Examples with AtomTypeNotKnownFromInputListException de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException used on opensource projects

Example 1 with AtomTypeNotKnownFromInputListException

use of de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException in project MetFragRelaunched by ipb-halle.

the class DownloadEntriesFromPubChem method downloadFromString.

public static void downloadFromString(String idString) {
    String[] ids = idString.trim().split(",");
    MetFragGlobalSettings settings = new MetFragGlobalSettings();
    settings.set(VariableNames.PRECURSOR_DATABASE_IDS_NAME, ids);
    OnlineExtendedPubChemDatabase db = new OnlineExtendedPubChemDatabase(settings);
    CandidateList candidates = null;
    try {
        candidates = db.getCandidateByIdentifier(db.getCandidateIdentifiers());
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    for (int i = 0; i < candidates.getNumberElements(); i++) {
        ICandidate candidate = candidates.getElement(i);
        try {
            System.out.println(candidate.getIdentifier() + "|" + candidate.getInChI() + "|" + candidate.getMolecularFormula().toString() + "|" + candidate.getMolecularFormula().getMonoisotopicMass() + "|" + candidate.getProperty(VariableNames.PUBCHEM_XLOGP_NAME) + "|" + candidate.getProperty(VariableNames.INCHI_KEY_1_NAME) + "|" + candidate.getProperty(VariableNames.INCHI_KEY_2_NAME) + "|" + candidate.getProperty(VariableNames.PUBCHEM_NUMBER_PATENTS_NAME) + "|" + candidate.getProperty(VariableNames.PUBCHEM_NUMBER_PUBMED_REFERENCES_NAME) + "|" + candidate.getProperty(VariableNames.SMILES_NAME));
        } catch (AtomTypeNotKnownFromInputListException e) {
            e.printStackTrace();
        }
    }
}

Example 2 with AtomTypeNotKnownFromInputListException

use of de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException in project MetFragRelaunched by ipb-halle.

the class CandidateListWriterLossFragmentSmilesCompletePSV method calculateMassOfFormula.

private double calculateMassOfFormula(String formula) {
    String part1 = formula.replaceAll("\\[([A-Za-z0-9]*).*\\].*", "$1");
    String charge = formula.substring(formula.length() - 1);
    java.util.ArrayList<String> elementsToAdd = new java.util.ArrayList<String>();
    java.util.ArrayList<String> timesToAdd = new java.util.ArrayList<String>();
    java.util.ArrayList<String> signsForAdd = new java.util.ArrayList<String>();
    for (int i = 0; i < formula.length() - 1; i++) {
        if (formula.charAt(i) == '+' || formula.charAt(i) == '-') {
            signsForAdd.add(formula.charAt(i) + "");
            boolean numberFinished = false;
            String number = "";
            String element = "";
            for (int k = (i + 1); k < formula.length() - 1; k++) {
                if (!numberFinished && Character.isDigit(formula.charAt(k)))
                    number += formula.charAt(k);
                else if (!numberFinished && !Character.isDigit(formula.charAt(k))) {
                    if (number.equals(""))
                        number = "1";
                    numberFinished = true;
                }
                if (Character.isLowerCase(formula.charAt(k)) && !element.equals(""))
                    element += formula.charAt(k);
                if (Character.isUpperCase(formula.charAt(k)) && element.equals(""))
                    element += formula.charAt(k);
                if (Character.isUpperCase(formula.charAt(k)) && !element.equals(""))
                    break;
                if (Character.isDigit(formula.charAt(k)) && numberFinished)
                    break;
                if (!Character.isUpperCase(formula.charAt(k)) && !Character.isLowerCase(formula.charAt(k)) && !Character.isDigit(formula.charAt(k)))
                    break;
            }
            elementsToAdd.add(element);
            timesToAdd.add(number);
        }
    }
    double mass = 0.0;
    try {
        boolean isPositive = charge.equals("-") ? false : true;
        double chargeMass = Constants.getChargeMassByType(isPositive);
        ByteMolecularFormula bmf = new ByteMolecularFormula(part1);
        for (int i = 0; i < elementsToAdd.size(); i++) {
            byte atomIndex = (byte) Constants.ELEMENTS.indexOf(elementsToAdd.get(i));
            short amount = Short.parseShort(signsForAdd.get(i) + timesToAdd.get(i));
            bmf.changeNumberElementsFromByte(atomIndex, amount);
        }
        mass = bmf.getMonoisotopicMass() + chargeMass;
    } catch (AtomTypeNotKnownFromInputListException e) {
        e.printStackTrace();
    }
    return mass;
}

Example 3 with AtomTypeNotKnownFromInputListException

use of de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException in project MetFragRelaunched by ipb-halle.

the class MetfRag method scoreMoleculesAgainstSpectrum.

/**
 * fragment and score molecules stored in a sdf file
 *
 * @param _pathToSDF
 * @param _masses
 * @param _intensities
 * @param _exactMass
 * @param _numberThreads
 * @param _mzabs
 * @param _mzppm
 * @param _searchppm
 * @param _posCharge
 * @param _mode
 * @param _treeDepth
 * @return
 */
public static IAtomContainer[] scoreMoleculesAgainstSpectrum(IAtomContainer[] atomContainerArray, double[] _masses, double[] _intensities, double _exactMass, int _numberThreads, double _mzabs, double _mzppm, boolean _posCharge, int _mode, int _treeDepth, String[] scoreNames, double[] scoreWeights) {
    Logger.getLogger("net.sf.jnati.deploy.artefact.ConfigManager").setLevel(Level.ERROR);
    Logger.getLogger("net.sf.jnati.deploy.repository.ClasspathRepository").setLevel(Level.ERROR);
    Logger.getLogger("net.sf.jnati.deploy.repository.LocalRepository").setLevel(Level.ERROR);
    Logger.getLogger("net.sf.jnati.deploy.artefact.ManifestReader").setLevel(Level.ERROR);
    Logger.getLogger("net.sf.jnati.deploy.NativeArtefactLocator").setLevel(Level.ERROR);
    Logger.getLogger("net.sf.jnati.deploy.NativeLibraryLoader").setLevel(Level.ERROR);
    Logger.getLogger("net.sf.jnati.deploy.resolver.ArtefactResolver").setLevel(Level.ERROR);
    Logger.getLogger("net.sf.jnati.deploy.source.JarSource").setLevel(Level.ERROR);
    double mzabs = _mzabs;
    double mzppm = _mzppm;
    double exactMass = _exactMass;
    int treeDepth = _treeDepth;
    int mode = _mode;
    int numberThreads = _numberThreads;
    boolean posCharge = _posCharge;
    double[] masses = _masses;
    double[] intensities = _intensities;
    IAtomContainer[] resultMols = new IAtomContainer[0];
    if (masses == null)
        return resultMols;
    if (intensities == null)
        return resultMols;
    if (masses.length != intensities.length)
        return resultMols;
    if (exactMass <= 0.0)
        return resultMols;
    if (numberThreads < -1 || numberThreads > 8)
        return resultMols;
    if (mzabs < 0.0 || mzppm < 0.0)
        return resultMols;
    if (mode != -1 && mode != 0 && mode != 1)
        return resultMols;
    if (treeDepth < 1 || treeDepth > 5)
        return resultMols;
    String peaksString = "";
    if (masses.length > 0)
        peaksString += masses[0] + " " + intensities[0];
    for (int i = 1; i < masses.length; i++) {
        peaksString += "\n" + masses[i] + " " + intensities[i];
    }
    Double[] scoreWeightsObject = new Double[scoreWeights.length];
    for (int i = 0; i < scoreWeightsObject.length; i++) scoreWeightsObject[i] = Double.valueOf(scoreWeights[i]);
    MetFragGlobalSettings settings = new MetFragGlobalSettings();
    settings.set(VariableNames.MOLECULES_IN_MEMORY, atomContainerArray);
    settings.set(VariableNames.PEAK_LIST_STRING_NAME, peaksString);
    settings.set(VariableNames.METFRAG_DATABASE_TYPE_NAME, "LocalInMemoryDatabase");
    settings.set(VariableNames.METFRAG_PEAK_LIST_READER_NAME, "de.ipbhalle.metfraglib.peaklistreader.FilteredStringTandemMassPeakListReader");
    settings.set(VariableNames.METFRAG_SCORE_TYPES_NAME, scoreNames);
    settings.set(VariableNames.METFRAG_SCORE_WEIGHTS_NAME, scoreWeightsObject);
    settings.set(VariableNames.RELATIVE_MASS_DEVIATION_NAME, mzppm);
    settings.set(VariableNames.ABSOLUTE_MASS_DEVIATION_NAME, mzabs);
    settings.set(VariableNames.IS_POSITIVE_ION_MODE_NAME, posCharge);
    settings.set(VariableNames.PRECURSOR_ION_MODE_NAME, mode);
    settings.set(VariableNames.PRECURSOR_NEUTRAL_MASS_NAME, exactMass);
    settings.set(VariableNames.MAXIMUM_TREE_DEPTH_NAME, (byte) treeDepth);
    CombinedMetFragProcess mp = new CombinedMetFragProcess(settings);
    try {
        mp.retrieveCompounds();
    } catch (Exception e2) {
        System.err.println("Error retrieving candidates");
        e2.printStackTrace();
        return new IAtomContainer[0];
    }
    try {
        mp.run();
    } catch (Exception e) {
        System.err.println("Error running MetFrag process");
        e.printStackTrace();
        return new IAtomContainer[0];
    }
    SortedScoredCandidateList scoredCandidateList = (SortedScoredCandidateList) mp.getCandidateList();
    resultMols = new IAtomContainer[scoredCandidateList.getNumberElements()];
    int numberOfPeaksUsed = scoredCandidateList.getNumberPeaksUsed();
    for (int i = 0; i < scoredCandidateList.getNumberElements(); i++) {
        ICandidate candidate = scoredCandidateList.getElement(i);
        IAtomContainer tmp = null;
        try {
            tmp = candidate.getAtomContainer();
            MoleculeFunctions.prepareAtomContainer(tmp, false);
        } catch (Exception e1) {
            e1.printStackTrace();
            continue;
        }
        if (candidate.getProperties().containsKey(VariableNames.INCHI_KEY_1_NAME) && candidate.getProperty(VariableNames.INCHI_KEY_1_NAME) != null)
            tmp.setProperty(VariableNames.INCHI_KEY_1_NAME, candidate.getProperty(VariableNames.INCHI_KEY_1_NAME));
        if (candidate.getProperties().containsKey(VariableNames.INCHI_KEY_2_NAME) && candidate.getProperty(VariableNames.INCHI_KEY_2_NAME) != null)
            tmp.setProperty(VariableNames.INCHI_KEY_2_NAME, candidate.getProperty(VariableNames.INCHI_KEY_2_NAME));
        if (candidate.getProperties().containsKey(VariableNames.INCHI_KEY_NAME) && candidate.getProperty(VariableNames.INCHI_KEY_NAME) != null)
            tmp.setProperty(VariableNames.INCHI_KEY_NAME, candidate.getProperty(VariableNames.INCHI_KEY_NAME));
        tmp.setProperty(VariableNames.IDENTIFIER_NAME, candidate.getIdentifier());
        IMolecularFormula molFormula = MolecularFormulaManipulator.getMolecularFormula(tmp);
        Double massDoubleOrig = null;
        try {
            massDoubleOrig = candidate.getMolecularFormula().getMonoisotopicMass();
        } catch (AtomTypeNotKnownFromInputListException e) {
            e.printStackTrace();
        }
        massDoubleOrig = (double) Math.round((massDoubleOrig) * 10000) / 10000;
        tmp.setProperty(VariableNames.MONOISOTOPIC_MASS_NAME, massDoubleOrig);
        tmp.setProperty(VariableNames.FINAL_SCORE_COLUMN_NAME, candidate.getProperty(VariableNames.FINAL_SCORE_COLUMN_NAME));
        for (int ii = 0; ii < scoreNames.length; ii++) {
            String scoreClassName = scoreNames[ii];
            tmp.setProperty(scoreClassName, candidate.getProperty(scoreClassName));
            tmp.setProperty(scoreClassName + "_Values", candidate.getProperty(scoreClassName + "_Values"));
        }
        if (candidate.getMatchList() != null)
            tmp.setProperty(VariableNames.NUMBER_EXPLAINED_PEAKS_COLUMN, candidate.getMatchList().getNumberElements());
        String peaksExplained = "";
        String sumFormulasOfFragmentsExplainedPeaks = "";
        if (candidate.getMatchList() != null) {
            for (int ii = 0; ii < candidate.getMatchList().getNumberElements(); ii++) {
                try {
                    peaksExplained += candidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + "_" + candidate.getMatchList().getElement(ii).getMatchedPeak().getIntensity() + ";";
                } catch (RelativeIntensityNotDefinedException e1) {
                    e1.printStackTrace();
                }
                sumFormulasOfFragmentsExplainedPeaks += candidate.getMatchList().getElement(ii).getMatchedPeak().getMass() + ":" + candidate.getMatchList().getElement(ii).getBestMatchedFragment().getMolecularFormula(candidate.getPrecursorMolecule()) + ";";
            }
            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 (sumFormulasOfFragmentsExplainedPeaks.length() == 0)
                sumFormulasOfFragmentsExplainedPeaks = "NA";
            tmp.setProperty(VariableNames.EXPLAINED_PEAKS_COLUMN, peaksExplained);
            tmp.setProperty(VariableNames.FORMULAS_OF_PEAKS_EXPLAINED_COLUMN, sumFormulasOfFragmentsExplainedPeaks);
        }
        tmp.setProperty(VariableNames.MOLECULAR_FORMULA_NAME, MolecularFormulaManipulator.getString(molFormula));
        tmp.setProperty(VariableNames.NUMBER_EXPLAINED_PEAKS_COLUMN, numberOfPeaksUsed);
        resultMols[i] = tmp;
    }
    return resultMols;
}

Example 4 with AtomTypeNotKnownFromInputListException

use of de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException in project MetFragRelaunched by ipb-halle.

the class ByteMolecularFormula method parseMolecularFormula.

protected void parseMolecularFormula(String formula) throws AtomTypeNotKnownFromInputListException {
    String splitableFormula = formula.trim().replaceAll("(\\[*[0-9]*[A-Z][a-z]{0,3}\\]*)([0-9]*)", "$1;$2\\|");
    String[] parts = splitableFormula.split("\\|");
    int numberElements = 0;
    for (int i = 0; i < parts.length; i++) if (!parts[i].split(";")[0].equals("H") && !parts[i].split(";")[0].equals("D"))
        numberElements++;
    this.atomsAsIndeces = new byte[numberElements];
    this.numberOfAtoms = new short[numberElements];
    this.numberHydrogens = 0;
    int index = 0;
    for (int i = 0; i < parts.length; i++) {
        String[] tmp = parts[i].split(";");
        short count = 1;
        if (tmp.length > 1 && tmp[1].length() != 0)
            count = Short.parseShort(tmp[1]);
        if (tmp[0].equals("H"))
            this.numberHydrogens = count;
        else if (tmp[0].equals("D"))
            this.numberHydrogens = count;
        else {
            byte byteToAtomSymbol = (byte) Constants.ELEMENTS.indexOf(tmp[0]);
            if (byteToAtomSymbol == 0 || byteToAtomSymbol == 1)
                this.containsC = true;
            if (byteToAtomSymbol == -1) {
                throw new de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException(tmp[0] + " not found (" + formula + ")");
            }
            this.atomsAsIndeces[index] = byteToAtomSymbol;
            this.numberOfAtoms[index] = count;
            index++;
        }
    }
}

Example 5 with AtomTypeNotKnownFromInputListException

use of de.ipbhalle.metfraglib.exceptions.AtomTypeNotKnownFromInputListException in project MetFragRelaunched by ipb-halle.

the class SiriusNodePeakList method parseDotFile.

/**
 * generate SiriusNodePeakList from dot file
 *
 * @param filename
 * @return
 */
public void parseDotFile(String filename) {
    java.util.Hashtable<String, SiriusNodePeak> nodes = new java.util.Hashtable<String, SiriusNodePeak>();
    double maxIntensity = 0.0;
    try {
        java.io.BufferedReader breader = new java.io.BufferedReader(new java.io.FileReader(new java.io.File(filename)));
        String line = breader.readLine();
        while ((line = breader.readLine()) != null) {
            line = line.trim();
            if (line.length() == 1)
                continue;
            if (line.contains("->")) {
                String[] tmp = line.split("\\s+");
                SiriusNodePeak curChild = nodes.get(tmp[2].trim());
                SiriusNodePeak curFather = nodes.get(tmp[0].trim());
                try {
                    curChild.setLossFormula(new ByteMolecularFormula(tmp[3].replaceFirst("\\[label=\"", "").replace("\"];", "").trim()));
                } catch (AtomTypeNotKnownFromInputListException e) {
                    e.printStackTrace();
                }
                curChild.setFather(curFather);
                curFather.addChild(curChild);
            } else {
                String properties = line.replaceFirst(".*label=\"", "").replace("\"];", "");
                String id = line.split("\\s+")[0].trim();
                String[] tmp = properties.split("\\\\n");
                String fragmentFormula = tmp[0];
                double mass = Double.parseDouble(tmp[1].split("\\s+")[0].trim());
                double intensity = 0.0;
                try {
                    intensity = Double.parseDouble(properties.split("Intensity=")[1].split("\\\\n")[0]);
                } catch (java.lang.ArrayIndexOutOfBoundsException e) {
                    // precursor has no intensity
                    intensity = 0.0;
                }
                if (intensity > maxIntensity)
                    maxIntensity = intensity;
                SiriusNodePeak curNode = null;
                try {
                    curNode = new SiriusNodePeak(mass, fragmentFormula, intensity);
                } catch (AtomTypeNotKnownFromInputListException e) {
                    e.printStackTrace();
                }
                curNode.setCompleteNodeLabel(properties);
                curNode.setIntensity(intensity);
                curNode.setSiriusID(id);
                nodes.put(id, curNode);
                /*
					 * add peak sorted
					 */
                this.addElement(curNode);
            }
        }
        breader.close();
    } catch (java.io.FileNotFoundException e) {
        e.printStackTrace();
    } catch (java.io.IOException e) {
        e.printStackTrace();
    }
    java.util.Enumeration<SiriusNodePeak> elems = nodes.elements();
    while (elems.hasMoreElements()) {
        SiriusNodePeak node = elems.nextElement();
        try {
            node.setIntensity((node.getIntensity() / maxIntensity) * 999.0);
        } catch (RelativeIntensityNotDefinedException e) {
            e.printStackTrace();
        }
        if (node.isRoot()) {
            this.root = node;
        }
        if (node.isLeaf())
            this.leaves.add(node);
    }
}