[gmx-users] Parsing g_rms binary rmsd comparison matrix

[Mark Abraham]

OK great. Do bear in mind that float32 would likely not work if g_rms were
running in double precision.

Mark


On Wed, Mar 5, 2014 at 2:40 PM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> 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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