PDBParser chainid segid / set groups

[yuyuan871111]

Fixes #4948 #2874

Changes made in this Pull Request:

• extract the segid from columns 73-76 in PDB files (instead of columns 67-76)
• deal with conflicts between chainids and segids
  • generate warnings when chainids and segids are different
  • generate warnings if chainids is prior to segids when loading into the AtomGroup/ResidueGroup/SegmentGroup in the universe
  • add an argument force_chainids_to_segids in PDBReader to forcibly reading the chain ID into the segment ID (PDB specific method)
  • add a function in the universe set_groups to update the topology and groups in the universe when atomwise resids/segids is given (more generalized method across different file type)

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--4965.org.readthedocs.build/en/4965/

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.42%. Comparing base (35d9d2e) to head (a594aaf).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4965      +/-   ##
===========================================
- Coverage    93.42%   93.42%   -0.01%     
===========================================
  Files          177      189      +12     
  Lines        21859    22969    +1110     
  Branches      3078     3084       +6     
===========================================
+ Hits         20422    21459    +1037     
- Misses         986     1059      +73     
  Partials       451      451              

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[yuyuan871111]

might need to update the user guide as well if this PR is accepted
https://userguide.mdanalysis.org/stable/formats/reference/pdb.html#reading-in

[yuyuan871111]

Hi @lilyminium, I update the codes based on your comment in the issue #4948 (comment).

let me know if it works for you.

u = mda.Universe("test.pdb")
# try
u.guess_or_set_segments() # default guess chainIDs
# or
u.guess_or_set_segments(custom_segids=u.atoms.chainIDs) # or use any atomwise list you would like to set

# might possibly add it to the guess_TopologyAttrs, as you suggested below 
# u.guess_TopologyAttrs(to_guess=["segids"], force_guess=["segids"])
# (or just let it stay outside, I am not sure which one is better)

[lilyminium]

Thanks for trying that out, @yuyuan871111!

As @tylerjereddy mentioned I think there are some design decisions still to be resolved. I'll reply on the parent issue just to centralize discussion

[yuyuan871111]

Hi @lilyminium @tylerjereddy

I believe the design decisions have been finalized #4948 (comment). Can we proceed with the pull request?

[yuyuan871111]

Hi @orbeckst @yuxuanzhuang,

As we have discussed this improvement in #4948, would you mind giving some feedback from the perspective of the codes?

I know it is a busy time for MDAnalysis core members (on GSoC application, MDAnalysis UserGuide/Document updates), but I hope this helpful improvement for MDAnlaysis users will not become a stale PR. Please let me know any suggestions and I am happy to clarify any unclear part (or improve codes).

[orbeckst]

No concerns with tightening the SEGID columns that are read in PDB to 73-76, see #4948 (comment)