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@marinegor marinegor commented Nov 6, 2025

Fixes #5141 and perhaps fixes #5089

Changes made in this Pull Request:
Adds option to explicitly read pdb directly with gemmi, with format='pdb_gemmi' upon Universe creation:

import MDAnalysis as mda
u = mda.Universe(mmcif_filename, format="pdb_gemmi")

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!)

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


📚 Documentation preview 📚: https://mdanalysis--5142.org.readthedocs.build/en/5142/

@marinegor marinegor linked an issue Nov 6, 2025 that may be closed by this pull request
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codecov bot commented Nov 6, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.75%. Comparing base (5c7c480) to head (9c3884e).

Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #5142      +/-   ##
===========================================
+ Coverage    92.68%   92.75%   +0.07%     
===========================================
  Files          180      182       +2     
  Lines        22452    22520      +68     
  Branches      3186     3190       +4     
===========================================
+ Hits         20809    20888      +79     
- Misses        1169     1176       +7     
+ Partials       474      456      -18     

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@marinegor
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converted to draft since #4712 is not yet merged

@marinegor marinegor mentioned this pull request Nov 13, 2025
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Add option for gemmi backend for PDB reading Parse hexadecimal resid from OpenMM in PDBParser

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