Here you are
Le 01/02/2016 15:36, Jason Swails a écrit :
> Can you provide the mdout file that failed here?
>
> On Mon, Feb 1, 2016 at 9:32 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
>> 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
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
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>>>>
>>>
>>
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>
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Received on Mon Feb 01 2016 - 07:00:06 PST
