Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -222,7 +222,7 @@ def pdb(input_set, mode, impute):
             data = response.json()
             st.write(list(list(list(data.values())[0].values())[0].keys()))
             return list(list(list(data.values())[0].values())[0].keys())
-        print(fetch_uniprot_ids('5K5T'))
+        
         for search in pdbs:
             # Step 1: Fetch the PDB file
             pdb_url = f"https://files.rcsb.org/download/{search}.pdb"
@@ -274,12 +274,12 @@ def pdb(input_set, mode, impute):
                     if chain_id in pdb_data_list:
                     # Print UniProt IDs, chain ID, and resolution for the current model
                         chain_id = chain.get_id()
-                        st.write(f"---- Information for Chain {chain_id} in Model {i} ----")
-                        st.write(f"UniProt IDs: {', '.join(uniprot_ids)}")
-                        st.write(f"Chain ID: {chain_id}")
-                        st.write(f"PDB ID: {search.upper()}")
-                        st.write(f"Resolution: {resolution}")
-                        st.write(f"Sequence: {sequence}")
+                        #st.write(f"---- Information for Chain {chain_id} in Model {i} ----")
+                        #st.write(f"UniProt IDs: {', '.join(uniprot_ids)}")
+                        #st.write(f"Chain ID: {chain_id}")
+                        #st.write(f"PDB ID: {search.upper()}")
+                        #st.write(f"Resolution: {resolution}")
+                        #st.write(f"Sequence: {sequence}")
                         pdb_fasta.at[index, 'pdbID'] = search
                         pdb_fasta.at[index, 'chain'] = chain_id
                         pdb_fasta.at[index, 'pdbSequence'] = str(seqs[chain_id])
@@ -437,6 +437,10 @@ def pdb(input_set, mode, impute):
         print('Aligning sequences...\n')
         aligned_m = final_stage(dfM, annotation_list, Path(path_to_output_files / 'alignment_files'))
         aligned_nm = final_stage(dfNM, annotation_list, Path(path_to_output_files / 'alignment_files'))
+        st.write('aligned_m')
+        st.write(aligned_m)
+        st.write('aligned_nm')
+        st.write(aligned_nm)
         # When PDB sequence is nan, it is wrongly aligned to the UniProt sequence. Fix them.
         for i in aligned_m.index:
             if aligned_m.at[i, 'pdbSequence'] == 'nan':