org.jmol.modelsetbio
Class PhosphorusPolymer

java.lang.Object
  org.jmol.modelset.Polymer
      org.jmol.modelsetbio.BioPolymer
          org.jmol.modelsetbio.PhosphorusPolymer

 class PhosphorusPolymer
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

PhosphorusPolymer(Monomer[] monomers)

Method Summary

void	getPdbData(Viewer viewer, char ctype, char qtype, int mStep, int derivType, BitSet bsAtoms, BitSet bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, OutputStringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsWritten)

Methods inherited from class org.jmol.modelsetbio.BioPolymer

allocateBioPolymer, calcEtaThetaAngles, 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, calcRasmolHydrogenBonds, calculateStructures, calculateStruts, getType, setStructureList

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PhosphorusPolymer

PhosphorusPolymer(Monomer[] monomers)

Method Detail

getPdbData

public void getPdbData(Viewer viewer,
                       char ctype,
                       char qtype,
                       int mStep,
                       int derivType,
                       BitSet bsAtoms,
                       BitSet bsSelected,
                       boolean bothEnds,
                       boolean isDraw,
                       boolean addHeader,
                       LabelToken[] tokens,
                       OutputStringBuffer pdbATOM,
                       StringBuffer pdbCONECT,
                       BitSet bsWritten)

Overrides:

getPdbData in class Polymer