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Merged
ijpulidos merged 14 commits into from
Dec 23, 2025
Merged

Protein mutation protocol #132

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90d49a8
WIP -- Skeleton for protein mutation protocol.
ijpulidos Aug 15, 2024
4d52587
Tests for capped AAs (#92)
ijpulidos Oct 21, 2024
f15592a
Convergence tests for protein mutation protocol (#95)
ijpulidos Oct 28, 2024
00c1f15
Test expected failing or unhandled cases (#96)
ijpulidos Nov 7, 2024
570ec7c
Protein mutation support in Neq Cycling Setup Unit (#106)
ijpulidos Dec 19, 2025
a56913a
Merge branch 'main' into protein-mutation-protocol
ijpulidos Dec 19, 2025
968d122
Fixed parenthesis missing in conflict merge
ijpulidos Dec 19, 2025
bceb37b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 19, 2025
8e609ca
Fixed parenthesis missing in conflict merge
ijpulidos Dec 19, 2025
f95fc55
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 19, 2025
b22a598
Changelog update for v0.2.0
ijpulidos Dec 19, 2025
0b7a9bb
We only support one mapping for now.
ijpulidos Dec 19, 2025
561c588
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 19, 2025
e18af6a
Removing unused protein mapping template/module.
ijpulidos Dec 19, 2025
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10 changes: 8 additions & 2 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,6 @@ jobs:
matrix:
os: ["ubuntu"]
python-version:
- "3.10"
- "3.11"
- "3.12"
include:
Expand Down Expand Up @@ -80,7 +79,14 @@ jobs:
# Set the OFE_SLOW_TESTS to True if running a Cron job
OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
run: |
pytest -n auto -v --cov=feflow --cov-report=xml --durations=10
if [ "$RUNNER_OS" == "macOS" ]; then
echo "Running test in serial for macOS (known limitations)..."
pytest -n 0 -v --cov=feflow --cov-report=xml --durations=10
else
echo "Running tests in parallel with xdist..."
pytest -n logical -v --cov=feflow --cov-report=xml --durations=10
fi


- name: codecov
if: ${{ github.repository == 'OpenFreeEnergy/feflow'
Expand Down
10 changes: 5 additions & 5 deletions devtools/conda-envs/test_env.yaml
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Expand Up @@ -4,16 +4,16 @@ channels:
- openeye
dependencies:
# Base depends
- gufe >=1.7.1, <2
- gufe ~=1.7.1
- numpy
- openfe >=1.1.0 # TODO: Remove once we don't depend on openfe
- openfe ~=1.8.0 # TODO: Remove once we don't depend on openfe
- openff-units
- openmm
- openmmforcefields >=0.14.1 # TODO: remove when upstream deps fix this
- pymbar >4.0
- pydantic >=1.10.17
- openmmtools >=0.23.0
- pymbar ~=4.0
- pydantic >=1.10.17, <3
- python

# Testing (optional deps)
- espaloma_charge ==0.0.8 # To use Espaloma FF in tests
- torchdata <0.10
Expand Down
8 changes: 8 additions & 0 deletions docs/CHANGELOG.rst
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Expand Up @@ -4,6 +4,14 @@ feflow Change Log

.. current developments

v0.2.0
====================
Most changes come from supporting protein mutations in the Nonequilibrium cycling protocol.

- Single point protein mutation support for the Nonequilibrium Cycling protocol, in its ``SetupUnit`` (`PR #106 <https://github.com/OpenFreeEnergy/feflow/pull/106>`_)
- Hybrid Topology Factory optimizations adopted from `openfe codebase <https://github.com/OpenFreeEnergy/openfe/>`_ (`PR #128 <https://github.com/OpenFreeEnergy/feflow/pull/128>`_).
- Dropping use of deprecated openff quantity models for type hinting, in favor of ``GufeQuantity`` from ``gufe`` (`PR #130 <https://github.com/OpenFreeEnergy/feflow/pull/130>`_).

v0.1.4
====================
- Dropping use of deprecated ``openff-models``. Using vendored ``gufe`` implementation instead (`PR #123 <https://github.com/OpenFreeEnergy/feflow/pull/123>`_)
Expand Down
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4,315 changes: 4,315 additions & 0 deletions docs/tutorials/inputs/abl1_structure.pdb
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160 changes: 160 additions & 0 deletions docs/tutorials/inputs/imatinib_ligand.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,160 @@
LIG
-OEChem-09082123573D

70 74 0 0 0 0 0 0 0999 V2000
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66.0044 55.7021 13.5868 H 0 0 0 0 0 0 0 0 0 0 0 0
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M CHG 2 29 1 32 1
M END
> <bio:pdb:part:site>
1

> <bio:pdb:part:order>
1

> <bio:pdb:ligand>
true

$$$$
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