[gmx-developers] Re: [Fsatom] Re: CML and macromolecules

Erik Lindahl lindahl at csb.stanford.edu
Sun Oct 26 18:29:29 CET 2003

Hi Geoff,

> 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).

OpenBabel is a great idea, but I think the C++ really hurts adoption :-)

It works great to link C/C++ on a standard PC, but on many platforms 
the C++ compilers are either bad or nonexistent (embedded CPUs, for 
instance). This means we can't *rely* on babel for our IO routines, 
although it might be nice to have as an optional plugin.



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