Package org.openscience.cdk.config

Examples of org.openscience.cdk.config.IsotopeFactory.configure()

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      int c = (int)mol.getBondOrderSum(a);
      if(a.getFormalCharge() == 1 || a.getFormalCharge() == -1) c += 1;
      int hr = 4 - c;
      for(int j=0;j<hr;j++) {
        IAtom ha = new Atom("H");
        isotopeFactory.configure(ha);
        IBond b = new Bond(a, ha);
        mol.addAtom(ha);
        mol.addBond(b);
      }
    }
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    this.atom.setSymbol(symbol);
    try {
      IsotopeFactory ifac = XMLIsotopeFactory.getInstance(atom.getBuilder());
      this.atom.setMassNumber(ifac.getMajorIsotope(symbol).getMassNumber());
      chemModelRelay.updateAtom(atom);
      ifac.configure(atom);
    } catch (OptionalDataException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } catch (IOException e) {
      // TODO Auto-generated catch block
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    this.atom.setSymbol(formerSymbol);
    try {
      IsotopeFactory ifac = XMLIsotopeFactory.getInstance(atom.getBuilder());
      this.atom.setMassNumber(ifac.getMajorIsotope(formerSymbol).getMassNumber());
      chemModelRelay.updateAtom(atom);
      ifac.configure(atom);
    } catch (OptionalDataException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } catch (IOException e) {
      // TODO Auto-generated catch block
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