// delete Atoms from both modelList and viewer.
public void deleteAtoms(int currentModelIndex, String key, int atomPosition) {
modelList.get(currentModelIndex).removeAtom(key);
// modelList.get(currentModelIndex).getAtomHash().remove(key);
viewer.evalString(
"delete atomno=" + atomPosition + " && modelindex=" + viewer.getDisplayModelIndex());
toolPanel.setModelText(modelList);
}
public void notifyUpdated(AbstractParticle[] particles) {
List<Atom> atomsUpdated = new ArrayList<Atom>();
// When the two particles are part of common model
if (modelList.size() != 0) {
for (int i = 0; i < particles.length; i++) {
if (particles[i] instanceof Atom) { // if particle is Atom type
// get the updated atom from model
atomsUpdated.add(
modelList
.get(0)
.getAtomHash()
.get(modelList.get(0).getModelName() + ((Atom) particles[i]).getChainSeqNum()));
}
}
// update atoms in jmol display
for (int i = 0; i < atomsUpdated.size(); i++) {
Atom atom = atomsUpdated.get(i);
float xOffset =
(float) atom.getPosition().x - viewer.getAtomPoint3f(atom.getChainSeqNum() - 1).x;
float yOffset =
(float) atom.getPosition().y - viewer.getAtomPoint3f(atom.getChainSeqNum() - 1).y;
float zOffset =
(float) atom.getPosition().z - viewer.getAtomPoint3f(atom.getChainSeqNum() - 1).z;
viewer.evalString("select atomno=" + atom.getChainSeqNum());
viewer.evalString("translateSelected {" + xOffset + " " + yOffset + " " + zOffset + "}");
}
}
}
private String getAuxiliaryFileData() {
String fName = fileName.substring(fileName.lastIndexOf("/") + 1);
fName = fName.substring(fName.lastIndexOf("\\") + 1);
return "; Created by: Jmol "
+ Viewer.getJmolVersion()
+ "\n; Creation date: "
+ getExportDate()
+ "\n; File created: "
+ fileName
+ " ("
+ out.getByteCount()
+ " bytes)\n\n"
+ (commandLineOptions != null
? commandLineOptions
: "\n; Jmol state: (embedded in input file)"
+ "\nInput_File_Name="
+ fName
+ "\nOutput_to_File=true"
+ "\nOutput_File_Type=N"
+ "\nOutput_File_Name="
+ fName
+ ".png"
+ "\nWidth="
+ screenWidth
+ "\nHeight="
+ screenHeight
+ "\nAntialias=true"
+ "\nAntialias_Threshold=0.1"
+ "\nDisplay=true"
+ "\nPause_When_Done=true"
+ "\nWarning_Level=5"
+ "\nVerbose=false"
+ "\n");
}
// called by JMolSelectionListener.java to set the selected Atoms list
public void setSelectedAtoms(BS values) {
// System.out.println("Selected: " + values);
if (selectedAtoms == null) selectedAtoms = new ArrayList<Atom>();
else selectedAtoms.clear();
String[] valueGet = values.toString().split("[{ }]");
if (modelList != null) {
Model currentModel = modelList.get(viewer.getDisplayModelIndex());
for (int i = 0; i < valueGet.length; i++) {
if (valueGet[i].compareTo("") != 0) {
// if its list of continuous atoms
if (valueGet[i].contains(":")) {
int start = Integer.parseInt(valueGet[i].split(":")[0]) + 1;
int end = Integer.parseInt(valueGet[i].split(":")[1]) + 1;
for (int j = start; j <= end; j++) {
selectedAtoms.add(currentModel.getAtomHash().get(currentModel.getModelName() + j));
}
} else {
selectedAtoms.add(
currentModel
.getAtomHash()
.get(currentModel.getModelName() + (Integer.parseInt(valueGet[i]) + 1)));
}
}
}
}
}
// 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: ");
}
// define minimizer, for minimizing molecule.
public void minimizeModel() {
// viewer.ms.setAtomCoord(0, 0.0f, 0.0f, 0.0f);
Minimizer minimizer = new Minimizer(this);
minimizer.setupMinimizing(modelList.get(viewer.getDisplayModelIndex()));
minimizer.startMinimizing();
System.out.println(DataManager.modelToPDB(modelList));
minimizeMode = false;
}
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);
}
}
}
}
// 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);
}
// every mouse state and detection called here.
// to cater for future self-created display.
public void setMouseState(int x, int y, int mode) {
GestureManager.setMouseState(x, y, mode, mouseState);
if (viewer.getInMotion(false)) {
/*String mouseGesture = "";
mouseGesture += "Mouse Mode: " + mouseState.getMouseMode() + "\n";
mouseGesture += "Mouse Start Position: X-Pos=" + mouseState.getStartPosX() + " Y-Pos=" + mouseState.getStartPosY() + "\n";
mouseGesture += "Mouse End Position: X-Pos=" + mouseState.getEndPosX() + " Y-Pos=" + mouseState.getEndPosY() + "\n";*/
// System.out.println(mouseGesture);
mouseState.clearState();
}
if (minimizeMode && mode == 16640) { // when mouse drag stopped.
System.out.println("Entering minimizing stage...");
minimizeModel();
}
}
public void steepestDescentInitialize(int stepMax, double criterion) {
this.stepMax = stepMax; // 1000
// The criterion must be in the units of the calculation.
// However, the user is setting this, so they will be in Minimizer units.
//
this.criterion = criterion / toUserUnits(1); // 1e-3
currentStep = 0;
clearForces();
calc.setLoggingEnabled(true);
calc.setLoggingEnabled(stepMax == 0 || Logger.isActiveLevel(Logger.LEVEL_DEBUGHIGH));
String s =
name
+ " "
+ calc.getDebugHeader(-1)
+ "Jmol Minimization Version "
+ Viewer.getJmolVersion()
+ "\n";
calc.appendLogData(s);
Logger.info(s);
calc.getConstraintList();
if (calc.loggingEnabled)
calc.appendLogData(calc.getAtomList("S T E E P E S T D E S C E N T"));
dE = 0;
calc.setPreliminary(stepMax > 0);
e0 = energyFull(false, false);
s =
TextFormat.sprintf(
" Initial "
+ name
+ " E = %10.3f "
+ minimizer.units
+ " criterion = %8.6f max steps = "
+ stepMax,
new Object[] {Float.valueOf(toUserUnits(e0)), Float.valueOf(toUserUnits(criterion))});
minimizer.report(s, false);
calc.appendLogData(s);
}
/**
* legacy apps will use this
*
* @param vwr
* @param g
* @param size
*/
@Deprecated
static void renderScreenImage(PlatformViewer vwr, Object g, Object size) {
((Viewer) vwr).renderScreenImage(g, ((Dimension) size).width, ((Dimension) size).height);
}
@Override
protected void outputHeader() {
initVars();
output("// ******************************************************\n");
output("// Created by Jmol " + Viewer.getJmolVersion() + "\n");
output("//\n");
output("// This script was generated on " + getExportDate() + "\n");
output("// ******************************************************\n");
try {
output(viewer.getWrappedStateScript());
} catch (Exception e) {
// tough luck
}
output("\n");
output("// ******************************************************\n");
output("// Declare the resolution, camera, and light sources.\n");
output("// ******************************************************\n");
output("\n");
output("// NOTE: if you plan to render at a different resolution,\n");
output("// be sure to update the following two lines to maintain\n");
output("// the correct aspect ratio.\n" + "\n");
output("#declare Width = " + screenWidth + ";\n");
output("#declare Height = " + screenHeight + ";\n");
output("#declare minScreenDimension = " + minScreenDimension + ";\n");
output("#declare showAtoms = true;\n");
output("#declare showBonds = true;\n");
output("#declare noShadows = true;\n");
output("camera{\n");
output(" orthographic\n");
output(" location < " + screenWidth / 2f + ", " + screenHeight / 2f + ", 0>\n" + "\n");
output(" // Negative right for a right hand coordinate system.\n");
output("\n");
output(" sky < 0, -1, 0 >\n");
output(" right < -" + screenWidth + ", 0, 0>\n");
output(" up < 0, " + screenHeight + ", 0 >\n");
output(" look_at < " + screenWidth / 2f + ", " + screenHeight / 2f + ", 1000 >\n");
output("}\n");
output("\n");
output("background { color rgb <" + rgbFractionalFromColix(backgroundColix) + "> }\n");
output("\n");
// light source
float distance = Math.max(screenWidth, screenHeight);
output(
"light_source { <"
+ lightSource.x * distance
+ ","
+ lightSource.y * distance
+ ", "
+ (-1 * lightSource.z * distance)
+ "> "
+ " rgb <0.6,0.6,0.6> }\n");
output("\n");
output("\n");
output("// ***********************************************\n");
output("// macros for common shapes\n");
output("// ***********************************************\n");
output("\n");
writeMacros();
}
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");
}