// 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);
}
}
}
// from biojava structure, convert to own user model
public void createUserModel(Structure struc) {
// read default MMFFtypes for atoms
if (modelList == null) modelList = new ArrayList<Model>();
Model model = null;
for (int i = 0; i < struc.nrModels(); i++) {
// for each model, create and add to model list
model = new Model();
model.setModelName("Model" + (i + 1));
model.setMolecule(struc.getModel(i)); // set the model
modelList.add(model);
}
}