boltz-small-molecule-adme

Workflow

If boltz-api is missing from PATH, use boltz-cli-setup for install/update guidance before retrying. If a command reports missing or expired authentication, use boltz-cli-setup to start boltz-api auth login --device-code before retrying; do not ask permission first. If the agent host sandbox blocks boltz-api install/auth/API calls, use boltz-cli-setup to request the host sandbox bypass/escalation needed for user-wide CLI install, browser login, credential storage, temp files, or API access before retrying.

Use this skill for standalone ADME triage on SMILES the user already has. No protein target is involved. If the user is also screening or docking those molecules against a target, prefer boltz-small-molecule-screen — it returns the same ADME block free as part of the screen.

1. Normalize the molecules from raw SMILES, a CSV (auto-detect the SMILES column), .smi, or .txt into the molecules list. Each entry is {smiles, id?}; the optional id is echoed back as external_id on each result so you can map results to inputs.
2. Hard cap: 128 molecules per request. If the list exceeds 128, split into batches of ≤128 and submit one request per batch (suffix the run name, for example -b1, -b2), then merge results. Never send more than 128 in one call — the API rejects it with VALIDATION_ERROR: input.molecules must contain at most 128 items.
3. Author the payload YAML or JSON, run estimate-cost, show the USD cost, wait for explicit confirmation. ADME is priced at $0.01 per molecule (size-independent); estimate-cost returns the authoritative total — always quote it.
4. run to submit and wait — ADME finishes in seconds, so it is synchronous and needs no background polling. run persists results locally under --root-dir/<run-name>/.
5. Report from <output-root>/<run-name>/run.json → output.molecules[]. For each molecule show external_id (or smiles), solubility, permeability, and lipophilicity. The three values live under each molecule's adme object. Call out any molecule with status: failed and its error (an object {code, message}, e.g. code adme_enumeration_failed, message Invalid SMILES) — adme is null there; one bad SMILES fails only that molecule, not the batch. Read references/results.md for the output layout and references/api.md for the payload and batching details.