org.openscience.cdk.ringsearch

Class AllRingsFinder

java.lang.Object

org.openscience.cdk.ringsearch.AllRingsFinder

public final class AllRingsFinder
extends Object

Compute the set of all rings in a molecule. This set includes every cyclic path of atoms. As the set is exponential it can be very large and is often impractical (e.g. fullerenes). To avoid combinatorial explosion there is a configurable threshold, at which the computation aborts. The AllRingsFinder.Threshold values have been precomputed on PubChem-Compound and can be used with the usingThreshold(Threshold). Alternatively, other ring sets which are a subset of this set offer a tractable alternative.

 AllRingsFinder arf = new AllRingsFinder();
 for (IAtomContainer m : ms) {
     try {
         IRingSet rs = arf.findAllRings(m);
     } catch (CDKException e) {
         // molecule was too complex, handle error
     }
 }
 

Author:

steinbeck, johnmay

See Also:

AllCycles

Source code:

master

Belongs to CDK module:

standard

Keywords:

rings, all rings

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AllRingsFinder.Threshold The threshold values provide a limit at which the computation stops.

Constructor Summary

Constructors

Constructor and Description
AllRingsFinder() Default constructor using a threshold of AllRingsFinder.Threshold.PubChem_99.
AllRingsFinder(boolean logging) Deprecated. turn logging off by setting the level in the logger implementation

Method Summary

Modifier and Type	Method and Description
void	checkTimeout() Deprecated. timeout not used
IRingSet	findAllRings(IAtomContainer container) Compute all rings in the given IAtomContainer.
IRingSet	findAllRings(IAtomContainer container, int maxRingSize) Compute all rings up to and including the maxRingSize.
IRingSet	findAllRingsInIsolatedRingSystem(IAtomContainer container) Compute all rings in the given IAtomContainer.
IRingSet	findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer, int maxRingSize) Compute all rings up to an including the maxRingSize.
long	getTimeout() Deprecated. timeout not used
AllRingsFinder	setTimeout(long timeout) Deprecated. use the new threshold (during construction)
static AllRingsFinder	usingThreshold(AllRingsFinder.Threshold threshold) Create an AllRingsFinder instance using the given threshold.

Methods inherited from class java.lang.Object

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

Constructor Detail

AllRingsFinder

@Deprecated
public AllRingsFinder(boolean logging)

Deprecated. turn logging off by setting the level in the logger implementation

Constructor for the AllRingsFinder.

Parameters:

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

AllRingsFinder

public AllRingsFinder()

Default constructor using a threshold of AllRingsFinder.Threshold.PubChem_99.

Method Detail

findAllRings

public IRingSet findAllRings(IAtomContainer container)
                      throws CDKException

Compute all rings in the given IAtomContainer. The container is first partitioned into ring systems which are then processed separately. If the molecule has already be partitioned, consider using findAllRingsInIsolatedRingSystem(IAtomContainer).

Parameters:

container - The AtomContainer to be searched for rings

Returns:

A RingSet with all rings in the AtomContainer

Throws:

CDKException - An exception thrown if the threshold was exceeded

See Also:

findAllRings(IAtomContainer, int), findAllRingsInIsolatedRingSystem(IAtomContainer)

findAllRings

public IRingSet findAllRings(IAtomContainer container,
                             int maxRingSize)
                      throws CDKException

Compute all rings up to and including the maxRingSize. The container is first partitioned into ring systems which are then processed separately. If the molecule has already be partitioned, consider using findAllRingsInIsolatedRingSystem(IAtomContainer, int).

Parameters:

container - 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 the threshold was exceeded

findAllRingsInIsolatedRingSystem

public IRingSet findAllRingsInIsolatedRingSystem(IAtomContainer container)
                                          throws CDKException

Compute all rings in the given IAtomContainer. No pre-processing is done on the container.

Parameters:

container - The Atom Container to find the ring systems of

Returns:

RingSet for the container

Throws:

CDKException - An exception thrown if the threshold was exceeded

findAllRingsInIsolatedRingSystem

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

Compute all rings up to an including the maxRingSize. No pre-processing is done on the container.

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 the threshold was exceeded

checkTimeout

@Deprecated
public void checkTimeout()
                              throws CDKException

Deprecated. timeout not used

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

@Deprecated
public AllRingsFinder setTimeout(long timeout)

Deprecated. use the new threshold (during construction)

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

@Deprecated
public long getTimeout()

Deprecated. timeout not used

Gets the timeout values in milliseconds of the AllRingsFinder object

Returns:

The timeout value

usingThreshold

public static AllRingsFinder usingThreshold(AllRingsFinder.Threshold threshold)

Create an AllRingsFinder instance using the given threshold.

 // import static AllRingsFinder.Threshold.PubChem_99;
 AllRingsFinder arf = AllRingsFinder.usingThreshold(PubChem_99);
 

Parameters:

threshold - the threshold value

Returns:

instance with the set threshold