// called by JMolSelectionListener.java to set the selected Atoms list
  public void setSelectedAtoms(BS values) {
    // System.out.println("Selected: " + values);
    if (selectedAtoms == null) selectedAtoms = new ArrayList<Atom>();
    else selectedAtoms.clear();

    String[] valueGet = values.toString().split("[{ }]");
    if (modelList != null) {
      Model currentModel = modelList.get(viewer.getDisplayModelIndex());
      for (int i = 0; i < valueGet.length; i++) {
        if (valueGet[i].compareTo("") != 0) {
          // if its list of continuous atoms
          if (valueGet[i].contains(":")) {
            int start = Integer.parseInt(valueGet[i].split(":")[0]) + 1;
            int end = Integer.parseInt(valueGet[i].split(":")[1]) + 1;
            for (int j = start; j <= end; j++) {
              selectedAtoms.add(currentModel.getAtomHash().get(currentModel.getModelName() + j));
            }
          } else {
            selectedAtoms.add(
                currentModel
                    .getAtomHash()
                    .get(currentModel.getModelName() + (Integer.parseInt(valueGet[i]) + 1)));
          }
        }
      }
    }
  }
 // set the model's bonds using Jmol display.
 public void setModelBonds() {
   int currModel = 0, prevModel = 0;
   Atom atom1, atom2;
   Bond bond;
   String index1, index2;
   ArrayList<Bond> ownbonds = new ArrayList<Bond>();
   org.jmol.modelset.Bond[] bonds = viewer.ms.bo;
   for (int i = 0; i < bonds.length; i++) {
     prevModel = currModel;
     currModel = bonds[i].getAtom1().getModelNumber();
     Model model = modelList.get(currModel - 1);
     if (currModel != prevModel && i != 0) {
       modelList.get(prevModel - 1).setBonds(ownbonds);
       ownbonds.clear();
     }
     index1 = model.getModelName() + bonds[i].getAtom1().atomSite;
     index2 = model.getModelName() + bonds[i].getAtom2().atomSite;
     atom1 = model.getAtomHash().get(index1);
     atom2 = model.getAtomHash().get(index2);
     if (atom1 == null || atom2 == null) continue;
     bond = new Bond(atom1, atom2);
     ownbonds.add(bond);
     atom1.setBond(bond);
     atom2.setBond(bond);
     if (i == bonds.length - 1) {
       modelList.get(currModel - 1).setBonds(ownbonds);
     }
   }
 }