[WIP] Parameter coverage iPython notebook

[j-wags]

Summary

This PR adds a parameter coverage checker hosted in an iPython notebook. This notebook produces a detailed report of which chemical groups a ForceField object is unable to parameterize. These chemistries are reported as

• 2D molecule images, with unparameterizable groups highlighted (generated by RDKit)
• tagged SMILES
• tuples of atom indices

These results are printed out in the iPython notebook itself, and the final cells provide functionality to write to file as well.

My hope is that the Open Force Field industry partners can use this tool on a small dataset which encapsulates the diversity of the compounds they might simulate, and report critical areas where our force fields lack coverage. Industry partners probably can not reveal whole molecules from internal data sets, so I have tried to design this notebook such that it is easy to take screenshots of relevant chemistry, without revealing the whole molecule.

This notebook is suitable for analysis of hundreds to thousands of molecules, but probably not much more than that. It takes about 1 core-second per molecule, though I do offer a parallelized checker as well. Significant speedups past 0.1 sec/molecule would require several additional days of engineering, affect internal OFF Toolkit code, and decrease code readability. Thus, while we probably want to make a "fast" version of this some day, it would not be in the form of an interactive notebook.

Checklist

• Closes Make an example notebook/script that analyzes molecule dataset coverage #413
• Fix Molecule.from_file with RDKit backend doesn't resepect allow_undefined_stereo #417
• Fix Molecule.from_file reading SMILES using RDKit backend ignores first molecule #418
• Change MissingValenceParameterException to also contain relevant TopologyAtoms for exception handling
• Add parameter coverage example notebook
  • Provide SMILES test set
  • Provide mol2 test set
  • Provide SDF test set
  • Provide in-notebook description of missing parameters
  • Output easily-readable, file-based summary of parameter coverage results
• Update docstrings/documentation, if applicable
• Update changelog

Status

• Ready for review
• Ready for merge

[lgtm-com]

This pull request introduces 1 alert and fixes 1 when merging a40dca1 into fe87bae - view on LGTM.com

new alerts:

• 1 for Syntax error

fixed alerts:

• 1 for Suspicious unused loop iteration variable

[codecov-io]

Codecov Report

Merging #419 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #419   +/-   ##
=======================================
  Coverage   49.25%   49.25%           
=======================================
  Files          35       35           
  Lines        9577     9577           
=======================================
  Hits         4717     4717           
  Misses       4860     4860

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[j-wags]

Closed and reopened -- Trying to get travis to resume building this PR

[lgtm-com]

This pull request introduces 1 alert and fixes 1 when merging 501a1d8 into fe87bae - view on LGTM.com

new alerts:

• 1 for Syntax error

fixed alerts:

• 1 for Suspicious unused loop iteration variable