Examples of org.jmol.api.JmolMolecule

      getMolecules();
    List V = new ArrayList();
    BitSet bsTemp = new BitSet();
    for (int i = 0; i < moleculeCount; i++) {
      bsTemp = BitSetUtil.copy(bsAtoms);
      JmolMolecule m = molecules[i];
      bsTemp.and(m.atomList);
      if (bsTemp.length() > 0) {
        Hashtable info = new Hashtable();
        info.put("mf", m.getMolecularFormula(false));
        info.put("number", new Integer(m.moleculeIndex + 1)); //for now
        info.put("modelNumber", getModelNumberDotted(m.modelIndex));
        info.put("numberInModel", new Integer(m.indexInModel + 1));
        info.put("nAtoms", new Integer(m.atomCount));
        info.put("nElements", new Integer(m.nElements));

    BitSet bsOK = viewer.transformAtoms(firstPass);
    if (firstPass && slabByMolecule && slabbing) {
      JmolMolecule[] molecules = modelSet.getMolecules();
      int moleculeCount = modelSet.getMoleculeCountInModel(-1);
      for (int i = 0; i < moleculeCount; i++) {
        JmolMolecule m = molecules[i];
        int j = 0;
        int pt = m.firstAtomIndex;
        if (!bsOK.get(pt))
          continue;
        for (; j < m.atomCount; j++, pt++)

Related Classes of org.jmol.api.JmolMolecule

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