Class 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 Detail

      • noBondSym

        private boolean noBondSym
      • tokens

        private java.lang.String[] tokens
      • htEdges

        private java.util.Map<Atom,​javajs.util.V3[]> htEdges
      • lastName

        private java.lang.String lastName
      • edgeData

        private javajs.util.Lst<java.lang.String> edgeData
      • vecs

        private static final javajs.util.V3[] vecs
    • Constructor Detail

      • CgdReader

        public CgdReader()
    • Method Detail

      • checkLine

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

        private java.lang.String group​(java.lang.String name)
      • atom

        private void atom()
      • getName

        private java.lang.String getName​(java.lang.String name)
      • 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)