yapf and cleanup (74414af3) · Commits · 钟慕尧 / deepchem

deepchem/models/tensorgraph/layers.py

+2 −8

Original line number	Diff line number	Diff line
		@@ -3287,20 +3287,14 @@ class ANIFeat(Layer):
		# d = tf.nn.relu(d) # fix numerical instabilities about diagonal
		# d = tf.sqrt(d) # does this have negative elements? may be unstable for diagonals

		# d = d * flags

		max_atoms = self.max_atoms
		tensor1 = tf.stack([coordinates] * max_atoms, axis=1)
		tensor2 = tf.stack([coordinates] * max_atoms, axis=2)

		# Calculate pairwise distance
		# d = tf.sqrt(
		# tf.nn.relu(
		# tf.reduce_sum(tf.squared_difference(tensor1, tensor2), axis=3)))
		d = tf.sqrt(
		tf.reduce_sum(tf.squared_difference(tensor1, tensor2), axis=3) + 1e-7)
		# d = tf.reduce_sum(tf.squared_difference(tensor1, tensor2), axis=3)
		# Masking for valid atom index

		d = d * flags
		return d

+6 −9

Original line number	Diff line number	Diff line
		@@ -15,20 +15,17 @@ class TestANIRegression(unittest.TestCase):

		max_atoms = 4

		X = np.array([
		[
		X = np.array([[
		[1, 5.0, 3.2, 1.1],
		[6, 1.0, 3.4, -1.1],
		[1, 2.3, 3.4, 2.2],
		[0, 0, 0, 0],
		],
		[
		], [
		[8, 2.0, -1.4, -1.1],
		[7, 6.3, 2.4, 3.2],
		[0, 0, 0, 0],
		[0, 0, 0, 0],
		]
		])
		]])

		y = np.array([2.0, 1.1])