Examples with DefaultBitArrayFragment de.ipbhalle.metfraglib.fragment.DefaultBitArrayFragment used on opensource projects

Example 1 with DefaultBitArrayFragment

use of de.ipbhalle.metfraglib.fragment.DefaultBitArrayFragment in project MetFragRelaunched by ipb-halle.

the class CollectCommuniesAndFragmentPeaks method main.

public static void main(String[] args) {
    MetFragGlobalSettings settings = new MetFragGlobalSettings();
    settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, args[0]);
    LocalPSVDatabase db = new LocalPSVDatabase(settings);
    java.util.ArrayList<String> ids = null;
    try {
        ids = db.getCandidateIdentifiers();
    } catch (MultipleHeadersFoundInInputDatabaseException e1) {
        e1.printStackTrace();
    } catch (Exception e1) {
        e1.printStackTrace();
    }
    CandidateList candidates = db.getCandidateByIdentifier(ids);
    ArrayList<Double> masses = new ArrayList<Double>();
    ArrayList<ArrayList<String>> vector_formulas = new ArrayList<ArrayList<String>>();
    ArrayList<ArrayList<String>> vector_smiles = new ArrayList<ArrayList<String>>();
    ArrayList<ArrayList<String>> vector_eawagids = new ArrayList<ArrayList<String>>();
    ArrayList<ArrayList<Double>> vector_intensities = new ArrayList<ArrayList<Double>>();
    ArrayList<Integer> occurences = new ArrayList<Integer>();
    ArrayList<ArrayList<FingerPrintFragmentCollection>> matchingFragments = new ArrayList<ArrayList<FingerPrintFragmentCollection>>();
    for (int i = 0; i < candidates.getNumberElements(); i++) {
        // System.out.println(candidates.getElement(i).getIdentifier());
        try {
            candidates.getElement(i).initialisePrecursorCandidate();
        } catch (AtomTypeNotKnownFromInputListException e) {
            e.printStackTrace();
        } catch (Exception e) {
            e.printStackTrace();
        }
        CommunityCalculation c = new CommunityCalculation((BitArrayPrecursor) candidates.getElement(i).getPrecursorMolecule());
        DefaultBitArrayFragment[] communityFragments = c.getCommunityFragments();
        String[] formulas = ((String) candidates.getElement(i).getProperties().get("FormulasOfExplPeaks")).split(";");
        String eawagID = (String) candidates.getElement(i).getProperties().get("EawagID");
        String[] smiles = ((String) candidates.getElement(i).getProperties().get("SmilesOfExplPeaks")).split(";");
        String[] explPeaks = ((String) candidates.getElement(i).getProperties().get("ExplPeaks")).split(";");
        boolean debug = false;
        for (int k = 0; k < formulas.length; k++) {
            String[] tmp_formula = formulas[k].split(":");
            String[] tmp_smiles = smiles[k].split(":");
            String[] tmp_intensity = explPeaks[k].split("_");
            if (tmp_formula.length != 2 || tmp_smiles.length != 2 || tmp_intensity.length != 2)
                continue;
            double intensity = Double.parseDouble(tmp_intensity[1]);
            if (intensity < intensityThreshold)
                continue;
            double mass = Double.parseDouble(tmp_formula[0]);
            int index = containsDouble(masses, mass, 5.0, 0.001, debug);
            if (index == -1) {
                int addedIndex = addMassSorted(masses, mass, debug);
                /*
					 * how often we have ssen this peak mass 
					 * here: only once as initial add
					 */
                occurences.add(addedIndex, 1);
                /*
					 * add the fragment
					 */
                addFragmentsAddPositionInitial(candidates.getElement(i).getPrecursorMolecule(), addedIndex, matchingFragments, communityFragments, candidates.getElement(i).getIdentifier());
                ArrayList<String> tmp_formulas = new ArrayList<String>();
                ArrayList<String> tmp_smiless = new ArrayList<String>();
                ArrayList<Double> tmp_intensities = new ArrayList<Double>();
                ArrayList<String> tmp_eawagids = new ArrayList<String>();
                tmp_formulas.add(tmp_formula[1]);
                tmp_smiless.add(tmp_smiles[1]);
                tmp_intensities.add(Double.parseDouble(tmp_intensity[1]));
                tmp_eawagids.add(eawagID);
                vector_formulas.add(addedIndex, tmp_formulas);
                vector_smiles.add(addedIndex, tmp_smiless);
                vector_intensities.add(addedIndex, tmp_intensities);
                vector_eawagids.add(addedIndex, tmp_eawagids);
            } else {
                masses.set(index, (masses.get(index) + mass) / 2.0);
                occurences.set(index, occurences.get(index) + 1);
                addFragmentsAddPosition(candidates.getElement(i).getPrecursorMolecule(), index, matchingFragments, communityFragments, candidates.getElement(i).getIdentifier());
                vector_formulas.get(index).add(tmp_formula[1]);
                vector_smiles.get(index).add(tmp_smiles[1]);
                vector_intensities.get(index).add(Double.parseDouble(tmp_intensity[1]));
                vector_eawagids.get(index).add(eawagID);
            }
        }
    }
    printMasses(masses);
    java.io.BufferedWriter bwriter;
    java.io.BufferedWriter smilesBwriter;
    try {
        smilesBwriter = new java.io.BufferedWriter(new java.io.FileWriter(new java.io.File(args[2])));
        bwriter = new java.io.BufferedWriter(new java.io.FileWriter(new java.io.File(args[1])));
        for (int i = 0; i < masses.size(); i++) {
            // System.out.println(masses.get(i));
            bwriter.write(masses.get(i) + "");
            bwriter.newLine();
            for (int k = 0; k < vector_formulas.get(i).size(); k++) {
                // System.out.println("\t" + vector_eawagids.get(i).get(k) + ": " + vector_formulas.get(i).get(k) + " " + vector_smiles.get(i).get(k) + " " + vector_intensities.get(i).get(k));
                bwriter.write("\t" + vector_eawagids.get(i).get(k) + ": " + vector_formulas.get(i).get(k) + " " + vector_smiles.get(i).get(k) + " " + vector_intensities.get(i).get(k));
                smilesBwriter.write(vector_smiles.get(i).get(k));
                smilesBwriter.newLine();
                bwriter.newLine();
            }
            // System.out.print("\t");
            bwriter.write("\t");
            for (int k = 0; k < vector_formulas.get(i).size(); k++) {
                // System.out.print(vector_eawagids.get(i).get(k) + ".png ");
                bwriter.write(vector_eawagids.get(i).get(k) + ".png ");
            }
            // System.out.println();
            bwriter.newLine();
            bwriter.newLine();
        // System.out.println();
        }
        bwriter.close();
        smilesBwriter.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
    try {
        java.io.BufferedWriter bwriterComms = new java.io.BufferedWriter(new java.io.FileWriter(new java.io.File(args[3])));
        for (int i = 0; i < matchingFragments.size(); i++) {
            bwriterComms.write(masses.get(i) + " " + occurences.get(i));
            bwriterComms.newLine();
            ArrayList<FingerPrintFragmentCollection> collections = matchingFragments.get(i);
            for (int j = 0; j < collections.size(); j++) {
                FingerPrintFragmentCollection collection = collections.get(j);
                bwriterComms.write("\t");
                bwriterComms.write(collection.toString());
                bwriterComms.newLine();
            }
        }
        bwriterComms.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 2 with DefaultBitArrayFragment

use of de.ipbhalle.metfraglib.fragment.DefaultBitArrayFragment in project MetFragRelaunched by ipb-halle.

the class CommunityCalculation method calculateCommunities.

private void calculateCommunities() {
    String nodeString = "";
    for (int i = 0; i < this.precursor.getNonHydrogenAtomCount(); i++) {
        short[] connectedAtomIndexes = this.precursor.getConnectedAtomIndecesOfAtomIndex((short) i);
        for (int k = 0; k < connectedAtomIndexes.length; k++) {
            if (i < connectedAtomIndexes[k])
                nodeString += "," + (i + 1) + "," + (connectedAtomIndexes[k] + 1);
        }
    }
    nodeString = nodeString.substring(1);
    String command1 = "g <- graph(c(" + nodeString + "),directed=F)";
    String command2 = "comms <- fastgreedy.community(g)";
    String command3 = "membership(comms)";
    double[] membershipDouble = null;
    if (Rsession.isSessionLoaded())
        membershipDouble = Rsession.giveMemberships(command1, command2, command3);
    this.memberships = new int[membershipDouble.length];
    this.numberCommunities = 0;
    for (int i = 0; i < membershipDouble.length; i++) {
        this.memberships[i] = (int) membershipDouble[i] - 1;
        if (this.memberships[i] + 1 > this.numberCommunities)
            this.numberCommunities = this.memberships[i] + 1;
    }
    FastBitArray[] atomFastBitArrays = new FastBitArray[this.numberCommunities];
    for (int i = 0; i < this.numberCommunities; i++) atomFastBitArrays[i] = new FastBitArray(this.memberships.length, false);
    for (int i = 0; i < this.memberships.length; i++) {
        atomFastBitArrays[this.memberships[i]].set(i);
    }
    this.communityFragments = new DefaultBitArrayFragment[this.numberCommunities];
    for (int i = 0; i < this.communityFragments.length; i++) {
        this.communityFragments[i] = new DefaultBitArrayFragment(this.precursor, atomFastBitArrays[i]);
    }
}

Example 3 with DefaultBitArrayFragment

use of de.ipbhalle.metfraglib.fragment.DefaultBitArrayFragment 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;
}