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<p align="center"><a href="https://api.naturalproducts.net/" target="_blank"><img src="/public/img/logo.png" width="400" alt="CMS Logo"></a></p>

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## Overview of Cheminformatics Microservice :globe_with_meridians:

This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics. Generally, it is designed to work with SMILES-based inputs and could be used to translate between different machine-readable representations, get Natural Product (NP) likeliness scores, visualize chemical structures, and generate descriptors. In addition, the microservices also host an instance of [STOUT](https://github.com/Kohulan/Smiles-TO-iUpac-Translator) and another instance of [DECIMER](https://github.com/Kohulan/DECIMER-Image_Transformer) (two deep learning models for IUPAC name generation and optical chemical structure recognition, respectively).

## Documentation :book:

https://docs.api.naturalproducts.net/
# Cheminformatics Microservice

<p align="center">
<a href="https://api.naturalproducts.net/" target="_blank">
<img src="/public/img/logo.png" width="400" alt="CMS Logo">
</a>
</p>

<p align="center">
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</p>

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<a href="https://fastapi.tiangolo.com/"><img src="https://img.shields.io/badge/Framework-FastAPI-blue?style" alt="framework"></a>
<a href="https://api.naturalproducts.net/v1/docs#/"><img src="https://img.shields.io/badge/docs-fastapi-blue" alt="FastAPI Documentation"></a>
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<a href="https://doi.org/10.5281/zenodo.7745987"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.7745987.svg" alt="DOI"></a>
</p>

## 🌐 Overview

The Cheminformatics Microservice is a set of essential and valuable services designed to support cheminformatics through API calls. It primarily works with SMILES-based inputs and offers functionalities such as:

- Translating between different machine-readable representations
- Calculating Natural Product (NP) likeliness scores
- Visualizing chemical structures
- Generating descriptors

Additionally, it hosts instances of:
- [STOUT](https://github.com/Kohulan/Smiles-TO-iUpac-Translator): A deep learning model for IUPAC name generation
- [DECIMER](https://github.com/Kohulan/DECIMER-Image_Transformer): A deep learning model for optical chemical structure recognition

## 📚 Documentation

Comprehensive documentation is available at: [https://docs.api.naturalproducts.net/](https://docs.api.naturalproducts.net/)

### API Swagger Docs

Production: https://api.naturalproducts.net/latest/docs
- Production: [https://api.naturalproducts.net/latest/docs](https://api.naturalproducts.net/latest/docs)
- Development: [https://dev.api.naturalproducts.net/latest/docs](https://dev.api.naturalproducts.net/latest/docs)

Development: https://dev.api.naturalproducts.net/latest/docs
## 💻 Installation

## Installation :computer:
You can run Cheminformatics Microservice in multiple ways:

You can run Cheminformatics Microservice as a standalone application using Python virtual environment or via Docker, or deploy to a Kubernetes cluster utilising [Helm charts](https://github.com/NFDI4Chem/repo-helm-charts/tree/main/charts). Please follow the links below for step-by-step instructions.
1. As a standalone application using a Python virtual environment
2. Via Docker
3. Deploy to a Kubernetes cluster using [Helm charts](https://github.com/NFDI4Chem/repo-helm-charts/tree/main/charts)

**Docker**
https://docs.api.naturalproducts.net/docker.html
For detailed instructions, please refer to:

**Kubernetes - Cluster deployment**
https://docs.api.naturalproducts.net/cluster-deployment.html
- [Docker Installation Guide](https://docs.api.naturalproducts.net/docker.html)
- [Kubernetes Cluster Deployment Guide](https://docs.api.naturalproducts.net/cluster-deployment.html)
- [Standalone Installation Guide](https://docs.api.naturalproducts.net/standalone.html)

**Standalone**
https://docs.api.naturalproducts.net/standalone.html
## 📈 Load Ramping Test Results

## Load ramping test results - 29 September 2023 :chart_with_upwards_trend:
https://github.com/Steinbeck-Lab/cheminformatics-microservice/discussions/413
View the latest load ramping test results from September 29, 2023: [Test Results Discussion](https://github.com/Steinbeck-Lab/cheminformatics-microservice/discussions/413)

## License :scroll:
## 📜 License

This project is licensed under the MIT License - see the [LICENSE](https://github.com/Steinbeck-Lab/cheminformatics-microservice/blob/main/LICENSE) file for details
This project is licensed under the MIT License. See the [LICENSE](https://github.com/Steinbeck-Lab/cheminformatics-microservice/blob/main/LICENSE) file for details.

## Citation :newspaper:
## 📰 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
### 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](https://doi.org/10.1186/s13321-023-00762-4)

*Software*
- Venkata, C., Sharma, N., & Rajan, K. (2023). Cheminformatics Microservice (Version v1.6.0) [Computer software]. https://doi.org/10.5281/zenodo.8336440
### Software
Venkata, C., Sharma, N., & Rajan, K. (2023). Cheminformatics Microservice (Version v1.6.0) [Computer software]. [https://doi.org/10.5281/zenodo.8336440](https://doi.org/10.5281/zenodo.8336440)

## Maintained by :wrench:
## 🔧 Maintenance

Cheminformatics Microservice and [Natural Products Online](https://naturalproducts.net) are developed and maintained by the [Steinbeck group](https://cheminf.uni-jena.de) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany.

The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT). Copyright © CC-BY-SA 2023
<p align="center"><a href="https://cheminf.uni-jena.de/" target="_blank"><img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/blob/master/assets/CheminfGit.png" width="800" alt="cheminf Logo"></a></p>

## Acknowledgments :bulb:
<p align="center">
<a href="https://cheminf.uni-jena.de/" target="_blank">
<img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/blob/master/assets/CheminfGit.png" width="800" alt="cheminf Logo">
</a>
</p>

## 💡 Acknowledgments

Funded by the [Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)](https://www.dfg.de/) under the [National Research Data Infrastructure – NFDI4Chem](https://nfdi4chem.de/) – Project number: **441958208** and [ChemBioSys](https://www.chembiosys.de/en/) (Project INF) - Project number: **239748522 - SFB 1127**.
Funded by the [Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)](https://www.dfg.de/) under the [National Research Data Infrastructure – NFDI4Chem](https://nfdi4chem.de/) – Project number: **441958208** and [ChemBioSys](https://www.chembiosys.de/en/) (Project INF) - Project number: **239748522 - SFB 1127**.

<div style="display: flex; justify-content: space-between;">
<a href="https://www.dfg.de/" target="_blank">
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