Now do it in memory (42038c29) · Commits · 钟慕尧 / deepchem

deepchem/utils/rdkit_util.py

+16 −6

Original line number	Diff line number	Diff line
		@@ -9,6 +9,11 @@ from rdkit.Chem import AllChem
		from pdbfixer import PDBFixer
		from simtk.openmm.app import PDBFile

		try:
		from StringIO import StringIO
		except ImportError:
		from io import StringIO


		class MoleculeLoadException(Exception):

		@@ -34,13 +39,18 @@ def get_xyz_from_mol(mol):
		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)
		pdbblock = Chem.MolToPDBBlock(mol)
		pdb_stringio = StringIO()
		pdb_stringio.write(pdbblock)
		pdb_stringio.seek(0)
		fixer = PDBFixer(pdbfile=pdb_stringio)
		fixer.addMissingHydrogens(7.4)
		PDBFile.writeFile(fixer.topology, fixer.positions, open(molecule_file, 'w'))
		return Chem.MolFromPDBFile(
		str(molecule_file), sanitize=False, removeHs=False)

		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)
		except ValueError as e:
		logging.warning("Unable to add hydrogens", e)
		raise MoleculeLoadException(e)