Move rfe protocol by IAlibay · Pull Request #1769 · OpenFreeEnergy/openfe

IAlibay · 2026-01-03T01:05:08Z

Blocked by #1740 and #1768

Towards protocol continuations - moves some files around to make things easier to work it.

IMPORTANT: This is not a finalized layout for all the files, so please don't lose time bikeshedding here - we can reformat everything later (especially as we move towards a 2.0).

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/.

…validate-rfe

IAlibay · 2026-01-03T01:05:19Z

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IAlibay · 2026-01-06T16:41:35Z

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IAlibay · 2026-01-06T16:50:26Z

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IAlibay · 2026-01-06T16:53:09Z

openfe/protocols/openmm_rfe/hybridtop_protocols.py

I might be being a bit premature with this one - I haven't done this move with the AFE protocols. I was partly being motivated by the fact that eventually we might have "full cycle" protocols that do the whole RHFE/RBFE, they will mostly inherit the same base class and have lightweight changes to their validation & construction methods. In that case it makes sense to have them live in a separate file somewhere so it's easier to see the subclasses.

hannahbaumann

Thanks @IAlibay lgtm! Just two comments. Do we have a document somewhere where we're listing all the ideas for changes for the 2.0 or is that too premature?

openfe/protocols/openmm_rfe/equil_rfe_methods.py

hannahbaumann · 2026-01-07T09:37:03Z

openfe/protocols/openmm_rfe/hybridtop_units.py

+
+Acknowledgements
+----------------
+These ProtocolUnits are based on, and leverage components originating from


I wonder whether the file name could also be hybridtop_protocol_units.py to be more similar to the other files?

That's a pretty good idea - I've added it to #1785. I might circle back and make the change once we're done with all the other PRs for the hybridtop protocol (changing this file name specifically will cause some headaches 😓 ).

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>

github-actions · 2026-01-07T12:32:11Z

No API break detected ✅

codecov · 2026-01-07T12:58:40Z

Codecov Report

❌ Patch coverage is 91.14833% with 37 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.21%. Comparing base (990b77b) to head (77acfbe).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_rfe/hybridtop_units.py	85.20%	25 Missing ⚠️
...protocols/openmm_rfe/hybridtop_protocol_results.py	85.91%	10 Missing ⚠️
openfe/protocols/openmm_rfe/hybridtop_protocols.py	98.82%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1769      +/-   ##
==========================================
- Coverage   95.40%   93.21%   -2.20%     
==========================================
  Files         190      193       +3     
  Lines       16818    16838      +20     
==========================================
- Hits        16046    15695     -351     
- Misses        772     1143     +371

Flag	Coverage Δ
fast-tests	`93.21% <91.14%> (?)`
slow-tests	`?`

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Move RFE protocol files around

* 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

Add charge validation for smcs when dealing with ismorphic molecules

d1bd736

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

e0a8e2a

Fix missing import

b826803

Fix comp getter

063e8ce

IAlibay added 2 commits December 30, 2025 09:46

update module name

a98c799

fix duecredit tests

cadc6d6

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This was referenced Jan 3, 2026

Breakdown rfe protocolunit #1770

Merged

Moving AFE Protocols around a bit #1775

Merged

IAlibay added 2 commits January 6, 2026 11:26

fix typo

863098f

add in review fixes from #1740

ce5c529

Merge branch 'main' into move-rfe-protocol

529ac51

[pre-commit.ci] auto fixes from pre-commit.com hooks

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IAlibay commented Jan 6, 2026

View reviewed changes

IAlibay marked this pull request as ready for review January 6, 2026 16:53

hannahbaumann approved these changes Jan 7, 2026

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IAlibay mentioned this pull request Jan 7, 2026

Protocol modules renaming #1785

Open

IAlibay and others added 2 commits January 7, 2026 12:31

Update openfe/protocols/openmm_rfe/equil_rfe_methods.py

c4e9a09

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>

Merge branch 'main' into move-rfe-protocol

77acfbe

IAlibay merged commit acd6d58 into main Jan 7, 2026
11 of 12 checks passed

IAlibay deleted the move-rfe-protocol branch January 7, 2026 13:15

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

Move rfe protocol (#1769)

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Move RFE protocol files around

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Move rfe protocol#1769

Move rfe protocol#1769
IAlibay merged 39 commits intomainfrom
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