org.jmol.modelset

Class Polymer

java.lang.Object

org.jmol.modelset.Polymer

Direct Known Subclasses:

BioPolymer

public abstract class Polymer
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
int	bioPolymerIndexInModel
protected javax.vecmath.Point3f[]	controlPoints
protected int[]	leadAtomIndices
protected javax.vecmath.Point3f[]	leadMidpoints
protected javax.vecmath.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 javax.vecmath.Vector3f[]	wingVectors

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Polymer()

Method Summary

Methods

Modifier and Type	Method and Description
void	addSecondaryStructure(EnumStructure type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
void	calcRasmolHydrogenBonds(Polymer polymer, java.util.BitSet bsA, java.util.BitSet bsB, java.util.List<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
void	calcSelectedMonomersCount(java.util.BitSet bsSelected)
void	calculateStructures(boolean alphaOnly)
java.lang.String	calculateStructures(Polymer[] bioPolymers, int bioPolymerCount, java.util.List<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
java.util.List<Atom[]>	calculateStruts(ModelSet modelSet, java.util.BitSet bs1, java.util.BitSet bs2, java.util.List<Atom> vCA, float thresh, int delta, boolean allowMultiple)
void	clearStructures()
void	getConformation(java.util.BitSet bsConformation, int conformationIndex)
Group[]	getGroups()
javax.vecmath.Point3f[]	getLeadMidpoints()
void	getPdbData(Viewer viewer, 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)
void	getRange(java.util.BitSet bs)
void	getRangeGroups(int residues, java.util.BitSet bs, java.util.BitSet bsResult)
java.lang.String	getSequence()
int	getType()
boolean	isDna()
boolean	isRna()
void	recalculateLeadMidpointsAndWingVectors()
void	setConformation(java.util.BitSet bsConformation)
void	setStructureList(java.util.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 javax.vecmath.Point3f[] leadMidpoints

leadPoints

protected javax.vecmath.Point3f[] leadPoints

controlPoints

protected javax.vecmath.Point3f[] controlPoints

wingVectors

protected javax.vecmath.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(java.util.BitSet bs)

Parameters:

bs -

getPolymerPointsAndVectors

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

Parameters:

last -

bs -

vList -

isTraceAlpha -

sheetSmoothing -

Returns:

number of points

addSecondaryStructure

public void addSecondaryStructure(EnumStructure type,
                         java.lang.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 java.lang.String calculateStructures(Polymer[] bioPolymers,
                                   int bioPolymerCount,
                                   java.util.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 java.lang.String getSequence()

getPolymerInfo

public java.util.Map<java.lang.String,java.lang.Object> getPolymerInfo(java.util.BitSet bs)

Parameters:

bs -

Returns:

info

setConformation

public void setConformation(java.util.BitSet bsConformation)

Parameters:

bsConformation -

calcRasmolHydrogenBonds

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

Parameters:

polymer -

bsA -

bsB -

vHBonds -

nMaxPerResidue -

min -

checkDistances -

dsspIgnoreHydrogens -

calcSelectedMonomersCount

public void calcSelectedMonomersCount(java.util.BitSet bsSelected)

Parameters:

bsSelected -

getPolymerSequenceAtoms

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

Parameters:

group1 -

nGroups -

bsInclude -

bsResult -

getLeadMidpoints

public javax.vecmath.Point3f[] getLeadMidpoints()

recalculateLeadMidpointsAndWingVectors

public void recalculateLeadMidpointsAndWingVectors()

getPdbData

public void getPdbData(Viewer viewer,
              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)

Parameters:

viewer -

ctype -

qtype -

mStep -

derivType -

bsAtoms -

bsSelected -

bothEnds -

isDraw -

addHeader -

tokens -

pdbATOM -

pdbCONECT -

bsWritten -

calculateStruts

public java.util.List<Atom[]> calculateStruts(ModelSet modelSet,
                                     java.util.BitSet bs1,
                                     java.util.BitSet bs2,
                                     java.util.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,
                  java.util.BitSet bs,
                  java.util.BitSet bsResult)

Parameters:

residues -

bs -

bsResult -

getGroups

public Group[] getGroups()

setStructureList

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

Parameters:

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

getConformation

public void getConformation(java.util.BitSet bsConformation,
                   int conformationIndex)

Parameters:

bsConformation -

conformationIndex -