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Merge branch 'main' into feat/add_worker_based_execution
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‎.pre-commit-config.yaml‎

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files: (^notebooks)
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repos:
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 26.3.1
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rev: 26.5.1
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hooks:
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- id: black
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 26.5.1
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- id: black-jupyter

‎abfe_tutorial/abfe_analysis.ipynb‎

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"text": [
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" % Total % Received % Xferd Average Speed Time Time Time Current\n",
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" Dload Upload Total Spent Left Speed\n",
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"100 3092k 100 3092k 0 0 432k 0 0:00:07 0:00:07 --:--:-- 501k\n",
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"100 3092k 100 3092k 0 0 1588k 0 0:00:01 0:00:01 --:--:-- 1587k\n",
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"Archive: abfe_results.zip\n",
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" inflating: abfe_results/README.md \n",
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" inflating: abfe_results/abfe_results_single_unit/results_2/1.json \n",
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"!unzip -o abfe_results.zip"
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]
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},
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{
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"cell_type": "markdown",
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"id": "0e15f538-1471-440f-b590-866a2258f0c7",
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"metadata": {},
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"source": [
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"## Analysing results from the command line\n",
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"\n",
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"The quickest way to get free energies out of your `openfe quickrun` results is\n",
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"`openfe gather-abfe`, which reads the result JSON files and prints a report\n",
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"directly. The default `--report dg` gives the overall binding free energy per\n",
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"ligand; `--report raw` gives the per-leg (complex and solvent) values. Add\n",
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"`-o out.tsv` to write a tab-separated file instead of printing, and\n",
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"`--allow-partial` to skip incomplete edges with a warning.\n",
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"\n",
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"*Note: `openfe gather-abfe` is currently experimental and may change in a future\n",
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"openfe release. It will also print an experimental-feature warning to stderr.*"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "7bb3c09c-4aff-4e6a-9b39-4d0318b2a71b",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\u001b[33mWARNING! Gathering of ABFE results with `openfe gather-abfe` is an experimental feature and is subject to change in a future release of openfe.\u001b[0m\n",
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"┌────────┬───────────────┬────────────────────────────────┐\n",
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"│\u001b[1m \u001b[0m\u001b[1mligand\u001b[0m\u001b[1m \u001b[0m│\u001b[1m \u001b[0m\u001b[1mDG (kcal/mol)\u001b[0m\u001b[1m \u001b[0m│\u001b[1m \u001b[0m\u001b[1mstd dev uncertainty (kcal/mol)\u001b[0m\u001b[1m \u001b[0m│\n",
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"├────────┼───────────────┼────────────────────────────────┤\n",
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"│ 1 │ -20.87 │ 0.58 │\n",
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"└────────┴───────────────┴────────────────────────────────┘\n"
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]
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}
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],
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"source": [
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"# overall binding free energy (DG) per ligand\n",
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"!openfe gather-abfe abfe_results/abfe_results_multiple_units --report dg"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "89f51d9d-1ea8-4d12-8d7c-7bce2dd6666a",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\u001b[33mWARNING! Gathering of ABFE results with `openfe gather-abfe` is an experimental feature and is subject to change in a future release of openfe.\u001b[0m\n",
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"┌──────────────────────────┬────────┬───────────────┬──────────────────────────┐\n",
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"│\u001b[1m \u001b[0m│\u001b[1m \u001b[0m│\u001b[1m \u001b[0m│\u001b[1m \u001b[0m\u001b[1mMBAR uncertainty \u001b[0m\u001b[1m \u001b[0m│\n",
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"│\u001b[1m \u001b[0m\u001b[1mleg \u001b[0m\u001b[1m \u001b[0m│\u001b[1m \u001b[0m\u001b[1mligand\u001b[0m\u001b[1m \u001b[0m│\u001b[1m \u001b[0m\u001b[1mDG (kcal/mol)\u001b[0m\u001b[1m \u001b[0m│\u001b[1m \u001b[0m\u001b[1m(kcal/mol) \u001b[0m\u001b[1m \u001b[0m│\n",
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"├──────────────────────────┼────────┼───────────────┼──────────────────────────┤\n",
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"│ complex │ 1 │ 36.34 │ 0.91 │\n",
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"│ complex │ 1 │ 36.17 │ 0.80 │\n",
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"│ complex │ 1 │ 34.77 │ 0.81 │\n",
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"│ solvent │ 1 │ 6.5 │ 1.4 │\n",
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"│ solvent │ 1 │ 5.4 │ 1.4 │\n",
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"│ solvent │ 1 │ 5.5 │ 1.4 │\n",
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"│ standard_state_correcti… │ 1 │ -8.9 │ 0.0 │\n",
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"│ standard_state_correcti… │ 1 │ -9.3 │ 0.0 │\n",
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"│ standard_state_correcti… │ 1 │ -9.0 │ 0.0 │\n",
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"└──────────────────────────┴────────┴───────────────┴──────────────────────────┘\n"
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]
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}
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],
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"source": [
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"# raw per-leg (complex, solvent, and Boresch-restraint analytical correction) values\n",
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"!openfe gather-abfe abfe_results/abfe_results_multiple_units --report raw"
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]
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},
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{
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"cell_type": "markdown",
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"id": "7e0ce0ab-0777-44b2-b865-7eaedaba57d9",
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"metadata": {},
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"source": [
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"## Analysing results with the Python API\n",
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"\n",
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"For more control over how results are combined and analysed, you can work with\n",
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"the result JSONs directly in Python, as shown in the rest of this notebook."
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]
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},
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"cell_type": "markdown",
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"id": "f2cff1e7-cf62-4839-b53d-62b59b7189b6",
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