Examples with AtomContainerSet org.openscience.cdk.AtomContainerSet used on opensource projects

Example 26 with AtomContainerSet

use of org.openscience.cdk.AtomContainerSet in project cdk by cdk.

the class MoSSOutputReaderTest method testExampleFile_MolReading.

@Test
public void testExampleFile_MolReading() throws Exception {
    String filename = "TKO.mossoutput";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    MoSSOutputReader reader = new MoSSOutputReader(ins);
    IAtomContainerSet moleculeSet = new AtomContainerSet();
    moleculeSet = reader.read(moleculeSet);
    Assert.assertEquals(19, moleculeSet.getAtomContainerCount());
    for (IAtomContainer mol : moleculeSet.atomContainers()) {
        Assert.assertEquals(Integer.valueOf(mol.getProperty("atomCount").toString()).intValue(), mol.getAtomCount());
        Assert.assertEquals(Integer.valueOf(mol.getProperty("bondCount").toString()).intValue(), mol.getBondCount());
    }
}

Example 27 with AtomContainerSet

use of org.openscience.cdk.AtomContainerSet in project cdk by cdk.

the class SMILESReaderTest method testReading.

@Test
public void testReading() throws Exception {
    String filename = "smiles.smi";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    SMILESReader reader = new SMILESReader(ins);
    IAtomContainerSet som = reader.read(new AtomContainerSet());
    Assert.assertEquals(8, som.getAtomContainerCount());
}

Example 28 with AtomContainerSet

use of org.openscience.cdk.AtomContainerSet in project cdk by cdk.

the class SMILESReaderTest method testReadingSmiFile_2.

@Test
public void testReadingSmiFile_2() throws Exception {
    String filename = "smiles.smi";
    logger.info("Testing: " + filename);
    InputStream ins = this.getClass().getResourceAsStream(filename);
    SMILESReader reader = new SMILESReader(ins);
    IAtomContainerSet som = reader.read(new AtomContainerSet());
    IAtomContainer thisMol = som.getAtomContainer(1);
    Assert.assertNull(thisMol.getProperty("SMIdbNAME"));
}

Example 29 with AtomContainerSet

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

the class SmilesDeuteriumGeneration method main.

public static void main(String[] args) throws Exception {
    boolean withAromaticRings = false;
    boolean combinatorial = false;
    /*
		 * read input inchis
		 */
    ArrayList<String> smiles = new ArrayList<String>();
    ArrayList<Integer> numberToAddDeuteriums = new ArrayList<Integer>();
    ArrayList<String> identifiers = new ArrayList<String>();
    File input = new File(args[0]);
    BufferedReader breader = null;
    if (!input.exists()) {
        smiles.add(args[0]);
        identifiers.add("1");
    } else
        breader = new BufferedReader(new FileReader(input));
    String line = "";
    int identifier = 1;
    if (breader != null)
        while ((line = breader.readLine()) != null) {
            String[] tmp = line.trim().split("\\s+");
            smiles.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++;
        }
    if (breader != null)
        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 < smiles.size(); j++) {
        /*
			 * build the atom container
			 */
        IAtomContainer its = MoleculeFunctions.parseSmilesImplicitHydrogen(smiles.get(j));
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(its);
        try {
            adder.addImplicitHydrogens(its);
        } catch (Exception e) {
            System.out.println("missed " + smiles.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;
                IAtomContainer itsNew = MoleculeFunctions.parseSmilesImplicitHydrogen(smiles.get(j));
                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++) {
                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));
                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)));
            }
        }
        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);
        if (numberToAddDeuteriums.size() == 0 || numberDeuteriums == numberToAddDeuteriums.get(j)) {
            InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(its);
            String inchi = gen.getInchi();
            String inchiKey = gen.getInchiKey();
            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());
            double mass = MathTools.round(formula.getMonoisotopicMass());
            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);
            its.setProperty("M+H", MathTools.round(mass + Constants.getMonoisotopicMassOfAtom("H") - Constants.ELECTRON_MASS));
            its.setProperty("M+D", MathTools.round(mass + Constants.getMonoisotopicMassOfAtom("D") - Constants.ELECTRON_MASS));
            its.setProperty("M-H", MathTools.round(mass - Constants.getMonoisotopicMassOfAtom("H") + Constants.ELECTRON_MASS));
            its.setProperty("M-D", MathTools.round(mass - Constants.getMonoisotopicMassOfAtom("D") + Constants.ELECTRON_MASS));
            IAtomContainer con = MoleculeFunctions.removeHydrogens(its, toExchange);
            its.setProperty("DeuteratedSMILES", MoleculeFunctions.generateSmiles(con).replaceAll("\\[H\\]", "[2H]"));
            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 30 with AtomContainerSet

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

the class CandidateListWriterSDF method writeFile.

public boolean writeFile(File file, IList list, Settings settings) throws Exception {
    IAtomContainerSet set = new AtomContainerSet();
    CandidateList candidateList = null;
    int numberOfPeaksUsed = 0;
    if (list instanceof ScoredCandidateList || list instanceof SortedScoredCandidateList) {
        candidateList = (ScoredCandidateList) list;
        numberOfPeaksUsed = ((ScoredCandidateList) list).getNumberPeaksUsed();
    }
    if (list instanceof CandidateList) {
        candidateList = (CandidateList) list;
    }
    if (candidateList == null)
        return false;
    for (int i = 0; i < candidateList.getNumberElements(); i++) {
        ICandidate candidate = candidateList.getElement(i);
        if (settings != null)
            candidate.setUseSmiles((Boolean) settings.get(VariableNames.USE_SMILES_NAME));
        try {
            candidate.initialisePrecursorCandidate();
        } catch (Exception e) {
            continue;
        }
        IAtomContainer candidateAtomContainer = null;
        try {
            candidateAtomContainer = candidate.getAtomContainer();
        } catch (Exception e1) {
            System.err.println("Error saving: " + candidateList.getElement(i).getIdentifier());
            continue;
        }
        ICandidate scoredCandidate = candidateList.getElement(i);
        if (scoredCandidate.getMatchList() != null) {
            MatchList matchList = scoredCandidate.getMatchList();
            int countExplainedPeaks = 0;
            for (int l = 0; l < matchList.getNumberElements(); l++) {
                try {
                    matchList.getElement(l).getMatchedPeak().getIntensity();
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                countExplainedPeaks++;
            }
            candidateAtomContainer.setProperty("NumberPeaksExplained", countExplainedPeaks);
        }
        String peaksExplained = "";
        String sumFormulasOfFragmentsExplainedPeaks = "";
        String fragmentAtomArrays = "";
        String fragmentBondArrays = "";
        String fragmentBrokenBondArrays = "";
        if (scoredCandidate.getMatchList() != null) {
            for (int ii = 0; ii < scoredCandidate.getMatchList().getNumberElements(); ii++) {
                try {
                    double intensity = scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getIntensity();
                    peaksExplained += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + "_" + intensity + ";";
                } catch (RelativeIntensityNotDefinedException e1) {
                    continue;
                }
                String formula = scoredCandidate.getMatchList().getElement(ii).getModifiedFormulaStringOfBestMatchedFragment(scoredCandidate.getPrecursorMolecule());
                sumFormulasOfFragmentsExplainedPeaks += scoredCandidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + ":" + formula + ";";
                fragmentAtomArrays += ((DefaultBitArrayFragment) scoredCandidate.getMatchList().getElement(ii).getBestMatchedFragment()).getAtomsFastBitArray() + ";";
                fragmentBondArrays += ((DefaultBitArrayFragment) scoredCandidate.getMatchList().getElement(ii).getBestMatchedFragment()).getBondsFastBitArray() + ";";
                fragmentBrokenBondArrays += ((DefaultBitArrayFragment) scoredCandidate.getMatchList().getElement(ii).getBestMatchedFragment()).getBrokenBondsFastBitArray() + ";";
            }
            if (sumFormulasOfFragmentsExplainedPeaks.length() != 0)
                sumFormulasOfFragmentsExplainedPeaks = sumFormulasOfFragmentsExplainedPeaks.substring(0, sumFormulasOfFragmentsExplainedPeaks.length() - 1);
            if (peaksExplained.length() != 0)
                peaksExplained = peaksExplained.substring(0, peaksExplained.length() - 1);
            if (peaksExplained.length() == 0)
                peaksExplained = "NA";
            if (fragmentAtomArrays.length() != 0)
                fragmentAtomArrays = fragmentAtomArrays.substring(0, fragmentAtomArrays.length() - 1);
            if (fragmentBondArrays.length() != 0)
                fragmentBondArrays = fragmentBondArrays.substring(0, fragmentBondArrays.length() - 1);
            if (fragmentBrokenBondArrays.length() != 0)
                fragmentBrokenBondArrays = fragmentBrokenBondArrays.substring(0, fragmentBrokenBondArrays.length() - 1);
            if (sumFormulasOfFragmentsExplainedPeaks.length() == 0)
                sumFormulasOfFragmentsExplainedPeaks = "NA";
            candidateAtomContainer.setProperty("PeaksExplained", peaksExplained);
            candidateAtomContainer.setProperty("FragmentMolecularFormulas", sumFormulasOfFragmentsExplainedPeaks);
        }
        for (java.util.Enumeration<String> keys = candidate.getProperties().keys(); keys.hasMoreElements(); ) {
            String key = keys.nextElement();
            String propertyValue = checkEmptyProperty(candidate.getProperty(key)).toString();
            if (key.equals(VariableNames.IDENTIFIER_NAME))
                propertyValue = propertyValue.replaceAll("\\|[0-9]+", "");
            candidateAtomContainer.setProperty(key, propertyValue);
        }
        candidateAtomContainer.setProperty("NumberPeaksUsed", numberOfPeaksUsed);
        MoleculeFunctions.prepareAtomContainer(candidateAtomContainer, true);
        MoleculeFunctions.convertExplicitToImplicitHydrogens(candidateAtomContainer);
        set.addAtomContainer(candidateAtomContainer);
    }
    SDFWriter writer = new SDFWriter(new FileWriter(file));
    writer.write(set);
    writer.close();
    return true;
}