andmastro / protein-ligand-gnn Goto Github PK

Hello,
Thank you so much for this public available repo.
I want to train or test these models on my structures. However, there is no script for generating the input files (i.e., the protein, ligand, and interaction_graph.json) for training or testing. Could you kindly provide the scripts to generate these files?
Thanks!
Li

Hi,

Congratulations on your fantastic work! I successfully run the command "python trainer_script.py" and "python explainer_script.py" with all default settings, but failed to run the command "python top_k_computation.py". It shows that there is something missing:

File "top_k_computation.py", line 51, in generate_pli_dataset_dict_reduced
with open(data_path + interaction_name + "/" + interaction_name + "_interaction_graph.json", 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'data//dataset/.ipynb_checkpoints/.ipynb_checkpoints_interaction_graph.json'

a json file in the dataset folder, i double checked the downloaded pdbbind (1).tgz , and there is no such file. i wonder how i can get that particular file