There is no indication in the babel-1.6 source tree that I could find to indicate that it is not FOSS. It looks like openbabel-2.1.1 is in the package tree, and it would be worth checking out I take it. In fact, thank you for the excellent suggestions!
Regards, On 25 Aug, Geoffrey Hutchison wrote: > > 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 -- Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab: 410-614-3179 fax: 410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -----BEGIN GEEK CODE BLOCK----- Version: 3.1 GMU/S d+@ s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e++++ h--- r+++ y++++ ------END GEEK CODE BLOCK------
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