFilter Class is used to parse and store molecular mechanics data from keyword/property and parameter (*.PRM) files.
ForceFieldFilter(CompositeConfiguration) - Constructor for class ffx.potential.parsers.ForceFieldFilter: Constructor for ForceFieldFilter.
forceFieldURL - Variable in class ffx.potential.parameters.ForceField: URL to the force field parameter file.
format(LogRecord) - Method in class ffx.ui.LogFormatter
formatEnergy(double) - Method in class ffx.algorithms.optimize.RotamerOptimization: Utility method for formatting energies, using 16 spaces with 8 digits of precision.
FormFactor - Interface in ffx.xray: FormFactor interface.
FORWARD - Enum constant in enum class ffx.algorithms.optimize.RotamerOptimization.Direction
FORWARDS - Enum constant in enum class ffx.numerics.estimator.Zwanzig.Directionality
FOTOESQ - Static variable in interface ffx.xray.SplineEnergy.Type
FourBodyEnergyRegion - Class in ffx.algorithms.optimize.manybody: Compute 4-Body energies.
FourBodyEnergyRegion(RotamerOptimization, DistanceMatrix, EnergyExpansion, EliminatedRotamers, Residue[], List<Residue>, double) - Constructor for class ffx.algorithms.optimize.manybody.FourBodyEnergyRegion
Fr - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
fractionalCount() - Method in class ffx.potential.MolecularAssembly: Count the number of fractional coordinate entities in the system.
fractionalMultipole - Variable in class ffx.potential.nonbonded.ParticleMeshEwald: Fractional multipoles in the global frame with dimensions of [nsymm][nAtoms][10]
frame() - Method in class ffx.ui.MainPanel: frame
frameAtomTypes - Variable in class ffx.potential.parameters.MultipoleType: Atom types that define the local frame of this multipole.
frameDefinition - Variable in class ffx.potential.parameters.MultipoleType: Local frame definition method.
free() - Method in class ffx.potential.ForceFieldEnergyOpenMM.State
free() - Method in class ffx.potential.ForceFieldEnergyOpenMM.System: Destroy the system.
freeEnergyDiff - Variable in enum class ffx.potential.parameters.TitrationUtils.Titration
freeR - Variable in class ffx.xray.DiffractionRefinementData: Array of R free flags;
FROM_JOB_BACKEND - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job backend process.
FROM_JOB_FRONTEND - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job frontend process.
FROM_JOB_LAUNCHER - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job launcher process.
FROM_JOB_SCHEDULER - Static variable in class edu.rit.pj.cluster.Message: The message tag for a message from a job scheduler process.
fromRank - Variable in class edu.rit.pj.CommStatus: The rank of the source process that sent the message.
frontend - Variable in class edu.rit.pj.cluster.JobInfo: Reference to the job frontend process.
frontendAddress - Variable in class edu.rit.pj.cluster.ProcessInfo: Host/port to which the job backend process is listening for the frontend communicator, or null if the frontend communicator does not exist.
FrontendFileReader - Class in edu.rit.pj.cluster: Class FrontendFileReader provides an object that reads sequential files in the job frontend process.
FrontendFileReader(JobFrontend) - Constructor for class edu.rit.pj.cluster.FrontendFileReader: Construct a new frontend file reader.
FrontendFileWriter - Class in edu.rit.pj.cluster: Class FrontendFileWriter provides an object that writes sequential files in the job frontend process.
FrontendFileWriter(JobFrontend) - Constructor for class edu.rit.pj.cluster.FrontendFileWriter: Construct a new frontend file writer.
fs - Variable in class ffx.xray.DiffractionRefinementData: Calculated bulk solvent structure factors.
FSEC_TO_PSEC - Static variable in class ffx.utilities.Constants: Constant FSEC_TO_PSEC=0.001
fsF(int) - Method in class ffx.xray.DiffractionRefinementData: fsF
fSigFCutoff - Variable in class ffx.xray.DiffractionRefinementData
fsPhi(int) - Method in class ffx.xray.DiffractionRefinementData: fsPhi
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Adiabatic: The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Berendsen: The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Bussi: The full-step temperature correction.
fullStep(double) - Method in class ffx.algorithms.dynamics.thermostats.Thermostat: The full-step temperature correction.
FunctionDataCurve - Class in ffx.numerics.integrate: A FunctionDataCurve represents a set of points along a 1-dimensional, analytically integrable function.
FunctionDataCurve() - Constructor for class ffx.numerics.integrate.FunctionDataCurve
fwDec(double, int, int) - Static method in class ffx.utilities.StringUtils: Prints a fixed-width decimal, similar to String.format(%width.precf, val), but ensuring the resulting string is never longer than width.
fwFpDec(double, int, int) - Static method in class ffx.utilities.StringUtils: Prints a fixed-width decimal using String.format conventions, throwing an error if the value cannot be formatted within that space.
fwFpTrunc(double, int, int) - Static method in class ffx.utilities.StringUtils: Prints a fixed-width decimal using String.format conventions, reducing the value if necessary to fit within the width.
fX(double) - Method in class ffx.numerics.integrate.CompositeCurve: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.CosineWave: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.FunctionDataCurve: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.PolynomialCurve: Evaluates the function at x.
fX(double) - Method in class ffx.numerics.integrate.SinWave: Evaluates the function at x.

G

G - Enum constant in enum class ffx.potential.bonded.AminoAcidUtils.AminoAcid1
G - Enum constant in enum class ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
G - Variable in class ffx.crystal.Crystal: The direct space metric matrix.
Ga - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
gamma - Variable in class ffx.crystal.Crystal: The interaxial lattice angle between a and b.
gamma - Variable in class ffx.potential.nonbonded.VanDerWaalsForm: First constant suggested by Halgren for the Buffered-14-7 potential.
gather(int, int, Buf, Buf[]) - Method in class edu.rit.pj.Comm: Gather messages from all processes in this communicator using the given message tag.
gather(int, Buf, Buf[]) - Method in class edu.rit.pj.Comm: Gather messages from all processes in this communicator.
GAUSS_DISP - Enum constant in enum class ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
GAUSSIAN - Enum constant in enum class ffx.xray.CrystalReciprocalSpace.SolventModel: Smooth the boundary of the classic model using Gaussians.
GaussVol - Class in ffx.potential.nonbonded.implicit: GaussVol implements a description molecular volume and surface area described by overlapping Gaussian spheres.
GaussVol(Atom[], ForceField, ParallelTeam) - Constructor for class ffx.potential.nonbonded.implicit.GaussVol: Creates/Initializes a GaussVol instance.
Gd - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
Ge - Enum constant in enum class ffx.potential.bonded.Atom.ElementSymbol
GeneralizedKirkwood - Class in ffx.potential.nonbonded: This Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a NeighborList.
GeneralizedKirkwood(ForceField, Atom[], ParticleMeshEwald, Crystal, ParallelTeam, double) - Constructor for class ffx.potential.nonbonded.GeneralizedKirkwood: Constructor for GeneralizedKirkwood.
GeneralizedKirkwood.NonPolarModel - Enum Class in ffx.potential.nonbonded
generate(int, double, double) - Method in enum class ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules: Creates an AnnealingSchedule corresponding to this enum and provided values.
generateFsigFfromAnomalousFsigF(double[][]) - Method in class ffx.xray.DiffractionRefinementData: Generate average F/sigF from anomalous F/sigF.
generateLoops(int, int) - Method in class ffx.potential.utils.Loop: generateLoops.
generateLoops(int, int, double[]) - Method in class ffx.potential.utils.Loop: generateLoops.
generateRFree() - Method in class ffx.xray.DiffractionRefinementData: Mark 5% of reflections for cross validation (R free flags).
GenerateRotamers - Class in ffx.algorithms.misc: The GenerateRotamers class helps generate a rotamer library (particularly for nonstandard amino acids) for a Residue.
GenerateRotamers(MolecularAssembly, Potential, Residue, File, int, AlgorithmListener) - Constructor for class ffx.algorithms.misc.GenerateRotamers: Intended to create rotamer sets for nonstandard amino acids.
GenerateRotamers(MolecularAssembly, Potential, Residue, File, int, AlgorithmListener, RotamerLibrary) - Constructor for class ffx.algorithms.misc.GenerateRotamers: Intended to create rotamer sets for nonstandard amino acids.
generateSource(GKSource.GK_TENSOR_MODE, GKSource.GK_MULTIPOLE_ORDER, double, double, double) - Method in class ffx.numerics.multipole.GKSource: Generate source terms for the Kirkwood version of the Challacombe et al.
generateTensor() - Method in class ffx.numerics.multipole.MultipoleTensor: Generate the tensor using hard-coded methods or via recursion.
generateTensor(double[]) - Method in class ffx.numerics.multipole.MultipoleTensor: For the MultipoleTensorTest class and testing.
generateTestData_v1() - Static method in class ffx.numerics.integrate.Integration: generateTestData_v1.
generateXPoints(double, double, int, boolean) - Static method in class ffx.numerics.integrate.Integrate1DNumeric: Generates a set of points along x.
GEOMETRIC - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.EPSILON_RULE
GEOMETRIC - Enum constant in enum class ffx.potential.nonbonded.VanDerWaalsForm.RADIUS_RULE
get() - Method in class edu.rit.pj.reduction.SharedBoolean: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedByte: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedCharacter: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedDouble: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedFloat: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedInteger: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedLong: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedObject: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.reduction.SharedShort: Returns this reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedBoolean: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.replica.ReplicatedByte: Returns this replicated, shared reduction variable's current value.
get() - Method in class edu.rit.pj.