[gmx-users] A simple XVG viewer

[Michael Lerner]

On Thu, Nov 5, 2009 at 10:23 AM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> Hi,
>
> So, what's the advantage over using e.g. (xm)grace?
>

I'm not sure. The last time I tried, xmgrace refused to install on my Mac.

This certainly isn't a big analysis/plotting package. It's just a quick way
to step through XVG files.


>
> /Erik
>
> Michael Lerner skrev:
>
>> Hi,
>>
>> (My apologies if this shows up several times. I sent it yesterday, but it
>> appears that it won't go through to the list if I include a screenshot.)
>>
>> I wanted a quick way to plot the data in XVG files, so I wrote a quick
>> little GUI viewer in Python this morning. You point it at an XVG file and it
>> pops up a GUI where you can click buttons to step through the columns of
>> data, plot individual columns from the XVG file, or make a plot of
>> everything in the XVG file.
>>
>> This makes it easy to dump all the information from an .edr/trr/xtc/etc
>> file and step through it visually in 30 seconds. That, in turn, makes me way
>> more likely to look at as much information as possible as part of my normal
>> workflow.
>>
>> I've only tested this on a few of my own XVG files, so it's possible that
>> my simple XVG parser doesn't cover everything.
>>
>> Here's the help output. Let me know if anyone finds it useful.
>>
>>
>> Michael-Lerners-MacBook-Pro-2: ~ mglerner$ ./xvgviewer.py --help
>> Usage: Just a simple XVG viewer.
>>
>> For each column in the XVG file, we plot
>>
>>  - the raw data (light blue)
>>  - a running average (black)
>>  - block averages (green)
>>
>> We also print out
>>
>>  - the average over the simulation
>>  - standard error over the blocks
>>  - average of the standard deviations within each block
>>
>> Block length is reported in number of frames, and its meaning will
>> therefore depend on the settings in your .mdp file as well as the
>> arguments you used when making the .xvg file.
>>
>> We attempt to get units out of the XVG file, and we convert times to
>> nanoseconds before plotting.
>>
>> This program requires
>>
>>  - Python 2.5 or 2.6
>>  - wxPython 2.8.7.1+ (http://www.wxpython.org/)
>>  - numpy 1.3.0+ (http://numpy.scipy.org/)
>>  - matplotlib 0.99.0+ (http://matplotlib.sourceforge.net/)
>>  - traits 3.2.0+ (http://code.enthought.com/projects/traits/)
>>
>> All of which will be installed for you if you use the Enthought Python
>> Distribution (http://enthought.com/).
>>
>> I mostly wrote this as a quick way to figure out how to use the Traits
>> GUI, but feel free to email me (m g lerner atsign gmail dot com) if
>> you have any questions.
>>
>>
>> Options:
>>  -h, --help            show this help message and exit
>>  -f FILE, --file=FILE  The XVG file [default energy.xvg]
>>
>>
>> Cheers,
>>
>> -Michael
>>
>> --
>> Michael Lerner, Ph.D.
>> IRTA Postdoctoral Fellow
>> Laboratory of Computational Biology NIH/NHLBI
>> 5635 Fishers Lane, Room T909, MSC 9314
>> Rockville, MD 20852 (UPS/FedEx/Reality)
>> Bethesda MD 20892-9314 (USPS)
>> ------------------------------------------------------------------------
>>
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>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
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-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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