alexanderkroll / prosmith Goto Github PK

It seems like the transformer model trained for ESP prediction is not included in the repo or in the Zenodo folder. I can only find the pretrained KM prediction model and the BindingDB model. Could you upload the trained ESP transformer model (ESP_1gpus_bs24_1e-05_layers6.txt.pkl)?

Thanks,
Max

Could you, please, fix a little typo in the training.py file? in the training.py in line 94 the parser code for --pretrained model is missing its name, need to paste [--pretrained model] into empty " " for the code to actually run.

Calculating protein embeddings:
Traceback (most recent call last):
File "code/preprocessing/preprocessing.py", line 58, in
calculate_protein_embeddings(all_sequences, args.outpath, args.prot_emb_no)
NameError: name 'calculate_protein_embeddings' is not defined

Could you take a look?

Thanks,
Yang

Dear Alexander,
I hope you are doing well,
would you please upload the missing data folder.
Best,
Vahid