Changes (76b6a1ab) · Commits · 钟慕尧 / deepchem

deepchem/feat/base_classes.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -117,12 +117,12 @@ class ComplexFeaturizer(object):
		raise NotImplementedError('Featurizer is not defined.')


		class MolecularFeaturizer(object):
		class MolecularFeaturizer(Featurizer):
		"""Abstract class for calculating a set of features for a
		molecule.

		The defining feature of a `MolecularFeaturizer` is that it
		uses SMILES strings and RDKIT molecule objecgs to represent
		uses SMILES strings and RDKIT molecule objects to represent
		small molecules. All other featurizers which are subclasses of
		this class should plan to process input which comes as smiles
		strings or RDKIT molecules.

+12 −4

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		Basic molecular features.
		"""

		import numpy as np
		from deepchem.feat.base_classes import MolecularFeaturizer


		@@ -12,7 +13,6 @@ class MolecularWeight(MolecularFeaturizer):
		----
		This class requires RDKit to be installed.
		"""
		name = ['mw', 'molecular_weight']

		def _featurize(self, mol):
		"""
		@@ -22,6 +22,10 @@ class MolecularWeight(MolecularFeaturizer):
		----------
		mol : RDKit Mol
		Molecule.

		Returns
		-------
		np.ndarray of length 1 containing the molecular weight.
		"""
		try:
		from rdkit.Chem import Descriptors
		@@ -29,7 +33,7 @@ class MolecularWeight(MolecularFeaturizer):
		raise ValueError("This class requires RDKit to be installed.")
		wt = Descriptors.ExactMolWt(mol)
		wt = [wt]
		return wt
		return np.asarray(wt)


		class RDKitDescriptors(MolecularFeaturizer):
		@@ -40,11 +44,15 @@ class RDKitDescriptors(MolecularFeaturizer):
		See http://rdkit.org/docs/GettingStartedInPython.html
		#list-of-available-descriptors.

		Attributes
		----------
		descriptors: list
		List of RDKit descriptor names used in this class.

		Note
		----
		This class requires RDKit to be installed.
		"""
		name = 'descriptors'

		# (ytz): This is done to avoid future compatibility issues like inclusion of
		# the 3D descriptors or changing the feature size.
		@@ -105,4 +113,4 @@ class RDKitDescriptors(MolecularFeaturizer):
		rval = []
		for desc_name, function in self.descList:
		rval.append(function(mol))
		return rval
		return np.asarray(rval)

+2 −2

Original line number	Diff line number	Diff line
		@@ -16,8 +16,8 @@ class RawFeaturizer(MolecularFeaturizer):
		def __init__(self, smiles=False):
		"""Initialize this featurizer.

		Parameter
		---------
		Parameters
		----------
		smiles: bool, optional (default False)
		If True, encode this molecule as a SMILES string. Else as a RDKit mol.
		"""