Field Detail

• MAX_COUNT

  private static final int MAX_COUNT

  maximum allowable supercell

  See Also:

  Constant Field Values

• SLOP0014

  private static final float SLOP0014

  maximum allowable distance fx, fy ,fz for atom finder

• SLOP001

  private static final float SLOP001

  tolerance for fractional coord and

  See Also:

  Constant Field Values

• SLOP0001

  private static final float SLOP0001

  tolerance for fractional coord and

  See Also:

  Constant Field Values

• GROUP_COUNT

  private static int GROUP_COUNT

• OP_COUNT

  private static int OP_COUNT

• bsOpGroups

  private static javajs.util.BS[] bsOpGroups

• bsGroupOps

  private static javajs.util.BS[] bsGroupOps

• groupNames

  private static java.lang.String[] groupNames

• opXYZ

  private static java.lang.String[] opXYZ

• ops

  private static SymmetryOperation[] ops

• rdr

  private static java.io.BufferedReader rdr

• atoms

  private SpaceGroupFinder.SGAtom[] atoms

• nAtoms

  private int nAtoms

• pt

  private javajs.util.P3 pt

Constructor Detail

• SpaceGroupFinder

  public SpaceGroupFinder()

Method Detail

• findSpaceGroup

  public java.lang.Object findSpaceGroup​(Viewer vwr,
                                         javajs.util.BS atoms0,
                                         java.lang.String xyzList,
                                         float[] unitCellParams,
                                         SymmetryInterface uc,
                                         boolean asString,
                                         boolean isAssign)

  Parameters:

  vwr -

  atoms0 -

  xyzList -

  unitCellParams -

  uc -

  asString -

  isAssign -

  Returns:

  SpaceGroup or null if isAssign, spacegroup information map if

• removeDuplicates

  private void removeDuplicates​(javajs.util.BS bs)

• dumpBasis

  private void dumpBasis​(javajs.util.BS ops,
                         javajs.util.BS bs1,
                         javajs.util.BS bsPoints)

• checkBasis

  private boolean checkBasis​(javajs.util.BS uncheckedOps,
                             javajs.util.BS bsPoints,
                             javajs.util.BS targets)

• filterGroups

  private void filterGroups​(javajs.util.BS bsGroups,
                            float[] params)

  Remove possibilities based on unit cells. No attempt is made to permute axes. Rhombohedral groups are never included. orthorhombic = 16 - 74 (a, b, c, 90, 90, 90) tetragonal = 75 - 142 (a, a, c, 90, 90, 90) trigonal = 143 - 194 (a, a, c, 90, 90, 120) cubic = 195 - 230 (a, a, a, 90, 90, 90)

  Parameters:

  bsGroups -

  params -

• scanTo

  private static int scanTo​(int i,
                            java.lang.String num)

• getGroupsWithOps

  private java.lang.Object getGroupsWithOps​(java.lang.String xyzList,
                                            float[] unitCellParams,
                                            boolean isAssign)

  Find all space groups that match EXACTLY or contain all of the operations specified. Operation need not be in Jmol-canonical form. For instance, "1-x,-y,-z" will be matched to "-x,-y,-z". Could be the result of spacegroup(nameOrXYZList, unitcellParametersArray) or MODELKIT ASSIGN SPACEGROUP "nameOrXYZList" other than P1

  Parameters:

  xyzList - a semicolon-separated list of possible space groups, such as "-x,-y,-z;x,-y,-z" or a space group ID such as "133:2"; if a list, prefixing or postfixing the list with "&" or joining with "&" indicates that a partial match is desired, returning a list of names of space groups that have at least the specified operations

  unitCellParams -

  isAssign - from ModelKit

  Returns:

  an array of space group IDs if not isAssign and not "="; a SpaceGroup or null if isAssign; a single space group ID as a string if "=" and a string starting and ending with "?" if an xyz operator is of an invalid form.

• toFractional

  javajs.util.P3 toFractional​(Atom a,
                              SymmetryInterface uc)

• getOp

  private static SymmetryOperation getOp​(int iop)

• checkSupercell

  public SymmetryInterface checkSupercell​(Viewer vwr,
                                          SymmetryInterface uc,
                                          javajs.util.BS bsPoints,
                                          int abc,
                                          javajs.util.P3 scaling)

  Look for a supercell and adjust lattice down if necessary.

  Parameters:

  vwr -

  uc -

  bsPoints -

  abc - 1==a, 2==b, 3==c

  scaling - set to [na, nb, nc]

  Returns:

  revised unit cell

• approx0

  private boolean approx0​(float f)

• approx000

  private boolean approx000​(float f)

• approx0014

  private boolean approx0014​(float f)

• approxInt

  private int approxInt​(float finv)

• findEquiv

  private int findEquiv​(int iop,
                        SymmetryOperation op,
                        int i,
                        javajs.util.BS bsPoints,
                        javajs.util.P3 pt,
                        boolean andClear)

• latticeShift

  private boolean latticeShift​(javajs.util.P3 a,
                               javajs.util.P3 b)

  Look for true {1 0 0}, {0 1 0}, {0 0 1} difference. This comes from issues with SimpleCell.unitize and our methods here, I think.

  Parameters:

  a -

  b -

  Returns:

  true if a lattice shift

• main

  public static void main​(java.lang.String[] args)

• loadData

  private static boolean loadData​(Viewer vwr,
                                  java.lang.Object me)

• getList

  private static java.lang.String[] getList​(Viewer vwr,
                                            java.lang.Object me,
                                            java.lang.String[] list,
                                            java.lang.String fileName)
                                     throws java.io.IOException

  Throws:

  java.io.IOException