Pumas doesn’t do drug discovery, it does drug development. Those are different parts of the process with different tools.
For similar drug discovery stuff there’s Chemellia:
And that’s where you’ll find all of the stuff like atomic graph nets and graph transformers.
https://github.com/Chemellia/AtomicGraphNets.jl
https://github.com/Chemellia/GraphTransformer.jl
These build on the GeometricFlux.jl tool for graph neural networks.