Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -223,16 +223,18 @@ def pdb(input_set, mode, impute):
             shutil.rmtree('obsolete')
         except OSError as e:
             pass
-        existing_pdb = list(Path(path_to_output_files / 'pdb_structures').glob("*"))
-        st.write('existing_pdb')
-        st.write(existing_pdb)
-        existing_pdb = [str(i) for i in existing_pdb]
-        existing_pdb = [i.split('/')[-1].split('.')[0].lower() for i in existing_pdb]
+        #existing_pdb = list(Path(path_to_output_files / 'pdb_structures').glob("*"))
+        #st.write('existing_pdb')
+        #st.write(existing_pdb)
+        #existing_pdb = [str(i) for i in existing_pdb]
+        #existing_pdb = [i.split('/')[-1].split('.')[0].lower() for i in existing_pdb]
         cnt = 0
         st.write('this is the pdbs', pdbs)
         for search in pdbs:
             st.write('searching for pdb:', search)
             try:
+                file = pdb_list.retrieve_pdb_file(search,  file_format="pdb")
+                """
                 path_pdb = 'out_files/pdb/pdb_structures'
                 st.write('path for pdb: ', path_pdb)
                 file = pdbl.retrieve_pdb_file(search, pdir=path_pdb, file_format="pdb")
@@ -265,7 +267,7 @@ def pdb(input_set, mode, impute):
                     #    st.write('ERROR')
                     
 
-                    """
+                    
                     from huggingface_hub import Hf
                     api = HfApi()
                     st.write('api', API)
@@ -276,7 +278,7 @@ def pdb(input_set, mode, impute):
                         repo_id="HUBioDataLab/ASCARIS",
                         repo_type="space")
                     st.write(f"PDB file {search}.pdb downloaded successfully.")
-                    """
+                    
 
                     # Aug 23
                     content = response.content.decode("utf-8")  # Decode the content if it's not already a string
@@ -298,7 +300,7 @@ def pdb(input_set, mode, impute):
                 existing_pdb = list(Path(path_to_output_files / 'pdb_structures').glob("*"))
                 st.write('existing_pdb3', existing_pdb)
 
-                
+                """
         
                 resolution_method = parser.get_structure(search, file)
                 for record in SeqIO.parse(file, "pdb-seqres"):
@@ -319,6 +321,8 @@ def pdb(input_set, mode, impute):
                 pdb_info.at[index, 'resolution'] = 'nan'
             cnt += 1
         print()
+        st.write()
+        st.write(pdb_info)
         print('PDB file processing finished..')
         for filename in list(Path(path_to_output_files / 'pdb_structures').glob("*")):
             try: