org.openscience.cdk.inchi

Class InChIGeneratorFactory

java.lang.Object

org.openscience.cdk.inchi.InChIGeneratorFactory

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

Source code:

master

Belongs to CDK module:

inchi

Method Summary

Modifier and Type	Method and Description
boolean	getIgnoreAromaticBonds() Deprecated.
InChIGenerator	getInChIGenerator(IAtomContainer container) Gets an Standard InChI generator for a IAtomContainer.
InChIGenerator	getInChIGenerator(IAtomContainer container, io.github.dan2097.jnainchi.InchiFlag... flags) Get an InChI generator providing flags to customise the generation.
InChIGenerator	getInChIGenerator(IAtomContainer container, io.github.dan2097.jnainchi.InchiOptions options) Get an InChI generator providing flags to customise the generation.
InChIGenerator	getInChIGenerator(IAtomContainer container, List<INCHI_OPTION> options) Deprecated. use getInChIGenerator(org.openscience.cdk.interfaces.IAtomContainer, io.github.dan2097.jnainchi.InchiOptions)
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.
void	setIgnoreAromaticBonds(boolean ignore) Deprecated. "the use of aromatic bonds is strongly discouraged" - InChI FAQ, the InChI will fail for many compounds if ignore aromatic bonds is not enabled and the compound have aromatic flags.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

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

setIgnoreAromaticBonds

@Deprecated
public void setIgnoreAromaticBonds(boolean ignore)

Deprecated. "the use of aromatic bonds is strongly discouraged" - InChI FAQ, the InChI will fail for many compounds if ignore aromatic bonds is not enabled and the compound have aromatic flags.

Sets whether aromatic bonds should be treated as single and double bonds for the InChI generation. The bond type INCHI_BOND_TYPE.ALTERN is considered special in contrast to single, double, and triple bonds, and is not bulletproof. If the molecule has clearly defined single and double bonds, the option can be used to force the class not to use the alternating bond type.

http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html#16.3

Parameters:

ignore - if aromatic bonds should be treated as bonds of type single and double

getIgnoreAromaticBonds

@Deprecated
public boolean getIgnoreAromaticBonds()

Deprecated.

Returns whether aromatic bonds are treated as single and double bonds for the InChI generation.

Returns:

if aromatic bonds are treated as bonds of type single and double

getInChIGenerator

public InChIGenerator getInChIGenerator(IAtomContainer container)
                                 throws CDKException

Gets an Standard InChI generator for a IAtomContainer. AuxInfo is not generated by this method, please use getInChIGenerator(IAtomContainer, List) with no options specified if you would like to generate AuxInfo.

Parameters:

container - AtomContainer to generate InChI for.

Returns:

the InChI generator object

Throws:

CDKException - if the generator cannot be instantiated

getInChIGenerator

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

@Deprecated
public InChIGenerator getInChIGenerator(IAtomContainer container,
                                                    List<INCHI_OPTION> options)
                                             throws CDKException

Deprecated. use getInChIGenerator(org.openscience.cdk.interfaces.IAtomContainer, io.github.dan2097.jnainchi.InchiOptions)

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

getInChIGenerator

public InChIGenerator getInChIGenerator(IAtomContainer container,
                                        io.github.dan2097.jnainchi.InchiFlag... flags)
                                 throws CDKException

Get an InChI generator providing flags to customise the generation. If you need to provide a timeout the method that accepts an InchiOptions should be used.

Parameters:

container - the molecule

flags - the option flags

Returns:

the InChI generator

Throws:

CDKException - something went wrong

See Also:

getInChIGenerator(org.openscience.cdk.interfaces.IAtomContainer, io.github.dan2097.jnainchi.InchiOptions)

getInChIGenerator

public InChIGenerator getInChIGenerator(IAtomContainer container,
                                        io.github.dan2097.jnainchi.InchiOptions options)
                                 throws CDKException

Get an InChI generator providing flags to customise the generation.

Parameters:

container - the molecule

options - the inchi option flags

Returns:

the InChI generator

Throws:

CDKException - something went wrong

getInChIToStructure

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

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

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