public abstract class BioPolymer extends Polymer
Modifier and Type | Field and Description |
---|---|
(package private) java.util.BitSet |
bsSelectedMonomers |
protected boolean |
hasWingPoints |
boolean |
haveParameters |
protected boolean |
invalidControl |
private boolean |
invalidLead |
(package private) Monomer[] |
monomers |
private static java.lang.String[] |
qColor |
private int |
selectedMonomerCount |
protected float |
sheetSmoothing |
private javax.vecmath.Vector3f |
unitVectorX |
bioPolymerIndexInModel, controlPoints, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NOBONDING, TYPE_NUCLEIC, wingVectors
Constructor and Description |
---|
BioPolymer(Monomer[] monomers) |
Modifier and Type | Method and Description |
---|---|
(package private) static BioPolymer |
allocateBioPolymer(Group[] groups,
int firstGroupIndex,
boolean checkConnections) |
protected boolean |
calcEtaThetaAngles() |
private void |
calcLeadMidpointsAndWingVectors() |
boolean |
calcParameters() |
protected boolean |
calcPhiPsiAngles() |
void |
calcSelectedMonomersCount(java.util.BitSet bsSelected) |
protected float |
calculateRamachandranHelixAngle(int m,
char qtype) |
java.lang.String |
calculateStructures(Polymer[] bioPolymers,
int bioPolymerCount,
java.util.List vHBonds,
boolean doReport,
boolean dsspIgnoreHydrogens,
boolean setStructure) |
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,
java.util.BitSet bsWritten,
boolean isDraw,
boolean isRamachandran,
boolean calcRamachandranStraightness,
boolean useQuaternionStraightness,
boolean writeRamachandranStraightness,
boolean quaternionStraightness,
float factor,
boolean isAmino,
boolean isRelativeAlias,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT) |
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,
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) |
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() |
(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) |
addSecondaryStructure, calcRasmolHydrogenBonds, calculateStructures, calculateStruts, getPdbData, getType, setStructureList
Monomer[] monomers
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)
static BioPolymer allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections)
public void clearStructures()
clearStructures
in class Polymer
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)
getConformation
in class Polymer
public void setConformation(java.util.BitSet bsSelected)
setConformation
in class Polymer
public void recalculateLeadMidpointsAndWingVectors()
recalculateLeadMidpointsAndWingVectors
in class Polymer
protected void resetHydrogenPoints()
public javax.vecmath.Point3f[] getLeadMidpoints()
getLeadMidpoints
in class Polymer
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)
calcSelectedMonomersCount
in class Polymer
boolean isMonomerSelected(int i)
public int getPolymerPointsAndVectors(int last, java.util.BitSet bs, java.util.List vList, boolean isTraceAlpha, float sheetSmoothing)
getPolymerPointsAndVectors
in class Polymer
public java.lang.String getSequence()
getSequence
in class Polymer
public java.util.Map getPolymerInfo(java.util.BitSet bs)
getPolymerInfo
in class Polymer
public void getPolymerSequenceAtoms(int group1, int nGroups, java.util.BitSet bsInclude, java.util.BitSet bsResult)
getPolymerSequenceAtoms
in class Polymer
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, boolean isDraw, java.util.BitSet bsAtoms, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, boolean bothEnds, 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, java.util.BitSet bsWritten, boolean isDraw, boolean isRamachandran, boolean calcRamachandranStraightness, boolean useQuaternionStraightness, boolean writeRamachandranStraightness, boolean quaternionStraightness, float factor, boolean isAmino, boolean isRelativeAlias, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT)
viewer
- m0
- mStep
- p
- ctype
- qtype
- derivType
- bsAtoms
- bsSelected
- bsWritten
- isDraw
- isRamachandran
- calcRamachandranStraightness
- useQuaternionStraightness
- writeRamachandranStraightness
- quaternionStraightness
- NOT USEDfactor
- isAmino
- isRelativeAlias
- pdbATOM
- pdbCONECT
- 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 void getRangeGroups(int nResidues, java.util.BitSet bsAtoms, java.util.BitSet bsResult)
getRangeGroups
in class Polymer
public java.lang.String calculateStructures(Polymer[] bioPolymers, int bioPolymerCount, java.util.List vHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)
calculateStructures
in class Polymer
vHBonds
- TODO