org.jmol.modelset
public abstract class AtomCollection extends Object
| Field Summary | |
|---|---|
| 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 | |
|---|---|
| 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