[gmx-developers] Re: markup for macromolecules in biology

Michael Banck mbanck at gmx.net
Tue Oct 14 19:28:10 CEST 2003

On Mon, Oct 13, 2003 at 06:44:25PM -0700, Erik Lindahl wrote:
> I'm also working with Warren DeLano to add Gromacs support in Pymol. 


> We are somewhat hesitant on using XML "everywhere" - at least not as a 
> default format. It would be fairly straightforward to allow input 
> parameters (number of steps, cutoff radius, etc) as XML, but it really 
> doesn't buy us much, and it would be harder for the users to always 
> edit proper XML files in their input. 

IMHO XML is not really useful as an input file format, at least not in
general (there might be nice XML editors and emacs-modes, but that would
cut off general easy editing). It's really good for data files though.

> The same goes for writing coordinates, trajectories and energies: we
> have have very compact and portable binary formats that we probably
> want to stick to.

Comparing your binary format to gzipped XML might be worthwhile -
OpenOffice and gnumeric do that for example. A lot of applications can
read/write gzipped data on the fly - even if they are not open source,

> One issue is how detailed the markup should be. If it isn't the default 
> format it might make sense to have it very detailed for coordinate 
> files, but trajectories and compressed trajectories should probably be 
> binary for size reasons. We have extremely efficient code for 
> reading/writing compressed coordinates that we could release completely 
> free (BSD license or something...)



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