Segid columns change to 73-76 for PDBParser

[yuyuan871111]

Fixes #4948 (comment) issue 1.

Changes made in this Pull Request:

• extract the segid from columns 73-76 in PDB files (instead of columns 67-76)
• add warnings related to reading the segids

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• package/CHANGELOG file updated?
• 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--5001.org.readthedocs.build/en/5001/

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.41%. Comparing base (66e7e5c) to head (830f7cd).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5001      +/-   ##
===========================================
- Coverage    93.42%   93.41%   -0.02%     
===========================================
  Files          177      189      +12     
  Lines        21859    22931    +1072     
  Branches      3078     3079       +1     
===========================================
+ Hits         20422    21421     +999     
- Misses         986     1059      +73     
  Partials       451      451              

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[Copilot]

Pull Request Overview

This pull request updates the PDB segid handling to extract the segment ID from columns 73-76, along with updating the related documentation and adding warnings for when the segid does not match related values.

• Update segid extraction from PDB files in the parser
• Add warning messages for mismatched or missing segids in the topology parser
• Update documentation in the PDB coordinate reader to reflect the new segid column locations

Reviewed Changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated no comments.

File	Description
package/MDAnalysis/topology/PDBParser.py	Extract segid from columns 73-76 and add warnings accordingly.
package/MDAnalysis/coordinates/PDB.py	Update documentation to reflect the new segid column positions.

Files not reviewed (1)

• package/AUTHORS: Language not supported

[orbeckst]

Thanks for splitting the PR.

• CHANGELOG entry
• test case (something that fails with the old code and passes with the new one ... eg a file that has something else in 67-72)
• I am not a fan of too many warnings: When running in workflows, they are virtually invisible, when running interactively they can be very distracting when they show up for most "normal" cases. I suggest to use logging instead. We then also want some testing for the cases that trigger the warnings/logging events. We have code that shows how to test that messages are logged (or warnings emitted).

[orbeckst]

This PR is relevant for a GSOC application so it would actually be really good if @cbouy (and @talagayev ) could get involved.

I'll take over the managing of the PR.

(@marinegor and @lilyminium quick reviews would be greatly appreciated, too!)

[orbeckst]

Looking really good, just some minor issues to fix.

(Eventually we should use logging more consistently in the PDBParser but that can be for another PR.)

[orbeckst]

Nice work!

[orbeckst]

Congratulations @yuyuan871111 — first contribution!