org.openscience.cdk.isomorphism

Class Pattern

java.lang.Object

org.openscience.cdk.isomorphism.Pattern

Direct Known Subclasses:

DfPattern, SmartsPattern, SmartsPattern, Ullmann, VentoFoggia

public abstract class Pattern
extends Object

A structural pattern for finding an exact matching in a target compound.

Author:

John May

Belongs to CDK module:

isomorphism

Constructor Summary

Constructors

Constructor and Description
Pattern()

Method Summary

Modifier and Type	Method and Description
static Pattern	findIdentical(IAtomContainer query) Create a pattern which can be used to find molecules which are the same as the query structure.
static Pattern	findSubstructure(IAtomContainer query) Create a pattern which can be used to find molecules which contain the query structure.
abstract int[]	match(IAtomContainer target) Find a matching of this pattern in the target.
abstract Mappings	matchAll(IAtomContainer target) Find all mappings of this pattern in the target.
Mappings	matchAll(IReaction target) Find all mappings of this pattern in the target reaction.
boolean	matches(IAtomContainer target) Determine if there is a mapping of this pattern in the target.
boolean	matches(IReaction target) Determine if there is a mapping of this pattern in the target reaction.

Methods inherited from class java.lang.Object

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

Constructor Detail

Pattern

public Pattern()

Method Detail

match

public abstract int[] match(IAtomContainer target)

Find a matching of this pattern in the target. If no such order exist an empty mapping is returned. Depending on the implementation stereochemistry may be checked (recommended).

 Pattern        pattern = ...; // create pattern
 for (IAtomContainer m : ms) {
     int[] mapping = pattern.match(m);
     if (mapping.length > 0) {
         // found mapping!
     }
 }
 

Parameters:

target - the container to search for the pattern in

Returns:

the mapping from the pattern to the target or an empty array

matches

public boolean matches(IAtomContainer target)

Determine if there is a mapping of this pattern in the target. Depending on the implementation stereochemistry may be checked (recommended).

 Pattern        pattern = ...; // create pattern
 for (IAtomContainer m : ms) {
     if (pattern.matches(m)) {
         // found mapping!
     }
 }
 

Parameters:

target - the container to search for the pattern in

Returns:

the mapping from the pattern to the target

matches

public final boolean matches(IReaction target)

Determine if there is a mapping of this pattern in the target reaction.

 Pattern        pattern = ...; // create pattern
 for (IReaction r : rs) {
     if (pattern.matches(r)) {
         // found mapping!
     }
 }
 

Parameters:

target - the reaction to search for the pattern in

Returns:

the mapping from the pattern to the target

matchAll

public abstract Mappings matchAll(IAtomContainer target)

Find all mappings of this pattern in the target. Stereochemistry should not be checked to allow filtering with Mappings.stereochemistry().

 Pattern pattern = Pattern.findSubstructure(query);
 for (IAtomContainer m : ms) {
     for (int[] mapping : pattern.matchAll(m)) {
         // found mapping
     }
 }
 

Using the fluent interface (see Mappings) we can search and manipulate the mappings. Here's an example of finding the first 5 mappings and creating an array. If the mapper is lazy other states are simply not explored.

 // find only the first 5 mappings and store them in an array
 Pattern pattern  = Pattern.findSubstructure(query);
 int[][] mappings = pattern.matchAll(target)
                           .limit(5)
                           .toArray();
 

Parameters:

target - the container to search for the pattern in

Returns:

the mapping from the pattern to the target

See Also:

Mappings

matchAll

public final Mappings matchAll(IReaction target)

Find all mappings of this pattern in the target reaction.

 Pattern pattern = Pattern.findSubstructure(query);
 for (IReaction r : rs) {
     for (int[] mapping : pattern.matchAll(r)) {
         // found mapping
     }
 }
 

The reaction is inlined into a molecule and vs mapped id's correspond to the absolute atom index in the reaction when considered as reactants, agents, products ReactionManipulator.toMolecule(org.openscience.cdk.interfaces.IReaction).

Parameters:

target - the reaction to search for the pattern in

Returns:

the mapping from the pattern to the target

See Also:

Mappings, ReactionManipulator.toMolecule(IReaction)

findSubstructure

public static Pattern findSubstructure(IAtomContainer query)

Create a pattern which can be used to find molecules which contain the query structure. The default structure search implementation is VentoFoggia.

Parameters:

query - the substructure to find

Returns:

a pattern for finding the query

See Also:

VentoFoggia

findIdentical

public static Pattern findIdentical(IAtomContainer query)

Create a pattern which can be used to find molecules which are the same as the query structure. The default structure search implementation is VentoFoggia.

Parameters:

query - the substructure to find

Returns:

a pattern for finding the query

See Also:

VentoFoggia