RDKitConverter improvements

[cbouy]

Part of #3996

Changes made in this Pull Request:

• moved some variables (MONATOMIC_CATION_CHARGES and STANDARDIZATION_REACTIONS) out of the related functions to allow users fine tuning them if necessary.
• changed the sorting of heavy atoms when inferring bond orders and charges: previously only based on the number of unpaired electrons, now based on this and the number of heavy atom neighbors.
• use RDKit's RunReactantInPlace for the standardization reactions, which should result in a significant speed improvement as we don't need to use bespoke code to transfer atomic properties from the non-standardized mol to the standardized one.
• added more test cases for bond order and charges inferring for molecules that failed in the benchmark previously.

Ideally I need to run the benchmark again to make sure that their are no regression from these changes, and I'd also like to make a comparison between the develop branch and these changes as there should be a significant speed improvement from using RunReactantInPlace.

PR Checklist

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

---

📚 Documentation preview 📚: https://readthedocs-preview--4082.org.readthedocs.build/en/4082/

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.07 ⚠️

Comparison is base (e63c396) 93.65% compared to head (dc5f92a) 93.59%.

❗ Current head dc5f92a differs from pull request most recent head 65601de. Consider uploading reports for the commit 65601de to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4082      +/-   ##
===========================================
- Coverage    93.65%   93.59%   -0.07%     
===========================================
  Files           14      192     +178     
  Lines         1104    25109   +24005     
  Branches         0     4050    +4050     
===========================================
+ Hits          1034    23500   +22466     
- Misses          70     1092    +1022     
- Partials         0      517     +517     

Impacted Files	Coverage Δ
package/MDAnalysis/converters/RDKit.py	98.97% <100.00%> (ø)

... and 178 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

[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/5089795892/jobs/9147847656

---

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

[richardjgowers]

thanks @cbouy ! these changes look sane to me. I'd be curious how this approach compares to the new rdDetermineBond functions, but I think that's a long conversation to be had elsewhere

[cbouy]

Yes it would be nice to have it as an alternative bond-inferring solution as well, and try it on the benchmark that I had set up some time ago. Might give it a go someday