Package org.openscience.cdk.formula

Examples of org.openscience.cdk.formula.MolecularFormula

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    while (true) {

      if (isCanceled())
        return;

      MolecularFormula cdkFormula = generator.getNextFormula();

      if (cdkFormula == null)
        break;

      // Mass is ok, so test other constraints
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        }

      }

      if (currentMass >= minMass) {
        MolecularFormula cdkFormula = generateCDKFormula();
        testedCombinations++;
        increaseCounter(0);
        return cdkFormula;
      }
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  }

  private MolecularFormula generateCDKFormula() {

    MolecularFormula cdkFormula = new MolecularFormula();

    for (int i = 0; i < elementRules.length; i++) {
      if (currentCounts[i] == 0)
        continue;
      cdkFormula.addIsotope(elementRules[i].getElementObject(),
          currentCounts[i]);
    }

    return cdkFormula;
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        if (isCanceled()) {
          return;
        }

        MolecularFormula cdkFormula = generator.getNextFormula();

        if (cdkFormula == null) {
          break;
        }
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          .getToleranceRange(neutralLoss);

      FormulaGenerator msmsEngine = new FormulaGenerator(msmsTargetRange,
          msmsElementRules);

      MolecularFormula formula = msmsEngine.getNextFormula();
      if (formula != null) {
        String formulaString = MolecularFormulaManipulator
            .getString(formula);
        msmsAnnotations.put(dp, formulaString);
        interpretedMSMSpeaks++;
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Related Classes of org.openscience.cdk.formula.MolecularFormula

  • net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.FormulaGenerator
  • net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.SingleRowPredictionTask
  • net.sf.mzmine.modules.peaklistmethods.identification.formulapredictionpeaklist.FormulaPredictionPeakListTask
  • net.sf.mzmine.modules.peaklistmethods.msms.msmsscore.MSMSScoreCalculator
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