Examples of addIsotope()

Examples of org.openscience.cdk.formula.MolecularFormula.addIsotope()

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    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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Examples of org.openscience.cdk.interfaces.IMolecularFormula.addIsotope()

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    Iterator<IAtomContainer> containers = ChemModelManipulator
        .getAllAtomContainers(chemModel).iterator();
    int implicitHs = 0;
    while (containers.hasNext()) {
      for (IAtom atom : containers.next().atoms()) {
        wholeModel.addIsotope(atom);
        if (atom.getImplicitHydrogenCount() != null) {
          implicitHs += atom.getImplicitHydrogenCount();
        }
      }
    }
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Examples of org.openscience.cdk.interfaces.IMolecularFormula.addIsotope()

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        }
      }
    }
    try {
      if (implicitHs > 0)
        wholeModel
            .addIsotope(XMLIsotopeFactory.getInstance(
                wholeModel.getBuilder()).getMajorIsotope(1),
                implicitHs);
    } catch (IOException e) {
      // do nothing
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Examples of org.openscience.cdk.interfaces.IMolecularFormula.addIsotope()

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        Iterator<IAtomContainer> containers = ChemModelManipulator
            .getAllAtomContainers(theJcpp.get2DHub().getIChemModel()).iterator();
        int implicitHs = 0;
        while (containers.hasNext()) {
            for (IAtom atom : containers.next().atoms()) {
                wholeModel.addIsotope(atom);
                if (atom.getImplicitHydrogenCount() != null) {
                    implicitHs += atom.getImplicitHydrogenCount();
                }
            }
        }
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Examples of org.openscience.cdk.interfaces.IMolecularFormula.addIsotope()

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                }
            }
        }
        try {
            if (implicitHs > 0)
                wholeModel.addIsotope(XMLIsotopeFactory.getInstance(
                        wholeModel.getBuilder()).getMajorIsotope(1),
                        implicitHs);
        } catch (IOException e) {
        // do nothing
        }
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