Smiles TO iUpac Translator Web Application

About • Deployment • License • Citation • Maintenance • Acknowledgments

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About

STOUT (Smiles TO iUpac Translator) Web Application

This repository contains the code running on stout.decimer.ai

🧪 STOUT-V2 is a powerful tool that can:

• Translate SMILES to IUPAC names
• Convert IUPAC names back to valid SMILES strings

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Deployment 🚀

Prerequisites

• Docker
• Docker Compose
• Git

Local Deployment Steps

1. Clone the repository

git clone https://github.com/Kohulan/STOUT_WebApp.git
cd STOUT_WebApp

2. Build and start the containers

docker-compose up -d --build

Accessing the Application

Once the containers are running, you can access:

• Frontend: http://localhost:80
• Backend API: http://localhost:3000
• API Documentation: http://localhost:3000/docs

Container Structure

The application runs two main containers:

• frontend: Vue.js application served by Nginx (Port 80)
• backend: FastAPI application running with uvicorn (Port 3000)

Managing the Application

To stop the containers:

docker-compose down

Troubleshooting

If you encounter any issues:

1. Check container status:

docker-compose ps

2. View container logs:

# All containers
docker-compose logs

# Specific container
docker-compose logs frontend
docker-compose logs backend

3. Common issues:
   • Port conflicts: Ensure ports 80 and 3000 are available
   • Network issues: Check if the stout-network is created properly
   • Build errors: Make sure all dependencies are properly listed in requirements.txt and package.json

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Training Details 🧠

STOUT V2 uses a transformer-based sequence-to-sequence model

Training tutorial could be found here: STOUT Training

Hardware Requirements

Minimum Requirements (Inference)

• CPU: 4 cores
• RAM: 8GB
• Storage: 5GB

Recommended Requirements (Training)

• TPU v3-8 or equivalent
• High-speed internet connection for dataset downloads

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License 📜

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

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Citation 📰

Software:

Rajan, K., Zielesny, A., & Steinbeck, C. (2024). STOUT_WebApp (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.1234

Paper

Rajan, K., Zielesny, A. & Steinbeck, C. STOUT V2.0: SMILES to IUPAC name conversion using transformer models. J Cheminform 16, 146 (2024). https://doi.org/10.1186/s13321-024-00941-x

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Maintenance 🔧

🔬 STOUT and DECIMER are developed and maintained by Kohulan Rajan at the Steinbeck group, Friedrich Schiller University Jena, Germany.

The code for this web application is released under the MIT license. Copyright © CC-BY-SA 2023

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Acknowledgments 💡

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the ChemBioSys (Project INF) - Project number: 239748522 - SFB 1127.

Research supported with Cloud TPUs from Google's TPU Research Cloud (TRC)

Made with ❤️ by the Steinbeck Group