Check for enpty coordinates in RDKit converter

[RMeli]

Fixes #4813

Changes made in this Pull Request:

• Embed molecule created from SMILES

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--4824.org.readthedocs.build/en/4824/

[pep8speaks]

Hello @RMeli! 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 369:80: E501 line too long (82 > 79 characters)
Line 370:80: E501 line too long (81 > 79 characters)

Comment last updated at 2024-12-08 12:57:28 UTC

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.66%. Comparing base (83f702f) to head (1c7ac6b).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4824      +/-   ##
===========================================
+ Coverage    86.08%   93.66%   +7.57%     
===========================================
  Files          177      189      +12     
  Lines        21743    22809    +1066     
  Branches      3055     3055              
===========================================
+ Hits         18718    21363    +2645     
+ Misses        2593     1000    -1593     
- Partials       432      446      +14     

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[cbouy]

Mmmh it might be relevant to extend the if np.isnan(ag.positions).any() check in the convert method to also handle the case where all atoms have coordinates 0, 0, 0 so that we don't try to assign these coordinates (and ultimately assign stereo from these dummy coordinates) when that happens?

[RMeli]

Thanks @cbouy, good suggestion.

[cbouy]

LGTM! Thank you 🙌

[IAlibay]

lgtm thanks!

[IAlibay]

CI failure is known, going ahead with merge.