com.chemaxon.mapper

Class AutoMapper

java.lang.Object

com.chemaxon.mapper.AutoMapper

All Implemented Interfaces:

Mapper<RxnMolecule>

public final class AutoMapper
extends Object
implements Mapper<RxnMolecule>

AutoMapper is a tool that performs automated chemical reaction mapping. The term mapping refers to the association of reactant side atoms to product side atoms. It can also identify and mark the reaction center during mapping.

AutoMapper supports three mapping styles:

• Mapper.MappingStyle.COMPLETE (default)
• Mapper.MappingStyle.CHANGING
• Mapper.MappingStyle.MATCHING

Helper functions are added to support concurrent mapping of reactions coming from various sources, such as

• files
• collections (Collection)
• iterators (Iterator).

API usage examples

Basic example, shows how to map a single reaction:

 RxnMolecule reaction = RxnMolecule.getReaction(MolImporter
                .importMol("COC1OC(CO)C(OC)C(O)C1O.OS(O)(=O)=O>>COC1OC(COS(O)(=O)=O)C(OC)C(O)C1O.[H]O[H]"));
 AutoMapper mapper = new AutoMapper();
 mapper.map(reaction);
 System.out.println(MolExporter.exportToFormat(reaction, "smiles"));
 

Map all reactions in a file, and mark the reaction centers:

 MolImporter importer = new MolImporter("unmapped.smiles");
 MolExporter exporter = new MolExporter("mapped.mrv", "mrv");
 AutoMapper.mapReaction(importer, exporter, new AutoMapper.Options().setMarkBonds(true));
 importer.close();
 exporter.close();
 

Map reactions during iteration:

 MolImporter importer = new MolImporter("unmapped.smiles");
 Iterator<Molecule> mappedMoleculeIterator = AutoMapper.iterator(importer.iterator());
 while (mappedMoleculeIterator.hasNext()) {
        Molecule mappedReaction = mappedMoleculeIterator.next();
        // do something with the mapped reaction ...
 }
 importer.close();
 

In concurrent mode reactions are cached. The default cache size is 1000, which can be overridden with "chemaxon.automapper.AutoMapper.cacheSize" Java system property. In case of invalid cache size (not positive, or not a valid number) the default value is used.

Since:

6.0

Author:

Istvan Rabel, Rita Vereb

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AutoMapper.Options Option object for set common options when mapping called by static way.

Nested classes/interfaces inherited from interface com.chemaxon.mapper.Mapper

Mapper.MappingStyle

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_CACHE_SIZE default cache size
static String	DEFAULT_CACHE_SIZE_PROPERTY cache size property key

Constructor Summary

Constructors

Constructor and Description
AutoMapper() Initializes an AutoMapper object

Method Summary

Methods

Modifier and Type	Method and Description
Mapper.MappingStyle	getMappingStyle() Returns the mapping style of the mapper.
boolean	isKeepMapping() Returns if the mapper will keep the initial mapping or not.
boolean	isMarkBonds() Returns if the mapper marks the reaction center bonds or not.
static Iterator<Molecule>	iterator(Iterator<Molecule> iterator) Returns an iterator that will return the mapped molecules from the specified iterator. NOTE: the returned iterator provides the same molecule instances with maps added
static Iterator<Molecule>	iterator(Iterator<Molecule> iterator, AutoMapper.Options options) Returns an iterator that will return the mapped molecules from the specified iterator using the specified number of threads for mapping. NOTE: the returned iterator provides the same molecule instances with maps added
static Iterator<Molecule>	iterator(Iterator<Molecule> iterator, Mapper<RxnMolecule>... mappers) Returns an iterator that will return the mapped molecules from the specified iterator using the specified mappers for mapping.
boolean	map(RxnMolecule reaction) Maps the reaction.
static void	mapReaction(AutoMapper.Options options, Molecule... reactions) Maps the reactions in the specified collection using the specified options.
static void	mapReaction(Collection<Molecule> reactions) Maps the reactions in the specified collection using multiple threads if possible.
static void	mapReaction(Collection<Molecule> reactions, AutoMapper.Options options) Maps the reactions in the specified collection using the specified options.
static void	mapReaction(Collection<Molecule> reactions, Mapper<RxnMolecule>... mappers) Maps the reactions in the specified collection using the specified mappers in multiple threads.
static void	mapReaction(Mapper<RxnMolecule>[] mappers, Molecule... reactions) Maps the reactions in the specified collection using the specified mappers in multiple threads.
static void	mapReaction(Molecule... reactions) Maps the reactions in the specified collection using multiple threads if possible.
static void	mapReaction(MolImporter importer, MolExporter exporter) Reads the reactions from the importer, maps them, and writes to the exporter.
static void	mapReaction(MolImporter importer, MolExporter exporter, AutoMapper.Options options) Reads the reactions from the importer, maps them, and writes to the exporter.
static void	mapReaction(MolImporter importer, MolExporter exporter, Mapper<RxnMolecule>... mappers) Reads the reactions from the importer, maps them, and writes to the exporter.
void	setKeepMapping(boolean keepMapping) Sets if the initial mapping of the given object should be kept or not.
void	setMappingStyle(Mapper.MappingStyle style) Sets the mapping style
void	setMarkBonds(boolean markResult) Sets if the changing bonds should be marked or not.
static void	unmap(Molecule item) Remove atom maps from the given structure

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_CACHE_SIZE_PROPERTY

public static final String DEFAULT_CACHE_SIZE_PROPERTY

cache size property key

See Also:

Constant Field Values

DEFAULT_CACHE_SIZE

public static final int DEFAULT_CACHE_SIZE

default cache size

See Also:

Constant Field Values

Constructor Detail

AutoMapper

public AutoMapper()

Initializes an AutoMapper object

Method Detail

mapReaction

public static void mapReaction(Molecule... reactions)

Maps the reactions in the specified collection using multiple threads if possible.

Parameters:

reactions - the array of reactions to map

mapReaction

public static void mapReaction(AutoMapper.Options options,
               Molecule... reactions)

Maps the reactions in the specified collection using the specified options.

Parameters:

options - the mapping options to use

reactions - the array of reactions to map

See Also:

AutoMapper.Options

mapReaction

public static void mapReaction(Mapper<RxnMolecule>[] mappers,
               Molecule... reactions)

Maps the reactions in the specified collection using the specified mappers in multiple threads. The number of mappers specifies the number of threads to use.

Parameters:

mappers - the mappers to use

reactions - the collections of reactions to map

mapReaction

public static void mapReaction(Collection<Molecule> reactions)

Maps the reactions in the specified collection using multiple threads if possible.

Parameters:

reactions - the collection of reactions to map

mapReaction

public static void mapReaction(Collection<Molecule> reactions,
               AutoMapper.Options options)

Maps the reactions in the specified collection using the specified options.

Parameters:

reactions - the collections of reactions to map

options - the mapping options to use

See Also:

AutoMapper.Options

mapReaction

public static void mapReaction(Collection<Molecule> reactions,
               Mapper<RxnMolecule>... mappers)

Maps the reactions in the specified collection using the specified mappers in multiple threads. The number of mappers specifies the number of threads to use.

Parameters:

reactions - the collections of reactions to map

mappers - the mappers to use

mapReaction

public static void mapReaction(MolImporter importer,
               MolExporter exporter)
                        throws MolExportException,
                               IOException

Reads the reactions from the importer, maps them, and writes to the exporter. Uses multiple threads for mapping if possible.

Parameters:

importer - the importer to read reactions from

exporter - the exporter to write mapped reactions to

Throws:

MolExportException - on export failure

IOException - on export failure

mapReaction

public static void mapReaction(MolImporter importer,
               MolExporter exporter,
               AutoMapper.Options options)
                        throws MolExportException,
                               IOException

Reads the reactions from the importer, maps them, and writes to the exporter. Uses the specified number of threads for mapping.

Parameters:

importer - the importer to read reactions from

exporter - the exporter to write mapped reactions to

options - the mapping options to use for mapping

Throws:

MolExportException - on export failure

IOException - on export failure

See Also:

AutoMapper.Options

mapReaction

public static void mapReaction(MolImporter importer,
               MolExporter exporter,
               Mapper<RxnMolecule>... mappers)
                        throws MolExportException,
                               IOException

Reads the reactions from the importer, maps them, and writes to the exporter. Uses the specified mappers for mapping. The number of mappers specified the number of threads to use.

Parameters:

importer - the importer to read reactions from

exporter - the exporter to write mapped reactions to

mappers - the mappers to use

Throws:

MolExportException - on export failure

IOException - on export failure

iterator

public static Iterator<Molecule> iterator(Iterator<Molecule> iterator)

Returns an iterator that will return the mapped molecules from the specified iterator.
NOTE: the returned iterator provides the same molecule instances with maps added

Parameters:

iterator - the input data iterator

Returns:

an iterator that provides the mapped molecules, may not support Iterator.remove().

iterator

public static Iterator<Molecule> iterator(Iterator<Molecule> iterator,
                          AutoMapper.Options options)

Returns an iterator that will return the mapped molecules from the specified iterator using the specified number of threads for mapping.
NOTE: the returned iterator provides the same molecule instances with maps added

Parameters:

iterator - the input data iterator

options - the mapping options to use

Returns:

an iterator that provides the mapped molecules, may not support Iterator.remove().

See Also:

AutoMapper.Options

iterator

public static Iterator<Molecule> iterator(Iterator<Molecule> iterator,
                          Mapper<RxnMolecule>... mappers)

Returns an iterator that will return the mapped molecules from the specified iterator using the specified mappers for mapping. The number of mappers specifies the number of threads to use.
NOTE: the returned iterator provides the same molecule instances with maps added

Parameters:

iterator - the input data iterator

mappers - the mappers to use

Returns:

an iterator that provides the mapped molecules, may not support Iterator.remove().

map

public boolean map(RxnMolecule reaction)

Maps the reaction.

Specified by:

map in interface Mapper<RxnMolecule>

Parameters:

reaction - is the reaction to be mapped

Returns:

true if mapping was successful

setMappingStyle

public void setMappingStyle(Mapper.MappingStyle style)

Sets the mapping style

Specified by:

setMappingStyle in interface Mapper<RxnMolecule>

Parameters:

style - the mapping style to set

See Also:

Mapper.MappingStyle.COMPLETE, Mapper.MappingStyle.CHANGING, Mapper.MappingStyle.MATCHING

getMappingStyle

public Mapper.MappingStyle getMappingStyle()

Returns the mapping style of the mapper.

Returns:

the mapping style of the mapper

setMarkBonds

public void setMarkBonds(boolean markResult)

Description copied from interface: Mapper

Sets if the changing bonds should be marked or not.

Specified by:

setMarkBonds in interface Mapper<RxnMolecule>

Parameters:

markResult - if the reaction center should be marked or not

isMarkBonds

public boolean isMarkBonds()

Returns if the mapper marks the reaction center bonds or not.

Returns:

if the mapper marks the reaction center bonds or not

setKeepMapping

public void setKeepMapping(boolean keepMapping)

Description copied from interface: Mapper

Sets if the initial mapping of the given object should be kept or not.

Specified by:

setKeepMapping in interface Mapper<RxnMolecule>

Parameters:

keepMapping - if the initial mapping of the given object should be kept or not

isKeepMapping

public boolean isKeepMapping()

Returns if the mapper will keep the initial mapping or not.

Returns:

if the mapper will keep the initial mapping or not

unmap

public static void unmap(Molecule item)

Remove atom maps from the given structure

Parameters:

item - the structure to unmap