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 ");
}
public void atomMoved() {
for (Atom atm : modelList.get(viewer.getDisplayModelIndex()).getAtomHash().values()) {
for (int i = 0; i < viewer.ms.at.length; i++) {
if (atm.getAtomSeqNum() == (i + 1)) {
double[] coords = {viewer.ms.at[i].x, viewer.ms.at[i].y, viewer.ms.at[i].z};
atm.setCoordinates(coords);
}
}
}
}