[Fsatom] Re: CML and macromolecules

[Geoff Hutchison]

On Oct 19, 2003, at 6:15 PM, Peter Murray-Rust wrote:
>> The remainder (mainly REMARK stuff) is most likely less interesting. 
>> If
>> CML would provide the stuff listed above we don't have to worry about
>> reading pdb files anymore, and we could even use the bond information
>> that babel provides.
>
> I have provided core functionality only for Babel. I do not know what 
> additional data structure they provide for PDB-like elements. If it's 
> easy I can probably hack it. I doubt they support BIso. The problem 
> with all conversion programs is that you are constrained by the data 
> structures they provide. Not their fault...

One advantage with an open conversion program is that you can add other 
data structures (or suggest that they be added).

Open Babel has pages for bugs and for feature requests. ;-)
http://openbabel.sourceforge.net/

Since you can add per-molecule, per-residue, per-bond, or per-atom 
custom information, it's a matter of agreeing to data format and coding 
the OBGeneric class. Something like the process of extending CML, 
though of course there's some C++ involved.

Certainly if you feel there's something inadequate in Open Babel, we'd 
rather you complain bitterly about it than to just mumble so that we 
never know what's wrong. In particular with conversion programs, some 
of the developers are coding formats that we don't use much (if at 
all).

Cheers,
-Geoff

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