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

Field Summary

Fields

Modifier and Type	Field and Description
(package private) java.util.BitSet	bsSelectedMonomers
protected boolean	hasWingPoints
boolean	haveParameters
protected boolean	invalidControl
private boolean	invalidLead
(package private) Monomer[]	monomers
private static java.lang.String[]	qColor
private int	selectedMonomerCount
protected float	sheetSmoothing
private javax.vecmath.Vector3f	unitVectorX

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

Constructor Summary

Constructors

Constructor and Description
BioPolymer(Monomer[] monomers)

Method Summary

Methods

Modifier and Type	Method and Description
(package private) static BioPolymer	allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections)
protected boolean	calcEtaThetaAngles()
private void	calcLeadMidpointsAndWingVectors()
boolean	calcParameters()
protected boolean	calcPhiPsiAngles()
void	calcSelectedMonomersCount(java.util.BitSet bsSelected)
protected float	calculateRamachandranHelixAngle(int m, char qtype)
java.lang.String	calculateStructures(Polymer[] bioPolymers, int bioPolymerCount, java.util.List<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)
void	clearStructures()
void	findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, java.util.BitSet bsNot)
private static float	get3DStraightness(java.lang.String id, Quaternion dq, Quaternion dqnext)
void	getConformation(java.util.BitSet bsConformation, int conformationIndex)
protected javax.vecmath.Point3f	getControlPoint(int i, javax.vecmath.Vector3f v)
javax.vecmath.Point3f[]	getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
protected javax.vecmath.Point3f[]	getControlPoints(float sheetSmoothing)
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, boolean isDraw, boolean isRamachandran, boolean calcRamachandranStraightness, boolean useQuaternionStraightness, boolean writeRamachandranStraightness, boolean quaternionStraightness, float factor, boolean isAmino, boolean isRelativeAlias, LabelToken[] tokens, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsWritten)
Group[]	getGroups()
(package private) int	getIndex(char chainID, int seqcode)
(package private) javax.vecmath.Point3f	getInitiatorPoint()
int[]	getLeadAtomIndices()
(package private) void	getLeadMidPoint(int groupIndex, javax.vecmath.Point3f midPoint)
javax.vecmath.Point3f[]	getLeadMidpoints()
(package private) javax.vecmath.Point3f	getLeadPoint(int monomerIndex)
(package private) void	getLeadPoint(int groupIndex, javax.vecmath.Point3f midPoint)
(package private) javax.vecmath.Point3f[]	getLeadPoints()
static void	getPdbData(Viewer viewer, BioPolymer p, char ctype, char qtype, int mStep, int derivType, java.util.BitSet bsAtoms, java.util.BitSet bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsWritten)
java.util.Map<java.lang.String,java.lang.Object>	getPolymerInfo(java.util.BitSet bs)
int	getPolymerPointsAndVectors(int last, java.util.BitSet bs, java.util.List<javax.vecmath.Point3f[]> vList, boolean isTraceAlpha, float sheetSmoothing)
void	getPolymerSequenceAtoms(int group1, int nGroups, java.util.BitSet bsInclude, java.util.BitSet bsResult)
ProteinStructure	getProteinStructure(int monomerIndex)
private static float	getQuaternionStraightness(java.lang.String id, Quaternion dq, Quaternion dqnext)
void	getRange(java.util.BitSet bs)
void	getRangeGroups(int nResidues, java.util.BitSet bsAtoms, java.util.BitSet bsResult)
(package private) int	getSelectedMonomerCount()
java.lang.String	getSequence()
private static float	getStraightness(float cosHalfTheta)
(package private) javax.vecmath.Point3f	getTerminatorPoint()
(package private) javax.vecmath.Point3f	getWingPoint(int polymerIndex)
javax.vecmath.Vector3f[]	getWingVectors()
boolean	isDna()
(package private) boolean	isMonomerSelected(int i)
boolean	isRna()
void	recalculateLeadMidpointsAndWingVectors()
(package private) void	removeProteinStructure(int monomerIndex, int count)
protected void	resetHydrogenPoints()
void	setConformation(java.util.BitSet bsSelected)

Methods inherited from class org.jmol.modelset.Polymer

addSecondaryStructure, calcRasmolHydrogenBonds, calculateStructures, calculateStruts, getPdbData, getType, setStructureList

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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

Constructor Detail

BioPolymer

BioPolymer(Monomer[] monomers)

Method Detail

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<javax.vecmath.Point3f[]> 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<java.lang.String,java.lang.Object> 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,
              java.util.BitSet bsAtoms,
              java.util.BitSet bsSelected,
              boolean bothEnds,
              boolean isDraw,
              boolean addHeader,
              LabelToken[] tokens,
              OutputStringBuffer pdbATOM,
              java.lang.StringBuffer pdbCONECT,
              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,
           boolean isDraw,
           boolean isRamachandran,
           boolean calcRamachandranStraightness,
           boolean useQuaternionStraightness,
           boolean writeRamachandranStraightness,
           boolean quaternionStraightness,
           float factor,
           boolean isAmino,
           boolean isRelativeAlias,
           LabelToken[] tokens,
           OutputStringBuffer pdbATOM,
           java.lang.StringBuffer pdbCONECT,
           java.util.BitSet bsWritten)

Parameters:

viewer -

m0 -

mStep -

p -

ctype -

qtype -

derivType -

bsAtoms -

bsSelected -

isDraw -

isRamachandran -

calcRamachandranStraightness -

useQuaternionStraightness -

writeRamachandranStraightness -

quaternionStraightness - NOT USED

factor -

isAmino -

isRelativeAlias -

tokens -

pdbATOM -

pdbCONECT -

bsWritten -

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 only

dq -

dqnext -

Returns:

calculated straightness

getQuaternionStraightness

private static float getQuaternionStraightness(java.lang.String id,
                              Quaternion dq,
                              Quaternion dqnext)

Parameters:

id - for debugging only

dq -

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<Bond> vHBonds,
                                   boolean doReport,
                                   boolean dsspIgnoreHydrogens,
                                   boolean setStructure)

Overrides:

calculateStructures in class Polymer

vHBonds - TODO

Returns:

DSSP report