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!


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.)
>> 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:
> Cheers,
> -Geoff

Michael L. Love Ph.D
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