Package etomica.molecule.iterator

Class MoleculeIteratorMolecule

java.lang.Object

etomica.molecule.iterator.MoleculeIteratorArrayListSimple

etomica.molecule.iterator.MoleculeIteratorMolecule

All Implemented Interfaces:

AtomsetIterator, AtomsetIteratorDirectable, MoleculeIterator, MoleculeIteratorBoxDependent, MoleculesetIterator, MoleculesetIteratorBoxDependent, MoleculesetIteratorPDT, MoleculesetIteratorTargetable

public class MoleculeIteratorMolecule
extends MoleculeIteratorArrayListSimple
implements MoleculesetIteratorPDT, MoleculeIteratorBoxDependent

Iterator for the molecules of a single species in a box. Can be targeted to give the molecule containing a specific atom (if consistent with the species), or all molecules of the species in a box.
This class is used by PotentialMaster to iterate over molecules for single-body potentials.

See Also:

Serialized Form

Field Summary

Fields inherited from class etomica.molecule.iterator.MoleculeIteratorArrayListSimple

atomSetSinglet, cursor, list

Constructor Summary

Constructors

Constructor	Description
MoleculeIteratorMolecule(ISpecies species)

Method Summary

Modifier and Type	Method	Description
void	reset()	Puts iterator in state ready to begin iteration.
void	setBox(Box newBox)	Sets the box containing the molecules for iteration.
void	setDirection(IteratorDirective.Direction direction)	Has no effect, but is included as part of the AtomsetIteratorPDT interface.
void	setTarget(IMolecule newTargetAtom)	Specifies molecule returned by this iterator, as the one containing the given target atom.

Methods inherited from interface etomica.atom.iterator.AtomsetIterator

nBody, size, unset

Methods inherited from interface etomica.molecule.iterator.MoleculeIterator

nextMolecule

Methods inherited from class etomica.molecule.iterator.MoleculeIteratorArrayListSimple

nBody, next, nextMolecule, setList, size, unset

Methods inherited from interface etomica.molecule.iterator.MoleculesetIterator

next

Methods inherited from class java.lang.Object

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

Constructor Detail

MoleculeIteratorMolecule

public MoleculeIteratorMolecule(ISpecies species)

Parameters:

species - species for which molecules are returned as iterates. species must not be null.

Method Detail

setBox

public void setBox(Box newBox)

Sets the box containing the molecules for iteration. A null box conditions iterator to give no iterates.

Specified by:

setBox in interface MoleculesetIteratorBoxDependent

Throws:

java.lang.NullPointerException - if the Box is null

reset

public void reset()

Description copied from class: MoleculeIteratorArrayListSimple

Puts iterator in state ready to begin iteration.

Specified by:

reset in interface AtomsetIterator

Overrides:

reset in class MoleculeIteratorArrayListSimple

setTarget

public void setTarget(IMolecule newTargetAtom)

Specifies molecule returned by this iterator, as the one containing the given target atom. Only the first element of the array is relevant. If argument is null, of zero length, or if targetAtom[0] is null, then no target atom is specified and all molecules of the species in the box will be given on iteration.

Specified by:

setTarget in interface MoleculesetIteratorTargetable

Throws:

java.lang.NullPointerException - if targetAtom is null

java.lang.IllegalArgumentException - if targetAtom.count() is not 0 or 1

setDirection

public void setDirection(IteratorDirective.Direction direction)

Has no effect, but is included as part of the AtomsetIteratorPDT interface.

Specified by:

setDirection in interface AtomsetIteratorDirectable