Error when using script partial_noise_reconstruct.py

[tanoramb]

Hello,

It is a good idea to incorporate a script to produce variants from starting structures (aka. inpaiting). I was trying to run the script partial_noise_reconstruct.py but I got the following error:

$ python ../bin/partial_noise_reconstruct.py protein1.pdb protein2.pdb output.json

INFO:root:Detected huggingface repo ID wukevin/foldingdiff_cath
Fetching 6 files: 100%|█████████████████████| 6/6 [00:00<00:00, 23410.07it/s]
INFO:root:Using downloaded model at /home/tn/.cache/huggingface/hub/models--wukevin--foldingdiff_cath/snapshots/98d77b1e68468db5ca03cdba1c0a90f2a2a33edc
INFO:root:Loading dataset from 2 pdb files
INFO:root:Clean dataset class: <class 'foldingdiff.datasets.CathCanonicalAnglesOnlyDataset'>
Traceback (most recent call last):
  File "../bin/partial_noise_reconstruct.py", line 132, in <module>
    main()
  File "../bin/partial_noise_reconstruct.py", line 116, in main
    scores = get_reconstruction_error(
  File "../bin/partial_noise_reconstruct.py", line 94, in get_reconstruction_error
    dset = load_dataset(pdb_files, model)
  File "../bin/partial_noise_reconstruct.py", line 34, in load_dataset
    dset = clean_dset_class(
  File "/home/tn/foldingdiff/foldingdiff/datasets.py", line 499, in __init__
    super().__init__(*args, **kwargs)
  File "/home/tn/foldingdiff/foldingdiff/datasets.py", line 123, in __init__
    fnames = self.__get_pdb_fnames(pdbs)
  File "/home/tn/foldingdiff/foldingdiff/datasets.py", line 238, in __get_pdb_fnames
    if Path(pdbs).is_dir():
  File "/home/tn/.conda/envs/foldingdiff/lib/python3.8/pathlib.py", line 1042, in __new__
    self = cls._from_parts(args, init=False)
  File "/home/tn/.conda/envs/foldingdiff/lib/python3.8/pathlib.py", line 683, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/home/tn/.conda/envs/foldingdiff/lib/python3.8/pathlib.py", line 667, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not list

Could you please help on this issue?

[wukevin]

Hi, we don't currently officially support inpainting - the partial_noise_reconstruct.py script is largely experimental dev code.

[tanoramb]

Anyway, could you please find out to have some idea of the issue?

Thank you