Merge pull request #1874 from deepchem/conda_env_rtd (48d40fc9) · Commits · 钟慕尧 / deepchem

deepchem/feat/graph_features.py

+12 −6

Original line number	Diff line number	Diff line
		import numpy as np
		from rdkit import Chem

		import deepchem as dc
		from deepchem.feat import Featurizer
		@@ -55,11 +54,9 @@ possible_atom_list = [
		possible_numH_list = [0, 1, 2, 3, 4]
		possible_valence_list = [0, 1, 2, 3, 4, 5, 6]
		possible_formal_charge_list = [-3, -2, -1, 0, 1, 2, 3]
		possible_hybridization_list = [
		Chem.rdchem.HybridizationType.SP, Chem.rdchem.HybridizationType.SP2,
		Chem.rdchem.HybridizationType.SP3, Chem.rdchem.HybridizationType.SP3D,
		Chem.rdchem.HybridizationType.SP3D2
		]
		# To avoid importing rdkit, this is a placeholder list of the correct
		# length. These will be replaced with rdkit HybridizationType below
		possible_hybridization_list = ["SP", "SP2", "SP3", "SP3D", "SP3D2"]
		possible_number_radical_e_list = [0, 1, 2]
		possible_chirality_list = ['R', 'S']

		@@ -84,6 +81,14 @@ def get_feature_list(atom):
		atom: RDKit.rdchem.Atom
		Atom to get features for
		"""
		# Replace the hybridization
		from rdkit import Chem
		global possible_hybridization_list
		possible_hybridization_list = [
		Chem.rdchem.HybridizationType.SP, Chem.rdchem.HybridizationType.SP2,
		Chem.rdchem.HybridizationType.SP3, Chem.rdchem.HybridizationType.SP3D,
		Chem.rdchem.HybridizationType.SP3D2
		]
		features = 6 * [0]
		features[0] = safe_index(possible_atom_list, atom.GetSymbol())
		features[1] = safe_index(possible_numH_list, atom.GetTotalNumHs())
		@@ -91,6 +96,7 @@ def get_feature_list(atom):
		features[3] = safe_index(possible_formal_charge_list, atom.GetFormalCharge())
		features[4] = safe_index(possible_number_radical_e_list,
		atom.GetNumRadicalElectrons())

		features[5] = safe_index(possible_hybridization_list, atom.GetHybridization())
		return features

deepchem/feat/tests/test_graph_features.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -22,7 +22,7 @@ class TestConvMolFeaturizer(unittest.TestCase):
		# Note there is a central nitrogen of degree 4, with 4 carbons
		# of degree 1 (connected only to central nitrogen).
		raw_smiles = ['C[N+](C)(C)C']
		import rdkit
		import rdkit.Chem
		mols = [rdkit.Chem.MolFromSmiles(s) for s in raw_smiles]
		featurizer = ConvMolFeaturizer()
		mols = featurizer.featurize(mols)
		@@ -70,7 +70,7 @@ class TestConvMolFeaturizer(unittest.TestCase):
		def test_alkane(self):
		"""Test on simple alkane"""
		raw_smiles = ['CCC']
		import rdkit
		import rdkit.Chem
		mols = [rdkit.Chem.MolFromSmiles(s) for s in raw_smiles]
		featurizer = ConvMolFeaturizer()
		mol_list = featurizer.featurize(mols)

docs/conf.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@
		#
		import os
		import sys
		sys.path.insert(0, os.path.abspath('..'))

		# -- Project information -----------------------------------------------------

docs/requirements.txt

+6 −0

Original line number	Diff line number	Diff line
		sphinx_rtd_theme
		numpy
		pandas
		sklearn
		tensorflow
		pillow
		tensorflow_probability

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