Package org.jmol.symmetry

Class SymmetryOperation

java.lang.Object
javajs.util.M34
javajs.util.M4
org.jmol.symmetry.SymmetryOperation
public class SymmetryOperation extends M4

  • Field Details

    • subsystemCode

      public String subsystemCode

    • opIsLong

      public boolean opIsLong

  • Method Details

    • setSigma

      public void setSigma(String subsystemCode, Matrix sigma)

    • getxyzTrans

      public String getxyzTrans(T3 t)

    • getMatrixFromXYZ

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

    • getMatrixFromString

      public static String getMatrixFromString(SymmetryOperation op, String xyz, float[] linearRotTrans, boolean allowScaling, boolean halfOrLess, boolean retString)
      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 -
      Returns:
      canonized Jones-Faithful string

    • getXYZFromMatrix

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

    • getXYZFromMatrixFrac

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

    • 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)

    • 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

    • 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)

    • 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 periodicity)

    • normalize12ths

      public static void normalize12ths(V3 vtrans)

    • getCode

      public String getCode()

    • getGlideFromTrans

      public static char getGlideFromTrans(T3 ftrans, T3 ax1)

    • getTransformABC

      public static String getTransformABC(Object transform, boolean normalize)