IAtomContainer (cdk 2.5 API)

All Superinterfaces:

Cloneable, ICDKObject, IChemObject, IChemObjectListener

All Known Subinterfaces:

IAminoAcid, IBioPolymer, ICrystal, IMonomer, IPDBMonomer, IPDBPolymer, IPolymer, IQueryAtomContainer, IRing, IStrand

All Known Implementing Classes:

AminoAcid, AminoAcid, AtomContainer, AtomContainer, BioPolymer, BioPolymer, ChargeGroup, Crystal, Crystal, DebugAminoAcid, DebugAtomContainer, DebugBioPolymer, DebugCrystal, DebugMonomer, DebugPDBMonomer, DebugPDBPolymer, DebugPolymer, DebugRing, DebugStrand, MDMolecule, Monomer, Monomer, PDBMonomer, PDBMonomer, PDBPolymer, PDBPolymer, PDBStrand, PharmacophoreQuery, Polymer, Polymer, QueryAtomContainer, Residue, Ring, Ring, Strand, Strand
```
public interface IAtomContainer
extends IChemObject, IChemObjectListener
```
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.

Looping over all IBonds in the IAtomContainer is typically done like:
```
  for (IBond bond : atomContainer.bonds()) {
    // do something
  }
  
```
If you do need an explicit Iterator then use
```
 Iterator<IBond> bondIter = atomContainer.bonds().iterator();
 
```
Author:

steinbeck

Source code:
master

Belongs to CDK module:
interfaces

Created on:

2000-10-02

Method Summary

All Methods Instance Methods Abstract Methods Deprecated Methods
Modifier and Type	Method and 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(IBond bond)` Adds a Bond to this AtomContainer.
`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`	`addElectronContainer(IElectronContainer electronContainer)` Adds a ElectronContainer to this AtomContainer.
`void`	`addLonePair(ILonePair lonePair)` Adds a lone pair to this AtomContainer.
`void`	`addLonePair(int atomID)` Adds a LonePair to this Atom.
`void`	`addSingleElectron(int atomID)` Adds a SingleElectron to this Atom.
`void`	`addSingleElectron(ISingleElectron singleElectron)` Adds a single electron to this AtomContainer.
`void`	`addStereoElement(IStereoElement element)` 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()` Returns a deep clone of 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 lonePair)` True, if the AtomContainer contains the given LonePair object.
`boolean`	`contains(ISingleElectron singleElectron)` 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 < `getAtomCount()`.
`int`	`getAtomCount()` Returns the number of Atoms in this Container.
`int`	`getAtomNumber(IAtom atom)` Deprecated. use `indexOf(IAtom)`
`IBond`	`getBond(IAtom atom1, IAtom atom2)` Returns the bond that connects the two given atoms.
`IBond`	`getBond(int idx)` Get the bond at the specified idx, the index should be in the range 0 ≤ idx < `getBondCount()`.
`int`	`getBondCount()` Returns the number of Bonds in this Container.
`int`	`getBondNumber(IAtom atom1, IAtom atom2)` Deprecated. use `indexOf(IBond)`
`int`	`getBondNumber(IBond bond)` Deprecated. use `indexOf(IBond)`
`double`	`getBondOrderSum(IAtom atom)` Returns the sum of the bond orders for a given Atom.
`int`	`getConnectedAtomsCount(IAtom atom)` Deprecated. use `getConnectedBondsCount(IAtom)`
`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.
`int`	`getConnectedBondsCount(int idx)` Returns the number of connected bonds (explicit degree) to atom at the specified index.
`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()` Deprecated. use `getAtom(int)`
`IAtom`	`getLastAtom()` Deprecated. use `getAtom(int)`
`ILonePair`	`getLonePair(int idx)` Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < `getLonePairCount()`.
`int`	`getLonePairCount()` Returns the number of LonePairs in this Container.
`int`	`getLonePairNumber(ILonePair lonePair)` Deprecated. use `indexOf(ILonePair)`
`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.
`ISingleElectron`	`getSingleElectron(int idx)` Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < `getSingleElectronCount()`.
`int`	`getSingleElectronCount()` Returns the number of the single electrons in this container.
`int`	`getSingleElectronNumber(ISingleElectron singleElectron)` Deprecated. use `indexOf(ISingleElectron)`
`String`	`getTitle()` Access the title of the record.
`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`	`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`	`removeAtom(int pos)` Safely remove an atom from the container.
`void`	`removeAtomAndConnectedElectronContainers(IAtom atom)` Deprecated. Method has be renamed `removeAtom(IAtom)`.
`void`	`removeAtomOnly(IAtom atom)` Unsafely remove atom.
`void`	`removeAtomOnly(int position)` Unsafely remove atom at index.
`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.
`IBond`	`removeBond(int position)` Removes the bond at the given position from the AtomContainer.
`void`	`removeElectronContainer(IElectronContainer electronContainer)` Removes this ElectronContainer from this container.
`IElectronContainer`	`removeElectronContainer(int position)` Removes the bond at the given position from this container.
`void`	`removeLonePair(ILonePair lonePair)` Removes the lone pair from the AtomContainer.
`ILonePair`	`removeLonePair(int position)` Removes the lone pair at the given position from the AtomContainer.
`ISingleElectron`	`removeSingleElectron(int position)` Removes the single electron at the given position from the AtomContainer.
`void`	`removeSingleElectron(ISingleElectron singleElectron)` Removes the single electron from the AtomContainer.
`void`	`setAtom(int idx, 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`	`setBonds(IBond[] bonds)` Sets the array of bonds of this AtomContainer.
`void`	`setStereoElements(List<IStereoElement> elements)` Set the stereo elements - this will replace the existing instance with a new instance.
`void`	`setTitle(String title)` Modify the title of the record.
`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 interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder

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

- Method Detail
  - addStereoElement
```
void addStereoElement(IStereoElement element)
```
    Adds a stereo element to this container.
    
    Parameters:
    
    element - The new IStereoElement for this container
    
    See Also:
    
    stereoElements()
  - setStereoElements
```
void setStereoElements(List<IStereoElement> elements)
```
    Set the stereo elements - this will replace the existing instance with a new instance.
    
    Parameters:
    
    elements - the new stereo elements
  - stereoElements
```
Iterable<IStereoElement> stereoElements()
```
    Returns the stereo elements defined for this atom container.
    
    Returns:
    
    An Iterable of IStereoElements.
    
    See Also:
    
    addStereoElement(IStereoElement)
  - setAtoms
```
void setAtoms(IAtom[] atoms)
```
    Sets the array of atoms of this AtomContainer.
    
    Parameters:
    
    atoms - The array of atoms to be assigned to this AtomContainer
    
    See Also:
    
    atoms()
  - setBonds
```
void setBonds(IBond[] bonds)
```
    Sets the array of bonds of this AtomContainer.
    
    Parameters:
    
    bonds - The array of bonds to be assigned to this AtomContainer
    
    See Also:
    
    bonds()
  - setAtom
```
void setAtom(int idx,
             IAtom atom)
```
    Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
    
    Parameters:
    
    idx - The index of the atom to be set.
    
    atom - The atom to be stored at position idx
    
    Throws:
    
    IndexOutOfBoundsException - index is out of bounds
    
    IllegalArgumentException - the atom could not be set
    
    See Also:
    
    getAtom(int)
  - getAtom
```
IAtom getAtom(int idx)
```
    Get the atom at the specified idx, the index should be in the range 0 ≤ idx < getAtomCount().
    
    Parameters:
    
    idx - atom index
    
    Returns:
    
    the atom stored at the index
    
    Throws:
    
    IndexOutOfBoundsException - the index is out of range
    
    See Also:
    
    setAtom(int, org.openscience.cdk.interfaces.IAtom)
  - getBond
```
IBond getBond(int idx)
```
    Get the bond at the specified idx, the index should be in the range 0 ≤ idx < getBondCount().
    
    Parameters:
    
    idx - bond index
    
    Returns:
    
    the bond stored at the index
    
    Throws:
    
    IndexOutOfBoundsException - the index is out of range
  - getLonePair
```
ILonePair getLonePair(int idx)
```
    Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < getLonePairCount().
    
    Parameters:
    
    idx - lone pair index
    
    Returns:
    
    the lone pair stored at the index
    
    Throws:
    
    IndexOutOfBoundsException - the index is out of range
  - getSingleElectron
```
ISingleElectron getSingleElectron(int idx)
```
    Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < getSingleElectronCount().
    
    Parameters:
    
    idx - single electron index
    
    Returns:
    
    the single electron stored at the index
    
    Throws:
    
    IndexOutOfBoundsException - the index is out of range
  - atoms
```
Iterable<IAtom> atoms()
```
    Returns an Iterable for looping over all atoms in this container.
    
    Returns:
    
    An Iterable with the atoms in this container
  - bonds
```
Iterable<IBond> bonds()
```
    Returns an Iterable for looping over all bonds in this container.
    
    Returns:
    
    An Iterable with the bonds in this container
  - lonePairs
```
Iterable<ILonePair> lonePairs()
```
    Returns an Iterable for looping over all lone pairs in this container.
    
    Returns:
    
    An Iterable with the lone pairs in this container
  - singleElectrons
```
Iterable<ISingleElectron> singleElectrons()
```
    Returns an Iterable for looping over all single electrons in this container.
    
    Returns:
    
    An Iterable with the single electrons in this container
  - electronContainers
```
Iterable<IElectronContainer> electronContainers()
```
    Returns an Iterable for looping over all electron containers in this container.
    
    Returns:
    
    An Iterable with the electron containers in this container
  - getFirstAtom
```
@Deprecated
IAtom getFirstAtom()
```
    Deprecated. use getAtom(int)
    
    Returns the atom at position 0 in the container.
    
    Returns:
    
    The atom at position 0 .
  - getLastAtom
```
@Deprecated
IAtom getLastAtom()
```
    Deprecated. use getAtom(int)
    
    Returns the atom at the last position in the container.
    
    Returns:
    
    The atom at the last position
  - getAtomNumber
```
@Deprecated
int getAtomNumber(IAtom atom)
```
    Deprecated. use indexOf(IAtom)
    
    Returns the position of a given atom in the atoms array. It returns -1 if the atom atom does not exist.
    
    Parameters:
    
    atom - The atom to be sought
    
    Returns:
    
    The Position of the atom in the atoms array in [0,..].
  - getBondNumber
```
@Deprecated
int getBondNumber(IAtom atom1,
                              IAtom atom2)
```
    Deprecated. use indexOf(IBond)
    
    Returns the position of the bond between two given atoms in the electronContainers array. It returns -1 if the bond does not exist.
    
    Parameters:
    
    atom1 - The first atom
    
    atom2 - The second atom
    
    Returns:
    
    The Position of the bond between a1 and a2 in the electronContainers array.
  - getBondNumber
```
@Deprecated
int getBondNumber(IBond bond)
```
    Deprecated. use indexOf(IBond)
    
    Returns the position of a given bond in the electronContainers array. It returns -1 if the bond does not exist.
    
    Parameters:
    
    bond - The bond to be sought
    
    Returns:
    
    The Position of the bond in the electronContainers array in [0,..].
  - getLonePairNumber
```
@Deprecated
int getLonePairNumber(ILonePair lonePair)
```
    Deprecated. use indexOf(ILonePair)
    
    Returns the position of a given lone pair in the lone pair array. It returns -1 if the lone pair does not exist.
    
    Parameters:
    
    lonePair - The lone pair to be sought
    
    Returns:
    
    The Position of the lone pair in the array..
  - getSingleElectronNumber
```
int getSingleElectronNumber(ISingleElectron singleElectron)
```
    Deprecated. use indexOf(ISingleElectron)
    
    Returns the position of a given single electron in the single electron array. It returns -1 if the single electron does not exist.
    
    Parameters:
    
    singleElectron - The single electron to be sought
    
    Returns:
    
    The Position of the single electron in the array.
  - indexOf
```
int indexOf(IAtom atom)
```
    Access the storage index of an atom.
    
    Parameters:
    
    atom - atom instance to find
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
int indexOf(IBond bond)
```
    Access the storage index of a bond.
    
    Parameters:
    
    bond - bond instance to find
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
int indexOf(ISingleElectron electron)
```
    Access the storage index of a single electron (radical).
    
    Parameters:
    
    electron - the electron
    
    Returns:
    
    the index, -1 if not found
  - indexOf
```
int indexOf(ILonePair pair)
```
    Access the storage index of a long pair.
    
    Parameters:
    
    pair - the long pair
    
    Returns:
    
    the index, -1 if not found
  - getElectronContainer
```
IElectronContainer getElectronContainer(int number)
```
    Returns the ElectronContainer at position number in the container.
    
    Parameters:
    
    number - The position of the ElectronContainer to be returned.
    
    Returns:
    
    The ElectronContainer at position number.
    
    See Also:
    
    addElectronContainer(IElectronContainer)
  - getBond
```
IBond getBond(IAtom atom1,
              IAtom atom2)
```
    Returns the bond that connects the two given atoms.
    
    Parameters:
    
    atom1 - The first atom
    
    atom2 - The second atom
    
    Returns:
    
    The bond that connects the two atoms
  - getAtomCount
```
int getAtomCount()
```
    Returns the number of Atoms in this Container.
    
    Returns:
    
    The number of Atoms in this Container
  - getBondCount
```
int getBondCount()
```
    Returns the number of Bonds in this Container.
    
    Returns:
    
    The number of Bonds in this Container
  - getLonePairCount
```
int getLonePairCount()
```
    Returns the number of LonePairs in this Container.
    
    Returns:
    
    The number of LonePairs in this Container
  - getSingleElectronCount
```
int getSingleElectronCount()
```
    Returns the number of the single electrons in this container.
    
    Returns:
    
    The number of SingleElectron objects of this AtomContainer
  - getElectronContainerCount
```
int getElectronContainerCount()
```
    Returns the number of ElectronContainers in this Container.
    
    Returns:
    
    The number of ElectronContainers in this Container
  - getConnectedAtomsList
```
List<IAtom> getConnectedAtomsList(IAtom atom)
```
    Returns the atoms connected connected to the specified atom by a bond.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected atoms
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedBondsList
```
List<IBond> getConnectedBondsList(IAtom atom)
```
    Returns the bonds connected connected to the specified atom.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected bonds
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedLonePairsList
```
List<ILonePair> getConnectedLonePairsList(IAtom atom)
```
    Returns the lone pairs connected connected to the specified atom.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected lone pairs
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedSingleElectronsList
```
List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)
```
    Returns the single electrons connected connected to the specified atom.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected lone pairs
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedElectronContainersList
```
List<IElectronContainer> getConnectedElectronContainersList(IAtom atom)
```
    Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    connected lone pairs
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedAtomsCount
```
@Deprecated
int getConnectedAtomsCount(IAtom atom)
```
    Deprecated. use getConnectedBondsCount(IAtom)
    
    Returns the number of connected atoms (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedBondsCount
```
int getConnectedBondsCount(IAtom atom)
```
    Returns the number of connected bonds (explicit degree) to the specified atom. This does not include bonds to implicit hydrogens.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedBondsCount
```
int getConnectedBondsCount(int idx)
```
    Returns the number of connected bonds (explicit degree) to atom at the specified index. This does not include bonds to implicit hydrogens.
    
    Parameters:
    
    idx - the atom idx
    
    Returns:
    
    number of connected bonds
    
    Throws:
    
    IndexOutOfBoundsException - the index is not in range
  - getConnectedLonePairsCount
```
int getConnectedLonePairsCount(IAtom atom)
```
    Returns the number of lone pairs connected to the specified atom.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getConnectedSingleElectronsCount
```
int getConnectedSingleElectronsCount(IAtom atom)
```
    Returns the number of single electrons connected to the specified atom.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    number of connected bonds
    
    Throws:
    
    NoSuchElementException - the atom is not present
  - getBondOrderSum
```
double getBondOrderSum(IAtom atom)
```
    Returns the sum of the bond orders for a given Atom.
    
    Parameters:
    
    atom - The atom
    
    Returns:
    
    The number of bondorders for this atom
  - getMaximumBondOrder
```
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.
    
    Parameters:
    
    atom - The atom
    
    Returns:
    
    The maximum bond order that this atom currently has
    
    Throws:
    
    NoSuchElementException - atom does not belong to this container
  - getMinimumBondOrder
```
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.
    
    Parameters:
    
    atom - The atom
    
    Returns:
    
    The minimum bond order that this atom currently has
    
    Throws:
    
    NoSuchElementException - atom does not belong to this container
  - add
```
void add(IAtomContainer atomContainer)
```
    Adds all atoms and electronContainers of a given atomcontainer to this container.
    
    Parameters:
    
    atomContainer - The atomcontainer to be added
  - addAtom
```
void addAtom(IAtom atom)
```
    Adds an atom to this container.
    
    Parameters:
    
    atom - The atom to be added to this container
  - addBond
```
void addBond(IBond bond)
```
    Adds a Bond to this AtomContainer.
    
    Parameters:
    
    bond - The bond to added to this container
    
    Throws:
    
    NoSuchAtomException - optionally thrown if the atoms of the bond have not yet been added
  - addLonePair
```
void addLonePair(ILonePair lonePair)
```
    Adds a lone pair to this AtomContainer.
    
    Parameters:
    
    lonePair - The LonePair to added to this container
  - addSingleElectron
```
void addSingleElectron(ISingleElectron singleElectron)
```
    Adds a single electron to this AtomContainer.
    
    Parameters:
    
    singleElectron - The SingleElectron to added to this container
  - addElectronContainer
```
void addElectronContainer(IElectronContainer electronContainer)
```
    Adds a ElectronContainer to this AtomContainer.
    
    Parameters:
    
    electronContainer - The ElectronContainer to added to this container
  - remove
```
void remove(IAtomContainer atomContainer)
```
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    
    Parameters:
    
    atomContainer - The atomcontainer to be removed
  - removeAtomOnly
```
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.
    
    Parameters:
    
    position - The position of the atom to be removed.
  - removeAtomOnly
```
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.
    
    Parameters:
    
    atom - The atom to be removed
  - removeBond
```
IBond removeBond(int position)
```
    Removes the bond at the given position from the AtomContainer.
    
    Parameters:
    
    position - The position of the bond to be removed.
    
    Returns:
    
    the bond at the given position
  - removeBond
```
IBond removeBond(IAtom atom1,
                 IAtom atom2)
```
    Removes the bond that connects the two given atoms.
    
    Parameters:
    
    atom1 - The first atom
    
    atom2 - The second atom
    
    Returns:
    
    The bond that connects the two atoms
  - removeBond
```
void removeBond(IBond bond)
```
    Removes the bond from this container.
    
    Parameters:
    
    bond - The bond to be removed.
  - removeLonePair
```
ILonePair removeLonePair(int position)
```
    Removes the lone pair at the given position from the AtomContainer.
    
    Parameters:
    
    position - The position of the LonePair to be removed.
    
    Returns:
    
    The removed ILonePair.
  - removeLonePair
```
void removeLonePair(ILonePair lonePair)
```
    Removes the lone pair from the AtomContainer.
    
    Parameters:
    
    lonePair - The LonePair to be removed.
  - removeSingleElectron
```
ISingleElectron removeSingleElectron(int position)
```
    Removes the single electron at the given position from the AtomContainer.
    
    Parameters:
    
    position - The position of the SingleElectron to be removed.
    
    Returns:
    
    The removed ISingleElectron
  - removeSingleElectron
```
void removeSingleElectron(ISingleElectron singleElectron)
```
    Removes the single electron from the AtomContainer.
    
    Parameters:
    
    singleElectron - The SingleElectron to be removed.
  - removeElectronContainer
```
IElectronContainer removeElectronContainer(int position)
```
    Removes the bond at the given position from this container.
    
    Parameters:
    
    position - The position of the bond in the electronContainers array
    
    Returns:
    
    the IElectronContainer that was removed
  - removeElectronContainer
```
void removeElectronContainer(IElectronContainer electronContainer)
```
    Removes this ElectronContainer from this container.
    
    Parameters:
    
    electronContainer - The electronContainer to be removed
  - removeAtom
```
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 remove(IAtomContainer).
    If you are removing hydrogens one of the utility methods (e.g. AtomContainerManipulator.removeHydrogens(IAtomContainer)) is preferable.
    
    Parameters:
    
    atom - the atom to be removed
  - removeAtom
```
void removeAtom(int pos)
```
    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 remove(IAtomContainer).
    If you are removing hydrogens one of the utility methods (e.g. AtomContainerManipulator.removeHydrogens(IAtomContainer)) is preferable.
    
    Parameters:
    
    pos - the position of the atom to be removed
  - removeAtomAndConnectedElectronContainers
```
@Deprecated
void removeAtomAndConnectedElectronContainers(IAtom atom)
```
    Deprecated. Method has be renamed removeAtom(IAtom).
    
    Safely remove an atom from the container.
    
    See Also:
    
    removeAtom(IAtom)
  - removeAllElements
```
void removeAllElements()
```
    Removes all atoms, bonds and stereo elements from this container.
  - removeAllElectronContainers
```
void removeAllElectronContainers()
```
    Removes electronContainers from this container.
  - removeAllBonds
```
void removeAllBonds()
```
    Removes all Bonds from this container.
  - addBond
```
void addBond(int atom1,
             int atom2,
             IBond.Order order,
             IBond.Stereo stereo)
```
    Adds a bond to this container.
    
    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
```
void addBond(int atom1,
             int atom2,
             IBond.Order order)
```
    Adds a bond to this container.
    
    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
```
void addLonePair(int atomID)
```
    Adds a LonePair to this Atom.
    
    Parameters:
    
    atomID - The atom number to which the LonePair is added in [0,..]
  - addSingleElectron
```
void addSingleElectron(int atomID)
```
    Adds a SingleElectron to this Atom.
    
    Parameters:
    
    atomID - The atom number to which the SingleElectron is added in [0,..]
  - contains
```
boolean contains(IAtom atom)
```
    True, if the AtomContainer contains the given atom object.
    
    Parameters:
    
    atom - the atom this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given atom object
  - contains
```
boolean contains(IBond bond)
```
    True, if the AtomContainer contains the given bond object.
    
    Parameters:
    
    bond - the bond this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given bond object
  - contains
```
boolean contains(ILonePair lonePair)
```
    True, if the AtomContainer contains the given LonePair object.
    
    Parameters:
    
    lonePair - the LonePair this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given LonePair object
  - contains
```
boolean contains(ISingleElectron singleElectron)
```
    True, if the AtomContainer contains the given SingleElectron object.
    
    Parameters:
    
    singleElectron - the SingleElectron this AtomContainer is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given SingleElectron object
  - contains
```
boolean contains(IElectronContainer electronContainer)
```
    True, if the AtomContainer contains the given ElectronContainer object.
    
    Parameters:
    
    electronContainer - ElectronContainer that is searched for
    
    Returns:
    
    True, if the AtomContainer contains the given bond object
  - isEmpty
```
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.
    
    Returns:
    
    whether the container is empty
  - getTitle
```
String getTitle()
```
    Access the title of the record.
    
    Returns:
    
    the title
  - setTitle
```
void setTitle(String title)
```
    Modify the title of the record.
    
    Parameters:
    
    title - the title
  - clone
```
IAtomContainer clone()
              throws CloneNotSupportedException
```
    Returns a deep clone of this IChemObject.
    
    Specified by:
    
    clone in interface IChemObject
    
    Returns:
    
    Object the clone of this IChemObject.
    
    Throws:
    
    CloneNotSupportedException - if the IChemObject cannot be cloned

Interface IAtomContainer

Method Summary

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

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

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

Method Detail

addStereoElement

setStereoElements

stereoElements

setAtoms

setBonds

setAtom

getAtom

getBond

getLonePair

getSingleElectron

atoms

bonds

lonePairs

singleElectrons

electronContainers

getFirstAtom

getLastAtom

getAtomNumber

getBondNumber

getBondNumber

getLonePairNumber

getSingleElectronNumber

indexOf

indexOf

indexOf

indexOf

getElectronContainer

getBond

getAtomCount

getBondCount

getLonePairCount

getSingleElectronCount

getElectronContainerCount

getConnectedAtomsList

getConnectedBondsList

getConnectedLonePairsList

getConnectedSingleElectronsList

getConnectedElectronContainersList

getConnectedAtomsCount

getConnectedBondsCount

getConnectedBondsCount

getConnectedLonePairsCount

getConnectedSingleElectronsCount

getBondOrderSum

getMaximumBondOrder

getMinimumBondOrder

add

addAtom

addBond

addLonePair

addSingleElectron

addElectronContainer

remove

removeAtomOnly

removeAtomOnly

removeBond

removeBond

removeBond

removeLonePair

removeLonePair

removeSingleElectron

removeSingleElectron

removeElectronContainer

removeElectronContainer

removeAtom

removeAtom

removeAtomAndConnectedElectronContainers

removeAllElements

removeAllElectronContainers

removeAllBonds

addBond

addBond

addLonePair

addSingleElectron