Renames and PR cleanups (147fc92a) · Commits · 钟慕尧 / deepchem

deepchem/utils/rdkit_util.py

+15 −7

Original line number	Diff line number	Diff line
		@@ -3,6 +3,7 @@ import logging
		import os
		import numpy as np
		import tempfile
		import shutil
		from rdkit import Chem
		from rdkit.Chem import AllChem
		from pdbfixer import PDBFixer
		@@ -30,17 +31,24 @@ def get_xyz_from_mol(mol):
		return (xyz)


		def add_hydrogens_f(mol):
		def add_hydrogens_to_mol(mol):
		molecule_file = None
		try:
		molecule_file = str(tempfile.NamedTemporaryFile().name)
		Chem.MolToPDBFile(mol, molecule_file)
		try:
		fixer = PDBFixer(filename=molecule_file)
		fixer.addMissingHydrogens(7.4)
		PDBFile.writeFile(fixer.topology, fixer.positions, open(molecule_file, 'w'))
		return Chem.MolFromPDBFile(
		str(molecule_file), sanitize=False, removeHs=False)
		except ValueError as e:
		print(e)
		logging.warning("Unable to add hydrogens", e)
		raise MoleculeLoadException(e)
		return Chem.MolFromPDBFile(str(molecule_file), sanitize=False, removeHs=False)
		finally:
		try:
		os.remove(molecule_file)
		except (OSError, TypeError):
		pass


		def compute_charges(mol):
		@@ -73,10 +81,10 @@ def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True):
		raise ValueError("Unable to read non None Molecule Object")

		if calc_charges:
		my_mol = add_hydrogens_f(my_mol)
		my_mol = add_hydrogens_to_mol(my_mol)
		compute_charges(my_mol)
		elif add_hydrogens:
		my_mol = add_hydrogens_f(my_mol)
		my_mol = add_hydrogens_to_mol(my_mol)
		compute_charges(my_mol)

		xyz = get_xyz_from_mol(my_mol)