molcompose-mcp

An agent-safe MCP server that exposes the MolCompose figure workflow in UCSF ChimeraX as typed tools. Agents call the same canonical molcompose commands as the GUI panel — versioned presets, validated inputs, and a complete provenance record for every exported figure.

Requirements

  1. UCSF ChimeraX 1.12 with the ChimeraX-MolCompose bundle installed.
  2. Start the REST bridge inside ChimeraX:
remotecontrol rest start port 3000 json true

(Image export requires a windowed ChimeraX on macOS; analysis tools also work with --nogui.)

Run

pip install molcompose-mcp
molcompose-mcp --chimerax-url http://127.0.0.1:3000

Register the command above as an MCP stdio server in whichever client you use. The protocol is open and this server is not written against any one client; a command-line client is enough.

Most clients take the same shape of config:

{
  "mcpServers": {
    "molcompose": {
      "command": "molcompose-mcp",
      "args": ["--chimerax-url", "http://127.0.0.1:3000"]
    }
  }
}

Check your client's documentation for its configuration-file location rather than trusting a path written here, since client conventions change.

Optional: PythiaStudio ΔΔG

predict_ddg_pythiastudio fetches binding/stability ΔΔG from the PythiaStudio REST API and writes a tabular file that load_ddg then loads into ChimeraX. This is the only networked tool — the bundle itself never calls out, which keeps its zero-service dependency profile intact while the agent acts as the integration layer. Set PYTHIASTUDIO_API_KEY or pass a key explicitly.

Safety model

  • Figure work goes through the typed molcompose tools only.
  • Native passthrough is limited to an enumerated display-only whitelist (open, close, view, select, color, show, hide, ...).
  • Coordinate- or file-modifying commands are rejected with a structured error.
  • Every export writes <figure>.provenance.json with the client identity, timestamps, and the full command recipe.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.1.2)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for ChiaChunL from gravatar.com ChiaChunL

License expression

BSD-3-Clause
View SPDX License List

Requires

Python >=3.11

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