On Thursday 13 July 2006 16:07, Bob Hanson wrote: > Sounds like I should just hold off on this and see what comes of Miguel > Rojas's work.
Miguel is mostly done, I think. > Can you summarize for me how the CDK, Bioeclipse, and Jmol fit together? Please download Bioclipse 0.9.2 and see for your self (1.0 will be released next week.) Start it, and do Window -> Show View -> Other -> Jmol View. Bioclipse is a workbench for chemoinformatics and bioinformatics. See the bioclipse website to see where things are going. > Which parts of Jmol are utilized? Jmol is used for what Jmol is good at: scriptable visualisation. Jmol IO is currently not used, but this could be enabled. > Which parts are replaced with the CDK version? There is nothing really replaced, though you might consider reading files as such. The CDK library (and possibly *any* other library) is used as backend for doing chemoinformatics stuff, just like it uses BioJava for sequence stuff. For example, I am supervising a summer student who is working on integration of ghemical via JNI, so Bioclipse will be able to calculate QM properties too. Since Jmol is the visualizer we use right now for 3D molecular content, Jmol is used for rendering the optimized structure. In case of partial charges, the CDK plugin would hook in a 'calculate charges' action for the molecular resources so that one could open a XYZ file, and then calculate partial charges with the CDK plugin, and visualize it on top of a surface shown in the Jmol View. Check out my latest blog on the Jmol View with 'context help' refering to a static copy of your command reference: http://chem-bla-ics.blogspot.com/2006/07/context-help-in-bioclipse.html The Jmol plugin also provides (sorry for repeating myself for the second time), a Jmol script file editor, with syntax highlighting and autocompletion. So, just type 'cart' press Ctrl^Space and pick 'cartoon' from the popup list :) (No, it does not give the full syntax yet.) And run this resource by simply clicking the 'run' button in the toolbar. Lot's of possibilities. With respect to the current application (and I'm sure I've posted this too before), only the AtomSetChooser is really missing at this moment... Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
