Read chainID from PDBQT

[pgbarletta]

Fixes #4207

The user also complained about lacking elements, but given that the PDBQT format replaced the element field from the PDB ATOM record, I guess is fair that we don't try to create the from the atomtype. In any case, the solution given to the user could be made a FAQ (if it's indeed a FAQ).

Changes made in this Pull Request:

• Use the chain ID read from the atoms to create the proper chainIDs attribute instead of just discarding them.

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.

---

📚 Documentation preview 📚: https://mdanalysis--4284.org.readthedocs.build/en/4284/

[github-actions]

Linter Bot Results:

Hi @pgbarletta! Thanks for making this PR. We linted your code and found the following:

There are currently no issues detected! 🎉

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (2197a2c) 93.40% compared to head (e76db8b) 93.40%.

Additional details and impacted files

@@            Coverage Diff             @@
##           develop    #4284     +/-   ##
==========================================
  Coverage    93.40%   93.40%             
==========================================
  Files          170      184     +14     
  Lines        22255    23364   +1109     
  Branches      4071     4071             
==========================================
+ Hits         20788    21824   +1036     
- Misses         951     1024     +73     
  Partials       516      516             

Files Changed	Coverage Δ
package/MDAnalysis/topology/PDBQTParser.py	100.00% <100.00%> (ø)

... and 14 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[lilyminium]

Thanks @pgbarletta for opening this PR! I assume the PDBQT format doesn't include a segment column, or else that would be preferenced for segids? I was worried about what the PDBQT writer would do if the chainIDs and segids conflict -- looks like it tries to write chainIDs first, and then uses the last (not first...) letter of the segids.

There's a test for the segid attribute:

mdanalysis/testsuite/MDAnalysisTests/coordinates/test_pdbqt.py

Lines 41 to 45 in 16647cb

	def test_segid(self, universe):
	sel = universe.select_atoms('segid A')
	assert_equal(sel.n_atoms, 909, "failed to select segment A")
	sel = universe.select_atoms('segid B')
	assert_equal(sel.n_atoms, 896, "failed to select segment B")

Would it be possible to add one for chainIDs too? Otherwise LGTM.

[pgbarletta]

I assume the PDBQT format doesn't include a segment column, or else that would be preferenced for segids?

PDBQT has the concept of chainID, but not of segments. Taken from the PDBQT reference:

ATOM%5d%-4s%1s%-3s%1s%4d%1s%8.3f%8.3f%8.3f%6.2f%6.2f%4s%6.3f%2s \n",
atom_serial_num, atom_name, alt_loc, res_name, chain_id, res_num, ins_code, x, y, z,
occupancy, temp_factor, footnote, partial_charge, atom_type

I've seen the occupancy and temp_factor columns used for vdW and Elec, but never the footnote for segments, though I don't have that much experience with this format.

Would it be possible to add one for chainIDs too?

Done. Didn't add it at first since both segid and chainID read the same info.

[lilyminium]

Thanks @pgbarletta! Everything LGTM!

[orbeckst]

ALong the lines of MDAnalysis/UserGuide#312 — please (1) raise an issue to document in the User Guide and then (2) do the documenting.

[orbeckst]

@lilyminium I tentatively assigned you to merge because you reviewed but please feel free to punt.