[gmx-users] A simple XVG viewer

[Erik Marklund]

Hi,

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

/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