#OpenBabel is dead, long live #RDKit!
https://github.com/RMeli/spyrmsd/issues/149
On a more serius note, it would be cool to have a cheminformatics library that actually works. Don't get me wrong, RDKit is very cool - but you can feel all the underlying problems it has when using it.
Good work is easy and fun to review - I just sent a golden recommendation to accept (with minor changes 😜) for "Cheminformatics Python Microservice (CPM): unifying access to open cheminformatics toolkits"
preprint: https://doi.org/10.26434/chemrxiv-2023-hk8zn)
code: https://github.com/Steinbeck-Lab/cheminformatics-python-microservice
service: https://api.naturalproducts.net/latest/docs
#cheminformatics #rdkit #openbabel #indigo #cdk #microservice #smiles #inchi #ocsr
@Kohulan @steinbeck good work, all
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
OffSequence
rastinza
Charles Tapley Hoyt