org.openscience.cdk.ringsearch

Class SSSRFinder

java.lang.Object

org.openscience.cdk.ringsearch.SSSRFinder

Deprecated.

Use the Cycles API Cycles.sssr(IAtomContainer)

@Deprecated
public class SSSRFinder
extends Object

Finds the Smallest Set of Smallest Rings. This is an implementation of an algorithm by Franziska Berger, Peter Gritzmann, and Sven deVries, TU München, [Berger, F. and Gritzmann, P. and De Vries, S., Minimum cycle bases for network graphs, Algorithmica, 2004, ?:51-62].

Additional related algorithms from [Berger, F. and Gritzmann, P. and De Vries, S., Cyclic Invariants for Molecular Graphs, 2004, Lehrstuhl für Angewandte Geometrie und Diskrete Mathematik, Technische Universität München, http://www-m9.ma.tum.de/dm/cycles/].

Author:

Ulrich Bauer <ulrich.bauer@alumni.tum.de>

Dictionary pointer(s):

findSmallestSetOfSmallestRings_Berger in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:findSmallestSetOfSmallestRings_Berger]

Source code:

master

Belongs to CDK module:

standard

Keywords:

smallest-set-of-rings, ring search

Constructor Summary

Constructors

Constructor and Description
SSSRFinder(IAtomContainer container) Deprecated. Constructs a SSSRFinder for a specified molecule.

Method Summary

Methods

Modifier and Type	Method and Description
List	findEquivalenceClasses() Deprecated. Finds the "interchangeability" equivalence classes.
IRingSet	findEssentialRings() Deprecated. Finds the Set of Essential Rings.
IRingSet	findRelevantRings() Deprecated. Finds the Set of Relevant Rings.
IRingSet	findSSSR() Deprecated. Finds a Smallest Set of Smallest Rings.
int[]	getEquivalenceClassesSizeVector() Deprecated. Returns a vector containing the size of the "interchangeability" equivalence classes.
int[]	getSSSRWeightVector() Deprecated. Returns a vector containing the lengths of the rings in a SSSR.

Methods inherited from class java.lang.Object

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

Constructor Detail

SSSRFinder

public SSSRFinder(IAtomContainer container)

Deprecated.

Constructs a SSSRFinder for a specified molecule.

Parameters:

container - the molecule to be searched for rings

Method Detail

findSSSR

public IRingSet findSSSR()

Deprecated.

Finds a Smallest Set of Smallest Rings. The returned set is not uniquely defined.

Returns:

a RingSet containing the SSSR

findEssentialRings

public IRingSet findEssentialRings()

Deprecated.

Finds the Set of Essential Rings. These rings are contained in every possible SSSR. The returned set is uniquely defined.

Returns:

a RingSet containing the Essential Rings

findRelevantRings

public IRingSet findRelevantRings()

Deprecated.

Finds the Set of Relevant Rings. These rings are contained in every possible SSSR. The returned set is uniquely defined.

Returns:

a RingSet containing the Relevant Rings

findEquivalenceClasses

public List findEquivalenceClasses()

Deprecated.

Finds the "interchangeability" equivalence classes. The interchangeability relation is described in [GLS00].

Returns:

a List of RingSets containing the rings in an equivalence class

getSSSRWeightVector

public int[] getSSSRWeightVector()

Deprecated.

Returns a vector containing the lengths of the rings in a SSSR. The vector is uniquely defined for any SSSR of a molecule.

Returns:

An int[] containing the length of the rings in a SSSR

getEquivalenceClassesSizeVector

public int[] getEquivalenceClassesSizeVector()

Deprecated.

Returns a vector containing the size of the "interchangeability" equivalence classes. The vector is uniquely defined for any SSSR of a molecule.

Returns:

An int[] containing the size of the equivalence classes in a SSSR