[gmx-users] A simple XVG viewer

Thu Nov 5 17:40:16 CET 2009

Very nice!

Your termsize function doesn't seem to work on my Mac, but the one from here
(http://www.finalcog.com/terminal-size-python) does.

On Thu, Nov 5, 2009 at 11:19 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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 <mglerner%2Bgromacs 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!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> 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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>

-- 
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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