Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@Mol-MCP generate 3D coordinates for ethanol (CCO)"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
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.
Modular agent and tool system
Extensible via configuration and plugins
Designed for quantum chemistry and molecular computation
Related MCP server: ChemMCP
src/
molmcp/ # Main package
agents/ # Agent servers
tools/ # Tool servers
tests/ # Test suite
pyproject.toml # Project metadata and dependencies
README.md # Project documentationuvx --from git+https://github.com/lukasmki/mol-mcp mol-mcp serve --helpTo use the built-in interactive agent with mol-mcp tools,
uv run mol-mcp goCurrently, 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.
Install uv
# macOS
brew install uv
# Linux/WSL2
curl -LsSf https://astral.sh/uv/install.sh | shThe calc and geometry servers depend on tblite and require a Fortran compiler to complete installation.
# macOS
brew install gfortran
# Linux/WSL2
sudo apt install gfortranIn your project directory, install with uv
uv add git+https://github.com/lukasmki/mol-mcpor
uv pip install git+https://github.com/lukasmki/mol-mcpYou can also run it as a uv tool outside of a project!
uvx --from git+https://github.com/lukasmki/mol-mcp mol-mcp serve --helpor install it to use it anywhere
uv tool install --from git+https://github.com/lukasmki/mol-mcp
mol-mcp serve --helpuvx: MCP-JSON Supporting ClientsAdd 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",
]
}
}
}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",
]
}
}
}Contributions are welcome! Please open issues or submit pull requests for bug fixes, new features, or improvements.
This project is licensed under the MIT License.
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