Uses of Class
ffx.crystal.Crystal

Packages that use Crystal

Package	Description
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.optimize.manybody
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	The Crystal package implements space group symmetry and periodic boundary condition support.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
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
ffx.potential.nonbonded.pme
ffx.potential.openmm
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.realspace.parsers	The Parsers package reads and writes CCP4 map files.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.parsers	The Parsers package reads CNS files and reads/writes MTZ files.

Uses of Crystal in ffx.algorithms.dynamics

Methods in ffx.algorithms.dynamics that return Crystal

Modifier and Type	Method	Description
Crystal	Barostat.getCrystal()

Methods in ffx.algorithms.dynamics with parameters of type Crystal

Modifier and Type	Method	Description
void	Barostat.setCrystal(Crystal crystal)

Uses of Crystal in ffx.algorithms.optimize.manybody

Methods in ffx.algorithms.optimize.manybody with parameters of type Crystal

Modifier and Type	Method	Description
boolean	ManyBodyCell.anyRotamerInsideCell(Residue residue, Crystal crystal, SymOp symOp, boolean variableOnly)	Checks if any rotamer of a Residue is inside this BoxOptCell.
boolean	ManyBodyCell.atomInsideCell(Atom atom, Crystal crystal, SymOp symOp)	Checks if an Atom would be contained inside this cell.
boolean	ManyBodyCell.residueInsideCell(Residue residue, Crystal crystal, SymOp symOp, boolean variableOnly)	Checks if a Residue is inside this BoxOptCell.

Constructors in ffx.algorithms.optimize.manybody with parameters of type Crystal

Modifier	Constructor	Description
	DistanceRegion(int nt, int nResidues, Crystal crystal, int[][][] lists, IntegerSchedule schedule)

Uses of Crystal in ffx.algorithms.thermodynamics

Methods in ffx.algorithms.thermodynamics that return Crystal

Modifier and Type	Method	Description
Crystal	OrthogonalSpaceTempering.getCrystal()

Methods in ffx.algorithms.thermodynamics with parameters of type Crystal

Modifier and Type	Method	Description
void	OrthogonalSpaceTempering.setCrystal(Crystal crystal)

Uses of Crystal in ffx.crystal

Subclasses of Crystal in ffx.crystal

Modifier and Type	Class	Description
class	NCSCrystal	The NCSCrystal class extends Crystal to support non-crystallographic symmetry (NCS).
class	ReplicatesCrystal	The ReplicatesCrystal class extends Crystal to generate additional symmetry operators needed to describe a "replicated" super-cell.

Fields in ffx.crystal declared as Crystal

Modifier and Type	Field	Description
final Crystal	ReflectionList.crystal	The Crystal instance.

Methods in ffx.crystal that return Crystal

Modifier and Type	Method	Description
static Crystal	Crystal.checkProperties(org.apache.commons.configuration2.CompositeConfiguration properties)	checkProperties
Crystal	CrystalPotential.getCrystal()
Crystal	Crystal.getUnitCell()	The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
Crystal	NCSCrystal.getUnitCell()	The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
Crystal	ReplicatesCrystal.getUnitCell()	The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
static Crystal	SpaceGroupConversions.hrConversion(double a, double b, double c, double alpha, double beta, double gamma, SpaceGroup currentSG)	Convert between hexagonal and rhombohedral space groups.
static Crystal	SpaceGroupConversions.hrConversion(Crystal crystal)	Convert between hexagonal and rhombohedral space groups.
static Crystal	NCSCrystal.NCSCrystalFactory(Crystal unitCell, List<SymOp> symOps)	Returns an NCSCrystal by expanding the orignal unit cell with the symmetry operators provided by the BIOMT records in the PDB files.
static Crystal	ReplicatesCrystal.replicatesCrystalFactory(Crystal unitCell, double cutOff2)	Returns a ReplicatesCrystal large enough to satisfy the minimum image convention for the specified unit cell and cutoff criteria.
static Crystal	ReplicatesCrystal.replicatesCrystalFactory(Crystal unitCell, double cutOff2, int[] replicatesVector)	Returns a ReplicatesCrystal large enough to satisfy the minimum image convention for the specified unit cell and cutoff criteria.

Methods in ffx.crystal with parameters of type Crystal

Modifier and Type	Method	Description
static Crystal	SpaceGroupConversions.hrConversion(Crystal crystal)	Convert between hexagonal and rhombohedral space groups.
static Crystal	NCSCrystal.NCSCrystalFactory(Crystal unitCell, List<SymOp> symOps)	Returns an NCSCrystal by expanding the orignal unit cell with the symmetry operators provided by the BIOMT records in the PDB files.
static Crystal	ReplicatesCrystal.replicatesCrystalFactory(Crystal unitCell, double cutOff2)	Returns a ReplicatesCrystal large enough to satisfy the minimum image convention for the specified unit cell and cutoff criteria.
static Crystal	ReplicatesCrystal.replicatesCrystalFactory(Crystal unitCell, double cutOff2, int[] replicatesVector)	Returns a ReplicatesCrystal large enough to satisfy the minimum image convention for the specified unit cell and cutoff criteria.
void	CrystalPotential.setCrystal(Crystal crystal)

Constructors in ffx.crystal with parameters of type Crystal

Modifier	Constructor	Description
	ReflectionList(Crystal crystal, Resolution resolution)	Constructor for ReflectionList.
	ReflectionList(Crystal crystal, Resolution resolution, org.apache.commons.configuration2.CompositeConfiguration properties)	Constructor for ReflectionList.
	ReplicatesCrystal(Crystal unitCell, int l, int m, int n, double cutOff2)	Constructor for a ReplicatesCrystal.

Uses of Crystal in ffx.potential

Methods in ffx.potential that return Crystal

Modifier and Type	Method	Description
Crystal	DualTopologyEnergy.getCrystal()
Crystal	ForceFieldEnergy.getCrystal()
Crystal	MolecularAssembly.getCrystal()	getCrystal
Crystal	QuadTopologyEnergy.getCrystal()

Methods in ffx.potential with parameters of type Crystal

Modifier and Type	Method	Description
void	DualTopologyEnergy.setCrystal(Crystal crystal)
void	ForceFieldEnergy.setCrystal(Crystal crystal)
void	ForceFieldEnergy.setCrystal(Crystal crystal, boolean checkReplicatesCell)	Set the boundary conditions for this calculation.
void	MolecularAssembly.setCrystal(Crystal crystal)	Set the Crystal for the Potential of this MolecularAssembly.
void	QuadTopologyEnergy.setCrystal(Crystal crystal)

Uses of Crystal in ffx.potential.bonded

Constructors in ffx.potential.bonded with parameters of type Crystal

Modifier	Constructor	Description
	RestrainDistance(Atom a1, Atom a2, Crystal crystal, boolean lambdaTerm, double lamStart, double lamEnd, UnivariateSwitchingFunction sf)	Creates a distance restraint between two Atoms.

Uses of Crystal in ffx.potential.nonbonded

Fields in ffx.potential.nonbonded declared as Crystal

Modifier and Type	Field	Description
protected Crystal	SpatialDensityRegion.crystal

Methods in ffx.potential.nonbonded with parameters of type Crystal

Modifier and Type	Method	Description
void	GeneralizedKirkwood.setCrystal(Crystal crystal)	Setter for the field crystal.
void	NeighborList.setCrystal(Crystal crystal)	The NeighborList will be re-configured, if necessary, for the supplied Crystal.
void	ParticleMeshEwald.setCrystal(Crystal crystal)
void	ReciprocalSpace.setCrystal(Crystal crystal)	Setter for the field crystal.
final void	RowRegion.setCrystal(Crystal crystal, int gX, int gY, int gZ)	Setter for the field crystal.
final void	SliceRegion.setCrystal(Crystal crystal, int gX, int gY, int gZ)	Setter for the field crystal.
final void	SpatialDensityRegion.setCrystal(Crystal crystal, int gX, int gY, int gZ)	Setter for the field crystal.
void	VanDerWaals.setCrystal(Crystal crystal)	If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated.
void	VanDerWaalsTornado.setCrystal(Crystal crystal)	If the crystal being passed in is not equal to the current crystal, then some Van der Waals data structures may need to updated.

Constructors in ffx.potential.nonbonded with parameters of type Crystal

Modifier	Constructor	Description
	GeneralizedKirkwood(ForceField forceField, Atom[] atoms, ParticleMeshEwald particleMeshEwald, Crystal crystal, ParallelTeam parallelTeam, double gkCutoff)	Constructor for GeneralizedKirkwood.
	NCSRestraint(Atom[] atoms, ForceField forceField, Crystal crystal)	This NCSRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
	NeighborList(MaskingInterface maskingRules, Crystal crystal, Atom[] atoms, double cutoff, double buffer, ParallelTeam parallelTeam)	Constructor for the NeighborList class.
	ParticleMeshEwald(Atom[] atoms, int[] molecule, ForceField forceField, Crystal crystal, NeighborList neighborList, ForceField.ELEC_FORM elecForm, double ewaldCutoff, double gkCutoff, ParallelTeam parallelTeam)	ParticleMeshEwald constructor.
	ReciprocalSpace(ParticleMeshEwald particleMeshEwald, Crystal crystal, ForceField forceField, Atom[] atoms, double aewald, ParallelTeam fftTeam, ParallelTeam parallelTeam)	Reciprocal Space PME contribution.
	SpatialDensityRegion(int gX, int gY, int gZ, double[] grid, int basisSize, int nSymm, int minWork, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates)	Constructor for SpatialDensityRegion.
	VanDerWaals(Atom[] atoms, int[] molecule, boolean[] neuralNetwork, Crystal crystal, ForceField forceField, ParallelTeam parallelTeam, double vdwCutoff, double neighborListCutoff)	The VanDerWaals class constructor.
	VanDerWaalsTornado(Atom[] atoms, Crystal crystal, ForceField forceField, double vdwCutoff)	The VanDerWaalsTornado class constructor.

Uses of Crystal in ffx.potential.nonbonded.implicit

Methods in ffx.potential.nonbonded.implicit with parameters of type Crystal

Modifier and Type	Method	Description
void	BornGradRegion.init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, double[] unscaledBornIntegral, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born, AtomicDoubleArray3D grad, AtomicDoubleArray sharedBornGrad)
void	BornRadiiRegion.init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born)
void	DispersionRegion.init(Atom[] atoms, Crystal crystal, boolean[] use, int[][][] neighborLists, double[] x, double[] y, double[] z, double cut2, boolean gradient, AtomicDoubleArray3D grad)	Initialize the DispersionRegion for energy calculation.
void	GKEnergyRegion.init(Atom[] atoms, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] baseRadius, double[] born, boolean gradient, ParallelTeam parallelTeam, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad)
void	InducedGKFieldRegion.init(Atom[] atoms, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] born, AtomicDoubleArray3D sharedGKField, AtomicDoubleArray3D sharedGKFieldCR)
void	PermanentGKFieldRegion.init(Atom[] atoms, double[][][] globalMultipole, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] born, AtomicDoubleArray3D sharedGKField)

Uses of Crystal in ffx.potential.nonbonded.pme

Fields in ffx.potential.nonbonded.pme declared as Crystal

Modifier and Type	Field	Description
Crystal	AlchemicalParameters.vaporCrystal	Boundary conditions for the vapor end of the alchemical path.

Methods in ffx.potential.nonbonded.pme with parameters of type Crystal

Modifier and Type	Method	Description
void	ExpandInducedDipolesRegion.init(Atom[] atoms, Crystal crystal, double[][][] inducedDipole, double[][][] inducedDipoleCR)
void	InducedDipoleFieldRegion.init(Atom[] atoms, Crystal crystal, boolean[] use, int[] molecule, double[] ipdamp, double[] thole, double[][][] coordinates, RealSpaceNeighborParameters realSpaceNeighborParameters, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean reciprocalSpaceTerm, ReciprocalSpace reciprocalSpace, LambdaMode lambdaMode, EwaldParameters ewaldParameters, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, PMETimings pmeTimings)
void	InitializationRegion.init(boolean lambdaTerm, ExtendedSystem esvSystem, Atom[] atoms, double[][][] coordinates, Crystal crystal, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[] polarizability, double[] titrationPolarizability, double[] tautomerPolarizability, double[] thole, double[] ipdamp, boolean[] use, int[][][] neighborLists, int[][][] realSpaceLists, int[][][] vaporLists, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque)
void	PCGSolver.init(Atom[] atoms, double[][][] coordinates, double[] polarizability, double[] ipdamp, double[] thole, boolean[] use, Crystal crystal, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] directDipole, double[][] directDipoleCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, EwaldParameters ewaldParameters, double dieletric, ParallelTeam parallelTeam, IntegerSchedule realSpaceSchedule, long[] realSpaceSCFTime)
void	PermanentFieldRegion.init(Atom[] atoms, Crystal crystal, double[][][] coordinates, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, int[][][] neighborLists, ScaleParameters scaleParameters, boolean[] use, int[] molecule, double[] ipdamp, double[] thole, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, LambdaMode lambdaMode, boolean reciprocalSpaceTerm, ReciprocalSpace reciprocalSpace, EwaldParameters ewaldParameters, PCGSolver pcgSolver, IntegerSchedule permanentSchedule, RealSpaceNeighborParameters realSpaceNeighborParameters, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, PMETimings pmeTimings)
void	RealSpaceEnergyRegion.init(Atom[] atoms, Crystal crystal, ExtendedSystem extendedSystem, boolean esvTerm, double[][][] coordinates, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean[] use, int[] molecule, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, int[][] mask15, boolean[] isSoft, double[] ipdamp, double[] thole, RealSpaceNeighborParameters realSpaceNeighborParameters, boolean gradient, boolean lambdaTerm, boolean nnTerm, LambdaMode lambdaMode, Polarization polarization, EwaldParameters ewaldParameters, ScaleParameters scaleParameters, AlchemicalParameters alchemicalParameters, long[] realSpaceEnergyTime, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
void	ReciprocalEnergyRegion.init(Atom[] atoms, Crystal crystal, boolean gradient, boolean lambdaTerm, boolean esvTerm, boolean[] use, double[][][] globalMultipole, double[][][] globalFracMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][] cartMultipolePhi, double[][] fracMultipolePhi, Polarization polarization, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, double[][] fracInducedDipolePhi, double[][] fracInducedDipolePhiCR, ReciprocalSpace reciprocalSpace, AlchemicalParameters alchemicalParameters, ExtendedSystem extendedSystem, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)

Uses of Crystal in ffx.potential.openmm

Methods in ffx.potential.openmm with parameters of type Crystal

Modifier and Type	Method	Description
void	OpenMMEnergy.setCrystal(Crystal crystal)
void	OpenMMContext.setPeriodicBoxVectors(Crystal crystal)	Set the periodic box vectors for a context based on the crystal instance.

Uses of Crystal in ffx.potential.parsers

Methods in ffx.potential.parsers with parameters of type Crystal

Modifier and Type	Method	Description
boolean	DYNFilter.readDYN(File dynFile, Crystal crystal, double[] x, double[] v, double[] a, double[] ap)	readDYN
boolean	DYNFilter.writeDYN(File dynFile, Crystal crystal, double[] x, double[] v, double[] a, double[] ap)	writeDYN
boolean	XPHFilter.writeFileAsP1(File saveFile, boolean append, Crystal crystal)	writeFileAsP1
boolean	XPHFilter.writeFileAsP1(File saveFile, boolean append, Crystal crystal, String[] extraLines)	writeFileAsP1
boolean	XYZFilter.writeFileAsP1(File saveFile, boolean append, Crystal crystal)	writeFileAsP1
boolean	XYZFilter.writeFileAsP1(File saveFile, boolean append, Crystal crystal, int[] lmn, String[] extraLines)	Write file as a P1 system in XYZ format.
boolean	XYZFilter.writeFileAsP1(File saveFile, boolean append, Crystal crystal, String[] extraLines)	writeFileAsP1

Uses of Crystal in ffx.realspace

Methods in ffx.realspace that return Crystal

Modifier and Type	Method	Description
Crystal[]	RealSpaceData.getCrystal()	Getter for the field crystal.
Crystal	RealSpaceEnergy.getCrystal()

Methods in ffx.realspace with parameters of type Crystal

Modifier and Type	Method	Description
void	RealSpaceData.setCrystal(Crystal[] crystal)	Setter for the field crystal.
void	RealSpaceEnergy.setCrystal(Crystal crystal)

Uses of Crystal in ffx.realspace.parsers

Methods in ffx.realspace.parsers that return Crystal

Modifier and Type	Method	Description
Crystal	CCP4MapFilter.getCrystal(String fileName, org.apache.commons.configuration2.CompositeConfiguration properties)	getCrystal
Crystal	RealSpaceFileFilter.getCrystal(String filename, org.apache.commons.configuration2.CompositeConfiguration properties)	getCrystal

Uses of Crystal in ffx.xray

Methods in ffx.xray that return Crystal

Modifier and Type	Method	Description
Crystal[]	DiffractionData.getCrystal()	Getter for the field crystal.
Crystal	RefinementEnergy.getCrystal()
Crystal	XRayEnergy.getCrystal()

Methods in ffx.xray with parameters of type Crystal

Modifier and Type	Method	Description
void	RefinementEnergy.setCrystal(Crystal crystal)
void	XRayEnergy.setCrystal(Crystal crystal)

Constructors in ffx.xray with parameters of type Crystal

Modifier	Constructor	Description
	BulkSolventDensityRegion(int gX, int gY, int gZ, double[] grid, int basisSize, int nSymm, int minWork, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.
	BulkSolventList(Crystal crystal, Atom[] atoms, double cutoff, ParallelTeam parallelTeam)	Constructor for the NeighborList class.
	BulkSolventRowRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.
	BulkSolventSliceRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.

Uses of Crystal in ffx.xray.parsers

Methods in ffx.xray.parsers with parameters of type Crystal

Modifier and Type	Method	Description
double	CIFFilter.getResolution(File cifFile, Crystal crystal)	Attempt to determine resolution of reflection file.
double	CNSFilter.getResolution(File cnsFile, Crystal crystal)	Attempt to determine resolution of reflection file.
double	DiffractionFileFilter.getResolution(File file, Crystal crystal)	Attempt to determine resolution of reflection file.
double	MTZFilter.getResolution(File mtzFile, Crystal crystal)	Attempt to determine resolution of reflection file.

Constructors in ffx.xray.parsers with parameters of type Crystal

Modifier	Constructor	Description
	CCP4MapWriter(int orix, int oriy, int oriz, int extx, int exty, int extz, int nx, int ny, int nz, Crystal crystal, String filename)	Constructor for CCP4MapWriter.
	CCP4MapWriter(int extx, int exty, int extz, Crystal crystal, String filename)	construct mapwriter object
	CNSMapWriter(int nx, int ny, int nz, Crystal crystal, String filename)	Constructor for CNSMapWriter.