AssertionError

[adithigr]

Please guide me with this error. Please!
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/5jqwA/5jqwA.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/5jy1C/5jy1C.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/5k2xA/5k2xA.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/5nulA/5nulA.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/6a3hA/6a3hA.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/6gsyB/6gsyB.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/7aatA/7aatA.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/7acnA/7acnA.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/7stdB/7stdB.npz,corresponding pdb likely could not be parsed
WARNING:root:HTMD featurization file not found: C:UsersAdithiDownloadsbindDeeplyTough-masterDeeplyTough-master/processed/htmd/TOUGH-M1/TOUGH-M1_dataset/9abpA/9abpA.npz,corresponding pdb likely could not be parsed
Traceback (most recent call last):
File "/mnt/c/Users/Adithi/Downloads/bind/DeeplyTough-master/DeeplyTough-master/deeplytough/scripts/train.py", line 311, in
main()
File "/mnt/c/Users/Adithi/Downloads/bind/DeeplyTough-master/DeeplyTough-master/deeplytough/scripts/train.py", line 95, in main
exclude_Vertex_from_train=args.db_exclude_vertex, exclude_Prospeccts_from_train=args.db_exclude_prospeccts
File "/mnt/c/Users/Adithi/Downloads/bind/DeeplyTough-master/DeeplyTough-master/deeplytough/engine/datasets.py", line 319, in create_tough_dataset
augm_decoy_prob=args.augm_decoy_prob, db_pairs_limit=-args.db_size_limit)
File "/mnt/c/Users/Adithi/Downloads/bind/DeeplyTough-master/DeeplyTough-master/deeplytough/engine/datasets.py", line 125, in init
super().init(pdb_list, box_size, augm_rot, augm_mirror_prob)
File "/mnt/c/Users/Adithi/Downloads/bind/DeeplyTough-master/DeeplyTough-master/deeplytough/engine/datasets.py", line 46, in init
assert len(self.pdb_list) > 0, f'No HTMD could be found but {len(pdb_list)}'
AssertionError: No HTMD could be found but 6042PDB files were given, please call preprocess_once() on the dataset

[JoshuaMeyers]

It appears you haven't installed HTMD correctly, this dependency is highly out of date.

If you would truly like to use deeplytough, I would suggest starting from our image on Dockerhub, or building the docker image yourself since this repo has a few stale dependencies now which can be a bit fiddly to install (docker pull joshuameyers/deeplytough)

[adithigr]

Thank you for your input. Do you think there are any other tools like DeeplyTough currently? We are trying to figure it out, but all the tools seemed to be outdated.

[JoshuaMeyers]

Yep good point, I'm not working in this realm at the moment but I'd say the masif suite would be a step in the right direction 👍