Package etomica.molecule.iterator

Interface Summary

Interface	Description
MoleculeIterator	Interface for classes that loop over a set of atoms.
MoleculeIteratorBoxDependent	Interface indicating that an atom iterator can determine appropriate atoms for iteration given an arbitrary box.
MoleculeIteratorMoleculeDependent	Interface for an atom iterator that can be altered by setting of an atom.
MoleculesetIterator	Interface for classes that loop over a set of atoms.
MoleculesetIteratorBasisDependent	Interface for an MoleculeIterator that can be conditioned with target and basis molecules.
MoleculesetIteratorBoxDependent	Interface indicating that an iterator can determine appropriate atoms for iteration given an arbitrary box.
MoleculesetIteratorPDT	This is an interface for iterators that are box dependent, directable, and targetable.
MoleculesetIteratorTargetable	Interface for an iterator that can be targeted at one or more atoms.

Class Summary

Class	Description
IteratorFactory	Class for construction of iterators of molecules.
MoleculeIteratorAll	Iterator for all the molecules of a set of species in a box.
MoleculeIteratorAllMolecules	Iterator for all the molecules in a box.
MoleculeIteratorArrayList	An atom iterator of the elements from an AtomArrayList (in proper sequence).
MoleculeIteratorArrayListSimple	An atom iterator of the elements from an AtomArrayList (in proper sequence).
MoleculeIteratorMolecule	Iterator for the molecules of a single species in a box.
MoleculeIteratorSinglet	Iterator that expires after returning a single atom, which is specified by a call to the setAtom method, or via the constructor.
MpiInnerFixed	Pair iterator synthesized from two atom iterators, such that the inner-loop iteration is independent of the outer-loop atom.
MpiInnerVariable	Pair iterator synthesized from two atom iterators, such that the inner-loop iteration depends on the outer-loop atom.
MpiInterArrayList	Returns all pairs formed from two different untabbed lists of molecules.
MpiInterspecies1A	Gives pairs formed from the molecules of two different species in a box, taking one molecule of one species with all molecules of the other.
MpiInterspeciesAA	Gives pairs formed from the molecules of two different species in a box.
MpiIntraArrayList	Returns all pairs formed from a single list of molecules.
MpiIntraspecies1A	Gives pairs formed from the molecules of a species in a box, taking one molecule the species with all of its other molecules.
MpiIntraspeciesAA	Gives pairs formed from the molecules of a single species in a box.
MpiMolecule	Adapater class that wraps three atomPair iterators, one suitable for iterating over all molecule pairs in a box (AA), another suitable for iterating over all molecule pairs formed with a target molecule (1A), and the third suitable for iterating over a single molecule pair (11).