search

AndMastro / protein-ligand-GNN

This repository contains the code for the work on protein-ligand interaction with GNNs and XAI
GNU General Public License v3.0
33 stars 4 forks source link

json file not found #4

Closed a1e-the closed 2 months ago

a1e-the commented 2 months ago

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

AndMastro commented 2 months ago

Hello, thanks for reaching out! 😎

It looks like in the downloaded pdbbind dataset, into the dataset folder, there is a .ipynb_checkpoints folder you can safely delete. The code searches for all directories in that folder, and it finds the directory .ipynb_checkpoints. Ensure that the dataset folder contains only folders related to protein-ligand complexes, and you should be fine👌

a1e-the commented 2 months ago

I appreciate your reply, it really solved my problem. I successfully generated the svg files. Wish you all the best!😎