public void updateViewerCoord() {
for (Atom atm : modelList.get(viewer.getDisplayModelIndex()).getAtomHash().values()) {
viewer.ms.setAtomCoord(
(atm.getAtomSeqNum() - 1),
atm.getCoordinates()[0],
atm.getCoordinates()[1],
atm.getCoordinates()[2]);
}
jmolPanel.getViewer().refresh(3, "minimization step ");
}
// 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);
}