Enable user defn boresch restraints in ABFE Protocol by IAlibay · Pull Request #2019 · OpenFreeEnergy/openfe

IAlibay · 2026-06-16T10:34:49Z

Fixes #2002

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.
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…/openfe into abfe_user_defn_restraints

codecov · 2026-06-16T11:54:58Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.57%. Comparing base (ffc1cb9) to head (10ccce3).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2019      +/-   ##
==========================================
- Coverage   95.15%   90.57%   -4.58%     
==========================================
  Files         213      213              
  Lines       20950    21104     +154     
==========================================
- Hits        19934    19114     -820     
- Misses       1016     1990     +974

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IAlibay · 2026-06-17T12:17:14Z

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IAlibay · 2026-06-17T13:11:38Z

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hannahbaumann

Thanks @IAlibay , this looks great, just added a few comments.

hannahbaumann · 2026-06-19T06:25:29Z

+    host_restraint_ids: tuple[int, int, int] | None = None
+    """
+    The indices of the host component atoms to restrain.
+    The entries define the H0, H1, and H2 atoms in order.


Would it be helpful to add how the restraints are defined, since people use different definitions of H0 vs H2 (meaning, is the bond between H0 and G0 or between H2 and G0?)

I'll double check but I think the docstring gets inherited from

openfe/src/openfe/protocols/restraint_utils/settings.py

Line 92 in dab402b

class BoreschRestraintSettings(BaseRestraintSettings):

Which has the whole description of the restraints including my attempt at ASCII art.

Looks like the class docstring wasn't getting inherited, so I've added it.

hannahbaumann · 2026-06-19T06:29:26Z

+    """
+    guest_restraint_ids: tuple[int, int, int] | None = None
+    """
+    The indices of the guest component atoms to restraint.


This is based on the only ligand indices (from the sdf), correct? Maybe worth adding that this are not the indices the ligand would have in the complex (probably obvious since the complex is not created yet, but maybe just to be extra clear).

hannahbaumann · 2026-06-19T06:30:25Z

+
+    errmsg = "``guest_atoms`` and ``host_atoms`` cannot have negative indices."
+    with pytest.raises(ValueError, match=errmsg):
+        setattr(setting, parameter, [1, 2, -3])


What happens if you pass in 4 integers?

It'll fail validation, I initially tried that test and was pleasantly surprised that pydantic was that good.

Added a test just in case.

IAlibay · 2026-07-28T14:17:40Z

@hannahbaumann something I've been thinking about is whether or not SepTop should be using two of these settings (one for each restraint) or if it always makes sense for the restraint to have the exact same settings? (i.e. I think if the settings are different, the restraint might not cancel out, but I'm not sure).

IAlibay · 2026-07-28T14:20:26Z

        return v


+class ABFEBoreschRestraintSettings(BoreschRestraintSettings):


I'd like to avoid having to proliferate more settings classes for SepTop - TBD with @hannahbaumann, how easily can we align things?

IAlibay · 2026-07-29T10:54:09Z

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…/openfe into abfe_user_defn_restraints

hannahbaumann · 2026-07-31T08:14:21Z


 .. module:: openfe.protocols.openmm_afe.equil_afe_settings

+


I just noticed looking at the API docs that this page openmm_protocol_settings.rst does not have a link to the ABFE protocol settings. Maybe we could add that in this PR?

hannahbaumann

Thanks @IAlibay lgtm! Just the one comment on adding the link to the ABFE ProtocolSettings in the OpenMM settings reference, but approving early!

@hannahbaumann

* User supplied restraints SepTop protocol * Apply suggestion from @hannahbaumann * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update test data * Update test data * Address review comments * [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>

IAlibay · 2026-08-13T11:56:00Z

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hannahbaumann

Thanks @IAlibay , lgtm!

github-actions · 2026-08-13T13:34:35Z

🚨 API breaking changes detected! 🚨

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Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main
src/openfe/protocols/openmm_septop/equil_septop_settings.py:0: SepTopSettings.complex_restraint_settings:
Public object was removed


$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main

IAlibay added 5 commits June 16, 2026 11:32

enable user defined restraints in abfe calculations

e47b90a

Merge branch 'abfe_user_defn_restraints' of github.com:OpenFreeEnergy…

c5425b9

…/openfe into abfe_user_defn_restraints

Merge branch 'main' into abfe_user_defn_restraints

82f3c94

Add something specific to abfe restraints

a453b53

fix some typing

12c509f

IAlibay changed the title ~~Enable user defn boresch restraints~~ Enable user defn boresch restraints in ABFE Protocol Jun 16, 2026

isolate restraints only for ABFEs for now

f593327

Add settings test

505f4b7

jameseastwood assigned IAlibay Jun 16, 2026

Add test for user defined restraints

6ddcba1

pre-commit-ci Bot and others added 2 commits June 17, 2026 12:17

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Add a news item

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IAlibay marked this pull request as ready for review June 17, 2026 12:19

IAlibay added 2 commits June 17, 2026 13:19

Merge branch 'main' into abfe_user_defn_restraints

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assign None if needed

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Merge branch 'main' into abfe_user_defn_restraints

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Merge branch 'main' into abfe_user_defn_restraints

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IAlibay requested a review from hannahbaumann June 18, 2026 14:12

hannahbaumann self-assigned this Jun 18, 2026

hannahbaumann requested changes Jun 19, 2026

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Merge branch 'main' into abfe_user_defn_restraints

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hannahbaumann mentioned this pull request Jul 3, 2026

Septop tutorial inquiry OpenFreeEnergy/ExampleNotebooks#315

Closed

Merge branch 'main' into abfe_user_defn_restraints

4eb3875

IAlibay commented Jul 28, 2026

View reviewed changes

IAlibay added 2 commits July 29, 2026 09:49

Merge branch 'main' into abfe_user_defn_restraints

34671f5

Add settings to docs

afe4059

IAlibay added 8 commits July 29, 2026 10:29

try something

ae0383a

top level docstring is not inherited

1ac92c2

switch ascii art style

c681756

some fixes

3fceef8

try this instead

f4c0b22

Fix old docstring

b286463

Add test for too many indices

9a28bb1

Add validation

0ae6a3e

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IAlibay requested a review from hannahbaumann July 29, 2026 10:54

IAlibay added 2 commits July 29, 2026 13:59

fix test

c10183a

Merge branch 'abfe_user_defn_restraints' of github.com:OpenFreeEnergy…

a4eaa23

…/openfe into abfe_user_defn_restraints

hannahbaumann reviewed Jul 31, 2026

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hannahbaumann approved these changes Jul 31, 2026

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hannahbaumann and others added 7 commits August 12, 2026 13:13

fix all the imports for the move back upstream

8a45df5

Merge branch 'main' into abfe_user_defn_restraints

8d83ef4

fix fixture name

3f7dc1c

some more fixes

23cda45

fix docs

0ddf97f

Add extra link

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IAlibay requested a review from hannahbaumann August 13, 2026 12:04

hannahbaumann approved these changes Aug 13, 2026

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Merge branch 'main' into abfe_user_defn_restraints

10ccce3

IAlibay merged commit d8a6d37 into main Aug 13, 2026
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IAlibay deleted the abfe_user_defn_restraints branch August 13, 2026 14:28

		return v


		class ABFEBoreschRestraintSettings(BoreschRestraintSettings):

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