Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -47,7 +47,6 @@ from add_interface_pos import *
 from standard import *
 from uniprotSequenceMatch import uniprotSequenceMatch
 from process_input import clean_data
-from huggingface_hub import hf_hub_download
 
 
 def pdb(input_set, mode, impute):
@@ -219,17 +218,21 @@ def pdb(input_set, mode, impute):
         try:
             shutil.rmtree('obsolete')
         except OSError as e:
-            pass
-        pdb_structures_path = path_to_output_files / 'log.txt'
+            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]
         cnt = 0
         for search in pdbs:
-            
+            st.write('searching for pdb:', search)
             try:
                 if search.lower() not in existing_pdb:
+                    st.write('path for pdb: ',Path(path_to_output_files / 'pdb_structures'))
                     file = pdbl.retrieve_pdb_file(search, pdir=Path(path_to_output_files / 'pdb_structures'), file_format="pdb")
+                    existing_pdb = list(Path(path_to_output_files/'pdb_structures').glob("*"))
+                    st.write('After retrieving existing pdb folder : ',existing_pdb)
                 else:
                     print('PDB structure file exists..')
                     for filename in list(Path(path_to_output_files / 'pdb_structures').glob("*")):
@@ -1306,13 +1309,11 @@ def pdb(input_set, mode, impute):
         existing_free_sasa = list(Path(path_to_output_files / 'freesasa_files').glob("*"))
         existing_free_sasa = [str(i) for i in existing_free_sasa]
         existing_free_sasa = [i.split('/')[-1].split('.')[0] for i in existing_free_sasa]
-        st.write('existing_free_sasa', existing_free_sasa)
         print('Calculation RSA for PDB Structure Files...\n')
 
         pdb_only = data[data.source == 'PDB']
         for pdbID in pdb_only.pdbID.to_list():
             if pdbID not in existing_free_sasa:
-                st.write('I am here')
                 (run_freesasa(Path(path_to_output_files / 'pdb_structures' / f'{pdbID.lower()}.pdb'),
                               Path(path_to_output_files / 'freesasa_files' / f'{pdbID.lower()}.txt'), include_hetatms=True,
                               outdir=None, force_rerun=False, file_type='pdb'))