deal with indices outside of the box in RdkitGridFeaturizer._voxelize (9b0afeee) · Commits · 钟慕尧 / deepchem

deepchem/feat/rdkit_grid_featurizer.py

+3 −7

Original line number	Diff line number	Diff line
		@@ -1095,7 +1095,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		channel_power=None,
		nb_channel=16,
		dtype="np.int8"):
		# TODO(enf): make array index checking not a try-catch statement.

		if channel_power is not None:
		if channel_power == 0:
		nb_channel = 1
		@@ -1115,22 +1115,18 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		for key, features in feature_dict.items():
		voxels = get_voxels(coordinates, key, self.box_width, self.voxel_width)
		for voxel in voxels:
		try:
		if ((voxel >= 0) & (voxel < self.voxels_per_edge)).all():
		if hash_function is not None:
		feature_tensor[voxel[0], voxel[1], voxel[2],
		hash_function(features, channel_power)] += 1.0
		else:
		feature_tensor[voxel[0], voxel[1], voxel[3], 0] += features
		except:
		continue
		elif feature_list is not None:
		for key in feature_list:
		voxels = get_voxels(coordinates, key, self.box_width, self.voxel_width)
		for voxel in voxels:
		try:
		if ((voxel >= 0) & (voxel < self.voxels_per_edge)).all():
		feature_tensor[voxel[0], voxel[1], voxel[2], 0] += 1.0
		except:
		continue

		return feature_tensor