RDKit converter inferring

[cbouy]

Fixes part of #3996

Changes made in this Pull Request:

• Refactored the RDKit converter code to move the inferring code in a separate RDKitInferring module. The bond order and charges inferer has been move to a MDAnalysisInferer dataclass in there.
• Renamed NoImplicit parameter to implicit_hydrogens and added a separate inferer argument (defaults to MDAnalysisInferer(). Passing NoImplicit to any of the relevant functions will issue a warning and make the necessary arrangements to execute the code in a backwards-compatible way (i.e. implicit_hydrogens=not NoImplicit and if NoImplicit is False: inferer=None).
• Added TemplateInferer that wraps around RDKit's AssignBondOrdersFromTemplate. There's an additional adjust_hydrogens parameter that when set to True allows one to assign bond orders from a template molecule with implicit hydrogens to an input molecule with explicit hydrogens (which won't work with the base AssignBondOrdersFromTemplate for charged molecules where the charged atom has a hydrogen). I originally had this code in ProLIF for dealing with PDBQT inputs, figured it would be worth here as well.
• Added RDKit's rdDetermineBonds inferring wrapper as showcased here.

PR Checklist

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

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4305.org.readthedocs.build/en/4305/

[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/converters/RDKit.py:

Line 430:80: E501 line too long (80 > 79 characters)

• In the file package/MDAnalysis/converters/RDKitInferring.py:

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• In the file testsuite/MDAnalysisTests/converters/test_rdkit.py:

Line 476:80: E501 line too long (80 > 79 characters)
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Comment last updated at 2024-04-01 18:48:41 UTC

[github-actions]

Linter Bot Results:

Hi @cbouy! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/8512234446/job/23313437678

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Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[codecov]

Codecov Report

Attention: Patch coverage is 98.47328% with 4 lines in your changes are missing coverage. Please review.

Project coverage is 93.66%. Comparing base (6ec838b) to head (ea26569).

Files	Patch %	Lines
package/MDAnalysis/converters/RDKit.py	95.74%	0 Missing and 2 partials ⚠️
package/MDAnalysis/converters/RDKitInferring.py	99.06%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4305      +/-   ##
===========================================
- Coverage    93.66%   93.66%   -0.01%     
===========================================
  Files          168      181      +13     
  Lines        21248    22414    +1166     
  Branches      3917     3943      +26     
===========================================
+ Hits         19902    20993    +1091     
- Misses         888      961      +73     
- Partials       458      460       +2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[cbouy]

No code changes here apart from refactoring all the different bond order inferring functions under this class, a deprecation warning if specifying max_iter anywhere else than in __init__, and some code formatting with black

[cbouy]

Just checking that the default to True sounds reasonable to everyone? Otherwise if you have a charged mol you'll need to add explicit hydrogens on the template to have an exact match with your input mol which may be a bit of a pain.
This was originally in ProLIF to read PDBQT files as valid RDKit mols, happy to add it here (and should be fine license-wise)

[cbouy]

RDKit now also has a DetermineBonds which could be interesting to add as an alternative to guess_bonds? Or at least in the RDKitConverter which requires bonds anyway

[IAlibay]

Thanks @cbouy ! From a quick look this seems great, I'll try to review it at some point over the next week (unless someone gets to it first).

P.S. For others that might review here - codecov seems to be throwing a bunch of "uncovered code" messages (when they seem like they are). Cycling the PR might clear them, but I don't think it's a major necessity right now.

[orbeckst]

@cbouy are you still working on the PR or is this ready for review?

[cbouy]

Should be ready for review, I'll just need to update the changelog when ready for merging

[orbeckst]

That's great.

Can you please add the CHANGELOG update right away, even if it will require resolving a merge conflict later? The summary there tends to be really helpful for assessing a PR.... and typically no reviewer will green-light such a PR without the CHANGELOG in place anyway.

[orbeckst]

@richardjgowers do you have capacity to shepherd the PR to completion? If not please let me know and un-assign yourself. Thanks!

[cbouy]

Sorry for the spam, should be good now!