📌Overview

Purpose: Molecule-MCP aims to facilitate integration between molecular science tools and Claude AI, enhancing molecule modeling through collaborative efforts.

Overview: Molecule-MCP serves as a model-context-protocol server that connects various molecular science tools to Claude AI, enabling direct interaction and control of these tools. This collaborative framework allows Claude to act as a co-scientist in the molecular modeling process, promoting efficient and informed decision-making in scientific research.

Key Features:

Integration with Claude AI: Directly connects molecular science tools like PyMOL and ChimeraX to Claude AI, enhancing the modeling experience and allowing AI-assisted workflows.
Model Context Protocol (MCP): Utilizes MCP to enable seamless communication between Claude and the connected tools, streamlining operations and improving overall efficiency in molecular modeling tasks.

Molecule-MCP

Molecule-MCP: A model-context-protocol server for molecules.

Molecule-MCP connects molecular science-related tools to Claude AI through the Model Context Protocol (MCP), allowing Claude to directly interact with and control these tools, acting as a co-scientist. This integration enables prompt-assisted molecule modeling.

Installation

⚠️ Note: Molecule-MCP requires Claude Desktop to be installed and running.

Go to Claude > Settings > Developer > Edit Config > claude_desktop_config.json to include the following:

{
  "mcpServers": {
    "pymol": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
      ]
    },
    "chimerax": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/chimerax_server.py"
      ]
    }
  }
}

Install mcp and get the script:
```
pip install mcp chatmol
which mcp
```
Replace /path/to/mcp with the displayed path.
Clone the repository and navigate to the directory:
```
git clone https://github.com/ChatMol/molecule-mcp.git
cd molecule-mcp
pwd
```
Replace /path/to/molecule-mcp with the displayed path.

Disclaimer

Molecule-MCP is provided "as is" without warranty of any kind. The authors and contributors disclaim all warranties, including implied warranties of merchantability and fitness for a particular purpose. Users employ this software at their own risk.

The authors bear no responsibility for any consequences arising from the use or misinterpretation of this software or its outputs. Results obtained through Molecule-MCP should be independently validated prior to use in research, publications, or decision-making processes.

This software is intended for research and educational purposes only. Users are responsible for ensuring compliance with applicable laws, regulations, and ethical standards in their jurisdiction.