[Cdk-devel] Re: [Joelib-devel] Re: [Open Babel] Atom types and protonation models

[Joerg K. W. <we...@in...>]

Hello Geoff,

thanks ! Have a nice exam !:-)

> There's also the FSAtom project: http://www.fsatom.org/ which looks 
> similar to what we're talking about.
I will have a look ... i know that Ghemical uses OElib(OpenBabel) also.

> Open Babel loads most of these from text files, which has enabled 
> workarounds for some bugs. They're all under the GPL and I'd be glad to 
> set aside a separate CVS repository for just these data files.
Perfect, that's what i thought !!!

>> 2. The assignemts should be defined in a transparent
>>    and reproducable way. Any suggestion? Which
>>    are practical ? Technical docu ?
> 
> 
> At least in Open Babel, the typing is either done by the program that 
> generated the file, or by a SMARTS pattern. Certainly the latter seems 
> pretty transparent and reproducible to me, assuming that everyone has 
> bug-free SMARTS code, of course. :-)
> 
> Now I can't say that external type assignments are necessarily 
> reproducible or transparent, but we can't easily solve that. (Until 
> everyone uses open file formats...) OTOH, Open Babel has a pretty 
> complete type translation table. It's not bug free, but it's getting 
> much better with continued testing (and roundtripping).
I agree, i think SMARTS will be transparent enough !!!

Thanks, for your efforts !

Regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Univ. Tuebingen, Computer Architecture, Sand 1, D-72076 Tuebingen, Germany
Tel. (+49/0) 7071 29 78970, Fax (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
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