42038c294a32f708b41255a7f29164e5d094eeba,deepchem/utils/rdkit_util.py,,add_hydrogens_to_mol,#Any#,34

Before Change

def add_hydrogens_to_mol(mol):
  molecule_file = None
  try:
    molecule_file = str(tempfile.NamedTemporaryFile().name)
    Chem.MolToPDBFile(mol, molecule_file)
    fixer = PDBFixer(filename=molecule_file)
    fixer.addMissingHydrogens(7.4)
    PDBFile.writeFile(fixer.topology, fixer.positions, open(molecule_file, "w"))

After Change

    fixer = PDBFixer(pdbfile=pdb_stringio)
    fixer.addMissingHydrogens(7.4)

    hydrogenated_io = StringIO()
    PDBFile.writeFile(fixer.topology, fixer.positions, hydrogenated_io)
    hydrogenated_io.seek(0)
    return Chem.MolFromPDBBlock(
        hydrogenated_io.read(), sanitize=False, removeHs=False)

Instances