On Aug 22, 2008, at 4:43 PM, [EMAIL PROTECTED] wrote: > It is my understanding that Babel is FOSS. If this is incorrect, > please be sure to let me know.
No, it is not. The original Babel (which you used) does not have any sort of open source license. It's free to distribute, but was blocked from Debian because of the license. This is separate from Open Babel, which is true GPL. (It's also better.) http://openbabel.org/ > beautifully. In order to address this problem of poor geometry, we > plan > to provide high quality minimized structures based on the pdb files > that we generate. You may find Open Babel 2.2 interesting, since it offers conformer searching and molecular mechanics. For drug-like molecules (i.e., no exotic elements), you could easily take the tools/obconformer code and run it over your PDB files. This will run MMFF94 conformer searching and geometry optimization. If you're likely to encounter more elements, you will probably want to try changing the force field to UFF. You may also want to consider working with Rajarshi and Indiana about their Pub3D database: http://www.chembiogrid.org/products/index.html Cheers, -Geoff ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
