org.openscience.cdk.smiles.smarts

Class SmartsPattern

java.lang.Object

org.openscience.cdk.isomorphism.Pattern

org.openscience.cdk.smiles.smarts.SmartsPattern

Deprecated.

@Deprecated
public final class SmartsPattern
extends Pattern

A Pattern for matching a single SMARTS query against multiple target compounds. The class should not be used for matching many queries against a single target as in substructure keyed fingerprints. The SMARTSQueryTool is currently a better option as less target initialistion is performed. Simple usage:

 Pattern ptrn = SmartsPattern.create("O[C@?H](C)CC");

 for (IAtomContainer ac : acs) {
   if (ptrn.matches(ac)) {
       // 'ac' contains the pattern
   }
 }
 

Obtaining a Mappings instance and determine the number of unique matches.

 Pattern ptrn = SmartsPattern.create("O[C@?H](C)CC");

 for (IAtomContainer ac : acs) {
   nUniqueHits += ptrn.matchAll(ac)
                      .countUnique();
 }
 

Author:

John May

Method Summary

Modifier and Type	Method and Description
static SmartsPattern	create(String smarts) Deprecated. Default SMARTS pattern constructor, passes in a null chem object builder.
static SmartsPattern	create(String smarts, IChemObjectBuilder builder) Deprecated. Create a Pattern that will match the given smarts query.
int[]	match(IAtomContainer container) Deprecated. Find a matching of this pattern in the target.
Mappings	matchAll(IAtomContainer target) Deprecated. Obtain the mappings of the query pattern against the target compound.
void	setPrepare(boolean doPrep) Deprecated. Sets whether the molecule should be "prepared" for a SMARTS match, including set ring flags and perceiving aromaticity.

Methods inherited from class org.openscience.cdk.isomorphism.Pattern

findIdentical, findSubstructure, matchAll, matches, matches

Methods inherited from class java.lang.Object

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

Method Detail

setPrepare

public void setPrepare(boolean doPrep)

Deprecated.

Sets whether the molecule should be "prepared" for a SMARTS match, including set ring flags and perceiving aromaticity. The main reason to skip preparation (via prepare(IAtomContainer)) is if it has already been done, for example when matching multiple SMARTS patterns.

Parameters:

doPrep - whether preparation should be done

match

public int[] match(IAtomContainer container)

Deprecated.

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!
     }
 }
 

Specified by:

match in class Pattern

Parameters:

container - the container to search for the pattern in

Returns:

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

matchAll

public Mappings matchAll(IAtomContainer target)

Deprecated.

Obtain the mappings of the query pattern against the target compound. Any initialisations required for the SMARTS match are automatically performed. The Daylight aromaticity model is applied clearing existing aromaticity. Do not use this for matching multiple SMARTS againsts the same container.

 Pattern ptrn = SmartsPattern.create("O[C@?H](C)CC");
 int nUniqueHits = 0;

 for (IAtomContainer ac : acs) {
   nUniqueHits += ptrn.matchAll(ac)
                      .countUnique();
 }
 

See Mappings for available methods.

Specified by:

matchAll in class Pattern

Parameters:

target - the target compound in which we want to match the pattern

Returns:

mappings of the query to the target compound

See Also:

Mappings

create

public static SmartsPattern create(String smarts,
                                   IChemObjectBuilder builder)
                            throws IOException

Deprecated.

Create a Pattern that will match the given smarts query.

Parameters:

smarts - SMARTS pattern string

builder - chem object builder used to create objects

Returns:

a new pattern

Throws:

IOException - the smarts could not be parsed

create

public static SmartsPattern create(String smarts)
                            throws IOException

Deprecated.

Default SMARTS pattern constructor, passes in a null chem object builder.

Parameters:

smarts - SMARTS pattern string

Returns:

a SMARTS pattern

Throws:

IOException - problem with SMARTS string syntax/semantics