[gmx-users] Parsing g_rms binary rmsd comparison matrix

[João Henriques]

Hi Mark,

Good to know that the binary dump is just plain data. Then I know that the
problem is uniquely due to the *data type*, which is *exactly* what I
couldn't figure out from the source file. Using the wrong data type due to
not knowing the size and byte-order of the items in the file was obviously
yielding faulty array length values, and that's why I started thinking that
the file may have a more complex structure.

Just now, I tested using "numpy.float32" (which should have been obvious,
were I not a newbie) as the dtype and it finally worked. The min and max
values correspond to the g_rms output and the array length is finally N**2,
with N being the side length of the symmetric rmsd matrix.

Thank you for your help,
Best regards,
João




On Wed, Mar 5, 2014 at 1:23 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Mar 4, 2014 9:19 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
> wrote:
> >
> > Hello everyone,
> >
> > Let me start by saying that I am unsure whether this is a question for
> the
> > gmx-users or gmx-developers mailing list, but here it goes:
> >
> > I have written a Python/NumPy script that parses the rmsd comparison
> matrix
> > dumped by g_rms in the .xpm format. However the "nlevels" are not
> > sufficient to give me the desired detail for posterior calculations.
> > Therefore I have decided to forget the .xpm and focus on the binary dump
> > produced by g_rms using the flag -bin. My sole purpose is to fetch the
> > binary rmsd data and pass it into an array, so that I can then do some
> > calculations over it.
> >
> > I am a total newbie in binary file parsing, but I know that I can, for
> > example, use something like "numpy.fromfile" for that purpose. The
> problem
> > is that I have absolutely no idea of what is the structure of the binary
> > rmsd comparison matrix file. I'm pretty sure that besides the actual
> data,
> > there are other stamps and stuff being written to the file, with
> > potentially different formats as well. I tried looking at gmx_rms.c but I
> > got lost very quickly.
>
> No, g_rms -bin is very plain, see
>
> http://redmine.gromacs.org/projects/gromacs/repository/revisions/master/entry/src/gromacs/gmxana/gmx_rms.c#L1073
>
> Do let us know how you go!
>
> Mark
>
> > Is there anyone out there that might be able to help me identify the
> > correct structure OR is there any Python or C++ routine capable of doing
> > similar things to what I need? I have no urge in "reinventing the wheel".
> >
> > P.S.: I know that there is the possibility of modifying g_rms itself, but
> > that is not what I'm looking for.
> >
> > Thank you in advance,
> > Best regards,
> > João Henriques
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