net.sf.octet.model
Interface Configuration

All Superinterfaces:

PaddleWheelCollection

All Known Implementing Classes:

BasicConfiguration

public interface Configuration

extends PaddleWheelCollection

A representation of atomic configuration - the spatial distribution of neighboring Atoms about a central Atom. Distinguishable atomic Configurations in two Molecules with the same bonding arrangements and Atom connectivities result from spatial arrangements not resulting from rotations about an AtomPair. In other words, tetrahedral carbon chirality may be represented by a Configuration, but biaryl chirality must be represented by a Conformation.

Configuration enables all forms of atomic configuration to be represented and queried in a uniform way. No distinction is made between tetrahedral atom chirality or other forms of configuration such as that found in octahedral complexes, trigonal bipyramidal transition states, or trigonal planar and pyrimidal configurations of amines and phosphines.

Each neighbor Atom to which a central Atom is connected has a PaddleWheel associated with it. This collection of PaddleWheels completely defines the configuration.

The Configuration interface is adapted from concepts presented in a paper by Andreas Dietz (J. Chem. Inf. Comput. Sci. 1995, 35 , 787).

Author:

Richard Apodaca

See Also:

Conformation

Method Summary

PaddleWheel

getPaddleWheel(Atom neighbor) Returns the PaddleWheel directed at neighbor.

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

containsPaddleWheel, containsPaddleWheel, countPaddleWheels, getPaddleWheel, getPaddleWheel, getPaddleWheelIndex, iteratePaddleWheels, toPaddleWheelArray

Method Detail

getPaddleWheel

public PaddleWheel getPaddleWheel(Atom neighbor)

Returns the PaddleWheel directed at neighbor.

Parameters:

neighbor - the Atom to which the returned PaddleWheel is directed

Returns:

the PaddleWheel directed toward neighbor

Throws:

NoSuchAtomException - if neighbor can not be found