org.jmol.modelset

Class Polymer

public abstract class Polymer extends Object

Field Summary
protected int[]leadAtomIndices
protected Point3f[]leadMidpoints
protected Point3f[]leadPoints
protected Point3f[]sheetPoints
protected Vector3f[]wingVectors
Constructor Summary
protected Polymer()
Method Summary
voidaddSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
voidcalcHydrogenBonds(BitSet bsA, BitSet bsB)
voidcalcSelectedMonomersCount(BitSet bsSelected)
voidcalculateStructures()
voidclearStructures()
voidfreeze()
Point3f[]getLeadMidpoints()
voidgetPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)
HashtablegetPolymerInfo(BitSet bs)
intgetPolymerPointsAndVectors(int last, BitSet bs, Vector vList, boolean isTraceAlpha, float sheetSmoothing)
voidgetPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, BitSet bsInclude, BitSet bsResult)
StringgetSequence()
voidrecalculateLeadMidpointsAndWingVectors()
voidsetConformation(BitSet bsConformation, int nAltLocs)

Field Detail

leadAtomIndices

protected int[] leadAtomIndices

leadMidpoints

protected Point3f[] leadMidpoints

leadPoints

protected Point3f[] leadPoints

sheetPoints

protected Point3f[] sheetPoints

wingVectors

protected Vector3f[] wingVectors

Constructor Detail

Polymer

protected Polymer()

Method Detail

addSecondaryStructure

public void addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)

calcHydrogenBonds

public void calcHydrogenBonds(BitSet bsA, BitSet bsB)

calcSelectedMonomersCount

public void calcSelectedMonomersCount(BitSet bsSelected)

calculateStructures

public void calculateStructures()

clearStructures

public void clearStructures()

freeze

public void freeze()

getLeadMidpoints

public Point3f[] getLeadMidpoints()

getPdbData

public void getPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)

getPolymerInfo

public Hashtable getPolymerInfo(BitSet bs)

getPolymerPointsAndVectors

public int getPolymerPointsAndVectors(int last, BitSet bs, Vector vList, boolean isTraceAlpha, float sheetSmoothing)

getPolymerSequenceAtoms

public void getPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, BitSet bsInclude, BitSet bsResult)

getSequence

public String getSequence()

recalculateLeadMidpointsAndWingVectors

public void recalculateLeadMidpointsAndWingVectors()

setConformation

public void setConformation(BitSet bsConformation, int nAltLocs)