org.jmol.modelsetbio

Class BioPolymer

public abstract class BioPolymer extends Polymer

Field Summary
BitSetbsSelectedMonomers
protected Modelmodel
intmonomerCount
Monomer[]monomers
static String[]qColor
intselectedMonomerCount
floatsheetSmoothing
Vector3funitVectorX
Constructor Summary
BioPolymer(Monomer[] monomers)
Method Summary
voidaddSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
static BioPolymerallocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections)
voidcalcHydrogenBonds(BitSet bsA, BitSet bsB)
voidcalcLeadMidpointsAndWingVectors(boolean getNewPoints)
protected booleancalcPhiPsiAngles()
voidcalcSelectedMonomersCount(BitSet bsSelected)
voidcalculateStructures()
voidclearStructures()
voidfindNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag)
Point3f[]getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
intgetIndex(char chainID, int seqcode)
Point3fgetInitiatorPoint()
int[]getLeadAtomIndices()
Point3f[]getLeadMidpoints()
voidgetLeadMidPoint(int groupIndex, Point3f midPoint)
Point3fgetLeadPoint(int monomerIndex)
voidgetLeadPoint(int groupIndex, Point3f midPoint)
Point3f[]getLeadPoints()
ModelgetModel()
intgetMonomerCount()
Monomer[]getMonomers()
static voidgetPdbData(BioPolymer p, char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)
Point3fgetPointPoint(int polymerIndex)
HashtablegetPolymerInfo(BitSet bs)
intgetPolymerPointsAndVectors(int last, BitSet bs, Vector vList, boolean isTraceAlpha, float sheetSmoothing)
voidgetPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, BitSet bsInclude, BitSet bsResult)
ProteinStructuregetProteinStructure(int monomerIndex)
intgetSelectedMonomerCount()
StringgetSequence()
Point3f[]getSheetPoints(float sheetSmoothing)
static floatgetStraightness(String id, Quaternion dqprev, Quaternion dq)
Point3fgetTerminatorPoint()
Point3fgetWingPoint(int polymerIndex)
Vector3f[]getWingVectors()
booleanhasWingPoints()
booleanisMonomerSelected(int i)
voidrecalculateLeadMidpointsAndWingVectors()
voidremoveProteinStructure(int monomerIndex, int count)
voidsetConformation(BitSet bsSelected, int nAltLocsInModel)

Field Detail

bsSelectedMonomers

BitSet bsSelectedMonomers

model

protected Model model

monomerCount

int monomerCount

monomers

Monomer[] monomers

qColor

private static final String[] qColor

selectedMonomerCount

private int selectedMonomerCount

sheetSmoothing

private float sheetSmoothing

unitVectorX

private final Vector3f unitVectorX

Constructor Detail

BioPolymer

BioPolymer(Monomer[] monomers)

Method Detail

addSecondaryStructure

public void addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)

allocateBioPolymer

static BioPolymer allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections)

calcHydrogenBonds

public void calcHydrogenBonds(BitSet bsA, BitSet bsB)

calcLeadMidpointsAndWingVectors

private final void calcLeadMidpointsAndWingVectors(boolean getNewPoints)

calcPhiPsiAngles

protected boolean calcPhiPsiAngles()

calcSelectedMonomersCount

public void calcSelectedMonomersCount(BitSet bsSelected)

calculateStructures

public void calculateStructures()

clearStructures

public void clearStructures()

findNearestAtomIndex

public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag)

getControlPoints

public Point3f[] getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)

getIndex

int getIndex(char chainID, int seqcode)

getInitiatorPoint

final Point3f getInitiatorPoint()

getLeadAtomIndices

public int[] getLeadAtomIndices()

getLeadMidpoints

public Point3f[] getLeadMidpoints()

getLeadMidPoint

void getLeadMidPoint(int groupIndex, Point3f midPoint)

getLeadPoint

final Point3f getLeadPoint(int monomerIndex)

getLeadPoint

void getLeadPoint(int groupIndex, Point3f midPoint)

getLeadPoints

Point3f[] getLeadPoints()

getModel

public Model getModel()

getMonomerCount

public int getMonomerCount()

getMonomers

public Monomer[] getMonomers()

getPdbData

public static final void getPdbData(BioPolymer p, char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)

getPointPoint

final Point3f getPointPoint(int polymerIndex)

getPolymerInfo

public Hashtable getPolymerInfo(BitSet bs)

getPolymerPointsAndVectors

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

getPolymerSequenceAtoms

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

getProteinStructure

public ProteinStructure getProteinStructure(int monomerIndex)

getSelectedMonomerCount

int getSelectedMonomerCount()

getSequence

public String getSequence()

getSheetPoints

private Point3f[] getSheetPoints(float sheetSmoothing)

getStraightness

private static float getStraightness(String id, Quaternion dqprev, Quaternion dq)

getTerminatorPoint

final Point3f getTerminatorPoint()

getWingPoint

final Point3f getWingPoint(int polymerIndex)

getWingVectors

public final Vector3f[] getWingVectors()

hasWingPoints

boolean hasWingPoints()

isMonomerSelected

boolean isMonomerSelected(int i)

recalculateLeadMidpointsAndWingVectors

public void recalculateLeadMidpointsAndWingVectors()

removeProteinStructure

void removeProteinStructure(int monomerIndex, int count)

setConformation

public void setConformation(BitSet bsSelected, int nAltLocsInModel)