feat: Add support for reading unit cell dimensions from MOL2 CRYSIN records

[Dreamstick9]

Fixes #3341

Changes made in this Pull Request:

Implemented logic in MOL2Parser (package/MDAnalysis/coordinates/MOL2.py) to parse @CRYSIN records.

Extracted unit cell dimensions (lengths and angles) from the CRYSIN block and assigned them to ts.dimensions.

Added a new test data file with a CRYSIN record: testsuite/MDAnalysisTests/data/mol2/test_crysin.mol2.

Registered the new test file in testsuite/MDAnalysisTests/datafiles.py.

Added a regression test test_mol2_crysin_dimensions in testsuite/MDAnalysisTests/coordinates/test_mol2.py to verify dimensions are loaded correctly.

PR Checklist
[x] Issue raised/referenced?

[x] Tests updated/added?

[ ] Documentation updated/added?

[x] package/CHANGELOG file updated?

[x] Is your name in package/AUTHORS? (If it is not, add it!)

Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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Documentation preview : https://mdanalysis--5187.org.readthedocs.build/en/5187/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.82%. Comparing base (6a1befe) to head (2effc53).
⚠️ Report is 40 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5187      +/-   ##
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- Coverage    93.83%   93.82%   -0.01%     
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  Files          182      182              
  Lines        22483    22487       +4     
  Branches      3195     3196       +1     
===========================================
+ Hits         21097    21099       +2     
- Misses         924      925       +1     
- Partials       462      463       +1     

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[orbeckst]

@Dreamstick9 can you link to the document that describes the @CRYSIN record? Can you show/link to examples mol2 files found "in the wild" that use it, e.g., from a database?

That may help with reviewing.

Also make sure that you address all points in the checklist (eg, add a note to the docs, add an entry to CHANGELOG). Reviewing PRs takes a lot of time and time is really precious so show reviewers that you've done all the necessary work.

[Dreamstick9]

I implemented this based on the official Tripos mol2 file format specification, the @crysin record is defined the the standard manual in page 17 of the pdf(https://github.com/UnixJunkie/mol2-file-format-spec/blob/master/mol2.pdf). the test case added in mol2_crysin was for this specification. this record is the standard method for defining periodic boundary conditions in the format (see "Data Record Format" in the spec).
i have updated the CHANGELOG and AUTHORS.

Thanks for the review @orbeckst

[orbeckst]

I have some inline comments/questions — please address those.

Update the docs where it says that MOL2 ignores CRYSIN to say that it ignores the spacegroup and settings. The unitcell is interpreted in the common crystallographic convention with box vector a parallel to X, b in the XY plane, and c with a positive Z component.

[Dreamstick9]

Thanks for the review @orbeckst, I've made the requested changes and also removed the try and except,

[Dreamstick9]

@tylerjereddy i've updated the CHANGELOG and also switched to assert_allclose in test_mol2.py
Thanks for the review!

[orbeckst]

Thank you for addressing my comments. I have two changes that I am going to make and then it's good to go from my end.

[orbeckst]

Congratulations @Dreamstick9 , your contribution is merged 🎉 ! Thank you!