Raised meaningful error for short peptide stretch #5163

spyke7 · 2025-11-30T13:52:19Z

Changes made in this Pull Request:

Added a block for raising value error inside init in dssp.py
Checked the length of ag.residues, and just raised a simple value error message showing the minimum required residues

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.

📚 Documentation preview 📚: https://mdanalysis--5163.org.readthedocs.build/en/5163/

spyke7 · 2025-11-30T13:53:41Z

@orbeckst @marinegor please check this, and do I need to add extra tests for this? and also codecov is failing, so I think it would be better if I add tests right?

and please tell me what to write in CHANGELOG, cause I'm confused about the format.... :-)

codecov · 2025-11-30T14:51:18Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.72%. Comparing base (1e7644f) to head (d711d20).
⚠️ Report is 2 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5163      +/-   ##
===========================================
- Coverage    92.72%   92.72%   -0.01%     
===========================================
  Files          180      180              
  Lines        22472    22474       +2     
  Branches      3188     3189       +1     
===========================================
+ Hits         20838    20839       +1     
- Misses        1176     1177       +1     
  Partials       458      458

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IAlibay

Please add:

Tests that trigger the error
Tests that check that the system passes with 6 residues (and that it returns correct results)
Update the docstring "Raises" section
Update relevant docs to make it clear that at least 6 residues are necessary
Update the changelog

package/MDAnalysis/analysis/dssp/dssp.py

IAlibay · 2025-11-30T16:50:25Z

and please tell me what to write in CHANGELOG, cause I'm confused about the format.... :-)

Please look at the instructions in the changelog (

mdanalysis/package/CHANGELOG

Lines 6 to 13 in bbcef1b

    
           The rules for this file: 
        
             * entries are sorted newest-first. 
        
             * summarize sets of changes - don't reproduce every git log comment here. 
        
             * don't ever delete anything. 
        
             * keep the format consistent (79 char width, M/D/Y date format) and do not 
        
               use tabs but use spaces for formatting 
        
             * accompany each entry with github issue/PR number (Issue #xyz) 
        
             * release numbers follow "Semantic Versioning" https://semver.org

), and try to add something. If something about the changelog is unclear, then ask us specifically about (edit: what is unclear).

spyke7 · 2025-11-30T17:03:48Z

If something about the changelog is unclear, then ask us specifically about the.

ok

spyke7 · 2025-12-02T08:36:09Z

@IAlibay hi!
Please check it, and do I need to update any other things related to docs?

spyke7 · 2025-12-04T14:02:44Z

Hi @marinegor @IAlibay if you are not busy, can you tell me any updates on this?

IAlibay · 2025-12-04T14:19:57Z

@spyke7 - I appreciate the ping. I won't get to this until the weekend at the very least. As per all core developers, we tend to not have time during the week days due to life priorities.

spyke7 · 2025-12-04T14:49:26Z

@spyke7 - I appreciate the ping. I won't get to this until the weekend at the very least. As per all core developers, we tend to not have time during the week days due to life priorities.

Sure. No problem with that.

orbeckst · 2025-12-12T20:56:40Z

@IAlibay I tentatively assigned you here, given that you've been reviewing already. If you don't have the bandwidth please unassign yourself.

spyke7 · 2025-12-13T20:14:02Z

Hi @IAlibay
Any other changes or updates required?!

spyke7

Yeah done

IAlibay · 2026-01-01T15:38:41Z

package/MDAnalysis/analysis/dssp/dssp.py

    ----------
    atoms : Union[Universe, AtomGroup]
-        input Universe or AtomGroup. In both cases, only protein residues will
+        input at least 6 Universe or AtomGroup. In both cases, only protein residues will


This sentence is incorrect, please fix.

ok, I need to remove at least 6 right?

You should mention "6 residues" somewhere, but this current sentence structure doesn't say that.

input Universe or AtomGroup with at least 6 protein residues. In both cases, only protein residues will
is this good?

I think so, I'll review when you push the commit.

package/CHANGELOG

IAlibay · 2026-01-01T15:45:36Z

testsuite/MDAnalysisTests/analysis/test_dssp.py

+    resids = protein.residues.resids
+
+    with pytest.raises(ValueError, match="DSSP requires at least 6 residues"):
+        res2 = u.select_atoms(f"protein and resid {resids[0]}-{resids[1]}")


Please use atomgroup maniuplations here (and below) instead of calling "select_atoms".

Please check it now.

IAlibay · 2026-01-01T18:15:39Z

testsuite/MDAnalysisTests/analysis/test_dssp.py

+    u = mda.Universe(TPR, XTC)
+
+    protein = u.select_atoms("protein")
+    resids = protein.residues.resids


Suggested change

resids = protein.residues.resids

No longer being used?

yeah removed now

Raised meaningful error for short peptide stretch

f002bde

Moved the logic for checking at the end of __init__()

0d8e6be

IAlibay requested changes Nov 30, 2025

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package/MDAnalysis/analysis/dssp/dssp.py Outdated Show resolved Hide resolved

Updated tests, changelog and dssp.py

8d0d67b

spyke7 requested a review from IAlibay November 30, 2025 20:23

Updated the parameters part of atoms

dc24b83

orbeckst assigned IAlibay Dec 12, 2025

spyke7 commented Dec 13, 2025

View reviewed changes

IAlibay requested changes Jan 1, 2026

View reviewed changes

spyke7 and others added 2 commits January 1, 2026 21:57

Merge branch 'MDAnalysis:develop' into error_msg_fix_DSSP

43d9335

Updated changelog, and test_dssp.py

07fdd15

spyke7 requested a review from IAlibay January 1, 2026 18:01

IAlibay requested changes Jan 1, 2026

View reviewed changes

updated test_dssp.py

d711d20

spyke7 requested a review from IAlibay January 1, 2026 18:32

IAlibay approved these changes Jan 1, 2026

View reviewed changes

IAlibay merged commit 8ff4d09 into MDAnalysis:develop Jan 1, 2026
24 checks passed

Raised meaningful error for short peptide stretch #5163

Raised meaningful error for short peptide stretch #5163

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