Examples with InChIGenerator org.openscience.cdk.inchi.InChIGenerator used on opensource projects

Example 36 with InChIGenerator

use of org.openscience.cdk.inchi.InChIGenerator in project MetFragRelaunched by ipb-halle.

the class GetRankOfCandidateCSV method calculateInchiKey.

/**
 * @param con
 * @return
 * @throws CDKException
 */
public static String calculateInchiKey(IAtomContainer con) throws CDKException {
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(con);
    CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(con.getBuilder());
    for (int i = 0; i < con.getAtomCount(); i++) {
        try {
            hAdder.addImplicitHydrogens(con, con.getAtom(i));
        } catch (CDKException e) {
            continue;
        }
    }
    AtomContainerManipulator.convertImplicitToExplicitHydrogens(con);
    InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
    InChIGenerator gen = factory.getInChIGenerator(con);
    return gen.getInchiKey().split("-")[0];
}

Example 37 with InChIGenerator

use of org.openscience.cdk.inchi.InChIGenerator in project MetFragRelaunched by ipb-halle.

the class GetRankOfCandidatePSV method calculateInchiKey.

/**
 * @param con
 * @return
 * @throws CDKException
 */
public static String calculateInchiKey(IAtomContainer con) throws CDKException {
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(con);
    CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(con.getBuilder());
    for (int i = 0; i < con.getAtomCount(); i++) {
        try {
            hAdder.addImplicitHydrogens(con, con.getAtom(i));
        } catch (CDKException e) {
            continue;
        }
    }
    AtomContainerManipulator.convertImplicitToExplicitHydrogens(con);
    InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
    InChIGenerator gen = factory.getInChIGenerator(con);
    return gen.getInchiKey().split("-")[0];
}

Example 38 with InChIGenerator

use of org.openscience.cdk.inchi.InChIGenerator in project bacting by egonw.

the class InChIManager method generate.

/**
 * Generates an InChI for the given {@link IMolecule}, using the given options.
 * This options String consists of one or more, space-delimited options, such as FixedH.
 *
 * @param molecule the {@link IMolecule} to create the InChI for
 * @return         an {@link InChI} object
 * @throws Exception
 */
public InChI generate(IMolecule molecule, String options) throws Exception {
    if (!isAvailable()) {
        return InChI.FAILED_TO_CALCULATE;
    }
    Object adapted = molecule.getAdapter(IAtomContainer.class);
    if (adapted != null) {
        IAtomContainer container = (IAtomContainer) adapted;
        IAtomContainer clone = (IAtomContainer) container.clone();
        // remove aromaticity flags
        for (IAtom atom : clone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
        for (IBond bond : clone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
        InChIGenerator gen = factory.getInChIGenerator(clone, options);
        InchiStatus status = gen.getStatus();
        if (status == InchiStatus.SUCCESS || status == InchiStatus.WARNING) {
            InChI inchi = new InChI();
            inchi.setValue(gen.getInchi());
            inchi.setKey(gen.getInchiKey());
            return inchi;
        } else {
            throw new InvalidParameterException("Error while generating InChI (" + status + "): " + gen.getMessage());
        }
    } else {
        throw new InvalidParameterException("Given molecule must be a CDKMolecule");
    }
}