NEEMP:Reports

Along with NEEMP we provide an handy python script to generate charge correlation graphs and quality assay reports, named nut-report.py.

SCRIPT BASIC USAGE: ./nut-report.py chg-stats-out-file

Requirements:

• Python (https://www.python.org/)

• R (https://www.r-project.org/)

NB: the script has been tested for both python 2.7 and python 3.4, as well as for R 3.2.

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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Once the script has been executed, a bunch of output files are generated in the chg-stats-out-file directory. In particular:

• csv files containing per-atom charge information and values for several performance evaluating metrics for each atomic type and molecule

• png files displaying the charge correlation graphs for the whole set and for each atomic type (as shown in figure 6 and figure 7 respectively)

• html file gathering together all the previous information in an interactive and more easily readable report page (see figure 8 and figure 9 or click here for a more comprehensive view)

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).