Package org.openscience.cdk.inchi

Class InChIToStructure

java.lang.Object

org.openscience.cdk.inchi.InChIToStructure

public class InChIToStructure
extends Object

This class generates a CDK IAtomContainer from an InChI string. It places calls to a JNI wrapper for the InChI C++ library.

The generated IAtomContainer will have all 2D and 3D coordinates set to 0.0, but may have atom parities set. Double bond and allene stereochemistry are not currently recorded.
Example usage // Generate factory - throws CDKException if native code does not load
InChIGeneratorFactory factory = new InChIGeneratorFactory();
// Get InChIToStructure
InChIToStructure intostruct = factory.getInChIToStructure(
inchi, DefaultChemObjectBuilder.getInstance()
);

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

IAtomContainer container = intostruct.getAtomContainer();

Author:

Sam Adams

Source code:

main

Belongs to CDK module:

inchi

Field Summary

Fields

Modifier and Type	Field	Description
protected IAtomContainer	molecule
protected io.github.dan2097.jnainchi.InchiOptions	options
protected io.github.dan2097.jnainchi.InchiInputFromInchiOutput	output

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	InChIToStructure(String inchi, IChemObjectBuilder builder)	Constructor.
protected	InChIToStructure(String inchi, IChemObjectBuilder builder, io.github.dan2097.jnainchi.InchiOptions options)	Constructor.
protected	InChIToStructure(String inchi, IChemObjectBuilder builder, String options)	Constructor.
protected	InChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected void	generateAtomContainerFromInchi(IChemObjectBuilder builder)	Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.
IAtomContainer	getAtomContainer()	Returns generated molecule.
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.
long[][]	getWarningFlags()	Returns warning flags, see INCHIDIFF in inchicmp.h.

Methods inherited from class java.lang.Object

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

Field Details

output

protected io.github.dan2097.jnainchi.InchiInputFromInchiOutput output

options

protected io.github.dan2097.jnainchi.InchiOptions options

molecule

protected IAtomContainer molecule

Constructor Details

InChIToStructure

protected InChIToStructure(String inchi,
 IChemObjectBuilder builder,
 io.github.dan2097.jnainchi.InchiOptions options)
                    throws CDKException

Constructor. Generates CDK AtomContainer from InChI.

Parameters:

inchi -

Throws:

CDKException

InChIToStructure

protected InChIToStructure(String inchi,
 IChemObjectBuilder builder)
                    throws CDKException

Constructor. Generates CDK AtomContainer from InChI.

Parameters:

inchi -

Throws:

CDKException

InChIToStructure

protected InChIToStructure(String inchi,
 IChemObjectBuilder builder,
 String options)
                    throws CDKException

Constructor. Generates CMLMolecule from InChI.

Parameters:

inchi -

options -

Throws:

CDKException

InChIToStructure

protected InChIToStructure(String inchi,
 IChemObjectBuilder builder,
 List<String> options)
                    throws CDKException

Constructor. Generates CMLMolecule from InChI.

Parameters:

inchi -

options -

Throws:

CDKException

Method Details

generateAtomContainerFromInchi

protected void generateAtomContainerFromInchi(IChemObjectBuilder builder)
                                       throws CDKException

Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.

Throws:

CDKException

getAtomContainer

public IAtomContainer getAtomContainer()

Returns generated molecule.

Returns:

An AtomContainer object

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

getMessage

public String getMessage()

Gets generated (error/warning) messages.

getLog

public String getLog()

Gets generated log.

getWarningFlags

public long[][] getWarningFlags()

Returns warning flags, see INCHIDIFF in inchicmp.h.

[x][y]:
x=0 => Reconnected if present in InChI otherwise Disconnected/Normal
x=1 => Disconnected layer if Reconnected layer is present
y=1 => Main layer or Mobile-H
y=0 => Fixed-H layer