org.openscience.cdk.isomorphism

Class ComponentGrouping

java.lang.Object

org.openscience.cdk.isomorphism.ComponentGrouping

All Implemented Interfaces:

com.google.common.base.Predicate<int[]>

public final class ComponentGrouping
extends Object
implements com.google.common.base.Predicate<int[]>

A predicate for verifying component level grouping in query/target structure matching. The grouping is used by SMARTS and is critical to querying reactions. The grouping specifies that substructures in the query should match to separate components in the target. The grouping specification is indicated by an int[] array of length (|V(query)| + 1). The final index indicates the maximum component group (in the query). A specification of '0' indicates there are no grouping restrictions.

 // grouping is actually set by SMARTS parser but this shows how it's stored
 query.setProperty(ComponentGrouping.KEY, grouping);

 IAtomContainer query, target;
 Pattern        pattern = ...; // create pattern for query

 // filter for mappings which respect component grouping in the query
 Iterables.filter(pattern.matchAll(target),
                  new ComponentGrouping(query, target));
 

Author:

John May

See Also:

Pattern

Belongs to CDK module:

isomorphism

Field Summary

Fields

Modifier and Type	Field and Description
static String	KEY Key indicates where the grouping should be store in the query properties.

Constructor Summary

Constructors

Constructor and Description
ComponentGrouping(IAtomContainer query, IAtomContainer target) Create a predicate to match components for the provided query and target.
ComponentGrouping(int[] grouping, int[] targetComponents) Create a predicate to match components for the provided query (grouping) and target (connected components).

Method Summary

Methods

Modifier and Type	Method and Description
boolean	apply(int[] mapping) Does the mapping respected the component grouping specified by the query.

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.google.common.base.Predicate

equals

Field Detail

KEY

public static final String KEY

Key indicates where the grouping should be store in the query properties.

See Also:

Constant Field Values

Constructor Detail

ComponentGrouping

public ComponentGrouping(IAtomContainer query,
                 IAtomContainer target)

Create a predicate to match components for the provided query and target. The target is converted to an adjacency list (GraphUtil.toAdjList(IAtomContainer)) and the query components extracted from the property KEY in the query.

Parameters:

query - query structure

target - target structure

ComponentGrouping

public ComponentGrouping(int[] grouping,
                 int[] targetComponents)

Create a predicate to match components for the provided query (grouping) and target (connected components).

Parameters:

grouping - query grouping

targetComponents - connected component of the target

Method Detail

apply

public boolean apply(int[] mapping)

Does the mapping respected the component grouping specified by the query.

Specified by:

apply in interface com.google.common.base.Predicate<int[]>

Parameters:

mapping - a permutation of the query vertices

Returns:

the mapping preserves the specified grouping