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

Constructors

Constructor and Description
PhosphorusPolymer(Monomer[] monomers)

Method Summary

Methods

Modifier and Type	Method and Description
void	getPdbData(Viewer viewer, char ctype, char qtype, int mStep, int derivType, boolean isDraw, java.util.BitSet bsAtoms, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, boolean bothEnds, java.util.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,
              boolean isDraw,
              java.util.BitSet bsAtoms,
              OutputStringBuffer pdbATOM,
              java.lang.StringBuffer pdbCONECT,
              java.util.BitSet bsSelected,
              boolean addHeader,
              boolean bothEnds,
              java.util.BitSet bsWritten)

Overrides:

getPdbData in class Polymer