added sanitize flag (00d80849) · Commits · 钟慕尧 / deepchem

deepchem/feat/rdkit_grid_featurizer.py

+36 −16

Original line number	Original line	Diff line number	Diff line
	@@ -910,6 +910,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
	voxel_width=1.0,		voxel_width=1.0,
	flatten=False,		flatten=False,
	verbose=True,		verbose=True,
			sanitize=False,
	**kwargs):		**kwargs):
	"""Parameters:		"""Parameters:
	-----------		-----------
	@@ -967,6 +968,10 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
	'box_x', 'box_y', 'box_z', 'save_intermediates', 'voxelize_features',		'box_x', 'box_y', 'box_z', 'save_intermediates', 'voxelize_features',
	'parallel', 'voxel_feature_types'		'parallel', 'voxel_feature_types'
	]		]

			# list of features that require sanitized molecules
			require_sanitized = ['pi_stack', 'cation_pi']

	for arg in deprecated_args:		for arg in deprecated_args:
	if arg in kwargs and verbose:		if arg in kwargs and verbose:
	warn('%s argument was removed and it is ignored,'		warn('%s argument was removed and it is ignored,'
	@@ -974,6 +979,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
	DeprecationWarning)		DeprecationWarning)

	self.verbose = verbose		self.verbose = verbose
			self.sanitize = sanitize
	self.flatten = flatten		self.flatten = flatten

	self.ecfp_degree = ecfp_degree		self.ecfp_degree = ecfp_degree
	@@ -1222,8 +1228,20 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
	# each entry is a tuple (is_flat, feature_name)		# each entry is a tuple (is_flat, feature_name)
	self.feature_types = []		self.feature_types = []

			# list of features that cannot be calculated with specified parameters
			# this list is used to define <flat/voxel/all>_combined subset
			ignored_features = []
			if self.sanitize is False:
			ignored_features += require_sanitized

	# parse provided feature types		# parse provided feature types
	for feature_type in feature_types:		for feature_type in feature_types:
			if self.sanitize is False and feature_type in require_sanitized:
			if self.verbose:
			warn('sanitize is set to False, %s feature will be ignored' %
			feature_type)
			continue

	if feature_type in self.FLAT_FEATURES:		if feature_type in self.FLAT_FEATURES:
	self.feature_types.append((True, feature_type))		self.feature_types.append((True, feature_type))
	if self.flatten is False:		if self.flatten is False:
	@@ -1235,28 +1253,28 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
	self.feature_types.append((False, feature_type))		self.feature_types.append((False, feature_type))

	elif feature_type == 'flat_combined':		elif feature_type == 'flat_combined':
	self.feature_types += list(		self.feature_types += [(True, ftype)
	zip([True] * len(self.FLAT_FEATURES),		for ftype in sorted(self.FLAT_FEATURES.keys())
	sorted(self.FLAT_FEATURES.keys())))		if ftype not in ignored_features]
	if self.flatten is False:		if self.flatten is False:
	if self.verbose:		if self.verbose:
	warn('flat features are used, output will be flattened')		warn('Flat features are used, output will be flattened')
	self.flatten = True		self.flatten = True

	elif feature_type == 'voxel_combined':		elif feature_type == 'voxel_combined':
	self.feature_types += list(		self.feature_types += [(False, ftype)
	zip([False] * len(self.VOXEL_FEATURES),		for ftype in sorted(self.VOXEL_FEATURES.keys())
	sorted(self.VOXEL_FEATURES.keys())))		if ftype not in ignored_features]
	elif feature_type == 'all_combined':		elif feature_type == 'all_combined':
	self.feature_types += list(		self.feature_types += [(True, ftype)
	zip([True] * len(self.FLAT_FEATURES),		for ftype in sorted(self.FLAT_FEATURES.keys())
	sorted(self.FLAT_FEATURES.keys())))		if ftype not in ignored_features]
	self.feature_types += list(		self.feature_types += [(False, ftype)
	zip([False] * len(self.VOXEL_FEATURES),		for ftype in sorted(self.VOXEL_FEATURES.keys())
	sorted(self.VOXEL_FEATURES.keys())))		if ftype not in ignored_features]
	if self.flatten is False:		if self.flatten is False:
	if self.verbose:		if self.verbose:
	warn('flat feature are used, output will be flattened')		warn('Flat feature are used, output will be flattened')
	self.flatten = True		self.flatten = True
	elif self.verbose:		elif self.verbose:
	warn('Ignoring unknown feature %s' % feature_type)		warn('Ignoring unknown feature %s' % feature_type)
	@@ -1333,7 +1351,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
	############################################################## TIMING		############################################################## TIMING

	if not self.ligand_only:		if not self.ligand_only:
	protein_xyz, protein_rdk = load_molecule(protein_pdb, calc_charges=True)		protein_xyz, protein_rdk = load_molecule(
			protein_pdb, calc_charges=True, sanitize=self.sanitize)
	############################################################## TIMING		############################################################## TIMING
	time2 = time.time()		time2 = time.time()
	log("TIMING: Loading protein coordinates took %0.3f s" % (time2 - time1),		log("TIMING: Loading protein coordinates took %0.3f s" % (time2 - time1),
	@@ -1342,7 +1361,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
	############################################################## TIMING		############################################################## TIMING
	time1 = time.time()		time1 = time.time()
	############################################################## TIMING		############################################################## TIMING
	ligand_xyz, ligand_rdk = load_molecule(ligand_file, calc_charges=True)		ligand_xyz, ligand_rdk = load_molecule(
			ligand_file, calc_charges=True, sanitize=self.sanitize)
	############################################################## TIMING		############################################################## TIMING
	time2 = time.time()		time2 = time.time()
	log("TIMING: Loading ligand coordinates took %0.3f s" % (time2 - time1),		log("TIMING: Loading ligand coordinates took %0.3f s" % (time2 - time1),

deepchem/feat/tests/test_rdkit_grid_features.py

+10 −10

Original line number	Original line	Diff line number	Diff line
	@@ -8,7 +8,7 @@ import unittest
	import numpy as np		import numpy as np
	np.random.seed(123)		np.random.seed(123)

	from rdkit.Chem import MolFromMolFile, MolFromSmiles, MolFromPDBFile, SDMolSupplier		from rdkit.Chem import MolFromSmiles
	from rdkit.Chem.AllChem import Mol, ComputeGasteigerCharges		from rdkit.Chem.AllChem import Mol, ComputeGasteigerCharges

	from deepchem.feat import rdkit_grid_featurizer as rgf		from deepchem.feat import rdkit_grid_featurizer as rgf
	@@ -205,15 +205,13 @@ class TestPiInteractions(unittest.TestCase):
	self.cycle4.Compute2DCoords()		self.cycle4.Compute2DCoords()

	# load and sanitize two real molecules		# load and sanitize two real molecules
	self.prot = MolFromPDBFile(		_, self.prot = rgf.load_molecule(
	os.path.join(current_dir, '3ws9_protein_fixer_rdkit.pdb'),		os.path.join(current_dir, '3ws9_protein_fixer_rdkit.pdb'),
	sanitize=True,		add_hydrogens=False, calc_charges=False, sanitize=True)
	removeHs=False)

	self.lig = SDMolSupplier(		_, self.lig = rgf.load_molecule(
	os.path.join(current_dir, '3ws9_ligand.sdf'),		os.path.join(current_dir, '3ws9_ligand.sdf'),
	sanitize=True,		add_hydrogens=False, calc_charges=False, sanitize=True)
	removeHs=False)[0]

	def test_compute_ring_center(self):		def test_compute_ring_center(self):
	# FIXME might break with different version of rdkit		# FIXME might break with different version of rdkit
	@@ -334,7 +332,7 @@ class TestFeaturizationFunctions(unittest.TestCase):
	self.ligand_file = os.path.join(current_dir, '3ws9_ligand.sdf')		self.ligand_file = os.path.join(current_dir, '3ws9_ligand.sdf')

	def test_compute_all_ecfp(self):		def test_compute_all_ecfp(self):
	mol = MolFromMolFile(self.ligand_file)		_, mol = rgf.load_molecule(self.ligand_file)
	num_atoms = mol.GetNumAtoms()		num_atoms = mol.GetNumAtoms()
	for degree in range(1, 4):		for degree in range(1, 4):
	# TODO test if dict contains smiles		# TODO test if dict contains smiles
	@@ -482,7 +480,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
	],		],
	ecfp_power=ecfp_power,		ecfp_power=ecfp_power,
	splif_power=splif_power,		splif_power=splif_power,
	flatten=True)		flatten=True,
			sanitize=True)
	self.assertIsInstance(featurizer, rgf.RdkitGridFeaturizer)		self.assertIsInstance(featurizer, rgf.RdkitGridFeaturizer)
	feature_tensor = featurizer.featurize_complexes([self.ligand_file],		feature_tensor = featurizer.featurize_complexes([self.ligand_file],
	[self.protein_file])		[self.protein_file])
	@@ -510,7 +509,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
	box_width=box_w,		box_width=box_w,
	ecfp_power=f_power,		ecfp_power=f_power,
	feature_types=['all_combined'],		feature_types=['all_combined'],
	flatten=True)		flatten=True,
			sanitize=True)

	prot_tensor = rgf_featurizer._voxelize(		prot_tensor = rgf_featurizer._voxelize(
	rgf.convert_atom_to_voxel,		rgf.convert_atom_to_voxel,

deepchem/utils/rdkit_util.py

+7 −2

Original line number	Original line	Diff line number	Diff line
	@@ -87,7 +87,8 @@ def compute_charges(mol):
	return mol		return mol


	def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True):		def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True,
			sanitize=False):
	"""		"""
	Converts molecule file to (xyz-coords, obmol object)		Converts molecule file to (xyz-coords, obmol object)

	@@ -99,7 +100,7 @@ def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True):
	:return: (xyz, mol)		:return: (xyz, mol)
	"""		"""
	if ".mol2" in molecule_file:		if ".mol2" in molecule_file:
	my_mol = Chem.MolFromMol2File(molecule_file)		my_mol = Chem.MolFromMol2File(molecule_file, sanitize=False, removeHs=False)
	elif ".sdf" in molecule_file:		elif ".sdf" in molecule_file:
	suppl = Chem.SDMolSupplier(str(molecule_file), sanitize=False)		suppl = Chem.SDMolSupplier(str(molecule_file), sanitize=False)
	my_mol = suppl[0]		my_mol = suppl[0]
	@@ -118,6 +119,10 @@ def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True):

	if add_hydrogens or calc_charges:		if add_hydrogens or calc_charges:
	my_mol = add_hydrogens_to_mol(my_mol)		my_mol = add_hydrogens_to_mol(my_mol)
			# TODO: mol should be always sanitized when charges are calculated
			# can't change it now because it would break a lot of examples
			if sanitize:
			Chem.SanitizeMol(my_mol)
	if calc_charges:		if calc_charges:
	compute_charges(my_mol)		compute_charges(my_mol)

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