Remove verbose and adjust featurizing classes (8bfa5990) · Commits · 钟慕尧 / deepchem

deepchem/feat/coulomb_matrices.py

+0 −2

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		"""
		Generate coulomb matrices for molecules.

		See Montavon et al., _New Journal of Physics_ __15__ (2013) 095003.
		"""
		import numpy as np
		import deepchem as dc

+8 −1

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		"""
		Implements featurizations for GraphConv and Weave Models.
		"""
		import numpy as np
		import deepchem as dc
		from deepchem.feat.base_classes import MolecularFeaturizer
		@@ -6,6 +9,8 @@ from deepchem.feat.mol_graphs import ConvMol, WeaveMol
		from deepchem.data import DiskDataset
		import logging

		logger = logging.getLogger(__name__)


		def one_of_k_encoding(x, allowable_set):
		"""Encodes elements of a provided set as integers.
		@@ -273,7 +278,9 @@ def atom_features(atom,
		use_chirality=False):
		"""Helper method used to compute per-atom feature vectors.

		Many different featurization methods compute per-atom features such as ConvMolFeaturizer, WeaveFeaturizer. This method computes such features.
		Many different featurization methods compute per-atom features
		such as ConvMolFeaturizer, WeaveFeaturizer. This method
		computes such features.

		Parameters
		----------

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		@@ -6,9 +6,12 @@ __copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import csv
		import logging
		import random
		import numpy as np

		logger = logging.getLogger(__name__)


		def cumulative_sum_minus_last(l, offset=0):
		"""Returns cumulative sums for set of counts, removing last entry.

+5 −0

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		"""
		Implements a simple one hot encoder for text models.
		"""
		import numpy as np
		from deepchem.feat.base_classes import MolecularFeaturizer

		logger = logging.getLogger(__name__)

		zinc_charset = [
		' ', '#', ')', '(', '+', '-', '/', '1', '3', '2', '5', '4', '7', '6', '8',
		'=', '@', 'C', 'B', 'F', 'I', 'H', 'O', 'N', 'S', '[', ']', '\\', 'c', 'l',

+12 −2

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		"""
		Encodes smiles/smarts as RDKIT objects directly.
		"""
		from deepchem.feat.base_classes import MolecularFeaturizer

		import logging
		from deepchem.feat import MolecularFeaturizer
		from deepchem.feat import ReactionFeaturizer


		class RawFeaturizer(MolecularFeaturizer):
		"""Encodes a molecule as a SMILES string or RDKit mol.
		@@ -45,10 +52,13 @@ class RawFeaturizer(MolecularFeaturizer):
		else:
		return mol

		class RawReactionFeaturizer(Featurizer):

		class RawReactionFeaturizer(ReactionFeaturizer):
		"""Featurize SMARTS as RDKit Reaction objects.

		This featurizer uses RDKit's `rdkit.Chem.rdChemReactions.ReactionFromSmarts` to parse in input SMARTS strings.
		This featurizer uses RDKit's
		`rdkit.Chem.rdChemReactions.ReactionFromSmarts` to parse in
		input SMARTS strings which encode reactions.
		"""

		def __init__(self, smarts=True):