PSFParser reads and converts string-Like residue number to the leading number

[yuxuanzhuang]

Fixes #2053 #4189

Changes made in this Pull Request:

• Updated PSFParser to convert string-like residue numbers to their leading number. If the conversion fails, the residue number defaults to 0.

In CHARMM PSF, residue identifiers (resids) can be any string, as discussed in #2053 (comment). Tools like CHARMM-GUI and psfgen often modify resids by including insertion codes from PDB files or converting large resids to hexadecimal numbers for placement in the resid block.

We should support reading it and this update aligns with the approach used by VMD for reading the leading number (atoi as in C) from string-like resids.

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--4582.org.readthedocs.build/en/4582/

[pep8speaks]

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

• In the file package/MDAnalysis/lib/util.py:

Line 2587:1: W293 blank line contains whitespace

• In the file package/MDAnalysis/topology/PSFParser.py:

Line 255:9: E731 do not assign a lambda expression, use a def

• In the file testsuite/MDAnalysisTests/topology/test_psf.py:

Line 162:1: E302 expected 2 blank lines, found 1
Line 165:51: W292 no newline at end of file

Comment last updated at 2024-05-30 03:52:24 UTC

[github-actions]

Linter Bot Results:

Hi @yuxuanzhuang! 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	⚠️ Possible failure

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/9296711606/job/25585650663

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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

All modified and coverable lines are covered by tests ✅

Project coverage is 93.17%. Comparing base (81062f3) to head (34810e6).
Report is 19 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4582      +/-   ##
===========================================
- Coverage    93.60%   93.17%   -0.44%     
===========================================
  Files          168       12     -156     
  Lines        21098     1069   -20029     
  Branches      3919        0    -3919     
===========================================
- Hits         19748      996   -18752     
+ Misses         892       73     -819     
+ Partials       458        0     -458     

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[hmacdope]

This looks good to me @yuxuanzhuang. Thanks! Would you be able to just add a quick test that the resids of the form 14F etc are able to be read from the test file?

[orbeckst]

@hmacdope please look after this PR! Thank you!

(As always, if it gets too much please say something an un-assign yourself.)

[hmacdope]

Looks good to me now @yuxuanzhuang! Thanks!

[d-beltran]

Hey @yuxuanzhuang,

Is the insertion code saved?
I don't find how to read it in the residue instance.

Thank you!