Class TopoCifParser.TopoLink

  • Enclosing class:
    TopoCifParser

    private class TopoCifParser.TopoLink
    extends Object
    A class to hold the _topol block 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.
    • Constructor Detail

      • TopoLink

        TopoLink​(Atom a1,
                 Atom a2,
                 int op1,
                 double[] t1,
                 int op2,
                 double[] t2,
                 double d,
                 String type)
    • Method Detail

      • setPrimitives

        void setPrimitives​(SymmetryInterface sym,
                           javajs.util.M4[] operations)
        Primitives are set by doing the operations and adding dt to the second point's position only. This works because we are going to unitize this anyway, so only the relative final lattice translation for point 1 and point 2 is needed.
        Parameters:
        sym -
        nOps -