public abstract class BioPolymer
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
int |
bioPolymerIndexInModel |
(package private) java.util.BitSet |
bsSelectedMonomers |
protected javax.vecmath.Point3f[] |
controlPoints |
protected boolean |
hasWingPoints |
boolean |
haveParameters |
protected boolean |
invalidControl |
private boolean |
invalidLead |
protected int[] |
leadAtomIndices |
protected javax.vecmath.Point3f[] |
leadMidpoints |
protected javax.vecmath.Point3f[] |
leadPoints |
Model |
model |
int |
monomerCount |
(package private) Monomer[] |
monomers |
private static java.lang.String[] |
qColor |
private int |
selectedMonomerCount |
protected float |
sheetSmoothing |
protected int |
type |
protected static int |
TYPE_AMINO |
protected static int |
TYPE_CARBOHYDRATE |
protected static int |
TYPE_NOBONDING |
protected static int |
TYPE_NUCLEIC |
private javax.vecmath.Vector3f |
unitVectorX |
protected javax.vecmath.Vector3f[] |
wingVectors |
Constructor and Description |
---|
BioPolymer(Monomer[] monomers) |
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) |
(package private) static BioPolymer |
allocateBioPolymer(Group[] groups,
int firstGroupIndex,
boolean checkConnections) |
protected boolean |
calcEtaThetaAngles() |
private void |
calcLeadMidpointsAndWingVectors() |
boolean |
calcParameters() |
protected boolean |
calcPhiPsiAngles() |
void |
calcRasmolHydrogenBonds(BioPolymer 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) |
protected float |
calculateRamachandranHelixAngle(int m,
char qtype) |
java.lang.String |
calculateStructures(BioPolymer[] bioPolymers,
int bioPolymerCount,
java.util.List<Bond> vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogens,
boolean setStructure) |
void |
calculateStructures(boolean alphaOnly) |
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 |
findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
short[] mads,
int myVisibilityFlag,
java.util.BitSet bsNot) |
private static float |
get3DStraightness(java.lang.String id,
Quaternion dq,
Quaternion dqnext) |
void |
getConformation(java.util.BitSet bsConformation,
int conformationIndex) |
protected javax.vecmath.Point3f |
getControlPoint(int i,
javax.vecmath.Vector3f v) |
javax.vecmath.Point3f[] |
getControlPoints(boolean isTraceAlpha,
float sheetSmoothing,
boolean invalidate) |
protected javax.vecmath.Point3f[] |
getControlPoints(float sheetSmoothing) |
private static void |
getData(Viewer viewer,
int m0,
int mStep,
BioPolymer p,
char ctype,
char qtype,
int derivType,
java.util.BitSet bsAtoms,
java.util.BitSet bsSelected,
boolean isDraw,
boolean isRamachandran,
boolean calcRamachandranStraightness,
boolean useQuaternionStraightness,
boolean writeRamachandranStraightness,
boolean quaternionStraightness,
float factor,
boolean isAmino,
boolean isRelativeAlias,
LabelToken[] tokens,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsWritten) |
Group[] |
getGroups() |
(package private) int |
getIndex(char chainID,
int seqcode) |
(package private) javax.vecmath.Point3f |
getInitiatorPoint() |
int[] |
getLeadAtomIndices() |
(package private) void |
getLeadMidPoint(int groupIndex,
javax.vecmath.Point3f midPoint) |
javax.vecmath.Point3f[] |
getLeadMidpoints() |
(package private) javax.vecmath.Point3f |
getLeadPoint(int monomerIndex) |
(package private) void |
getLeadPoint(int groupIndex,
javax.vecmath.Point3f midPoint) |
(package private) javax.vecmath.Point3f[] |
getLeadPoints() |
static void |
getPdbData(Viewer viewer,
BioPolymer p,
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) |
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) |
ProteinStructure |
getProteinStructure(int monomerIndex) |
private static float |
getQuaternionStraightness(java.lang.String id,
Quaternion dq,
Quaternion dqnext) |
void |
getRange(java.util.BitSet bs) |
void |
getRangeGroups(int nResidues,
java.util.BitSet bsAtoms,
java.util.BitSet bsResult) |
(package private) int |
getSelectedMonomerCount() |
java.lang.String |
getSequence() |
private static float |
getStraightness(float cosHalfTheta) |
(package private) javax.vecmath.Point3f |
getTerminatorPoint() |
int |
getType() |
(package private) javax.vecmath.Point3f |
getWingPoint(int polymerIndex) |
javax.vecmath.Vector3f[] |
getWingVectors() |
boolean |
isDna() |
(package private) boolean |
isMonomerSelected(int i) |
boolean |
isRna() |
void |
recalculateLeadMidpointsAndWingVectors() |
(package private) void |
removeProteinStructure(int monomerIndex,
int count) |
protected void |
resetHydrogenPoints() |
void |
setConformation(java.util.BitSet bsSelected) |
void |
setStructureList(java.util.Map<EnumStructure,float[]> structureList) |
Monomer[] monomers
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
private boolean invalidLead
protected boolean invalidControl
protected float sheetSmoothing
protected boolean hasWingPoints
private final javax.vecmath.Vector3f unitVectorX
private int selectedMonomerCount
java.util.BitSet bsSelectedMonomers
public boolean haveParameters
private static final java.lang.String[] qColor
BioPolymer(Monomer[] monomers)
public Group[] getGroups()
public void getRange(java.util.BitSet bs)
static BioPolymer allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections)
public void clearStructures()
void removeProteinStructure(int monomerIndex, int count)
public int[] getLeadAtomIndices()
int getIndex(char chainID, int seqcode)
final javax.vecmath.Point3f getLeadPoint(int monomerIndex)
final javax.vecmath.Point3f getInitiatorPoint()
final javax.vecmath.Point3f getTerminatorPoint()
void getLeadMidPoint(int groupIndex, javax.vecmath.Point3f midPoint)
void getLeadPoint(int groupIndex, javax.vecmath.Point3f midPoint)
final javax.vecmath.Point3f getWingPoint(int polymerIndex)
public void getConformation(java.util.BitSet bsConformation, int conformationIndex)
public void setConformation(java.util.BitSet bsSelected)
public void recalculateLeadMidpointsAndWingVectors()
protected void resetHydrogenPoints()
public javax.vecmath.Point3f[] getLeadMidpoints()
javax.vecmath.Point3f[] getLeadPoints()
public javax.vecmath.Point3f[] getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
protected javax.vecmath.Point3f[] getControlPoints(float sheetSmoothing)
protected javax.vecmath.Point3f getControlPoint(int i, javax.vecmath.Vector3f v)
i
- v
- public final javax.vecmath.Vector3f[] getWingVectors()
private final void calcLeadMidpointsAndWingVectors()
public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, java.util.BitSet bsNot)
int getSelectedMonomerCount()
public void calcSelectedMonomersCount(java.util.BitSet bsSelected)
boolean isMonomerSelected(int i)
public int getPolymerPointsAndVectors(int last, java.util.BitSet bs, java.util.List<javax.vecmath.Point3f[]> vList, boolean isTraceAlpha, float sheetSmoothing)
public java.lang.String getSequence()
public java.util.Map<java.lang.String,java.lang.Object> getPolymerInfo(java.util.BitSet bs)
public void getPolymerSequenceAtoms(int group1, int nGroups, java.util.BitSet bsInclude, java.util.BitSet bsResult)
public ProteinStructure getProteinStructure(int monomerIndex)
public boolean calcParameters()
protected boolean calcEtaThetaAngles()
protected boolean calcPhiPsiAngles()
public static final void getPdbData(Viewer viewer, BioPolymer p, 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)
private static void getData(Viewer viewer, int m0, int mStep, BioPolymer p, char ctype, char qtype, int derivType, java.util.BitSet bsAtoms, java.util.BitSet bsSelected, boolean isDraw, boolean isRamachandran, boolean calcRamachandranStraightness, boolean useQuaternionStraightness, boolean writeRamachandranStraightness, boolean quaternionStraightness, float factor, boolean isAmino, boolean isRelativeAlias, LabelToken[] tokens, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsWritten)
viewer
- m0
- mStep
- p
- ctype
- qtype
- derivType
- bsAtoms
- bsSelected
- isDraw
- isRamachandran
- calcRamachandranStraightness
- useQuaternionStraightness
- writeRamachandranStraightness
- quaternionStraightness
- NOT USEDfactor
- isAmino
- isRelativeAlias
- tokens
- pdbATOM
- pdbCONECT
- bsWritten
- protected float calculateRamachandranHelixAngle(int m, char qtype)
m
- qtype
- private static float get3DStraightness(java.lang.String id, Quaternion dq, Quaternion dqnext)
id
- for debugging onlydq
- dqnext
- private static float getQuaternionStraightness(java.lang.String id, Quaternion dq, Quaternion dqnext)
id
- for debugging onlydq
- dqnext
- private static float getStraightness(float cosHalfTheta)
public boolean isDna()
public boolean isRna()
public void getRangeGroups(int nResidues, java.util.BitSet bsAtoms, java.util.BitSet bsResult)
public java.lang.String calculateStructures(BioPolymer[] bioPolymers, int bioPolymerCount, java.util.List<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)
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 void calculateStructures(boolean alphaOnly)
alphaOnly
- public void calcRasmolHydrogenBonds(BioPolymer 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 setStructureList(java.util.Map<EnumStructure,float[]> structureList)
structureList
- protein only -- helix, sheet, turn definitionspublic 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 int getType()
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
-