net.sf.octet.model
Interface AtomGraph

All Superinterfaces:

AtomCollection, AtomPairCollection

All Known Subinterfaces:

BondingSystem, GammaSequence, Molecule

All Known Implementing Classes:

AtomGraphDecorator, BasicAtomGraph, BasicBondingSystem, BasicGammaSequence, MoleculeDecorator, SimpleBondingSystem

public interface AtomGraph

extends AtomCollection, AtomPairCollection

AtomGraph represents the graph theoretical construct of a graph as applied to a set of Atoms. AtomGraph places the additional restriction on the AtomCollection and AtomPairCollection interfaces that there are no duplicate items as determined by operator ==.

In graph theoretical terms, an AtomGraph is a simple, undirected, unweighted graph whose verticies are Atoms and whose edges are AtomPairs.

The Atoms and AtomPairs in an AtomGraph may or may not belong to a single Molecule, depending on implementation.

Author:

Richard Apodaca

Method Summary

int	countNeighbors(Atom atom) Returns the number of Atoms connected to atom in the context of this AtomGraph.
AtomIterator	iterateNeighbors(Atom atom) Returns an iterator over all neighbors of atom in the context of this AtomGraph.

Methods inherited from interface net.sf.octet.collection.AtomCollection

containsAtom, countAtoms, getAtom, getAtomIndex, iterateAtoms, toAtomArray

Methods inherited from interface net.sf.octet.collection.AtomPairCollection

containsAtomPair, containsAtomPair, countAtomPairs, getAtomPair, getAtomPair, getAtomPairIndex, iterateAtomPairs, toAtomPairArray

Method Detail

iterateNeighbors

public AtomIterator iterateNeighbors(Atom atom)

Returns an iterator over all neighbors of atom in the context of this AtomGraph. This iterator may contain only a subset of the Atoms returned by atom.iterateNeighbors(), depending on the nature of this AtomGraph.

Parameters:

atom - the Atom to examine

Returns:

an iterator over all neighbors of atom

Throws:

NoSuchAtomException - if the specified Atom can not be found

countNeighbors

public int countNeighbors(Atom atom)

Returns the number of Atoms connected to atom in the context of this AtomGraph. This value will be less than or equal to the value returned by atom.countNeighbors().

Parameters:

atom - the Atom to examine

Returns:

the number of neighbors of atom

Throws:

NoSuchAtomException - if the specified Atom can not be found