CDK Web Application

A web-based cheminformatics toolkit using the Chemistry Development Kit (CDK) for molecular visualization and chemical descriptor calculations.

Overview

This application provides a modern web interface for analyzing chemical molecules using the Chemistry Development Kit (CDK). It allows users to:

• Parse molecules from SMILES notation
• Generate 2D molecular visualizations
• Calculate chemical descriptors
• Organize descriptors into meaningful categories
• View and analyze molecular properties

Architecture

Backend

• Spring Boot: Java-based REST API
• CDK Library: Chemistry Development Kit for cheminformatics functions
• Maven: Build tool and dependency management

Frontend

• React: UI framework
• Bootstrap: CSS framework for responsive design
• Tailwind CSS: Utility-first CSS framework
• Axios: HTTP client for API communication

Deployment Options

There are multiple ways to deploy and run this application:

Option 1: Docker Deployment (Recommended)

Prerequisites

• Docker and Docker Compose installed
• Docker Desktop running (for macOS and Windows)

Setup and Start

1. Clone the repository

   git clone https://github.com/yourusername/CDK-iwomi-demo.git
   cd CDK-iwomi-demo

2. Start the application with Docker Compose

   docker-compose up

   To run in detached mode:

   docker-compose up -d

3. To rebuild containers after code changes:

   docker-compose down
   docker-compose up --build

Accessing the Application

• Frontend UI: http://localhost:3000
• Backend API: http://localhost:8080/api/molecules/health

Environment Configuration

The frontend communicates with the backend using the environment variable REACT_APP_BACKEND_URL, which is set to http://localhost:8080 in the Docker configuration.

Troubleshooting Docker Issues

If you encounter connection issues between frontend and backend:

1. Run the diagnostic script for detailed diagnostics:

   ./debug-docker-network.sh

2. Common issues and solutions:

   • Docker daemon not running: Start Docker Desktop
   • Container startup errors: Check logs with docker logs cdk-backend or docker logs cdk-frontend
   • Network connectivity: Make sure both containers are running on the same network
   • API errors: Check if backend API is accessible at /api/molecules/health endpoint

3. Restart application with cleaned environment:

   ./restart-app.sh

Option 2: Local Development Setup

Prerequisites

• Java 11 or higher
• Maven 3.6+
• Node.js 16+ and npm
• Git

Starting the Backend

1. Navigate to the backend directory:

   cd backend/cdk-webapp-backend

2. Build and run the Spring Boot application:

   # If Maven is installed
   mvn clean spring-boot:run
   
   # Or using Maven wrapper
   ./mvnw clean spring-boot:run

3. The backend server will start at http://localhost:8080.

Starting the Frontend

1. Navigate to the frontend directory:

   cd frontend/cdk-webapp-frontend

2. Install dependencies:

   npm install

3. Start the development server:

   npm start

4. The frontend development server will start at http://localhost:3000.

API Documentation

Core Endpoints

• GET /api/molecules/health: Check API health status
• POST /api/molecules/parse: Parse a molecule from SMILES notation

  {
    "smiles": "CC(=O)OC1=CC=CC=C1C(=O)O"
  }

• GET /api/molecules/descriptors: Get all available chemical descriptors
• GET /api/molecules/image?smiles={SMILES}: Generate a PNG image of a molecule

Development

Project Structure

cdk-webapp/
├── backend/                # Spring Boot application
│   └── cdk-webapp-backend/
│       ├── src/main/java/  # Java source code
│       ├── pom.xml         # Maven configuration
│       └── mvnw            # Maven wrapper
└── frontend/               # React application
    └── cdk-webapp-frontend/
        ├── public/         # Static files
        ├── src/            # React source code
        ├── package.json    # npm dependencies
        └── tailwind.config.js # Tailwind CSS config

Building for Production

Backend

cd backend/cdk-webapp-backend
mvn clean package

Frontend

cd frontend/cdk-webapp-frontend
npm run build

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• Chemistry Development Kit - The open-source cheminformatics toolkit