[gmx-users] other output format of Matrix Data than xpm format

[Tsjerk Wassenaar]

Hi Florian, Ran,

Isabelles script deals with the inproduct matrices from g_anaeig.
Though it doesn't directly write out a matrix in ascii format, it
could be made to do so. You could use convert though to convert the
.xpm to (human readable) .ppm, which is easily further processed by a
script. Alternatively, it is very simple to add a bit of code to make
the tools write ascii matrices, or .ppm/.pgm for that matter, which
are also very simple to handle. To do so, you may have to add the new
file types in $GMXSRC/include/types/filenames.h and
$GMXSRC/src/gmxlib/filenames.c (follow the examples, and make sure to
insert the file types in the same place). For generic matrices I use
efDAT usually, which is already present. If you want more of an
example, just let me know.

Best,

Tsjerk

On 4/4/07, Ran Friedman <r.friedman at bioc.unizh.ch> wrote:
> IIRC there's a script from Isabella Daidone to deal with the xpm of one
> of these programs. I don't remember more, but you can check the archives
> and try to work it out for other xpms.
>
> Ran.
>
> Berk Hess wrote:
> >
> >
> >
> >> From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
> >> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Subject: [gmx-users] other output format of Matrix Data than xpm format
> >> Date: Wed, 4 Apr 2007 16:14:57 +0100
> >>
> >> Hi,
> >>
> >> is there a build in option or an easy way to change the output not to
> >> be xpm
> >> files? I only want a matrix of the numbers and not plotted as xpm file.
> >>
> >> I only found
> >>
> >> http://www.gromacs.org/pipermail/gmx-developers/2004-April/000866.html
> >>
> >> Affected tools like
> >>
> >> g_rms
> >> g_anaeig
> >
> > Currently not...
> > We want to add an option to all tools that write xpm to
> > optionally write an ascii (or binary) matrix.
> >
> > Berk.
> >
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>
> --
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355593
> Email: r.friedman at bioc.unizh.ch
> Skype: ran.friedman
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623