org.jmol.modelset
Class Polymer

java.lang.Object
  extended by org.jmol.modelset.Polymer
Direct Known Subclasses:
BioPolymer

public abstract class Polymer
extends java.lang.Object


Field Summary
 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
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)
           
 
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 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 - 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 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 -