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

Example 1 with InChIGenerator

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

the class InChIDeuteriumGeneration method main.

public static void main(String[] args) throws Exception {
    boolean withAromaticRings = false;
    boolean combinatorial = true;
    /*
		 * read input inchis
		 */
    ArrayList<String> inchis = new ArrayList<String>();
    ArrayList<Integer> numberToAddDeuteriums = new ArrayList<Integer>();
    ArrayList<String> identifiers = new ArrayList<String>();
    BufferedReader breader = new BufferedReader(new FileReader(new File(args[0])));
    String line = "";
    int identifier = 1;
    while ((line = breader.readLine()) != null) {
        String[] tmp = line.trim().split("\\s+");
        inchis.add(tmp[0].trim());
        if (tmp.length >= 2)
            numberToAddDeuteriums.add(Integer.parseInt(tmp[1].trim()));
        if (tmp.length == 3)
            identifiers.add(tmp[2].trim());
        else
            identifiers.add(identifier + "");
        identifier++;
    }
    breader.close();
    /*
		 * generate deuterated version of inchi
		 */
    InChITautomerGenerator tg = new InChITautomerGenerator();
    java.io.BufferedWriter bwriter = null;
    if (args.length == 2) {
        bwriter = new java.io.BufferedWriter(new java.io.FileWriter(new java.io.File(args[1])));
    }
    CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
    for (int j = 0; j < inchis.size(); j++) {
        System.out.println(inchis.get(j));
        /*
			 * build the atom container
			 */
        IAtomContainer its = InChIGeneratorFactory.getInstance().getInChIToStructure(inchis.get(j), SilentChemObjectBuilder.getInstance()).getAtomContainer();
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(its);
        try {
            adder.addImplicitHydrogens(its);
        } catch (Exception e) {
            System.out.println("missed " + inchis.get(j) + " " + identifiers.get(j));
            continue;
        }
        AtomContainerManipulator.convertImplicitToExplicitHydrogens(its);
        int numberDeuteriums = 0;
        int numberDeuteriumsEasilyExchanged = 0;
        int numberDeuteriumsAromaticExchanged = 0;
        int[] toExchange = searchForDeuteriumExchangeablePositions(new String[] { "O", "N", "S" }, its);
        if (!combinatorial || (numberToAddDeuteriums.size() == 0 || toExchange.length <= numberToAddDeuteriums.get(j))) {
            for (int i = 0; i < toExchange.length; i++) {
                int numberExchanged = setAllExplicitDeuteriums(its, toExchange[i]);
                numberDeuteriums += numberExchanged;
                numberDeuteriumsEasilyExchanged += numberExchanged;
            }
        } else if (toExchange.length > numberToAddDeuteriums.get(j)) {
            ArrayList<IAtomContainer> deuteratedStrutures = new ArrayList<IAtomContainer>();
            ArrayList<Integer> numberDeuteriumsVec = new ArrayList<Integer>();
            ArrayList<Integer> numberDeuteriumsEasilyExchangedVec = new ArrayList<Integer>();
            // get all possible combinations of exchanges with given number
            // of exchangeable hydrogens
            int[][] combs = getCombinations(toExchange, numberToAddDeuteriums.get(j));
            for (int k = 0; k < combs.length; k++) {
                numberDeuteriumsEasilyExchanged = 0;
                numberDeuteriums = 0;
                InChIToStructure itsNew = InChIGeneratorFactory.getInstance().getInChIToStructure(inchis.get(j), SilentChemObjectBuilder.getInstance());
                IAtomContainer con = itsNew.getAtomContainer();
                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(con);
                java.util.List<IAtomContainer> tautos = tg.getTautomers(con);
                SmilesGenerator sg = new SmilesGenerator(SmiFlavor.Generic);
                for (IAtomContainer tautomer : tautos) {
                    System.out.println(sg.create(tautomer));
                }
                IAtomContainer jiosNew = itsNew.getAtomContainer();
                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(jiosNew);
                adder.addImplicitHydrogens(jiosNew);
                AtomContainerManipulator.convertImplicitToExplicitHydrogens(jiosNew);
                // System.out.println(Arrays.toString(combs[k]));
                for (int l = 0; l < combs[k].length; l++) {
                    addExplicitDeuterium(jiosNew, combs[k][l]);
                    numberDeuteriumsEasilyExchanged++;
                    numberDeuteriums++;
                }
                // System.out.println("JniInchiOutputStructure");
                // printInfo(jiosNew);
                numberDeuteriumsVec.add(numberDeuteriums);
                numberDeuteriumsEasilyExchangedVec.add(numberDeuteriumsEasilyExchanged);
                deuteratedStrutures.add(jiosNew);
            }
            for (int k = 0; k < deuteratedStrutures.size(); k++) {
                IAtomContainer con = deuteratedStrutures.get(k);
                InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(con);
                String inchi = gen.getInchi();
                String inchiKey = gen.getInchiKey();
                HDByteMolecularFormula formula = null;
                try {
                    formula = new HDByteMolecularFormula(inchi.split("/")[1]);
                } catch (Exception e) {
                    System.err.println(identifiers.get(j));
                    e.printStackTrace();
                    System.exit(1);
                }
                formula.setNumberHydrogens((short) formula.getNumberHydrogens());
                formula.setNumberDeuterium((short) (int) numberDeuteriumsVec.get(k));
                double mass = formula.getMonoisotopicMass();
                System.out.println(identifiers.get(j) + "-" + (k + 1) + "|" + inchi + "|" + formula.toString() + "|" + mass + "|" + inchiKey.split("-")[0] + "|" + inchiKey.split("-")[1] + "|" + numberDeuteriumsEasilyExchangedVec.get(k) + "|0|" + (toExchange.length - numberToAddDeuteriums.get(j)) + "|" + (mass + Constants.getMonoisotopicMassOfAtom("D") - Constants.ELECTRON_MASS) + "|" + (mass - Constants.getMonoisotopicMassOfAtom("D") + Constants.ELECTRON_MASS));
            }
            continue;
        }
        if (withAromaticRings || (numberToAddDeuteriums.size() != 0 && numberToAddDeuteriums.get(j) > numberDeuteriums)) {
            int numberMissing = numberToAddDeuteriums.get(j) - numberDeuteriums;
            numberDeuteriums += numberMissing;
            numberDeuteriumsAromaticExchanged += numberMissing;
        }
        HDByteMolecularFormula formula = null;
        try {
            formula = new HDByteMolecularFormula(MolecularFormulaManipulator.getString(MolecularFormulaManipulator.getMolecularFormula(its)));
        } catch (Exception e) {
            System.err.println(identifiers.get(j));
            e.printStackTrace();
            System.exit(1);
        }
        formula.setNumberHydrogens((short) formula.getNumberHydrogens());
        formula.setNumberDeuterium((short) numberDeuteriums);
        // Identifier|InChI|MolecularFormula|MonoisotopicMass|InChIKey1|InChIKey2|OSN-Deuteriums|AromaticDeuteriums
        if (numberToAddDeuteriums.size() == 0 || numberDeuteriums == numberToAddDeuteriums.get(j)) {
            InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(its);
            String inchi = gen.getInchi();
            String inchiKey = gen.getInchiKey();
            double mass = formula.getMonoisotopicMass();
            double negMass = mass - Constants.getMonoisotopicMassOfAtom("D") + Constants.ELECTRON_MASS;
            if (numberDeuteriumsEasilyExchanged + numberDeuteriumsAromaticExchanged == 0)
                negMass = mass - Constants.getMonoisotopicMassOfAtom("H") + Constants.ELECTRON_MASS;
            System.out.println(identifiers.get(j) + "|" + inchi + "|" + formula.toString() + "|" + mass + "|" + inchiKey.split("-")[0] + "|" + inchiKey.split("-")[1] + "|" + numberDeuteriumsEasilyExchanged + "|" + numberDeuteriumsAromaticExchanged + "|0" + "|" + (mass + Constants.getMonoisotopicMassOfAtom("D") - Constants.ELECTRON_MASS) + "|" + negMass);
            if (bwriter != null) {
                bwriter.write(identifiers.get(j) + "|" + inchi + "|" + formula.toString() + "|" + mass + "|" + inchiKey.split("-")[0] + "|" + inchiKey.split("-")[1] + "|" + numberDeuteriumsEasilyExchanged + "|" + numberDeuteriumsAromaticExchanged + "|0" + "|" + (mass + Constants.getMonoisotopicMassOfAtom("D") - Constants.ELECTRON_MASS) + "|" + negMass);
                bwriter.newLine();
            }
        } else if (!combinatorial)
            System.err.println("discarded to many easy exchangeable hydrogens " + numberDeuteriums + " " + identifiers.get(j));
    /*
			 * String[] masses = getAllFormulas(formula);
			 * 
			 * 
			 * for(int i = 0; i < masses.length; i++) { System.out.print(masses[i] + " "); }
			 * System.out.println();
			 */
    }
    if (bwriter != null)
        bwriter.close();
}

Example 2 with InChIGenerator

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

the class SDFDeuteriumGeneration method main.

public static void main(String[] args) throws Exception {
    boolean withAromaticRings = false;
    boolean combinatorial = true;
    /*
		 * read input inchis
		 */
    ArrayList<String> inchis = new ArrayList<String>();
    ArrayList<Integer> numberToAddDeuteriums = new ArrayList<Integer>();
    ArrayList<String> identifiers = new ArrayList<String>();
    BufferedReader breader = new BufferedReader(new FileReader(new File(args[0])));
    String line = "";
    int identifier = 1;
    while ((line = breader.readLine()) != null) {
        String[] tmp = line.trim().split("\\s+");
        inchis.add(tmp[0].trim());
        if (tmp.length >= 2)
            numberToAddDeuteriums.add(Integer.parseInt(tmp[1].trim()));
        if (tmp.length == 3)
            identifiers.add(tmp[2].trim());
        else
            identifiers.add(identifier + "");
        identifier++;
    }
    breader.close();
    /*
		 * generate deuterated version of inchi
		 */
    IAtomContainerSet set = new AtomContainerSet();
    SmilesGenerator sg = new SmilesGenerator(SmiFlavor.Generic);
    CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
    for (int j = 0; j < inchis.size(); j++) {
        /*
			 * build the inchi atom container
			 */
        IAtomContainer its = InChIGeneratorFactory.getInstance().getInChIToStructure(inchis.get(j), SilentChemObjectBuilder.getInstance()).getAtomContainer();
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(its);
        try {
            adder.addImplicitHydrogens(its);
        } catch (Exception e) {
            System.out.println("missed " + inchis.get(j) + " " + identifiers.get(j));
            continue;
        }
        AtomContainerManipulator.convertImplicitToExplicitHydrogens(its);
        int numberDeuteriums = 0;
        int numberDeuteriumsEasilyExchanged = 0;
        int numberDeuteriumsAromaticExchanged = 0;
        int[] toExchange = searchForDeuteriumExchangeablePositions(new String[] { "O", "N", "S" }, its);
        if (!combinatorial || (numberToAddDeuteriums.size() == 0 || toExchange.length <= numberToAddDeuteriums.get(j))) {
            for (int i = 0; i < toExchange.length; i++) {
                int numberExchanged = setAllExplicitDeuteriums(its, i);
                numberDeuteriums += numberExchanged;
                numberDeuteriumsEasilyExchanged += numberExchanged;
            }
        } else if (toExchange.length > numberToAddDeuteriums.get(j)) {
            ArrayList<IAtomContainer> deuteratedStrutures = new ArrayList<IAtomContainer>();
            ArrayList<Integer> numberDeuteriumsVec = new ArrayList<Integer>();
            ArrayList<Integer> numberDeuteriumsEasilyExchangedVec = new ArrayList<Integer>();
            // get all possible combinations of exchanges with given number
            // of exchangeable hydrogens
            int[][] combs = getCombinations(toExchange, numberToAddDeuteriums.get(j));
            for (int k = 0; k < combs.length; k++) {
                numberDeuteriumsEasilyExchanged = 0;
                numberDeuteriums = 0;
                IAtomContainer itsNew = InChIGeneratorFactory.getInstance().getInChIToStructure(inchis.get(j), SilentChemObjectBuilder.getInstance()).getAtomContainer();
                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(itsNew);
                adder.addImplicitHydrogens(itsNew);
                AtomContainerManipulator.convertImplicitToExplicitHydrogens(itsNew);
                for (int l = 0; l < combs[k].length; l++) {
                    addExplicitDeuterium(itsNew, combs[k][l]);
                    numberDeuteriumsEasilyExchanged++;
                    numberDeuteriums++;
                }
                numberDeuteriumsVec.add(numberDeuteriums);
                numberDeuteriumsEasilyExchangedVec.add(numberDeuteriumsEasilyExchanged);
                deuteratedStrutures.add(itsNew);
            }
            for (int k = 0; k < deuteratedStrutures.size(); k++) {
                String inchi = inchis.get(j);
                IAtomContainer con = deuteratedStrutures.get(k);
                HDByteMolecularFormula formula = null;
                try {
                    formula = new HDByteMolecularFormula(inchi.split("/")[1]);
                } catch (Exception e) {
                    System.err.println(identifiers.get(j));
                    e.printStackTrace();
                    System.exit(1);
                }
                formula.setNumberHydrogens((short) formula.getNumberHydrogens());
                formula.setNumberDeuterium((short) (int) numberDeuteriumsVec.get(k));
                InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(con);
                String inchiKey = gen.getInchiKey();
                con.setProperty(VariableNames.IDENTIFIER_NAME, identifiers.get(j) + "-" + (k + 1));
                con.setProperty(VariableNames.INCHI_NAME, inchi);
                // con.setProperty(VariableNames.SMILES_NAME, sg.create(deuteratedStrutures.get(k)));
                con.setProperty(VariableNames.MOLECULAR_FORMULA_NAME, formula.toString());
                con.setProperty(VariableNames.MONOISOTOPIC_MASS_NAME, formula.getMonoisotopicMass());
                con.setProperty(VariableNames.INCHI_KEY_1_NAME, inchiKey.split("-")[0]);
                con.setProperty(VariableNames.INCHI_KEY_2_NAME, inchiKey.split("-")[1]);
                con.setProperty("OSN-Deuteriums", numberDeuteriumsEasilyExchangedVec.get(k));
                con.setProperty("AromaticDeuteriums", 0);
                con.setProperty("MissedDeuteriums", (toExchange.length - numberToAddDeuteriums.get(j)));
                set.addAtomContainer(con);
                System.out.println(identifiers.get(j) + "-" + (k + 1) + "|" + inchi + "|" + sg.create(deuteratedStrutures.get(k)) + "|" + formula.toString() + "|" + formula.getMonoisotopicMass() + "|" + inchiKey.split("-")[0] + "|" + inchiKey.split("-")[1] + "|" + numberDeuteriumsEasilyExchangedVec.get(k) + "|0|" + (toExchange.length - numberToAddDeuteriums.get(j)));
            }
            continue;
        }
        if (withAromaticRings || (numberToAddDeuteriums.size() != 0 && numberToAddDeuteriums.get(j) > numberDeuteriums)) {
            int numberMissing = numberToAddDeuteriums.get(j) - numberDeuteriums;
            numberDeuteriums += numberMissing;
            numberDeuteriumsAromaticExchanged += numberMissing;
        }
        String inchi = inchis.get(j);
        InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(its);
        String inchiKey = gen.getInchiKey();
        HDByteMolecularFormula formula = null;
        try {
            formula = new HDByteMolecularFormula(inchi.split("/")[1]);
        } catch (Exception e) {
            System.err.println(identifiers.get(j));
            e.printStackTrace();
            System.exit(1);
        }
        formula.setNumberHydrogens((short) formula.getNumberHydrogens());
        formula.setNumberDeuterium((short) numberDeuteriums);
        if (numberToAddDeuteriums.size() == 0 || numberDeuteriums == numberToAddDeuteriums.get(j)) {
            System.out.println(identifiers.get(j) + "|" + inchi + "|" + sg.create(its) + "|" + formula.toString() + "|" + formula.getMonoisotopicMass() + "|" + inchiKey.split("-")[0] + "|" + inchiKey.split("-")[1] + "|" + numberDeuteriumsEasilyExchanged + "|" + numberDeuteriumsAromaticExchanged + "|0");
            its.setProperty(VariableNames.IDENTIFIER_NAME, identifiers.get(j));
            its.setProperty(VariableNames.INCHI_NAME, inchi);
            // its.setProperty(VariableNames.SMILES_NAME, sg.create(its));
            its.setProperty(VariableNames.MOLECULAR_FORMULA_NAME, formula.toString());
            its.setProperty(VariableNames.MONOISOTOPIC_MASS_NAME, formula.getMonoisotopicMass());
            its.setProperty(VariableNames.INCHI_KEY_1_NAME, inchiKey.split("-")[0]);
            its.setProperty(VariableNames.INCHI_KEY_2_NAME, inchiKey.split("-")[1]);
            its.setProperty("OSN-Deuteriums", numberDeuteriumsEasilyExchanged);
            its.setProperty("AromaticDeuteriums", numberDeuteriumsAromaticExchanged);
            its.setProperty("MissedDeuteriums", 0);
            set.addAtomContainer(its);
        } else if (!combinatorial)
            System.err.println("discarded to many easy exchangeable hydrogens " + numberDeuteriums + " " + identifiers.get(j));
    }
    try {
        SDFWriter writer = new SDFWriter(new java.io.FileWriter(new java.io.File(args[1])));
        writer.write(set);
        writer.close();
    } catch (java.io.IOException e) {
        e.printStackTrace();
    } catch (CDKException e) {
        e.printStackTrace();
    }
}

Example 3 with InChIGenerator

use of org.openscience.cdk.inchi.InChIGenerator in project ambit-mirror by ideaconsult.

the class CompoundLookup method atomcontainer2inchi.

public String[] atomcontainer2inchi(IAtomContainer c, String origin) throws ResourceException {
    try {
        Kekulization.kekulize(c);
        // inchi can't process aromatic bonds...
        for (IBond bond : c.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
        // now generate unique inchi, as SMILES are not
        searchType = _searchtype.inchi;
        InChIGeneratorFactory f = InChIGeneratorFactory.getInstance();
        InChIGenerator gen = f.getInChIGenerator(c);
        INCHI_RET status = gen.getReturnStatus();
        if (INCHI_RET.OKAY.equals(status) || INCHI_RET.WARNING.equals(status))
            return new String[] { gen.getInchi(), gen.getInchiKey() };
        else
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, String.format("Error converting to InChI: %s %s %s %s", status, gen.getMessage(), gen.getLog(), origin));
    } catch (ResourceException x) {
        throw x;
    } catch (InvalidSmilesException x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    } catch (CDKException x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    }
}

Example 4 with InChIGenerator

use of org.openscience.cdk.inchi.InChIGenerator in project ambit-mirror by ideaconsult.

the class StructureNormalizer method process.

public IStructureRecord process(IStructureRecord structure) throws AmbitException {
    if ((structure.getFormat() != null) && MOL_TYPE.NANO.name().equals(structure.getFormat())) {
        try {
            // fields
            return structure;
        /*
				 * Class clazz =
				 * FileInputState.class.getClassLoader().loadClass(
				 * "net.idea.ambit2.nano.NanoStructureNormalizer"); Method
				 * method = clazz.getMethod("normalizeNano",
				 * IStructureRecord.class); return (IStructureRecord)
				 * method.invoke(null, structure);
				 */
        } catch (Exception x) {
            if (x instanceof AmbitException)
                throw (AmbitException) x;
            else
                throw new AmbitException(x);
        }
    }
    // else process as chemical
    IAtomContainer molecule = molReader.process(structure);
    if ((molecule != null) && (molecule.getProperties() != null))
        structure.addRecordProperties(molecule.getProperties());
    if ((molecule == null) || (molecule.getAtomCount() == 0))
        structure.setType(STRUC_TYPE.NA);
    else {
        structure.setType(strucType.process(molecule));
        if (build2D)
            try {
                IAtomContainer newmol = build2d(molecule, structure.getType());
                if (newmol != null) {
                    molecule = newmol;
                    StringWriter w = new StringWriter();
                    SDFWriter writer = new SDFWriter(w);
                    try {
                        writer.write(molecule);
                    } catch (Exception x) {
                        logger.log(Level.WARNING, x.getMessage());
                    } finally {
                        writer.close();
                    }
                    structure.setType(strucType.process(molecule));
                    structure.setContent(w.toString());
                    structure.setFormat(MOL_TYPE.SDF.name());
                }
            } catch (Exception x) {
            }
    }
    try {
        if ((molecule != null) && (molecule.getAtomCount() > 0)) {
            structure.setSmiles(smilesKey.process(molecule));
            if ("".equals(structure.getSmiles()))
                structure.setSmiles(null);
        }
    } catch (Exception x) {
        logger.log(Level.SEVERE, x.getMessage());
        structure.setSmiles(null);
    }
    try {
        if (structure.getInchi() == null) {
            String inchi = null;
            String key = null;
            if ((molecule == null) || (molecule.getAtomCount() == 0)) {
                inchi = inchiKey.process(structure);
            } else
                try {
                    if (inchiProcessor == null)
                        inchiProcessor = new InchiProcessor();
                    boolean kekulize = false;
                    for (IBond bond : molecule.bonds()) if (bond.getFlag(CDKConstants.ISAROMATIC)) {
                        kekulize = true;
                        break;
                    }
                    IAtomContainer kekulized = (IAtomContainer) molecule;
                    if (kekulize)
                        try {
                            // inchi can't process aromatic bonds...
                            kekulized = (IAtomContainer) molecule.clone();
                            // the new kekulizer probably do not needs atom typing
                            // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(kekulized);
                            Kekulization.kekulize(kekulized);
                            for (IBond bond : kekulized.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
                        } catch (Exception x) {
                            logger.log(Level.FINE, x.getMessage(), x);
                            ;
                        }
                    InChIGenerator gen = inchiProcessor.process(kekulized);
                    if (INCHI_RET.OKAY.equals(gen.getReturnStatus()) || INCHI_RET.WARNING.equals(gen.getReturnStatus())) {
                        inchi = gen.getInchi();
                        key = gen.getInchiKey();
                    } else {
                        inchi = null;
                        key = String.format("ERROR:%s:%s", gen.getReturnStatus(), gen.getMessage());
                    }
                } catch (Exception x) {
                    inchi = null;
                    key = null;
                }
            if ("".equals(inchi))
                inchi = null;
            structure.setInchi(inchi);
            structure.setInchiKey(key);
        }
    } catch (Exception x) {
        structure.setInchi(null);
        structure.setInchiKey("ERROR:" + x.getMessage());
    }
    if ((molecule != null) && (molecule.getAtomCount() > 0))
        try {
            IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(molecule);
            structure.setFormula(formula == null ? null : MolecularFormulaManipulator.getString(formula));
        } catch (Exception x) {
            structure.setFormula(null);
        }
    if (DXParser.hasDxProperties(structure)) {
        if (dxParser == null)
            dxParser = new DXParser();
        structure = dxParser.process(structure);
    }
    return structure;
}

Example 5 with InChIGenerator

use of org.openscience.cdk.inchi.InChIGenerator in project ambit-mirror by ideaconsult.

the class InchiProcessorTest method testProcessExplicitH.

@Test
public void testProcessExplicitH() throws Exception {
    List<INCHI_OPTION> options = new ArrayList<INCHI_OPTION>();
    options.add(INCHI_OPTION.FixedH);
    options.add(INCHI_OPTION.SAbs);
    options.add(INCHI_OPTION.SAsXYZ);
    options.add(INCHI_OPTION.SPXYZ);
    options.add(INCHI_OPTION.FixSp3Bug);
    options.add(INCHI_OPTION.AuxNone);
    SmilesParser p = new SmilesParser(SilentChemObjectBuilder.getInstance());
    IAtomContainer mol = p.parseSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C");
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
    CDKHydrogenAdder.getInstance(mol.getBuilder()).addImplicitHydrogens(mol);
    IAtomContainer molH = mol.clone();
    MoleculeTools.convertImplicitToExplicitHydrogens(molH);
    InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
    InChIGenerator gen = factory.getInChIGenerator(mol, options);
    Assert.assertEquals(INCHI_RET.OKAY, gen.getReturnStatus());
    InChIGenerator genH = factory.getInChIGenerator(mol, options);
    Assert.assertEquals(INCHI_RET.OKAY, genH.getReturnStatus());
    Assert.assertEquals(gen.getInchi(), genH.getInchi());
}