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Classes | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Static Protected Member Functions | Protected Attributes | Static Protected Attributes | Package Functions | Static Package Functions | Package Attributes | Private Member Functions | Static Private Member Functions | Private Attributes | Static Private Attributes

org::jmol::modelsetbio::AminoPolymer Class Reference

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List of all members.

Classes

class  Bridge

Public Member Functions

void addSecondaryStructure (byte type, String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
boolean calcParameters ()
void calcRasmolHydrogenBonds (Polymer polymer, BitSet bsA, BitSet bsB, List vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
void calcSelectedMonomersCount (BitSet bsSelected)
void calculateStructures (boolean alphaOnly)
String calculateStructures (Polymer[] bioPolymers, int bioPolymerCount, List vHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)
List calculateStruts (ModelSet modelSet, Atom[] atoms, BitSet bs1, BitSet bs2, List vCA, float thresh, int delta, boolean allowMultiple)
void clearStructures ()
void findNearestAtomIndex (int xMouse, int yMouse, Atom[] closest, short[] mads, int myVisibilityFlag, BitSet bsNot)
void getConformation (BitSet bsConformation, int conformationIndex)
Point3f[] getControlPoints (boolean isTraceAlpha, float sheetSmoothing, boolean invalidate)
Group[] getGroups ()
int[] getLeadAtomIndices ()
Point3f[] getLeadMidpoints ()
void getPdbData (Viewer viewer, char ctype, char qtype, int mStep, int derivType, boolean isDraw, BitSet bsAtoms, OutputStringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, boolean bothEnds, BitSet bsWritten)
Map getPolymerInfo (BitSet bs)
int getPolymerPointsAndVectors (int last, BitSet bs, List vList, boolean isTraceAlpha, float sheetSmoothing)
void getPolymerSequenceAtoms (int group1, int nGroups, BitSet bsInclude, BitSet bsResult)
ProteinStructure getProteinStructure (int monomerIndex)
void getRange (BitSet bs)
void getRangeGroups (int nResidues, BitSet bsAtoms, BitSet bsResult)
String getSequence ()
int getType ()
final Vector3f[] getWingVectors ()
boolean isDna ()
boolean isRna ()
void recalculateLeadMidpointsAndWingVectors ()
void setConformation (BitSet bsSelected)
void setStructureList (float[][] structureList)

Static Public Member Functions

final static void getPdbData (Viewer viewer, BioPolymer p, char ctype, char qtype, int mStep, int derivType, boolean isDraw, BitSet bsAtoms, OutputStringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, boolean bothEnds, BitSet bsWritten)

Public Attributes

int bioPolymerIndexInModel
boolean haveParameters
Model model
int monomerCount

Protected Member Functions

void addSecondaryStructure (byte type, String structureID, int serialID, int strandCount, int indexStart, int indexEnd)
boolean calcEtaThetaAngles ()
boolean calcPhiPsiAngles ()
float calculateRamachandranHelixAngle (int m, char qtype)
Point3f getControlPoint (int i, Vector3f v)
Point3f[] getControlPoints (float sheetSmoothing)
void resetHydrogenPoints ()

Static Protected Member Functions

static String calculateStructuresDssp (Polymer[] bioPolymers, int bioPolymerCount, List vHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)

Protected Attributes

Point3f[] controlPoints
boolean hasWingPoints
boolean invalidControl = false
int[] leadAtomIndices
Point3f[] leadMidpoints
Point3f[] leadPoints
float sheetSmoothing
int type = TYPE_NOBONDING
Vector3f[] wingVectors

Static Protected Attributes

static final int TYPE_AMINO = 1
static final int TYPE_CARBOHYDRATE = 3
static final int TYPE_NOBONDING = 0
static final int TYPE_NUCLEIC = 2

Package Functions

 AminoPolymer (Monomer[] monomers)
int getIndex (char chainID, int seqcode)
final Point3f getInitiatorPoint ()
void getLeadMidPoint (int groupIndex, Point3f midPoint)
final Point3f getLeadPoint (int monomerIndex)
void getLeadPoint (int groupIndex, Point3f midPoint)
Point3f[] getLeadPoints ()
int getSelectedMonomerCount ()
final Point3f getTerminatorPoint ()
final Point3f getWingPoint (int polymerIndex)
boolean isMonomerSelected (int i)
void removeProteinStructure (int monomerIndex, int count)

Static Package Functions

static BioPolymer allocateBioPolymer (Group[] groups, int firstGroupIndex, boolean checkConnections)

Package Attributes

BitSet bsSelectedMonomers
Monomer[] monomers

Private Member Functions

void addResidueHydrogenBond (Atom nitrogen, Atom oxygen, int indexAminoGroup, int indexCarbonylGroup, float energy, List vHBonds)
int calcHbondEnergy (Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target, boolean checkDistances)
void calcPhiPsiAngles (AminoMonomer residue1, AminoMonomer residue2)
void checkRasmolHydrogenBond (AminoMonomer source, Polymer polymer, int indexDonor, Point3f hydrogenPoint, BitSet bsB, List vHBonds, int[][] min, boolean checkDistances)
String dumpSummary (char[] labels)
String dumpTags (String lines, BitSet bsBad, int mode)
String findHelixes (int[][][] min, int iPolymer, BitSet bsDone, char[] labels, boolean doReport, boolean setStructure, List vHBonds, BitSet bsBad)
String findHelixes (int pitch, int[][][] min, int thisIndex, byte subtype, int type, BitSet bsDone, BitSet bsTurn, char[] labels, boolean doReport, boolean setStructure, List vHBonds, BitSet bsBad)
boolean isHelix (float psi, float phi)
boolean isSheet (float psi, float phi)
boolean isTurn (float psi, float phi)
void setStructure (BitSet bs, byte type)
void setTag (char[] tags, BitSet bs, char ch)

Static Private Member Functions

static void addHbond (List vHBonds, Monomer donor, Monomer acceptor, int iEnergy, int type, Map htTemp)
static boolean checkBridge (Bridge bridge, Map htBridges, Map htLadders, boolean isAntiparallel, int n1, int n2)
static void checkBulge (Bridge bridge, Map htBridges, Map htLadders, boolean isAntiparallel, int dir)
static boolean checkPhiPsi (float[] list, float psi, float phi)
static void createLadders (List bridges, Map htBridges, Map htLadders, boolean isAntiparallel)
static Bridge getBridge (int[][][][] min, int p1, int a, int p2, int b, List bridges, Atom atom1, Atom atom2, AminoPolymer ap1, AminoPolymer ap2, List vHBonds, Map htTemp, boolean isAntiparallel, Map htLadders)
static void getBridges (Polymer[] bioPolymers, int[][][][] min, List bridgesA, List bridgesP, Map htBridges, Map htLadders, BitSet bsBad, List vHBonds, BitSet[] bsDone)
static int[][][][] getDualHydrogenBondArray (Polymer[] bioPolymers, int bioPolymerCount, boolean dsspIgnoreHydrogens)
static void getSheetStructures (Polymer[] bioPolymers, List bridgesA, List bridgesP, Map htBridges, Map htLadders, char[][] labels, BitSet[] bsDone, boolean doReport, boolean setStructure)
static int[] isHbonded (int indexDonor, int indexAcceptor, int pDonor, int pAcceptor, int[][][][] min)

Private Attributes

float[][] structureList

Static Private Attributes

static final float maxHbondAlphaDistance = 9
static final float maxHbondAlphaDistance2
static final float minimumHbondDistance2 = 0.5f * 0.5f
static int[][] sheetOffsets

Detailed Description

Definition at line 52 of file AminoPolymer.java.


The documentation for this class was generated from the following file:

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