org.openscience.cdk.ringsearch

Class AllRingsFinderMod

java.lang.Object

org.openscience.cdk.ringsearch.AllRingsFinderMod

@TestClass(value="org.openscience.cdk.ringsearch.AllRingsFinderTest")
public class AllRingsFinderMod
extends Object

Finds the Set of all Rings. This is an implementation of the algorithm published in . Some of the comments refer to pseudo code fragments listed in this article. The concept is that a regular molecular graph is converted into a path graph first, i.e. a graph where the edges are actually paths, i.e. can list several nodes that are implicitly connecting the two nodes between the path is formed. The paths that join one endnode are step by step fused and the joined nodes deleted from the pathgraph. What remains is a graph of paths that have the same start and endpoint and are thus rings.

WARNING: This class has now a timeout of 5 seconds, after which it aborts its ringsearch. The timeout value can be customized by the setTimeout() method of this class.
Also, by using the optional argument "maxRingSize" timeouts can possibly be avoided because recursion depth will be limited accordingly. Example: given a complex atom container and a maxRingSize of six, the find method will return all rings only of size six or smaller.

Author:

steinbeck

Created on:

2002-06-23

Field Summary

Fields

Modifier and Type	Field and Description
boolean	debug

Constructor Summary

Constructors

Constructor and Description
AllRingsFinderMod() Constructor for the AllRingsFinder with logging.
AllRingsFinderMod(boolean logging) Constructor for the AllRingsFinder.

Method Summary

Methods

Modifier and Type	Method and Description
void	checkTimeout() Checks if the timeout has been reached and throws an exception if so.
IRingSet	findAllRings(IAtomContainer atomContainer) Returns a ringset containing all rings in the given AtomContainer Calls findAllRings(org.openscience.cdk.interfaces.IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes)
IRingSet	findAllRings(IAtomContainer atomContainer, Integer maxRingSize) Returns a ringset containing all rings up to a provided maximum size in a given AtomContainer
IRingSet	findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer) Fings the set of all rings in a molecule Calls findAllRingsInIsolatedRingSystem(org.openscience.cdk.interfaces.IAtomContainer,Integer) with max ring size argument set to null (=unlimited ring sizes)
IRingSet	findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer, Integer maxRingSize) Finds the set of all rings in a molecule
long	getTimeout() Gets the timeout values in milliseconds of the AllRingsFinder object
AllRingsFinderMod	setTimeout(long timeout) Sets the timeout value in milliseconds of the AllRingsFinder object This is used to prevent this AllRingsFinder to run for ages in certain rare cases with ring systems of large size or special topology

Methods inherited from class java.lang.Object

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

Field Detail

debug

public boolean debug

Constructor Detail

AllRingsFinderMod

public AllRingsFinderMod(boolean logging)

Constructor for the AllRingsFinder.

Parameters:

logging - true=logging will be done (slower), false = no logging.

AllRingsFinderMod

public AllRingsFinderMod()

Constructor for the AllRingsFinder with logging.

Method Detail

findAllRings

@TestMethod(value="testFindAllRings_IAtomContainer,testBondsWithinRing")
public IRingSet findAllRings(IAtomContainer atomContainer)
                      throws CDKException

Returns a ringset containing all rings in the given AtomContainer Calls findAllRings(org.openscience.cdk.interfaces.IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes)

Parameters:

atomContainer - The AtomContainer to be searched for rings

Returns:

A RingSet with all rings in the AtomContainer

Throws:

CDKException - An exception thrown if something goes wrong or if the timeout limit is reached

findAllRings

public IRingSet findAllRings(IAtomContainer atomContainer,
                    Integer maxRingSize)
                      throws CDKException

Returns a ringset containing all rings up to a provided maximum size in a given AtomContainer

Parameters:

atomContainer - The AtomContainer to be searched for rings

maxRingSize - Maximum ring size to consider. Provides a possible breakout from recursion for complex compounds.

Returns:

A RingSet with all rings in the AtomContainer

Throws:

CDKException - An exception thrown if something goes wrong or if the timeout limit is reached

findAllRingsInIsolatedRingSystem

public IRingSet findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer)
                                          throws CDKException

Fings the set of all rings in a molecule Calls findAllRingsInIsolatedRingSystem(org.openscience.cdk.interfaces.IAtomContainer,Integer) with max ring size argument set to null (=unlimited ring sizes)

Parameters:

atomContainer - the molecule to be searched for rings

Returns:

a RingSet containing the rings in molecule

Throws:

CDKException - An exception thrown if something goes wrong or if the timeout limit is reached

findAllRingsInIsolatedRingSystem

public IRingSet findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer,
                                        Integer maxRingSize)
                                          throws CDKException

Finds the set of all rings in a molecule

Parameters:

atomContainer - the molecule to be searched for rings

maxRingSize - Maximum ring size to consider. Provides a possible breakout from recursion for complex compounds.

Returns:

a RingSet containing the rings in molecule

Throws:

CDKException - An exception thrown if something goes wrong or if the timeout limit is reached

checkTimeout

@TestMethod(value="testCheckTimeout")
public void checkTimeout()
                  throws CDKException

Checks if the timeout has been reached and throws an exception if so. This is used to prevent this AllRingsFinder to run for ages in certain rare cases with ring systems of large size or special topology.

Throws:

CDKException - The exception thrown in case of hitting the timeout

setTimeout

@TestMethod(value="testSetTimeout_long")
public AllRingsFinderMod setTimeout(long timeout)

Sets the timeout value in milliseconds of the AllRingsFinder object This is used to prevent this AllRingsFinder to run for ages in certain rare cases with ring systems of large size or special topology

Parameters:

timeout - The new timeout value

Returns:

a reference to the instance this method was called for

getTimeout

@TestMethod(value="testGetTimeout")
public long getTimeout()

Gets the timeout values in milliseconds of the AllRingsFinder object

Returns:

The timeout value