Changes (ae9b5670) · Commits · 钟慕尧 / deepchem

deepchem/feat/base_classes.py

+18 −14

Original line number	Diff line number	Diff line
		@@ -44,9 +44,11 @@ class Featurizer(object):
		for i, point in enumerate(datapoints):
		if i % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % i)
		if point is not None:
		try:
		features.append(self._featurize(point))
		else:
		except:
		logger.warning(
		"Failed to featurize datapoint %d. Appending empty array")
		features.append(np.array([]))

		features = np.asarray(features)
		@@ -139,12 +141,12 @@ class MolecularFeaturizer(Featurizer):
		In general, subclasses of this class will require RDKit to be installed.
		"""

		def featurize(self, mols, log_every_n=1000):
		def featurize(self, molecules, log_every_n=1000):
		"""Calculate features for molecules.

		Parameters
		----------
		mols : RDKit Mol / SMILES string /iterable
		molecules: RDKit Mol / SMILES string /iterable
		RDKit Mol, or SMILES string or iterable sequence of RDKit mols/SMILES
		strings.

		@@ -159,22 +161,24 @@ class MolecularFeaturizer(Featurizer):
		except ModuleNotFoundError:
		raise ValueError("This class requires RDKit to be installed.")
		# Special case handling of single molecule
		if isinstance(mols, str) or isinstance(mols, Mol):
		mols = [mols]
		if isinstance(molecules, str) or isinstance(molecules, Mol):
		molecules = [molecules]
		else:
		# Convert iterables to list
		mols = list(mols)
		molecutes = list(molecules)
		features = []
		for i, mol in enumerate(mols):
		for i, mol in enumerate(molecules):
		if i % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % i)
		if mol is not None:
		try:
		# Process only case of SMILES strings.
		if isinstance(mol, str):
		# mol must be a SMILES string so parse
		mol = Chem.MolFromSmiles(mol)
		features.append(self._featurize(mol))
		else:
		except:
		logger.warning(
		"Failed to featurize datapoint %d. Appending empty array")
		features.append(np.array([]))

		features = np.asarray(features)
		@@ -191,16 +195,16 @@ class MolecularFeaturizer(Featurizer):
		"""
		raise NotImplementedError('Featurizer is not defined.')

		def __call__(self, mols):
		def __call__(self, molecules):
		"""
		Calculate features for molecules.

		Parameters
		----------
		mols : iterable
		RDKit Mol objects.
		molecules: iterable
		An iterable yielding RDKit Mol objects or SMILES strings.
		"""
		return self.featurize(mols)
		return self.featurize(molecules)


		class UserDefinedFeaturizer(Featurizer):

deepchem/feat/graph_features.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -115,7 +115,7 @@ def safe_index(l, e):


		class GraphConvConstants(object):
		"""Allowed Atom Types."""
		"""This class defines a collection of constants which are useful for graph convolutions on molecules."""
		possible_atom_list = [
		'C', 'N', 'O', 'S', 'F', 'P', 'Cl', 'Mg', 'Na', 'Br', 'Fe', 'Ca', 'Cu',
		'Mc', 'Pd', 'Pb', 'K', 'I', 'Al', 'Ni', 'Mn'

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