agentic-pymol

by Arcadia-Science · Python · ★ 78

A Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface to your agent (Claude Code/Desktop, Codex, or any MCP-compatible client)

Install

pip install git+https://github.com/Arcadia-Science/agentic-pymol.git

Auto-generated from the repo's primary language — check the repo's own README for its exact install instructions.

Claude Desktop config

A starting point for your claude_desktop_config.json (auto-generated — the repo's README may specify a published package name or required env vars):

{
  "mcpServers": {
    "agentic-pymol": {
      "command": "uvx",
      "args": [
        "git+https://github.com/Arcadia-Science/agentic-pymol.git"
      ]
    }
  }
}

From the README

https://github.com/user-attachments/assets/43524828-0fcc-44e5-bcd6-c912e7f865b1 A lightweight Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface for general-purpose agents. Use it with Claude Code, Claude Desktop, Codex, or any MCP-compatible client to let your agent control an open PyMOL session, inspect molecular structures, run PyMOL-native analyses, and render what it sees. Agentic PyMOL is not an embedded chatbot and not a molecular workbench. It is a small bridge between a capable agent and the PyMOL session you already use. Ask your agent to use PyMOL dir…

Read full README on GitHub →

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