Chemspace MCP Server

# chemspace-mcp A Model Context Protocol (MCP) server that provides a wrapper for the Chemspace API, enabling AI agents to search for synthesizable building blocks and screening compounds through exact, substructure, and similarity searches. ## Features - **Exact Search**: Find exact molecular matches by SMILES - **Substructure Search**: Find compounds containing a specific substructure - **Similarity Search**: Find structurally similar compounds by SMILES - **Multiple Product Categories**: Search across in-stock and make-on-demand compounds - **Global Shipping**: Specify shipping countries with ISO country codes ## Requirements - Python 3.13+ - Chemspace API key ## Installation ### Prerequisites Install `uv`: ```sh # macOS brew install uv # Linux/WSL2 curl -LsSf https://astral.sh/uv/install.sh | sh ``` ### Setup 1. Clone the repository and navigate to the project directory 2. Set your Chemspace API key as an environment variable: ```bash export CHEMSPACE_API_KEY="your-api-key-here" ``` 3. Install dependencies and run: ```bash uv run chemspace-mcp ``` ## Configuration ### For use with FastAgent Configure `example/fastagent.secrets.yaml`. Environment variables set here will override the ones in your shell: ```yaml anthropic: api_key: your-anthropic-api-key mcp: servers: chemspace: env: CHEMSPACE_API_KEY: your-chemspace-api-key ``` Then run the example interface with FastAgent: ```bash cd example uv run --extra agent agent.py ``` ## Usage The MCP server exposes the following tools: ### search_exact Searches for exact molecular matches by SMILES string. **Parameters:** - `smiles` (string): The SMILES string to search for - `shipToCountry` (string): Two-letter ISO country code (default: "US") - `count` (integer): Maximum results per page (default: 10) - `page` (integer): Page number for pagination (default: 1) - `categories` (list): Product categories to search: - `CSSB`: In-stock building blocks - `CSSS`: In-stock screening compounds - `CSMB`: Make-on-demand building blocks - `CSMS`: Make-on-demand screening compounds - `CSCS`: Custom requests ### search_substructure Searches for compounds containing a specific substructure. **Parameters:** Same as `search_exact` ### search_similarity Searches for structurally similar compounds. **Parameters:** Same as `search_exact` ## Project Structure ``` chemspace-mcp/ ├── src/ │ └── chemspace_mcp/ │ ├── __init__.py # Entry point and MCP server initialization │ ├── tools.py # Tool definitions for chemical searches │ └── tokenmanager.py # Token management for API authentication ├── example/ │ ├── agent.py # Example FastAgent integration │ ├── fastagent.config.yaml # FastAgent configuration │ └── fastagent.secrets.yaml # Secrets configuration (not in version control) ├── pyproject.toml # Project metadata and dependencies └── README.md # This file ``` ## Development ### Dependencies - `fastmcp>=2.13.1`: Core MCP server framework - `fast-agent-mcp>=0.2.25`: FastAgent integration ## License MIT License ## Support For issues or questions, please open an issue on the project repository.