Package org.jmol.adapter.writers

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