[gmx-users] numerical matrix from xpm file

[Tsjerk Wassenaar]

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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>>>
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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