gcorso
installation issue
Hi,
When trying to run diffdock using the command below, I got this error. Please advice how to fix this:
(diffdock) [root@oric-zCHS3IvgQd:~/DiffDock]# python -m inference --config default_inference_args.yaml --protein_path /root/DiffDock/examples/1a46_protein_processed.pdb --ligand /root/DiffDock/examples/1a46_lig
and.sdf --out_dir results/user_predictions_small
Traceback (most recent call last):
File "/root/anaconda3/envs/diffdock/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/root/anaconda3/envs/diffdock/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/root/DiffDock/inference.py", line 3, in
I'm having the same issue. It seems that when setting up the environment with the command conda env create --file environment.yml, it doesn't install many packages such as pytorch and rdkit even though these are listed in the environment.yml file.
So when I try to run the inference.py file, it gives errors of missing packages.
I can second to this, followed the installation procedure and PyTorch and RDKIT were missing among others...
Debian Bookworm on WLS2
I also ran into a similar issue. As far as I can tell gradio and requests are the only thing that actually got installed from conda env create --file environment.yml. Purportedly, these packages get installed because they are in the last pip block of the environment.yml file.
I am not familiar with the proper file format so I can't propose a true fix, but you can just pip install each chunk manually to get all the dependencies.
