[gmx-users] A simple XVG viewer

[Tsjerk Wassenaar]

Hi,

Well, if we're exchanging xvg viewers... This one I wrote for quickly
viewing xvg files in a terminal. It converts the graph to ascii,
fitting automatically to the terminal size. It can also be used to
generate (ramachandran) density plots. Should still add proper help
info, but the options are:

-f xvg file
-g [optional] second xvg file to plot one against the other
-c column to plot
-d [optional] column to plot, will plot one column against the other,
or use this column from second xvg file if given
-x minimum x value
-X maximum X value
-y minimum y value
-Y maximum y value
--square force square display
--angles set x=-180, X=180, y=-180, Y=180

Hope it's of some use to some one :)

Tsjerk

On Thu, Nov 5, 2009 at 4:29 PM, Michael Lerner
<mglerner+gromacs at gmail.com> wrote:
>
>
> 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)
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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