Difference between revisions of "Applications Embedding Jmol"

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* [http://bioclipse.net/ BioClipse]
 
* [http://bioclipse.net/ BioClipse]
 
* [http://www.mathematik.uni-bielefeld.de/~CaGe/ 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.)
 
* [http://www.mathematik.uni-bielefeld.de/~CaGe/ 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.)
 +
* [http://homepage.mac.com/swain/Sites/Macinchem/page6/page6.html iBabel] - A GUI for cheminfomatics toolkit Openbabel, iBabel uses embeded applets to display structures
 
* [http://mw.concord.org/modeler/index.html Molecular Workbench] - A Molecular Simulation Tool
 
* [http://mw.concord.org/modeler/index.html Molecular Workbench] - A Molecular Simulation Tool
 
* [http://pfaat.sourceforge.net/ PFAAT] - Protein Family Alignment Annotation Tool.
 
* [http://pfaat.sourceforge.net/ PFAAT] - Protein Family Alignment Annotation Tool.
 +
* [http://homepage.mac.com/eludens/proyectos/htmls/proteinglimpseen.html 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.
 
* [http://www.efamily.org.uk/software/dasclients/spice/spice.shtml Spice] - Spice is a DAS client for distributed annotation of protein sequences and structures. A java webstart version can be run from online.
 
* [http://www.efamily.org.uk/software/dasclients/spice/spice.shtml Spice] - Spice is a DAS client for distributed annotation of protein sequences and structures. A java webstart version can be run from online.
 
* [http://3d-alignment.eu STRAP] - Alignment Program for Proteins and workbench for protein structures
 
* [http://3d-alignment.eu STRAP] - Alignment Program for Proteins and workbench for protein structures
 
* [http://taverna.sourceforge.net/ Taverna]
 
* [http://taverna.sourceforge.net/ Taverna]
* [http://homepage.mac.com/swain/Sites/Macinchem/page6/page6.html iBabel] - A GUI for cheminfomatics toolkit Openbabel, iBabel uses embeded applets to display structures
 
  
 
=== How to embed Jmol into an application ===
 
=== How to embed Jmol into an application ===

Revision as of 12:32, 19 January 2008

Jmol / JSmol Applications

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.)
  • 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

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.