fix inclusion of PRO in secondary structure #5065

orbeckst · 2025-06-12T00:22:19Z

Changes made in this Pull Request:

ported fix from PyDSSP 0.9.1 by @ShintaroMinami to analysis.dssp.DSSP (see also Wrong assignment or prolines? ShintaroMinami/PyDSSP#2)
new kwarg ignore_proline_donor=True for DSSP (the new default changes the behavior and implements the fix, False recovers old behavior); the kwarg also exists in PyDSSP
updated docs
minimal regression tests
updated CHANGELOG

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--5065.org.readthedocs.build/en/5065/

@ShintaroMinami

- fix #4913 - ported fix from PyDSSP 0.9.1 by @ShintaroMinami to analysis.dssp.DSSP (see also ShintaroMinami/PyDSSP#2) - new kwarg ignore_proline_donor=True for DSSP (the new default changes the behavior and implements the fix, False recovers old behavior); the kwarg also exists in PyDSSP - updated docs - minimal regression tests - updated CHANGELOG

orbeckst

This is a quick draft. I'd be more than happy if someone continued and completed it.

(EDIT: ... and I am also grateful for any comments that would help me to continue working on it.)

orbeckst · 2025-06-12T00:26:07Z

package/MDAnalysis/analysis/dssp/dssp.py

+        self._donor_mask: Optional[np.ndarray] = (
+            ag.residues.resnames != "PRO" if ignore_proline_donor else None
+        )


This may not be correct. The code runs ... but I am not sure if I should be masking corresponding atoms.

if the question is about shape of the donor mask (i.e. make it for residues or for atoms), then it seems to be correct -- pydssp makes it of shape l (line) and l is the number of residues (link). However, the notation I made in pydssp_numpy.py is wrong, hence I renamed it in the commit below.

package/MDAnalysis/analysis/dssp/pydssp_numpy.py

orbeckst · 2025-06-12T00:29:28Z

package/MDAnalysis/analysis/dssp/pydssp_numpy.py

+        if donor_mask is not None
+        else np.ones(n_atoms, dtype=float)
+    )
+    donor_mask = np.tile(donor_mask[:, np.newaxis], (1, n_atoms))


Is the donor_mask (one element for each residue) really correct for this tiling????

package/MDAnalysis/analysis/dssp/pydssp_numpy.py

orbeckst · 2025-06-12T00:32:34Z

testsuite/MDAnalysisTests/analysis/test_dssp.py

 def test_file_guess_hydrogens(pdb_filename, client_DSSP):
+    # run 2.9.0 tests (which include PRO)
+    # ignore_proline_donor=False
+    # TODO: update reference data for ignore_proline_donor=True


We should really have correct reference data. About half of the files do not show a difference between ignore_proline_donor=True and ignore_proline_donor=False.

after some while, I figured what's the problem: the updated pydssp just gives different results now! Namely, take 3e8mA.pdb:

0.9.0: -----EEEE-----------EE-----EE-----HHHHHHHHHHH---EEEEE-----HHHHHHHHH----EEE-----HHHHHHHHHHHH---HHHEEEE---HHHHHHH----EEE------HHHH--------------HHHHHHHHH----HHHHHHH-- 3e8mA.pdb 0.9.1: -----EEEE-----------EE-----EE-----HHHHHHHHHHH----EEEE-----HHHHHHHHH----EEE-----HHHHHHHHHHHH---HHHEEEE---HHHHHHH----EEE------HHHH--------------HHHHHHHHH----HHHHHHH-- X `` In this particular case it used to (incorrectly) assign `E` (sheet) char to P48, and now it correctly assigns it to `-` (loop). The author didn't catch it since their test checks only correlation between pydssp and original assignment, which is still high enough since 0.9.0 changes only PRO assignment (and not even always).

testsuite/MDAnalysisTests/analysis/test_dssp.py

codecov · 2025-06-12T00:37:37Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.73%. Comparing base (5c7c480) to head (1679258).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5065      +/-   ##
===========================================
+ Coverage    92.68%   92.73%   +0.05%     
===========================================
  Files          180      180              
  Lines        22452    22457       +5     
  Branches      3186     3186              
===========================================
+ Hits         20809    20825      +16     
- Misses        1169     1176       +7     
+ Partials       474      456      -18

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

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Copilot

Pull Request Overview

This PR fixes the treatment of proline residues in secondary structure assignment by implementing the DSSP algorithm more correctly. The fix ports changes from PyDSSP 0.9.1 that properly handles proline residues by not considering their HN atoms as hydrogen bond donors.

Adds ignore_proline_donor parameter to DSSP class with default True for correct behavior
Updates the hydrogen bond calculation to mask proline donors when requested
Maintains backward compatibility through the new parameter

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
package/MDAnalysis/analysis/dssp/dssp.py	Adds `ignore_proline_donor` parameter and creates donor mask for proline residues
package/MDAnalysis/analysis/dssp/pydssp_numpy.py	Updates hydrogen bond functions to accept and use donor mask for filtering
testsuite/MDAnalysisTests/analysis/test_dssp.py	Adds regression tests and updates existing tests for the new proline handling
package/CHANGELOG	Documents the fix and new parameter

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

testsuite/MDAnalysisTests/analysis/test_dssp.py

package/MDAnalysis/analysis/dssp/pydssp_numpy.py

orbeckst · 2025-10-30T23:05:39Z

@marinegor if you can spare a moment to look at this PR then that would be great; I think you're really the person with best insight into the DSSP code. Feel free to tell me that all these changes are rubbish and we need to redo everything.

marinegor · 2025-11-02T21:11:19Z

@orbeckst I don't think it's all rubbish -- when this change was introduced to pydssp, I also made a similar attempt of introducing it to MDAnalysis.

My main concern is how to combine it with a workaround I introduced when PRO fix wasn't yet available. I have a feeling that in principle we should just get rid of that (I mean roughly this part) and rely purely on pydssp. I'll have a closer look.

- fixed variable names from `n_atoms` to `n_residues` - updated some docs, and most importantly - added updated `dssp` files.

marinegor

Quick summary: pydssp in 0.9.1 fixed the proline bug and changed (in correct direction) assignment of prolines. For example, for P48 in 3e8mA.pdb assignment used to be E, and now it's correctly -. Also the dssp output file in the original repo annotates P48 as -.

I suggest in this PR we:

change test files following up the pydssp update
remove the ignore_proline_donor option in function signature (i.e. make it always True, since the previous implementation was plain wrong)

@orbeckst while reviewing the PR, I made few commits on top of your branch -- namely, fixed variable names from n_atoms to n_residues, updated some docs, and most importantly, added updated dssp files. They're in here, feel free to pull them for yourself: //github.com/marinegor/mdanalysis/pull/new/update-dssp-proline-fix

marinegor · 2025-11-04T21:14:13Z

package/MDAnalysis/analysis/dssp/dssp.py

+        self._donor_mask: Optional[np.ndarray] = (
+            ag.residues.resnames != "PRO" if ignore_proline_donor else None
+        )


if the question is about shape of the donor mask (i.e. make it for residues or for atoms), then it seems to be correct -- pydssp makes it of shape l (line) and l is the number of residues (link). However, the notation I made in pydssp_numpy.py is wrong, hence I renamed it in the commit below.

package/MDAnalysis/analysis/dssp/pydssp_numpy.py

testsuite/MDAnalysisTests/analysis/test_dssp.py

marinegor · 2025-11-04T22:17:05Z

testsuite/MDAnalysisTests/analysis/test_dssp.py

 def test_file_guess_hydrogens(pdb_filename, client_DSSP):
+    # run 2.9.0 tests (which include PRO)
+    # ignore_proline_donor=False
+    # TODO: update reference data for ignore_proline_donor=True


after some while, I figured what's the problem: the updated pydssp just gives different results now! Namely, take 3e8mA.pdb:

0.9.0: -----EEEE-----------EE-----EE-----HHHHHHHHHHH---EEEEE-----HHHHHHHHH----EEE-----HHHHHHHHHHHH---HHHEEEE---HHHHHHH----EEE------HHHH--------------HHHHHHHHH----HHHHHHH-- 3e8mA.pdb 0.9.1: -----EEEE-----------EE-----EE-----HHHHHHHHHHH----EEEE-----HHHHHHHHH----EEE-----HHHHHHHHHHHH---HHHEEEE---HHHHHHH----EEE------HHHH--------------HHHHHHHHH----HHHHHHH-- X `` In this particular case it used to (incorrectly) assign `E` (sheet) char to P48, and now it correctly assigns it to `-` (loop). The author didn't catch it since their test checks only correlation between pydssp and original assignment, which is still high enough since 0.9.0 changes only PRO assignment (and not even always).

orbeckst · 2025-11-05T02:18:46Z

@marinegor thank you for the detailed review. Could you please directly update this PR with your changes? I’d really appreciate that!

I’m not sure if I get to working on the PR before the UGM this weekend. Please feel free to make any changes necessary!

thanks again !!

marinegor · 2025-11-05T11:30:49Z

@orbeckst sure, I've pushed them on top of this branch.

orbeckst · 2025-11-05T16:01:15Z

Thanks!!

…

On Nov 5, 2025, at 04:31, Egor Marin ***@***.***> wrote: marinegor left a comment (MDAnalysis/mdanalysis#5065) <#5065 (comment)> @orbeckst <https://github.com/orbeckst> sure, I've pushed them on top of this branch. — Reply to this email directly, view it on GitHub <#5065 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB2DHGLGDX4FYVKHCRCBQL33HNX7AVCNFSM6AAAAAB7D57EXGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIOJQGY4DIOJZGU>. You are receiving this because you were mentioned.

-- Oliver Beckstein (he/his/him) ***@***.***

orbeckst

Thank you for pushing the PR across the finish line @marinegor !

I'll just push a minor doc fix and then we can squash-merge. Please feel free to do the honors. When I squash-merge I typically clean up the log and format it something like

title

- fix #xxx
- summary of changes (typically from PR summary) and/or CHANGELOG
- other important changes (from comments)
- tests updated
- docs updated
- CHANGELOG updated

---
lines identifying code contributors as provided by GH

package/MDAnalysis/analysis/dssp/pydssp_numpy.py

marinegor · 2025-11-14T10:40:58Z

@orbeckst thanks, did my best! Initiation PR, I guess🥳

orbeckst · 2025-11-14T14:50:53Z

Awesome, great work @marinegor !

orbeckst force-pushed the update-dssp-proline-fix branch from b38e9db to 005100f Compare June 12, 2025 00:23

orbeckst commented Jun 12, 2025

View reviewed changes

Merge branch 'develop' into update-dssp-proline-fix

df31c86

orbeckst mentioned this pull request Jun 26, 2025

Update secondary structure assignment in DSSP after an upstream fix #4913

Closed

orbeckst added 2 commits July 14, 2025 13:33

Merge branch 'develop' into update-dssp-proline-fix

87810eb

Merge branch 'develop' into update-dssp-proline-fix

cf1f6aa

orbeckst requested review from RMeli and Copilot September 4, 2025 00:49

Copilot AI reviewed Sep 4, 2025

View reviewed changes

testsuite/MDAnalysisTests/analysis/test_dssp.py Show resolved Hide resolved

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

orbeckst requested a review from marinegor October 30, 2025 23:02

Merge branch 'develop' into update-dssp-proline-fix

e9df025

fix variable names and update dssp files after pydssp 0.9.1

66eeda0

- fixed variable names from `n_atoms` to `n_residues` - updated some docs, and most importantly - added updated `dssp` files.

marinegor requested changes Nov 4, 2025

View reviewed changes

marinegor added 2 commits November 5, 2025 12:29

remove ignore_proline_donors

3eab2fe

add myself to the changelog

2c77c84

marinegor approved these changes Nov 6, 2025

View reviewed changes

orbeckst commented Nov 14, 2025

View reviewed changes

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

doc fix with release number

1679258

orbeckst assigned marinegor Nov 14, 2025

marinegor merged commit 4a525ee into develop Nov 14, 2025
23 of 24 checks passed

marinegor deleted the update-dssp-proline-fix branch November 14, 2025 10:41

fix inclusion of PRO in secondary structure #5065

fix inclusion of PRO in secondary structure #5065

Uh oh!

Conversation

orbeckst commented Jun 12, 2025 • edited by github-actions bot Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

PR Checklist

Developers Certificate of Origin

Uh oh!

orbeckst left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

orbeckst Jun 12, 2025

Choose a reason for hiding this comment

Uh oh!

marinegor Nov 4, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

orbeckst Jun 12, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

orbeckst Jun 12, 2025

Choose a reason for hiding this comment

Uh oh!

marinegor Nov 4, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

codecov bot commented Jun 12, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull Request Overview

Reviewed Changes

Uh oh!

Uh oh!

Uh oh!

orbeckst commented Oct 30, 2025

Uh oh!

marinegor commented Nov 2, 2025

Uh oh!

marinegor left a comment

Choose a reason for hiding this comment

Uh oh!

marinegor Nov 4, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

marinegor Nov 4, 2025

Choose a reason for hiding this comment

Uh oh!

orbeckst commented Nov 5, 2025

Uh oh!

marinegor commented Nov 5, 2025

Uh oh!

orbeckst commented Nov 5, 2025 via email

Uh oh!

orbeckst left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

marinegor commented Nov 14, 2025

Uh oh!

orbeckst commented Nov 14, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

orbeckst commented Jun 12, 2025 •

edited by github-actions bot

Loading

orbeckst left a comment •

edited

Loading

codecov bot commented Jun 12, 2025 •

edited

Loading