Class SymmetryOperation

Method Details

• getOpDesc

  public String getOpDesc()

• setSigma

  public void setSigma(String subsystemCode, Matrix sigma)

  Sets sigma and the subsystem code for modulated CIF

  Parameters:

  subsystemCode -

  sigma -

• getXyz

  public String getXyz(boolean normalized)

• getxyzTrans

  public String getxyzTrans(T3 t)

• setSpin

  public void setSpin(String s)

• getMatrixFromXYZ

  public static M4 getMatrixFromXYZ(String xyz, float[] v, boolean halfOrLess)

• getMatrixFromXYZScaled

  public static M4 getMatrixFromXYZScaled(String xyz, float[] v, boolean halfOrLess)

• getRotTransArrayAndXYZ

  public static String getRotTransArrayAndXYZ(SymmetryOperation op, String xyz, float[] linearRotTrans, boolean allowScaling, boolean halfOrLess, boolean retString, String labels)

  Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format

  Parameters:

  op -

  xyz -

  linearRotTrans -

  allowScaling -

  halfOrLess -

  retString -

  labels -

  Returns:

  canonized Jones-Faithful string

• getXYZFromMatrix

  public static final String getXYZFromMatrix(M4 mat, boolean is12ths, boolean allPositive, boolean halfOrLess)

• rotateAxes

  public V3[] rotateAxes(V3[] vectors, UnitCell unitcell, P3 ptTemp, M3 mTemp)

• fcoord

  public static String fcoord(T3 p, String sep)

  Get string version of fraction

  Parameters:

  p -

  sep - space or comma

  Returns:

  "1/2" for example

• getXYZFromRsVs

  public static String getXYZFromRsVs(Matrix rs, Matrix vs, boolean is12ths)

• isTranslation

  public static boolean isTranslation(M4 op)

• getSpinString

  public static String getSpinString(M34 m, boolean isUVW, boolean withParens)

  allows for 3x3 rotation-only matrix;

  Parameters:

  m -

  isUVW - will allow 0.577.... not changing that to a fraction

  withParens -

  Returns:

  full x,y,...(u,v,....) or just u,v,w

• getInfo

  public Map<String,Object> getInfo()

• normalizeOperationToCentroid

  public static void normalizeOperationToCentroid(int dim, M4 m, P3[] fracPts, int i0, int n)

  Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.

  Parameters:

  dim -

  m -

  fracPts -

  i0 - first index

  n - number of atoms

• getLatticeCentering

  public static Lst<P3> getLatticeCentering(SymmetryOperation[] ops)

• getLatticeCenteringStrings

  public static Lst<String> getLatticeCenteringStrings(SymmetryOperation[] ops)

• getOpIsCCW

  public Boolean getOpIsCCW()

• getOpType

  public int getOpType()

• getOpOrder

  public int getOpOrder()

• getOpPoint

  public P3 getOpPoint()

• getOpAxis

  public V3 getOpAxis()

• getOpPoint2

  public P3 getOpPoint2()

• getOpTrans

  public V3 getOpTrans()

• getAdditionalOperations

  public static SymmetryOperation[] getAdditionalOperations(SymmetryOperation[] ops, int per_dim)

• normalize12ths

  public static void normalize12ths(V3 vtrans)

• getCode

  public String getCode()

• getGlideFromTrans

  public static char getGlideFromTrans(T3 ftrans, T3 ax1)

  note = this method will return 'n' for SG 161 do an operator's odd 1/2 -1/2 1/2 glide (but only for additional operations, not the basic set but ITA says "tetragonal and cubic only" in Table ITA1969 4.1.6

  Parameters:

  ftrans -

  ax1 -

  Returns:

  one of a b c d g n

• getTransformXYZ

  public static String getTransformXYZ(M4 op)

• getTransformUVW

  public static String getTransformUVW(M4 spin)

• getTransformABC

  public static String getTransformABC(M4 transform, boolean normalize)

  This method properly transposes the matrix for ABC format, converting columns to rows before passing the information to getXYZFromMatrixFrac(...,"ABC").

  Parameters:

  transform -

  normalize - only set to true by (undocumented?) script unitcell(m4,true); normalize translation to interval (-1/2,1/2]

  Returns:

  a,b,c format for the given matrix

• getTransformABCd

  public static String getTransformABCd(M4 transform, boolean normalize, boolean fractionAsDecimal)

• matrixToRationalString

  public static String matrixToRationalString(M34 matrix)

  rxyz option creates tab-separated string representation of a 3x4 (r,t) or 3x3 matrix with rational fractions adds "|" prior to translation; does NOT add last row of 0 0 0 1 ( 1 -1 0 | 1/2 0 0 1 | -1/2 0 1 0 | 0 )

  Parameters:

  matrix -

  Returns:

  string representation

• rotateSpin

  public void rotateSpin(T3 vib)

• staticConvertOperation

  public static Object staticConvertOperation(String xyz, M34 matrix34, String labels)

• toString

  public String toString()

  Description copied from class: M4

  Returns a string that contains the values of this Matrix4f.

  Overrides:

  toString in class M4

  Returns:

  the String representation

• getSUVW

  public String getSUVW()