Package org.openscience.cdk.tautomers
Class InChITautomerGenerator
java.lang.Object
org.openscience.cdk.tautomers.InChITautomerGenerator
Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI.
Algorithm described in [Thalheim, T. et. al.. J. Chem. Inf. Model.. 2010. 50].
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.
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:
- main
- Belongs to CDK module:
- tautomer
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
Generate InChI with -KET (keto-enol tautomers) option.static final int
Generate InChI with -15T (1,5-shift tautomers) option. -
Constructor Summary
ConstructorsConstructorDescriptionCreate 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
Modifier and TypeMethodDescriptionPublic method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.getTautomers
(IAtomContainer mol, String inchi) Deprecated.
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Field Details
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KETO_ENOL
public static final int KETO_ENOLGenerate InChI with -KET (keto-enol tautomers) option.- See Also:
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ONE_FIVE_SHIFT
public static final int ONE_FIVE_SHIFTGenerate InChI with -15T (1,5-shift tautomers) option.- See Also:
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Constructor Details
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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
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InChITautomerGenerator
public InChITautomerGenerator()Create a tautomer generator, keto-enol (-KET) and 1,5-shifts (-15T) are disabled.
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Method Details
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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
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getTautomers
@Deprecated public List<IAtomContainer> getTautomers(IAtomContainer mol, String inchi) throws CDKException, CloneNotSupportedException Deprecated.usegetTautomers(IAtomContainer)
directlyThis method is slower than recalculating the InChI withgetTautomers(IAtomContainer)
as the mapping between the two can be found more efficiently.- Parameters:
mol
-inchi
-- Returns:
- Throws:
CDKException
CloneNotSupportedException
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getTautomers(IAtomContainer)
directly