Add structural analysis to the SepTop protocol by hannahbaumann · Pull Request #1982 · OpenFreeEnergy/openfe

hannahbaumann · 2026-05-28T10:05:26Z

Checklist

All new code is appropriately documented (user-facing code must have complete docstrings).
Added a news entry, or the changes are not user-facing.
Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

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packaging tests: run this for any large feature PRs or PRs that add test data.

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I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

hannahbaumann · 2026-05-28T10:06:06Z

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hannahbaumann · 2026-05-29T11:04:42Z

This is what it would look like for the complex right now.

codecov · 2026-05-29T13:30:30Z

Codecov Report

❌ Patch coverage is 96.98276% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.60%. Comparing base (c9505a8) to head (3f2da12).

Files with missing lines	Patch %	Lines
src/openfe/protocols/openmm_septop/base_units.py	93.06%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1982      +/-   ##
==========================================
- Coverage   94.93%   90.60%   -4.34%     
==========================================
  Files         216      217       +1     
  Lines       20498    20725     +227     
==========================================
- Hits        19459    18777     -682     
- Misses       1039     1948     +909

Flag	Coverage Δ
fast-tests	`90.60% <96.98%> (?)`
slow-tests	`?`

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hannahbaumann · 2026-06-02T09:12:02Z

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hannahbaumann · 2026-06-02T09:34:13Z

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hannahbaumann · 2026-06-10T14:13:53Z

As discussed offline, CI is currently breaking since the prev. openfe 1.11 results files for gather do not have the new analysis_settings. Should we turn them on by default to keep backward compatibility or remove the old test files and break backward compatibility? @IAlibay

Co-authored-by: Josh Horton <joshua.horton@openforcefield.org> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

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hannahbaumann · 2026-06-11T09:10:30Z

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…reeEnergy/openfe into structural_analysis_septop

IAlibay

overall looks good - just the one blocker for me re: settings

hannahbaumann · 2026-06-11T13:43:57Z

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github-actions · 2026-06-12T08:56:35Z

No API break detected ✅

IAlibay

lgtm, thanks!

First pass at adding structural analysis to the SepTop protocol

ea6e58a

hannahbaumann marked this pull request as draft May 28, 2026 10:05

hannahbaumann changed the title ~~Add structural analysis to the SepTop protocol~~ [WIP] Add structural analysis to the SepTop protocol May 28, 2026

pre-commit-ci Bot and others added 3 commits May 28, 2026 10:06

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Small fix

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Small fix

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hannahbaumann self-assigned this May 28, 2026

hannahbaumann added 3 commits May 29, 2026 09:43

Fix ligand indices mapping

14381f9

Fix complex alignment

811a1b6

Small fix

54d4839

Add ligand indices to test

e1c101e

hannahbaumann added 2 commits June 1, 2026 15:40

Some updates

14ce7fd

Add tests for structural analysis

d953848

hannahbaumann marked this pull request as ready for review June 2, 2026 09:12

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fix mypy

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Update env

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hannahbaumann requested review from IAlibay and jthorton June 2, 2026 12:41

jameseastwood assigned IAlibay and unassigned hannahbaumann Jun 3, 2026

jthorton reviewed Jun 3, 2026

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Comment thread src/openfe/protocols/openmm_septop/base_units.py Outdated

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Comment thread src/openfe/protocols/openmm_septop/base_units.py Outdated

Update SepTop user guide to add strucural analysis

54b7c53

hannahbaumann requested review from IAlibay and jthorton June 10, 2026 11:13

Update septop results for gather test

4207d4a

jthorton reviewed Jun 11, 2026

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Comment thread src/openfe/tests/protocols/openmm_septop/test_septop_protocol_analysis.py

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Comment thread docs/guide/protocols/septop.rst Outdated

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Comment thread docs/guide/protocols/septop.rst Outdated

IAlibay reviewed Jun 11, 2026

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Comment thread src/openfe/protocols/openmm_septop/equil_septop_settings.py Outdated

hannahbaumann and others added 3 commits June 11, 2026 11:02

Apply suggestions from code review

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Co-authored-by: Josh Horton <joshua.horton@openforcefield.org> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

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Add test for skip

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Merge branch 'structural_analysis_septop' of https://github.com/OpenF…

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…reeEnergy/openfe into structural_analysis_septop

Update tests

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hannahbaumann and others added 2 commits June 11, 2026 15:37

Address review comments

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Merge branch 'main' into structural_analysis_septop

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Merge branch 'main' into structural_analysis_septop

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Add ToDo comment on Exception

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hannahbaumann requested review from IAlibay and jthorton June 12, 2026 08:56

IAlibay approved these changes Jun 15, 2026

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hannahbaumann merged commit 58d1e00 into main Jun 15, 2026
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hannahbaumann deleted the structural_analysis_septop branch June 15, 2026 14:21

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