MoleculeX 🧬# MoleculeX 🧬

AI-powered pharmaceutical intelligence platform for discovering clinical trials, analyzing patent landscapes, and exploring scientific literature.AI-Driven Pharmaceutical Insight Discovery Platform

---MoleculeX is a sophisticated web application that leverages multi-agent AI systems to analyze pharmaceutical opportunities, clinical trials, patents, and market intelligence. Built with FastAPI and React, it provides real-time analysis with beautiful animations and downloadable PDF reports.

🚀 Quick Start---

Backend## 🎯 Features

cd backend- **Multi-Agent Analysis**: Master agent orchestrates specialized workers (Clinical Trials, Patent, Web Intelligence)

python -m venv venv- **Real-Time Updates**: WebSocket-powered live progress tracking

venv\Scripts\activate  # Windows: venv\Scripts\activate | Mac/Linux: source venv/bin/activate- **Clinical Trial Data**: Live integration with ClinicalTrials.gov API

pip install -r requirements.txt- **Beautiful UI**: Smooth Framer Motion animations with TailwindCSS styling

uvicorn main:app --reload- **PDF Reports**: Comprehensive analysis reports with professional formatting

```- **No Database Required**: Simple JSON file-based job storage

Backend runs at: **http://localhost:8000**  - **No Docker Required**: Easy local setup and deployment

API docs: **http://localhost:8000/docs**

---

### Frontend

```bash## 🏗️ Architecture

cd frontend

npm install### Backend (FastAPI)

npm run dev```

```backend/

Frontend runs at: **http://localhost:5173**├── main.py                 # FastAPI app entry point

├── routes.py              # API endpoints

---├── models.py              # Pydantic data models

├── job_manager.py         # Job lifecycle management

## ✨ Features├── master_agent.py        # Master orchestrator

├── websocket_manager.py   # WebSocket connection handler

- 🔬 **Clinical Trials Search** - Live ClinicalTrials.gov integration├── report_generator.py    # PDF generation

- 📄 **Patent Analysis** - Patent landscape insights├── agents/

- 🌐 **Web Intelligence** - Scientific literature analysis│   ├── clinical_trials_agent.py  # ClinicalTrials.gov integration

- 📊 **Real-time Updates** - WebSocket-powered progress tracking│   ├── patent_agent.py           # Patent search (placeholder)

- 📈 **PDF Reports** - Professional analysis reports│   └── web_intel_agent.py        # Web intelligence (placeholder)

- 🎨 **Beautiful UI** - Smooth animations with Framer Motion├── templates/

│   └── report_template.html      # Jinja2 PDF template

---└── data/

    ├── jobs/              # Job state (JSON files)

## 🏗️ Project Structure    └── reports/           # Generated PDF reports


moleculeX/### Frontend (React + Vite)

├── backend/              # FastAPI backend```

│   ├── main.py          # Application entryfrontend/

│   ├── agents/          # Specialized agents├── src/

│   ├── data/            # Jobs & reports│   ├── App.jsx                    # Main application

│   └── templates/       # PDF templates│   ├── components/

└── frontend/            # React frontend│   │   ├── QueryCard.jsx         # Query input with examples

    └── src/│   │   ├── AgentStatusRow.jsx    # Agent progress chips

        ├── components/  # UI components│   │   ├── ResultsPanel.jsx      # Results display

        ├── api/         # API client│   │   └── ReportDownload.jsx    # PDF download button

        └── App.jsx      # Main app│   ├── api/

```│   │   └── client.js             # Axios API client

│   └── hooks/

---│       └── useWebSocket.js       # WebSocket hook

├── index.html

## 📖 Usage├── vite.config.js

├── tailwind.config.js

1. **Enter Query**: Type your pharmaceutical research question└── package.json

2. **Watch Progress**: Real-time agent status updates```

3. **Review Results**: Interactive results with detailed insights

4. **Download Report**: Get professionally formatted PDF---



### Example Queries## 🚀 Quick Start

- "Which respiratory diseases show low competition but high patient burden in India?"

- "What are emerging opportunities in cardiovascular drug development?"### Prerequisites

- "Find unmet medical needs in oncology with recent patent activity"- Python 3.9+

- Node.js 18+

---- npm or yarn



## 🔌 Key API Endpoints### Backend Setup



```http1. **Navigate to backend directory:**

POST /api/query          # Submit new query   ```bash

GET  /api/status/{id}    # Get job status   cd backend

GET  /api/result/{id}    # Get results   ```

WS   /ws/jobs/{id}       # Real-time updates

GET  /api/reports/{id}   # Download PDF2. **Create virtual environment:**

```   ```bash

   python -m venv venv

Full API documentation: **http://localhost:8000/docs**   ```



---3. **Activate virtual environment:**

   - Windows:

## 🛠️ Tech Stack     ```cmd

     venv\Scripts\activate

- **Backend**: FastAPI, Python 3.11, WebSockets     ```

- **Frontend**: React 18, Vite 5, TailwindCSS 3, Framer Motion   - Mac/Linux:

- **APIs**: ClinicalTrials.gov     ```bash

- **Storage**: JSON-based job storage     source venv/bin/activate

     ```

---

4. **Install dependencies:**

## 🐛 Troubleshooting   ```bash

   pip install -r requirements.txt

**Port already in use:**   ```

```bash

# Windows5. **Run the FastAPI server:**

netstat -ano | findstr :8000   ```bash

taskkill /PID <PID> /F   python main.py

Mac/Linux

lsof -ti:8000 | xargs kill -9 The API will be available at http://localhost:8000

``` - API docs: http://localhost:8000/docs

Health check: http://localhost:8000/

Module not found:


# Activate venv and reinstall

pip install -r requirements.txt1. **Navigate to frontend directory:**

```   ```bash

   cd frontend

**WebSocket issues:**   ```

- Ensure backend is running on port 8000

- Check browser console for errors2. **Install dependencies:**

   ```bash

---   npm install

📝 License

Run the development server:

npm run dev

--- ```

Built for pharmaceutical researchers with ❤️ The app will be available at http://localhost:5173

📖 Usage

1. Enter Your Query

Type a pharmaceutical research question, such as:

"Which respiratory diseases show low competition but high patient burden in India?"
"What are the emerging opportunities in cardiovascular drug development in Asia?"
"Find unmet medical needs in oncology with recent patent activity"

2. Watch Agent Progress

Real-time status updates show each agent's progress:

🎯 Master Agent: Query analysis and orchestration
🔬 Clinical Trials Agent: Fetching live data from ClinicalTrials.gov
📄 Patent Agent: Patent landscape analysis
🌐 Web Intel Agent: Market intelligence gathering

3. Review Results

Interactive results panel with:

Executive summary
Key findings
Clinical trials table
Patent landscape
Web intelligence sources

4. Download Report

Get a professionally formatted PDF report with all findings.

🔌 API Endpoints

Query Submission

POST /api/query
Content-Type: application/json

{
  "query": "Your pharmaceutical research question"
}

Response: {
  "job_id": "uuid",
  "status": "queued",
  "message": "Query submitted successfully",
  "created_at": "2024-01-01T00:00:00"
}

Job Status

GET /api/status/{job_id}

Response: {
  "job_id": "uuid",
  "status": "running",
  "query": "...",
  "agents": [...],
  "progress": 45,
  "created_at": "...",
  "updated_at": "..."
}

Job Results

GET /api/result/{job_id}

Response: {
  "job_id": "uuid",
  "query": "...",
  "executive_summary": "...",
  "key_findings": [...],
  "clinical_trials": [...],
  "patents": [...],
  "web_intel": [...],
  "report_url": "/api/reports/job_{id}.pdf"
}

WebSocket

ws://localhost:8000/ws/jobs/{job_id}

Messages: {
  "job_id": "uuid",
  "event_type": "agent_update",
  "data": {...},
  "timestamp": "..."
}

Download Report

GET /api/reports/job_{job_id}.pdf

🎨 UI Components

QueryCard

Large textarea for query input
4 example queries with click-to-fill
Animated submit button with loading state

AgentStatusRow

4 agent status chips with icons
Color-coded status (idle/running/completed/failed)
Pulse animation for running agents
Result count display

ResultsPanel

Slide-in animation from right
Collapsible sections
Interactive data tables
Color-coded trial statuses

ReportDownload

Pulsing download button
Animated PDF icon
One-click report download

🔧 Configuration

Backend Configuration

Edit backend/main.py:

# CORS origins
allow_origins=["http://localhost:5173", "http://localhost:3000"]

# Server port
uvicorn.run("main:app", host="0.0.0.0", port=8000)

Frontend Configuration

Edit frontend/vite.config.js:

server: {
  port: 5173,
  proxy: {
    '/api': 'http://localhost:8000',
    '/ws': 'ws://localhost:8000'
  }
}

🧪 Testing Example Queries

Competition Analysis:

Which respiratory diseases show low competition but high patient burden in India?

Opportunity Detection:

What are the emerging opportunities in cardiovascular drug development?

Clinical Trial Analysis:

Show me clinical trials for diabetes treatments with less than 5 active competitors

Market Research:

Find unmet medical needs in oncology with recent patent activity

📊 Data Sources

Phase 1 (Current)

✅ ClinicalTrials.gov API: Live clinical trial data (no API key required)
🔄 Patent Agent: Placeholder with dummy data
🔄 Web Intel Agent: Placeholder with dummy data

Future Enhancements

🔮 USPTO Patent API integration
🔮 PubMed/NIH research paper analysis
🔮 WHO disease burden statistics
🔮 FDA drug approval databases

🐛 Troubleshooting

Backend Issues

"Module not found" error:

# Ensure virtual environment is activated
# Then reinstall dependencies
pip install -r requirements.txt

"Port 8000 already in use":

# Find and kill the process
# Windows:
netstat -ano | findstr :8000
taskkill /PID <PID> /F

# Mac/Linux:
lsof -ti:8000 | xargs kill -9

PDF generation fails:

# Install WeasyPrint dependencies (Windows)
# WeasyPrint requires GTK3
# Fallback to xhtml2pdf will be used automatically

Frontend Issues

"npm install" fails:

# Clear npm cache
npm cache clean --force
# Delete node_modules and package-lock.json
rm -rf node_modules package-lock.json
# Reinstall
npm install

WebSocket connection fails:

Ensure backend is running on port 8000
Check browser console for CORS errors
Verify WebSocket URL in useWebSocket.js

🚢 Deployment

Backend Deployment

# Production server
pip install gunicorn
gunicorn main:app -w 4 -k uvicorn.workers.UvicornWorker --bind 0.0.0.0:8000

Frontend Deployment

# Build for production
npm run build

# Serve static files
npm install -g serve
serve -s dist -p 5173

📝 License

MIT License - feel free to use this for your pharmaceutical research projects!

🤝 Contributing

Contributions welcome! Areas for improvement:

Additional worker agents (Patent API, PubMed integration)
Enhanced NLP for query parsing
Database integration for job persistence
User authentication and history
Export to multiple formats (Excel, CSV)
Advanced data visualization charts

📧 Support

For issues and questions:

Open an issue on GitHub
Check API documentation at /docs
Review logs in backend console

Built with ❤️ for pharmaceutical researchers

MoleculeX - Discovering pharmaceutical insights through AI-powered multi-agent analysis

Name		Name	Last commit message	Last commit date
Latest commit History 14 Commits
backend		backend
data		data
frontend		frontend
.gitignore		.gitignore
DESIGN_README.md		DESIGN_README.md
ENHANCED_DESIGN.md		ENHANCED_DESIGN.md
FIXES_APPLIED.md		FIXES_APPLIED.md
FRONTEND_REDESIGN.md		FRONTEND_REDESIGN.md
GEMINI_SETUP.md		GEMINI_SETUP.md
MULTI_SOURCE_APIS.md		MULTI_SOURCE_APIS.md
README.md		README.md
render.yaml		render.yaml

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MoleculeX 🧬# MoleculeX 🧬

🚀 Quick Start---

Backend## 🎯 Features

Mac/Linux

📝 License

📖 Usage

1. Enter Your Query

2. Watch Agent Progress

3. Review Results

4. Download Report

🔌 API Endpoints

Query Submission

Job Status

Job Results

WebSocket

Download Report

🎨 UI Components

QueryCard

AgentStatusRow

ResultsPanel

ReportDownload

🔧 Configuration

Backend Configuration

Frontend Configuration

🧪 Testing Example Queries

📊 Data Sources

Phase 1 (Current)

Future Enhancements

🐛 Troubleshooting

Backend Issues

Frontend Issues

🚢 Deployment

Backend Deployment

Frontend Deployment

📝 License

🤝 Contributing

📧 Support

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