[gmx-developers] Hi and Gmx library development

David van der Spoel spoel at xray.bmc.uu.se
Sat Jul 14 22:33:43 CEST 2007

Daniel Gutson wrote:
> Hi Gmx developers,
>   we'd need to use some Gmx functionality (such as rmsd) from our programs.
> It would be very nice to get such functionality as a library, and I
> saw in the wiki that there are 2 related projects:
>    * Analysis-Library
>    * Analysis-Related
> Are these projects intended for encapsulating the functionality as we 
> need it?
> If so, what's the status of the projects? We could contribute to that,
> if it provides any help.
> Additionally, our programs are written in C++, so if a library is to
> be done, we could provide a thin (mostly inlined) C++ wrapping library
> as well.

all the analysis programs are already compiled into one library, so you 
can for instance call a function gmx_rmsd(int argc,char *argv[]);
Obviously that is almost the same as doing a system call.

What I would like to have is distinction between the low level and the 
high level. such that you can call e.g. the rdf function for a single 
coordinate set and then get the results back. It would also be great if 
there could be online visualization but that is not crucial for a start.

I'm not sure how familiar you are with GROMACS, but for most analyses we 
use index files containing atom numbers, e.g. the atoms used for the RDF 
calculation. Since we want to bring this to a new level of abstraction 
we'd also need something like "dynamic indices", such that one at each 
step determines, e.g. which are the oxygen atoms in a protein. This is 
necessary when the number of atoms is dynamic as well.

Calling C-funtions from C++ is trivial as you are aware.

Please give us some more details on what you could contribute with and 
what the aim of your project is.
> Thanks!
>   Daniel.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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