Create setup, run, and analysis units for HybridTop Protocol by IAlibay · Pull Request #1773 · OpenFreeEnergy/openfe

IAlibay · 2026-01-03T02:00:25Z

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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 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).

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…validate-rfe

IAlibay · 2026-01-03T02:07:53Z

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openfe/protocols/openmm_rfe/hybridtop_units.py

openfe/protocols/openmm_utils/serialization.py

hannahbaumann

Thanks @IAlibay , this looks great! One thing I was wondering is whether you noticed any slowdowns having the three units instead of the one unit, e.g. due to serialization of things or recreation of the reporter?

hannahbaumann · 2026-01-09T07:59:57Z

openfe/protocols/openmm_rfe/__init__.py

 from .hybridtop_protocols import RelativeHybridTopologyProtocol
-from .hybridtop_units import RelativeHybridTopologyProtocolUnit
+from .hybridtop_units import (
+    HybridTopologyMultiStateAnalysisUnit,


Re unit names, do we already know how we would name the simulation and analysis units if we had a nonequilibrium protocol and would that match well with these names?

I was just going to call them HybridTopologyNEQUnit. BUT these names are not set in stone, we can redo them later.

hannahbaumann · 2026-01-09T08:08:36Z

openfe/protocols/openmm_rfe/hybridtop_units.py

+        # Get the relevant inputs
+        system = deserialize(setup_results.outputs["system"])
+        positions = to_openmm(np.load(setup_results.outputs["positions"]) * offunit.nm)
+        selection_indices = setup_results.outputs["selection_indices"]


We'll somewhere have to document well which unit stores what to be easily findable for users.

Ideally I would like to expose everything you would need in the analysis unit results - anything else we should add there?

Ah, hadn't seen the selection_indices down there, those were mostly what I was thinking of!

IAlibay · 2026-01-09T12:58:08Z

any slowdowns

Not that I saw, the intermediate steps are rather quick so you shouldn't see much overhead.

* fix test to have slightly better mocking * add try/except nightmare --------- Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>

IAlibay · 2026-01-15T19:07:03Z

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openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py

IAlibay · 2026-01-15T19:35:05Z

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github-actions · 2026-01-15T19:58:22Z

No API break detected ✅

codecov · 2026-01-15T20:31:47Z

Codecov Report

❌ Patch coverage is 81.51261% with 66 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.52%. Comparing base (7a897ad) to head (eba94fd).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_rfe/hybridtop_units.py	62.50%	30 Missing ⚠️
...tests/protocols/openmm_rfe/test_hybrid_top_slow.py	0.00%	18 Missing ⚠️
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	86.95%	15 Missing ⚠️
openfe/protocols/openmm_utils/serialization.py	93.10%	2 Missing ⚠️
...protocols/openmm_rfe/hybridtop_protocol_results.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1773      +/-   ##
==========================================
- Coverage   95.50%   92.52%   -2.98%     
==========================================
  Files         196      197       +1     
  Lines       16910    17046     +136     
==========================================
- Hits        16150    15772     -378     
- Misses        760     1274     +514

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slow-tests	`?`

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* Turn Hybrid Topology protocol into 3 units. --------- Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

* 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 and others added 30 commits December 5, 2025 13:18

Migrate validation to Protocol._validate

43d6007

some fixes

2cd56ba

Merge branch 'main' into validate-rfe

70e6d7a

move some things around

f330562

Merge branch 'main' into validate-rfe

95b92b3

add validate endstate tests

1e0153e

Merge branch 'validate-rfe' of github.com:OpenFreeEnergy/openfe into …

fe2b879

…validate-rfe

validate mapping tests

fbc4554

net charge validation tests

c2f49d2

more stuff

c50f99c

remove old tests

9e0d29b

make hybrid samplers not rely on htf

2fe8ff9

fix up test

4a0bd26

fix up some slow tests

5848adc

Merge branch 'main' into multistate-nohtf

1aaef87

Fix up the one test

b6d5ecd

fix a few things

0605d11

fix the remaining tests

48106a2

cleanup imports

5af66e8

Merge branch 'validate-rfe' into move-rfe-protocol

ad0b5fb

Merge branch 'multistate-nohtf' into move-rfe-protocol

45e004c

Migrate protocol, units, and results for the hybridtop protocol

58dd71c

Add news item

792996e

Merge branch 'validate-rfe' into move-rfe-protocol

91f1788

Merge branch 'main' into validate-rfe

527b870

fix redefine

7d17998

start modularising everything

43eb947

Add charge validation for smcs when dealing with ismorphic molecules

d1bd736

break down the rfe units into bits

51a6de1

more broadly disallow oechem as a backend when creating systems

6a5a76a

pre-commit-ci bot and others added 3 commits January 3, 2026 02:08

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remove redundant list declarations

1588b53

move integrator out of the try/except

c15ba01

IAlibay commented Jan 7, 2026

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IAlibay marked this pull request as ready for review January 9, 2026 00:24

IAlibay commented Jan 9, 2026

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Update openfe/protocols/openmm_rfe/hybridtop_units.py

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IAlibay requested review from hannahbaumann and jthorton January 9, 2026 00:28

IAlibay added 2 commits January 9, 2026 01:29

make mypy happy

7d8ff06

Move serialization from septop to utils

0b060be

hannahbaumann reviewed Jan 9, 2026

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IAlibay and others added 2 commits January 15, 2026 18:23

Merge branch 'main' into multi-unit-rfe

759ed6f

[WIP] fixing cli test for protocol refactor (#1788)

607d752

* fix test to have slightly better mocking * add try/except nightmare --------- Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>

IAlibay commented Jan 15, 2026

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pre-commit-ci bot and others added 2 commits January 15, 2026 19:35

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Merge branch 'main' into multi-unit-rfe

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IAlibay merged commit d3a5927 into main Jan 15, 2026
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IAlibay deleted the multi-unit-rfe branch January 15, 2026 21:35

atravitz mentioned this pull request Jan 16, 2026

update docs for multiple protocol units #1793

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

Create setup, run, and analysis units for HybridTop Protocol (#1773)

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* Turn Hybrid Topology protocol into 3 units. --------- Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

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