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, IChemObjectListener, Serializable, Cloneable

Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.

Looping over all Bonds in the AtomContainer is typically done like:

 Iterator iter = atomContainer.bonds();
 while (iter.hasNext()) {
   IBond aBond = (IBond) iter.next();
 }
 

Author:

steinbeck

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

data

Created on:

2000-10-02

Field Summary

Fields

Modifier and Type	Field and Description
protected int	atomCount Number of atoms contained by this object.
protected IAtom[]	atoms Internal array of atoms.
protected int	bondCount Number of bonds contained by this object.
protected IBond[]	bonds Internal array of bonds.
protected int	growArraySize Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
protected int	lonePairCount Number of lone pairs contained by this object.
protected ILonePair[]	lonePairs Internal array of lone pairs.
protected int	singleElectronCount Number of single electrons contained by this object.
protected ISingleElectron[]	singleElectrons Internal array of single electrons.
protected Set<IStereoElement>	stereoElements Internal list of atom parities.

Constructor Summary

Constructors

Constructor and Description
AtomContainer() Constructs an empty AtomContainer.
AtomContainer(IAtomContainer container) Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
AtomContainer(int atomCount, int bondCount, int lpCount, int seCount) Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.

Method Summary

Modifier and Type	Method and Description
void	add(IAtomContainer that)
void	addAtom(IAtom atom)
void	addBond(IBond bond)
void	addBond(int atom1, int atom2, IBond.Order order)
void	addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo)
void	addElectronContainer(IElectronContainer electronContainer)
void	addLonePair(ILonePair lonePair)
void	addLonePair(int atomID)
void	addSingleElectron(int atomID)
void	addSingleElectron(ISingleElectron singleElectron)
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 singleElectron)
Iterable<IElectronContainer>	electronContainers()
IAtom	getAtom(int idx)
int	getAtomCount()
int	getAtomNumber(IAtom atom)
IBond	getBond(IAtom atom1, IAtom atom2)
IBond	getBond(int idx)
int	getBondCount()
int	getBondNumber(IAtom atom1, IAtom atom2)
int	getBondNumber(IBond bond)
double	getBondOrderSum(IAtom atom)
int	getConnectedAtomsCount(IAtom atom)
List<IAtom>	getConnectedAtomsList(IAtom atom)
int	getConnectedBondsCount(IAtom atom)
int	getConnectedBondsCount(int idx)
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()
void	remove(IAtomContainer atomContainer)
void	removeAllBonds()
void	removeAllElectronContainers()
void	removeAllElements()
void	removeAtom(IAtom atom)
void	removeAtom(int pos)
void	removeAtomAndConnectedElectronContainers(IAtom atom) Deprecated.
void	removeAtomOnly(IAtom atom)
void	removeAtomOnly(int position)
IBond	removeBond(IAtom atom1, IAtom atom2)
void	removeBond(IBond bond)
IBond	removeBond(int position)
void	removeElectronContainer(IElectronContainer electronContainer)
IElectronContainer	removeElectronContainer(int number)
void	removeLonePair(ILonePair lonePair)
ILonePair	removeLonePair(int position)
ISingleElectron	removeSingleElectron(int position)
void	removeSingleElectron(ISingleElectron singleElectron)
void	setAtom(int idx, IAtom atom)
void	setAtoms(IAtom[] newAtoms)
void	setBonds(IBond[] newBonds)
void	setStereoElements(List<IStereoElement> elements)
void	setTitle(String title)
Iterable<ISingleElectron>	singleElectrons()
void	stateChanged(IChemObjectChangeEvent event)
Iterable<IStereoElement>	stereoElements()
String	toString()

Methods inherited from class org.openscience.cdk.ChemObject

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

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

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

getBuilder

Field Detail

atomCount

protected int atomCount

Number of atoms contained by this object.

bondCount

protected int bondCount

Number of bonds contained by this object.

lonePairCount

protected int lonePairCount

Number of lone pairs contained by this object.

singleElectronCount

protected int singleElectronCount

Number of single electrons contained by this object.

growArraySize

protected int growArraySize

Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.

atoms

protected IAtom[] atoms

Internal array of atoms.

bonds

protected IBond[] bonds

Internal array of bonds.

lonePairs

protected ILonePair[] lonePairs

Internal array of lone pairs.

singleElectrons

protected ISingleElectron[] singleElectrons

Internal array of single electrons.

stereoElements

protected Set<IStereoElement> stereoElements

Internal list of atom parities.

Constructor Detail

AtomContainer

public AtomContainer()

Constructs an empty AtomContainer.

AtomContainer

public AtomContainer(IAtomContainer container)

Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).

Parameters:

container - An AtomContainer to copy the atoms and electronContainers from

AtomContainer

public AtomContainer(int atomCount,
                     int bondCount,
                     int lpCount,
                     int seCount)

Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers. It will set the starting array lengths to the defined values, but will not create any Atom or ElectronContainer's.

Parameters:

atomCount - Number of atoms to be in this container

bondCount - Number of bonds to be in this container

lpCount - Number of lone pairs to be in this container

seCount - Number of single electrons to be in this container

Method Detail

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 atom1,
                         IAtom atom2)

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 atom1,
                     IAtom atom2)

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

getConnectedBondsCount

public int getConnectedBondsCount(IAtom atom)

Specified by:

getConnectedBondsCount in interface IAtomContainer

getConnectedAtomsCount

public int getConnectedAtomsCount(IAtom atom)

Specified by:

getConnectedAtomsCount 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

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 lonePair)

Specified by:

addLonePair in interface IAtomContainer

addSingleElectron

public void addSingleElectron(ISingleElectron singleElectron)

Specified by:

addSingleElectron in interface IAtomContainer

addElectronContainer

public void addElectronContainer(IElectronContainer electronContainer)

Specified by:

addElectronContainer in interface IAtomContainer

remove

public void remove(IAtomContainer atomContainer)

Specified by:

remove in interface IAtomContainer

removeAtomOnly

public void removeAtomOnly(int position)

Specified by:

removeAtomOnly in interface IAtomContainer

removeAtomOnly

public void removeAtomOnly(IAtom atom)

Specified by:

removeAtomOnly in interface IAtomContainer

removeBond

public IBond removeBond(int position)

Specified by:

removeBond in interface IAtomContainer

removeBond

public IBond removeBond(IAtom atom1,
                        IAtom atom2)

Specified by:

removeBond in interface IAtomContainer

removeBond

public void removeBond(IBond bond)

Specified by:

removeBond in interface IAtomContainer

removeLonePair

public ILonePair removeLonePair(int position)

Specified by:

removeLonePair in interface IAtomContainer

removeLonePair

public void removeLonePair(ILonePair lonePair)

Specified by:

removeLonePair in interface IAtomContainer

removeSingleElectron

public ISingleElectron removeSingleElectron(int position)

Specified by:

removeSingleElectron in interface IAtomContainer

removeSingleElectron

public void removeSingleElectron(ISingleElectron singleElectron)

Specified by:

removeSingleElectron in interface IAtomContainer

removeElectronContainer

public IElectronContainer removeElectronContainer(int number)

Specified by:

removeElectronContainer in interface IAtomContainer

removeElectronContainer

public void removeElectronContainer(IElectronContainer electronContainer)

Specified by:

removeElectronContainer in interface IAtomContainer

removeAtomAndConnectedElectronContainers

@Deprecated
public void removeAtomAndConnectedElectronContainers(IAtom atom)

Deprecated.

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 atom1,
                    int atom2,
                    IBond.Order order,
                    IBond.Stereo stereo)

Specified by:

addBond in interface IAtomContainer

addBond

public void addBond(int atom1,
                    int atom2,
                    IBond.Order order)

Specified by:

addBond in interface IAtomContainer

addLonePair

public void addLonePair(int atomID)

Specified by:

addLonePair in interface IAtomContainer

addSingleElectron

public void addSingleElectron(int atomID)

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 singleElectron)

Specified by:

contains in interface IAtomContainer

contains

public boolean contains(IElectronContainer electronContainer)

Specified by:

contains in interface IAtomContainer

toString

public String toString()

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

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

getTitle

public String getTitle()

Specified by:

getTitle in interface IAtomContainer

setTitle

public void setTitle(String title)

Specified by:

setTitle in interface IAtomContainer