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 UpdateRegistry(JmolDisplay jmolPanel, ToolPanel toolPanel, List<Model> models) {
this.jmolPanel = jmolPanel;
this.viewer = jmolPanel.getViewer();
this.modelList = models;
this.toolPanel = toolPanel;
this.mouseState = new MouseState();
this.dragMode = -1;
this.addMode = false;
this.minimizeMode = false;
}
/** Create the main frame. */
public View(EventListener listener, Map<String, Object> config) {
super((String) config.get("name"));
this.listener = listener;
this.config = config;
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
setBounds(100, 100, 900, 600);
setLocationRelativeTo(null);
contentPane = new JPanel();
contentPane.setBorder(new EmptyBorder(5, 5, 5, 5));
contentPane.setLayout(new BorderLayout(0, 0));
setContentPane(contentPane);
// add JMol Panel
JmolDisplay jmolPanel = new JmolDisplay();
jmolPanel.setBorder(new EmptyBorder(5, 0, 5, 0));
contentPane.add(jmolPanel);
// add mediator
viewer = jmolPanel.getViewer();
viewer.evalString("set debug OFF;");
mediator = new UpdateRegistry(viewer);
jmolPanel.setMediator(mediator);
viewer.setPercentVdwAtom(20);
viewer.evalString("");
System.out.println((String) config.get("pdb"));
viewer.reset(true);
viewer.openStringInline((String) config.get("pdb"));
// viewer.evalString("load " + (String) config.get("dir") + "/" + (String) config.get("name") +
// "/" + (String) config.get("name") + ".gro");
viewer.evalString("wireframe only;wireframe reset;spacefill reset;");
// viewer.evalString("set mouseDragFactor 1.0");
jmolPanel.setMediator(mediator);
// add RHS Panel for user input
JPanel inputPanel = new JPanel();
inputPanel.setBorder(new EmptyBorder(0, 5, 0, 5));
contentPane.add(inputPanel, BorderLayout.EAST);
createSimulationPanel();
inputPanel.setLayout(new BorderLayout(0, 1));
inputPanel.add(simulationPanel, BorderLayout.NORTH);
createForcesPanel();
inputPanel.add(forcesPanel, BorderLayout.CENTER);
controlPanel = new JPanel();
controlPanel.setAlignmentX(LEFT_ALIGNMENT);
inputPanel.add(controlPanel, BorderLayout.SOUTH);
pauseButton = new JButton("Pause");
pauseButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (listener.getStatus() > 0) {
pauseButton.setText("Resume");
partialEnableSimulationPanel();
enableForcePanel();
listener.onPause();
} else {
pauseButton.setText("Pause");
saveParams();
disableForcePanel();
disableSimulationPanel();
listener.onResume();
}
}
});
controlPanel.add(pauseButton);
stopButton = new JButton("Stop");
stopButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (stopButton.getText().equals("Stop")) {
stopButton.setText("Start");
pauseButton.setEnabled(false);
enableConfig();
listener.onStop();
} else {
stopButton.setText("Stop");
pauseButton.setText("Pause");
pauseButton.setEnabled(true);
saveParams();
listener.onRestart();
System.out.println("restart done");
}
}
});
controlPanel.add(stopButton);
restartButton = new JButton("Restart");
restartButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
stopButton.setText("Stop");
pauseButton.setText("Pause");
pauseButton.setEnabled(true);
saveParams();
listener.onRestart();
}
});
controlPanel.add(restartButton);
// add text field for user input
// commandTextField = new JTextField();
// contentPane.add(commandTextField, BorderLayout.SOUTH);
// commandTextField.requestFocusInWindow();
this.setVisible(true);
}