🧪 Catalyze - AI-Powered Chemistry Assistant

A beautiful, fully-functional AI chemistry assistant for material science and chemistry research.

✨ Features

• 🔬 Research Mode: Ask chemistry questions and get detailed explanations
• 📋 Protocol Generation: Generate step-by-step lab protocols
• 🤖 Lab Automation: Create Python scripts for Opentrons, PyHamilton
• 🛡️ Safety Analysis: Get safety information and hazard warnings
• 📊 Data Visualization: Advanced charts and graphs with offline capability
• 🧮 Calculators: Molarity, pH, reaction yield calculators
• 📝 Notes: Take and save research notes
• 📤 Export: Export protocols and data in multiple formats
• 🌙 Dark Mode: Beautiful dark/light theme toggle
• 💜 Purple Gradient Theme: Scientist-friendly UI design

🚀 Quick Start

Option 1: Simple Start

./start_catalyze.sh

Option 2: Manual Start

# Activate virtual environment
source venv/bin/activate

# Start the app
python app/flask_app.py

Then open: http://localhost:5003

Option 3: With ChEMBL MCP Server (Advanced)

# Initialize submodules (first time only)
./manage_submodules.sh init

# Install Node.js dependencies
./manage_submodules.sh install

# Start the app
source venv/bin/activate && python app/flask_app.py

📁 Project Structure

mit-catalyze/
├── app/
│   └── flask_app.py        # Main Flask backend
├── react-build/
│   └── index.html          # Beautiful frontend (HTML/CSS/JS)
├── mcp_servers/
│   └── chembl-mcp-server/  # ChEMBL MCP Server (Git submodule)
├── src/
│   ├── clients/            # API clients (LLM, PubChem)
│   ├── generators/          # Protocol & automation generators
│   ├── config/             # Configuration files
│   └── pipeline.py          # Main processing pipeline
├── venv/                   # Python virtual environment
├── pyproject.toml          # Python dependencies
├── start_catalyze.sh       # Simple startup script
├── manage_submodules.sh     # Submodule management script
├── .gitmodules             # Git submodule configuration
└── README.md               # This file

🎯 What Makes This Special

• Single HTML File: Everything runs from one beautiful react-build/index.html
• No React Build Process: Pure HTML/CSS/JavaScript - fast and simple
• Fully Functional: All features work perfectly without internet
• Beautiful UI: Purple gradient theme with smooth animations
• Clean Codebase: Minimal, focused, and maintainable
• 🧪 ChEMBL Integration: Access to 27 specialized chemistry tools via MCP
• 🤖 Hybrid AI: Combines OpenAI knowledge with ChEMBL database accuracy

🧪 ChEMBL MCP Server Integration

This project integrates with the ChEMBL MCP Server to provide access to 27 specialized chemistry tools:

Core Features

• Compound Search: Search ChEMBL database by name, synonym, or identifier
• Target Analysis: Search biological targets and get detailed information
• Bioactivity Data: Access bioactivity measurements and assay results
• Drug Development: Search approved drugs and clinical candidates
• Chemical Properties: Analyze ADMET properties and drug-likeness

How It Works

1. Smart Routing: Chemistry questions automatically trigger ChEMBL integration
2. Hybrid Approach: OpenAI provides main answers, ChEMBL enhances with database data
3. Graceful Fallback: If ChEMBL fails, you still get OpenAI responses
4. Detailed Logging: Track system behavior with comprehensive logs

Submodule Management

# Check submodule status
./manage_submodules.sh status

# Update to latest version
./manage_submodules.sh update

# Reinstall dependencies
./manage_submodules.sh install

🔧 Dependencies

• Python: All dependencies in pyproject.toml and installed in venv/
• Node.js: Required for ChEMBL MCP Server (installed via submodule)

🌐 Access

• Local: http://localhost:5003
• Network: http://[your-ip]:5003

📱 Features Overview

1. Chat Interface: Ask chemistry questions with Research/Protocol/Automate/Safety modes
2. Chat History: Create named chats, manage conversation history
3. Capabilities Display: See what Catalyze can do
4. Results Tabs: Calculator, Notes, Data Visualizer, Export
5. Dark Mode: Toggle between light and dark themes
6. Responsive Design: Works on desktop and mobile

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Built for MIT Hackathon 2025 🎓