There is an error in initializing PDBManager in https://github.com/NVIDIA-Digital-Bio/la-proteina/blob/cde5de3ead6e4d76f367da6dc5174be9913ef6ca/proteinfoundation/datasets/pdb_data.py#L116 due to an outdated url used in the graphein library (http://ligand-expo.rcsb.org/dictionaries/cc-to-pdb.tdd, shown below) used to obtain the `$DATA_PATH/cc-to-pdb.tdd` file at https://github.com/a-r-j/graphein/blob/75ce145e66602872f652e4a3d8972fcb207d335a/graphein/ml/datasets/pdb_data.py#L76. (Also refer to issue https://github.com/a-r-j/graphein/issues/444 in graphein). <img width="1010" height="128" alt="Image" src="https://github.com/user-attachments/assets/97702f4a-e15b-4135-b3eb-5ab536481078" /> To solve this issue, please use the same file (downloaded before the url expired) at https://drive.google.com/file/d/1cfgzu5hWyUV9qoGqDjjdzpEfErWNxWlg/view?usp=sharing. If possible, would it be possible to also update the README to include a solution to this issue?
There is an error in initializing PDBManager in https://github.com/NVIDIA-Digital-Bio/la-proteina/blob/cde5de3ead6e4d76f367da6dc5174be9913ef6ca/proteinfoundation/datasets/pdb_data.py#L116 due to an outdated url used in the graphein library (http://ligand-expo.rcsb.org/dictionaries/cc-to-pdb.tdd, shown below) used to obtain the
$DATA_PATH/cc-to-pdb.tddfile at https://github.com/a-r-j/graphein/blob/75ce145e66602872f652e4a3d8972fcb207d335a/graphein/ml/datasets/pdb_data.py#L76. (Also refer to issue a-r-j/graphein#444 in graphein).To solve this issue, please use the same file (downloaded before the url expired) at https://drive.google.com/file/d/1cfgzu5hWyUV9qoGqDjjdzpEfErWNxWlg/view?usp=sharing.
If possible, would it be possible to also update the README to include a solution to this issue?