[gmx-developers] grompp .mdp processing

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 23 13:14:15 CET 2009

> I think XML is great when read/written from a script. Because there a 
> good libraries for all languages. So speical routines might not even be 
> neccassary. If we provide a library to write the mdp file, the scripts 
> are independent of the file format.
> Thus only editing by hand is influced by the format and my concern is 
> that XML makes it more difficult to edit by hand. Very few people use 
> XML editors for XML - most still use text editors. And I don't see what 
> XML would add as a benefit to the user. What does the user gain to have 
> the abstract data types in the code represented in the mdp file 
> structure? I think the current comments written in the mdout file 
> structure the file for humans as well as XML could do. In case we really 
> think we need some markup language - I would vote for something like 
> YAML to make it best human readable/editable.

My point (not explicitly stated) was to discourage all manual editing. 
It should be quite simple to make an inputrec editor if there is a 
proper API - once again: if there is a proper API and an application to 
edit content, the file format is irrelevant to the user.

By the way, we will probably turn on linking to libxml2 by default in 
4.1 (but not yet obligatory), and make it obligatory after that. I 
already have quite a bit of code using it (that is not in the main tree 
yet). I would not like having two different markup languages (even 
though YAML Ain't a Markup Language), and YAML is definitely not general 
enough for all future uses within GROMACS. Then it would be better to 
stick to the current mdp format (which we will need to support for a 
time to come anyway).

> Roland
> -- 
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <http://cmb.ornl.gov>
> 865-241-1537, ORNL PO BOX 2008 MS6309
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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