Mol-MCP: Computational Chemistry Interfaces for LLMs

[!WARNING] This project is a work in progress!

MolMCP is a modular set of interfaces for chemistry workflows. It provides a flexible architecture for building, configuring, and running agents and tools for chemical operatations.

Features

• Modular agent and tool system
• Extensible via configuration and plugins
• Designed for quantum chemistry and molecular computation

Project Structure

src/
  molmcp/           # Main package
    agents/         # Agent servers
    tools/          # Tool servers
tests/              # Test suite
pyproject.toml      # Project metadata and dependencies
README.md           # Project documentation

Usage

Tools

uvx --from git+https://github.com/lukasmki/mol-mcp mol-mcp serve --help

Chat TUI

To use the built-in interactive agent with mol-mcp tools,

uv run mol-mcp go

Currently, the interactive agent is setup to use the Anthropic API. If you want to use another, take a look at the src/molmcp/agents/interactive.py script for an example of using fast-agent.

Installation

Install uv

# macOS
brew install uv

# Linux/WSL2  
curl -LsSf https://astral.sh/uv/install.sh | sh

The calc and geometry servers depend on tblite and require a Fortran compiler to complete installation.

# macOS
brew install gfortran

# Linux/WSL2
sudo apt install gfortran

In your project directory, install with uv

uv add git+https://github.com/lukasmki/mol-mcp

or

uv pip install git+https://github.com/lukasmki/mol-mcp

You can also run it as a uv tool outside of a project!

uvx --from git+https://github.com/lukasmki/mol-mcp mol-mcp serve --help

or install it to use it anywhere

uv tool install --from git+https://github.com/lukasmki/mol-mcp
mol-mcp serve --help

Easy Install with uvx: MCP-JSON Supporting Clients

Add the server into your MCP config:

{
    "mcpServers": {
        "MolMCP": {
            "command": "uvx",
            "args": [
                "-from",
                "git+https://github.com/lukasmki/mol-mcp",
                "mol-mcp",
                "serve",
                "smiles",
                "geometry",
            ]
        }
    }
}

On Windows with WSL2,

{
    "mcpServers": {
        "MolMCP": {
            "command": "wsl",
            "args": [
                "--shell_type",
                "login",
                "uvx",
                "-from",
                "git+https://github.com/lukasmki/mol-mcp",
                "mol-mcp",
                "serve",
                "smiles",
                "geometry",
            ]
        }
    }
}

Development Install

Clone the repository.

{
    "mcpServers": {
        "MolMCP": {
            "command": "uv",
            "args": [
                "run",
                "--project",
                "/path/to/mol-mcp",
                "mol-mcp",
                "serve",
                "smiles",
                "geometry",
            ]
        }
    }
}

On Windows with WSL2,

{
    "mcpServers": {
        "MolMCP": {
            "command": "wsl",
            "args": [
                "--shell_type",
                "login",
                "uv",
                "run",
                "--project",
                "/path/to/mol-mcp",
                "mol-mcp"
                "serve",
                "smiles",
                "geometry",
            ]
        }
    }
}

Contributing

Contributions are welcome! Please open issues or submit pull requests for bug fixes, new features, or improvements.

License

This project is licensed under the MIT License.