org.jmol.modelset
Class Polymer
public abstract
class
Polymer
extends Object
Method Summary |
void | addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode) |
void | calcHydrogenBonds(BitSet bsA, BitSet bsB) |
void | calcSelectedMonomersCount(BitSet bsSelected) |
void | calculateStructures() |
void | clearStructures() |
void | freeze() |
Point3f[] | getLeadMidpoints() |
void | getPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten) |
Hashtable | getPolymerInfo(BitSet bs) |
int | getPolymerPointsAndVectors(int last, BitSet bs, Vector vList, boolean isTraceAlpha, float sheetSmoothing) |
void | getPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, BitSet bsInclude, BitSet bsResult) |
String | getSequence() |
void | recalculateLeadMidpointsAndWingVectors() |
void | setConformation(BitSet bsConformation, int nAltLocs) |
protected int[] leadAtomIndices
protected Point3f[] leadMidpoints
protected Point3f[] leadPoints
protected Point3f[] sheetPoints
protected Vector3f[] wingVectors
protected Polymer()
public void addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
public void calcHydrogenBonds(BitSet bsA, BitSet bsB)
public void calcSelectedMonomersCount(BitSet bsSelected)
public void calculateStructures()
public void clearStructures()
public void freeze()
public Point3f[] getLeadMidpoints()
public void getPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)
public Hashtable getPolymerInfo(BitSet bs)
public int getPolymerPointsAndVectors(int last, BitSet bs, Vector vList, boolean isTraceAlpha, float sheetSmoothing)
public void getPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, BitSet bsInclude, BitSet bsResult)
public String getSequence()
public void recalculateLeadMidpointsAndWingVectors()
public void setConformation(BitSet bsConformation, int nAltLocs)