Merge pull request #1769 from VIGS25/weave-chirality (e4325ff5) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -128,7 +128,8 @@ def get_user_specified_features(df, featurizer, verbose=True):
		time1 = time.time()
		df[featurizer.feature_fields] = df[featurizer.feature_fields].apply(
		pd.to_numeric)
		X_shard = df.as_matrix(columns=featurizer.feature_fields)
		df_fields = df[featurizer.feature_fields]
		X_shard = df_fields.values
		time2 = time.time()
		log("TIMING: user specified processing took %0.3f s" % (time2 - time1),
		verbose)

+14 −9

Original line number	Diff line number	Diff line
		@@ -73,6 +73,8 @@ reference_lists = [
		]

		intervals = get_intervals(reference_lists)
		possible_bond_stereo = ["STEREONONE", "STEREOANY", "STEREOZ", "STEREOE"]
		bond_fdim_base = 6


		def get_feature_list(atom):
		@@ -210,8 +212,7 @@ def bond_features(bond, use_chirality=False):
		]
		if use_chirality:
		bond_feats = bond_feats + one_of_k_encoding_unk(
		str(bond.GetStereo()),
		["STEREONONE", "STEREOANY", "STEREOZ", "STEREOE"])
		str(bond.GetStereo()), possible_bond_stereo)
		return np.array(bond_feats)


		@@ -396,6 +397,10 @@ class WeaveFeaturizer(Featurizer):
		self.explicit_H = explicit_H
		# If uses use_chirality
		self.use_chirality = use_chirality
		if self.use_chirality:
		self.bt_len = bond_fdim_base + len(possible_bond_stereo)
		else:
		self.bt_len = bond_fdim_base

		def _featurize(self, mol):
		"""Encodes mol as a WeaveMol object."""
		@@ -430,7 +435,7 @@ class WeaveFeaturizer(Featurizer):
		mol,
		edge_list,
		canon_adj_list,
		bt_len=6,
		bt_len=self.bt_len,
		graph_distance=self.graph_distance)

		return WeaveMol(nodes, pairs)