drop: buildin logger

apps/protein_folding/helixfold3/helixfold/data/mmcif_parsing_paddle.py

@@ -22,7 +22,7 @@
 from Bio import PDB
 import numpy as np
 import time
-import logging
+from absl import logging
 from helixfold.common.residue_constants import crystallization_aids, ligand_exclusion_list
 
 # Type aliases:

apps/protein_folding/helixfold3/helixfold/data/tools/utils.py

@@ -16,7 +16,7 @@
 
 import contextlib
 import shutil
-import logging
+from absl import logging
 import tempfile
 import time
 from typing import Optional

apps/protein_folding/helixfold3/helixfold/infer_scripts/preprocess.py

@@ -165,20 +165,21 @@ def _get_supported_formats(self) -> Tuple[str]:
         return tuple(formats)
 
     def _perform_conversion(self, input_type: str, input_value: str) -> Chem.Mol:
-        with tempfile.NamedTemporaryFile(suffix=".mol2") as temp_file:
-            with utils.timing(f'converting {input_type} to mol2: {input_value}'):
-                if input_type == 'smiles':
-                    obabel_cmd = f"{self.obabel_bin} -:'{input_value}' -omol2 -O{temp_file.name} --gen3d"
-                    if len(input_value)>60:
-                        logging.warning(f'This takes a while ...')
-                else:
-                    obabel_cmd = f"{self.obabel_bin} -i {input_type} {input_value} -omol2 -O{temp_file.name} --gen3d"
-                ret = subprocess.run(obabel_cmd, shell=True, capture_output=True, text=True)
-                mol = Chem.MolFromMol2File(temp_file.name, sanitize=False)
-                if '3D coordinate generation failed' in ret.stderr:
-                    mol = generate_ETKDGv3_conformer(mol)
-                optimal_mol_wo_H = Chem.RemoveAllHs(mol, sanitize=False)
-                return optimal_mol_wo_H
+        with tempfile.NamedTemporaryFile(suffix=".mol2") as temp_file, utils.timing(f'converting {input_type} to mol2: {input_value}'):
+            if input_type == 'smiles':
+                obabel_cmd = f"{self.obabel_bin} -:'{input_value}' -omol2 -O{temp_file.name} --gen3d"
+                if len(input_value)>60:
+                    logging.warning(f'This takes a while ...')
+            else:
+                obabel_cmd = f"{self.obabel_bin} -i {input_type} {input_value} -omol2 -O{temp_file.name} --gen3d"
+            logging.debug(f'Launching command: `{obabel_cmd}`')
+            ret = subprocess.run(obabel_cmd, shell=True, capture_output=True, text=True)
+            mol = Chem.MolFromMol2File(temp_file.name, sanitize=False)
+            if '3D coordinate generation failed' in ret.stderr:
+                mol = generate_ETKDGv3_conformer(mol)
+            optimal_mol_wo_H = Chem.RemoveAllHs(mol, sanitize=False)
+
+            return optimal_mol_wo_H
 
     def _convert_to_mol(self, input_type: str, input_value: str) -> Chem.Mol:
         if input_type not in self.supported_formats:

apps/protein_folding/helixfold3/helixfold/inference.py

@@ -22,7 +22,6 @@
 import pickle
 import pathlib
 import shutil
-import logging
 import numpy as np
 import shutil