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); } } } }