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
 
Fields inherited from class org.jmol.modelsetbio.BioPolymer
bsSelectedMonomers, hasWingPoints, haveParameters, invalidControl, monomers, sheetSmoothing
 
Fields inherited from class org.jmol.modelset.Polymer
bioPolymerIndexInModel, controlPoints, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NOBONDING, TYPE_NUCLEIC, wingVectors
 
Constructor Summary
NucleicPolymer(Monomer[] monomers)
           
 
Method Summary
protected static int addHydrogenBond(java.util.List<Bond> vAtoms, Atom atom1, Atom atom2)
           
protected  boolean calcEtaThetaAngles()
           
 void calcRasmolHydrogenBonds(Polymer polymer, java.util.BitSet bsA, java.util.BitSet bsB, java.util.List<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
           
(package private)  Atom getNucleicPhosphorusAtom(int monomerIndex)
           
 void getPdbData(Viewer viewer, char ctype, char qtype, int mStep, int derivType, java.util.BitSet bsAtoms, java.util.BitSet bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsWritten)
           
 
Methods inherited from class org.jmol.modelsetbio.BioPolymer
allocateBioPolymer, calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, calculateStructures, clearStructures, findNearestAtomIndex, getConformation, getControlPoint, getControlPoints, getControlPoints, getGroups, getIndex, getInitiatorPoint, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoint, getLeadPoints, getPdbData, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getTerminatorPoint, getWingPoint, getWingVectors, isDna, isMonomerSelected, isRna, recalculateLeadMidpointsAndWingVectors, removeProteinStructure, resetHydrogenPoints, setConformation
 
Methods inherited from class org.jmol.modelset.Polymer
addSecondaryStructure, calculateStructures, calculateStruts, getType, setStructureList
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NucleicPolymer

NucleicPolymer(Monomer[] monomers)
Method Detail

getNucleicPhosphorusAtom

Atom getNucleicPhosphorusAtom(int monomerIndex)

calcEtaThetaAngles

protected boolean calcEtaThetaAngles()
Overrides:
calcEtaThetaAngles in class BioPolymer

calcRasmolHydrogenBonds

public void calcRasmolHydrogenBonds(Polymer polymer,
                                    java.util.BitSet bsA,
                                    java.util.BitSet bsB,
                                    java.util.List<Bond> vAtoms,
                                    int nMaxPerResidue,
                                    int[][][] min,
                                    boolean checkDistances,
                                    boolean dsspIgnoreHydrogens)
Overrides:
calcRasmolHydrogenBonds in class Polymer

addHydrogenBond

protected static int addHydrogenBond(java.util.List<Bond> vAtoms,
                                     Atom atom1,
                                     Atom atom2)

getPdbData

public void getPdbData(Viewer viewer,
                       char ctype,
                       char qtype,
                       int mStep,
                       int derivType,
                       java.util.BitSet bsAtoms,
                       java.util.BitSet bsSelected,
                       boolean bothEnds,
                       boolean isDraw,
                       boolean addHeader,
                       LabelToken[] tokens,
                       OutputStringBuffer pdbATOM,
                       java.lang.StringBuffer pdbCONECT,
                       java.util.BitSet bsWritten)
Overrides:
getPdbData in class Polymer