NEEMP:Reports: Difference between revisions

Revision as of 08:49, 29 June 2016

Along with NEEMP we provide an handy python script to generate charge correlation graphs and quality assay reports, namely nut-report.py. To run the above-mentioned script, python and R packages must be installed in the system. Figure 5 displays the required input file in which for each atom the difference between the reference QM charge and the EEM charge is calculated. Such a file can be obtained running NEEMP in quality validation mode with the option --chg-stats-out (see example or quality validation for details).

**Figure 5:** Close-up from charge statistics file. Along with statistics for each molecule, *ab-initio* charges (3rd column), *EEM* charges (4th column) and their difference (5th column) are also printed out.

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To generate the graphs the scripts must be called in the simple following way:

First:

./nut-report.py charge-stat-file

Figure 6 and 7 demonstrate as the correlation graphs include both all atom and individual atomic types dependency.


Figure 6: All atom correlation graph between QM charges (x axis) and EEM charges (y axis).	Figure 7: Correlation graph between QM charges (x axis) and EEM charges (y axis) for O1 atomic type (oxygen with just single bonds).

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-All the graphs in '''NEEMP''''s article showing the correlation between reference charges and EEM charges, have been generated employing two python scripts, ''nut-report.py'' and ''nut.plot.py''. The required input file must contain the charge statistics as shown in '''''figure 5''''' and  can be obtained running '''NEEMP''' in ''quality validation'' mode with the option <code>--chg-stats-out</code> (see [[NEEMP:Examples#Example 8 - Quality validation | here]] for details).
+Along with '''NEEMP''' we provide an handy python script to generate charge correlation graphs and quality assay reports, namely '''''nut-report.py'''''. To run the above-mentioned script, ''python'' and ''R'' packages must be installed in the system.
+'''''Figure 5''''' displays the required input file in which for each atom the difference between the ''reference QM charge'' and the ''EEM charge'' is calculated. Such a file can be obtained running '''NEEMP''' in ''quality validation'' mode with the option <code>--chg-stats-out</code> (see [[NEEMP:Examples#Example 8 - Quality validation | example]] or [[NEEMP:Modes#Quality validation | quality validation]] for details).
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