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

org::jmol::modelset::BondCollection Class Reference

Inheritance diagram for org::jmol::modelset::BondCollection:
Inheritance graph
Collaboration diagram for org::jmol::modelset::BondCollection:
Collaboration graph

List of all members.

Public Member Functions

void assignAromaticBonds ()
Bond bondAtoms (Atom atom1, Atom atom2, int order, short mad, BitSet bsBonds, float energy, boolean isNew)
Point3f[][] calculateHydrogens (BitSet bs, int[] nTotal, boolean doAll, boolean justCarbon, List vConnect)
Point3f[] calculateSurface (BitSet bsSelected, float envelopeRadius)
float calculateVolume (BitSet bs, int iType)
void clearBfactorRange ()
void deleteBonds (BitSet bsBond, boolean isFullModel)
BitSet findAtomsInRectangle (Rectangle rect, BitSet bsModels)
String getAtomChain (int i)
short getAtomColix (int i)
int getAtomCount ()
float[] getAtomicCharges ()
void getAtomicPropertyState (StringBuffer commands, byte type, BitSet bs, String label, float[] fData)
String getAtomicPropertyState (int taintWhat, BitSet bsSelected)
int getAtomIndexFromAtomNumber (int atomNumber, BitSet bsVisibleFrames)
int[] getAtomIndices (BitSet bs)
String getAtomInfo (int i, String format)
String getAtomInfoXYZ (int i, boolean useChimeFormat)
int getAtomModelIndex (int i)
String getAtomName (int i)
int getAtomNumber (int i)
Point3f getAtomPoint3f (int i)
List getAtomPointVector (BitSet bs)
float getAtomRadius (int i)
String getAtomSequenceCode (int i)
BitSet getAtomsWithin (float distance, Point4f plane)
String[] getAtomTypes ()
float getAtomVdwRadius (int i, int iType)
int getBfactor100Hi ()
int getBfactor100Lo ()
short[] getBFactors ()
Bond getBondAt (int bondIndex)
Atom getBondAtom1 (int i)
Atom getBondAtom2 (int i)
short getBondColix1 (int i)
short getBondColix2 (int i)
int getBondCount ()
BondIterator getBondIterator (BitSet bsSelected)
BondIterator getBondIterator (int bondType, BitSet bsSelected)
int getBondModelIndex (int i)
int getBondOrder (int i)
float getBondRadius (int i)
Bond[] getBonds ()
BitSet getBondsForSelectedAtoms (BitSet bsAtoms, boolean bondSelectionModeOr)
BitSet getClickableSet ()
int getElementNumber (int i)
String getElementSymbol (int i)
Object[] getEllipsoid (int i)
Object getHelixData (BitSet bs, int tokType)
String getHybridizationAndAxes (int atomIndex, Vector3f z, Vector3f x, String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ)
float[] getIonicRadii ()
float getMaxVanderwaalsRadius ()
float[] getPartialCharges ()
Quaternion getQuaternion (int i, char qtype)
int getSurfaceDistanceMax ()
BitSet getTaintedAtoms (byte type)
float getVibrationCoord (int atomIndex, char c)
Vector3f getVibrationVector (int atomIndex, boolean forceNew)
BitSet getVisibleSet ()
boolean isAtomHidden (int iAtom)
boolean modelSetHasVibrationVectors ()
void resetAromatic ()
void setAtomCoord (int atomIndex, float x, float y, float z)
void setAtomCoord (BitSet bs, int tokType, Object xyzValues)
void setAtomCoordRelative (int atomIndex, float x, float y, float z)
void setAtomData (int type, String name, String dataString, boolean isDefault)
void setAtomProperty (BitSet bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
BitSet setBondOrder (int bondIndex, char type)
void setBsHidden (BitSet bs)
void setFormalCharges (BitSet bs, int formalCharge)
void setHaveStraightness (boolean TF)
void setPreserveState (boolean TF)
void setTaintedAtoms (BitSet bs, byte type)
void taint (BitSet bsAtoms, byte type)
void unTaintAtoms (BitSet bs, byte type)

Static Public Member Functions

static int getUserSettableType (String dataType)

Public Attributes

Atom[] atoms
Vector3f[] vibrationVectors
Viewer viewer

Static Public Attributes

final static byte TAINT_ATOMNAME = 0
final static byte TAINT_ATOMNO = 12
final static byte TAINT_ATOMTYPE = 1
final static byte TAINT_COORD = 2
final static byte TAINT_ELEMENT = 3
static final byte TAINT_FORMALCHARGE = 4
final static byte TAINT_MAX = 13

Protected Member Functions

int addHBond (Atom atom1, Atom atom2, int order, float energy)
void assignAromaticBonds (boolean isUserCalculation, BitSet bsBonds)
Bond bondMutually (Atom atom, Atom atomOther, int order, short mad, float energy)
boolean checkValencesAndBond (Atom atomA, Atom atomB, int order, short mad, BitSet bsBonds)
void deleteAllBonds ()
int[] deleteConnections (float minDistance, float maxDistance, int order, BitSet bsA, BitSet bsB, boolean isBonds, boolean matchNull, float minDistanceSquared, float maxDistanceSquared)
void deleteModelAtoms (int firstAtomIndex, int nAtoms, BitSet bs)
void fillAtomData (AtomData atomData, int mode)
void findMaxRadii ()
void findNearestAtomIndex (int x, int y, Atom[] closest, BitSet bsNot)
BitSet getAtomBits (int tokType, Object specInfo)
int getBondCountInModel (int modelIndex)
short getBondOrder (float bondingRadiusA, float bondingRadiusB, float distance2, float minBondDistance2, float bondTolerance)
BitSet getChainBits (char chain)
String getChimeInfo (int tok, BitSet bs)
short getDefaultMadFromOrder (int order)
boolean getHaveStraightness ()
float getRadiusVdwJmol (Atom atom)
BitSet getSeqcodeBits (int seqcode, boolean returnEmpty)
void mergeAtomArrays (AtomCollection mergeModelSet)
void releaseModelSet ()
void removeUnnecessaryBonds (Atom atom, boolean deleteAtom)
void setAtomCoordRelative (BitSet bs, float x, float y, float z)
void setAtomName (int atomIndex, String name)
boolean setAtomNumber (int atomIndex, int atomno)
void setAtomType (int atomIndex, String type)
boolean setBFactor (int atomIndex, float bfactor)
Bond setBond (int index, Bond bond)
void setElement (Atom atom, int atomicNumber)
void setEllipsoid (int atomIndex, Object[] ellipsoid)
boolean setIonicRadius (int atomIndex, float radius)
boolean setOccupancy (int atomIndex, int occupancy)
boolean setPartialCharge (int atomIndex, float partialCharge)
void setVibrationVector (int atomIndex, float x, float y, float z)
void taint (int atomIndex, byte type)

Protected Attributes

int bondCount
Bond[] bonds
BitSet bsAromatic = new BitSet()
BitSet bsHBondsRasmol
Bspf bspf
short defaultCovalentMad
Object[][] ellipsoids
Bond[][][] freeBonds = new Bond[MAX_BONDS_LENGTH_TO_CACHE][][]
Graphics3D g3d
boolean haveStraightness
float maxBondingRadius = Float.MIN_VALUE
int moleculeCount
JmolMolecule[] molecules = new JmolMolecule[4]
int[] numCached = new int[MAX_BONDS_LENGTH_TO_CACHE]
boolean preserveState = true
int[] surfaceDistance100s
BitSet[] tainted

Static Protected Attributes

static final int BOND_GROWTH_INCREMENT = 250
static final int MAX_BONDS_LENGTH_TO_CACHE = 5
static final int MAX_NUM_TO_CACHE = 200

Package Functions

 [instance initializer]
String getElementName (int i)
void getRasmolHydrogenBonds (Model m, BitSet bsA, BitSet bsB, List vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens)
int getSurfaceDistance100 (int atomIndex)
boolean isCursorOnTopOf (Atom contender, int x, int y, int radius, Atom champion)

Static Package Functions

 [static initializer]

Package Attributes

int atomCount
String[] atomNames
int[] atomSerials
String[] atomTypes
short[] bfactor100s
float[] ionicRadii
byte[] occupancies
float[] partialCharges

Private Member Functions

void addBondToAtom (Atom atom, Bond bond)
Bond[] addToBonds (Bond newBond, Bond[] oldBonds)
boolean assignAromaticDouble (Bond bond)
boolean assignAromaticDouble (Atom atom)
void assignAromaticNandO (BitSet bsSelected)
boolean assignAromaticSingle (Bond bond)
boolean assignAromaticSingle (Atom atom, int notBondIndex)
boolean assignAromaticSingleHetero (Atom atom)
Bond getOrAddBond (Atom atom, Atom atomOther, int order, short mad, BitSet bsBonds, float energy, boolean overrideBonding)

Private Attributes

BitSet bsAromaticDouble
BitSet bsAromaticSingle
boolean haveWarned = false

Detailed Description

Definition at line 41 of file BondCollection.java.

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

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