Applications Embedding Jmol

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Revision as of 00:05, 7 April 2007 by Christoph.gille (talk | contribs) (Applications using Jmol)
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Jmol / JSmol Applications

Applications using Jmol

Jmol users, please add here your favorite Java applications that embed 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.)
  • Molecular Workbench - A Molecular Simulation Tool
  • PFAAT - Protein Family Alignment Annotation Tool.
  • 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

Most interaction with Jmol will happen by sending RasmolScript - like commands to Jmol. This is nicely documented by the 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.