Update app.py

app.py

@@ -276,7 +276,7 @@ def predict_peptide(base_model_path, finetuned_model_path, input_seqs, peptide_l
     
     return results_df, PPC
 
-def predict_peptide_from_file(base_model_path, finetuned_model_path, file_obj, max_peptide_length=15, num_binders=5, top_k=3, plddt_iptm_yes="no"):
+def predict_peptide_from_file(base_model_path, finetuned_model_path, file_obj, max_peptide_length=15, num_binders=5, plddt_iptm_yes="no"):
     start = time.time()
     # Load the model
     loaded_model = AutoModelForMaskedLM.from_pretrained(finetuned_model_path)  #.to(device)
@@ -308,6 +308,8 @@ def predict_peptide_from_file(base_model_path, finetuned_model_path, file_obj, m
 
         results.append([protein_seq, peptide_seq, ppl, plddt, iptm, 1]) # flag 1 for ground truth peptide
 
+        # set top_k mutations for each AA position
+        top_k=3
         #predict peptides
         binders = generate_peptide_for_single_sequence(loaded_model, tokenizer, protein_seq, peptide_length, top_k, num_binders, plddt_iptm_yes)