You can download the processed data geom_drug.tar.gz (~2GB) from here and unzip them (tar -zxvf)
in the data folder as:
data
├── geom_drug
│ ├── mol_summary.csv
│ ├── split_by_molid.pt
│ ├── processed.lmdb
│ └── processed_molid2idx.ptIf you want to process the data from the sdf files, you have to further download the sdf.tar.gz (~4GB) from here. Unzip it (~28GB after unzipping) in the data/geom_drug folder and remove the processed.lmdb and processed_molid2idx.pt:
data
├── geom_drug
│ ├── mol_summary.csv
│ ├── split_by_molid.pt
│ └── sdf
│ ├── 0.sdf
│ ├── ...Then by running any sampling, training or evaluation script, the data will be processed automatically.