org.openscience.cdk.smsd.ring

Class HanserRingFinder

java.lang.Object

org.openscience.cdk.smsd.ring.HanserRingFinder

All Implemented Interfaces:

RingFinder

Deprecated.

Use CDK AllRingsFinder. A more recent version of SMSD is available at http://github.com/asad/smsd.

@Deprecated
public class HanserRingFinder
extends Object
implements RingFinder

Finds the Set of all Rings. This is an implementation of the algorithm published in [Hanser, Th. and Jauffret, Ph. and Kaufmann, G., A New Algorithm for Exhaustive Ring Perception in a Molecular Graph, J. Chem. Inf. Comput. Sci., 1996, 36:1146-1152]. Some of the comments refer to pseudo code fragments listed in this article. The concept is that a regular molecular graph is first converted into a path graph (refer PathGraph.java), i.e. a graph where the edges are actually paths. This can list several nodes that are implicitly connecting the two nodes between the path is formed (refer PathEdge.java). The paths that join source and sink node are step by step fused and the joined nodes are deleted from the path graph (collapsed path). What remains is a graph of paths that have the same start and endpoint and are thus rings (source=sink=ring).

Author:

Syed Asad Rahman <asad@ebi.ac.uk> 2009-2010

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
HanserRingFinder() Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
Collection<List<IAtom>>	findRings(IAtomContainer molecule) Deprecated. Returns a collection of rings.
IRingSet	getRingSet(IAtomContainer molecule) Deprecated. Returns Ring set based on Hanser Ring Finding method

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HanserRingFinder

public HanserRingFinder()

Deprecated.

Method Detail

findRings

public Collection<List<IAtom>> findRings(IAtomContainer molecule)

Deprecated.

Returns a collection of rings.

Specified by:

findRings in interface RingFinder

Parameters:

molecule -

Returns:

a Collection of Lists containing one ring each

See Also:

RingFinder.findRings(org.openscience.cdk.interfaces.IAtomContainer)

getRingSet

public IRingSet getRingSet(IAtomContainer molecule)
                    throws CDKException

Deprecated.

Returns Ring set based on Hanser Ring Finding method

Specified by:

getRingSet in interface RingFinder

Parameters:

molecule -

Returns:

report collected the rings

Throws:

CDKException

See Also:

RingFinder.getRingSet(org.openscience.cdk.interfaces.IAtomContainer)