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

Related MCP server: PubChem MCP Server

Requirements

• Python 3.13+

• Chemspace API key

Installation

Prerequisites

Install uv:

# 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:

   export CHEMSPACE_API_KEY="your-api-key-here"

3. Install dependencies and run:

   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:

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:

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.