Molecular Docking

Required: prepared receptor and ligand PDBQT paths, binding box and preparation provenance, approved local resource budget. Output: molecular_docking_preflight/v1, molecular_docking_run/v1 and real pose/score files.

HOLD: Missing inputs or failed contract gates. Prepared OMH routing is not execution or approval.

Why This Exists

Input validation and tutorial numbers are not measured docking. Require a real engine search and digest-bound poses, finite energies and replay settings.

First Steps

• Read toolkit/README.md and references/execution-and-qa.md. Use the explicitly invoked standalone Vina Python helper, not an invented ToolUniverse tool or hidden core execution service.
• Recover prepared file paths, source/license and preparation receipts, angstrom binding box, seed, CPU, new output directory and host deadline. Never guess a site, silently prepare a molecule or install dependencies on skill load. If the person has a SMILES or a PDB id rather than PDBQT, stop and list the preparation steps they must approve (protonation state, charges, tautomer, receptor cleanup, box) with a named converter such as Meeko or ADFR; do not convert silently.
• Use --validate-only for dependency-free prerequisites, or explicitly invoke actual docking in an approved environment with a host-enforced timeout and stdout/stderr capture. Missing dependencies must refuse, not produce guessed findings.

Contract: references/full-contract.md, loaded before analysis. Procedure: references/procedure.md. These are working methods, not an OMH runtime operation.

Safety Rules