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Datasets:
djh992
/
pdbbind_complex_GB2022

Tags:
molecules
Chemistry
SMILES
Protein
Ligand
Complexes
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The dataset viewer is not available for this dataset.
Cannot get the config names for the dataset.
Error code:   ConfigNamesError
Exception:    FileNotFoundError
Message:      Couldn't find a dataset script at /src/services/worker/djh992/pdbbind_complex_GB2022/pdbbind_complex_GB2022.py or any data file in the same directory. Couldn't find 'djh992/pdbbind_complex_GB2022' on the Hugging Face Hub either: FileNotFoundError: No (supported) data files or dataset script found in djh992/pdbbind_complex_GB2022. 
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 55, in compute_config_names_response
                  for config in sorted(get_dataset_config_names(path=dataset, token=hf_token))
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 351, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1508, in dataset_module_factory
                  raise FileNotFoundError(
              FileNotFoundError: Couldn't find a dataset script at /src/services/worker/djh992/pdbbind_complex_GB2022/pdbbind_complex_GB2022.py or any data file in the same directory. Couldn't find 'djh992/pdbbind_complex_GB2022' on the Hugging Face Hub either: FileNotFoundError: No (supported) data files or dataset script found in djh992/pdbbind_complex_GB2022.

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To generate the dataset

Register for an account at https://www.pdbbind.org.cn/, confirm the validation email, then login and download

the Index files (1) the general protein-ligand complexes (2) the refined protein-ligand complexes (3) Extract those files in pdbbind_complex_GB2022/data

Run the script pdbbind.py in a compute job on an MPI-enabled cluster (e.g., mpirun -n 64 pdbbind.py).

Output will be tar files in train/, val/ and test/ folders, following the split direction which is from EquiBind manuscript.

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