Problems with Angle Distribution in water dynamics module

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Elías C

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Nov 7, 2021, 11:00:12 AM11/7/21
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Estimated MDAnalysis group. I would like to make an angle distribution analysis, so, I follow the tutorial presented in https://docs.mdanalysis.org/stable/documentation_pages/analysis/waterdynamics.html

A common warning that I have is:

/lib/python3.8/site-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0.

But, it is not seen to be something problematic. In the original line:

for bin in range(bins):
        print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(AD_analysis.graph0=AD_analysis.graph[0][bin], AD_analysis.graph1=AD_analysis.graph[1][bin],AD_analysis.graph2=AD_analysis.graph[2][bin]))

I had by separate, after modificate the code, two errors:

1) print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(AD_analysis.graph0=AD_analysis.graph[0][bin], AD_analysis.graph1=AD_analysis.graph[1][bin],AD_analysis.graph2=AD_analysis.graph[2][bin]))
                                                                    ^
SyntaxError: expression cannot contain assignment, perhaps you meant "=="?

2) print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(AD_analysis.graph0==AD_analysis.graph[0][bin], AD_analysis.graph1==AD_analysis.graph[1][bin],AD_analysis.graph2==AD_analysis.graph[2][bin]))
AttributeError: 'AngularDistribution' object has no attribute 'graph0'

In my final code, modifications are highlighted with black::

for bin in range(bins):
      print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(AD_analysis.graph[0]==AD_analysis.graph[0][bin], AD_analysis.graph[1]==AD_analysis.graph[1][bin],AD_analysis.graph[2]==AD_analysis.graph[2][bin]))

After change that I get the next error:

print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(AD_analysis.graph[0]==AD_analysis.graph[0][bin], AD_analysis.graph[1]==AD_analysis.graph[1][bin],AD_analysis.graph[2]==AD_analysis.graph[2][bin]))
KeyError: 'AD_analysisOH'

I am not sure how to solve it. Thank you for your time and help.

Paul Smith

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Nov 7, 2021, 12:05:59 PM11/7/21
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Hi,

I'm not very familiar with this module but I can try to help you out:

A common warning that I have is:
>     /lib/python3.8/site-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0.

This is nothing to worry about. It's letting you know that the hbond_autocorrel module has been moved to a different location, so you would need to import it from MDAnalysis.analysis.hydrogenbonds instead of MDAnalysis.analysis.hbonds.

I had by separate, after modificate the code, two errors:
>     1) print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(AD_analysis.graph0=AD_analysis.graph[0][bin], AD_analysis.graph1=AD_analysis.graph[1][bin],AD_analysis.graph2=AD_analysis.graph[2][bin]))
            SyntaxError: expression cannot contain assignment, perhaps you meant "=="?

There's a couple of typos in the formatting of the string. I think it should be:

for bin in range(bins):
    print("{AD_analysisOH} {AD_analysisHH} {AD_analysisDip}".format(
        AD_analysisOH=AD_analysis.graph[0][bin],
        AD_analysisHH=AD_analysis.graph[1][bin],
        AD_analysisDip=AD_analysis.graph[2][bin])
    )

This is using string formatting with named parameters, e.g.:

    "{named_thing_1},  {named_thing_2}".format(named_thing_1=10, named_thing_2=20)

will create a string "10, 20".

Cheers,
Paul


Elías C

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Nov 7, 2021, 12:18:48 PM11/7/21
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Thank you very much! This has worked perfectly!

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