Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -223,9 +223,9 @@ def pdb(input_set, mode, impute):
                 response = requests.get(f"https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{pdb_code}")
                 response.raise_for_status()  # Check for a successful response
                 data = response.json()
+                st.write(list(list(list(data.values())[0].values())[0].keys()))
                 return list(list(list(data.values())[0].values())[0].keys())
-            except requests.exceptions.RequestException as e:
-                print(f"Failed to retrieve UniProt data for PDB code {pdb_code}: {e}")
+            except :
                 return []
         for search in pdbs:
             # Step 1: Fetch the PDB file
@@ -233,8 +233,7 @@ def pdb(input_set, mode, impute):
             try:
                 response = requests.get(pdb_url)
                 response.raise_for_status()  # Check for a successful response
-            except requests.exceptions.RequestException as e:
-                print(f"Failed to retrieve data for PDB code {search}: {e}")
+            except :
                 continue  # Skip to the next PDB code if fetching fails
                 
             # Step 2: Parse the PDB file from memory
@@ -265,37 +264,12 @@ def pdb(input_set, mode, impute):
                     pdb_fasta.at[index, 'pdbID'] = search
                     pdb_fasta.at[index, 'chain'] = chain_id
                     pdb_fasta.at[index, 'pdbSequence'] = str(sequence)
-                    pdb_info.at[index, 'uniprotID'] = record.dbxrefs[0].split(':')[1]
+                    pdb_info.at[index, 'uniprotID'] = ', '.join(uniprot_ids)
                     pdb_info.at[index, 'pdbID'] = search
                     pdb_info.at[index, 'chain'] = chain_id
                     pdb_info.at[index, 'resolution'] = resolution
                 index += 1
 
-                """
-        
-                resolution_method = parser.get_structure(search, file)
-                st.write(resolution_method)
-                for record in SeqIO.parse(file, "pdb-seqres"):
-                    st.write('rec', record)
-                    if record.dbxrefs[0].split(':')[0] == 'UNP':
-                        st.write(record.id.split(':')[0])
-                        st.write(record.id.split(':')[1])
-                        pdb_fasta.at[index, 'pdbID'] = record.id.split(':')[0]
-                        pdb_fasta.at[index, 'chain'] = record.id.split(':')[1]
-                        pdb_fasta.at[index, 'pdbSequence'] = str(record.seq)
-                        pdb_info.at[index, 'uniprotID'] = record.dbxrefs[0].split(':')[1]
-                        pdb_info.at[index, 'pdbID'] = record.id.split(':')[0]
-                        pdb_info.at[index, 'chain'] = record.annotations["chain"]
-                        pdb_info.at[index, 'resolution'] = resolution_method.header['resolution']
-                    index += 1
-            except:
-                IndexError
-                pdb_info.at[index, 'uniprotID'] = 'nan'
-                pdb_info.at[index, 'pdbID'] = 'nan'
-                pdb_info.at[index, 'chain'] = 'nan'
-                pdb_info.at[index, 'resolution'] = 'nan'
-            cnt += 1
-            """
         print()
         st.write()
         st.write(pdb_info)