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Saoge123 / PocketFlow

an autoregressive flow model incorporated with chemical acknowledge for generating drug-like molecules inside protein pockets
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KeyError: 'OG1' #8

Closed indazole closed 1 month ago

indazole commented 1 month ago

Hello, Thank you for posting your code - nice work! I have installed and tested, with success, a few of the sample pocket pdbs. When trying to generate my own pocket pdb files, I run into the following error:

PocketFlow# python create_pocket_pdb.py --protein test.pdb --ligand test_lig.sdf PyMOL not running, entering library mode (experimental) Traceback (most recent call last): File "create_pocket_pdb.py", line 32, in main() File "create_pocket_pdb.py", line 25, in main pocketblock, = SplitPocket._split_pocket_with_surface_atoms( File "/PocketFlow/pocket_flow/utils/process_raw.py", line 68, in _split_pocket_with_surface_atoms protein.compute_surface_atoms() File "/PocketFlow/pocket_flow/utils/ParseFile.py", line 480, in compute_surface_atoms res.atom_dict[a.name].is_surf = True KeyError: 'OG1'

Any help is appreciated.

Saoge123 commented 1 month ago

Hi, the error is lead by dismatching between the atom names of residues in your pdb and those at line 37 in utils/residues_base.py.

indazole commented 1 month ago

Ah, yes! Missing atoms. Thank you.