Public Member Functions |
| void | add (IAtomContainer atomContainer) |
| void | addAtom (IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand) |
| void | addAtom (IAtom oAtom, IMonomer oMonomer) |
| void | addAtom (IAtom oAtom) |
| void | addAtom (IPDBAtom oAtom) |
| void | addAtom (IAtom oAtom, IStrand oStrand) |
| void | addAtom (IAtom oAtom, IMonomer oMonomer, IStrand oStrand) |
| void | addAtomParity (IAtomParity parity) |
| void | addBond (IBond bond) |
| void | addBond (int atom1, int atom2, IBond.Order order, int stereo) |
| void | addBond (int atom1, int atom2, IBond.Order order) |
| void | addElectronContainer (IElectronContainer electronContainer) |
| void | addListener (IChemObjectListener col) |
| void | addLonePair (int atomID) |
| void | addLonePair (ILonePair lonePair) |
| void | addSingleElectron (ISingleElectron singleElectron) |
| void | addSingleElectron (int atomID) |
| void | addStructure (IPDBStructure structure) |
| Iterable< IAtom > | atoms () |
| Iterable< IBond > | bonds () |
| Object | clone () throws CloneNotSupportedException |
| boolean | contains (IAtom atom) |
| boolean | contains (IBond bond) |
| boolean | contains (ILonePair lonePair) |
| boolean | contains (ISingleElectron singleElectron) |
| boolean | contains (IElectronContainer electronContainer) |
| Iterable< IElectronContainer > | electronContainers () |
| IAtom | getAtom (int number) |
| int | getAtomCount () |
| int | getAtomNumber (IAtom atom) |
| IAtomParity | getAtomParity (IAtom atom) |
| IBond | getBond (int number) |
| IBond | getBond (IAtom atom1, IAtom atom2) |
| int | getBondCount () |
| int | getBondNumber (IAtom atom1, IAtom atom2) |
| int | getBondNumber (IBond bond) |
| double | getBondOrderSum (IAtom atom) |
| IChemObjectBuilder | getBuilder () |
| int | getConnectedAtomsCount (IAtom atom) |
| List< IAtom > | getConnectedAtomsList (IAtom atom) |
| int | getConnectedBondsCount (IAtom atom) |
| int | getConnectedBondsCount (int atomnumber) |
| List< IBond > | getConnectedBondsList (IAtom atom) |
| List< IElectronContainer > | getConnectedElectronContainersList (IAtom atom) |
| int | getConnectedLonePairsCount (IAtom atom) |
| List< ILonePair > | getConnectedLonePairsList (IAtom atom) |
| int | getConnectedSingleElectronsCount (IAtom atom) |
| List< ISingleElectron > | getConnectedSingleElectronsList (IAtom atom) |
| IElectronContainer | getElectronContainer (int number) |
| int | getElectronContainerCount () |
| IAtom | getFirstAtom () |
| boolean | getFlag (int flag_type) |
| boolean[] | getFlags () |
| String | getID () |
| IAtom | getLastAtom () |
| int | getListenerCount () |
| ILonePair | getLonePair (int number) |
| int | getLonePairCount () |
| int | getLonePairNumber (ILonePair lonePair) |
| Order | getMaximumBondOrder (IAtom atom) |
| Order | getMinimumBondOrder (IAtom atom) |
| IMonomer | getMonomer (String monName, String strandName) |
| IMonomer | getMonomer (String cName) |
| int | getMonomerCount () |
| Collection< String > | getMonomerNames () |
| boolean | getNotification () |
| Map< Object, Object > | getProperties () |
| Object | getProperty (Object description) |
| ISingleElectron | getSingleElectron (int number) |
| int | getSingleElectronCount () |
| int | getSingleElectronNumber (ISingleElectron singleElectron) |
| IStrand | getStrand (String cName) |
| int | getStrandCount () |
| Collection< String > | getStrandNames () |
| Map< String, IStrand > | getStrands () |
| Collection< IPDBStructure > | getStructures () |
| Iterable< ILonePair > | lonePairs () |
| void | notifyChanged () |
| void | notifyChanged (IChemObjectChangeEvent evt) |
| void | remove (IAtomContainer atomContainer) |
| void | removeAllBonds () |
| void | removeAllElectronContainers () |
| void | removeAllElements () |
| void | removeAtom (int position) |
| void | removeAtom (IAtom atom) |
| void | removeAtomAndConnectedElectronContainers (IAtom atom) |
| IBond | removeBond (int position) |
| IBond | removeBond (IAtom atom1, IAtom atom2) |
| void | removeBond (IBond bond) |
| void | removeElectronContainer (IElectronContainer electronContainer) |
| IElectronContainer | removeElectronContainer (int position) |
| void | removeListener (IChemObjectListener col) |
| ILonePair | removeLonePair (int position) |
| void | removeLonePair (ILonePair lonePair) |
| void | removeMonomer (String name) |
| void | removeProperty (Object description) |
| void | removeSingleElectron (ISingleElectron singleElectron) |
| ISingleElectron | removeSingleElectron (int position) |
| void | removeStrand (String name) |
| void | setAtom (int number, IAtom atom) |
| void | setAtoms (IAtom[] atoms) |
| void | setBonds (IBond[] bonds) |
| void | setFlag (int flag_type, boolean flag_value) |
| void | setFlags (boolean[] flagsNew) |
| void | setID (String identifier) |
| void | setNotification (boolean bool) |
| void | setProperties (Map< Object, Object > properties) |
| void | setProperty (Object description, Object property) |
| Iterable< ISingleElectron > | singleElectrons () |
| void | stateChanged (IChemObjectChangeEvent event) |
| String | toString () |
