ABFE protocol by IAlibay · Pull Request #1045 · OpenFreeEnergy/openfe

IAlibay · 2024-12-11T14:00:54Z

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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/.

github-actions · 2024-12-11T14:01:10Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-11T14:09:42Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-11T14:45:31Z

🚨 API breaking changes detected! 🚨

openfe/protocols/openmm_utils/omm_settings.py

codecov · 2025-02-27T23:46:41Z

Codecov Report

❌ Patch coverage is 87.18775% with 159 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.88%. Comparing base (b7a49df) to head (5c8ef53).
⚠️ Report is 83 commits behind head on main.

Files with missing lines	Patch %	Lines
.../tests/protocols/openmm_abfe/test_abfe_energies.py	29.16%	68 Missing ⚠️
...enfe/tests/protocols/openmm_abfe/test_abfe_slow.py	17.74%	51 Missing ⚠️
...e/protocols/openmm_afe/equil_binding_afe_method.py	94.95%	16 Missing ⚠️
.../tests/protocols/openmm_abfe/test_abfe_protocol.py	93.87%	15 Missing ⚠️
openfe/protocols/openmm_afe/base.py	82.35%	6 Missing ⚠️
.../tests/protocols/openmm_abfe/test_abfe_settings.py	93.93%	2 Missing ⚠️
...enfe/tests/protocols/openmm_ahfe/test_ahfe_slow.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1045      +/-   ##
==========================================
- Coverage   95.46%   92.88%   -2.58%     
==========================================
  Files         174      183       +9     
  Lines       14584    15765    +1181     
==========================================
+ Hits        13923    14644     +721     
- Misses        661     1121     +460

Flag	Coverage Δ
fast-tests	`92.88% <87.18%> (?)`
slow-tests	`?`

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… abfe_protocol

openfe/protocols/openmm_afe/equil_binding_afe_method.py

hannahbaumann

@IAlibay I'll approve the PR, pending the lambda restraints discussion on Monday!

IAlibay · 2025-10-20T15:24:04Z

openfe/protocols/openmm_afe/base.py

+        # interacting (which would be non-interacting for us)
+        lambdas['lambda_electrostatics'] = [1-x for x in lambda_elec]
+        lambdas['lambda_sterics'] = [1-x for x in lambda_vdw]
+        lambdas['lambda_restraints'] = [x for x in lambda_rest]


Just double checking @hannahbaumann - this is correct now right? I.e. the factory expects 0 as not applied and 1 as fully interacting, so we just let it be the way it is.

Yes, this looks good!

hannahbaumann

Thanks @IAlibay , the restraints settings look good to me! just left a spelling suggestion and a question regarding some comments, but will already approve since those are not that important.

hannahbaumann · 2025-10-21T06:11:40Z

openfe/protocols/openmm_afe/base.py

+        # interacting (which would be non-interacting for us)
+        lambdas['lambda_electrostatics'] = [1-x for x in lambda_elec]
+        lambdas['lambda_sterics'] = [1-x for x in lambda_vdw]
+        lambdas['lambda_restraints'] = [x for x in lambda_rest]


Yes, this looks good!

hannahbaumann · 2025-10-21T06:12:27Z

openfe/protocols/openmm_afe/equil_binding_afe_method.py

+                    0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+                    0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1.0],
+                lambda_restraints=[
+                    0.0, 0.2, 0.4, 0.6, 0.8, 1.0,


Yes, this is matching now!

openfe/protocols/openmm_afe/equil_afe_settings.py

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

github-actions · 2025-10-21T08:23:12Z

No API break detected ✅

IAlibay added 2 commits December 11, 2024 13:18

Towards ABFE protocol

5d0b683

Add base code for settings

22fbc37

Fix up the units a bit

e1ef18c

Deal with the restraint addition

158ce40

IAlibay commented Dec 11, 2024

View reviewed changes

openfe/protocols/openmm_utils/omm_settings.py Outdated Show resolved Hide resolved

IAlibay added 11 commits December 14, 2024 02:00

Merge branch 'omm-restraints' into abfe_protocol

deac61d

Merge branch 'omm-restraints' into abfe_protocol

2dd883a

Merge branch 'omm-restraints' into abfe_protocol

67abff1

Add various fixes

06f84c5

Merge branch 'omm-restraints' into abfe_protocol

8506db2

some QoL updates

6ecec87

Fix a few things with the restraint addition

f5369c6

Merge branch 'omm-restraints' into abfe_protocol

0e93e00

fix regex match test

6f5a4e0

Fix the case where we don't have a restraint parameter

9f1cc46

Enforce the periodic box when getting state to avoid NaNs

0d32568

IAlibay added 10 commits February 28, 2025 09:40

Fix up some protocol results things

4aa6151

Add some tests and validation

c0d3d58

Merge branch 'omm-restraints' into abfe_protocol

7db8ac6

Some reformatting

a856403

Merge branch 'omm-restraints' into abfe_protocol

a28cc59

fix return type hint

6d0a51d

Add test for complex equil output indices

ecad789

Allow generation of results for ABFEs

d901204

add settings_cls

86fc509

Merge branch 'omm-restraints' into abfe_protocol

f976de0

Merge branch 'abfe_protocol' of github.com:OpenFreeEnergy/openfe into…

2bdb6a9

… abfe_protocol

IAlibay commented Oct 17, 2025

View reviewed changes

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

IAlibay added 5 commits October 17, 2025 12:46

Address some review comments

9f802d1

Add an extra note for the solvent lambda settings

c2bff25

Merge branch 'main' into abfe_protocol

d7e0da9

try to make myppy happy

3fb1036

you happy now mypy?

a29dbc0

IAlibay requested a review from hannahbaumann October 17, 2025 11:55

IAlibay added 3 commits October 17, 2025 12:56

And again...

acd1f6b

Add net charge check test

b25f86e

remove early termination

ec04f3a

hannahbaumann approved these changes Oct 17, 2025

View reviewed changes

IAlibay added 5 commits October 20, 2025 12:09

Merge branch 'main' into abfe_protocol

23ed15e

Merge branch 'main' into abfe_protocol

6b87bab

fix tests

fa02671

fix restraints

a174ef2

fix settings validation for lambdas

5fff298

atravitz requested a review from hannahbaumann October 20, 2025 15:10

IAlibay commented Oct 20, 2025

View reviewed changes

IAlibay added 5 commits October 20, 2025 20:21

update results

9d22909

Merge branch 'main' into abfe_protocol

ef634a0

Update for new settings

7cec9e2

Merge branch 'main' into abfe_protocol

ec5ecd2

Merge branch 'main' into abfe_protocol

9765bf1

hannahbaumann approved these changes Oct 21, 2025

View reviewed changes

IAlibay and others added 2 commits October 21, 2025 09:22

Update openfe/protocols/openmm_afe/equil_afe_settings.py

8e1b2ee

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

Merge branch 'main' into abfe_protocol

5c8ef53

IAlibay merged commit 66d14f6 into main Oct 21, 2025
12 of 13 checks passed

IAlibay deleted the abfe_protocol branch October 21, 2025 10:45

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IAlibay commented Dec 11, 2024 •

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