public abstract class BioPolymer extends Object
Modifier and Type | Field and Description |
---|---|
int |
bioPolymerIndexInModel |
(package private) BS |
bsSelectedMonomers |
protected javajs.util.P3[] |
controlPoints |
protected boolean |
hasWingPoints |
boolean |
haveParameters |
protected boolean |
invalidControl |
private boolean |
invalidLead |
protected int[] |
leadAtomIndices |
protected javajs.util.P3[] |
leadMidpoints |
protected javajs.util.P3[] |
leadPoints |
Model |
model |
int |
monomerCount |
Monomer[] |
monomers |
private static 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 javajs.util.V3 |
unitVectorX |
protected javajs.util.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,
javajs.util.List<Bond> vHBonds,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens) |
void |
calcSelectedMonomersCount(BS bsSelected) |
protected float |
calculateRamachandranHelixAngle(int m,
char qtype) |
javajs.util.List<Atom[]> |
calculateStruts(ModelSet modelSet,
BS bs1,
BS bs2,
javajs.util.List<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(String id,
Quaternion dq,
Quaternion dqnext) |
void |
getConformation(BS bsConformation,
int conformationIndex) |
protected javajs.util.P3 |
getControlPoint(int i,
javajs.util.V3 v) |
javajs.util.P3[] |
getControlPoints(boolean isTraceAlpha,
float sheetSmoothing,
boolean invalidate) |
private javajs.util.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,
javajs.util.OC pdbATOM,
javajs.util.SB pdbCONECT,
BS bsWritten) |
Group[] |
getGroups() |
protected int |
getIndex(int chainID,
int seqcode,
int istart,
int iend) |
private javajs.util.P3 |
getInitiatorPoint() |
int[] |
getLeadAtomIndices() |
(package private) void |
getLeadMidPoint(int groupIndex,
javajs.util.P3 midPoint) |
javajs.util.P3[] |
getLeadMidpoints() |
(package private) javajs.util.P3 |
getLeadPoint(int monomerIndex) |
(package private) javajs.util.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,
javajs.util.OC pdbATOM,
javajs.util.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,
javajs.util.OC pdbATOM,
javajs.util.SB pdbCONECT,
BS bsWritten) |
Map<String,Object> |
getPolymerInfo(BS bs) |
int |
getPolymerPointsAndVectors(int last,
BS bs,
javajs.util.List<javajs.util.P3[]> vList,
boolean isTraceAlpha,
float sheetSmoothing) |
void |
getPolymerSequenceAtoms(int group1,
int nGroups,
BS bsInclude,
BS bsResult) |
ProteinStructure |
getProteinStructure(int monomerIndex) |
private static float |
getQuaternionStraightness(String id,
Quaternion dq,
Quaternion dqnext) |
void |
getRange(BS bs) |
void |
getRangeGroups(int nResidues,
BS bsAtoms,
BS bsResult) |
(package private) int |
getSelectedMonomerCount() |
String |
getSequence() |
private static float |
getStraightness(float cosHalfTheta) |
private javajs.util.P3 |
getTerminatorPoint() |
int |
getType() |
(package private) javajs.util.P3 |
getWingPoint(int polymerIndex) |
javajs.util.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(Map<EnumStructure,float[]> structureList) |
public Monomer[] monomers
public Model model
protected javajs.util.P3[] leadMidpoints
protected javajs.util.P3[] leadPoints
protected javajs.util.P3[] controlPoints
protected javajs.util.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 javajs.util.V3 unitVectorX
private int selectedMonomerCount
BS bsSelectedMonomers
public boolean haveParameters
private static final 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 javajs.util.P3 getLeadPoint(int monomerIndex)
private final javajs.util.P3 getInitiatorPoint()
private final javajs.util.P3 getTerminatorPoint()
void getLeadMidPoint(int groupIndex, javajs.util.P3 midPoint)
final javajs.util.P3 getWingPoint(int polymerIndex)
public void getConformation(BS bsConformation, int conformationIndex)
public void setConformation(BS bsSelected)
public void recalculateLeadMidpointsAndWingVectors()
protected void resetHydrogenPoints()
public javajs.util.P3[] getLeadMidpoints()
javajs.util.P3[] getLeadPoints()
public javajs.util.P3[] getControlPoints(boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
private javajs.util.P3[] getControlPoints2(float sheetSmoothing)
protected javajs.util.P3 getControlPoint(int i, javajs.util.V3 v)
i
- v
- public final javajs.util.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, javajs.util.List<javajs.util.P3[]> vList, boolean isTraceAlpha, float sheetSmoothing)
public String getSequence()
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, javajs.util.OC pdbATOM, javajs.util.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, javajs.util.OC pdbATOM, javajs.util.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(String id, Quaternion dq, Quaternion dqnext)
id
- for debugging onlydq
- dqnext
- private static float getQuaternionStraightness(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 calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, javajs.util.List<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
polymer
- bsA
- bsB
- vHBonds
- nMaxPerResidue
- min
- checkDistances
- dsspIgnoreHydrogens
- public void setStructureList(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, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, BS bsWritten)
viewer
- ctype
- qtype
- mStep
- derivType
- bsAtoms
- bsSelected
- bothEnds
- isDraw
- addHeader
- tokens
- pdbATOM
- pdbCONECT
- bsWritten
- public int getType()