Uses of Class
ffx.crystal.SymOp

Packages that use SymOp
Package
Description
 
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.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.
    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.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.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.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.