org.openscience.cdk.inchi

Class InChIToStructure

java.lang.Object

org.openscience.cdk.inchi.InChIToStructure

@TestClass(value="org.openscience.cdk.inchi.InChIToStructureTest")
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

Method Summary

Methods

Modifier and Type	Method and Description
IAtomContainer	getAtomContainer() Returns generated molecule.
String	getLog() Gets generated log.
String	getMessage() Gets generated (error/warning) messages.
net.sf.jniinchi.INCHI_RET	getReturnStatus() Gets return status from InChI process.
long[][]	getWarningFlags() Returns warning flags, see INCHIDIFF in inchicmp.h.

Methods inherited from class java.lang.Object

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

Method Detail

getAtomContainer

@TestMethod(value="testGetAtomContainer")
public IAtomContainer getAtomContainer()

Returns generated molecule.

Returns:

An AtomContainer object

getReturnStatus

@TestMethod(value="testGetReturnStatus_EOF")
public net.sf.jniinchi.INCHI_RET getReturnStatus()

Gets return status from InChI process. OKAY and WARNING indicate InChI has been generated, in all other cases InChI generation has failed.

getMessage

@TestMethod(value="testGetMessage")
public String getMessage()

Gets generated (error/warning) messages.

getLog

@TestMethod(value="testGetLog")
public String getLog()

Gets generated log.

getWarningFlags

@TestMethod(value="testGetWarningFlags")
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