Class TopoCifParser.TLink

Enclosing class:
TopoCifParser

private class TopoCifParser.TLink extends Bond
A class to hold the TOPOL_LINK data item information and transform it as needed. A key field is the primitives array of TopoPrimitives. These structures allow us to create a set of "primitive" operation results that operate specifically on the links themselves. Rather than showing those links (as with the Jmol script commented at the end of this class), we choose to first create the standard Jmol atom set using, for example, load hcb.cif PACKED or load xxx.cif {1 1 1} or load xxx.cif {444 666 1}, etc. Then we match those atoms with link edges by unitizing the atom back to its unit cell 555 site and then comparing with the primitive associated with a given operator.
  • Field Details

    • id

      String id
    • nodeIds

      String[] nodeIds
    • nodeLabels

      String[] nodeLabels
    • symops

      int[] symops
    • translations

      javajs.util.P3[] translations
    • netID

      String netID
    • netLabel

      String netLabel
    • type

      String type
    • multiplicity

      int multiplicity
    • topoOrder

      int topoOrder
    • voronoiAngle

      float voronoiAngle
    • cartesianDistance

      float cartesianDistance
    • idx

      int idx
    • net

    • linkNodes

      TopoCifParser.TNode[] linkNodes
    • typeBondOrder

      int typeBondOrder
    • tatoms

      javajs.util.Lst<TopoCifParser.TAtom> tatoms
    • bsAtoms

      javajs.util.BS bsAtoms
    • bsBonds

      javajs.util.BS bsBonds
    • line

      private String line
    • finalized

      boolean finalized
    • mf

      private String mf
  • Constructor Details

    • TLink

      public TLink()
  • Method Details

    • setLink

      boolean setLink(int[] t1, int[] t2, String line)
    • addAtom

    • finalizeLink

      void finalizeLink() throws Exception
      Take all actions prior to applying symmetry. Specifically, create any nodes and atoms
      Throws:
      Exception
    • finalizeLinkNode

      private void finalizeLinkNode(int index) throws Exception
      Parameters:
      index - 0 or 1
      Throws:
      Exception
    • getNodeWithSym

      private TopoCifParser.TNode getNodeWithSym(String nodeID, String nodeLabel, int op, javajs.util.P3 trans)
      Find a node that already matches this id and symmetry
      Parameters:
      nodeID -
      nodeLabel -
      op - a symmetry operation [9...N-1] or -1 to ignore op and trans
      trans - the translation, ignored if op invalid input: '<' 0
      Returns:
      found node or null
    • getLinkInfo

      Map<String,Object> getLinkInfo()
    • info

      String info()
    • toString

      public String toString()
      Overrides:
      toString in class Bond