Agent skills for Claude Code and Codex

The MoleculeDesk skill teaches a coding agent how to use the moldesk CLI. Ask in plain language, for example "predict the structure of this sequence" or "which models can my Mac run?", and the agent:

installs MoleculeDesk if it's missing (after asking you);
checks your hardware with moldesk doctor and moldesk list before choosing a model;
prepares input files from your data or the shipped examples, and runs the model;
summarizes outputs, confidence scores, and where the 3D report is;
follows workflows such as design-then-fold (ProteinMPNN → Boltz-2) and ligand docking.

The skill is written to keep you in control. The agent asks before installing models (some are over 15 GB), before sending sequences to a public MSA server, and before anything that costs money. It never asks for or handles cloud API keys.

Claude Code

$ claude plugin install moldesk --marketplace pooriyapfn/moldesk

On Claude Code older than 2.1.275, use two steps instead:

claude plugin marketplace add pooriyapfn/moldesk
claude plugin install moldesk@moldesk

Start a new session. Claude uses the skill automatically when a task matches; you can also call it directly with /moldesk:moldesk. Inside a session, /plugin install moldesk --marketplace pooriyapfn/moldesk does the same.

Update later with claude plugin marketplace update moldesk, then claude plugin update moldesk@moldesk.

Codex

$ codex plugin marketplace add pooriyapfn/moldesk

Then open Codex, enter /plugins, choose the MoleculeDesk marketplace, and install moldesk. The skill is available in the next session. Mention it explicitly with $moldesk, or just describe the task.

Without a plugin manager

The skill is a plain folder with a SKILL.md file, so you can copy it directly. For Codex:

$ mkdir -p ~/.agents/skills && curl -fsSL https://codeload.github.com/pooriyapfn/moldesk/tar.gz/main | tar -xz -C ~/.agents/skills --strip-components=4 moldesk-main/plugins/moldesk/skills/moldesk

For Claude Code, use the same command with ~/.claude/skills instead of ~/.agents/skills. Run it again to update.

The source is in the repository under plugins/moldesk/skills/moldesk.

What the skill covers

Topic	What the agent learns
Installation	The one-command installer, `MOLDESK_HOME` for GPU servers, updating
CLI	Every command and flag, `--json` output, exit codes
Compatibility	Reading `moldesk doctor` and `moldesk list`, which models run on Apple Silicon and which need Linux + NVIDIA
Models	Input formats, parameters, and example inputs for Boltz-2, OpenDDE, DiffDock-L, BindCraft2, ProteinMPNN, and LigandMPNN
Workflows	Smoke test, structure prediction, complex and affinity, docking, design-then-fold, binder campaigns, viewing structures
Cloud	Runpod quotes, explicit cost approval, and cleanup. Cloud execution is still disabled, and the skill says so

Safety rules in the skill

Ask before installing MoleculeDesk or a model, and show download and disk sizes.
Ask before sending sequences off the machine (MSA server options, cloud uploads).
For cloud runs: quote with --dry-run first, show the cost and the shutdown warning, and only continue after an explicit yes. Never pass the risk acknowledgment flags on its own.
Never ask for, type, or store API keys. You run moldesk cloud connect runpod yourself.
Report predictions as predictions, with confidence scores and the need for experimental validation.
Respect model licenses, such as BindCraft2's hosting restriction.