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HannesStark / EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
MIT License
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Keep getting the OSError #62

Closed Nailo closed 2 years ago

Nailo commented 2 years ago

I tried to reproduce the training, I extracted the PDBBind folder and put it in the data folder. And use the command "python train.py --config=configs_clean/RDkitCoords_flexible_self_docking.yml" Then I get the errors listed below：

Traceback (most recent call last): File "train.py", line 304, in main_function() File "train.py", line 295, in main_function train_wrapper(args) File "train.py", line 141, in train_wrapper return train(args, run_dir) File "train.py", line 169, in train train_data = PDBBind(device=device, complex_names_path=args.train_names,lig_predictions_name=args.train_predictions_name, is_train_data=True, **args.dataset_params) File "C:\Users\Equibind\datasets\pdbbind.py", line 127, in init self.process() File "C:\Users\Equibind\datasets\pdbbind.py", line 227, in process remove_hs=self.remove_h) File "C:\Users\Equibind\commons\process_mols.py", line 1223, in read_molecule supplier = Chem.SDMolSupplier(molecule_file, sanitize=False, removeHs=False) OSError: File error: Bad input file data/PDBBind\3dpf\3dpf_ligand.sdf

vedantg-1311 commented 2 months ago

how did you solve the problem?