What about using CDK 2.9 (or soon 2.10) for fingerprint generation directly?

[egonw]

The idea is to just call the CDK fingerprint generation from Python directly, instead of via PaDEL. I have already ported a few CDK code examples to Python here: https://egonw.github.io/chempyformatics/

Alternatively, we have been working on a PaDEL based on CDK 2.9. See that here: cdk/nwo-openscience-2024#19

cc @RvdPloeg

[martin-sicho]

Hi @egonw! Thanks for the great suggestion! We were not aware of this when we implemented this a while back. I will give this a look and update this issue on the progress. Thanks again :)