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add placeholder for openfold confidence score analysis
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Lines changed: 70 additions & 46 deletions

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cookbook/assets/of3_tyk2_output/settings.yaml renamed to cookbook/assets/of3_tyk2_output/output_settings.yaml

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‎cookbook/openfold3_to_openfe.ipynb‎

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"output_writer_settings:\n",
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" # change output format to pdb (default: mmcif):\n",
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" structure_format: pdb\n",
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"```\n",
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"```"
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]
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{
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"cell_type": "markdown",
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"id": "f3e4b82a-716e-494a-90e0-bff5c567df50",
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"metadata": {},
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"source": [
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"#### Running OpenFold\n",
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"\n",
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"With all these inputs, you can now run OpenFold:\n",
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"\n",
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"`run_openfold predict --query_json=queries.json --runner_yaml output_settings.yml`"
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]
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},
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{
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"cell_type": "markdown",
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"id": "354f4601-d1eb-46a6-9d5f-b0cd586880a0",
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"metadata": {},
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"source": [
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"### Evaluating OpenFold outputs"
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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": 4,
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"id": "ebe05714-306a-4353-a682-1174aef6f116",
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"metadata": {},
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"outputs": [],
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"source": [
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"# confidence scores for each ligand are at assets/of3_tyk2_output/{lig_name}/*/*confidences*.json"
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]
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},
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"cell_type": "markdown",
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"text": [
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"/Users/atravitz/micromamba/envs/openfe-notebooks/lib/python3.13/site-packages/MDAnalysis/coordinates/PDB.py:885: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.\n",
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" warnings.warn(\n",
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"Generating charges: 100%|███████████████████████| 10/10 [00:05<00:00, 1.75it/s]\n"
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"Generating charges: 100%|███████████████████████| 10/10 [00:05<00:00, 1.77it/s]\n"
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"SmallMoleculeComponent(name=lig_jmc_27)"
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" ChemicalSystem(name=state_B, components={'protein': ProteinComponent(name=tyk2), 'solvent': SolventComponent(name=O, Na+, Cl-)}))"
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