org.openscience.cdk.tautomers

Class InChITautomerGenerator

java.lang.Object

org.openscience.cdk.tautomers.InChITautomerGenerator

@TestClass(value="org.openscience.cdk.tautomers.InChITautomerGeneratorTest")
public class InChITautomerGenerator
extends Object

Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI. Algorithm described in .
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 test case.

Author:

Mark Rijnbeek

Constructor Summary

Constructors

Constructor and Description
InChITautomerGenerator()

Method Summary

Methods

Modifier and Type	Method and Description
List<IAtomContainer>	getTautomers(IAtomContainer molecule) Public method to get tautomers for an input molecule, based on the InChI which will be calculated by jniinchi.
List<IAtomContainer>	getTautomers(IAtomContainer inputMolecule, String inchi) Overloaded getTautomers(IAtomContainer) to get tautomers for an input molecule with the InChI already provided as input argument.

Methods inherited from class java.lang.Object

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

Constructor Detail

InChITautomerGenerator

public InChITautomerGenerator()

Method Detail

getTautomers

@TestMethod(value="test_withJniInchi,testAdenine")
public List<IAtomContainer> getTautomers(IAtomContainer molecule)
                                  throws CDKException,
                                         CloneNotSupportedException

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

Parameters:

molecule - molecule for which to generate tautomers

Returns:

a list of tautomers, if any

Throws:

CDKException

CloneNotSupportedException

getTautomers

@TestMethod(value="test1,test2,test3")
public List<IAtomContainer> getTautomers(IAtomContainer inputMolecule,
                                                String inchi)
                                  throws CDKException,
                                         CloneNotSupportedException

Overloaded getTautomers(IAtomContainer) to get tautomers for an input molecule with the InChI already provided as input argument.

Parameters:

inputMolecule - and input molecule for which to generate tautomers

inchi - InChI for the inpute molecule

Returns:

a list of tautomers

Throws:

CDKException

CloneNotSupportedException