Update inputs.py (#142)

Author: amorehead

alphafold3_pytorch/inputs.py

@@ -28,7 +28,7 @@
 
 from pdbeccdutils.core import ccd_reader
 
-from rdkit import Chem, RDLogger
+from rdkit import Chem, rdBase
 from rdkit.Chem import AllChem, rdDetermineBonds
 from rdkit.Chem.rdchem import Atom, Mol
 from rdkit.Geometry import Point3D
@@ -66,10 +66,6 @@
 from alphafold3_pytorch.utils.model_utils import exclusive_cumsum
 from alphafold3_pytorch.utils.utils import default, exists, first, identity
 
-# silence RDKit's warnings
-
-RDLogger.DisableLog("rdApp.*")
-
 # constants
 
 IS_MOLECULE_TYPES = 5
@@ -1793,9 +1789,15 @@ def create_mol_from_atom_positions_and_types(
     for i, (x, y, z) in enumerate(atom_positions):
         conf.SetAtomPosition(i, Point3D(x, y, z))
 
+    # add the conformer to the molecule
+
     mol.AddConformer(conf)
     Chem.SanitizeMol(mol)
 
+    # block the RDKit logger
+
+    blocker = rdBase.BlockLogs()
+
     # finalize molecule by inferring bonds
 
     determined_bonds = False
@@ -1817,6 +1819,10 @@ def create_mol_from_atom_positions_and_types(
                 "Failed to determine bonds in the input molecule. Skipping bond assignment."
             )
 
+    # unblock the RDKit logger
+
+    del blocker
+
     mol = Chem.RemoveHs(mol)
     Chem.SanitizeMol(mol)