org.jmol.modelset
Class Polymer
java.lang.Object
org.jmol.modelset.Polymer
- Direct Known Subclasses:
- BioPolymer
public abstract class Polymer
- extends java.lang.Object
Constructor Summary |
protected |
Polymer()
|
Method Summary |
void |
addSecondaryStructure(byte type,
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 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 |
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
Polymer
protected Polymer()
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,
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 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)