org.jmol.modelsetbio
Class NucleicPolymer

java.lang.Object
  extended by org.jmol.modelset.Polymer
      extended by org.jmol.modelsetbio.BioPolymer
          extended by org.jmol.modelsetbio.NucleicPolymer

public class NucleicPolymer
extends BioPolymer


Field Summary
private static short HBOND_MASK
           
 
Fields inherited from class org.jmol.modelsetbio.BioPolymer
bsSelectedMonomers, model, monomerCount, monomers
 
Fields inherited from class org.jmol.modelset.Polymer
leadAtomIndices, leadMidpoints, leadPoints, sheetPoints, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NUCLEIC, TYPE_OTHER, wingVectors
 
Constructor Summary
NucleicPolymer(Monomer[] monomers)
           
 
Method Summary
 void calcHydrogenBonds(Polymer polymer, java.util.BitSet bsA, java.util.BitSet bsB)
           
(package private)  Atom getNucleicPhosphorusAtom(int monomerIndex)
           
 void getPdbData(char ctype, char qtype, int derivType, boolean isDraw, java.util.BitSet bsAtoms, java.lang.StringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, java.util.BitSet bsWritten)
           
(package private)  boolean hasWingPoints()
           
(package private)  void lookForHbonds(NucleicPolymer other, java.util.BitSet bsA, java.util.BitSet bsB)
           
 
Methods inherited from class org.jmol.modelsetbio.BioPolymer
allocateBioPolymer, calcPhiPsiAngles, calcSelectedMonomersCount, clearStructures, findNearestAtomIndex, getControlPoints, getIndex, getInitiatorPoint, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoint, getLeadPoints, getMonomerCount, getMonomers, getPdbData, getPointPoint, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getSelectedMonomerCount, getSequence, getTerminatorPoint, getWingPoint, getWingVectors, isMonomerSelected, recalculateLeadMidpointsAndWingVectors, removeProteinStructure, setConformation
 
Methods inherited from class org.jmol.modelset.Polymer
addSecondaryStructure, calculateStructures, freeze, getType
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

HBOND_MASK

private static final short HBOND_MASK
See Also:
Constant Field Values
Constructor Detail

NucleicPolymer

NucleicPolymer(Monomer[] monomers)
Method Detail

getNucleicPhosphorusAtom

Atom getNucleicPhosphorusAtom(int monomerIndex)

hasWingPoints

boolean hasWingPoints()
Overrides:
hasWingPoints in class BioPolymer

calcHydrogenBonds

public void calcHydrogenBonds(Polymer polymer,
                              java.util.BitSet bsA,
                              java.util.BitSet bsB)
Overrides:
calcHydrogenBonds in class Polymer

lookForHbonds

void lookForHbonds(NucleicPolymer other,
                   java.util.BitSet bsA,
                   java.util.BitSet bsB)

getPdbData

public void getPdbData(char ctype,
                       char qtype,
                       int derivType,
                       boolean isDraw,
                       java.util.BitSet bsAtoms,
                       java.lang.StringBuffer pdbATOM,
                       java.lang.StringBuffer pdbCONECT,
                       java.util.BitSet bsSelected,
                       boolean addHeader,
                       java.util.BitSet bsWritten)
Overrides:
getPdbData in class Polymer