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(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)
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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 vList,
boolean isTraceAlpha,
float sheetSmoothing)
- Parameters:
last
- bs
- vList
- isTraceAlpha
- sheetSmoothing
-
- Returns:
- number of points
addSecondaryStructure
public void addSecondaryStructure(byte 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 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 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 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,
boolean isDraw,
java.util.BitSet bsAtoms,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
boolean bothEnds,
java.util.BitSet bsWritten)
- Parameters:
viewer
- ctype
- qtype
- mStep
- derivType
- isDraw
- bsAtoms
- pdbATOM
- pdbCONECT
- bsSelected
- addHeader
- bothEnds
- bsWritten
-
calculateStruts
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)
- Parameters:
modelSet
- atoms
- 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(float[][] structureList)
- Parameters:
structureList
- protein only -- helix, sheet, turn definitions
getConformation
public void getConformation(java.util.BitSet bsConformation,
int conformationIndex)
- Parameters:
bsConformation
- conformationIndex
-