[gmx-developers] Hi and Gmx library development

[Daniel Gutson]

Hi again David,
 sorry that I´m making a so basic question, but, please I beg you to
correct if I´m wrong. There is no random access to XTC files, right?
In other words, there are no indexes, as I saw so far.
And, I understand from your email that you refer to atom-level indexes, right?
Would adding per-xtc indexes be desirable? For example, given the
step, get the xtc, something like

extern int read_random_xtc(int fp, int ip, int step,
			  int *natoms,real *time,
			  matrix box,rvec **x,real *prec,bool *bOK);

(or maybe ´read_xtc_by_step´)

where ´step´ is provided, and ´ip´ would be a handler to an index
files, where the ´seek´ position is retrieved. This would require yet
2 other functions to generate and read indexes:

extern int index_xtc(const char *filename, const char* indexfile);
extern int open_indexes(char *filename,char *mode);
extern int close_indexes(int ip);

what do you think?
Would this be useful?

Sorry if I´m asking too basic questions, and thanks for the understanding.

   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.
> > _______________________________________________
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>
>
> --
> 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
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-- 
Daniel Gutson
Presidente / Director Informática
FuDePAN