Examples with MSMSScore net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScore used on opensource projects

Example 1 with MSMSScore

use of net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScore in project mzmine2 by mzmine.

the class SingleRowPredictionTask method checkConstraints.

private void checkConstraints(IMolecularFormula cdkFormula) {
    // Check elemental ratios
    if (checkRatios) {
        boolean check = ElementalHeuristicChecker.checkFormula(cdkFormula, ratiosParameters);
        if (!check)
            return;
    }
    Double rdbeValue = RDBERestrictionChecker.calculateRDBE(cdkFormula);
    // Check RDBE condition
    if (checkRDBE && (rdbeValue != null)) {
        boolean check = RDBERestrictionChecker.checkRDBE(rdbeValue, rdbeParameters);
        if (!check)
            return;
    }
    // Calculate isotope similarity score
    final IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
    final String stringFormula = MolecularFormulaManipulator.getString(cdkFormula);
    final String adjustedFormula = FormulaUtils.ionizeFormula(stringFormula, ionType, charge);
    final double isotopeNoiseLevel = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopeNoiseLevel).getValue();
    // Fixed min abundance
    final double minPredictedAbundance = 0.00001;
    final IsotopePattern predictedIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula, minPredictedAbundance, charge, ionType.getPolarity());
    Double isotopeScore = null;
    if ((checkIsotopes) && (detectedPattern != null)) {
        isotopeScore = IsotopePatternScoreCalculator.getSimilarityScore(detectedPattern, predictedIsotopePattern, isotopeParameters);
        final double minScore = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopePatternScoreThreshold).getValue();
        if (isotopeScore < minScore)
            return;
    }
    // MS/MS evaluation is slowest, so let's do it last
    Double msmsScore = null;
    Feature bestPeak = peakListRow.getBestPeak();
    RawDataFile dataFile = bestPeak.getDataFile();
    Map<DataPoint, String> msmsAnnotations = null;
    int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
    if ((checkMSMS) && (msmsScanNumber > 0)) {
        Scan msmsScan = dataFile.getScan(msmsScanNumber);
        String massListName = msmsParameters.getParameter(MSMSScoreParameters.massList).getValue();
        MassList ms2MassList = msmsScan.getMassList(massListName);
        if (ms2MassList == null) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("The MS/MS scan #" + msmsScanNumber + " in file " + dataFile.getName() + " does not have a mass list called '" + massListName + "'");
            return;
        }
        MSMSScore score = MSMSScoreCalculator.evaluateMSMS(cdkFormula, msmsScan, msmsParameters);
        double minMSMSScore = msmsParameters.getParameter(MSMSScoreParameters.msmsMinScore).getValue();
        if (score != null) {
            msmsScore = score.getScore();
            msmsAnnotations = score.getAnnotation();
            // Check the MS/MS condition
            if (msmsScore < minMSMSScore)
                return;
        }
    }
    // Create a new formula entry
    final ResultFormula resultEntry = new ResultFormula(cdkFormula, predictedIsotopePattern, rdbeValue, isotopeScore, msmsScore, msmsAnnotations);
    // Add the new formula entry
    resultWindow.addNewListItem(resultEntry);
    foundFormulas++;
}

Example 2 with MSMSScore

use of net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScore in project mzmine2 by mzmine.

the class FormulaPredictionPeakListTask method checkConstraints.

private boolean checkConstraints(IMolecularFormula cdkFormula, PeakListRow peakListRow) {
    // Check elemental ratios
    if (checkRatios) {
        boolean check = ElementalHeuristicChecker.checkFormula(cdkFormula, ratiosParameters);
        if (!check) {
            return false;
        }
    }
    Double rdbeValue = RDBERestrictionChecker.calculateRDBE(cdkFormula);
    // Check RDBE condition
    if (checkRDBE && (rdbeValue != null)) {
        boolean check = RDBERestrictionChecker.checkRDBE(rdbeValue, rdbeParameters);
        if (!check) {
            return false;
        }
    }
    // Calculate isotope similarity score
    IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
    IsotopePattern predictedIsotopePattern = null;
    Double isotopeScore = null;
    if ((checkIsotopes) && (detectedPattern != null)) {
        String stringFormula = MolecularFormulaManipulator.getString(cdkFormula);
        String adjustedFormula = FormulaUtils.ionizeFormula(stringFormula, ionType, charge);
        final double isotopeNoiseLevel = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopeNoiseLevel).getValue();
        final double detectedPatternHeight = detectedPattern.getHighestDataPoint().getIntensity();
        final double minPredictedAbundance = isotopeNoiseLevel / detectedPatternHeight;
        predictedIsotopePattern = IsotopePatternCalculator.calculateIsotopePattern(adjustedFormula, minPredictedAbundance, charge, ionType.getPolarity());
        isotopeScore = IsotopePatternScoreCalculator.getSimilarityScore(detectedPattern, predictedIsotopePattern, isotopeParameters);
        final double minScore = isotopeParameters.getParameter(IsotopePatternScoreParameters.isotopePatternScoreThreshold).getValue();
        if (isotopeScore < minScore) {
            return false;
        }
    }
    // MS/MS evaluation is slowest, so let's do it last
    Double msmsScore = null;
    Feature bestPeak = peakListRow.getBestPeak();
    RawDataFile dataFile = bestPeak.getDataFile();
    int msmsScanNumber = bestPeak.getMostIntenseFragmentScanNumber();
    if ((checkMSMS) && (msmsScanNumber > 0)) {
        Scan msmsScan = dataFile.getScan(msmsScanNumber);
        String massListName = msmsParameters.getParameter(MSMSScoreParameters.massList).getValue();
        MassList ms2MassList = msmsScan.getMassList(massListName);
        if (ms2MassList == null) {
            setStatus(TaskStatus.ERROR);
            setErrorMessage("The MS/MS scan #" + msmsScanNumber + " in file " + dataFile.getName() + " does not have a mass list called '" + massListName + "'");
            return false;
        }
        MSMSScore score = MSMSScoreCalculator.evaluateMSMS(cdkFormula, msmsScan, msmsParameters);
        double minMSMSScore = msmsParameters.getParameter(MSMSScoreParameters.msmsMinScore).getValue();
        if (score != null) {
            msmsScore = score.getScore();
            // Check the MS/MS condition
            if (msmsScore < minMSMSScore) {
                return false;
            }
        }
    }
    return true;
}