Applications Embedding Jmol

Jmol / JSmol Applications

• Websites Using J(S)mol
• J(S)mol in the Classroom
• Journals Using J(S)mol
• J(S)mol Literature
• Articles Using J(S)mol
• Books Using J(S)mol
• Wikis Using J(S)mol
• Blogs Using J(S)mol
• CMS Using J(S)mol (Moodle and others)
  Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms
• Applications Embedding Jmol
• Distributions Including Jmol
• Blue Obelisk

Applications using Jmol

Jmol users, please add here your favorite Java applications that embed Jmol.

(There is another page for operating systems and software suites that include Jmol.)

• BioClipse.
• CaGe - the "Chemical & abstract Graph environment", currently using an ancient version of JmolApplet (0.6.1) as one of its molecule viewers. (Old, but the developer might find time next to his regular job to extend the project. Incorporating a current Jmol version is on his wish list.)
• ChemPad renders in Jmol 3D models calculated on-the-fly from a formula sketched by hand in a tablet PC.
• iBabel - A GUI for cheminfomatics toolkit Openbabel, iBabel uses embeded applets to display structures.
• Molecular Workbench - A Molecular Simulation Tool.
• PFAAT - Protein Family Alignment Annotation Tool.
• ProteinGlimpse is a free widget for visualizing macromolecules retrieved from the Protein Data Bank or from local disk. It is a dashboard application for Mac OS X that uses the JmolApplet.
• Spice - Spice is a DAS client for distributed annotation of protein sequences and structures. A java webstart version can be run from online.
• STRAP - Alignment Program for Proteins and workbench for protein structures.
• Taverna.

How to embed Jmol into an application

• a very good start is the Integration.java out of Jmol SVN.
• to see how Spice is integrating Jmol, please have a look here.
• a special page is devoted to using Jmol as 3D viewer for CDK based projects: Jmol Cdk Integration.

Most interaction with Jmol will happen by sending RasmolScript - like commands to Jmol. This is nicely documented by the Integration.java example. It is also possible to get data back out of Jmol. This can be done by accessing the JmolViewer class. This might be replaced by an Interface in the future.

One example of getting data out of Jmol is by adding a MouseListener to the Panel that contains the JmolViewer instance. e.g.

 public void mouseMoved(MouseEvent e) {
 
   int pos = viewer.findNearestAtomIndex( e.getX(), e.getY() );
   if ( pos == -1 ) { return ; }
 
   String chainId = viewer.getAtomChain( pos ) ;
   String seqCode = viewer.getAtomSequenceCode( pos ) ;
   // ... do something in your application
 }

When retreiving the "seqCode" for an Atom, the Insertion Code of PDB files is appended. Note the Jmol notation of insertion codes: e.g. 122^A, to distinguish from the Rasmol command 122A, which would select residue 122 of chain A.

A Note on JmolStatusListener

If your application needs to be notified of Jmol events, then you must create an interface to Jmol by implementing org.jmol.api.JmolStatusListener. I stumbled for some time before discovering that the notifyFrameChanged() event handler must include updateComputedMenus() on the JmolPopup object. Without this, the menu will mostly contain ghosted items.

Contributors

AngelHerraez, Pierocanepa, Yodah134, Ssorgatem, Mhampton, Kirby, Chris, NicolasVervelle, Pimpim, Nvcleemp, Tzontonel, Christoph.gille, Andorsch, Martin.guetlein