public abstract class Polymer
extends java.lang.Object
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 |
Modifier | Constructor and Description |
---|---|
protected |
Polymer() |
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) |
public Model model
protected javax.vecmath.Point3f[] leadMidpoints
protected javax.vecmath.Point3f[] leadPoints
protected javax.vecmath.Point3f[] controlPoints
protected javax.vecmath.Vector3f[] wingVectors
protected int[] leadAtomIndices
protected int type
public int bioPolymerIndexInModel
public int monomerCount
protected static final int TYPE_NOBONDING
protected static final int TYPE_AMINO
protected static final int TYPE_NUCLEIC
protected static final int TYPE_CARBOHYDRATE
public int getType()
public void getRange(java.util.BitSet bs)
bs
- public int getPolymerPointsAndVectors(int last, java.util.BitSet bs, java.util.List<javax.vecmath.Point3f[]> vList, boolean isTraceAlpha, float sheetSmoothing)
last
- bs
- vList
- isTraceAlpha
- sheetSmoothing
- public void addSecondaryStructure(EnumStructure type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
type
- structureID
- serialID
- strandCount
- startChainID
- startSeqcode
- endChainID
- endSeqcode
- public java.lang.String calculateStructures(Polymer[] bioPolymers, int bioPolymerCount, java.util.List<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure)
bioPolymers
- bioPolymerCount
- vHBonds
- TODOdoReport
- dsspIgnoreHydrogen
- setStructure
- public void calculateStructures(boolean alphaOnly)
alphaOnly
- public void clearStructures()
public java.lang.String getSequence()
public java.util.Map<java.lang.String,java.lang.Object> getPolymerInfo(java.util.BitSet bs)
bs
- public void setConformation(java.util.BitSet bsConformation)
bsConformation
- 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)
polymer
- bsA
- bsB
- vHBonds
- nMaxPerResidue
- min
- checkDistances
- dsspIgnoreHydrogens
- public void calcSelectedMonomersCount(java.util.BitSet bsSelected)
bsSelected
- public void getPolymerSequenceAtoms(int group1, int nGroups, java.util.BitSet bsInclude, java.util.BitSet bsResult)
group1
- nGroups
- bsInclude
- bsResult
- public javax.vecmath.Point3f[] getLeadMidpoints()
public void recalculateLeadMidpointsAndWingVectors()
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)
viewer
- ctype
- qtype
- mStep
- derivType
- bsAtoms
- bsSelected
- bothEnds
- isDraw
- addHeader
- tokens
- pdbATOM
- pdbCONECT
- bsWritten
- 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)
modelSet
- bs1
- bs2
- vCA
- thresh
- delta
- allowMultiple
- public boolean isDna()
public boolean isRna()
public void getRangeGroups(int residues, java.util.BitSet bs, java.util.BitSet bsResult)
residues
- bs
- bsResult
- public Group[] getGroups()
public void setStructureList(java.util.Map<EnumStructure,float[]> structureList)
structureList
- protein only -- helix, sheet, turn definitionspublic void getConformation(java.util.BitSet bsConformation, int conformationIndex)
bsConformation
- conformationIndex
-