Programmatic Access to Jmol - Revision history

Emaillenin at 09:08, 15 September 2009

2009-09-15T09:08:25Z

Emaillenin: changing the method name - so new developers can understand easily

2009-09-15T08:39:26Z

changing the method name - so new developers can understand easily

Emaillenin at 08:19, 15 September 2009

2009-09-15T08:19:15Z

Emaillenin: The current source code requires biojava to be in the classpath.. I will change the code so that this program run without biojava requirement.. Lenin

2009-09-15T08:18:19Z

The current source code requires biojava to be in the classpath.. I will change the code so that this program run without biojava requirement.. Lenin

NicolasVervelle: Formatting

2009-08-02T10:29:14Z

Formatting

Emaillenin: code editing

2009-07-30T04:53:37Z

code editing

Emaillenin: First entry

2009-07-28T05:58:21Z

First entry

New page

Jmol can be [[Applications Embedding Jmol|embedded]] in your existing Java applications. After embedding the Jmol Viewer in your application, it can be accessed programmatically. This allows developers to accomplish every thing in Jmol by running scripts.

To embed Jmol and to show the structure of a molecule having its PDB file, can be done using the following example.
(Biojava should be in your classpath. Get it from [http://www.biojava.org/wiki/BioJava:Download Biojava Downloads Page])

package org.jmoltest;

import java.awt.Container;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import javax.swing.JFrame;
import javax.swing.JPanel;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.io.PDBFileReader;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAdapter;
import org.jmol.api.JmolSimpleViewer;

public class SimpleJmolExample {
JmolSimpleViewer viewer;
Structure structure;

JmolPanel jmolPanel;
JFrame frame ;

public static void main(String[] args){
try {

PDBFileReader pdbr = new PDBFileReader();
pdbr.setPath("/Path/To/PDBFiles/");

String pdbCode = "5pti";

Structure struc = pdbr.getStructureById(pdbCode);

SimpleJmolExample ex = new SimpleJmolExample();
ex.setStructure(struc);

} catch (Exception e){
e.printStackTrace();
}
}

public SimpleJmolExample() {
frame = new JFrame();
frame.addWindowListener(new ApplicationCloser());
Container contentPane = frame.getContentPane();
jmolPanel = new JmolPanel();

jmolPanel.setPreferredSize(new Dimension(200,200));
contentPane.add(jmolPanel);

frame.pack();
frame.setVisible(true);

}
public void setStructure(Structure s) {

frame.setName(s.getPDBCode());

// actually this is very simple
// just convert the structure to a PDB file

String pdb = s.toPDB();

structure = s;
JmolSimpleViewer viewer = jmolPanel.getViewer();

// Jmol could also read the file directly from your file system
//viewer.openFile("/Path/To/PDB/1tim.pdb");

// send the PDB file to Jmol.
// there are also other ways to interact with Jmol, but they require more
// code. See the link to SPICE above...
viewer.openStringInline(pdb);
viewer.evalString("select *; spacefill off; wireframe off; backbone 0.4; ");
viewer.evalString("color chain; ");
this.viewer = viewer;

}

public void setTitle(String label){
frame.setTitle(label);
}

public JmolSimpleViewer getViewer(){

return jmolPanel.getViewer();
}

static class ApplicationCloser extends WindowAdapter {
public void windowClosing(WindowEvent e) {
System.exit(0);
}
}

static class JmolPanel extends JPanel {
/**
*
*/
private static final long serialVersionUID = -3661941083797644242L;
JmolSimpleViewer viewer;
JmolAdapter adapter;
JmolPanel() {
adapter = new SmarterJmolAdapter();
viewer = JmolSimpleViewer.allocateSimpleViewer(this, adapter);

}

public JmolSimpleViewer getViewer() {
return viewer;
}

public void executeCmd(String rasmolScript){
viewer.evalString(rasmolScript);
}

final Dimension currentSize = new Dimension();
final Rectangle rectClip = new Rectangle();

public void paint(Graphics g) {
getSize(currentSize);
g.getClipBounds(rectClip);
viewer.renderScreenImage(g, currentSize, rectClip);
}
}

}

@@ Line 26: / Line 26: @@
      JFrame jframe;
-     public MyJmolViewer{
+     public MyJmolViewer() {
          try {
@@ Line 36: / Line 36: @@
              Structure struc = pdbr.getStructureById(pdbCode);
-             SimpleJmolExample ex = new SimpleJmolExample();
+             initializeJmolPanel ex = new initializeJmolPanel();
              ex.setStructure(struc);
@@ Line 46: / Line 46: @@
-     public SimpleJmolExample() {
+     public initializeJmolPanel() {
          frame = new JFrame();
          frame.addWindowListener(new ApplicationCloser());

@@ Line 3: / Line 3: @@
 To embed Jmol and to show the structure of a molecule using its PDB file, follow the example below.
-package org.jmoltest;
+ package org.jmoltest;
-<br/><br/>
-import java.awt.Container;<br/>
-import java.awt.Dimension;<br/>
+ import java.awt.Container;
-import java.awt.Graphics;<br/>
+ import java.awt.Dimension;
-import java.awt.Rectangle;<br/>
+ import java.awt.Graphics;
-import java.awt.event.WindowAdapter;<br/>
+ import java.awt.Rectangle;
-import java.awt.event.WindowEvent;<br/>
+ import java.awt.event.WindowAdapter;
-import javax.swing.JFrame;<br/>
+ import java.awt.event.WindowEvent;
-import javax.swing.JPanel;<br/>
+ import javax.swing.JFrame;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;<br/>
+ import javax.swing.JPanel;
-import org.jmol.api.JmolAdapter;<br/>
+ import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.api.JmolSimpleViewer;<br/>
+ import org.jmol.api.JmolAdapter;
+ import org.jmol.api.JmolSimpleViewer;
 public class MyJmolViewer {
+ public class MyJmolViewer {
      private String title = "Programmatic Access to Jmol";
      JmolSimpleViewer viewer;
@@ Line 130: / Line 131: @@
+         }
+     }
-−
+  }
 For a shorter example, use Biojava. For more details, visit [http://www.biojava.org/wiki/BioJava:CookBook:PDB:Jmol Biojava Cookbook].

@@ Line 58: / Line 58: @@
          frame.setVisible(true);
+     }
      public void setTitle(String label){
          frame.setTitle(label);

@@ Line 57: / Line 57: @@
          frame.pack();
          frame.setVisible(true);
+     }

@@ Line 59: / Line 59: @@
+     }
-    public void setStructure(Structure s) {
      public void setTitle(String label){
          frame.setTitle(label);
@@ Line 89: / Line 65: @@
      public JmolSimpleViewer getViewer(){
          return jmolPanel.getViewer();
+     }
@@ Line 101: / Line 76: @@
      static class JmolPanel extends JPanel {
          private static final long serialVersionUID = -3661941083797644242L;
          JmolSimpleViewer viewer;