RDKitConverter bugfix on HIP residue

[cbouy]

Currently HIP residues are likely to have a single double bond a a negatively charged carbon instead of 2 double bonds and a positive nitrogen

Changes made in this Pull Request:

• Adds a new SMARTS reaction to fix the protonated histidine residue HIP

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[pep8speaks]

Hello @cbouy! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/coordinates/RDKit.py:

Line 606:80: E501 line too long (100 > 79 characters)
Line 608:80: E501 line too long (100 > 79 characters)
Line 610:80: E501 line too long (100 > 79 characters)
Line 612:80: E501 line too long (100 > 79 characters)
Line 614:80: E501 line too long (100 > 79 characters)
Line 616:80: E501 line too long (100 > 79 characters)
Line 618:80: E501 line too long (100 > 79 characters)
Line 620:80: E501 line too long (100 > 79 characters)
Line 622:80: E501 line too long (100 > 79 characters)
Line 624:80: E501 line too long (100 > 79 characters)
Line 626:80: E501 line too long (100 > 79 characters)
Line 628:1: W293 blank line contains whitespace

Comment last updated at 2020-09-15 18:04:16 UTC

[codecov]

Codecov Report

Merging #2941 into develop will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #2941   +/-   ##
========================================
  Coverage    93.02%   93.02%           
========================================
  Files          187      187           
  Lines        24962    24962           
  Branches      3261     3261           
========================================
  Hits         23220    23220           
  Misses        1694     1694           
  Partials        48       48           

Impacted Files	Coverage Δ
package/MDAnalysis/coordinates/RDKit.py	97.31% <ø> (ø)

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[orbeckst]

Can you add a comment to the tests for the new SMILES that they are related to this fix?

(I don't think that this requires a CHANGELOG entry as it is updating an unreleased feature.)

@IAlibay @fiona-naughton anything else that you see?

[orbeckst]

Thanks @cbouy – unless anyone else sees something obvious, anyone can merge it when convenient (just wait for CI).