Uses of Class
ffx.crystal.SymOp

Packages that use SymOp

Package	Description
ffx.algorithms.optimize.manybody	The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
ffx.crystal	The Crystal package implements space group symmetry and periodic boundary condition support.

Uses of SymOp in ffx.algorithms.optimize.manybody

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

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.
double	DistanceMatrix.interResidueDistance(double[][] resi, double[][] resj, SymOp symOp)	Calculates the minimum distance between two sets of coordinates in a given symmetry operator.
boolean	ManyBodyCell.residueInsideCell(Residue residue, Crystal crystal, SymOp symOp, boolean variableOnly)	Checks if a Residue is inside this BoxOptCell.

Uses of SymOp in ffx.crystal

Fields in ffx.crystal with type parameters of type SymOp

Modifier and Type	Field	Description
final List<SymOp>	SpaceGroup.symOps	A List of SymOp instances.

Methods in ffx.crystal that return SymOp

Modifier and Type	Method	Description
SymOp	SymOp.append(SymOp symOp)	Return the combined SymOp that is equivalent to first applying this SymOp and then the argument.
static SymOp	SymOp.combineSymOps(SymOp symOp1, SymOp symOp2)	Return the combined SymOp that is equivalent to first applying symOp1 and then SymOp2.
SymOp	SpaceGroup.getSymOp(int i)	Return the ith symmetry operator.
static SymOp	SymOp.invertSymOp(SymOp symOp)	Invert a symmetry operator.
static SymOp	SymOp.parse(String s)	Create a SymOp from an input String.
SymOp	SymOp.prepend(SymOp symOp)	Return the combined SymOp that is equivalent to first applying the argument and then this SymOp.
static SymOp	SymOp.randomSymOpFactory(double scalar)	Generate a random Cartesian Symmetry Operator.
static SymOp	SymOp.randomSymOpFactory(double[] tr)	Generate a random Cartesian Symmetry Operator.

Methods in ffx.crystal with parameters of type SymOp

Modifier and Type	Method	Description
SymOp	SymOp.append(SymOp symOp)	Return the combined SymOp that is equivalent to first applying this SymOp and then the argument.
static void	SymOp.applyCartesianSymOp(double[] xyz, double[] mate, SymOp symOp)	Apply a cartesian symmetry operator to an array of coordinates.
static void	SymOp.applyCartesianSymOp(double[] xyz, double[] mate, SymOp symOp, boolean[] mask)	Apply a cartesian symmetry operator to an array of coordinates.
static void	SymOp.applyCartesianSymRot(double[] xyz, double[] mate, SymOp symOp)	Apply a Cartesian symmetry rotation to an array of Cartesian coordinates.
static void	SymOp.applyCartesianSymRot(double[] xyz, double[] mate, SymOp symOp, boolean[] mask)	Apply a Cartesian symmetry rotation to an array of Cartesian coordinates.
static void	SymOp.applyCartSymOp(int n, double[] x, double[] y, double[] z, double[] mateX, double[] mateY, double[] mateZ, SymOp symOp)	Apply a Cartesian symmetry operator to an array of Cartesian coordinates.
static void	SymOp.applyFracSymOp(double[] xyz, double[] mate, SymOp symOp)	Apply a fractional symmetry operator to one set of coordinates.
void	Crystal.applySymOp(double[] xyz, double[] mate, SymOp symOp)	Apply a fractional symmetry operator to one set of cartesian coordinates.
void	Crystal.applySymOp(int n, double[] x, double[] y, double[] z, double[] mateX, double[] mateY, double[] mateZ, SymOp symOp)	Apply a fractional symmetry operator to an array of Cartesian coordinates.
static void	SymOp.applySymOp(int h, int k, int l, int[] mate, SymOp symOp, int nx, int ny, int nz)	Apply a symmetry operator to one set of coordinates.
void	Crystal.applySymRot(double[] xyz, double[] mate, SymOp symOp)	Apply a fractional symmetry operator to one set of cartesian coordinates.
static void	SymOp.applySymRot(HKL hkl, HKL mate, SymOp symOp)	Apply a symmetry operator to one HKL.
void	Crystal.applyTransSymRot(int n, double[] x, double[] y, double[] z, double[] mateX, double[] mateY, double[] mateZ, SymOp symOp, double[][] rotmat)	Apply the transpose of a symmetry rotation to an array of Cartesian coordinates.
static void	SymOp.applyTransSymRot(HKL hkl, HKL mate, SymOp symOp)	Apply a transpose rotation symmetry operator to one HKL.
static String	SymOp.asMatrixString(SymOp symOp)	Print a Sym Op matrix as a continued line string.
static SymOp	SymOp.combineSymOps(SymOp symOp1, SymOp symOp2)	Return the combined SymOp that is equivalent to first applying symOp1 and then SymOp2.
void	Crystal.getTransformationOperator(SymOp symOp, double[][] rotmat)	Compute the total transformation operator R = ToCart * Rot * ToFrac.
static SymOp	SymOp.invertSymOp(SymOp symOp)	Invert a symmetry operator.
SymOp	SymOp.prepend(SymOp symOp)	Return the combined SymOp that is equivalent to first applying the argument and then this SymOp.

Method parameters in ffx.crystal with type arguments of type SymOp

Modifier and Type	Method	Description
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.

Constructors in ffx.crystal with parameters of type SymOp

Modifier	Constructor	Description
protected	SpaceGroup(int number, int numSymEquiv, int numPrimitiveSymEquiv, String shortName, String pointGroupName, String pdbName, CrystalSystem crystalSystem, LatticeSystem latticeSystem, LaueSystem laueSystem, ASULimit[] asuLimitOperators, double[] asuLimits, SymOp... symOps)	Immutable SpaceGroup instances are made available only through the factory method so this constructor is private.