org.jmol.modelset
public abstract class AtomCollection extends Object
Field Summary | |
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int | atomCount |
String[] | atomNames |
Atom[] | atoms |
int[] | atomSerials |
int | bfactor100Hi |
int | bfactor100Lo |
short[] | bfactor100s |
BitSet | bsEmpty |
BitSet | bsFoundRectangle |
BitSet | bsHidden |
protected Bspf | bspf |
BitSet | bsSurface |
Object[] | clientAtomReferences |
Object[][] | ellipsoids |
Graphics3D | g3d |
boolean | hasBfactorRange |
protected float | maxBondingRadius |
float | maxVanderwaalsRadius |
static int | minimumPixelSelectionRadius |
int | nSurfaceAtoms |
byte[] | occupancies |
float[] | partialCharges |
protected static boolean | showRebondTimes |
byte[] | specialAtomIDs |
protected int[] | surfaceDistance100s |
int | surfaceDistanceMax |
protected BitSet[] | tainted |
static byte | TAINT_COORD |
static byte | TAINT_FORMALCHARGE |
static byte | TAINT_MAX |
static byte | TAINT_OCCUPANCY |
static byte | TAINT_PARTIALCHARGE |
static byte | TAINT_TEMPERATURE |
static byte | TAINT_VALENCE |
static byte | TAINT_VANDERWAALS |
static byte | TAINT_VIBRATION |
static String[] | userSettableValues |
Vector3f[] | vibrationVectors |
Viewer | viewer |
Method Summary | |
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void | calcBfactorRange(BitSet bs) |
void | calcSurfaceDistances() |
Point3f[] | calculateSurface(BitSet bsSelected, float envelopeRadius) |
void | clearBfactorRange() |
void | deleteAtoms(int firstAtomIndex, int nAtoms, BitSet bs) |
protected void | fillAtomData(AtomData atomData, int mode) |
BitSet | findAtomsInRectangle(Rectangle rect, BitSet bsModels) |
protected void | findMaxRadii() |
protected void | findNearestAtomIndex(int x, int y, Atom[] closest) |
protected Point3f[][] | getAdditionalHydrogens(BitSet atomSet, int[] nTotal) |
Atom | getAtomAt(int atomIndex) |
protected BitSet | getAtomBits(int tokType, Object specInfo)
general unqualified lookup of atom set type |
String | getAtomChain(int i) |
short | getAtomColix(int i) |
int | getAtomCount() |
protected int | getAtomCountInModel(int modelIndex) |
String | getAtomicPropertyState(int taintWhat, BitSet bsSelected) |
static void | getAtomicPropertyState(StringBuffer commands, Atom[] atoms, int atomCount, byte type, BitSet bs, String label, float[] fData) |
int | getAtomIndexFromAtomNumber(int atomNumber) |
int[] | getAtomIndices(BitSet bs) |
String | getAtomInfo(int i, String format) |
String | getAtomInfoXYZ(int i, boolean useChimeFormat) |
int | getAtomModelIndex(int i) |
String | getAtomName(int i) |
String[] | getAtomNames() |
int | getAtomNumber(int i) |
Point3f | getAtomPoint3f(int i) |
float | getAtomRadius(int i) |
Atom[] | getAtoms() |
BitSet | getAtomsWithin(float distance, Point4f plane) |
String | getAtomSequenceCode(int i) |
float | getAtomVdwRadius(int i) |
float | getAtomX(int i) |
float | getAtomY(int i) |
float | getAtomZ(int i) |
int | getBfactor100Hi() |
int | getBfactor100Lo() |
short[] | getBFactors() |
protected BitSet | getChainBits(char chain) |
protected String | getChimeInfo(int tok, BitSet bs) |
BitSet | getClickableSet() |
String | getElementName(int i) |
int | getElementNumber(int i) |
String | getElementSymbol(int i) |
Object[] | getEllipsoid(int i) |
String | getHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoTypeRaw, boolean hybridizationCompatible) |
BitSet | getIdentifierOrNull(String identifier)
overhauled by RMH Nov 1, 2006.
|
float | getMaxVanderwaalsRadius() |
BitSet | getModelBitSet(BitSet atomList) |
float[] | getPartialCharges() |
Quaternion | getQuaternion(int i, char qtype) |
protected float | getRadiusVdwJmol(Atom atom) |
protected BitSet | getSeqcodeBits(int seqcode, boolean returnEmpty) |
BitSet | getSpecName(String name) |
BitSet | getSpecNameOrNull(String name, boolean checkStar) |
int | getSurfaceDistance100(int atomIndex) |
int | getSurfaceDistanceMax() |
BitSet | getTaintedAtoms(byte type) |
static int | getUserSettableType(String dataType) |
float | getVibrationCoord(int atomIndex, char c) |
Vector3f | getVibrationVector(int atomIndex) |
BitSet | getVisibleSet() |
boolean | isAtomHidden(int iAtom) |
boolean | isAtomNameMatch(Atom atom, String strPattern, boolean checkStar) |
boolean | isCursorOnTopOf(Atom contender, int x, int y, int radius, Atom champion)
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability |
protected boolean | isInLatticeCell(int i, Point3f cell) |
void | loadCoordinates(String data, boolean isVibrationVectors) |
void | loadData(int type, String name, String dataString) |
protected void | merge(AtomCollection mergeModelSet) |
boolean | modelSetHasVibrationVectors() |
protected void | releaseModelSet() |
void | setAtomCoord(BitSet bs, int tokType, Object xyzValues) |
void | setAtomCoord(int atomIndex, float x, float y, float z) |
void | setAtomCoordRelative(int atomIndex, float x, float y, float z) |
protected void | setAtomCoordRelative(BitSet atomSet, float x, float y, float z) |
void | setAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values) |
void | setAtomVibrationVector(int atomIndex, float x, float y, float z) |
protected void | setBFactor(int atomIndex, float bfactor) |
void | setBsHidden(BitSet bs) |
protected void | setEllipsoid(int atomIndex, Object[] ellipsoid) |
void | setFormalCharges(BitSet bs, int formalCharge) |
protected void | setOccupancy(int atomIndex, int occupancy) |
protected void | setPartialCharge(int atomIndex, float partialCharge) |
void | setTaintedAtoms(BitSet bs, byte type) |
protected void | setVibrationVector(int atomIndex, float x, float y, float z) |
void | setVibrationVector(int atomIndex, int tok, float fValue) |
protected void | taint(int atomIndex, byte type) |
void | untaint(int i, byte type) |
Parameters: tokType specInfo
Returns: BitSet; or null if we mess up the type
Parameters: identifier
Returns: null or bs
Parameters: contender x y radius champion
Returns: true if user is pointing to this atom