org.openscience.cdk

Class Association

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ElectronContainer

org.openscience.cdk.Association

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemObject, IElectronContainer

public class Association
extends ElectronContainer
implements Serializable, Cloneable

Base class for storing interactions like hydrogen bonds and ionic interactions. The ElectronContainer contains zero electrons by default.

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

extra

Keywords:

orbital, association, bond

Field Summary

Fields

Modifier and Type	Field and Description
protected int	atomCount
protected IAtom[]	atoms The atoms which take part in the association.
protected int	electronCount Number of electrons in the association.

Constructor Summary

Constructors

Constructor and Description
Association() Constructs an empty association.
Association(IAtom atom1, IAtom atom2) Constructs an association between two Atom's.

Method Summary

Modifier and Type	Method and Description
boolean	contains(IAtom atom) Returns true if the given atom participates in this Association.
IAtom	getAtomAt(int position) Returns an Atom from this Association.
int	getAtomCount() Returns the number of Atoms in this Association.
IAtom[]	getAtoms() Returns the array of atoms making up this Association.
Integer	getElectronCount() Returns the number of electrons in a Association.
void	setAtomAt(IAtom atom, int position) Sets an Atom in this Association.
void	setAtoms(IAtom[] atoms) Sets the array of atoms making up this Association.
String	toString() Returns a one line string representation of this Container.

Methods inherited from class org.openscience.cdk.ElectronContainer

clone, setElectronCount

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

electronCount

protected final int electronCount

Number of electrons in the association.

See Also:

Constant Field Values

atoms

protected IAtom[] atoms

The atoms which take part in the association.

atomCount

protected int atomCount

Constructor Detail

Association

public Association(IAtom atom1,
                   IAtom atom2)

Constructs an association between two Atom's.

Parameters:

atom1 - An atom to be associated with another atom

atom2 - An atom to be associated with another atom

See Also:

Atom

Association

public Association()

Constructs an empty association.

See Also:

Atom

Method Detail

getAtoms

public IAtom[] getAtoms()

Returns the array of atoms making up this Association.

Returns:

An array of atoms participating in this Association

See Also:

setAtoms(org.openscience.cdk.interfaces.IAtom[])

setAtoms

public void setAtoms(IAtom[] atoms)

Sets the array of atoms making up this Association.

Parameters:

atoms - An array of atoms that forms this Association

See Also:

getAtoms()

getAtomCount

public int getAtomCount()

Returns the number of Atoms in this Association.

Returns:

The number of Atoms in this Association

getElectronCount

public Integer getElectronCount()

Returns the number of electrons in a Association.

Specified by:

getElectronCount in interface IElectronContainer

Overrides:

getElectronCount in class ElectronContainer

Returns:

The number of electrons in a Association.

See Also:

ElectronContainer.setElectronCount(java.lang.Integer)

getAtomAt

public IAtom getAtomAt(int position)

Returns an Atom from this Association.

Parameters:

position - The position in this bond where the atom is

Returns:

The atom at the specified position

See Also:

setAtomAt(org.openscience.cdk.interfaces.IAtom, int)

contains

public boolean contains(IAtom atom)

Returns true if the given atom participates in this Association.

Parameters:

atom - The atom to be tested if it participates in this Association

Returns:

true if the atom participates in this Association

setAtomAt

public void setAtomAt(IAtom atom,
                      int position)

Sets an Atom in this Association.

Parameters:

atom - The atom to be set

position - The position in this Association where the atom is to be inserted

See Also:

getAtomAt(int)

toString

public String toString()

Returns a one line string representation of this Container. This method is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class ElectronContainer

Returns:

The string representation of this Container