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BenevolentAI / DeeplyTough

DeeplyTough: Learning Structural Comparison of Protein Binding Sites
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AssertionError #27

Open adithigr opened 1 week ago

adithigr commented 1 week ago

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 commented 1 week ago

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)