Class PDBWriter

  • All Implemented Interfaces:
    JmolWriter

    public class PDBWriter
    extends java.lang.Object
    implements JmolWriter
    An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
    • Constructor Summary

      Constructors 
      Constructor Description
      PDBWriter()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      private int fixPDBFormat​(javajs.util.Lst<java.lang.String> lines, java.util.Map<java.lang.String,​java.lang.Integer> map, javajs.util.OC out, int[] firstAtomIndexNew, int modelPt)
      must re-order by resno and then renumber atoms and add TER records based on BioPolymers note: 3hbt has a break between residues 39 and 51 with no TER record, but Jmol will put that in.
      private java.lang.String pdbKey​(int np)  
      void set​(Viewer viewer, javajs.util.OC oc, java.lang.Object[] data)  
      java.lang.String toString()  
      java.lang.String write​(javajs.util.BS bs)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Field Detail

      • oc

        private javajs.util.OC oc
      • isPQR

        private boolean isPQR
      • doTransform

        private boolean doTransform
      • allTrajectories

        private boolean allTrajectories
    • Constructor Detail

      • PDBWriter

        public PDBWriter()
    • Method Detail

      • set

        public void set​(Viewer viewer,
                        javajs.util.OC oc,
                        java.lang.Object[] data)
        Specified by:
        set in interface JmolWriter
      • write

        public java.lang.String write​(javajs.util.BS bs)
        Specified by:
        write in interface JmolWriter
      • pdbKey

        private java.lang.String pdbKey​(int np)
      • fixPDBFormat

        private int fixPDBFormat​(javajs.util.Lst<java.lang.String> lines,
                                 java.util.Map<java.lang.String,​java.lang.Integer> map,
                                 javajs.util.OC out,
                                 int[] firstAtomIndexNew,
                                 int modelPt)
        must re-order by resno and then renumber atoms and add TER records based on BioPolymers note: 3hbt has a break between residues 39 and 51 with no TER record, but Jmol will put that in.
        Parameters:
        lines -
        map -
        out -
        modelPt -
        firstAtomIndexNew -
        Returns:
        new modelPt
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object