org.jmol.modelset
Class Polymer

java.lang.Object
  extended by org.jmol.modelset.Polymer
Direct Known Subclasses:
BioPolymer

public abstract class Polymer
extends java.lang.Object


Field Summary
protected  int[] leadAtomIndices
           
protected  javax.vecmath.Point3f[] leadMidpoints
           
protected  javax.vecmath.Point3f[] leadPoints
           
protected  javax.vecmath.Point3f[] sheetPoints
           
protected  int type
           
protected static int TYPE_AMINO
           
protected static int TYPE_CARBOHYDRATE
           
protected static int TYPE_NUCLEIC
           
protected static int TYPE_OTHER
           
protected  javax.vecmath.Vector3f[] wingVectors
           
 
Constructor Summary
protected Polymer()
           
 
Method Summary
 void addSecondaryStructure(byte type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
           
 void calcHydrogenBonds(Polymer polymer, java.util.BitSet bsA, java.util.BitSet bsB)
           
 void calcSelectedMonomersCount(java.util.BitSet bsSelected)
           
 void calculateStructures()
           
 void clearStructures()
           
 void freeze()
           
 javax.vecmath.Point3f[] getLeadMidpoints()
           
 void getPdbData(char ctype, char qtype, int mStep, int derivType, boolean isDraw, java.util.BitSet bsAtoms, java.lang.StringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, java.util.BitSet bsWritten)
           
 java.util.Hashtable getPolymerInfo(java.util.BitSet bs)
           
 int getPolymerPointsAndVectors(int last, java.util.BitSet bs, java.util.Vector vList, boolean isTraceAlpha, float sheetSmoothing)
           
 void getPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, java.util.BitSet bsInclude, java.util.BitSet bsResult)
           
 java.lang.String getSequence()
           
 int getType()
           
 void recalculateLeadMidpointsAndWingVectors()
           
 void setConformation(java.util.BitSet bsConformation, int nAltLocs)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

leadMidpoints

protected javax.vecmath.Point3f[] leadMidpoints

leadPoints

protected javax.vecmath.Point3f[] leadPoints

sheetPoints

protected javax.vecmath.Point3f[] sheetPoints

wingVectors

protected javax.vecmath.Vector3f[] wingVectors

leadAtomIndices

protected int[] leadAtomIndices

type

protected int type

TYPE_OTHER

protected static final int TYPE_OTHER
See Also:
Constant Field Values

TYPE_AMINO

protected static final int TYPE_AMINO
See Also:
Constant Field Values

TYPE_NUCLEIC

protected static final int TYPE_NUCLEIC
See Also:
Constant Field Values

TYPE_CARBOHYDRATE

protected static final int TYPE_CARBOHYDRATE
See Also:
Constant Field Values
Constructor Detail

Polymer

protected Polymer()
Method Detail

getType

public int getType()

getPolymerPointsAndVectors

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

addSecondaryStructure

public void addSecondaryStructure(byte type,
                                  java.lang.String structureID,
                                  int serialID,
                                  int strandCount,
                                  char startChainID,
                                  int startSeqcode,
                                  char endChainID,
                                  int endSeqcode)

freeze

public void freeze()

calculateStructures

public void calculateStructures()

clearStructures

public void clearStructures()

getSequence

public java.lang.String getSequence()

getPolymerInfo

public java.util.Hashtable getPolymerInfo(java.util.BitSet bs)

setConformation

public void setConformation(java.util.BitSet bsConformation,
                            int nAltLocs)

calcHydrogenBonds

public void calcHydrogenBonds(Polymer polymer,
                              java.util.BitSet bsA,
                              java.util.BitSet bsB)

calcSelectedMonomersCount

public void calcSelectedMonomersCount(java.util.BitSet bsSelected)

getPolymerSequenceAtoms

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

getLeadMidpoints

public javax.vecmath.Point3f[] getLeadMidpoints()

recalculateLeadMidpointsAndWingVectors

public void recalculateLeadMidpointsAndWingVectors()

getPdbData

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