Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -1379,14 +1379,10 @@ def pdb(input_set, mode, impute):
         data['pdbSequence'] = data['pdbSequence'].str.replace('U', 'C')
         st.write('HERE')
         for i in data.index:
-            st.write('i',i)
-            st.write(data.at[i, 'source'])
             id_ = data.at[i, 'pdbID'].lower()
-            st.write('id_', id_)
             up_id_ = data.at[i, 'uniprotID']
-            st.write('up_id_', up_id_)
             score_ = str(data.at[i, 'score'])
-            st.write('score_', score_)
+         
             if data.at[i, 'source'] == 'PDB':
                 pdb_path = Path(path_to_output_files / 'pdb_structures' / f'{id_}.pdb')
             elif data.at[i, 'source'] == 'MODBASE':
@@ -1394,18 +1390,12 @@ def pdb(input_set, mode, impute):
             elif data.at[i, 'source'] == 'SWISSMODEL':
                 pdb_path = Path(path_to_output_files / 'swissmodel_structures' / f'{up_id_}_{id_}_{score_}.txt')
             pdbSequence = data.at[i, 'pdbSequence']
-            st.write('pdbSequence', pdbSequence)
-
-            st.write(uniprotID)
-            st.write(pdb_path)
-            st.write(source)
-            st.write(chain)
-            st.write(pdbID)
-            st.write(mode)
-            st.write(Path(path_to_output_files / '3D_alignment'))
-            x = pr('ik')
-
-            st.write(x)
+            source = data.at[i, 'source']
+            chain = data.at[i, 'chain']
+            uniprotID = data.at[i, 'uniprotID']
+            pdbID = data.at[i, 'pdbID']
+
+            
             alignments = get_alignments_3D(uniprotID, 'nan', pdb_path, pdbSequence, source, chain, pdbID, mode, Path(path_to_output_files / '3D_alignment'), file_format = 'gzip')
             mutPos = data.at[i, 'mutationPositionOnPDB']
             try: