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Protein mutation protocol (#132)
* Base implementation for the protein mutation support for nonequilibrium cycling protocol.
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‎.github/workflows/ci.yaml‎

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matrix:
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os: ["ubuntu"]
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python-version:
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- "3.10"
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- "3.11"
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- "3.12"
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include:
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# Set the OFE_SLOW_TESTS to True if running a Cron job
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OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
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run: |
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pytest -n auto -v --cov=feflow --cov-report=xml --durations=10
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if [ "$RUNNER_OS" == "macOS" ]; then
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echo "Running test in serial for macOS (known limitations)..."
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pytest -n 0 -v --cov=feflow --cov-report=xml --durations=10
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else
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echo "Running tests in parallel with xdist..."
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pytest -n logical -v --cov=feflow --cov-report=xml --durations=10
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fi
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- name: codecov
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if: ${{ github.repository == 'OpenFreeEnergy/feflow'

‎devtools/conda-envs/test_env.yaml‎

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- openeye
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dependencies:
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# Base depends
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- gufe >=1.7.1, <2
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- gufe ~=1.7.1
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- numpy
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- openfe >=1.1.0 # TODO: Remove once we don't depend on openfe
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- openfe ~=1.8.0 # TODO: Remove once we don't depend on openfe
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- openff-units
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- openmm
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- openmmforcefields >=0.14.1 # TODO: remove when upstream deps fix this
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- pymbar >4.0
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- pydantic >=1.10.17
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- openmmtools >=0.23.0
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- pymbar ~=4.0
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- pydantic >=1.10.17, <3
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- python
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# Testing (optional deps)
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- espaloma_charge ==0.0.8 # To use Espaloma FF in tests
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- torchdata <0.10

‎docs/CHANGELOG.rst‎

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.. current developments
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v0.2.0
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====================
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Most changes come from supporting protein mutations in the Nonequilibrium cycling protocol.
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- Single point protein mutation support for the Nonequilibrium Cycling protocol, in its ``SetupUnit`` (`PR #106 <https://github.com/OpenFreeEnergy/feflow/pull/106>`_)
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- Hybrid Topology Factory optimizations adopted from `openfe codebase <https://github.com/OpenFreeEnergy/openfe/>`_ (`PR #128 <https://github.com/OpenFreeEnergy/feflow/pull/128>`_).
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- 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>`_).
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v0.1.4
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====================
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- Dropping use of deprecated ``openff-models``. Using vendored ``gufe`` implementation instead (`PR #123 <https://github.com/OpenFreeEnergy/feflow/pull/123>`_)

‎docs/tutorials/abl1_imatinib.png‎

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‎docs/tutorials/inputs/abl1_structure.pdb‎

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‎docs/tutorials/inputs/imatinib_ligand.sdf‎

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1+
LIG
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-OEChem-09082123573D
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70 74 0 0 0 0 0 0 0999 V2000
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64.1560 50.8350 18.3690 C 0 0 0 0 0 0 0 0 0 0 0 0
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60.1800 58.0950 13.7210 N 0 0 0 0 0 0 0 0 0 0 0 0
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59.3060 58.3230 14.7280 C 0 0 0 0 0 0 0 0 0 0 0 0
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57.5700 59.7550 15.8520 C 0 0 0 0 0 0 0 0 0 0 0 0
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55.5170 62.7980 14.8260 C 0 0 0 0 0 0 0 0 0 0 0 0
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54.6660 62.8220 13.6500 N 0 3 0 0 0 0 0 0 0 0 0 0
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53.0530 61.5960 12.2140 C 0 0 0 0 0 0 0 0 0 0 0 0
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52.2570 62.8380 12.2300 N 0 3 0 0 0 0 0 0 0 0 0 0
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51.6290 62.8120 10.9250 C 0 0 0 0 0 0 0 0 0 0 0 0
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53.0920 63.9910 12.3580 C 0 0 0 0 0 0 0 0 0 0 0 0
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53.7320 63.9520 13.7600 C 0 0 0 0 0 0 0 0 0 0 0 0
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59.2040 57.5660 15.6480 O 0 0 0 0 0 0 0 0 0 0 0 0
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65.1760 54.9810 13.5260 C 0 0 0 0 0 0 0 0 0 0 0 0
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63.3153 47.0563 18.7468 H 0 0 0 0 0 0 0 0 0 0 0 0
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64.4026 51.8825 18.2776 H 0 0 0 0 0 0 0 0 0 0 0 0
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64.7893 48.2000 20.3264 H 0 0 0 0 0 0 0 0 0 0 0 0
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63.7465 54.7667 16.3778 H 0 0 0 0 0 0 0 0 0 0 0 0
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64.2364 56.9468 11.9739 H 0 0 0 0 0 0 0 0 0 0 0 0
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62.1427 58.2340 12.0496 H 0 0 0 0 0 0 0 0 0 0 0 0
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60.9733 56.0937 15.5053 H 0 0 0 0 0 0 0 0 0 0 0 0
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59.9862 58.5441 12.8488 H 0 0 0 0 0 0 0 0 0 0 0 0
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54.8826 62.6920 15.7184 H 0 0 0 0 0 0 0 0 0 0 0 0
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56.0705 63.7470 14.8803 H 0 0 0 0 0 0 0 0 0 0 0 0
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55.2333 62.9478 12.8362 H 0 0 0 0 0 0 0 0 0 0 0 0
60+
54.6386 60.7221 13.4726 H 0 0 0 0 0 0 0 0 0 0 0 0
61+
53.2737 61.4297 14.4016 H 0 0 0 0 0 0 0 0 0 0 0 0
62+
53.7067 61.5830 11.3294 H 0 0 0 0 0 0 0 0 0 0 0 0
63+
52.3833 60.7238 12.1878 H 0 0 0 0 0 0 0 0 0 0 0 0
64+
51.5711 62.8055 12.9570 H 0 0 0 0 0 0 0 0 0 0 0 0
65+
50.9938 63.7021 10.8054 H 0 0 0 0 0 0 0 0 0 0 0 0
66+
52.4046 62.8077 10.1450 H 0 0 0 0 0 0 0 0 0 0 0 0
67+
51.0117 61.9062 10.8333 H 0 0 0 0 0 0 0 0 0 0 0 0
68+
53.8766 63.9730 11.5872 H 0 0 0 0 0 0 0 0 0 0 0 0
69+
52.4893 64.9044 12.2464 H 0 0 0 0 0 0 0 0 0 0 0 0
70+
52.9758 63.7689 14.5376 H 0 0 0 0 0 0 0 0 0 0 0 0
71+
54.2650 64.8887 13.9802 H 0 0 0 0 0 0 0 0 0 0 0 0
72+
65.2778 54.2372 14.3300 H 0 0 0 0 0 0 0 0 0 0 0 0
73+
65.2031 54.4728 12.5508 H 0 0 0 0 0 0 0 0 0 0 0 0
74+
66.0044 55.7021 13.5868 H 0 0 0 0 0 0 0 0 0 0 0 0
75+
1 2 2 0 0 0 0
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2 3 1 0 0 0 0
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2 39 1 0 0 0 0
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3 4 2 0 0 0 0
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14 19 1 0 0 0 0
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16 17 2 0 0 0 0
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26 27 2 0 0 0 0
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29 30 1 0 0 0 0
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29 55 1 0 0 0 0
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30 31 1 0 0 0 0
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30 56 1 0 0 0 0
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30 57 1 0 0 0 0
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31 32 1 0 0 0 0
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31 58 1 0 0 0 0
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31 59 1 0 0 0 0
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32 33 1 0 0 0 0
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32 34 1 0 0 0 0
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32 60 1 0 0 0 0
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33 61 1 0 0 0 0
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33 62 1 0 0 0 0
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33 63 1 0 0 0 0
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34 35 1 0 0 0 0
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34 64 1 0 0 0 0
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34 65 1 0 0 0 0
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35 66 1 0 0 0 0
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35 67 1 0 0 0 0
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37 68 1 0 0 0 0
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37 69 1 0 0 0 0
148+
37 70 1 0 0 0 0
149+
M CHG 2 29 1 32 1
150+
M END
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> <bio:pdb:part:site>
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1
153+
154+
> <bio:pdb:part:order>
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1
156+
157+
> <bio:pdb:ligand>
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true
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160+
$$$$

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