org.jmol.modelset
Class Polymer
java.lang.Object
org.jmol.modelset.Polymer
- Direct Known Subclasses:
- BioPolymer
public abstract class Polymer
- extends java.lang.Object
Constructor Summary |
protected |
Polymer()
|
Method Summary |
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()
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void |
recalculateLeadMidpointsAndWingVectors()
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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 |
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
Polymer
protected Polymer()
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
- TODOdoReport
- 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
-