[gmx-developers] Hi and Gmx library development

[Daniel Gutson]

Hi,
  we're developing some clusterring applications for structures analysis.
If I come up with something that looks useful, I'll send it to you. I
understand the layering scheme you are saying, but since I'm not
actually very familiar with Gromacs, so I can't promise something as
the quality as you would develop it :)
We are a little bit tight of schedule. What I will use is the xtcio
part, and maybe the rmsd but deeper than the args[] interface
(therefore here there could be some API development useful, as maybe a
kick off starting contribution).

About the dynamic indexes, let me look with more detail about it.

Thanks for your help, I'll come back once I got something that
deserves to be shared :)

   Daniel.

On 7/14/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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.
> >
> Hi,
>
> 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.
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-developers-request at gromacs.org.
>
>
> --
> David.
> ________________________________________________________________________
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>