Package net.sf.octet.model

Basic functionality needed to represent molecular representations.

See:
Description

Interface Summary

Atom	A representation of the chemical concept of an atom.
AtomGraph	AtomGraph represents the graph theoretical construct of a graph as applied to a set of Atoms.
AtomicSymbol	A representation of the concept of an atomic symbol.
AtomicSystem	A system of symbols, masses, isotopes, and periodic classification for atoms.
AtomPair	An AtomPair represents a pair of Atoms.
BondingSystem	BondingSystem reflects a conceptually general model of chemical bonding.
Configuration	A representation of atomic configuration - the spatial distribution of neighboring Atoms about a central Atom.
Conformation	Representation of molecular conformation.
Electron	A representation of an electron.
GammaSequence	An acyclic Molecular subgraph used in representing molecular conformation.
HalfPlane	A representation of the half plane concept.
IsotopicDistribution	A distribution of Nuclei.
Molecule	A representation of the chemical concept of a molecule.
MoleculeConvertor	Transforms a Molecule into a set of instructions for a RepresentationBuilder.
NonbondingShell	A representation of the concept of an atom's valence shell of nonbonding electrons.
Nucleus	A representation of a nucleus.
Orbital	An implementation of the concept of an atomic orbital.
PaddleWheel	A representation of the paddle wheel concept.

Class Summary

AtomGraphDecorator	A decorator for an AtomGraph.
BasicAtomGraph	A default implementation of the AtomGraph interface that is suitable for representing Molecule subgraphs.
BasicAtomicSystem	A default implementation of the AtomicSystem interface.
BasicAtomPair	A default implementation of the AtomPair interface.
BasicBondingSystem	A default implementation of the BondingSystem interface.
BasicConfiguration	A default implementation of the Configuration interface.
BasicConformation	A default implementation of the Conformation interface.
BasicElectron	A default implementation of the Electron interface.
BasicGammaSequence	A default implementation of the BasicGammaSequence interface.
BasicHalfPlane	A default implementation of the HalfPlane interface.
BasicMoleculeConvertor	A default implementation of the MoleculeConvertor interface.
BasicNonbondingShell	A default implementation of the NonbondingShell interface.
BasicOrbital	A default implementation of the Orbital interface.
BasicPaddleWheel	A default implementation of the PaddleWheel interface.
MoleculeDecorator	MoleculeDecorator forwards all requests to a Molecule that it decorates.
SimpleBondingSystem	An implementation of the BondingSystem interface that is optimized for two- Atom bonding.
SimpleHalfPlane	An implementation of the HalfPlane interface that is optimized for those cases in which a HalfPlane contains only one Atom.

Package net.sf.octet.model Description

Basic functionality needed to represent molecular representations.

Package Specification