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ValueError: Encountered valid chain id that was not present in the LM embeddings #41

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OlgaKoont opened this issue Dec 12, 2024 · 0 comments

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@OlgaKoont
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OlgaKoont commented Dec 12, 2024

Hello, thank you so much for your work!

I ran the script screening.py along with the file ligandFile_with_protein_path.csv through the .sh file:
#!/bin/sh
python screening.py
--protein_ligand_csv ligandFile_with_protein_path.csv
--model_dir workdir/big_score_model_sanyueqi_with_time
--savings_per_complex 40
--inference_steps 20 \

Please tell me how I can fix this error:
parse receptor: 0%| | 0/1 [00:00<?, ?it/s]
parse receptor: 0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/mnt/tank/scratch/okonovalova/DynamicBind/screening/screening.py", line 138, in
test_dataset = PDBBindScoring(transform=None, root='', name_list=name_list, protein_path_list=protein_path_list, ligand_descriptions=ligand_descriptions,
File "/mnt/tank/scratch/okonovalova/DynamicBind/screening/datasets/pdbbind.py", line 500, in init
self.ligand_graphs, self.receptor_graphs, self.rdkit_ligands, self.receptor_pdbs = self.inference_preprocessing()
File "/mnt/tank/scratch/okonovalova/DynamicBind/screening/datasets/pdbbind.py", line 644, in inference_preprocessing
rec, rec_coords, c_alpha_coords, n_coords, c_coords, chis, chi_masks, lm_embeddings = extract_receptor_structure(copy.deepcopy(rec_model), None, lm_embedding_chains=lm_embeddings_chains_all[i])
File "/mnt/tank/scratch/okonovalova/DyValueError: Encountered valid chain id that was not present in the LM embeddings
namicBind/screening/datasets/process_mols.py", line 256, in extract_receptor_structure
raise ValueError('Encountered valid chain id that was not present in the LM embeddings')

Thank you for your help!

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