Package org.jmol.adapter.writers

Class PDBWriter

java.lang.Object
org.jmol.adapter.writers.PDBWriter
All Implemented Interfaces:
JmolWriter
public class PDBWriter extends Object implements JmolWriter
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html

  • Field Details

    • vwr

      private Viewer vwr

    • oc

      private javajs.util.OC oc

    • isPQR

      private boolean isPQR

    • doTransform

      private boolean doTransform

    • allTrajectories

      private boolean allTrajectories

  • Constructor Details

    • PDBWriter

      public PDBWriter()

  • Method Details

    • set

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

    • write

      public String write(javajs.util.BS bs)
      Specified by:
      write in interface JmolWriter

    • pdbKey

      private String pdbKey(int np)

    • fixPDBFormat

      private int fixPDBFormat(javajs.util.Lst<String> lines, Map<String,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 String toString()
      Overrides:
      toString in class Object