Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -1397,20 +1397,21 @@ def pdb(input_set, mode, impute):
             id_ = data.at[i, 'pdbID'].lower()
             up_id_ = data.at[i, 'uniprotID']
             score_ = str(data.at[i, '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':
                 pdb_path = Path(path_to_output_files / 'modbase_structures_individual' / f'{id_}.txt')
             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']
             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')
+            alignments = get_alignments_3D(uniprotID, 'nan', pdbSequence, source, chain, pdbID, mode,
+                                            file_format='gzip')
             mutPos = data.at[i, 'mutationPositionOnPDB']
             try:
                 coordMut = get_coords(mutPos, alignments, 'nan', 'nan', mode)[0]