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by modelcontextprotocol
by gpu-bridge
by hamflx
RDKit Chemical Informatics Server
FreeMaintained# MCP RDKit Project ## Overview The `mcp_rdkit` project integrates the RDKit library with the MCP (Model Context Protocol) framework to provide advanced chemica
About
MCP RDKit Project ## Overview The mcp_rdkit project integrates the RDKit library with the MCP (Model Context Protocol) framework to provide advanced chemical informatics tools. It includes functionalities for molecular visualization, descriptor calculation, and interaction with an MCP server. ## Features - Molecular Visualization: Generate images of molecules using RDKit. - Descriptor Calculation: Compute molecular descriptors such as molecular weight, logP, and more. - MCP Server Integration: Communicate with an MCP server for advanced chemical informatics tasks. ## Project Structure - mcp_rdkit/ - __main__.py: Entry point for the application. It initializes the MCP server and runs it in "stdio" mode. - rdkit_helper.py: Contains helper functions for RDKit operations, including: - Converting PIL images to base64. - Interfacing with the MCP server. - Utilizing RDKit for chemical computations. - setup.py: Configuration for packaging and distribution. ## Requirements - Python 3.8 or higher - RDKit library - MCP framework ## Installation 1. Install the package using pip: bash pip install mcp-rdkit 2. Run the application: bash python -m mcp_rdkit ## Demo You can integrate this directly into Claude App: 
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## Usage - Run the MCP server: The application starts an MCP server that can process chemical informatics tasks. - Generate molecular images: Use the RDKit helper functions to visualize molecules. - Calculate descriptors: Leverage RDKit's descriptor calculation tools for chemical analysis. ## MCP Configuration Example To use the RDKit server with MCP, add the following configuration to your mcp config file: json "rdkit-server": { "type": "stdio", "command": "python", "args": [ "-m", "mcp_rdkit" ] }
README
Smithery CLI connects your agents to thousands of skills and MCP servers directly from the command line. To get started, simply run npx skills add smithery/cli.
Installation
npm install -g smithery@latest
Requires Node.js 20+.
Commands
MCP Servers
smithery mcp search [term] # Search the Smithery registry
smithery mcp add <url> # Add an MCP server connection
smithery mcp list # List your connections
smithery mcp remove <ids...> # Remove connections
Tools
Interact with tools from MCP servers connected via smithery mcp.
smithery tool list [connection] # List tools from your connected MCP servers
smithery tool find [query] # Search tools by name or intent
smithery tool get <connection> <tool> # Show full details for one tool
smithery tool call <connection> <tool> [args] # Call a tool
Skills
Browse skills on the Smithery Skills Registry and install them with the upstream installer:
npx skills add <skill> # e.g. npx skills add smithery-ai/cli
Auth
smithery auth login # Login with Smithery (OAuth)
smithery auth logout # Log out
smithery auth whoami # Check current user
smithery auth token # Mint a service token
smithery auth token --policy '<json>' # Mint a restricted token
Namespaces
smithery namespace list # List your namespaces
smithery namespace use <name> # Set current namespace
Publishing
smithery mcp publish <url> -n <org/server> # Publish an MCP server URL
smithery mcp publish <bundle.mcpb> -n <org/server> # Publish an MCP bundle
Examples
# Search and connect to an MCP server
smithery mcp search "github"
smithery mcp add github --id github
# Find and call tools from your connected MCP servers
smithery tool find "create issue"
smithery tool call github create_issue '{"title":"Bug fix","body":"..."}'
# Browse and install skills
smithery skill search "frontend" --json --page 2
smithery skill add anthropics/frontend-design --agent claude-code
# Publish your MCP server URL
smithery mcp publish https://my-mcp-server.com -n myorg/my-server
# Publish a built MCP bundle
smithery mcp publish ./server.mcpb -n myorg/my-server
Development
git clone https://github.com/smithery-ai/cli
cd cli && pnpm install && pnpm run build
npx . --help
Contributing
Contributions welcome! Please submit a Pull Request.
How to install
Run in your terminal:
claude mcp add mcp-rdkit -- npx -y @smithery/cli run s20ss/mcp_rdkitRelated MCPs
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