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:


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