org.jmol.modelsetbio
Class BioPolymer
java.lang.Object
org.jmol.modelset.Polymer
org.jmol.modelsetbio.BioPolymer
- Direct Known Subclasses:
- AlphaPolymer, CarbohydratePolymer, NucleicPolymer, PhosphorusPolymer
public abstract class BioPolymer
- extends Polymer
Method Summary |
(package private) static BioPolymer |
allocateBioPolymer(Group[] groups,
int firstGroupIndex,
boolean checkConnections)
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private void |
calcLeadMidpointsAndWingVectors(boolean getNewPoints)
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protected boolean |
calcPhiPsiAngles()
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void |
calcSelectedMonomersCount(java.util.BitSet bsSelected)
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void |
clearStructures()
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void |
findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
short[] mads,
int myVisibilityFlag)
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javax.vecmath.Point3f[] |
getControlPoints(boolean isTraceAlpha,
float sheetSmoothing,
boolean invalidate)
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(package private) int |
getIndex(char chainID,
int seqcode)
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(package private) javax.vecmath.Point3f |
getInitiatorPoint()
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int[] |
getLeadAtomIndices()
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(package private) void |
getLeadMidPoint(int groupIndex,
javax.vecmath.Point3f midPoint)
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javax.vecmath.Point3f[] |
getLeadMidpoints()
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(package private) javax.vecmath.Point3f |
getLeadPoint(int monomerIndex)
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(package private) void |
getLeadPoint(int groupIndex,
javax.vecmath.Point3f midPoint)
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(package private) javax.vecmath.Point3f[] |
getLeadPoints()
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int |
getMonomerCount()
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Monomer[] |
getMonomers()
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static void |
getPdbData(BioPolymer p,
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)
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(package private) javax.vecmath.Point3f |
getPointPoint(int polymerIndex)
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java.util.Hashtable |
getPolymerInfo(java.util.BitSet bs)
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int |
getPolymerPointsAndVectors(int last,
java.util.BitSet bs,
java.util.Vector vList,
boolean isTraceAlpha,
float sheetSmoothing)
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void |
getPolymerSequenceAtoms(int iModel,
int iPolymer,
int group1,
int nGroups,
java.util.BitSet bsInclude,
java.util.BitSet bsResult)
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ProteinStructure |
getProteinStructure(int monomerIndex)
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private static float |
getQuaternionStraightness(java.lang.String id,
Quaternion dqprev,
Quaternion dq)
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(package private) int |
getSelectedMonomerCount()
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java.lang.String |
getSequence()
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private javax.vecmath.Point3f[] |
getSheetPoints(float sheetSmoothing)
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(package private) javax.vecmath.Point3f |
getTerminatorPoint()
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(package private) javax.vecmath.Point3f |
getWingPoint(int polymerIndex)
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javax.vecmath.Vector3f[] |
getWingVectors()
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(package private) boolean |
hasWingPoints()
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(package private) boolean |
isMonomerSelected(int i)
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void |
recalculateLeadMidpointsAndWingVectors()
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(package private) void |
removeProteinStructure(int monomerIndex,
int count)
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void |
setConformation(java.util.BitSet bsSelected,
int nAltLocsInModel)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
monomers
Monomer[] monomers
monomerCount
int monomerCount
model
protected Model model
sheetSmoothing
private float sheetSmoothing
unitVectorX
private final javax.vecmath.Vector3f unitVectorX
selectedMonomerCount
private int selectedMonomerCount
bsSelectedMonomers
java.util.BitSet bsSelectedMonomers
qColor
private static final java.lang.String[] qColor
BioPolymer
BioPolymer(Monomer[] monomers)
getMonomers
public Monomer[] getMonomers()
getMonomerCount
public int getMonomerCount()
allocateBioPolymer
static BioPolymer allocateBioPolymer(Group[] groups,
int firstGroupIndex,
boolean checkConnections)
clearStructures
public void clearStructures()
- Overrides:
clearStructures
in class Polymer
removeProteinStructure
void removeProteinStructure(int monomerIndex,
int count)
getLeadAtomIndices
public int[] getLeadAtomIndices()
getIndex
int getIndex(char chainID,
int seqcode)
getLeadPoint
final javax.vecmath.Point3f getLeadPoint(int monomerIndex)
getInitiatorPoint
final javax.vecmath.Point3f getInitiatorPoint()
getTerminatorPoint
final javax.vecmath.Point3f getTerminatorPoint()
getLeadMidPoint
void getLeadMidPoint(int groupIndex,
javax.vecmath.Point3f midPoint)
getLeadPoint
void getLeadPoint(int groupIndex,
javax.vecmath.Point3f midPoint)
hasWingPoints
boolean hasWingPoints()
getWingPoint
final javax.vecmath.Point3f getWingPoint(int polymerIndex)
getPointPoint
final javax.vecmath.Point3f getPointPoint(int polymerIndex)
setConformation
public void setConformation(java.util.BitSet bsSelected,
int nAltLocsInModel)
- Overrides:
setConformation
in class Polymer
recalculateLeadMidpointsAndWingVectors
public void recalculateLeadMidpointsAndWingVectors()
- Overrides:
recalculateLeadMidpointsAndWingVectors
in class Polymer
getLeadMidpoints
public javax.vecmath.Point3f[] getLeadMidpoints()
- Overrides:
getLeadMidpoints
in class Polymer
getLeadPoints
javax.vecmath.Point3f[] getLeadPoints()
getControlPoints
public javax.vecmath.Point3f[] getControlPoints(boolean isTraceAlpha,
float sheetSmoothing,
boolean invalidate)
getSheetPoints
private javax.vecmath.Point3f[] getSheetPoints(float sheetSmoothing)
getWingVectors
public final javax.vecmath.Vector3f[] getWingVectors()
calcLeadMidpointsAndWingVectors
private final void calcLeadMidpointsAndWingVectors(boolean getNewPoints)
findNearestAtomIndex
public void findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
short[] mads,
int myVisibilityFlag)
getSelectedMonomerCount
int getSelectedMonomerCount()
calcSelectedMonomersCount
public void calcSelectedMonomersCount(java.util.BitSet bsSelected)
- Overrides:
calcSelectedMonomersCount
in class Polymer
isMonomerSelected
boolean isMonomerSelected(int i)
getPolymerPointsAndVectors
public int getPolymerPointsAndVectors(int last,
java.util.BitSet bs,
java.util.Vector vList,
boolean isTraceAlpha,
float sheetSmoothing)
- Overrides:
getPolymerPointsAndVectors
in class Polymer
getSequence
public java.lang.String getSequence()
- Overrides:
getSequence
in class Polymer
getPolymerInfo
public java.util.Hashtable getPolymerInfo(java.util.BitSet bs)
- Overrides:
getPolymerInfo
in class Polymer
getPolymerSequenceAtoms
public void getPolymerSequenceAtoms(int iModel,
int iPolymer,
int group1,
int nGroups,
java.util.BitSet bsInclude,
java.util.BitSet bsResult)
- Overrides:
getPolymerSequenceAtoms
in class Polymer
getProteinStructure
public ProteinStructure getProteinStructure(int monomerIndex)
calcPhiPsiAngles
protected boolean calcPhiPsiAngles()
getPdbData
public static final void getPdbData(BioPolymer p,
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)
getQuaternionStraightness
private static float getQuaternionStraightness(java.lang.String id,
Quaternion dqprev,
Quaternion dq)