Moving AFE Protocols around a bit by IAlibay · Pull Request #1775 · OpenFreeEnergy/openfe

IAlibay · 2026-01-03T14:25:54Z

Similar to #1769
The idea here is just to move a few things around to make it easier to do multi-unit and then restarts, it is not the defenitive module structure.

Checklist

All new code is appropriately documented (user-facing code must have complete docstrings).
[N/A] Added a news entry, or the changes are not user-facing.
Ran pre-commit by making a comment with pre-commit.ci autofix before requesting review.

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).

GPU integration tests
example notebook testing
packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

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

IAlibay · 2026-01-03T14:58:58Z

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IAlibay · 2026-01-04T19:30:54Z

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… into move-afe-protocols

hannahbaumann

Thanks @IAlibay , lgtm! Already approving, given tests will pass later!

openfe/protocols/openmm_afe/afe_protocol_results.py

jthorton · 2026-01-14T14:14:20Z

openfe/protocols/openmm_afe/abfe_units.py

+    @staticmethod
+    def _get_mda_universe(
+        topology: omm_topology,
+        positions: ommunit.Quantity,


Can we type this as optional as its not used if the trajectory file is present?

jthorton · 2026-01-14T14:36:16Z

openfe/protocols/openmm_afe/afe_protocol_results.py

+        vac_dGs = []
+        solv_dGs = []
+
+        for pus in self.data["vacuum"].values():
+            vac_dGs.append((pus[0].outputs["unit_estimate"], pus[0].outputs["unit_estimate_error"]))
+
+        for pus in self.data["solvent"].values():
+            solv_dGs.append(
+                (pus[0].outputs["unit_estimate"], pus[0].outputs["unit_estimate_error"])
+            )
+
+        return {"solvent": solv_dGs, "vacuum": vac_dGs}


We could rewrite this as a loop and use the bound and unbound class variables making this robust to the values changing in future.

Suggested change

vac_dGs = []

solv_dGs = []

for pus in self.data["vacuum"].values():

vac_dGs.append((pus[0].outputs["unit_estimate"], pus[0].outputs["unit_estimate_error"]))

for pus in self.data["solvent"].values():

solv_dGs.append(

(pus[0].outputs["unit_estimate"], pus[0].outputs["unit_estimate_error"])

)

return {"solvent": solv_dGs, "vacuum": vac_dGs}

estimates = {}

# Loop through `bound_state` and `unbound_state`

for state in [self.bound_state, self.unbound_state]:

state_dGs = [

(pus[0].outputs["unit_estimate"], pus[0].outputs["unit_estimate_error"])

for pus in self.data[state].values()

]

estimates[state] = state_dGs

return estimates

good call - done

P.S. Sorry I didn't merge your suggestion in, there was some formatting that was easier done locally.

jthorton

LGTM very minor optional changes!

codecov · 2026-01-14T19:01:19Z

Codecov Report

❌ Patch coverage is 94.84848% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.29%. Comparing base (907cefd) to head (1e6eb1e).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...penfe/protocols/openmm_afe/afe_protocol_results.py	90.41%	14 Missing ⚠️
openfe/protocols/openmm_afe/abfe_units.py	97.41%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1775      +/-   ##
==========================================
- Coverage   95.45%   93.29%   -2.16%     
==========================================
  Files         193      196       +3     
  Lines       16935    16910      -25     
==========================================
- Hits        16165    15777     -388     
- Misses        770     1133     +363

Flag	Coverage Δ
fast-tests	`93.29% <94.84%> (?)`
slow-tests	`?`

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openfe/protocols/openmm_afe/abfe_units.py

IAlibay · 2026-01-15T14:51:22Z

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github-actions · 2026-01-15T14:52:55Z

No API break detected ✅

* move the protocols results to a single file and deduplicate * rename base units file * move units out of method files * move a few things in init

* update install instructions (#1744) * update manifest to include all .gz files (#1746) * update manifest to include all .gz files * add min openmmforcefields pin * bump cuda version to 11.8 (#1749) * fix deprecation warning on view_components_3d (#1750) * expose KartografAtomMapper alongside other AtomMappers (#1751) * fix psutils import (#1779) * fix psutils import * swap import order * [pre-commit.ci] pre-commit autoupdate (#1778) updates: - [github.com/tox-dev/pyproject-fmt: v2.8.0 → v2.11.1](tox-dev/pyproject-fmt@v2.8.0...v2.11.1) - [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.10](astral-sh/ruff-pre-commit@v0.13.3...v0.14.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Disable NAGL as a partial charge backend when OEToolkit is installed but not chosen as the registry backend. (#1762) * NAGL can no longer be used with oechem installed if you are using the rdkit backend. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * rename openfecli fixture to avoid duplication with openfe fixture (#1755) Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * openfe gather: add progress bar for loading JSONs (#1786) * all the profiling * make progress bar pretty * revert typing thing * news * all the profiling * make progress bar pretty * revert typing thing * news * update expected outputs * update expected outputs * add dill mock to fix openfe docs build (#1792) * Fix issue 1795 (#1796) * Update method name in CLI YAML documentation * Fix command option case in CLI YAML guide * manually add absolute settings news item to changelog (#1821) * manually add absolute settings news item to changelog * add link * Fixes docstring to clarify argument does not have a default (#1819) * Fixes docstring to clarify argument does not have a default * Modernize typing * fix ligand network cropping bug (#1822) * fix ligand network cropping bug * move to upstream func * whitespace * fix pydantic deprecation of copy method * fix pydantic deprecation of dict method - septop (#1831) * Updated CHANGELOG for 1.8.1 * fix changelog links * add openeye w/ python 3.13 test to CI (#1745) * add openeye w/ python 3.13 test to CI * only run openeye on unbuntu w/ python 3.13 * add explicit openeye no * bump python version for conda cron (#1748) * remove mypy rdkit pin (#1753) * remove mypy rdkit pin * try more explicit import * Revert "try more explicit import" This reverts commit 00cc2a3. * disallow attr-defined error code * try globally disabling attr-defined * try specific override * per-line ignores * Make the multistate hybrid topology samplers not require the HybridTopologyFactory (#1768) * make hybrid samplers not rely on htf but instead on the system & positions. * Migrate validation to Protocol._validate in HybridTopologyProtocol (#1740) * Migrate & add validation to Protocol._validate for hybrid topology Protocol --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> * Move rfe protocol (#1769) Move RFE protocol files around * HybridTop Unit methods (#1770) * Break down the Hybrid Top protocol unit into various methods. --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> * Have two separate system generators for state A & B in hybrid protocol (#1772) Make it so that the states A and B are generated using two different SystemGenerator objects, allowing for partial charge transformations. * HybridTop structural analysis via API rather than CLI (#1771) * change structural analysis from using CLI to using API * making some language clearer on github-facing things (#1758) * making some language clearer on github-facing things * : * add pre-commit link * clean up * Moving AFE Protocols around a bit (#1775) * move the protocols results to a single file and deduplicate * rename base units file * move units out of method files * move a few things in init * Create setup, run, and analysis units for HybridTop Protocol (#1773) * Turn Hybrid Topology protocol into 3 units. --------- Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * update docs for multiple protocol units (#1793) * Update docstring for hybridtop classes (#1794) * Update docstring for classes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Small improvement in RelativeHybridTopologyProtocol docstring (#1797) Updated class docstring to clarify the use of Hybrid Topology scheme. * turn off zenodo retry (#1802) * turn off zenodo retry * remove retry_if_failed arg * only run CI on macos python 3.12 (#1803) * Turn AFE protocols into multiple units (#1776) * Split the AFE protocol units into setup, simulation, and analysis. * move to src layout (#1805) * Move openfe project layout to `src`. * Temporarily build pooch from main w/ hotfix (#1806) * build with pooch@main to see if hotfix works * add link * make CLI starting guide easier to find from the landing page (#1787) * make CLI starting guide easier to find from the landing page * Python API -> API Docs * bump ci * bump example notebooks pin to 2026.01.26 * change a word * clarifying language * Update pyproject.toml (#1813) * Update pyproject.toml * update classifiers * refactor: clean up test data handling (#1815) * import pooch_cache from conftest * remove unused files from pooch cache * move zenodo cache to conftest * remove duplicate code * min pin pooch to fix data fetching (#1820) * fix ligand network cropping bug (#1822) * fix ligand network cropping bug * move to upstream func * whitespace * fix api break check path (#1825) * fix pydantic deprecation of copy method (#1829) * fix scope mismatch with zenodo data (#1828) * fix scope mismatch with zenodo data * fix session scope --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>

IAlibay added 7 commits January 1, 2026 09:23

move the protocols results to a single file and deduplicate

49ede96

rename base units file

6b504a8

fix some imports

8abf04f

import fix

a3e228f

fix some more imports

efcee64

update some docstring

d11ab5a

move units out of method files

0f0ce12

pre-commit-ci bot and others added 2 commits January 3, 2026 14:59

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move a few things in init

dd56a7d

pre-commit-ci bot and others added 3 commits January 4, 2026 19:31

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make mypy happy

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Merge branch 'move-afe-protocols' of github.com:OpenFreeEnergy/openfe…

3cce3b0

… into move-afe-protocols

IAlibay mentioned this pull request Jan 4, 2026

Turn AFE protocols into multiple units #1776

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hannahbaumann approved these changes Jan 14, 2026

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Merge branch 'main' into move-afe-protocols

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IAlibay mentioned this pull request Jan 15, 2026

Choose better name to define states in AFE results #1791

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IAlibay commented Jan 15, 2026

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openfe/protocols/openmm_afe/abfe_units.py Show resolved Hide resolved

Add test to cover the new None handle

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IAlibay merged commit 7a897ad into main Jan 15, 2026
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IAlibay deleted the move-afe-protocols branch January 15, 2026 19:41

atravitz pushed a commit that referenced this pull request Feb 5, 2026

Moving AFE Protocols around a bit (#1775)

1bc6abe

* move the protocols results to a single file and deduplicate * rename base units file * move units out of method files * move a few things in init

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Moving AFE Protocols around a bit#1775

Moving AFE Protocols around a bit#1775
IAlibay merged 16 commits intomainfrom
move-afe-protocols

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