[WIP] first draft of PDBx Reader

[richardjgowers]

Fixes #

Changes made in this Pull Request:

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--4303.org.readthedocs.build/en/4303/

[github-actions]

Linter Bot Results:

Hi @richardjgowers! 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	✅ Passed

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/6429099481/job/17457515242

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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: 64 lines in your changes are missing coverage. Please review.

Comparison is base (427f1a7) 93.40% compared to head (837b861) 93.15%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4303      +/-   ##
===========================================
- Coverage    93.40%   93.15%   -0.26%     
===========================================
  Files          170      186      +16     
  Lines        22257    23429    +1172     
  Branches      4071     4079       +8     
===========================================
+ Hits         20790    21825    +1035     
- Misses         951     1088     +137     
  Partials       516      516              

Files	Coverage Δ
package/MDAnalysis/coordinates/PDBx.py	0.00% <0.00%> (ø)
package/MDAnalysis/topology/PDBxParser.py	0.00% <0.00%> (ø)

... and 14 files with indirect coverage changes

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[pep8speaks]

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

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

Line 28:80: E501 line too long (98 > 79 characters)
Line 29:80: E501 line too long (113 > 79 characters)
Line 62:80: E501 line too long (80 > 79 characters)

[orbeckst]

Do you want reviews on this, @richardjgowers ?