conda create -n target python=3.8
conda activate target
conda install pytorch==2.0.1 pytorch-cuda=11.7 -c pytorch -c nvidia
conda install pyg -c pyg
pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
conda install rdkit openbabel tensorboard pyyaml easydict python-lmdb -c conda-forge
# For Vina Docking
pip install meeko==0.1.dev3 scipy pdb2pqr vina==1.2.2 
python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3

python gen_data.py

python scripts/train_ipo.py configs/training_ipo.yml

python scripts/sample_diffusion.py configs/sampling.yml --data_id {i} # Replace {i} with the index of the data. i should be between 0 and 99 for the testset.

python scripts/evaluate_diffusion.py {OUTPUT_DIR} --docking_mode vina_score --protein_root data/test_set