public abstract class BioPolymer
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
int |
bioPolymerIndexInModel |
(package private) BS |
bsSelectedMonomers |
protected P3[] |
controlPoints |
protected boolean |
hasWingPoints |
boolean |
haveParameters |
protected boolean |
invalidControl |
private boolean |
invalidLead |
protected int[] |
leadAtomIndices |
protected P3[] |
leadMidpoints |
protected P3[] |
leadPoints |
Model |
model |
int |
monomerCount |
(package private) Monomer[] |
monomers |
private static java.lang.String[] |
qColor |
BS |
reversed |
private int |
selectedMonomerCount |
protected float |
sheetSmoothing |
boolean |
twistedSheets |
protected int |
type |
protected static int |
TYPE_AMINO |
protected static int |
TYPE_CARBOHYDRATE |
protected static int |
TYPE_NOBONDING |
protected static int |
TYPE_NUCLEIC |
private V3 |
unitVectorX |
protected V3[] |
wingVectors |
Constructor and Description |
---|
BioPolymer(Monomer[] monomers) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
calcEtaThetaAngles() |
private void |
calcLeadMidpointsAndWingVectors() |
boolean |
calcParameters() |
protected boolean |
calcPhiPsiAngles() |
void |
calcRasmolHydrogenBonds(BioPolymer polymer,
BS bsA,
BS bsB,
JmolList<Bond> vHBonds,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens) |
void |
calcSelectedMonomersCount(BS bsSelected) |
java.lang.String |
calculateDssp(BioPolymer[] bioPolymers,
int bioPolymerCount,
JmolList<Bond> vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogens,
boolean setStructure) |
protected float |
calculateRamachandranHelixAngle(int m,
char qtype) |
JmolList<Atom[]> |
calculateStruts(ModelSet modelSet,
BS bs1,
BS bs2,
JmolList<Atom> vCA,
float thresh,
int delta,
boolean allowMultiple) |
void |
clearStructures() |
void |
findNearestAtomIndex(int xMouse,
int yMouse,
Atom[] closest,
short[] mads,
int myVisibilityFlag,
BS bsNot) |
private static float |
get3DStraightness(java.lang.String id,
Quaternion dq,
Quaternion dqnext) |
void |
getConformation(BS bsConformation,
int conformationIndex) |
protected P3 |
getControlPoint(int i,
V3 v) |
P3[] |
getControlPoints(boolean isTraceAlpha,
float sheetSmoothing,
boolean invalidate) |
private P3[] |
getControlPoints2(float sheetSmoothing) |
private static void |
getData(Viewer viewer,
int m0,
int mStep,
BioPolymer p,
char ctype,
char qtype,
int derivType,
BS bsAtoms,
BS bsSelected,
boolean isDraw,
boolean isRamachandran,
boolean calcRamachandranStraightness,
boolean useQuaternionStraightness,
boolean writeRamachandranStraightness,
boolean quaternionStraightness,
float factor,
boolean isAmino,
boolean isRelativeAlias,
LabelToken[] tokens,
OutputStringBuilder pdbATOM,
SB pdbCONECT,
BS bsWritten) |
Group[] |
getGroups() |
protected int |
getIndex(int chainID,
int seqcode,
int istart,
int iend) |
private P3 |
getInitiatorPoint() |
int[] |
getLeadAtomIndices() |
(package private) void |
getLeadMidPoint(int groupIndex,
P3 midPoint) |
P3[] |
getLeadMidpoints() |
(package private) P3 |
getLeadPoint(int monomerIndex) |
(package private) P3[] |
getLeadPoints() |
static void |
getPdbData(Viewer viewer,
BioPolymer p,
char ctype,
char qtype,
int mStep,
int derivType,
BS bsAtoms,
BS bsSelected,
boolean bothEnds,
boolean isDraw,
boolean addHeader,
LabelToken[] tokens,
OutputStringBuilder pdbATOM,
SB pdbCONECT,
BS bsWritten) |
void |
getPdbData(Viewer viewer,
char ctype,
char qtype,
int mStep,
int derivType,
BS bsAtoms,
BS bsSelected,
boolean bothEnds,
boolean isDraw,
boolean addHeader,
LabelToken[] tokens,
OutputStringBuilder pdbATOM,
SB pdbCONECT,
BS bsWritten) |
java.util.Map<java.lang.String,java.lang.Object> |
getPolymerInfo(BS bs) |
int |
getPolymerPointsAndVectors(int last,
BS bs,
JmolList<P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
void |
getPolymerSequenceAtoms(int group1,
int nGroups,
BS bsInclude,
BS bsResult) |
ProteinStructure |
getProteinStructure(int monomerIndex) |
private static float |
getQuaternionStraightness(java.lang.String id,
Quaternion dq,
Quaternion dqnext) |
void |
getRange(BS bs) |
void |
getRangeGroups(int nResidues,
BS bsAtoms,
BS bsResult) |
(package private) int |
getSelectedMonomerCount() |
java.lang.String |
getSequence() |
private static float |
getStraightness(float cosHalfTheta) |
private P3 |
getTerminatorPoint() |
int |
getType() |
(package private) P3 |
getWingPoint(int polymerIndex) |
V3[] |
getWingVectors() |
boolean |
isDna() |
(package private) boolean |
isMonomerSelected(int i) |
boolean |
isRna() |
void |
recalculateLeadMidpointsAndWingVectors() |
protected void |
removeProteinStructure(int monomerIndex,
int count) |
protected void |
resetHydrogenPoints() |
void |
setConformation(BS bsSelected) |
void |
setStructureList(java.util.Map<EnumStructure,float[]> structureList) |
Monomer[] monomers
public Model model
protected P3[] leadMidpoints
protected P3[] leadPoints
protected P3[] controlPoints
protected V3[] 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
public BS reversed
public boolean twistedSheets
private final V3 unitVectorX
private int selectedMonomerCount
BS bsSelectedMonomers
public boolean haveParameters
private static final java.lang.String[] qColor
BioPolymer(Monomer[] monomers)
public Group[] getGroups()
public void getRange(BS bs)
public void clearStructures()
protected void removeProteinStructure(int monomerIndex, int count)
public int[] getLeadAtomIndices()
protected int getIndex(int chainID, int seqcode, int istart, int iend)
final P3 getLeadPoint(int monomerIndex)
private final P3 getInitiatorPoint()
private final P3 getTerminatorPoint()
void getLeadMidPoint(int groupIndex, P3 midPoint)
final P3 getWingPoint(int polymerIndex)
public void getConformation(BS bsConformation, int conformationIndex)
public void setConformation(BS bsSelected)
public void recalculateLeadMidpointsAndWingVectors()
protected void resetHydrogenPoints()
public P3[] getLeadMidpoints()
P3[] getLeadPoints()
public P3[] getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
private P3[] getControlPoints2(float sheetSmoothing)
protected P3 getControlPoint(int i, V3 v)
i
- v
- public final V3[] getWingVectors()
private final void calcLeadMidpointsAndWingVectors()
public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, BS bsNot)
int getSelectedMonomerCount()
public void calcSelectedMonomersCount(BS bsSelected)
boolean isMonomerSelected(int i)
public int getPolymerPointsAndVectors(int last, BS bs, JmolList<P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
public java.lang.String getSequence()
public java.util.Map<java.lang.String,java.lang.Object> getPolymerInfo(BS bs)
public void getPolymerSequenceAtoms(int group1, int nGroups, BS bsInclude, BS 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, BS bsAtoms, BS bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, OutputStringBuilder pdbATOM, SB pdbCONECT, BS bsWritten)
private static void getData(Viewer viewer, int m0, int mStep, BioPolymer p, char ctype, char qtype, int derivType, BS bsAtoms, BS bsSelected, boolean isDraw, boolean isRamachandran, boolean calcRamachandranStraightness, boolean useQuaternionStraightness, boolean writeRamachandranStraightness, boolean quaternionStraightness, float factor, boolean isAmino, boolean isRelativeAlias, LabelToken[] tokens, OutputStringBuilder pdbATOM, SB pdbCONECT, BS 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 java.lang.String calculateDssp(BioPolymer[] bioPolymers, int bioPolymerCount, JmolList<Bond> vHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, JmolList<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, BS bsAtoms, BS bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, OutputStringBuilder pdbATOM, SB pdbCONECT, BS bsWritten)
viewer
- ctype
- qtype
- mStep
- derivType
- bsAtoms
- bsSelected
- bothEnds
- isDraw
- addHeader
- tokens
- pdbATOM
- pdbCONECT
- bsWritten
- public int getType()