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

[Geoff H. <hut...@ch...>]

Apologies that I haven't responded to you sooner, Joerg! I have an oral 
exam on Thursday and until a few days ago, I was working on the 
manuscript portion of it.

> different forums, i would recommend the Openbabel
> discussion list for a response (if this is o.k. !),

I agree that we probably need a list for discussing such inter-program 
"standards," but I certainly don't mind the Open Babel list used if 
other people follow it. Or, if you like, I'd be glad to start a new 
list. It would probably be worthwhile to talk about pseudo-code and 
algorithm development as well. Java and C++ are not so different and it 
would be silly to duplicate efforts!

There's also the FSAtom project: http://www.fsatom.org/ which looks 
similar to what we're talking about.

There's really a lot more than just atom typing that should be 
"hammered out," as there are some truly basic chemical concepts that 
are duplicated!
* periodic table
* isotopes (and masses--or else these are ignored completely)
* atom types
   - type translations from one program's syntax to another's
   - type rules
* test molecules (or other test sets?)
* residue info
* chemical MIME types, extensions, etc.
...

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.

> 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).

--
-Geoff Hutchison		<hut...@ch...>
Marks/Ratner Groups		(847) 491-3295
Northwestern Chemistry		<http://www.chem.northwestern.edu>