Package org.openscience.cdk

Class AtomContainer

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener

Direct Known Subclasses:

Crystal, Monomer, Polymer, Ring, Strand

public class AtomContainer
extends ChemObject
implements IAtomContainer

This class should not be used directly.

Author:

John Mayfield

See Also:

• Serialized Form

Field Summary

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

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
AtomContainer()	Constructs an empty AtomContainer.
AtomContainer(int numAtoms, int numBonds, int numLonePairs, int numSingleElectrons)	Create a new container with the specified capacities.
AtomContainer(IAtomContainer src)	Constructs a shallow copy of the provided IAtomContainer with the same atoms, bonds, electron containers and stereochemistry of another AtomContainer.

Method Summary

Modifier and Type	Method	Description
void	add(IAtomContainer that)
void	addAtom(IAtom atom)
void	addBond(int beg, int end, IBond.Order order, IBond.Display display)
void	addBond(int beg, int end, IBond.Order order, IBond.Stereo stereo)
void	addBond(IBond bond)
void	addElectronContainer(IElectronContainer ec)
void	addLonePair(int idx)
void	addLonePair(ILonePair lp)
void	addSingleElectron(int idx)
void	addSingleElectron(ISingleElectron e)
void	addStereoElement(IStereoElement element)
Iterable<IAtom>	atoms()
Iterable<IBond>	bonds()
IAtomContainer	clone()	Clones this IChemObject.
boolean	contains(IAtom atom)
boolean	contains(IBond bond)
boolean	contains(IElectronContainer electronContainer)
boolean	contains(ILonePair lonepair)
boolean	contains(ISingleElectron electron)
Iterable<IElectronContainer>	electronContainers()
IAtom	getAtom(int idx)
int	getAtomCount()
int	getAtomNumber(IAtom atom)
IBond	getBond(int idx)
IBond	getBond(IAtom beg, IAtom end)
int	getBondCount()
int	getBondNumber(IAtom beg, IAtom end)
int	getBondNumber(IBond bond)
double	getBondOrderSum(IAtom atom)
int	getConnectedAtomsCount(IAtom atom)
List<IAtom>	getConnectedAtomsList(IAtom atom)
int	getConnectedBondsCount(int idx)
int	getConnectedBondsCount(IAtom atom)
List<IBond>	getConnectedBondsList(IAtom atom)
List<IElectronContainer>	getConnectedElectronContainersList(IAtom atom)
int	getConnectedLonePairsCount(IAtom atom)
List<ILonePair>	getConnectedLonePairsList(IAtom atom)
int	getConnectedSingleElectronsCount(IAtom atom)
List<ISingleElectron>	getConnectedSingleElectronsList(IAtom atom)
IElectronContainer	getElectronContainer(int number)
int	getElectronContainerCount()
IAtom	getFirstAtom()
IAtom	getLastAtom()
ILonePair	getLonePair(int idx)
int	getLonePairCount()
int	getLonePairNumber(ILonePair lonePair)
IBond.Order	getMaximumBondOrder(IAtom atom)
IBond.Order	getMinimumBondOrder(IAtom atom)
ISingleElectron	getSingleElectron(int idx)
int	getSingleElectronCount()
int	getSingleElectronNumber(ISingleElectron singleElectron)
String	getTitle()
int	indexOf(IAtom atom)
int	indexOf(IBond bond)
int	indexOf(ILonePair pair)
int	indexOf(ISingleElectron electron)
boolean	isEmpty()
Iterable<ILonePair>	lonePairs()
IAtom	newAtom(int element, int numImplH)
IAtom	newAtom(IAtom atom)
IBond	newBond(IAtom beg, IAtom end, IBond.Order order)
void	remove(IAtomContainer atomContainer)
void	removeAllBonds()
void	removeAllElectronContainers()
void	removeAllElements()
void	removeAtom(int pos)
void	removeAtom(IAtom atom)
void	removeAtomAndConnectedElectronContainers(IAtom atom)
void	removeAtomOnly(int idx)
void	removeAtomOnly(IAtom atom)
IBond	removeBond(int idx)
IBond	removeBond(IAtom beg, IAtom end)
void	removeBond(IBond bond)
IElectronContainer	removeElectronContainer(int number)
void	removeElectronContainer(IElectronContainer ec)
ILonePair	removeLonePair(int idx)
void	removeLonePair(ILonePair lonePair)
ISingleElectron	removeSingleElectron(int idx)
void	removeSingleElectron(ISingleElectron electron)
void	setAtom(int idx, IAtom atom)
void	setAtoms(IAtom[] newatoms)
void	setBonds(IBond[] newbonds)
void	setStereoElements(List<IStereoElement> elements)
void	setTitle(String title)
IAtomContainer	shallowCopy()	Clones this IChemObject, but preserves references to Objects.
Iterable<ISingleElectron>	singleElectrons()
void	stateChanged(IChemObjectChangeEvent event)
Iterable<IStereoElement>	stereoElements()
String	toString()

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

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

addBond, newAtom, newAtom, newBond

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

getBuilder

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

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Constructor Details

AtomContainer

public AtomContainer(int numAtoms,
 int numBonds,
 int numLonePairs,
 int numSingleElectrons)

Create a new container with the specified capacities.

Parameters:

numAtoms - expected number of atoms

numBonds - expected number of bonds

numLonePairs - expected number of lone pairs

numSingleElectrons - expected number of single electrons

AtomContainer

public AtomContainer()

Constructs an empty AtomContainer.

AtomContainer

public AtomContainer(IAtomContainer src)

Constructs a shallow copy of the provided IAtomContainer with the same atoms, bonds, electron containers and stereochemistry of another AtomContainer. Removing atoms/bonds in this copy will not affect the original, however changing the properties will.

Parameters:

src - the source atom container

Method Details

addStereoElement

public void addStereoElement(IStereoElement element)

Specified by:

addStereoElement in interface IAtomContainer

setStereoElements

public void setStereoElements(List<IStereoElement> elements)

Specified by:

setStereoElements in interface IAtomContainer

stereoElements

public Iterable<IStereoElement> stereoElements()

Specified by:

stereoElements in interface IAtomContainer

setAtoms

public void setAtoms(IAtom[] newatoms)

Specified by:

setAtoms in interface IAtomContainer

setBonds

public void setBonds(IBond[] newbonds)

Specified by:

setBonds in interface IAtomContainer

setAtom

public void setAtom(int idx,
 IAtom atom)

Specified by:

setAtom in interface IAtomContainer

getAtom

public IAtom getAtom(int idx)

Specified by:

getAtom in interface IAtomContainer

getBond

public IBond getBond(int idx)

Specified by:

getBond in interface IAtomContainer

getLonePair

public ILonePair getLonePair(int idx)

Specified by:

getLonePair in interface IAtomContainer

getSingleElectron

public ISingleElectron getSingleElectron(int idx)

Specified by:

getSingleElectron in interface IAtomContainer

atoms

public Iterable<IAtom> atoms()

Specified by:

atoms in interface IAtomContainer

bonds

public Iterable<IBond> bonds()

Specified by:

bonds in interface IAtomContainer

lonePairs

public Iterable<ILonePair> lonePairs()

Specified by:

lonePairs in interface IAtomContainer

singleElectrons

public Iterable<ISingleElectron> singleElectrons()

Specified by:

singleElectrons in interface IAtomContainer

electronContainers

public Iterable<IElectronContainer> electronContainers()

Specified by:

electronContainers in interface IAtomContainer

getFirstAtom

public IAtom getFirstAtom()

Specified by:

getFirstAtom in interface IAtomContainer

getLastAtom

public IAtom getLastAtom()

Specified by:

getLastAtom in interface IAtomContainer

getAtomNumber

public int getAtomNumber(IAtom atom)

Specified by:

getAtomNumber in interface IAtomContainer

getBondNumber

public int getBondNumber(IAtom beg,
 IAtom end)

Specified by:

getBondNumber in interface IAtomContainer

getBondNumber

public int getBondNumber(IBond bond)

Specified by:

getBondNumber in interface IAtomContainer

getLonePairNumber

public int getLonePairNumber(ILonePair lonePair)

Specified by:

getLonePairNumber in interface IAtomContainer

getSingleElectronNumber

public int getSingleElectronNumber(ISingleElectron singleElectron)

Specified by:

getSingleElectronNumber in interface IAtomContainer

indexOf

public int indexOf(IAtom atom)

Specified by:

indexOf in interface IAtomContainer

indexOf

public int indexOf(IBond bond)

Specified by:

indexOf in interface IAtomContainer

indexOf

public int indexOf(ISingleElectron electron)

Specified by:

indexOf in interface IAtomContainer

indexOf

public int indexOf(ILonePair pair)

Specified by:

indexOf in interface IAtomContainer

getElectronContainer

public IElectronContainer getElectronContainer(int number)

Specified by:

getElectronContainer in interface IAtomContainer

getBond

public IBond getBond(IAtom beg,
 IAtom end)

Specified by:

getBond in interface IAtomContainer

getAtomCount

public int getAtomCount()

Specified by:

getAtomCount in interface IAtomContainer

getBondCount

public int getBondCount()

Specified by:

getBondCount in interface IAtomContainer

getLonePairCount

public int getLonePairCount()

Specified by:

getLonePairCount in interface IAtomContainer

getSingleElectronCount

public int getSingleElectronCount()

Specified by:

getSingleElectronCount in interface IAtomContainer

getElectronContainerCount

public int getElectronContainerCount()

Specified by:

getElectronContainerCount in interface IAtomContainer

getConnectedAtomsList

public List<IAtom> getConnectedAtomsList(IAtom atom)

Specified by:

getConnectedAtomsList in interface IAtomContainer

getConnectedBondsList

public List<IBond> getConnectedBondsList(IAtom atom)

Specified by:

getConnectedBondsList in interface IAtomContainer

getConnectedLonePairsList

public List<ILonePair> getConnectedLonePairsList(IAtom atom)

Specified by:

getConnectedLonePairsList in interface IAtomContainer

getConnectedSingleElectronsList

public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom)

Specified by:

getConnectedSingleElectronsList in interface IAtomContainer

getConnectedElectronContainersList

public List<IElectronContainer> getConnectedElectronContainersList(IAtom atom)

Specified by:

getConnectedElectronContainersList in interface IAtomContainer

getConnectedAtomsCount

public int getConnectedAtomsCount(IAtom atom)

Specified by:

getConnectedAtomsCount in interface IAtomContainer

getConnectedBondsCount

public int getConnectedBondsCount(IAtom atom)

Specified by:

getConnectedBondsCount in interface IAtomContainer

getConnectedBondsCount

public int getConnectedBondsCount(int idx)

Specified by:

getConnectedBondsCount in interface IAtomContainer

getConnectedLonePairsCount

public int getConnectedLonePairsCount(IAtom atom)

Specified by:

getConnectedLonePairsCount in interface IAtomContainer

getConnectedSingleElectronsCount

public int getConnectedSingleElectronsCount(IAtom atom)

Specified by:

getConnectedSingleElectronsCount in interface IAtomContainer

getBondOrderSum

public double getBondOrderSum(IAtom atom)

Specified by:

getBondOrderSum in interface IAtomContainer

getMaximumBondOrder

public IBond.Order getMaximumBondOrder(IAtom atom)

Specified by:

getMaximumBondOrder in interface IAtomContainer

getMinimumBondOrder

public IBond.Order getMinimumBondOrder(IAtom atom)

Specified by:

getMinimumBondOrder in interface IAtomContainer

add

public void add(IAtomContainer that)

Specified by:

add in interface IAtomContainer

newAtom

public IAtom newAtom(int element,
 int numImplH)

Specified by:

newAtom in interface IAtomContainer

newAtom

public IAtom newAtom(IAtom atom)

Specified by:

newAtom in interface IAtomContainer

newBond

public IBond newBond(IAtom beg,
 IAtom end,
 IBond.Order order)

Specified by:

newBond in interface IAtomContainer

addAtom

public void addAtom(IAtom atom)

Specified by:

addAtom in interface IAtomContainer

addBond

public void addBond(IBond bond)

Specified by:

addBond in interface IAtomContainer

addLonePair

public void addLonePair(ILonePair lp)

Specified by:

addLonePair in interface IAtomContainer

addSingleElectron

public void addSingleElectron(ISingleElectron e)

Specified by:

addSingleElectron in interface IAtomContainer

addElectronContainer

public void addElectronContainer(IElectronContainer ec)

Specified by:

addElectronContainer in interface IAtomContainer

remove

public void remove(IAtomContainer atomContainer)

Specified by:

remove in interface IAtomContainer

removeAtomOnly

public void removeAtomOnly(int idx)

Specified by:

removeAtomOnly in interface IAtomContainer

removeAtomOnly

public void removeAtomOnly(IAtom atom)

Specified by:

removeAtomOnly in interface IAtomContainer

removeBond

public IBond removeBond(int idx)

Specified by:

removeBond in interface IAtomContainer

removeBond

public IBond removeBond(IAtom beg,
 IAtom end)

Specified by:

removeBond in interface IAtomContainer

removeBond

public void removeBond(IBond bond)

Specified by:

removeBond in interface IAtomContainer

removeLonePair

public ILonePair removeLonePair(int idx)

Specified by:

removeLonePair in interface IAtomContainer

removeLonePair

public void removeLonePair(ILonePair lonePair)

Specified by:

removeLonePair in interface IAtomContainer

removeSingleElectron

public ISingleElectron removeSingleElectron(int idx)

Specified by:

removeSingleElectron in interface IAtomContainer

removeSingleElectron

public void removeSingleElectron(ISingleElectron electron)

Specified by:

removeSingleElectron in interface IAtomContainer

removeElectronContainer

public IElectronContainer removeElectronContainer(int number)

Specified by:

removeElectronContainer in interface IAtomContainer

removeElectronContainer

public void removeElectronContainer(IElectronContainer ec)

Specified by:

removeElectronContainer in interface IAtomContainer

removeAtomAndConnectedElectronContainers

public void removeAtomAndConnectedElectronContainers(IAtom atom)

Specified by:

removeAtomAndConnectedElectronContainers in interface IAtomContainer

removeAtom

public void removeAtom(IAtom atom)

Specified by:

removeAtom in interface IAtomContainer

removeAtom

public void removeAtom(int pos)

Specified by:

removeAtom in interface IAtomContainer

removeAllElements

public void removeAllElements()

Specified by:

removeAllElements in interface IAtomContainer

removeAllElectronContainers

public void removeAllElectronContainers()

Specified by:

removeAllElectronContainers in interface IAtomContainer

removeAllBonds

public void removeAllBonds()

Specified by:

removeAllBonds in interface IAtomContainer

addBond

public void addBond(int beg,
 int end,
 IBond.Order order,
 IBond.Stereo stereo)

Specified by:

addBond in interface IAtomContainer

addBond

public void addBond(int beg,
 int end,
 IBond.Order order,
 IBond.Display display)

Specified by:

addBond in interface IAtomContainer

addLonePair

public void addLonePair(int idx)

Specified by:

addLonePair in interface IAtomContainer

addSingleElectron

public void addSingleElectron(int idx)

Specified by:

addSingleElectron in interface IAtomContainer

contains

public boolean contains(IAtom atom)

Specified by:

contains in interface IAtomContainer

contains

public boolean contains(IBond bond)

Specified by:

contains in interface IAtomContainer

contains

public boolean contains(ILonePair lonepair)

Specified by:

contains in interface IAtomContainer

contains

public boolean contains(ISingleElectron electron)

Specified by:

contains in interface IAtomContainer

contains

public boolean contains(IElectronContainer electronContainer)

Specified by:

contains in interface IAtomContainer

getTitle

public String getTitle()

Specified by:

getTitle in interface IAtomContainer

setTitle

public void setTitle(String title)

Specified by:

setTitle in interface IAtomContainer

toString

public String toString()

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

shallowCopy

public IAtomContainer shallowCopy()

Description copied from class: ChemObject

Clones this IChemObject, but preserves references to Objects.

Overrides:

shallowCopy in class ChemObject

Returns:

Shallow copy of this IChemObject

See Also:

• ChemObject.clone()

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 ChemObject

Returns:

The cloned object

Throws:

CloneNotSupportedException

stateChanged

public void stateChanged(IChemObjectChangeEvent event)

Specified by:

stateChanged in interface IChemObjectListener

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface IAtomContainer