// 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: ");
}
// 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);
}
public void displayParticles(ArrayList<AbstractParticle> list) {
String pdb = "MODEL 1\n";
for (int i = 0; i < list.size(); i++) {
// String index = String.format("%4d", list.get(i).getGUID());
String index = String.format("%4d", i);
if (list.get(i) instanceof Atom) {
double scale = Math.pow(10, 10 + list.get(i).getPosition().metric);
Vector3D position = list.get(i).getPosition();
double x = capCoord(position.x * scale);
double y = capCoord(position.y * scale);
double z = capCoord(position.z * scale);
String coords = String.format("%8.3f%8.3f%8.3f", x, y, z);
String elementSymbol =
String.format("%-4s", ((Atom) list.get(i)).getElementSymbol().toUpperCase());
pdb +=
"HETATM " + index + " " + elementSymbol + " 1 " + coords + " 1.00 0.00\n";
} else if (list.get(i) instanceof Molecule) {
Molecule m = (Molecule) list.get(i);
if (World.simulationLvlAtomic == true) {
for (Atom a : m.getChains().get(0).atomSeq) {
double scale = Math.pow(10, 10 + list.get(i).getPosition().metric);
Vector3D position = a.getPosition();
double x = capCoord(position.x * scale);
double y = capCoord(position.y * scale);
double z = capCoord(position.z * scale);
String coords = String.format("%8.3f%8.3f%8.3f", x, y, z);
String elementSymbol = String.format("%-4s", a.getElementSymbol().toUpperCase());
pdb +=
"HETATM "
+ index
+ " "
+ elementSymbol
+ " 1 "
+ coords
+ " 1.00 0.00\n";
}
/*
pdb += "HETATM 1 NA TST A 1 5.000 5.000 5.000 1.00 0.00\n"+
"HETATM 2 CL TST A 1 6.400 6.400 6.400 1.00 0.00\n"+
"CONECT 1 2\n" +
"CONECT 2 1\n";
*/
} else {
double scale = Math.pow(10, 10 + list.get(i).getPosition().metric);
Vector3D position = list.get(i).getPosition();
double x = capCoord(position.x * scale);
double y = capCoord(position.y * scale);
double z = capCoord(position.z * scale);
String coords = String.format("%8.3f%8.3f%8.3f", x, y, z);
pdb += "HETATM 1 CS TST A 1 " + coords + " 1.00 0.00\n";
}
}
}
pdb += "ENDMDL";
if (World.displayUI) viewer.openStringInline(pdb);
try {
BufferedWriter writer = new BufferedWriter(new FileWriter("output.pdb"));
writer.write(pdb);
writer.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
World.simulationStatus = "restart";
}
if (World.displayUI) {
createUserModel(DataManager.readFile("output.pdb"));
}
}
/** 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);
}
private void reloadViewer() {
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");
}