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
Fields inherited from class org.jmol.modelset.Polymer |
bioPolymerIndexInModel, controlPoints, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NOBONDING, TYPE_NUCLEIC, wingVectors |
Method Summary |
(package private) static BioPolymer |
allocateBioPolymer(Group[] groups,
int firstGroupIndex,
boolean checkConnections)
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protected boolean |
calcEtaThetaAngles()
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private void |
calcLeadMidpointsAndWingVectors()
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boolean |
calcParameters()
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protected boolean |
calcPhiPsiAngles()
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void |
calcSelectedMonomersCount(java.util.BitSet bsSelected)
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protected float |
calculateRamachandranHelixAngle(int m,
char qtype)
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java.lang.String |
calculateStructures(Polymer[] bioPolymers,
int bioPolymerCount,
java.util.List vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogens,
boolean setStructure)
|
void |
clearStructures()
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void |
findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
short[] mads,
int myVisibilityFlag,
java.util.BitSet bsNot)
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private static float |
get3DStraightness(java.lang.String id,
Quaternion dq,
Quaternion dqnext)
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void |
getConformation(java.util.BitSet bsConformation,
int conformationIndex)
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protected javax.vecmath.Point3f |
getControlPoint(int i,
javax.vecmath.Vector3f v)
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javax.vecmath.Point3f[] |
getControlPoints(boolean isTraceAlpha,
float sheetSmoothing,
boolean invalidate)
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protected javax.vecmath.Point3f[] |
getControlPoints(float sheetSmoothing)
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private static void |
getData(Viewer viewer,
int m0,
int mStep,
BioPolymer p,
char ctype,
char qtype,
int derivType,
java.util.BitSet bsAtoms,
java.util.BitSet bsSelected,
java.util.BitSet bsWritten,
boolean isDraw,
boolean isRamachandran,
boolean calcRamachandranStraightness,
boolean useQuaternionStraightness,
boolean writeRamachandranStraightness,
boolean quaternionStraightness,
float factor,
boolean isAmino,
boolean isRelativeAlias,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT)
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Group[] |
getGroups()
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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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static void |
getPdbData(Viewer viewer,
BioPolymer p,
char ctype,
char qtype,
int mStep,
int derivType,
boolean isDraw,
java.util.BitSet bsAtoms,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
boolean bothEnds,
java.util.BitSet bsWritten)
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java.util.Map |
getPolymerInfo(java.util.BitSet bs)
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int |
getPolymerPointsAndVectors(int last,
java.util.BitSet bs,
java.util.List vList,
boolean isTraceAlpha,
float sheetSmoothing)
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void |
getPolymerSequenceAtoms(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 dq,
Quaternion dqnext)
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void |
getRange(java.util.BitSet bs)
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void |
getRangeGroups(int nResidues,
java.util.BitSet bsAtoms,
java.util.BitSet bsResult)
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(package private) int |
getSelectedMonomerCount()
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java.lang.String |
getSequence()
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private static float |
getStraightness(float cosHalfTheta)
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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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boolean |
isDna()
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(package private) boolean |
isMonomerSelected(int i)
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boolean |
isRna()
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void |
recalculateLeadMidpointsAndWingVectors()
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(package private) void |
removeProteinStructure(int monomerIndex,
int count)
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protected void |
resetHydrogenPoints()
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void |
setConformation(java.util.BitSet bsSelected)
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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
invalidLead
private boolean invalidLead
invalidControl
protected boolean invalidControl
sheetSmoothing
protected float sheetSmoothing
hasWingPoints
protected boolean hasWingPoints
unitVectorX
private final javax.vecmath.Vector3f unitVectorX
selectedMonomerCount
private int selectedMonomerCount
bsSelectedMonomers
java.util.BitSet bsSelectedMonomers
haveParameters
public boolean haveParameters
qColor
private static final java.lang.String[] qColor
BioPolymer
BioPolymer(Monomer[] monomers)
getGroups
public Group[] getGroups()
- Overrides:
getGroups
in class Polymer
getRange
public void getRange(java.util.BitSet bs)
- Overrides:
getRange
in class Polymer
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)
getWingPoint
final javax.vecmath.Point3f getWingPoint(int polymerIndex)
getConformation
public void getConformation(java.util.BitSet bsConformation,
int conformationIndex)
- Overrides:
getConformation
in class Polymer
setConformation
public void setConformation(java.util.BitSet bsSelected)
- Overrides:
setConformation
in class Polymer
recalculateLeadMidpointsAndWingVectors
public void recalculateLeadMidpointsAndWingVectors()
- Overrides:
recalculateLeadMidpointsAndWingVectors
in class Polymer
resetHydrogenPoints
protected void resetHydrogenPoints()
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)
getControlPoints
protected javax.vecmath.Point3f[] getControlPoints(float sheetSmoothing)
getControlPoint
protected javax.vecmath.Point3f getControlPoint(int i,
javax.vecmath.Vector3f v)
- Parameters:
i
- v
-
- Returns:
- the leadPoint unless a protein sheet residue (see AlphaPolymer)
getWingVectors
public final javax.vecmath.Vector3f[] getWingVectors()
calcLeadMidpointsAndWingVectors
private final void calcLeadMidpointsAndWingVectors()
findNearestAtomIndex
public void findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
short[] mads,
int myVisibilityFlag,
java.util.BitSet bsNot)
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.List vList,
boolean isTraceAlpha,
float sheetSmoothing)
- Overrides:
getPolymerPointsAndVectors
in class Polymer
- Returns:
- number of points
getSequence
public java.lang.String getSequence()
- Overrides:
getSequence
in class Polymer
getPolymerInfo
public java.util.Map getPolymerInfo(java.util.BitSet bs)
- Overrides:
getPolymerInfo
in class Polymer
- Returns:
- info
getPolymerSequenceAtoms
public void getPolymerSequenceAtoms(int group1,
int nGroups,
java.util.BitSet bsInclude,
java.util.BitSet bsResult)
- Overrides:
getPolymerSequenceAtoms
in class Polymer
getProteinStructure
public ProteinStructure getProteinStructure(int monomerIndex)
calcParameters
public boolean calcParameters()
calcEtaThetaAngles
protected boolean calcEtaThetaAngles()
calcPhiPsiAngles
protected boolean calcPhiPsiAngles()
getPdbData
public static final void getPdbData(Viewer viewer,
BioPolymer p,
char ctype,
char qtype,
int mStep,
int derivType,
boolean isDraw,
java.util.BitSet bsAtoms,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
boolean bothEnds,
java.util.BitSet bsWritten)
getData
private static void getData(Viewer viewer,
int m0,
int mStep,
BioPolymer p,
char ctype,
char qtype,
int derivType,
java.util.BitSet bsAtoms,
java.util.BitSet bsSelected,
java.util.BitSet bsWritten,
boolean isDraw,
boolean isRamachandran,
boolean calcRamachandranStraightness,
boolean useQuaternionStraightness,
boolean writeRamachandranStraightness,
boolean quaternionStraightness,
float factor,
boolean isAmino,
boolean isRelativeAlias,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT)
- Parameters:
viewer
- m0
- mStep
- p
- ctype
- qtype
- derivType
- bsAtoms
- bsSelected
- bsWritten
- isDraw
- isRamachandran
- calcRamachandranStraightness
- useQuaternionStraightness
- writeRamachandranStraightness
- quaternionStraightness
- NOT USEDfactor
- isAmino
- isRelativeAlias
- pdbATOM
- pdbCONECT
-
calculateRamachandranHelixAngle
protected float calculateRamachandranHelixAngle(int m,
char qtype)
- Parameters:
m
- qtype
-
- Returns:
- calculated value
get3DStraightness
private static float get3DStraightness(java.lang.String id,
Quaternion dq,
Quaternion dqnext)
- Parameters:
id
- for debugging onlydq
- dqnext
-
- Returns:
- calculated straightness
getQuaternionStraightness
private static float getQuaternionStraightness(java.lang.String id,
Quaternion dq,
Quaternion dqnext)
- Parameters:
id
- for debugging onlydq
- dqnext
-
- Returns:
- straightness
getStraightness
private static float getStraightness(float cosHalfTheta)
isDna
public boolean isDna()
- Overrides:
isDna
in class Polymer
isRna
public boolean isRna()
- Overrides:
isRna
in class Polymer
getRangeGroups
public void getRangeGroups(int nResidues,
java.util.BitSet bsAtoms,
java.util.BitSet bsResult)
- Overrides:
getRangeGroups
in class Polymer
calculateStructures
public java.lang.String calculateStructures(Polymer[] bioPolymers,
int bioPolymerCount,
java.util.List vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogens,
boolean setStructure)
- Overrides:
calculateStructures
in class Polymer
vHBonds
- TODO
- Returns:
- DSSP report