RosettaCommons / chaperone

# Chaperone: A Reliable and Efficient Protein Design Toolset Harness
Read the report: Reliable and Efficient Agentic Protein Design with Toolset Harnessing (PDF).
Chaperone is a unified framework for making structural biology tools interoperable.
Hook together design, sequencing, folding, and analysis into reproducible pipelines
with automatic SLURM orchestration, chunking, and path tracking.
Supported network blocks include RFD3NA, RFD3, RFD2, RFOptimization,
Proteina-Complexa, BindCraft, BoltzGen, Disco,
ProteinHunter, Protein/Ligand/FoundryMPNN, AF3, RF3, Boltz2, Chai1,
Protenix v2, OpenFold3, ESMFold2, E1, and ESM2.
Analysis blocks include RMSD, Foldseek, RASA, contact metrics, H-bond metrics,
and aromatic-neighbor scoring.
People have used Chaperone for PPI, symmetric design, and enzyme design — reach out to the respective experts if interested.
This repo ships with agent skills and project context (`AGENTS.md`) for writing, running, and debugging pipelines. The guides are Markdown files readable by Claude Code, Codex, and other coding agents; automatic discovery and slash commands depend on the agent installation.
> [!TIP]
> Read the Chaperone documentation. Start with the simple example and core examples.
## Installation (Agents)
First, install `uv` and a coding agent, either Claude Code or Codex:
- uv via `curl -LsSf https://astral.sh/uv/install.sh | sh`.
- Claude Code via `curl -fsSL https://claude.ai/install.sh | bash`, or
- Codex via `npm install -g @openai/codex`.
Then clone the repository and start your agent from its root:
 [code] 
Tell the agent: `Read .agents/skills/setup/SKILL.md and follow it.` If your agent discovers skills automatically, you can run the `setup` skill instead (for example `/setup`).
The setup guide walks through creating a venv, installing dependencies, choosing a compute environment, configuring a container backend, and installing selected block containers. Some tools or weights require a separate upstream download or access agreement.
`setup` is one of many skills Chaperone comes with, check out more below.
## Installation (Manual)
Requires Python 3.12+ and uv. The distribution name
is `chaperone-pipelines`; the import and CLI are `chaperone`. Install from this
repository until the production package is published.
 [code] 
Use a clean shell without a `PYTHONPATH` pointing at another checkout. To confirm which copy you are running:
 [code] 
Both paths should be inside this checkout.
Optional extras:
- **Jupyter kernel:** `python -m ipykernel install --user --name chaperone --display-name "Chaperone"`
- **PyRosetta** (only for the blocks that need it): set `PYROSETTA_PATH=/path/to/pyrosetta/setup` in `.env.local`, or run `python -c "import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()"`. IPD users can supply an untracked `.env.ipd` pointing to their shared install.
On IPD, place your site-provided `.env.ipd` in the checkout root; it is loaded when present and is not tracked in Git. Other systems