org.openscience.cdk.inchi

Class InChIGenerator

java.lang.Object

org.openscience.cdk.inchi.InChIGenerator

public class InChIGenerator
extends Object

This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer. It places calls to a JNI wrapper for the InChI C++ library.

If the atom container has 3D coordinates for all of its atoms then they will be used, otherwise 2D coordinates will be used if available.

Spin multiplicities and some aspects of stereochemistry are not currently handled completely. Example usage
// Generate factory - throws CDKException if native code does not load
InChIGeneratorFactory factory = new InChIGeneratorFactory();
// Get InChIGenerator
InChIGenerator gen = factory.getInChIGenerator(container);

INCHI_RET ret = gen.getReturnStatus();
if (ret == INCHI_RET.WARNING) {
// InChI generated, but with warning message
System.out.println("InChI warning: " + gen.getMessage());
} else if (ret != INCHI_RET.OKAY) {
// InChI generation failed
throw new CDKException("InChI failed: " + ret.toString()
+ " [" + gen.getMessage() + "]");
}

String inchi = gen.getInchi();
String auxinfo = gen.getAuxInfo();

TODO: distinguish between singlet and undefined spin multiplicity
TODO: double bond and allene parities
TODO: problem recognising bond stereochemistry

Author:

Sam Adams

Source code:

master

Belongs to CDK module:

inchi

Field Summary

Fields

Modifier and Type	Field and Description
protected IAtomContainer	atomContainer AtomContainer instance refers to.
protected io.github.dan2097.jnainchi.InchiInput	input
protected io.github.dan2097.jnainchi.InchiOptions	options
protected io.github.dan2097.jnainchi.InchiOutput	output

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds) Constructor.
protected	InChIGenerator(IAtomContainer atomContainer, io.github.dan2097.jnainchi.InchiOptions options, boolean ignoreAromaticBonds)
protected	InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> opts, boolean ignoreAromaticBonds) Deprecated.
protected	InChIGenerator(IAtomContainer atomContainer, String optStr, boolean ignoreAromaticBonds) Constructor.

Method Summary

Modifier and Type	Method and Description
String	getAuxInfo() Gets auxillary information.
String	getInchi() Gets generated InChI string.
String	getInchiKey() Gets generated InChIKey string.
String	getLog() Gets generated log.
String	getMessage() Gets generated (error/warning) messages.
INCHI_RET	getReturnStatus() Deprecated. use getStatus
io.github.dan2097.jnainchi.InchiStatus	getStatus() Access the status of the InChI output.

Methods inherited from class java.lang.Object

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

Field Detail

options

protected io.github.dan2097.jnainchi.InchiOptions options

input

protected io.github.dan2097.jnainchi.InchiInput input

output

protected io.github.dan2097.jnainchi.InchiOutput output

atomContainer

protected IAtomContainer atomContainer

AtomContainer instance refers to.

Constructor Detail

InChIGenerator

protected InChIGenerator(IAtomContainer atomContainer,
                         io.github.dan2097.jnainchi.InchiOptions options,
                         boolean ignoreAromaticBonds)
                  throws CDKException

Throws:

CDKException

InChIGenerator

protected InChIGenerator(IAtomContainer atomContainer,
                         boolean ignoreAromaticBonds)
                  throws CDKException

Constructor. Generates InChI from CDK AtomContainer.

Reads atoms, bonds etc from atom container and converts to format InChI library requires, then calls the library.

Parameters:

atomContainer - AtomContainer to generate InChI for.

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

Throws:

CDKException - if there is an error during InChI generation

InChIGenerator

protected InChIGenerator(IAtomContainer atomContainer,
                         String optStr,
                         boolean ignoreAromaticBonds)
                  throws CDKException

Constructor. Generates InChI from CDK AtomContainer.

Reads atoms, bonds etc from atom container and converts to format InChI library requires, then calls the library.

Parameters:

atomContainer - AtomContainer to generate InChI for.

optStr - Space delimited string of options to pass to InChI library. Each option may optionally be preceded by a command line switch (/ or -).

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

Throws:

CDKException

InChIGenerator

@Deprecated
protected InChIGenerator(IAtomContainer atomContainer,
                                     List<INCHI_OPTION> opts,
                                     boolean ignoreAromaticBonds)
                              throws CDKException

Deprecated.

Constructor. Generates InChI from CDK AtomContainer.

Reads atoms, bonds etc from atom container and converts to format InChI library requires, then calls the library.

Parameters:

atomContainer - AtomContainer to generate InChI for.

opts - List of INCHI_OPTION.

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

Throws:

CDKException

Method Detail

getReturnStatus

@Deprecated
public INCHI_RET getReturnStatus()

Deprecated. use getStatus

Gets return status from InChI process. OKAY and WARNING indicate InChI has been generated, in all other cases InChI generation has failed. This returns the JNI INCHI enum and requires the optional "cdk-jniinchi-support" module to be loaded (or the full JNI InChI lib to be on the class path).

getStatus

public io.github.dan2097.jnainchi.InchiStatus getStatus()

Access the status of the InChI output.

Returns:

the status

getInchi

public String getInchi()

Gets generated InChI string.

getInchiKey

public String getInchiKey()
                   throws CDKException

Gets generated InChIKey string.

Throws:

CDKException

getAuxInfo

public String getAuxInfo()

Gets auxillary information.

getMessage

public String getMessage()

Gets generated (error/warning) messages.

getLog

public String getLog()

Gets generated log.