Package org.jmol.adapter.readers.xtal

Class CgdReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.CgdReader
All Implemented Interfaces:
javajs.api.GenericLineReader
public class CgdReader extends AtomSetCollectionReader
A reader for TOPOS systre file Crystal Graph Data format. http://www.topos.samsu.ru/manuals.html http://gavrog.org/Systre-Help.html#file_formats H-M aliases from gavrov distribution geometry/sgtable.data

  • Field Details

    • noBondSym

      private boolean noBondSym

    • tokens

      private String[] tokens

    • htEdges

      private Map<Atom,javajs.util.V3[]> htEdges

    • lastName

      private String lastName

    • edgeData

      private javajs.util.Lst<String> edgeData

    • SG_ALIASES

      private static final String SG_ALIASES
      See Also:

    • vecs

      private static final javajs.util.V3[] vecs

  • Constructor Details

    • CgdReader

      public CgdReader()

  • Method Details

    • initializeReader

      public void initializeReader()
      Overrides:
      initializeReader in class AtomSetCollectionReader

    • checkLine

      protected boolean checkLine() throws Exception
      Overrides:
      checkLine in class AtomSetCollectionReader
      Returns:
      true if need to read new line
      Throws:
      Exception

    • group

      private String group(String name)

    • atom

      private void atom()

    • getName

      private String getName(String name)

    • finalizeSubclassReader

      public void finalizeSubclassReader() throws Exception
      Description copied from class: AtomSetCollectionReader
      optional reader-specific method run first.
      Overrides:
      finalizeSubclassReader in class AtomSetCollectionReader
      Throws:
      Exception

    • finalizeEdges

      private void finalizeEdges()
      Now that we have all the edge data we can add edges to atoms

    • getCoord

      private javajs.util.P3 getCoord(int i)

    • finalizeNet

      private void finalizeNet()
      Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges

    • findAtom

      private Atom findAtom(javajs.util.P3 pt)