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Using PharmacoNet's protein representation

Example scripts to use PharmacoNet's protein pharmacophore representation, which depend on torch-geometric.

# construct conda environment; pymol-open-source is not required.
conda create -n pmnet-dev python=3.10 openbabel=3.1.1
conda activate pmnet-dev
# install PharmacoNet & torch_geometric & wandb
pip install -e '.[dev]' --find-links https://data.pyg.org/whl/torch-2.3.1+cu121.html

Example datasets (100 or 1,000 pockets) can be available at Google Drive, which are constructed by CrossDocked2020 and QuickVina 2.1.