Installation

Requirements

mcp_pykingenie requires Python 3.11 or later. The MCP server depends on pykingenie and FastMCP, plus the scientific Python stack used for surface-based binding kinetics analysis. The server is intended only for surface-based binding data, such as Octet and Gator BLI experiments.

Run with uvx

Run the server directly with uvx:

uvx mcp_pykingenie

By default, generated plots and imported relative-path data are stored in a date-stamped folder under ~/user_data_mcp_pykingenie/<YYYY-MM-DD>/. To choose a different results folder, set RESULTS_DIR before starting the server. Use the print_data_dir MCP tool to inspect the active output folder.

RESULTS_DIR=~/Documents/user_data_mcp_pykingenie uvx mcp_pykingenie

Install from PyPI

Install the package with pip:

pip install --user mcp_pykingenie

Then run the server with:

mcp_pykingenie

If your shell cannot find the command, make sure your user-level Python scripts directory is on PATH.

You can use the same output-folder setting when running the installed command:

RESULTS_DIR=~/Documents/user_data_mcp_pykingenie mcp_pykingenie

Install from Source

Clone the repository and install the development environment with uv:

git clone https://github.com/osvalB/mcp_pykingenie.git
cd mcp_pykingenie
uv sync --extra dev --extra doc --extra test

Run Tests

Verify the development installation by running the test suite:

uv run pytest

Build Documentation

Create the local documentation build with:

uv run --extra doc make -C docs html

The generated HTML documentation is written to docs/_build/html/.