Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits

10 July 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present Cheminformatics Python Microservice (CPM). This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through CPM based on pre-existing tools. CPM also enables developers to extend the functionalities easily and seamlessly integrate with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net. The source code for CPM is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-python-microservice

Keywords

CDK
Chemistry Development Kit
RDKit
Open Babel
cheminformatics
microservice
toolkits

Supplementary weblinks

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.