Package org.jmol.adapter.smarter

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()

    • isWithinCell

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

    • scaleFractionalVibs

      public void scaleFractionalVibs()
      magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes. These have to be "fractionalized" in order to be properly handled by symmetry operations, then, in the end, turned into Cartesians. It is not clear to me at all how this would be handled if there are subsystems. This method must be run PRIOR to applying symmetry and thus prior to creation of modulation sets.

    • set

      public XtalSymmetry set(AtomSetCollectionReader reader)

    • setLatticeParameter

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

    • setSpinVectors

      public int setSpinVectors()

    • removePacking

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

    • setPartProperty

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

    • newFileSymmetry

      public XtalSymmetry.FileSymmetry newFileSymmetry()