java.lang.Object
- org.openscience.cdk.ChemObject
- - org.openscience.cdk.AtomContainer
  - - org.openscience.cdk.debug.DebugAtomContainer

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener
```
public class DebugAtomContainer
extends AtomContainer
implements IAtomContainer
```
Debugging data class.

Author:

egonw

See Also:

Serialized Form

Source code:
main

Belongs to CDK module:
datadebug

Field Summary
- Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
  ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors
Constructor	Description
`DebugAtomContainer()`
`DebugAtomContainer(int atomCount, int bondCount, int lonePairCount, int singleElectronCount)`
`DebugAtomContainer(IAtomContainer container)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`add(IAtomContainer atomContainer)`	Adds all atoms and electronContainers of a given atomcontainer to this container.
`void`	`addAtom(IAtom atom)`	Adds an atom to this container.
`void`	`addBond(int atom1, int atom2, IBond.Order order)`	Adds a bond to this container.
`void`	`addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo)`	Adds a bond to this container.
`void`	`addBond(IBond bond)`	Adds a Bond to this AtomContainer.
`void`	`addElectronContainer(IElectronContainer electronContainer)`	Adds a ElectronContainer to this AtomContainer.
`void`	`addListener(IChemObjectListener col)`	Use this to add yourself to this IChemObject as a listener.
`void`	`addLonePair(int atomID)`	Adds a LonePair to this Atom.
`void`	`addLonePair(ILonePair ec)`	Adds a lone pair to this AtomContainer.
`void`	`addProperties(Map<Object,Object> properties)`	Sets the properties of this object.
`void`	`addSingleElectron(int atomID)`	Adds a SingleElectron to this Atom.
`void`	`addSingleElectron(ISingleElectron ec)`	Adds a single electron to this AtomContainer.
`void`	`addStereoElement(IStereoElement parity)`	Adds a stereo element to this container.
`Iterable<IAtom>`	`atoms()`	Returns an Iterable for looping over all atoms in this container.
`Iterable<IBond>`	`bonds()`	Returns an Iterable for looping over all bonds in this container.
`IAtomContainer`	`clone()`	Clones this `IChemObject`.
`boolean`	`contains(IAtom atom)`	True, if the AtomContainer contains the given atom object.
`boolean`	`contains(IBond bond)`	True, if the AtomContainer contains the given bond object.
`boolean`	`contains(IElectronContainer electronContainer)`	True, if the AtomContainer contains the given ElectronContainer object.
`boolean`	`contains(ILonePair ec)`	True, if the AtomContainer contains the given LonePair object.
`boolean`	`contains(ISingleElectron ec)`	True, if the AtomContainer contains the given SingleElectron object.
`Iterable<IElectronContainer>`	`electronContainers()`	Returns an Iterable for looping over all electron containers in this container.
`IAtom`	`getAtom(int idx)`	Get the atom at the specified idx, the index should be in the range 0 ≤ idx < `IAtomContainer.getAtomCount()`.
`int`	`getAtomCount()`	Returns the number of Atoms in this Container.
`IBond`	`getBond(int idx)`	Get the bond at the specified idx, the index should be in the range 0 ≤ idx < `IAtomContainer.getBondCount()`.
`IBond`	`getBond(IAtom atom1, IAtom atom2)`	Returns the bond that connects the two given atoms.
`int`	`getBondCount()`	Returns the number of Bonds in this Container.
`double`	`getBondOrderSum(IAtom atom)`	Returns the sum of the bond orders for a given Atom.
`IChemObjectBuilder`	`getBuilder()`	Returns a `IChemObjectBuilder` for the data classes that extend this class.
`int`	`getConnectedAtomsCount(IAtom atom)`	Returns the number of connected atoms (explicit degree) to the specified atom.
`List<IAtom>`	`getConnectedAtomsList(IAtom atom)`	Returns the atoms connected connected to the specified atom by a bond.
`int`	`getConnectedBondsCount(IAtom atom)`	Returns the number of connected bonds (explicit degree) to the specified atom.
`List<IBond>`	`getConnectedBondsList(IAtom atom)`	Returns the bonds connected connected to the specified atom.
`List<IElectronContainer>`	`getConnectedElectronContainersList(IAtom atom)`	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
`int`	`getConnectedLonePairsCount(IAtom atom)`	Returns the number of lone pairs connected to the specified atom.
`List<ILonePair>`	`getConnectedLonePairsList(IAtom atom)`	Returns the lone pairs connected connected to the specified atom.
`int`	`getConnectedSingleElectronsCount(IAtom atom)`	Returns the number of single electrons connected to the specified atom.
`List<ISingleElectron>`	`getConnectedSingleElectronsList(IAtom atom)`	Returns the single electrons connected connected to the specified atom.
`IElectronContainer`	`getElectronContainer(int number)`	Returns the ElectronContainer at position `number` in the container.
`int`	`getElectronContainerCount()`	Returns the number of ElectronContainers in this Container.
`IAtom`	`getFirstAtom()`	Returns the atom at position 0 in the container.
`boolean`	`getFlag(int flagType)`	Returns the value of a given flag.
`boolean[]`	`getFlags()`	Returns the whole set of flags.
`String`	`getID()`	Returns the identifier (ID) of this object.
`IAtom`	`getLastAtom()`	Returns the atom at the last position in the container.
`int`	`getListenerCount()`	Returns the number of ChemObjectListeners registered with this object.
`ILonePair`	`getLonePair(int idx)`	Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < `IAtomContainer.getLonePairCount()`.
`int`	`getLonePairCount()`	Returns the number of LonePairs in this Container.
`IBond.Order`	`getMaximumBondOrder(IAtom atom)`	Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
`IBond.Order`	`getMinimumBondOrder(IAtom atom)`	Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
`Map<Object,Object>`	`getProperties()`	Returns a Map with the IChemObject's properties.
`<T> T`	`getProperty(Object description)`	Returns a property for the IChemObject.
`ISingleElectron`	`getSingleElectron(int idx)`	Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < `IAtomContainer.getSingleElectronCount()`.
`int`	`getSingleElectronCount()`	Returns the number of the single electrons in this container.
`int`	`indexOf(IAtom atom)`	Access the storage index of an atom.
`int`	`indexOf(IBond bond)`	Access the storage index of a bond.
`int`	`indexOf(ILonePair pair)`	Access the storage index of a long pair.
`int`	`indexOf(ISingleElectron electron)`	Access the storage index of a single electron (radical).
`boolean`	`isEmpty()`	Indicates whether this container is empty.
`Iterable<ILonePair>`	`lonePairs()`	Returns an Iterable for looping over all lone pairs in this container.
`void`	`notifyChanged()`	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
`void`	`notifyChanged(IChemObjectChangeEvent evt)`	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
`void`	`remove(IAtomContainer atomContainer)`	Removes all atoms and electronContainers of a given atomcontainer from this container.
`void`	`removeAllBonds()`	Removes all Bonds from this container.
`void`	`removeAllElectronContainers()`	Removes electronContainers from this container.
`void`	`removeAllElements()`	Removes all atoms, bonds and stereo elements from this container.
`void`	`removeAtom(IAtom atom)`	Safely remove an atom from the container.
`void`	`removeAtomOnly(int position)`	Unsafely remove atom at index.
`void`	`removeAtomOnly(IAtom atom)`	Unsafely remove atom.
`IBond`	`removeBond(int pos)`	Removes the bond at the given position from the AtomContainer.
`IBond`	`removeBond(IAtom atom1, IAtom atom2)`	Removes the bond that connects the two given atoms.
`void`	`removeBond(IBond bond)`	Removes the bond from this container.
`IElectronContainer`	`removeElectronContainer(int position)`	Removes the bond at the given position from this container.
`void`	`removeElectronContainer(IElectronContainer electronContainer)`	Removes this ElectronContainer from this container.
`void`	`removeListener(IChemObjectListener col)`	Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
`ILonePair`	`removeLonePair(int pos)`	Removes the lone pair at the given position from the AtomContainer.
`void`	`removeLonePair(ILonePair ec)`	Removes the lone pair from the AtomContainer.
`void`	`removeProperty(Object description)`	Removes a property for a IChemObject.
`ISingleElectron`	`removeSingleElectron(int pos)`	Removes the single electron at the given position from the AtomContainer.
`void`	`removeSingleElectron(ISingleElectron ec)`	Removes the single electron from the AtomContainer.
`void`	`setAtom(int number, IAtom atom)`	Set the atom at `idx`, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
`void`	`setAtoms(IAtom[] atoms)`	Sets the array of atoms of this AtomContainer.
`void`	`setFlag(int flagType, boolean flagValue)`	Sets the value of some flag.
`void`	`setFlags(boolean[] flagsNew)`	Sets the whole set of flags.
`void`	`setID(String identifier)`	Sets the identifier (ID) of this object.
`void`	`setProperty(Object description, Object property)`	Sets a property for a IChemObject.
`void`	`setStereoElements(List<IStereoElement> elements)`	Set the stereo elements - this will replace the existing instance with a new instance.
`Iterable<ISingleElectron>`	`singleElectrons()`	Returns an Iterable for looping over all single electrons in this container.
`Iterable<IStereoElement>`	`stereoElements()`	Returns the stereo elements defined for this atom container.

Methods inherited from class org.openscience.cdk.AtomContainer
getAtomNumber, getBondNumber, getBondNumber, getConnectedBondsCount, getLonePairNumber, getSingleElectronNumber, getTitle, newAtom, newAtom, newBond, removeAtom, removeAtomAndConnectedElectronContainers, setBonds, setTitle, shallowCopy, stateChanged, toString

Methods inherited from class org.openscience.cdk.ChemObject
clear, compare, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer
getAtomNumber, getBondNumber, getBondNumber, getConnectedBondsCount, getLonePairNumber, getSingleElectronNumber, getTitle, newAtom, newAtom, newAtom, newAtom, newBond, newBond, removeAtom, removeAtomAndConnectedElectronContainers, setBonds, setTitle

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
clear, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties, toString

Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener
stateChanged

- Constructor Detail
  - DebugAtomContainer
```
public DebugAtomContainer()
```
  - DebugAtomContainer
```
public DebugAtomContainer(int atomCount,
                          int bondCount,
                          int lonePairCount,
                          int singleElectronCount)
```
  - DebugAtomContainer
```
public DebugAtomContainer(IAtomContainer container)
```
- Method Detail
  - addStereoElement
```
public void addStereoElement(IStereoElement parity)
```
    Adds a stereo element to this container.
    
    Specified by:
    
    addStereoElement in interface IAtomContainer
    
    Overrides:
    
    addStereoElement in class AtomContainer
    
    Parameters:
    
    parity - The new IStereoElement for this container
    
    See Also:
    
    IAtomContainer.stereoElements()
  - setStereoElements
```
public void setStereoElements(List<IStereoElement> elements)
```
    Set the stereo elements - this will replace the existing instance with a new instance.
    
    Specified by:
    
    setStereoElements in interface IAtomContainer
    
    Overrides:
    
    setStereoElements in class AtomContainer
    
    Parameters:
    
    elements - the new stereo elements
  - stereoElements
```
public Iterable<IStereoElement> stereoElements()
```
    Returns the stereo elements defined for this atom container.
    
    Specified by:
    
    stereoElements in interface IAtomContainer
    
    Overrides:
    
    stereoElements in class AtomContainer
    
    Returns:
    
    An Iterable of IStereoElements.
    
    See Also:
    
    IAtomContainer.addStereoElement(IStereoElement)
  - setAtoms
```
public void setAtoms(IAtom[] atoms)
```
    Sets the array of atoms of this AtomContainer.
    
    Specified by:
    
    setAtoms in interface IAtomContainer
    
    Overrides:
    
    setAtoms in class AtomContainer
    
    Parameters:
    
    atoms - The array of atoms to be assigned to this AtomContainer
    
    See Also:
    
    IAtomContainer.atoms()
  - setAtom
```
public void setAtom(int number,
                    IAtom atom)
```
    Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
    
    Specified by:
    
    setAtom in interface IAtomContainer
    
    Overrides:
    
    setAtom in class AtomContainer
    
    Parameters:
    
    number - The index of the atom to be set.
    
    atom - The atom to be stored at position idx
    
    See Also:
    
    IAtomContainer.getAtom(int)
  - getAtom
```
public IAtom getAtom(int idx)
```
    Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
    
    Specified by:
    
    getAtom in interface IAtomContainer
    
    Overrides:
    
    getAtom in class AtomContainer
    
    Parameters:
    
    idx - atom index
    
    Returns:
    
    the atom stored at the index
    
    See Also:
    
    IAtomContainer.setAtom(int, org.openscience.cdk.interfaces.IAtom)
  - getBond
```
public IBond getBond(int idx)
```
    Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
    
    Specified by:
    
    getBond in interface IAtomContainer
    
    Overrides:
    
    getBond in class AtomContainer
    
    Parameters:
    
    idx - bond index
    
    Returns:
    
    the bond stored at the index
  - getLonePair
```
public ILonePair getLonePair(int idx)
```
    Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
    
    Specified by:
    
    getLonePair in interface IAtomContainer
    
    Overrides:
    
    getLonePair in class AtomContainer
    
    Parameters:
    
    idx - lone pair index
    
    Returns:
    
    the lone pair stored at the index
  - getSingleElectron
```
public ISingleElectron getSingleElectron(int idx)
```
    Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
    
    Specified by:
    
    getSingleElectron in interface IAtomContainer
    
    Overrides:
    
    getSingleElectron in class AtomContainer
    
    Parameters:
    
    idx - single electron index
    
    Returns:
    
    the single electron stored at the index
  - atoms
```
public Iterable<IAtom> atoms()
```
    Returns an Iterable for looping over all atoms in this container.
    
    Specified by:
    
    atoms in interface IAtomContainer
    
    Overrides:
    
    atoms in class AtomContainer
    
    Returns:
    
    An Iterable with the atoms in this container
  - bonds
```
public Iterable<IBond> bonds()
```
    Returns an Iterable for looping over all bonds in this container.
    
    Specified by:
    
    bonds in interface IAtomContainer
    
    Overrides:
    
    bonds in class AtomContainer
    
    Returns:
    
    An Iterable with the bonds in this container
  - lonePairs
```
public Iterable<ILonePair> lonePairs()
```
    Returns an Iterable for looping over all lone pairs in this container.
    
    Specified by:
    
    lonePairs in interface IAtomContainer
    
    Overrides:
    
    lonePairs in class AtomContainer
    
    Returns:
    
    An Iterable with the lone pairs in this container
  - singleElectrons
```
public Iterable<ISingleElectron> singleElectrons()
```
    Returns an Iterable for looping over all single electrons in this container.
    
    Specified by:
    
    singleElectrons in interface IAtomContainer
    
    Overrides:
    
    singleElectrons in class AtomContainer
    
    Returns:
    
    An Iterable with the single electrons in this container
  - electronContainers
```
public Iterable<IElectronContainer> electronContainers()
```
    Returns an Iterable for looping over all electron containers in this container.
    
    Specified by:
    
    electronContainers in interface IAtomContainer
    
    Overrides:
    
    electronContainers in class AtomContainer
    
    Returns:
    
    An Iterable with the electron containers in this container
  - getFirstAtom
```
public IAtom getFirstAtom()
```
    Returns the atom at position 0 in the container.
    
    Specified by:
    
    getFirstAtom in interface IAtomContainer
    
    Overrides:
    
    getFirstAtom in class AtomContainer
    
    Returns:
    
    The atom at position 0 .
  - getLastAtom
```
public IAtom getLastAtom()
```
    Returns the atom at the last position in the container.
    
    Specified by:
    
    getLastAtom in interface IAtomContainer
    
    Overrides:
    
    getLastAtom in class AtomContainer
    
    Returns:
    
    The atom at the last position
  - indexOf
```
public int indexOf(IAtom atom)
```
    Access the storage index of an atom.
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Overrides:
    
    indexOf in class AtomContainer
    
    Parameters:
    
    atom - atom instance to find
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
public int indexOf(IBond bond)
```
    Access the storage index of a bond.
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Overrides:
    
    indexOf in class AtomContainer
    
    Parameters:
    
    bond - bond instance to find
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
public int indexOf(ISingleElectron electron)
```
    Access the storage index of a single electron (radical).
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Overrides:
    
    indexOf in class AtomContainer
    
    Parameters:
    
    electron - the electron
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
public int indexOf(ILonePair pair)
```
    Access the storage index of a long pair.
    
    Specified by:
    
    indexOf in interface IAtomContainer
    
    Overrides:
    
    indexOf in class AtomContainer
    
    Parameters:
    
    pair - the long pair
    
    Returns:
    
    the index, -1 if not found
  - getElectronContainer
```
public IElectronContainer getElectronContainer(int number)
```
    Returns the ElectronContainer at position number in the container.
    
    Specified by:
    
    getElectronContainer in interface IAtomContainer
    
    Overrides:
    
    getElectronContainer in class AtomContainer
    
    Parameters:
    
    number - The position of the ElectronContainer to be returned.
    
    Returns:
    
    The ElectronContainer at position number.
    
    See Also:
    
    IAtomContainer.addElectronContainer(IElectronContainer)
  - getBond
```
public IBond getBond(IAtom atom1,
                     IAtom atom2)
```
    Returns the bond that connects the two given atoms.
    
    Specified by:
    
    getBond in interface IAtomContainer
    
    Overrides:
    
    getBond in class AtomContainer
    
    Parameters:
    
    atom1 - The first atom
    
    atom2 - The second atom
    
    Returns:
    
    The bond that connects the two atoms
  - getAtomCount
```
public int getAtomCount()
```
    Returns the number of Atoms in this Container.
    
    Specified by:
    
    getAtomCount in interface IAtomContainer
    
    Overrides:
    
    getAtomCount in class AtomContainer
    
    Returns:
    
    The number of Atoms in this Container
  - getBondCount
```
public int getBondCount()
```
    Returns the number of Bonds in this Container.
    
    Specified by:
    
    getBondCount in interface IAtomContainer
    
    Overrides:
    
    getBondCount in class AtomContainer
    
    Returns:
    
    The number of Bonds in this Container
  - getLonePairCount
```
public int getLonePairCount()
```
    Returns the number of LonePairs in this Container.
    
    Specified by:
    
    getLonePairCount in interface IAtomContainer
    
    Overrides:
    
    getLonePairCount in class AtomContainer
    
    Returns:
    
    The number of LonePairs in this Container
  - getSingleElectronCount
```
public int getSingleElectronCount()
```
    Returns the number of the single electrons in this container.
    
    Specified by:
    
    getSingleElectronCount in interface IAtomContainer
    
    Overrides:
    
    getSingleElectronCount in class AtomContainer
    
    Returns:
    
    The number of SingleElectron objects of this AtomContainer
  - getElectronContainerCount
```
public int getElectronContainerCount()
```
    Returns the number of ElectronContainers in this Container.
    
    Specified by:
    
    getElectronContainerCount in interface IAtomContainer
    
    Overrides:
    
    getElectronContainerCount in class AtomContainer
    
    Returns:
    
    The number of ElectronContainers in this Container
  - getConnectedAtomsList
```
public List<IAtom> getConnectedAtomsList(IAtom atom)
```
    Returns the atoms connected connected to the specified atom by a bond.
    
    Specified by:
    
    getConnectedAtomsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedAtomsList in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected atoms
  - getConnectedBondsList
```
public List<IBond> getConnectedBondsList(IAtom atom)
```
    Returns the bonds connected connected to the specified atom.
    
    Specified by:
    
    getConnectedBondsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedBondsList in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected bonds
  - getConnectedLonePairsList
```
public List<ILonePair> getConnectedLonePairsList(IAtom atom)
```
    Returns the lone pairs connected connected to the specified atom.
    
    Specified by:
    
    getConnectedLonePairsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedLonePairsList in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected lone pairs
  - getConnectedSingleElectronsList
```
public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)
```
    Returns the single electrons connected connected to the specified atom.
    
    Specified by:
    
    getConnectedSingleElectronsList in interface IAtomContainer
    
    Overrides:
    
    getConnectedSingleElectronsList in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected lone pairs
  - getConnectedElectronContainersList
```
public List<IElectronContainer> getConnectedElectronContainersList(IAtom atom)
```
    Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
    
    Specified by:
    
    getConnectedElectronContainersList in interface IAtomContainer
    
    Overrides:
    
    getConnectedElectronContainersList in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected lone pairs
  - getConnectedAtomsCount
```
public int getConnectedAtomsCount(IAtom atom)
```
    Returns the number of connected atoms (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.
    
    Specified by:
    
    getConnectedAtomsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedAtomsCount in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
  - getConnectedBondsCount
```
public int getConnectedBondsCount(IAtom atom)
```
    Returns the number of connected bonds (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.
    
    Specified by:
    
    getConnectedBondsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedBondsCount in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
  - getConnectedLonePairsCount
```
public int getConnectedLonePairsCount(IAtom atom)
```
    Returns the number of lone pairs connected to the specified atom.
    
    Specified by:
    
    getConnectedLonePairsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedLonePairsCount in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
  - getConnectedSingleElectronsCount
```
public int getConnectedSingleElectronsCount(IAtom atom)
```
    Returns the number of single electrons connected to the specified atom.
    
    Specified by:
    
    getConnectedSingleElectronsCount in interface IAtomContainer
    
    Overrides:
    
    getConnectedSingleElectronsCount in class AtomContainer
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
  - getBondOrderSum
```
public double getBondOrderSum(IAtom atom)
```
    Returns the sum of the bond orders for a given Atom.
    
    Specified by:
    
    getBondOrderSum in interface IAtomContainer
    
    Overrides:
    
    getBondOrderSum in class AtomContainer
    
    Parameters:
    
    atom - The atom
    
    Returns:
    
    The number of bondorders for this atom
  - getMaximumBondOrder
```
public IBond.Order getMaximumBondOrder(IAtom atom)
```
    Returns the maximum bond order that this atom currently has in the context of this AtomContainer. If the atom has no bonds but does have implicit hydrogens the minimum bond order is IBond.Order.SINGLE, otherwise the bond is unset IBond.Order.UNSET.
    
    Specified by:
    
    getMaximumBondOrder in interface IAtomContainer
    
    Overrides:
    
    getMaximumBondOrder in class AtomContainer
    
    Parameters:
    
    atom - The atom
    
    Returns:
    
    The maximum bond order that this atom currently has
  - getMinimumBondOrder
```
public IBond.Order getMinimumBondOrder(IAtom atom)
```
    Returns the minimum bond order that this atom currently has in the context of this AtomContainer. If the atom has no bonds but does have implicit hydrogens the minimum bond order is IBond.Order.SINGLE, otherwise the bond is unset IBond.Order.UNSET.
    
    Specified by:
    
    getMinimumBondOrder in interface IAtomContainer
    
    Overrides:
    
    getMinimumBondOrder in class AtomContainer
    
    Parameters:
    
    atom - The atom
    
    Returns:
    
    The minimum bond order that this atom currently has
  - add
```
public void add(IAtomContainer atomContainer)
```
    Adds all atoms and electronContainers of a given atomcontainer to this container.
    
    Specified by:
    
    add in interface IAtomContainer
    
    Overrides:
    
    add in class AtomContainer
    
    Parameters:
    
    atomContainer - The atomcontainer to be added
  - addAtom
```
public void addAtom(IAtom atom)
```
    Adds an atom to this container.
    
    Specified by:
    
    addAtom in interface IAtomContainer
    
    Overrides:
    
    addAtom in class AtomContainer
    
    Parameters:
    
    atom - The atom to be added to this container
  - addBond
```
public void addBond(IBond bond)
```
    Adds a Bond to this AtomContainer.
    
    Specified by:
    
    addBond in interface IAtomContainer
    
    Overrides:
    
    addBond in class AtomContainer
    
    Parameters:
    
    bond - The bond to added to this container
  - addLonePair
```
public void addLonePair(ILonePair ec)
```
    Adds a lone pair to this AtomContainer.
    
    Specified by:
    
    addLonePair in interface IAtomContainer
    
    Overrides:
    
    addLonePair in class AtomContainer
    
    Parameters:
    
    ec - The LonePair to added to this container
  - addSingleElectron
```
public void addSingleElectron(ISingleElectron ec)
```
    Adds a single electron to this AtomContainer.
    
    Specified by:
    
    addSingleElectron in interface IAtomContainer
    
    Overrides:
    
    addSingleElectron in class AtomContainer
    
    Parameters:
    
    ec - The SingleElectron to added to this container
  - addElectronContainer
```
public void addElectronContainer(IElectronContainer electronContainer)
```
    Adds a ElectronContainer to this AtomContainer.
    
    Specified by:
    
    addElectronContainer in interface IAtomContainer
    
    Overrides:
    
    addElectronContainer in class AtomContainer
    
    Parameters:
    
    electronContainer - The ElectronContainer to added to this container
  - remove
```
public void remove(IAtomContainer atomContainer)
```
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    
    Specified by:
    
    remove in interface IAtomContainer
    
    Overrides:
    
    remove in class AtomContainer
    
    Parameters:
    
    atomContainer - The atomcontainer to be removed
  - removeElectronContainer
```
public IElectronContainer removeElectronContainer(int position)
```
    Removes the bond at the given position from this container.
    
    Specified by:
    
    removeElectronContainer in interface IAtomContainer
    
    Overrides:
    
    removeElectronContainer in class AtomContainer
    
    Parameters:
    
    position - The position of the bond in the electronContainers array
    
    Returns:
    
    the IElectronContainer that was removed
  - removeElectronContainer
```
public void removeElectronContainer(IElectronContainer electronContainer)
```
    Removes this ElectronContainer from this container.
    
    Specified by:
    
    removeElectronContainer in interface IAtomContainer
    
    Overrides:
    
    removeElectronContainer in class AtomContainer
    
    Parameters:
    
    electronContainer - The electronContainer to be removed
  - removeAtomOnly
```
public void removeAtomOnly(int position)
```
    Unsafely remove atom at index.
    Removes the atom at the given position from the AtomContainer. Note that the electronContainers are unaffected: you also have to take care of removing all electronContainers to this atom from the container manually.
    
    Specified by:
    
    removeAtomOnly in interface IAtomContainer
    
    Overrides:
    
    removeAtomOnly in class AtomContainer
    
    Parameters:
    
    position - The position of the atom to be removed.
  - removeAtomOnly
```
public void removeAtomOnly(IAtom atom)
```
    Unsafely remove atom.
    Removes the given atom from the AtomContainer. Note that the electronContainers are unaffected: you also have to take care of removeing all electronContainers to this atom from the container.
    
    Specified by:
    
    removeAtomOnly in interface IAtomContainer
    
    Overrides:
    
    removeAtomOnly in class AtomContainer
    
    Parameters:
    
    atom - The atom to be removed
  - removeBond
```
public IBond removeBond(int pos)
```
    Removes the bond at the given position from the AtomContainer.
    
    Specified by:
    
    removeBond in interface IAtomContainer
    
    Overrides:
    
    removeBond in class AtomContainer
    
    Parameters:
    
    pos - The position of the bond to be removed.
    
    Returns:
    
    the bond at the given position
  - removeBond
```
public IBond removeBond(IAtom atom1,
                        IAtom atom2)
```
    Removes the bond that connects the two given atoms.
    
    Specified by:
    
    removeBond in interface IAtomContainer
    
    Overrides:
    
    removeBond in class AtomContainer
    
    Parameters:
    
    atom1 - The first atom
    
    atom2 - The second atom
    
    Returns:
    
    The bond that connects the two atoms
  - removeBond
```
public void removeBond(IBond bond)
```
    Removes the bond from this container.
    
    Specified by:
    
    removeBond in interface IAtomContainer
    
    Overrides:
    
    removeBond in class AtomContainer
    
    Parameters:
    
    bond - The bond to be removed.
  - removeLonePair
```
public ILonePair removeLonePair(int pos)
```
    Removes the lone pair at the given position from the AtomContainer.
    
    Specified by:
    
    removeLonePair in interface IAtomContainer
    
    Overrides:
    
    removeLonePair in class AtomContainer
    
    Parameters:
    
    pos - The position of the LonePair to be removed.
    
    Returns:
    
    The removed ILonePair.
  - removeLonePair
```
public void removeLonePair(ILonePair ec)
```
    Removes the lone pair from the AtomContainer.
    
    Specified by:
    
    removeLonePair in interface IAtomContainer
    
    Overrides:
    
    removeLonePair in class AtomContainer
    
    Parameters:
    
    ec - The LonePair to be removed.
  - removeSingleElectron
```
public ISingleElectron removeSingleElectron(int pos)
```
    Removes the single electron at the given position from the AtomContainer.
    
    Specified by:
    
    removeSingleElectron in interface IAtomContainer
    
    Overrides:
    
    removeSingleElectron in class AtomContainer
    
    Parameters:
    
    pos - The position of the SingleElectron to be removed.
    
    Returns:
    
    The removed ISingleElectron
  - removeSingleElectron
```
public void removeSingleElectron(ISingleElectron ec)
```
    Removes the single electron from the AtomContainer.
    
    Specified by:
    
    removeSingleElectron in interface IAtomContainer
    
    Overrides:
    
    removeSingleElectron in class AtomContainer
    
    Parameters:
    
    ec - The SingleElectron to be removed.
  - removeAtom
```
public void removeAtom(IAtom atom)
```
    Safely remove an atom from the container.
    Removes a single atom from the container updating all internal state to be consistent. All bonds connected to the atom will be deleted as well as all stereo elements. If multiple atoms/bonds are being deleted they should be gathered into a single transaction and removed with IAtomContainer.remove(IAtomContainer).
    If you are removing hydrogens one of the utility methods (e.g. AtomContainerManipulator.removeHydrogens(IAtomContainer)) is preferable.
    
    Specified by:
    
    removeAtom in interface IAtomContainer
    
    Overrides:
    
    removeAtom in class AtomContainer
    
    Parameters:
    
    atom - the atom to be removed
  - removeAllElements
```
public void removeAllElements()
```
    Removes all atoms, bonds and stereo elements from this container.
    
    Specified by:
    
    removeAllElements in interface IAtomContainer
    
    Overrides:
    
    removeAllElements in class AtomContainer
  - removeAllElectronContainers
```
public void removeAllElectronContainers()
```
    Removes electronContainers from this container.
    
    Specified by:
    
    removeAllElectronContainers in interface IAtomContainer
    
    Overrides:
    
    removeAllElectronContainers in class AtomContainer
  - removeAllBonds
```
public void removeAllBonds()
```
    Removes all Bonds from this container.
    
    Specified by:
    
    removeAllBonds in interface IAtomContainer
    
    Overrides:
    
    removeAllBonds in class AtomContainer
  - addBond
```
public void addBond(int atom1,
                    int atom2,
                    IBond.Order order,
                    IBond.Stereo stereo)
```
    Adds a bond to this container.
    
    Specified by:
    
    addBond in interface IAtomContainer
    
    Overrides:
    
    addBond in class AtomContainer
    
    Parameters:
    
    atom1 - Id of the first atom of the Bond in [0,..]
    
    atom2 - Id of the second atom of the Bond in [0,..]
    
    order - Bondorder
    
    stereo - Stereochemical orientation
  - addBond
```
public void addBond(int atom1,
                    int atom2,
                    IBond.Order order)
```
    Adds a bond to this container.
    
    Specified by:
    
    addBond in interface IAtomContainer
    
    Overrides:
    
    addBond in class AtomContainer
    
    Parameters:
    
    atom1 - Id of the first atom of the Bond in [0,..]
    
    atom2 - Id of the second atom of the Bond in [0,..]
    
    order - Bondorder
  - addLonePair
```
public void addLonePair(int atomID)
```
    Adds a LonePair to this Atom.
    
    Specified by:
    
    addLonePair in interface IAtomContainer
    
    Overrides:
    
    addLonePair in class AtomContainer
    
    Parameters:
    
    atomID - The atom number to which the LonePair is added in [0,..]
  - addSingleElectron
```
public void addSingleElectron(int atomID)
```
    Adds a SingleElectron to this Atom.
    
    Specified by:
    
    addSingleElectron in interface IAtomContainer
    
    Overrides:
    
    addSingleElectron in class AtomContainer
    
    Parameters:
    
    atomID - The atom number to which the SingleElectron is added in [0,..]
  - contains
```
public boolean contains(IAtom atom)
```
    True, if the AtomContainer contains the given atom object.
    
    Specified by:
    
    contains in interface IAtomContainer
    
    Overrides:
    
    contains in class AtomContainer
    
    Parameters:
    
    atom - the atom this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given atom object
  - contains
```
public boolean contains(IBond bond)
```
    True, if the AtomContainer contains the given bond object.
    
    Specified by:
    
    contains in interface IAtomContainer
    
    Overrides:
    
    contains in class AtomContainer
    
    Parameters:
    
    bond - the bond this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given bond object
  - contains
```
public boolean contains(ILonePair ec)
```
    True, if the AtomContainer contains the given LonePair object.
    
    Specified by:
    
    contains in interface IAtomContainer
    
    Overrides:
    
    contains in class AtomContainer
    
    Parameters:
    
    ec - the LonePair this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given LonePair object
  - contains
```
public boolean contains(ISingleElectron ec)
```
    True, if the AtomContainer contains the given SingleElectron object.
    
    Specified by:
    
    contains in interface IAtomContainer
    
    Overrides:
    
    contains in class AtomContainer
    
    Parameters:
    
    ec - the SingleElectron this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given SingleElectron object
  - contains
```
public boolean contains(IElectronContainer electronContainer)
```
    True, if the AtomContainer contains the given ElectronContainer object.
    
    Specified by:
    
    contains in interface IAtomContainer
    
    Overrides:
    
    contains in class AtomContainer
    
    Parameters:
    
    electronContainer - ElectronContainer that is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given bond object
  - addListener
```
public void addListener(IChemObjectListener col)
```
    Use this to add yourself to this IChemObject as a listener. In order to do so, you must implement the ChemObjectListener Interface.
    
    Specified by:
    
    addListener in interface IChemObject
    
    Overrides:
    
    addListener in class ChemObject
    
    Parameters:
    
    col - the ChemObjectListener
    
    See Also:
    
    ChemObject.removeListener(org.openscience.cdk.interfaces.IChemObjectListener)
  - getListenerCount
```
public int getListenerCount()
```
    Returns the number of ChemObjectListeners registered with this object.
    
    Specified by:
    
    getListenerCount in interface IChemObject
    
    Overrides:
    
    getListenerCount in class ChemObject
    
    Returns:
    
    the number of registered listeners.
  - removeListener
```
public void removeListener(IChemObjectListener col)
```
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject. It will then not be notified of change in this object anymore.
    
    Specified by:
    
    removeListener in interface IChemObject
    
    Overrides:
    
    removeListener in class ChemObject
    
    Parameters:
    
    col - The ChemObjectListener to be removed
    
    See Also:
    
    ChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)
  - notifyChanged
```
public void notifyChanged()
```
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    
    Specified by:
    
    notifyChanged in interface IChemObject
    
    Overrides:
    
    notifyChanged in class ChemObject
  - notifyChanged
```
public void notifyChanged(IChemObjectChangeEvent evt)
```
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.
    
    Specified by:
    
    notifyChanged in interface IChemObject
    
    Overrides:
    
    notifyChanged in class ChemObject
    
    Parameters:
    
    evt - A ChemObjectChangeEvent pointing to the source of where the change happened
  - setProperty
```
public void setProperty(Object description,
                        Object property)
```
    Sets a property for a IChemObject.
    
    Specified by:
    
    setProperty in interface IChemObject
    
    Overrides:
    
    setProperty in class ChemObject
    
    Parameters:
    
    description - An object description of the property (most likely a unique string)
    
    property - An object with the property itself
    
    See Also:
    
    ChemObject.getProperty(java.lang.Object), ChemObject.removeProperty(java.lang.Object)
  - removeProperty
```
public void removeProperty(Object description)
```
    Removes a property for a IChemObject.
    
    Specified by:
    
    removeProperty in interface IChemObject
    
    Overrides:
    
    removeProperty in class ChemObject
    
    Parameters:
    
    description - The object description of the property (most likely a unique string)
    
    See Also:
    
    ChemObject.setProperty(java.lang.Object, java.lang.Object), ChemObject.getProperty(java.lang.Object)
  - getProperty
```
public <T> T getProperty(Object description)
```
    Returns a property for the IChemObject.
    
    Specified by:
    
    getProperty in interface IChemObject
    
    Overrides:
    
    getProperty in class ChemObject
    
    Type Parameters:
    
    T - generic return type
    
    Parameters:
    
    description - An object description of the property (most likely a unique string)
    
    Returns:
    
    The object containing the property. Returns null if propert is not set.
    
    See Also:
    
    ChemObject.setProperty(java.lang.Object, java.lang.Object), ChemObject.removeProperty(java.lang.Object)
  - getProperties
```
public Map<Object,Object> getProperties()
```
    Returns a Map with the IChemObject's properties.
    
    Specified by:
    
    getProperties in interface IChemObject
    
    Overrides:
    
    getProperties in class ChemObject
    
    Returns:
    
    The object's properties as an Hashtable
    
    See Also:
    
    ChemObject.addProperties(java.util.Map<java.lang.Object, java.lang.Object>)
  - getID
```
public String getID()
```
    Returns the identifier (ID) of this object.
    
    Specified by:
    
    getID in interface IChemObject
    
    Overrides:
    
    getID in class ChemObject
    
    Returns:
    
    a String representing the ID value
    
    See Also:
    
    ChemObject.setID(java.lang.String)
  - setID
```
public void setID(String identifier)
```
    Sets the identifier (ID) of this object.
    
    Specified by:
    
    setID in interface IChemObject
    
    Overrides:
    
    setID in class ChemObject
    
    Parameters:
    
    identifier - a String representing the ID value
    
    See Also:
    
    ChemObject.getID()
  - setFlag
```
public void setFlag(int flagType,
                    boolean flagValue)
```
    Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC or IChemObject.VISITED). The flags are intrinsic internal properties and should not be used to store custom values, please use IChemObject.setProperty(Object, Object).
    // set this chem object to be aromatic chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE); // ... // indicate we have visited this chem object chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
    Specified by:
    
    setFlag in interface IChemObject
    
    Overrides:
    
    setFlag in class ChemObject
    
    Parameters:
    
    flagType - flag to set the value for
    
    flagValue - value to assign to flag
    
    See Also:
    
    IChemObject.getFlag(int)
  - getFlag
```
public boolean getFlag(int flagType)
```
    Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC).
    if(chemObject.getFlag(CDKConstants.ISAROMATIC)){ // handle aromatic flag on this chem object }
    Specified by:
    
    getFlag in interface IChemObject
    
    Overrides:
    
    getFlag in class ChemObject
    
    Parameters:
    
    flagType - flag to retrieve the value of
    
    Returns:
    
    true if the flag flag_type is set
    
    See Also:
    
    IChemObject.setFlag(int, boolean)
  - addProperties
```
public void addProperties(Map<Object,Object> properties)
```
    Sets the properties of this object.
    
    Specified by:
    
    addProperties in interface IChemObject
    
    Overrides:
    
    addProperties in class ChemObject
    
    Parameters:
    
    properties - a Hashtable specifying the property values
    
    See Also:
    
    ChemObject.getProperties()
  - getFlags
```
public boolean[] getFlags()
```
    Returns the whole set of flags.
    
    Specified by:
    
    getFlags in interface IChemObject
    
    Overrides:
    
    getFlags in class ChemObject
    
    Returns:
    
    the flags.
    
    See Also:
    
    ChemObject.setFlags(boolean[])
  - setFlags
```
public void setFlags(boolean[] flagsNew)
```
    Sets the whole set of flags.
    
    Specified by:
    
    setFlags in interface IChemObject
    
    Overrides:
    
    setFlags in class ChemObject
    
    Parameters:
    
    flagsNew - the new flags.
    
    See Also:
    
    ChemObject.getFlags()
  - clone
```
public IAtomContainer clone()
                     throws CloneNotSupportedException
```
    Clones this IChemObject. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.
    
    Specified by:
    
    clone in interface IAtomContainer
    
    Specified by:
    
    clone in interface IChemObject
    
    Overrides:
    
    clone in class AtomContainer
    
    Returns:
    
    The cloned object
    
    Throws:
    
    CloneNotSupportedException - if the IChemObject cannot be cloned
  - getBuilder
```
public IChemObjectBuilder getBuilder()
```
    Returns a IChemObjectBuilder for the data classes that extend this class.
    
    Specified by:
    
    getBuilder in interface ICDKObject
    
    Overrides:
    
    getBuilder in class ChemObject
    
    Returns:
    
    The IChemObjectBuilder matching this ICDKObject
  - isEmpty
```
public boolean isEmpty()
```
    Indicates whether this container is empty. The container is considered empty if there are no atoms. Bonds are not checked as a graph with no vertexes can not have edges.
    
    Specified by:
    
    isEmpty in interface IAtomContainer
    
    Overrides:
    
    isEmpty in class AtomContainer
    
    Returns:
    
    whether the container is empty

Class DebugAtomContainer

Field Summary

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.AtomContainer

Methods inherited from class org.openscience.cdk.ChemObject

Methods inherited from class java.lang.Object

Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener

Constructor Detail

DebugAtomContainer

DebugAtomContainer

DebugAtomContainer

Method Detail

addStereoElement

setStereoElements

stereoElements

setAtoms

setAtom

getAtom

getBond

getLonePair

getSingleElectron

atoms

bonds

lonePairs

singleElectrons

electronContainers

getFirstAtom

getLastAtom

indexOf

indexOf

indexOf

indexOf

getElectronContainer

getBond

getAtomCount

getBondCount

getLonePairCount

getSingleElectronCount

getElectronContainerCount

getConnectedAtomsList

getConnectedBondsList

getConnectedLonePairsList

getConnectedSingleElectronsList

getConnectedElectronContainersList

getConnectedAtomsCount

getConnectedBondsCount

getConnectedLonePairsCount

getConnectedSingleElectronsCount

getBondOrderSum

getMaximumBondOrder

getMinimumBondOrder

add

addAtom

addBond

addLonePair

addSingleElectron

addElectronContainer

remove

removeElectronContainer

removeElectronContainer

removeAtomOnly

removeAtomOnly

removeBond

removeBond

removeBond

removeLonePair

removeLonePair

removeSingleElectron

removeSingleElectron

removeAtom

removeAllElements

removeAllElectronContainers

removeAllBonds

addBond

addBond

addLonePair