org.jmol.modelsetbio
Class BioPolymer
public abstract
class
BioPolymer
extends Polymer
Method Summary |
void | addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode) |
static BioPolymer | allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections) |
void | calcHydrogenBonds(BitSet bsA, BitSet bsB) |
void | calcLeadMidpointsAndWingVectors(boolean getNewPoints) |
protected boolean | calcPhiPsiAngles() |
void | calcSelectedMonomersCount(BitSet bsSelected) |
void | calculateStructures() |
void | clearStructures() |
void | findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag) |
Point3f[] | getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate) |
int | getIndex(char chainID, int seqcode) |
Point3f | getInitiatorPoint() |
int[] | getLeadAtomIndices() |
Point3f[] | getLeadMidpoints() |
void | getLeadMidPoint(int groupIndex, Point3f midPoint) |
Point3f | getLeadPoint(int monomerIndex) |
void | getLeadPoint(int groupIndex, Point3f midPoint) |
Point3f[] | getLeadPoints() |
Model | getModel() |
int | getMonomerCount() |
Monomer[] | getMonomers() |
static void | getPdbData(BioPolymer p, char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten) |
Point3f | getPointPoint(int polymerIndex) |
Hashtable | getPolymerInfo(BitSet bs) |
int | getPolymerPointsAndVectors(int last, BitSet bs, Vector vList, boolean isTraceAlpha, float sheetSmoothing) |
void | getPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, BitSet bsInclude, BitSet bsResult) |
ProteinStructure | getProteinStructure(int monomerIndex) |
int | getSelectedMonomerCount() |
String | getSequence() |
Point3f[] | getSheetPoints(float sheetSmoothing) |
static float | getStraightness(String id, Quaternion dqprev, Quaternion dq) |
Point3f | getTerminatorPoint() |
Point3f | getWingPoint(int polymerIndex) |
Vector3f[] | getWingVectors() |
boolean | hasWingPoints() |
boolean | isMonomerSelected(int i) |
void | recalculateLeadMidpointsAndWingVectors() |
void | removeProteinStructure(int monomerIndex, int count) |
void | setConformation(BitSet bsSelected, int nAltLocsInModel) |
BitSet bsSelectedMonomers
int monomerCount
private static final String[] qColor
private int selectedMonomerCount
private float sheetSmoothing
private final Vector3f unitVectorX
public void addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
static
BioPolymer allocateBioPolymer(
Group[] groups, int firstGroupIndex, boolean checkConnections)
public void calcHydrogenBonds(BitSet bsA, BitSet bsB)
private final void calcLeadMidpointsAndWingVectors(boolean getNewPoints)
protected boolean calcPhiPsiAngles()
public void calcSelectedMonomersCount(BitSet bsSelected)
public void calculateStructures()
public void clearStructures()
public void findNearestAtomIndex(int xMouse, int yMouse,
Atom[] closest, short[] mads, int myVisibilityFlag)
public Point3f[] getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
int getIndex(char chainID, int seqcode)
final Point3f getInitiatorPoint()
public int[] getLeadAtomIndices()
public Point3f[] getLeadMidpoints()
void getLeadMidPoint(int groupIndex, Point3f midPoint)
final Point3f getLeadPoint(int monomerIndex)
void getLeadPoint(int groupIndex, Point3f midPoint)
Point3f[] getLeadPoints()
public int getMonomerCount()
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)
final Point3f getPointPoint(int polymerIndex)
public Hashtable getPolymerInfo(BitSet bs)
public int getPolymerPointsAndVectors(int last, BitSet bs, Vector vList, boolean isTraceAlpha, float sheetSmoothing)
public void getPolymerSequenceAtoms(int iModel, int iPolymer, int group1, int nGroups, BitSet bsInclude, BitSet bsResult)
int getSelectedMonomerCount()
public String getSequence()
private Point3f[] getSheetPoints(float sheetSmoothing)
final Point3f getTerminatorPoint()
final Point3f getWingPoint(int polymerIndex)
public final Vector3f[] getWingVectors()
boolean hasWingPoints()
boolean isMonomerSelected(int i)
public void recalculateLeadMidpointsAndWingVectors()
void removeProteinStructure(int monomerIndex, int count)
public void setConformation(BitSet bsSelected, int nAltLocsInModel)