Package etomica.molecule

Class Molecule

java.lang.Object

etomica.molecule.Molecule

All Implemented Interfaces:

IMolecule, java.io.Serializable

Direct Known Subclasses:

MoleculeOriented

public class Molecule
extends java.lang.Object
implements IMolecule, java.io.Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected AtomArrayList	childList
protected int	index
protected ISpecies	species

Constructor Summary

Constructors

Constructor	Description
Molecule(ISpecies species, int numLeafAtoms)

Method Summary

Modifier and Type	Method	Description
void	addChildAtom(IAtom newChildAtom)	Adds the given Atom as a child of this Atom.
IAtomList	getChildList()	Returns the atoms in the molecule as an IAtomList.
int	getIndex()	Returns this IMolecule's index, which is its place in the list of molecules of its ISpecies in its Box.
ISpecies	getType()	Returns the ISpecies of this IMolecule.
void	removeChildAtom(IAtom oldChildAtom)	Removes the given child Atom from this AtomGroup.
void	setIndex(int newIndex)	Informs the IMolecule of its index.
java.lang.String	signature()	Returns a string of digits that uniquely identifies this atom.
java.lang.String	toString()	Returns a string formed by concatenating the signature of this atom to a string that identifies it as a molecule.

Methods inherited from class java.lang.Object

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

Field Detail

index

protected int index

childList

protected final AtomArrayList childList

species

protected final ISpecies species

Constructor Detail

Molecule

public Molecule(ISpecies species,
                int numLeafAtoms)

Method Detail

signature

public java.lang.String signature()

Returns a string of digits that uniquely identifies this atom. String is formed by concatenating the ordinal of this atom to the signature given by the parent of this atom. If atom has no parent, forms a string from only the ordinal.

toString

public final java.lang.String toString()

Returns a string formed by concatenating the signature of this atom to a string that identifies it as a molecule.

Overrides:

toString in class java.lang.Object

addChildAtom

public void addChildAtom(IAtom newChildAtom)

Adds the given Atom as a child of this Atom. The given child Atom should be parentless when this method is called.

Throws:

java.lang.IllegalArgumentException - if the given atom already has a parent.

removeChildAtom

public void removeChildAtom(IAtom oldChildAtom)

Removes the given child Atom from this AtomGroup.

Throws:

java.lang.IllegalArgumentException - if the given atom is not a child.

getChildList

public final IAtomList getChildList()

Description copied from interface: IMolecule

Returns the atoms in the molecule as an IAtomList.

Specified by:

getChildList in interface IMolecule

Returns:

the childList

setIndex

public final void setIndex(int newIndex)

Description copied from interface: IMolecule

Informs the IMolecule of its index.

Specified by:

setIndex in interface IMolecule

getIndex

public final int getIndex()

Description copied from interface: IMolecule

Returns this IMolecule's index, which is its place in the list of molecules of its ISpecies in its Box.

Specified by:

getIndex in interface IMolecule

getType

public final ISpecies getType()

Description copied from interface: IMolecule

Returns the ISpecies of this IMolecule.

Specified by:

getType in interface IMolecule