org.jmol.modelset
Class Polymer

java.lang.Object
  org.jmol.modelset.Polymer

Direct Known Subclasses:

BioPolymer

public abstract class Polymer
extends Object

Field Summary

int	bioPolymerIndexInModel
protected Point3f[]	controlPoints
protected int[]	leadAtomIndices
protected Point3f[]	leadMidpoints
protected Point3f[]	leadPoints
Model	model
int	monomerCount
protected int	type
protected static int	TYPE_AMINO
protected static int	TYPE_CARBOHYDRATE
protected static int	TYPE_NOBONDING
protected static int	TYPE_NUCLEIC
protected Vector3f[]	wingVectors

Constructor Summary

protected

Polymer()

Method Summary

void	addSecondaryStructure(EnumStructure type, String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
void	calcRasmolHydrogenBonds(Polymer polymer, BitSet bsA, BitSet bsB, List<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
void	calcSelectedMonomersCount(BitSet bsSelected)
void	calculateStructures(boolean alphaOnly)
String	calculateStructures(Polymer[] bioPolymers, int bioPolymerCount, List<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
List<Atom[]>	calculateStruts(ModelSet modelSet, BitSet bs1, BitSet bs2, List<Atom> vCA, float thresh, int delta, boolean allowMultiple)
void	clearStructures()
void	getConformation(BitSet bsConformation, int conformationIndex)
Group[]	getGroups()
Point3f[]	getLeadMidpoints()
void	getPdbData(Viewer viewer, char ctype, char qtype, int mStep, int derivType, BitSet bsAtoms, BitSet bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, OutputStringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsWritten)
Map<String,Object>	getPolymerInfo(BitSet bs)
int	getPolymerPointsAndVectors(int last, BitSet bs, List<Point3f[]> vList, boolean isTraceAlpha, float sheetSmoothing)
void	getPolymerSequenceAtoms(int group1, int nGroups, BitSet bsInclude, BitSet bsResult)
void	getRange(BitSet bs)
void	getRangeGroups(int residues, BitSet bs, BitSet bsResult)
String	getSequence()
int	getType()
boolean	isDna()
boolean	isRna()
void	recalculateLeadMidpointsAndWingVectors()
void	setConformation(BitSet bsConformation)
void	setStructureList(Map<EnumStructure,float[]> structureList)

Methods inherited from class java.lang.Object

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

Field Detail

model

public Model model

leadMidpoints

protected Point3f[] leadMidpoints

leadPoints

protected Point3f[] leadPoints

controlPoints

protected Point3f[] controlPoints

wingVectors

protected Vector3f[] wingVectors

leadAtomIndices

protected int[] leadAtomIndices

type

protected int type

bioPolymerIndexInModel

public int bioPolymerIndexInModel

monomerCount

public int monomerCount

TYPE_NOBONDING

protected static final int TYPE_NOBONDING

See Also:

Constant Field Values

TYPE_AMINO

protected static final int TYPE_AMINO

See Also:

Constant Field Values

TYPE_NUCLEIC

protected static final int TYPE_NUCLEIC

See Also:

Constant Field Values

TYPE_CARBOHYDRATE

protected static final int TYPE_CARBOHYDRATE

See Also:

Constant Field Values

Constructor Detail

Polymer

protected Polymer()

Method Detail

getType

public int getType()

getRange

public void getRange(BitSet bs)

Parameters:

bs -

getPolymerPointsAndVectors

public int getPolymerPointsAndVectors(int last,
                                      BitSet bs,
                                      List<Point3f[]> vList,
                                      boolean isTraceAlpha,
                                      float sheetSmoothing)

Parameters:

last -

bs -

vList -

isTraceAlpha -

sheetSmoothing -

Returns:

number of points

addSecondaryStructure

public void addSecondaryStructure(EnumStructure type,
                                  String structureID,
                                  int serialID,
                                  int strandCount,
                                  char startChainID,
                                  int startSeqcode,
                                  char endChainID,
                                  int endSeqcode)

Parameters:

type -

structureID -

serialID -

strandCount -

startChainID -

startSeqcode -

endChainID -

endSeqcode -

calculateStructures

public String calculateStructures(Polymer[] bioPolymers,
                                  int bioPolymerCount,
                                  List<Bond> vHBonds,
                                  boolean doReport,
                                  boolean dsspIgnoreHydrogen,
                                  boolean setStructure)

Parameters:

bioPolymers -

bioPolymerCount -

vHBonds - TODO

doReport -

dsspIgnoreHydrogen -

setStructure -

Returns:

DSSP report

calculateStructures

public void calculateStructures(boolean alphaOnly)

Parameters:

alphaOnly -

clearStructures

public void clearStructures()

getSequence

public String getSequence()

getPolymerInfo

public Map<String,Object> getPolymerInfo(BitSet bs)

Parameters:

bs -

Returns:

info

setConformation

public void setConformation(BitSet bsConformation)

Parameters:

bsConformation -

calcRasmolHydrogenBonds

public void calcRasmolHydrogenBonds(Polymer polymer,
                                    BitSet bsA,
                                    BitSet bsB,
                                    List<Bond> vHBonds,
                                    int nMaxPerResidue,
                                    int[][][] min,
                                    boolean checkDistances,
                                    boolean dsspIgnoreHydrogens)

Parameters:

polymer -

bsA -

bsB -

vHBonds -

nMaxPerResidue -

min -

checkDistances -

dsspIgnoreHydrogens -

calcSelectedMonomersCount

public void calcSelectedMonomersCount(BitSet bsSelected)

Parameters:

bsSelected -

getPolymerSequenceAtoms

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

Parameters:

group1 -

nGroups -

bsInclude -

bsResult -

getLeadMidpoints

public Point3f[] getLeadMidpoints()

recalculateLeadMidpointsAndWingVectors

public void recalculateLeadMidpointsAndWingVectors()

getPdbData

public void getPdbData(Viewer viewer,
                       char ctype,
                       char qtype,
                       int mStep,
                       int derivType,
                       BitSet bsAtoms,
                       BitSet bsSelected,
                       boolean bothEnds,
                       boolean isDraw,
                       boolean addHeader,
                       LabelToken[] tokens,
                       OutputStringBuffer pdbATOM,
                       StringBuffer pdbCONECT,
                       BitSet bsWritten)

Parameters:

viewer -

ctype -

qtype -

mStep -

derivType -

bsAtoms -

bsSelected -

bothEnds -

isDraw -

addHeader -

tokens -

pdbATOM -

pdbCONECT -

bsWritten -

calculateStruts

public List<Atom[]> calculateStruts(ModelSet modelSet,
                                    BitSet bs1,
                                    BitSet bs2,
                                    List<Atom> vCA,
                                    float thresh,
                                    int delta,
                                    boolean allowMultiple)

Parameters:

modelSet -

bs1 -

bs2 -

vCA -

thresh -

delta -

allowMultiple -

Returns:

List [ {atom1, atom2}, {atom1, atom2}...]

isDna

public boolean isDna()

isRna

public boolean isRna()

getRangeGroups

public void getRangeGroups(int residues,
                           BitSet bs,
                           BitSet bsResult)

Parameters:

residues -

bs -

bsResult -

getGroups

public Group[] getGroups()

setStructureList

public void setStructureList(Map<EnumStructure,float[]> structureList)

Parameters:

structureList - protein only -- helix, sheet, turn definitions

getConformation

public void getConformation(BitSet bsConformation,
                            int conformationIndex)

Parameters:

bsConformation -

conformationIndex -