// delete Atoms from both modelList and viewer.
public void deleteAtoms(int currentModelIndex, String key, int atomPosition) {
modelList.get(currentModelIndex).removeAtom(key);
// modelList.get(currentModelIndex).getAtomHash().remove(key);
viewer.evalString(
"delete atomno=" + atomPosition + " && modelindex=" + viewer.getDisplayModelIndex());
toolPanel.setModelText(modelList);
}
// Method to load file from BioJava structure to Jmol Display
public void loadFileToJmol(Structure struc) {
createUserModel(struc);
String pdb = DataManager.modelToPDB(modelList);
viewer.openStringInline(pdb);
toolPanel.setModelText(modelList);
logger.log(Level.INFO, "After load File: ");
}
// copy atoms into new Atoms object from selected atoms
public void copyAtoms(int currentModelIndex, String key) {
if (savedAtoms == null) {
savedAtoms = new ArrayList<Atom>();
}
try {
Atom newAtom = (Atom) modelList.get(currentModelIndex).getAtomHash().get(key).clone();
savedAtoms.add(newAtom);
} catch (CloneNotSupportedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
toolPanel.setModelText(modelList);
}
// paste copied/cut atoms, not applicable when copied atoms are paste to same model.
public void pasteSavedAtoms(int modelIndex) {
if (savedAtoms == null)
JOptionPane.showMessageDialog(
jmolPanel,
"You have not copied or cut any atoms to paste!",
"Warning",
JOptionPane.WARNING_MESSAGE);
else {
boolean error = false;
for (int i = 0; i < savedAtoms.size(); i++) {
for (Atom atm : modelList.get(modelIndex).getAtomHash().values()) {
if (savedAtoms.get(i).getCoordinates()[0] == atm.getCoordinates()[0]
&& savedAtoms.get(i).getCoordinates()[1] == atm.getCoordinates()[1]
&& savedAtoms.get(i).getCoordinates()[2] == atm.getCoordinates()[2]) {
error = true;
break;
}
}
if (error) {
JOptionPane.showMessageDialog(
jmolPanel,
"You are trying to paste atoms in location occupied!",
"Warning",
JOptionPane.WARNING_MESSAGE);
break;
} else {
addAtom(modelIndex, savedAtoms.get(i));
}
}
String pdb = DataManager.modelToPDB(modelList);
System.out.println(pdb);
viewer.openStringInline(pdb);
viewer.setCurrentModelIndex(modelIndex);
}
toolPanel.setModelText(modelList);
}