Individual skill

omh-molecular-docking

[omh] Prepared PDBQT inputs: run bounded standalone Vina docking with real poses, scores and replay provenance; never infer efficacy or safety. Use when the user says: molecular-docking, rigid-receptor docking, PDBQT docking, ligand docking poses, AutoDock Vina.

agent-skills/omh-molecular-docking/SKILL.md

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Last checked: Nov 9, 2026

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Repository stars (not skill ratings): 5,309
Repository last updated: Nov 9, 2026
License: MIT

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agent Repository topic
ai Repository topic
ai-agent Repository topic
ai-tools Repository topic
claude-code Repository topic
codex Repository topic
hermes-agent Repository topic
hermes-skill Repository topic
skills Repository topic
engineering Derived category

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SKILL.mdcore · 7,043 bytes
SKILL.mdcore · 7,043 bytes
SKILL.mdcore · 7,043 bytes
references/execution-and-qa.mddoc · 5,357 bytes
references/full-contract.mddoc · 2,848 bytes
references/procedure.mddoc · 4,037 bytes
toolkit/NOTICE.mddoc · 1,647 bytes
toolkit/README.mddoc · 7,069 bytes
toolkit/examples/settings.jsonasset · 581 bytes
toolkit/scripts/dock.pyruns · 17,670 bytes
toolkit/upstream-manifest.jsonasset · 6,050 bytes

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# Molecular Docking

This is an OMH `molecular-docking` workflow skill, projected for Agent Skills hosts (Claude Code, Codex, Cursor, opencode, OpenClaw, pi).

## 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.
- 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.