Implementation of SugarSelection #4790

talagayev · 2024-11-14T19:11:57Z

Changes made in this Pull Request:

Creation of the SugarSelection class that allows the selection of sugars through
the access of known PDB, CHARMM and GLYCAM abbreviations
Addition of GLYCAM and SUGAR_PDB files in MDAnalysisTest.data
Addition of test_sugar_glycam_selection() and test_sugar_pdb_selection
in test_atomselections.py

Currently I used the following abbreviations:

https://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/index.html

In addition of using the GLYCAM Webserver to obtain the known Sugar abbreviations and also
included the aglycans that I obtained from the GLYCAM Weberserver.

The Pytest Files were retrieved from RCSB-PDB and the GLYCAM-Webserver:

https://glycam.org/

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--4790.org.readthedocs.build/en/4790/

Implementation of SugarSelection with the known abbreviations and aglycans obtained from the glycam webserver

pep8speaks · 2024-11-14T19:12:04Z

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

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2025-01-11 17:54:06 UTC

codecov · 2024-11-14T19:22:50Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.73%. Comparing base (4c12f15) to head (06ef329).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4790   +/-   ##
========================================
  Coverage    92.72%   92.73%           
========================================
  Files          180      180           
  Lines        22475    22483    +8     
  Branches      3190     3190           
========================================
+ Hits         20841    20849    +8     
  Misses        1177     1177           
  Partials       457      457

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pep fix 1

Added test files

Added tests for sugar selection

pep fix

talagayev · 2024-11-15T23:29:19Z

@hmacdope I will ping you here since you were one of the participants in the discussion that initiated the Issue that this PR is covering.

The main problem that I see currently, would be that the GLYCAM Abbreviations for the sugars due to the combinations have quite a lot of different names/abbreviations.

Some of them could lead to tricky cases, with the Allose Nomenclature having RNA as one of the abbreviations.

I checked the RCSB-PDB and found only one case, where a unique ligand was called RNA, but still could be dangerous if the
users call something "RNA" in their files.

As for the coverage, while looking at the PDBs in RCSB-PDB it covers NAG, GLC etc., which would be convenient if somebody wants to select those in the PDB Files, but does not cover for example Glycerol, which makes sense since it is not a sugar, but is quite common in crystal structures among those sugars as NAG, GLC. Does it make sense to have a selection that would somehow covers both cases of Glycerol and similar compounds together with sugars?

added changelog

added docs

Adds a minimal sugar selection that matches common GLYCAM06 hexose residue names (Glc, Gal, Man). This mirrors existing residue-based selectors in the codebase and intentionally limits the initial scope to well-documented cases. Closes MDAnalysis#4790.

RMeli

LGTM

IAlibay

Needs updating against main and a couple of small things, otherwise this is good.

package/MDAnalysis/core/selection.py

IAlibay · 2026-01-18T21:34:41Z

testsuite/MDAnalysisTests/data/6kya.pdb

gzip this file?

compressed the file to 6kya.pdb.gz

IAlibay · 2026-01-18T21:34:58Z

testsuite/MDAnalysisTests/data/GLYCAM_sugars.pdb

This is small enough to be ok non-gzipped.

IAlibay · 2026-01-18T21:35:36Z

testsuite/MDAnalysisTests/datafiles.py

 # DSSP testing: from https://github.com/ShintaroMinami/PyDSSP
 DSSP = (_data_ref / "dssp").as_posix()

+GLYCAM = (_data_ref / 'GLYCAM_sugars.pdb').as_posix()


Add some comments to describe these files?

Added the description :)

IAlibay · 2026-01-19T23:21:15Z

package/CHANGELOG

   directly passing them. (Issue #3520, PR #5006)

 Enhancements
+ * Addition of 'sugar' token for GLYCAM, PDB and CHARMM sugar selection (Issue #4790)


Sorry my bad - it should go in 2.11! (I forget what we have and haven't released)

All good, will adjust it :)

adjusted it t 2.11

talagayev · 2026-01-19T23:31:27Z

I also wanted to get your quick opinion on that PR @IAlibay, since when we implemented the water token in one the PRs you mentioned that there can be the case, that making the tokens will lead to users not carefully checking their files and thus deleting something, so that while it improved the user-friendliness it also led to a potential increase in user mistakes.

Here I have a small worry with this PR, that with the big amount of possible of abbrevations with 3 letters some may overlap with co-crystalized ligands. So for example something like NAG I only saw for the sugars in PDBs, so I would be suprised if a ligand would have that abbreviation, but something like 6lA or in that direction I would not be suprised to encounter in some PDB as the identifier for the co-crystalized ligand and thus may lead to the co-crystalized ligand being selected as soon as the user uses the sugar token.

What would be your opinion on that, how likely something like that could happen, espeically again with here the token covering every possible GLYCAM nomenclature, which leads to many ids falling under it 🤔

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

moved to 2.11.0

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Update selection.py

62a09ef

Implementation of SugarSelection with the known abbreviations and aglycans obtained from the glycam webserver

talagayev added 8 commits November 14, 2024 20:23

Update selection.py

95e8ae8

pep fix 1

Update selection.py

e395524

Update selection.py

9b50428

Added Test Files for GLYCAM and PDB sugars

137f69c

Update datafiles.py

70b70be

Added test files

Update test_atomselections.py

a56a95f

Added tests for sugar selection

Update test_atomselections.py

7639858

pep fix

Update datafiles.py

4cf52a4

talagayev mentioned this pull request Dec 18, 2024

Implementation of Water Selection token #4839

Closed

talagayev added 3 commits January 11, 2025 18:48

Merge branch 'develop' into sugar_selection

7539469

Update CHANGELOG

a21d40a

added changelog

Update selection.py

cf29e91

added docs

talagayev marked this pull request as ready for review January 11, 2025 17:54

MadhankumarAI mentioned this pull request Jan 17, 2026

SEL: add sugar atom selection based on GLYCAM residue names #5209

Closed

6 tasks

RMeli assigned hmacdope Jan 18, 2026

RMeli approved these changes Jan 18, 2026

View reviewed changes

IAlibay requested changes Jan 18, 2026

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Merge branch 'develop' into sugar_selection

2e81fd5

IAlibay reviewed Jan 19, 2026

View reviewed changes

talagayev and others added 5 commits January 21, 2026 22:52

Update package/MDAnalysis/core/selection.py

14be696

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Update CHANGELOG

fc42b6d

moved to 2.11.0

Update package/MDAnalysis/core/selection.py

e517482

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

compression of 6kya.pdb and addition of note about files in datafiles.py

38446d0

black formatting

a450a28

black formatting

06ef329

talagayev requested a review from IAlibay January 22, 2026 00:27

Implementation of SugarSelection #4790

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Implementation of SugarSelection #4790

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