Class XtalSymmetry

java.lang.Object
org.jmol.adapter.smarter.XtalSymmetry
public class XtalSymmetry extends Object
A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.

  • Constructor Details

    • XtalSymmetry

      public XtalSymmetry()

  • Method Details

    • addRotatedTensor

      public Tensor addRotatedTensor(Atom a, Tensor t, int iSym, boolean reset, XtalSymmetry.FileSymmetry symmetry)

    • applySymmetryBio

      public void applySymmetryBio(Map<String,Object> thisBiomolecule, boolean applySymmetryToBonds, String filter)

    • getBaseSymmetry

      public XtalSymmetry.FileSymmetry getBaseSymmetry()
      Get the symmetry that was in place prior to any supercell business.
      Returns:
      base symmetry

    • getOverallSpan

      public T3 getOverallSpan()

    • getSymmetry

      public XtalSymmetry.FileSymmetry getSymmetry()

    • isWithinSupercell

      public static boolean isWithinSupercell(int ndims, P3 pt, float minX, float maxX, float minY, float maxY, float minZ, float maxZ, float slop)

    • set

      public XtalSymmetry set(AtomSetCollectionReader reader)

    • setLatticeParameter

      public void setLatticeParameter(int latt)
      Shelx and Wien2k readers
      Parameters:
      latt -

    • finalizeMoments

      public void finalizeMoments(String spinFrame, String spinFrameExt)
      from XtalSymmetry.applySymmetryFromReader via CifReader and JanaReader doPreSymmetry
      Parameters:
      spinFrame -
      spinFrameExt -

    • setMagneticMoments

      public int setMagneticMoments(boolean isCartesian)
      One of the last things to do for a spin space group: Set the spin vectors, possibly based on spinFrameCartXYZ. From CifReader.finalizeSubclassSymmetry after supercell business.
      Parameters:
      isCartesian - TODO
      Returns:
      number of atoms with nonzero spin (atom.vib)

    • setPartProperty

      public void setPartProperty()
      create property_part for SHELX and CIF loaders

    • newFileSymmetry

      public XtalSymmetry.FileSymmetry newFileSymmetry()