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(byte 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 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 vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure) |
java.util.List |
calculateStruts(ModelSet modelSet,
Atom[] atoms,
java.util.BitSet bs1,
java.util.BitSet bs2,
java.util.List 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,
boolean isDraw,
java.util.BitSet bsAtoms,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
boolean bothEnds,
java.util.BitSet bsWritten) |
java.util.Map |
getPolymerInfo(java.util.BitSet bs) |
int |
getPolymerPointsAndVectors(int last,
java.util.BitSet bs,
java.util.List 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(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 vList, boolean isTraceAlpha, float sheetSmoothing)
last
- bs
- vList
- isTraceAlpha
- sheetSmoothing
- public void addSecondaryStructure(byte 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 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 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 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, boolean isDraw, java.util.BitSet bsAtoms, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, boolean bothEnds, java.util.BitSet bsWritten)
viewer
- ctype
- qtype
- mStep
- derivType
- isDraw
- bsAtoms
- pdbATOM
- pdbCONECT
- bsSelected
- addHeader
- bothEnds
- bsWritten
- public java.util.List calculateStruts(ModelSet modelSet, Atom[] atoms, java.util.BitSet bs1, java.util.BitSet bs2, java.util.List vCA, float thresh, int delta, boolean allowMultiple)
modelSet
- atoms
- 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(float[][] structureList)
structureList
- protein only -- helix, sheet, turn definitionspublic void getConformation(java.util.BitSet bsConformation, int conformationIndex)
bsConformation
- conformationIndex
-