[gmx-users] numerical matrix from xpm file

[João M. Damas]

Hi Tsjerk,

This is a very useful script. Just found a small bug that is only
noticeable if one is using higher -nlevels for the .xpm construction (in
g_rms, for example)

z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
should be
z = [colors[j[k:k+nb]] for k in range(0,nx*nb,nb)]
instead. At least that's working for me.

Thank you for sharing,
João

On Mon, Oct 4, 2010 at 12:05 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Anupam,
>
> I recently wrote a small python script to convert gromacs .xpm files
> to numbers. Maybe it'll be of some use to you:
>
> Cheers,
>
> Tsjerk
>
> ###
>
> #!/usr/bin/env python
>
> import sys
>
> def unquote(s):
>     return s[1+s.find('"'):s.rfind('"')]
>
> def uncomment(s):
>     return s[2+s.find('/*'):s.rfind('*/')]
>
> def col(c):
>     color = c.split('/*')
>     value = unquote(color[1])
>     color = unquote(color[0]).split()
>     sys.stderr.write("%s: %s %s %s\n"%(c.strip(),color[0], color[1],
> value))
>     return color[0], value
>
> # Open the xpm file for reading
> xpm = open(sys.argv[1])
>
> # Read in lines until we fidn the start of the array
> meta = [xpm.readline()]
> while not meta[-1].startswith("static char *gromacs_xpm[]"):
>     meta.append(xpm.readline())
>
> # The next line will contain the dimensions of the array
> dim = xpm.readline()
> # There are four integers surrounded by quotes
> nx, ny, nc, nb = [int(i) for i in unquote(dim).split()]
>
> # The next dim[2] lines contain the color definitions
> # Each pixel is encoded by dim[3] bytes, and a comment
> # at the end of the line contains the corresponding value
> colors = dict([col(xpm.readline()) for i in range(nc)])
>
> for i in xpm:
>     if i.startswith("/*"):
>         continue
>     j = unquote(i)
>     z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
>     sys.stdout.write(" ".join(z)+"\n")
>
> ###
>
> On Mon, Oct 4, 2010 at 12:33 PM, Anupam Nath Jha
> <anupam at mbu.iisc.ernet.in> wrote:
> >
> > right. I also came to see one of them but with no result.
> > and since it was done some time back so I thought if some one has come
> up with
> > some method to get that.
> >
> > right now I wanted the matrix information obtained from command
> g_mdmat.....
> > can you suggest some way to get that.
> >
> > thanks
> > anupam
> >
> >
> >> No, there's no ability to do this. I think there should be, though, and
> seem to
> >> recall discussion of it on one or other mailing list or the web page.
> >>
> >> Mark
> >>
> >> ----- Original Message -----
> >> From: Anupam Nath Jha <anupam at mbu.iisc.ernet.in>
> >> Date: Saturday, October 2, 2010 21:32
> >> Subject: [gmx-users] numerical matrix from xpm file
> >> To: gmx-users at gromacs.org
> >>
> >>>
> >>> Hi all
> >>>
> >>> Is it possible to obtain the matrix in numeric form from xpm
> >>> (obtained from
> >>> gromacs analysis) files.
> >>>
> >>> because it's not coming in options for ourput files.
> >>>
> >>> thanks with regards
> >>> anupam
> >>>
> >>> --
> >>>
> >>>
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> > --
> > Science is facts; just as houses are made of stone, so is science is
> made of
> > facts; but a pile of stones is not a house, and  a collection of facts
> is not
> > necessarily science.
> >
> > Anupam Nath Jha
> > Ph. D. Student
> > Saraswathi Vishveshwara Lab
> > Molecular Biophysics Unit
> > IISc,Bangalore-560012
> > Karnataka
> > Ph. no.-22932611
> >
> >
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613