org.openscience.cdk.inchi

Class InChIGeneratorFactory

java.lang.Object

org.openscience.cdk.inchi.InChIGeneratorFactory

@TestClass(value="org.openscience.cdk.inchi.InChIGeneratorFactoryTest")
public class InChIGeneratorFactory
extends Object

Factory providing access to InChIGenerator and InChIToStructure. See those classes for examples of use. These methods make use of the JNI-InChI library.

The InChIGeneratorFactory is a singleton class, which means that there exists only one instance of the class. An instance of this class is obtained with:

 InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
 

InChI/Structure interconversion is implemented in this way so that we can check whether or not the native code required is available. If the native code cannot be loaded during the first call to getInstance method (when the instance is created) a CDKException will be thrown. The most common problem is that the native code is not in the * the correct location. Java searches the locations in the PATH environmental variable, under Windows, and LD_LIBRARY_PATH under Linux, so the JNI-InChI native libraries must be in one of these locations. If the JNI-InChI jar file is being used and either the current working directory, or '.' are contained in PATH of LD_LIBRARY_PATH then the native code should be placed automatically. If the native files are in the correct location but fail to load, then they may need to be recompiled for your system. See:

• http://sourceforge.net/projects/jni-inchi
• http://www.iupac.org/inchi/

Author:

Sam Adams

Method Summary

Methods

Modifier and Type	Method and Description
InChIGenerator	getInChIGenerator(IAtomContainer container) Gets an Standard InChI generator for a IAtomContainer.
InChIGenerator	getInChIGenerator(IAtomContainer container, List<net.sf.jniinchi.INCHI_OPTION> options) Gets InChI generator for CDK IAtomContainer.
InChIGenerator	getInChIGenerator(IAtomContainer container, String options) Gets InChI generator for CDK IAtomContainer.
InChIToStructure	getInChIToStructure(String inchi, IChemObjectBuilder builder) Gets structure generator for an InChI string.
InChIToStructure	getInChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options) Gets structure generator for an InChI string.
InChIToStructure	getInChIToStructure(String inchi, IChemObjectBuilder builder, String options) Gets structure generator for an InChI string.
static InChIGeneratorFactory	getInstance() Gives the one InChIGeneratorFactory instance, if needed also creates it.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

@TestMethod(value="testGetInstance")
public static InChIGeneratorFactory getInstance()
                                         throws CDKException

Gives the one InChIGeneratorFactory instance, if needed also creates it.

Returns:

the one InChIGeneratorFactory instance

Throws:

CDKException - if unable to load native code when attempting to create the factory

getInChIGenerator

@TestMethod(value="testGetInChIGenerator_IAtomContainer")
public InChIGenerator getInChIGenerator(IAtomContainer container)
                                 throws CDKException

Gets an Standard InChI generator for a IAtomContainer.

Parameters:

container - AtomContainer to generate InChI for.

Returns:

the InChI generator object

Throws:

CDKException - if the generator cannot be instantiated

getInChIGenerator

@TestMethod(value="testGetInChIGenerator_IAtomContainer_String")
public InChIGenerator getInChIGenerator(IAtomContainer container,
                                               String options)
                                 throws CDKException

Gets InChI generator for CDK IAtomContainer.

Parameters:

container - AtomContainer to generate InChI for.

options - String of options for InChI generation.

Returns:

the InChI generator object

Throws:

CDKException - if the generator cannot be instantiated

getInChIGenerator

@TestMethod(value="testGetInChIGenerator_IAtomContainer_List")
public InChIGenerator getInChIGenerator(IAtomContainer container,
                                               List<net.sf.jniinchi.INCHI_OPTION> options)
                                 throws CDKException

Gets InChI generator for CDK IAtomContainer.

Parameters:

container - AtomContainer to generate InChI for.

options - List of options (net.sf.jniinchi.INCHI_OPTION) for InChI generation.

Returns:

the InChI generator object

Throws:

CDKException - if the generator cannot be instantiated

getInChIToStructure

@TestMethod(value="testGetInChIToStructure_String_IChemObjectBuilder")
public InChIToStructure getInChIToStructure(String inchi,
                                                   IChemObjectBuilder builder)
                                     throws CDKException

Gets structure generator for an InChI string.

Parameters:

inchi - InChI to generate structure from.

builder - the builder to use

Returns:

the InChI structure generator object

Throws:

CDKException - if the generator cannot be instantiated

getInChIToStructure

@TestMethod(value="testGetInChIToStructure_String_IChemObjectBuilder_NullString")
public InChIToStructure getInChIToStructure(String inchi,
                                                   IChemObjectBuilder builder,
                                                   String options)
                                     throws CDKException

Gets structure generator for an InChI string.

Parameters:

inchi - InChI to generate structure from.

builder - the builder to employ

options - String of options for structure generation.

Returns:

the InChI structure generator object

Throws:

CDKException - if the generator cannot be instantiated

getInChIToStructure

@TestMethod(value="testGetInChIToStructure_String_IChemObjectBuilder_List")
public InChIToStructure getInChIToStructure(String inchi,
                                                   IChemObjectBuilder builder,
                                                   List<String> options)
                                     throws CDKException

Gets structure generator for an InChI string.

Parameters:

inchi - InChI to generate structure from.

options - List of options (net.sf.jniinchi.INCHI_OPTION) for structure generation.

builder - the builder to employ

Returns:

the InChI structure generator object

Throws:

CDKException - if the generator cannot be instantiated