README_MODULAR.md

HITL Drug Discovery - Modular Architecture

🏗️ Project Structure

HITL_Drug_Discovery/
├── main.py                 # Main entry point
├── app.py                  # Legacy monolithic app (backup)
├── requirements.txt        # Dependencies
├── README.md              # Original README
├── README_MODULAR.md      # This file
└── src/                   # Modular source code
    ├── __init__.py
    ├── app.py             # Main application orchestrator
    ├── molecules/         # Molecular analysis and variations
    │   ├── __init__.py
    │   ├── analysis.py    # Molecular property calculations
    │   └── variations.py  # Structure variation generation
    ├── ai/                # AI services
    │   ├── __init__.py
    │   └── services.py    # AI chat and structure generation
    ├── ui/                # UI components and handlers
    │   ├── __init__.py
    │   ├── components.py  # UI component definitions
    │   └── handlers.py    # Event handlers and business logic
    └── config/            # Configuration and settings
        ├── __init__.py
        └── settings.py    # App configuration and constants

🚀 Running the Application

Option 1: Modular Version (Recommended)

python main.py

Option 2: Legacy Monolithic Version

python app.py

📁 Module Descriptions

src/molecules/

• analysis.py: Molecular property calculations, SMILES validation, drug-likeness assessment
• variations.py: Generation of multiple molecular structure visualizations

src/ai/

• services.py: AI-powered chat responses and structure generation using OpenAI GPT-OSS-20B

src/ui/

• components.py: Reusable UI component definitions for Gradio interface
• handlers.py: Event handlers, business logic, and state management

src/config/

• settings.py: Application configuration, constants, and styling

src/app.py

• Main orchestrator: Ties all modules together and creates the Gradio interface

🔧 Benefits of Modular Architecture

1. Maintainability: Each module has a single responsibility
2. Testability: Individual modules can be tested in isolation
3. Scalability: Easy to add new features without affecting existing code
4. Readability: Clear separation of concerns
5. Reusability: Components can be reused across different parts of the app
6. Professional: Industry-standard project structure

🧪 Key Features

• Molecular Analysis: SMILES validation, property calculations, drug-likeness assessment
• Chemical Variations: Multiple visualization styles and rendering options
• AI Structure Generation: AI-powered molecular structure suggestions
• Interactive UI: Clean, modern interface with real-time feedback
• Bookmarking: Save and manage favorite molecular structures

🔄 Migration from Monolithic

The original app.py (1082 lines) has been refactored into:

• 6 focused modules with clear responsibilities
• ~200 lines per module for better maintainability
• Clean imports and dependencies
• Preserved functionality with improved organization

🚀 Future Enhancements

With the modular structure, it's now easy to:

• Add new molecular analysis algorithms
• Implement additional AI models
• Create new UI components
• Add database integration
• Implement user authentication
• Add API endpoints
• Create unit tests for each module