nfdi4chem/cheminformatics-microservice repository overview

⁠Cheminformatics Microservice & UI

⁠🌐 Overview

A comprehensive cheminformatics solution consisting of:

1. Backend Microservices API that provides cheminformatics functionality through API calls:

   • Translating between different machine-readable representations
   • Calculating Natural Product (NP) likeliness scores
   • Visualizing chemical structures
   • Generating descriptors
   • Hosting instances of DECIMER⁠ for optical chemical structure recognition

2. Modern React Frontend that provides an intuitive user interface for:

   • Chemical structure analysis and validation
   • Format conversion (SMILES, InChI, IUPAC, etc.)
   • 2D and 3D molecular visualization
   • Optical Chemical Structure Recognition (OCSR)
   • Molecular property calculation

⁠📚 Documentation

⁠Backend API

Comprehensive documentation is available at: https://docs.api.naturalproducts.net/⁠

⁠API Swagger Docs

• Production: https://api.naturalproducts.net/latest/docs⁠
• Development: https://dev.api.naturalproducts.net/latest/docs⁠

⁠⚛️ Frontend Application

The frontend application provides a modern, user-friendly interface to the cheminformatics microservices.

⁠Key Features

• Chemical Analysis Tools:

  • Structure validation and standardization
  • Molecular descriptor calculation
  • Stereoisomer generation
  • Natural product likeness scoring
  • Functional group detection (Ertl)
  • Tautomer standardization
  • HOSE code generation
  • Tanimoto similarity calculation

• Format Conversion:

  • SMILES to various chemical formats (InChI, InChIKey, SELFIES, etc.)
  • IUPAC name to SMILES conversion
  • 2D/3D coordinate generation (Molblock)

• Molecule Depiction:

  • 2D molecule visualization with customizable settings
  • Interactive 3D molecule visualization
  • Batch depiction for multiple molecules

• OCSR (Optical Chemical Structure Recognition):

  • Convert chemical structure images to SMILES notation

⁠Technical Stack

• React 18: Core UI library
• React Router 6: Client-side routing
• Tailwind CSS: Utility-first styling
• Framer Motion: Enhanced UI animations
• Axios: API communication
• React Dropzone: File upload handling

⁠Frontend Architecture

• Component-Based Design: Modular components for reusability and maintainability
• Service Layer: Specialized services for API interaction
• Context API: Global state management for theme, recent molecules, etc.
• Responsive Design: Mobile-first approach with responsive layouts
• Dark/Light Theme: Full theme support with Tailwind dark mode

⁠Installation & Setup (Frontend)

# Clone the repository
git clone https://github.com/Steinbeck-Lab/cheminformatics-microservice.git
cd cheminformatics-microservice/frontend

# Install dependencies
npm install

# Start development server
npm start

# Build for production
npm run build

For detailed frontend configuration options, see the Frontend Documentation⁠.

⁠💻 Backend Installation

You can run Cheminformatics Microservice in multiple ways:

1. As a standalone application using a Python virtual environment
2. Via Docker
3. Deploy to a Kubernetes cluster using Helm charts⁠

For detailed instructions, please refer to:

• Docker Installation Guide⁠
• Kubernetes Cluster Deployment Guide⁠
• Standalone Installation Guide⁠

⁠📈 Load Ramping Test Results

View the latest load ramping test results from September 29, 2023: Test Results Discussion⁠

⁠📜 License

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

⁠📰 Citation

⁠Paper

Chandrasekhar, V., Sharma, N., Schaub, J. et al. Cheminformatics Microservice: unifying access to open cheminformatics toolkits. J Cheminform 15, 98 (2023). https://doi.org/10.1186/s13321-023-00762-4⁠

⁠Software

Venkata, C., Sharma, N., & Rajan, K. (2023). Cheminformatics Microservice (Version v2.6.0) [Computer software]. https://zenodo.org/records/13867839⁠

⁠🔧 Maintenance

Cheminformatics Microservice and Natural Products Online⁠ are developed and maintained by the Steinbeck group⁠ at the 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 National Research Data Infrastructure – NFDI4Chem⁠ – Project number: 441958208 and ChemBioSys⁠ (Project I