test_class.file: base/silent/src/test/java/org/openscience/cdk/silent/AtomContainerTest.java
test_class.identifier: AtomContainerTest
test_class.superclass: extends AbstractAtomContainerTest
test_case.body: @Test
      public void testAtomContainer() {
          // create an empty container with in the constructor defined array lengths
          IAtomContainer container = new AtomContainer();
  
          Assert.assertEquals(0, container.getAtomCount());
          Assert.assertEquals(0, container.getBondCount());
  
          // test whether the ElectronContainer is correctly initialized
          container.addBond(container.getBuilder().newInstance(IBond.class,
                  container.getBuilder().newInstance(IAtom.class, "C"),
                  container.getBuilder().newInstance(IAtom.class, "C"), IBond.Order.DOUBLE));
          container.addLonePair(container.getBuilder().newInstance(ILonePair.class,
                  container.getBuilder().newInstance(IAtom.class, "N")));
      }
test_case.class_method_signature: AtomContainerTest.testAtomContainer()
test_case.full_signature: @Test public void testAtomContainer()
test_case.identifier: testAtomContainer
test_case.invocations: assertEquals getAtomCount assertEquals getBondCount addBond newInstance getBuilder newInstance getBuilder newInstance getBuilder addLonePair newInstance getBuilder newInstance getBuilder
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAtomContainer()
focal_class.declarator: DEFAULT_CAPACITY = 20
focal_class.modifier: private static final
focal_class.original_string: private static final int DEFAULT_CAPACITY = 20;
focal_class.type: int
focal_class.var_name: DEFAULT_CAPACITY
focal_class.declarator: serialVersionUID = 5678100348445919254L
focal_class.modifier: private static final
focal_class.original_string: private static final long serialVersionUID = 5678100348445919254L;
focal_class.type: long
focal_class.var_name: serialVersionUID
focal_class.declarator: atomCount
focal_class.modifier: protected
focal_class.original_string: protected int atomCount;
focal_class.type: int
focal_class.var_name: atomCount
focal_class.declarator: bondCount
focal_class.modifier: protected
focal_class.original_string: protected int bondCount;
focal_class.type: int
focal_class.var_name: bondCount
focal_class.declarator: lonePairCount
focal_class.modifier: protected
focal_class.original_string: protected int lonePairCount;
focal_class.type: int
focal_class.var_name: lonePairCount
focal_class.declarator: singleElectronCount
focal_class.modifier: protected
focal_class.original_string: protected int singleElectronCount;
focal_class.type: int
focal_class.var_name: singleElectronCount
focal_class.declarator: growArraySize = 10
focal_class.modifier: protected
focal_class.original_string: protected int growArraySize = 10;
focal_class.type: int
focal_class.var_name: growArraySize
focal_class.declarator: atoms
focal_class.modifier: protected
focal_class.original_string: protected IAtom[] atoms;
focal_class.type: IAtom[]
focal_class.var_name: atoms
focal_class.declarator: bonds
focal_class.modifier: protected
focal_class.original_string: protected IBond[] bonds;
focal_class.type: IBond[]
focal_class.var_name: bonds
focal_class.declarator: lonePairs
focal_class.modifier: protected
focal_class.original_string: protected ILonePair[] lonePairs;
focal_class.type: ILonePair[]
focal_class.var_name: lonePairs
focal_class.declarator: singleElectrons
focal_class.modifier: protected
focal_class.original_string: protected ISingleElectron[] singleElectrons;
focal_class.type: ISingleElectron[]
focal_class.var_name: singleElectrons
focal_class.declarator: stereoElements
focal_class.modifier: protected
focal_class.original_string: protected Set<IStereoElement> stereoElements;
focal_class.type: Set<IStereoElement>
focal_class.var_name: stereoElements
focal_class.file: base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java
focal_class.identifier: AtomContainer
focal_class.interfaces: implements IAtomContainer, IChemObjectListener, Serializable, Cloneable
focal_class.class_method_signature: AtomContainer.AtomContainer()
focal_class.full_signature: public  AtomContainer()
focal_class.identifier: AtomContainer
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  AtomContainer()
focal_class.class_method_signature: AtomContainer.AtomContainer(IAtomContainer container)
focal_class.full_signature: public  AtomContainer(IAtomContainer container)
focal_class.identifier: AtomContainer
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container)
focal_class.signature:  AtomContainer(IAtomContainer container)
focal_class.class_method_signature: AtomContainer.AtomContainer(int atomCount, int bondCount, int lpCount,
                           int seCount)
focal_class.full_signature: public  AtomContainer(int atomCount, int bondCount, int lpCount,
                           int seCount)
focal_class.identifier: AtomContainer
focal_class.modifiers: public
focal_class.parameters: (int atomCount, int bondCount, int lpCount,
                           int seCount)
focal_class.signature:  AtomContainer(int atomCount, int bondCount, int lpCount,
                           int seCount)
focal_class.class_method_signature: AtomContainer.addStereoElement(IStereoElement element)
focal_class.full_signature: @Override public void addStereoElement(IStereoElement element)
focal_class.identifier: addStereoElement
focal_class.modifiers: @Override public
focal_class.parameters: (IStereoElement element)
focal_class.return: void
focal_class.signature: void addStereoElement(IStereoElement element)
focal_class.class_method_signature: AtomContainer.setStereoElements(List<IStereoElement> elements)
focal_class.full_signature: @Override public void setStereoElements(List<IStereoElement> elements)
focal_class.identifier: setStereoElements
focal_class.modifiers: @Override public
focal_class.parameters: (List<IStereoElement> elements)
focal_class.return: void
focal_class.signature: void setStereoElements(List<IStereoElement> elements)
focal_class.class_method_signature: AtomContainer.stereoElements()
focal_class.full_signature: @Override public Iterable<IStereoElement> stereoElements()
focal_class.identifier: stereoElements
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<IStereoElement>
focal_class.signature: Iterable<IStereoElement> stereoElements()
focal_class.class_method_signature: AtomContainer.setAtoms(IAtom[] newAtoms)
focal_class.full_signature: @Override public void setAtoms(IAtom[] newAtoms)
focal_class.identifier: setAtoms
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom[] newAtoms)
focal_class.return: void
focal_class.signature: void setAtoms(IAtom[] newAtoms)
focal_class.class_method_signature: AtomContainer.setBonds(IBond[] newBonds)
focal_class.full_signature: @Override public void setBonds(IBond[] newBonds)
focal_class.identifier: setBonds
focal_class.modifiers: @Override public
focal_class.parameters: (IBond[] newBonds)
focal_class.return: void
focal_class.signature: void setBonds(IBond[] newBonds)
focal_class.class_method_signature: AtomContainer.setAtom(int idx, IAtom atom)
focal_class.full_signature: @Override public void setAtom(int idx, IAtom atom)
focal_class.identifier: setAtom
focal_class.modifiers: @Override public
focal_class.parameters: (int idx, IAtom atom)
focal_class.return: void
focal_class.signature: void setAtom(int idx, IAtom atom)
focal_class.class_method_signature: AtomContainer.getAtom(int idx)
focal_class.full_signature: @Override public IAtom getAtom(int idx)
focal_class.identifier: getAtom
focal_class.modifiers: @Override public
focal_class.parameters: (int idx)
focal_class.return: IAtom
focal_class.signature: IAtom getAtom(int idx)
focal_class.class_method_signature: AtomContainer.getBond(int idx)
focal_class.full_signature: @Override public IBond getBond(int idx)
focal_class.identifier: getBond
focal_class.modifiers: @Override public
focal_class.parameters: (int idx)
focal_class.return: IBond
focal_class.signature: IBond getBond(int idx)
focal_class.class_method_signature: AtomContainer.getLonePair(int idx)
focal_class.full_signature: @Override public ILonePair getLonePair(int idx)
focal_class.identifier: getLonePair
focal_class.modifiers: @Override public
focal_class.parameters: (int idx)
focal_class.return: ILonePair
focal_class.signature: ILonePair getLonePair(int idx)
focal_class.class_method_signature: AtomContainer.getSingleElectron(int idx)
focal_class.full_signature: @Override public ISingleElectron getSingleElectron(int idx)
focal_class.identifier: getSingleElectron
focal_class.modifiers: @Override public
focal_class.parameters: (int idx)
focal_class.return: ISingleElectron
focal_class.signature: ISingleElectron getSingleElectron(int idx)
focal_class.class_method_signature: AtomContainer.atoms()
focal_class.full_signature: @Override public Iterable<IAtom> atoms()
focal_class.identifier: atoms
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<IAtom>
focal_class.signature: Iterable<IAtom> atoms()
focal_class.class_method_signature: AtomContainer.bonds()
focal_class.full_signature: @Override public Iterable<IBond> bonds()
focal_class.identifier: bonds
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<IBond>
focal_class.signature: Iterable<IBond> bonds()
focal_class.class_method_signature: AtomContainer.lonePairs()
focal_class.full_signature: @Override public Iterable<ILonePair> lonePairs()
focal_class.identifier: lonePairs
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<ILonePair>
focal_class.signature: Iterable<ILonePair> lonePairs()
focal_class.class_method_signature: AtomContainer.singleElectrons()
focal_class.full_signature: @Override public Iterable<ISingleElectron> singleElectrons()
focal_class.identifier: singleElectrons
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<ISingleElectron>
focal_class.signature: Iterable<ISingleElectron> singleElectrons()
focal_class.class_method_signature: AtomContainer.electronContainers()
focal_class.full_signature: @Override public Iterable<IElectronContainer> electronContainers()
focal_class.identifier: electronContainers
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterable<IElectronContainer>
focal_class.signature: Iterable<IElectronContainer> electronContainers()
focal_class.class_method_signature: AtomContainer.getFirstAtom()
focal_class.full_signature: @Override public IAtom getFirstAtom()
focal_class.identifier: getFirstAtom
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtom
focal_class.signature: IAtom getFirstAtom()
focal_class.class_method_signature: AtomContainer.getLastAtom()
focal_class.full_signature: @Override public IAtom getLastAtom()
focal_class.identifier: getLastAtom
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtom
focal_class.signature: IAtom getLastAtom()
focal_class.class_method_signature: AtomContainer.getAtomNumber(IAtom atom)
focal_class.full_signature: @Override public int getAtomNumber(IAtom atom)
focal_class.identifier: getAtomNumber
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int getAtomNumber(IAtom atom)
focal_class.class_method_signature: AtomContainer.getBondNumber(IAtom atom1, IAtom atom2)
focal_class.full_signature: @Override public int getBondNumber(IAtom atom1, IAtom atom2)
focal_class.identifier: getBondNumber
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom1, IAtom atom2)
focal_class.return: int
focal_class.signature: int getBondNumber(IAtom atom1, IAtom atom2)
focal_class.class_method_signature: AtomContainer.getBondNumber(IBond bond)
focal_class.full_signature: @Override public int getBondNumber(IBond bond)
focal_class.identifier: getBondNumber
focal_class.modifiers: @Override public
focal_class.parameters: (IBond bond)
focal_class.return: int
focal_class.signature: int getBondNumber(IBond bond)
focal_class.class_method_signature: AtomContainer.getLonePairNumber(ILonePair lonePair)
focal_class.full_signature: @Override public int getLonePairNumber(ILonePair lonePair)
focal_class.identifier: getLonePairNumber
focal_class.modifiers: @Override public
focal_class.parameters: (ILonePair lonePair)
focal_class.return: int
focal_class.signature: int getLonePairNumber(ILonePair lonePair)
focal_class.class_method_signature: AtomContainer.getSingleElectronNumber(ISingleElectron singleElectron)
focal_class.full_signature: @Override public int getSingleElectronNumber(ISingleElectron singleElectron)
focal_class.identifier: getSingleElectronNumber
focal_class.modifiers: @Override public
focal_class.parameters: (ISingleElectron singleElectron)
focal_class.return: int
focal_class.signature: int getSingleElectronNumber(ISingleElectron singleElectron)
focal_class.class_method_signature: AtomContainer.indexOf(IAtom atom)
focal_class.full_signature: @Override public int indexOf(IAtom atom)
focal_class.identifier: indexOf
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int indexOf(IAtom atom)
focal_class.class_method_signature: AtomContainer.indexOf(IBond bond)
focal_class.full_signature: @Override public int indexOf(IBond bond)
focal_class.identifier: indexOf
focal_class.modifiers: @Override public
focal_class.parameters: (IBond bond)
focal_class.return: int
focal_class.signature: int indexOf(IBond bond)
focal_class.class_method_signature: AtomContainer.indexOf(ISingleElectron electron)
focal_class.full_signature: @Override public int indexOf(ISingleElectron electron)
focal_class.identifier: indexOf
focal_class.modifiers: @Override public
focal_class.parameters: (ISingleElectron electron)
focal_class.return: int
focal_class.signature: int indexOf(ISingleElectron electron)
focal_class.class_method_signature: AtomContainer.indexOf(ILonePair pair)
focal_class.full_signature: @Override public int indexOf(ILonePair pair)
focal_class.identifier: indexOf
focal_class.modifiers: @Override public
focal_class.parameters: (ILonePair pair)
focal_class.return: int
focal_class.signature: int indexOf(ILonePair pair)
focal_class.class_method_signature: AtomContainer.getElectronContainer(int number)
focal_class.full_signature: @Override public IElectronContainer getElectronContainer(int number)
focal_class.identifier: getElectronContainer
focal_class.modifiers: @Override public
focal_class.parameters: (int number)
focal_class.return: IElectronContainer
focal_class.signature: IElectronContainer getElectronContainer(int number)
focal_class.class_method_signature: AtomContainer.getBond(IAtom atom1, IAtom atom2)
focal_class.full_signature: @Override public IBond getBond(IAtom atom1, IAtom atom2)
focal_class.identifier: getBond
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom1, IAtom atom2)
focal_class.return: IBond
focal_class.signature: IBond getBond(IAtom atom1, IAtom atom2)
focal_class.class_method_signature: AtomContainer.getAtomCount()
focal_class.full_signature: @Override public int getAtomCount()
focal_class.identifier: getAtomCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getAtomCount()
focal_class.class_method_signature: AtomContainer.getBondCount()
focal_class.full_signature: @Override public int getBondCount()
focal_class.identifier: getBondCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getBondCount()
focal_class.class_method_signature: AtomContainer.getLonePairCount()
focal_class.full_signature: @Override public int getLonePairCount()
focal_class.identifier: getLonePairCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getLonePairCount()
focal_class.class_method_signature: AtomContainer.getSingleElectronCount()
focal_class.full_signature: @Override public int getSingleElectronCount()
focal_class.identifier: getSingleElectronCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getSingleElectronCount()
focal_class.class_method_signature: AtomContainer.getElectronContainerCount()
focal_class.full_signature: @Override public int getElectronContainerCount()
focal_class.identifier: getElectronContainerCount
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getElectronContainerCount()
focal_class.class_method_signature: AtomContainer.getConnectedAtomsList(IAtom atom)
focal_class.full_signature: @Override public List<IAtom> getConnectedAtomsList(IAtom atom)
focal_class.identifier: getConnectedAtomsList
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: List<IAtom>
focal_class.signature: List<IAtom> getConnectedAtomsList(IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedBondsList(IAtom atom)
focal_class.full_signature: @Override public List<IBond> getConnectedBondsList(IAtom atom)
focal_class.identifier: getConnectedBondsList
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: List<IBond>
focal_class.signature: List<IBond> getConnectedBondsList(IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedLonePairsList(IAtom atom)
focal_class.full_signature: @Override public List<ILonePair> getConnectedLonePairsList(IAtom atom)
focal_class.identifier: getConnectedLonePairsList
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: List<ILonePair>
focal_class.signature: List<ILonePair> getConnectedLonePairsList(IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedSingleElectronsList(IAtom atom)
focal_class.full_signature: @Override public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)
focal_class.identifier: getConnectedSingleElectronsList
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: List<ISingleElectron>
focal_class.signature: List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedElectronContainersList(
          IAtom atom)
focal_class.full_signature: @Override public List<IElectronContainer> getConnectedElectronContainersList(
          IAtom atom)
focal_class.identifier: getConnectedElectronContainersList
focal_class.modifiers: @Override public
focal_class.parameters: (
          IAtom atom)
focal_class.return: List<IElectronContainer>
focal_class.signature: List<IElectronContainer> getConnectedElectronContainersList(
          IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedBondsCount(IAtom atom)
focal_class.full_signature: @Override public int getConnectedBondsCount(IAtom atom)
focal_class.identifier: getConnectedBondsCount
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int getConnectedBondsCount(IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedAtomsCount(IAtom atom)
focal_class.full_signature: @Override public int getConnectedAtomsCount(IAtom atom)
focal_class.identifier: getConnectedAtomsCount
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int getConnectedAtomsCount(IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedBondsCount(int idx)
focal_class.full_signature: @Override public int getConnectedBondsCount(int idx)
focal_class.identifier: getConnectedBondsCount
focal_class.modifiers: @Override public
focal_class.parameters: (int idx)
focal_class.return: int
focal_class.signature: int getConnectedBondsCount(int idx)
focal_class.class_method_signature: AtomContainer.getConnectedLonePairsCount(IAtom atom)
focal_class.full_signature: @Override public int getConnectedLonePairsCount(IAtom atom)
focal_class.identifier: getConnectedLonePairsCount
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int getConnectedLonePairsCount(IAtom atom)
focal_class.class_method_signature: AtomContainer.getConnectedSingleElectronsCount(IAtom atom)
focal_class.full_signature: @Override public int getConnectedSingleElectronsCount(IAtom atom)
focal_class.identifier: getConnectedSingleElectronsCount
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int getConnectedSingleElectronsCount(IAtom atom)
focal_class.class_method_signature: AtomContainer.getBondOrderSum(IAtom atom)
focal_class.full_signature: @Override public double getBondOrderSum(IAtom atom)
focal_class.identifier: getBondOrderSum
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: double
focal_class.signature: double getBondOrderSum(IAtom atom)
focal_class.class_method_signature: AtomContainer.getMaximumBondOrder(IAtom atom)
focal_class.full_signature: @Override public Order getMaximumBondOrder(IAtom atom)
focal_class.identifier: getMaximumBondOrder
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: Order
focal_class.signature: Order getMaximumBondOrder(IAtom atom)
focal_class.class_method_signature: AtomContainer.getMinimumBondOrder(IAtom atom)
focal_class.full_signature: @Override public Order getMinimumBondOrder(IAtom atom)
focal_class.identifier: getMinimumBondOrder
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: Order
focal_class.signature: Order getMinimumBondOrder(IAtom atom)
focal_class.class_method_signature: AtomContainer.add(IAtomContainer that)
focal_class.full_signature: @Override public void add(IAtomContainer that)
focal_class.identifier: add
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer that)
focal_class.return: void
focal_class.signature: void add(IAtomContainer that)
focal_class.class_method_signature: AtomContainer.addAtom(IAtom atom)
focal_class.full_signature: @Override public void addAtom(IAtom atom)
focal_class.identifier: addAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: void
focal_class.signature: void addAtom(IAtom atom)
focal_class.class_method_signature: AtomContainer.addBond(IBond bond)
focal_class.full_signature: @Override public void addBond(IBond bond)
focal_class.identifier: addBond
focal_class.modifiers: @Override public
focal_class.parameters: (IBond bond)
focal_class.return: void
focal_class.signature: void addBond(IBond bond)
focal_class.class_method_signature: AtomContainer.addLonePair(ILonePair lonePair)
focal_class.full_signature: @Override public void addLonePair(ILonePair lonePair)
focal_class.identifier: addLonePair
focal_class.modifiers: @Override public
focal_class.parameters: (ILonePair lonePair)
focal_class.return: void
focal_class.signature: void addLonePair(ILonePair lonePair)
focal_class.class_method_signature: AtomContainer.addSingleElectron(ISingleElectron singleElectron)
focal_class.full_signature: @Override public void addSingleElectron(ISingleElectron singleElectron)
focal_class.identifier: addSingleElectron
focal_class.modifiers: @Override public
focal_class.parameters: (ISingleElectron singleElectron)
focal_class.return: void
focal_class.signature: void addSingleElectron(ISingleElectron singleElectron)
focal_class.class_method_signature: AtomContainer.addElectronContainer(IElectronContainer electronContainer)
focal_class.full_signature: @Override public void addElectronContainer(IElectronContainer electronContainer)
focal_class.identifier: addElectronContainer
focal_class.modifiers: @Override public
focal_class.parameters: (IElectronContainer electronContainer)
focal_class.return: void
focal_class.signature: void addElectronContainer(IElectronContainer electronContainer)
focal_class.class_method_signature: AtomContainer.remove(IAtomContainer atomContainer)
focal_class.full_signature: @Override public void remove(IAtomContainer atomContainer)
focal_class.identifier: remove
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: void
focal_class.signature: void remove(IAtomContainer atomContainer)
focal_class.class_method_signature: AtomContainer.removeAtomOnly(int position)
focal_class.full_signature: @Override public void removeAtomOnly(int position)
focal_class.identifier: removeAtomOnly
focal_class.modifiers: @Override public
focal_class.parameters: (int position)
focal_class.return: void
focal_class.signature: void removeAtomOnly(int position)
focal_class.class_method_signature: AtomContainer.removeAtomOnly(IAtom atom)
focal_class.full_signature: @Override public void removeAtomOnly(IAtom atom)
focal_class.identifier: removeAtomOnly
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: void
focal_class.signature: void removeAtomOnly(IAtom atom)
focal_class.class_method_signature: AtomContainer.removeBond(int position)
focal_class.full_signature: @Override public IBond removeBond(int position)
focal_class.identifier: removeBond
focal_class.modifiers: @Override public
focal_class.parameters: (int position)
focal_class.return: IBond
focal_class.signature: IBond removeBond(int position)
focal_class.class_method_signature: AtomContainer.removeBond(IAtom atom1, IAtom atom2)
focal_class.full_signature: @Override public IBond removeBond(IAtom atom1, IAtom atom2)
focal_class.identifier: removeBond
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom1, IAtom atom2)
focal_class.return: IBond
focal_class.signature: IBond removeBond(IAtom atom1, IAtom atom2)
focal_class.class_method_signature: AtomContainer.removeBond(IBond bond)
focal_class.full_signature: @Override public void removeBond(IBond bond)
focal_class.identifier: removeBond
focal_class.modifiers: @Override public
focal_class.parameters: (IBond bond)
focal_class.return: void
focal_class.signature: void removeBond(IBond bond)
focal_class.class_method_signature: AtomContainer.removeLonePair(int position)
focal_class.full_signature: @Override public ILonePair removeLonePair(int position)
focal_class.identifier: removeLonePair
focal_class.modifiers: @Override public
focal_class.parameters: (int position)
focal_class.return: ILonePair
focal_class.signature: ILonePair removeLonePair(int position)
focal_class.class_method_signature: AtomContainer.removeLonePair(ILonePair lonePair)
focal_class.full_signature: @Override public void removeLonePair(ILonePair lonePair)
focal_class.identifier: removeLonePair
focal_class.modifiers: @Override public
focal_class.parameters: (ILonePair lonePair)
focal_class.return: void
focal_class.signature: void removeLonePair(ILonePair lonePair)
focal_class.class_method_signature: AtomContainer.removeSingleElectron(int position)
focal_class.full_signature: @Override public ISingleElectron removeSingleElectron(int position)
focal_class.identifier: removeSingleElectron
focal_class.modifiers: @Override public
focal_class.parameters: (int position)
focal_class.return: ISingleElectron
focal_class.signature: ISingleElectron removeSingleElectron(int position)
focal_class.class_method_signature: AtomContainer.removeSingleElectron(ISingleElectron singleElectron)
focal_class.full_signature: @Override public void removeSingleElectron(ISingleElectron singleElectron)
focal_class.identifier: removeSingleElectron
focal_class.modifiers: @Override public
focal_class.parameters: (ISingleElectron singleElectron)
focal_class.return: void
focal_class.signature: void removeSingleElectron(ISingleElectron singleElectron)
focal_class.class_method_signature: AtomContainer.removeElectronContainer(int number)
focal_class.full_signature: @Override public IElectronContainer removeElectronContainer(int number)
focal_class.identifier: removeElectronContainer
focal_class.modifiers: @Override public
focal_class.parameters: (int number)
focal_class.return: IElectronContainer
focal_class.signature: IElectronContainer removeElectronContainer(int number)
focal_class.class_method_signature: AtomContainer.removeElectronContainer(IElectronContainer electronContainer)
focal_class.full_signature: @Override public void removeElectronContainer(IElectronContainer electronContainer)
focal_class.identifier: removeElectronContainer
focal_class.modifiers: @Override public
focal_class.parameters: (IElectronContainer electronContainer)
focal_class.return: void
focal_class.signature: void removeElectronContainer(IElectronContainer electronContainer)
focal_class.class_method_signature: AtomContainer.removeAtomAndConnectedElectronContainers(IAtom atom)
focal_class.full_signature: @Override @Deprecated public void removeAtomAndConnectedElectronContainers(IAtom atom)
focal_class.identifier: removeAtomAndConnectedElectronContainers
focal_class.modifiers: @Override @Deprecated public
focal_class.parameters: (IAtom atom)
focal_class.return: void
focal_class.signature: void removeAtomAndConnectedElectronContainers(IAtom atom)
focal_class.class_method_signature: AtomContainer.removeAtom(IAtom atom)
focal_class.full_signature: @Override public void removeAtom(IAtom atom)
focal_class.identifier: removeAtom
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: void
focal_class.signature: void removeAtom(IAtom atom)
focal_class.class_method_signature: AtomContainer.removeAtom(int pos)
focal_class.full_signature: @Override public void removeAtom(int pos)
focal_class.identifier: removeAtom
focal_class.modifiers: @Override public
focal_class.parameters: (int pos)
focal_class.return: void
focal_class.signature: void removeAtom(int pos)
focal_class.class_method_signature: AtomContainer.removeAllElements()
focal_class.full_signature: @Override public void removeAllElements()
focal_class.identifier: removeAllElements
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void removeAllElements()
focal_class.class_method_signature: AtomContainer.removeAllElectronContainers()
focal_class.full_signature: @Override public void removeAllElectronContainers()
focal_class.identifier: removeAllElectronContainers
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void removeAllElectronContainers()
focal_class.class_method_signature: AtomContainer.removeAllBonds()
focal_class.full_signature: @Override public void removeAllBonds()
focal_class.identifier: removeAllBonds
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void removeAllBonds()
focal_class.class_method_signature: AtomContainer.addBond(int atom1, int atom2, IBond.Order order,
                          IBond.Stereo stereo)
focal_class.full_signature: @Override public void addBond(int atom1, int atom2, IBond.Order order,
                          IBond.Stereo stereo)
focal_class.identifier: addBond
focal_class.modifiers: @Override public
focal_class.parameters: (int atom1, int atom2, IBond.Order order,
                          IBond.Stereo stereo)
focal_class.return: void
focal_class.signature: void addBond(int atom1, int atom2, IBond.Order order,
                          IBond.Stereo stereo)
focal_class.class_method_signature: AtomContainer.addBond(int atom1, int atom2, IBond.Order order)
focal_class.full_signature: @Override public void addBond(int atom1, int atom2, IBond.Order order)
focal_class.identifier: addBond
focal_class.modifiers: @Override public
focal_class.parameters: (int atom1, int atom2, IBond.Order order)
focal_class.return: void
focal_class.signature: void addBond(int atom1, int atom2, IBond.Order order)
focal_class.class_method_signature: AtomContainer.addLonePair(int atomID)
focal_class.full_signature: @Override public void addLonePair(int atomID)
focal_class.identifier: addLonePair
focal_class.modifiers: @Override public
focal_class.parameters: (int atomID)
focal_class.return: void
focal_class.signature: void addLonePair(int atomID)
focal_class.class_method_signature: AtomContainer.addSingleElectron(int atomID)
focal_class.full_signature: @Override public void addSingleElectron(int atomID)
focal_class.identifier: addSingleElectron
focal_class.modifiers: @Override public
focal_class.parameters: (int atomID)
focal_class.return: void
focal_class.signature: void addSingleElectron(int atomID)
focal_class.class_method_signature: AtomContainer.contains(IAtom atom)
focal_class.full_signature: @Override public boolean contains(IAtom atom)
focal_class.identifier: contains
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean contains(IAtom atom)
focal_class.class_method_signature: AtomContainer.contains(IBond bond)
focal_class.full_signature: @Override public boolean contains(IBond bond)
focal_class.identifier: contains
focal_class.modifiers: @Override public
focal_class.parameters: (IBond bond)
focal_class.return: boolean
focal_class.signature: boolean contains(IBond bond)
focal_class.class_method_signature: AtomContainer.contains(ILonePair lonePair)
focal_class.full_signature: @Override public boolean contains(ILonePair lonePair)
focal_class.identifier: contains
focal_class.modifiers: @Override public
focal_class.parameters: (ILonePair lonePair)
focal_class.return: boolean
focal_class.signature: boolean contains(ILonePair lonePair)
focal_class.class_method_signature: AtomContainer.contains(ISingleElectron singleElectron)
focal_class.full_signature: @Override public boolean contains(ISingleElectron singleElectron)
focal_class.identifier: contains
focal_class.modifiers: @Override public
focal_class.parameters: (ISingleElectron singleElectron)
focal_class.return: boolean
focal_class.signature: boolean contains(ISingleElectron singleElectron)
focal_class.class_method_signature: AtomContainer.contains(IElectronContainer electronContainer)
focal_class.full_signature: @Override public boolean contains(IElectronContainer electronContainer)
focal_class.identifier: contains
focal_class.modifiers: @Override public
focal_class.parameters: (IElectronContainer electronContainer)
focal_class.return: boolean
focal_class.signature: boolean contains(IElectronContainer electronContainer)
focal_class.class_method_signature: AtomContainer.toString()
focal_class.full_signature: @Override public String toString()
focal_class.identifier: toString
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String toString()
focal_class.class_method_signature: AtomContainer.clone()
focal_class.full_signature: @Override public IAtomContainer clone()
focal_class.identifier: clone
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer clone()
focal_class.class_method_signature: AtomContainer.grow(T[] array, int required)
focal_class.full_signature: private static T[] grow(T[] array, int required)
focal_class.identifier: grow
focal_class.modifiers: private static
focal_class.parameters: (T[] array, int required)
focal_class.return: T[]
focal_class.signature: T[] grow(T[] array, int required)
focal_class.class_method_signature: AtomContainer.ensureAtomCapacity(int required)
focal_class.full_signature: private void ensureAtomCapacity(int required)
focal_class.identifier: ensureAtomCapacity
focal_class.modifiers: private
focal_class.parameters: (int required)
focal_class.return: void
focal_class.signature: void ensureAtomCapacity(int required)
focal_class.class_method_signature: AtomContainer.ensureBondCapacity(int required)
focal_class.full_signature: private void ensureBondCapacity(int required)
focal_class.identifier: ensureBondCapacity
focal_class.modifiers: private
focal_class.parameters: (int required)
focal_class.return: void
focal_class.signature: void ensureBondCapacity(int required)
focal_class.class_method_signature: AtomContainer.ensureElectronCapacity(int required)
focal_class.full_signature: private void ensureElectronCapacity(int required)
focal_class.identifier: ensureElectronCapacity
focal_class.modifiers: private
focal_class.parameters: (int required)
focal_class.return: void
focal_class.signature: void ensureElectronCapacity(int required)
focal_class.class_method_signature: AtomContainer.ensureLonePairCapacity(int required)
focal_class.full_signature: private void ensureLonePairCapacity(int required)
focal_class.identifier: ensureLonePairCapacity
focal_class.modifiers: private
focal_class.parameters: (int required)
focal_class.return: void
focal_class.signature: void ensureLonePairCapacity(int required)
focal_class.class_method_signature: AtomContainer.stateChanged(IChemObjectChangeEvent event)
focal_class.full_signature: @Override public void stateChanged(IChemObjectChangeEvent event)
focal_class.identifier: stateChanged
focal_class.modifiers: @Override public
focal_class.parameters: (IChemObjectChangeEvent event)
focal_class.return: void
focal_class.signature: void stateChanged(IChemObjectChangeEvent event)
focal_class.class_method_signature: AtomContainer.isEmpty()
focal_class.full_signature: @Override public boolean isEmpty()
focal_class.identifier: isEmpty
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isEmpty()
focal_class.class_method_signature: AtomContainer.getTitle()
focal_class.full_signature: @Override public String getTitle()
focal_class.identifier: getTitle
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getTitle()
focal_class.class_method_signature: AtomContainer.setTitle(String title)
focal_class.full_signature: @Override public void setTitle(String title)
focal_class.identifier: setTitle
focal_class.modifiers: @Override public
focal_class.parameters: (String title)
focal_class.return: void
focal_class.signature: void setTitle(String title)
focal_class.superclass: extends ChemObject
focal_method.body: public AtomContainer() {
          this(0, 0, 0, 0);
      }
focal_method.class_method_signature: AtomContainer.AtomContainer()
focal_method.full_signature: public  AtomContainer()
focal_method.identifier: AtomContainer
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  AtomContainer()