net.sf.octet.model
Interface Molecule

All Superinterfaces:

AtomCollection, AtomGraph, AtomPairCollection, BondingSystemCollection

All Known Implementing Classes:

MoleculeDecorator

public interface Molecule

extends AtomGraph, BondingSystemCollection

A representation of the chemical concept of a molecule. The purpose of the Molecule interface is to define behaviors relating to three fundamental molecular properties: constitution, configuration, and conformation.

Molecules are immutable. The methods defined in this interface can be expected to return the same results throughout the lifetime of any object implementing Molecule.

Author:

Richard Apodaca

See Also:

"Immutable Pattern (Grand98)"

Method Summary

int	countBondingSystems(Atom atom) Returns the number of BondingSystems in which the specified Atom particpates.
int	countImplicitHydrogens(Atom atom) Returns the number of implicit hydrogens associated with atom.
int	countNonbondingValenceElectrons(Atom atom) Returns the total number of nonbonding valence electrons associeated with atom.
Configuration	getConfiguration(Atom atom) Returns the Configuration of the specified Atom.
Conformation	getConformation() Returns the Conformation of this Molecule.
NonbondingShell	getNonbondingShell(Atom atom) Returns the NonbondingShell of the specified Atom.
BondingSystemIterator	iterateBondingSystems(Atom atom) Returns an iterator over all BondingSystems in which the specified Atom participates.

Methods inherited from interface net.sf.octet.model.AtomGraph

countNeighbors, iterateNeighbors

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

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

containsBondingSystem, countBondingSystems, getBondingSystem, getBondingSystemIndex, iterateBondingSystems, toBondingSystemArray

Method Detail

iterateBondingSystems

public BondingSystemIterator iterateBondingSystems(Atom atom)

Returns an iterator over all BondingSystems in which the specified Atom participates.

Specified by:

iterateBondingSystems in interface BondingSystemCollection

Parameters:

atom - the Atom

Returns:

an iterator over all BondingSystems in which the specified Atom participates

Throws:

NoSuchAtomException - if the specified Atom can not be found in this Molecule

countBondingSystems

public int countBondingSystems(Atom atom)

Returns the number of BondingSystems in which the specified Atom particpates.

Specified by:

countBondingSystems in interface BondingSystemCollection

Parameters:

atom - the Atom

Returns:

the number of BondingSystems in which the specified Atom particpates

Throws:

NoSuchAtomException - if the specified Atom can not be found in this Molecule

getConfiguration

public Configuration getConfiguration(Atom atom)

Returns the Configuration of the specified Atom. Configuration refers to the spatial arrangement of neighboring Atoms around a central Atom that do not result from rotation about an AtomPair.

Returns:

the Configuration of this Atom

Throws:

NoSuchAtomException - if the specified Atom can not be found in this Molecule

getConformation

public Conformation getConformation()

Returns the Conformation of this Molecule.

Returns:

the Conformation of this Molecule

getNonbondingShell

public NonbondingShell getNonbondingShell(Atom atom)

Returns the NonbondingShell of the specified Atom.

Parameters:

atom - the Atom

Returns:

the NonbondingShell of atom

Throws:

NoSuchAtomException - if the specified Atom can not be found in this Molecule

countImplicitHydrogens

public int countImplicitHydrogens(Atom atom)

Returns the number of implicit hydrogens associated with atom.

Parameters:

atom - the Atom

Returns:

the number of implicit hydrogens associated with atom

Throws:

NoSuchAtomException - if the specified Atom can not be found in this Molecule

countNonbondingValenceElectrons

public int countNonbondingValenceElectrons(Atom atom)

Returns the total number of nonbonding valence electrons associeated with atom. This number includes any electrons contained in the NonbondingShell of atom.

Parameters:

atom - the Atom

Returns:

the total number of nonbonding valence electrons associeated with atom

Throws:

NoSuchAtomException - if the specified Atom can not be found in this Molecule