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name: python-apis description: "Use when coding against AlphaFold 3 Python internals for input parsing, data pipeline/model config construction, model runner hooks, structure/mmCIF utilities, or generated resource inspection without running full inference." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

AlphaFold 3 Python APIs

Use this sub-skill when a task needs Python-level AlphaFold 3 internals rather than command-line operation.

Route Here For

• Inspecting alphafold3 package availability, version, JSON dialect/version, and key callable signatures.
• Parsing or emitting fold-input JSON with alphafold3.common.folding_input.Input.
• Constructing data-pipeline configuration objects or calling pipeline-only helpers safely.
• Building model configuration objects, wiring ModelRunner, or understanding inference hooks without accidentally starting model inference.
• Working with alphafold3.structure and mmCIF/CCD utilities at a high level.
• Diagnosing generated CCD pickle resources, package-data, C++ extension, JAX/GPU, model-directory, or resource-generation failures.

Do Not Handle Here

• For command-line prediction recipes, flags, output directory behavior, and split data-pipeline/inference runs, use ../running-predictions/.
• For AlphaFold 3 JSON schema, ligand/user CCD authoring, custom MSA/template fields, and input examples, use ../input-preparation/.
• For ranking scores, confidence JSON, embeddings, distograms, and output interpretation, use ../output-interpretation/.

Primary References

• Start with references/api-reference.md for verified signatures, safe snippets, and API caveats.
• Use references/troubleshooting.md for import/resource/JAX/model-dir failure modes.
• Run scripts/inspect_alphafold3_api.py --help to inspect an installed AlphaFold 3 package without performing inference.

Safety Rules

• Treat most Python APIs outside the JSON input classes as internal implementation surfaces; verify signatures against the installed package before generating durable code.
• Never instantiate ModelRunner.run_inference, predict_structure, or process_fold_input with a non-None model runner during harmless inspection.
• Prefer pipeline-only or parse-only examples when no model weights, GPU, databases, or external binaries are explicitly available.