Cool.
It's buggy however:
Traceback (most recent call last):
File "/home/djipey/SOFT/amber14/bin/mdout_analyzer.py", line 63, in
<module>
mdout = MdoutClass(f)
File
"/home/djipey/SOFT/amber14/lib/python2.7/site-packages/mdoutanalyzer/mdout.py",
line 82, in __init__
if self.properties['imin'] == 5:
KeyError: 'imin'
Le 01/02/2016 15:05, Jason Swails a écrit :
> If you're trying to plot data from mdout files, you can always try
> "mdout_analyzer.py". It's built on top of matplotlib and doesn't require
> any pre-processing step for mdout files (i.e., you can just type:
>
> mdout_analyzer.py mdout1 mdout2 ... mdoutN
> )
>
> HTH,
> Jason
>
> On Mon, Feb 1, 2016 at 8:57 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
>> "Plots generally look good"...Yeah maybe with a little formatting as you
>> suggested. Actually xmgrace has an old look on my platform, a bit like
>> xleap. That's why I will go for gnuplot.
>>
>> I had a bit of spare time, so I wrote a quick script:
>>
>> #!/usr/bin/python
>> # coding: utf-8
>>
>> help = """Plot.py
>>
>> Script to plot (x, y) data from files
>>
>> Usage:
>> plot.py <files>...
>>
>> Options:
>> -h --help Display help
>> """
>>
>>
>> from docopt import docopt
>> import matplotlib.pyplot as plt
>>
>> plt.style.use('ggplot')
>> plt.style.use('seaborn-poster')
>> plt.tick_params(left='off', bottom='off', top='off', right='off')
>>
>>
>> arguments = docopt(help)
>>
>> for arg in arguments['<files>']:
>> pts_x = []
>> pts_y = []
>>
>> with open(arg, 'r') as f:
>> for line in f.readlines():
>> res = [float(value.strip()) for value in line.split(' ')
>> if value.strip() != '']
>> if res:
>> pts_x.append(res[0])
>> pts_y.append(res[1])
>>
>> plt.plot(pts_x, pts_y, label=arg)
>>
>> plt.legend()
>> plt.show()
>>
>> Just to try docopt and the new version of matplotlib (which includes
>> styles). The graph formatting is clearly R-inspired (the devs of
>> matplotlib finally underestood...).
>>
>> Usage:
>> ./plot.py summary.EPTOT summary.ETOT
>>
>> Result:
>> http://i.imgur.com/FPdBfsz.png
>>
>> Le 01/02/2016 14:08, David A Case a écrit :
>>> On Mon, Feb 01, 2016, Lorenzo Gontrani wrote:
>>>
>>>> xmgrace is great..and lightweight.
>>> Just some (off-topic) comments about why I like xmgrace:
>>>
>>> 1. Plots generally look good and can be interactively edited if they
>> don't.
>>> Consider modifying your ~/.grace/templates/Default.agr file to specify
>>> Helvetica as "font 0" (the default) and change 'xaxis label char size'
>> to 1.25
>>> (from 1.0); same for yaxis.
>>>
>>> 2. A single .agr file has both the data and the formatting in a single
>> file.
>>> This is good if you come back months or years later and don't remember
>> your
>>> file naming conventions.
>>>
>>> 3. You can also write simple scripts to systematically modify lots of
>>> files, to replace the data but keep the formatting, etc. Once you grok
>> the
>>> file syntax (which is pretty straightforward), it's about as easy to
>> write
>>> scripts to create or manipulate xmgrace files as it is to write gnuplot
>> or
>>> matplotlib scripts.
>>>
>>> 4. Consider aliasing xmgrace to 'xmgrace -hdevice PDF'. This means that
>>> "print" will create a PDF file (rather than the default PostScript).
>> This is
>>> likely to be what most people want.
>>>
>>> ....dac
>>>
>>> (OK: I realize I've probably started a flame war here... Next up: why you
>>> should write all your code in LISP.)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Feb 01 2016 - 07:00:03 PST
