org.openscience.cdk.tautomers

Class InChITautomerGenerator

java.lang.Object

org.openscience.cdk.tautomers.InChITautomerGenerator

public final class InChITautomerGenerator
extends Object

Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI. Algorithm described in [Thalheim, T. and Vollmer, A. and Ebert, R. and Kuehne, R. and Schuurmann, G., Tautomer Identification and Tautomer Structure Generation Based on the InChI Code, J. Chem. Inf. Model., 2010, 50:1223-1232, doi:10.1021/ci1001179].
Provide your input molecules in Kekule form, and make sure atom type are perceived.
When creating an input molecule by reading an MDL file, make sure to set implicit hydrogens. See the InChITautomerGeneratorTest test case.

Author:

Mark Rijnbeek

Source code:

master

Belongs to CDK module:

tautomer

Field Summary

Fields

Modifier and Type	Field and Description
static int	KETO_ENOL Generate InChI with -KET (keto-enol tautomers) option.
static int	ONE_FIVE_SHIFT Generate InChI with -15T (1,5-shift tautomers) option.

Constructor Summary

Constructors

Constructor and Description
InChITautomerGenerator() Create a tautomer generator, keto-enol (-KET) and 1,5-shifts (-15T) are disabled.
InChITautomerGenerator(int flags) Create a tautomer generator specifygin whether to enable, keto-enol (-KET) and 1,5-shifts (-15T).

Method Summary

Methods

Modifier and Type	Method and Description
List<IAtomContainer>	getTautomers(IAtomContainer mol) Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.
List<IAtomContainer>	getTautomers(IAtomContainer mol, String inchi) Deprecated. use getTautomers(IAtomContainer) directly

Methods inherited from class java.lang.Object

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

Field Detail

KETO_ENOL

public static final int KETO_ENOL

Generate InChI with -KET (keto-enol tautomers) option.

See Also:

Constant Field Values

ONE_FIVE_SHIFT

public static final int ONE_FIVE_SHIFT

Generate InChI with -15T (1,5-shift tautomers) option.

See Also:

Constant Field Values

Constructor Detail

InChITautomerGenerator

public InChITautomerGenerator(int flags)

Create a tautomer generator specifygin whether to enable, keto-enol (-KET) and 1,5-shifts (-15T).

// enabled -KET option
 InChITautomerGenerator tautgen = new InChITautomerGenerator(InChITautomerGenerator.KETO_ENOL);
 // enabled both -KET and -15T
 InChITautomerGenerator tautgen = new InChITautomerGenerator(InChITautomerGenerator.KETO_ENOL | InChITautomerGenerator.ONE_FIVE_SHIFT);
 

Parameters:

flags - the options

InChITautomerGenerator

public InChITautomerGenerator()

Create a tautomer generator, keto-enol (-KET) and 1,5-shifts (-15T) are disabled.

Method Detail

getTautomers

public List<IAtomContainer> getTautomers(IAtomContainer mol)
                                  throws CDKException,
                                         CloneNotSupportedException

Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.

Parameters:

mol - molecule for which to generate tautomers

Returns:

a list of tautomers, if any

Throws:

CDKException

CloneNotSupportedException

getTautomers

@Deprecated
public List<IAtomContainer> getTautomers(IAtomContainer mol,
                                           String inchi)
                                  throws CDKException,
                                         CloneNotSupportedException

Deprecated. use getTautomers(IAtomContainer) directly

This method is slower than recalculating the InChI with getTautomers(IAtomContainer) as the mapping between the two can be found more efficiently.

Parameters:

mol -

inchi -

Returns:

Throws:

CDKException

CloneNotSupportedException