net.sf.octet.model
Interface GammaSequence

All Superinterfaces:

AtomCollection, AtomGraph, AtomPairCollection

All Known Implementing Classes:

BasicGammaSequence

public interface GammaSequence

extends AtomGraph

An acyclic Molecular subgraph used in representing molecular conformation. GammaSequence will in most cases consist of two Atoms. However, more than two Atoms may be present. For example, allenes will have GammaSequences containing three Atoms. GammaSequences with more Atoms will be very rare, but still allowed.

GammaSequence is modeled after the concept of the gamma-sequence first described in a paper by Dietz (J. Chem. Inf. Comput. Sci. 1995, 35 , 787).

Author:

Richard Apodaca

See Also:

Conformation

Method Summary

AtomPair

getAxis() Returns the AtomPair that contains the first Atom in this sequence as its source and the last Atom as its target.

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

Method Detail

getAxis

public AtomPair getAxis()

Returns the AtomPair that contains the first Atom in this sequence as its source and the last Atom as its target.

Returns:

the AtomPair that contains the first Atom in this sequence as its source and the last Atom as its target