AtomicConvFeaturizer test fixes (1fd3b05a) · Commits · 钟慕尧 / deepchem

deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+2 −5

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		Atomic coordinate featurizer.
		"""
		import logging
		import warnings

		import numpy as np

		@@ -242,10 +243,6 @@ class AtomicConvFeaturizer(ComplexFeaturizer):
		neighbor_list = compute_neighbor_list(coords, self.neighbor_cutoff,
		self.max_num_neighbors, None)
		# pad outputs
		if len(neighbor_list.keys()) < max_num_atoms:
		s = range(max_num_atoms) - neighbor_list.keys()
		for k in s:
		neighbor_list[k] = []
		z = self.get_Z_matrix(mol, max_num_atoms)
		z = pad_array(z, max_num_atoms)
		coords = pad_array(coords, (max_num_atoms, 3))
		@@ -285,7 +282,7 @@ class AtomicConvFeaturizer(ComplexFeaturizer):
		return coords, mol


		#################### Deprecation warnings for old atomic conv featurizer name ####################
		# Deprecation warnings for old atomic conv featurizer name #

		ATOMICCONV_DEPRECATION = "{} is deprecated and has been renamed to {} and will be removed in DeepChem 3.0."

deepchem/feat/tests/data/3zso_protein_noH.pdb

0 → 100644

+2876 −0

File added.

Preview size limit exceeded, changes collapsed.

deepchem/feat/tests/test_atomic_conv_feat.py

+16 −7

Original line number	Diff line number	Diff line
		@@ -5,6 +5,8 @@ Test atomic conv featurizer.
		import os
		import logging

		import numpy as np

		from deepchem.feat import AtomicConvFeaturizer

		logger = logging.getLogger(__name__)
		@@ -14,12 +16,12 @@ def test_atomic_conv_featurization():
		"""Unit test for AtomicConvFeaturizer."""
		dir_path = os.path.dirname(os.path.realpath(__file__))
		ligand_file = os.path.join(dir_path, "data/3zso_ligand_hyd.pdb")
		protein_file = os.path.join(dir_path, "data/3zso_protein.pdb")
		protein_file = os.path.join(dir_path, "data/3zso_protein_noH.pdb")
		# Pulled from PDB files. For larger datasets with more PDBs, would use
		# max num atoms instead of exact.
		frag1_num_atoms = 44 # for ligand atoms
		frag2_num_atoms = 2336 # for protein atoms
		complex_num_atoms = 2380 # in total
		frag2_num_atoms = 2334 # for protein atoms
		complex_num_atoms = 2378 # in total
		max_num_neighbors = 4
		# Cutoff in angstroms
		neighbor_cutoff = 4
		@@ -30,20 +32,27 @@ def test_atomic_conv_featurization():
		frag2_neighbor_list, frag2_z, complex_coords, complex_neighbor_list,
		complex_z) = complex_featurizer._featurize((ligand_file, protein_file))

		# Coords are padded, neighbor list and Z are not
		assert frag1_coords.shape == (frag1_num_atoms, 3)
		assert (sorted(list(frag1_neighbor_list.keys())) == list(
		range(frag1_num_atoms)))
		assert frag1_neighbor_list[0] == [1, 2, 14, 3]
		assert frag1_z.shape == (frag1_num_atoms,)
		assert np.array_equal(
		frag1_z,
		np.array([
		6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
		6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 8, 8, 8, 8, 8, 8, 8
		]))

		assert frag2_coords.shape == (frag2_num_atoms, 3)

		assert (sorted(list(frag2_neighbor_list.keys())) == list(
		range(frag2_num_atoms)))

		assert frag2_neighbor_list[0] == [1, 2, 4, 3]
		assert frag2_z.shape == (frag2_num_atoms,)
		assert complex_coords.shape == (complex_num_atoms, 3)

		assert complex_coords.shape == (complex_num_atoms, 3)
		assert (sorted(list(complex_neighbor_list.keys())) == list(
		range(complex_num_atoms)))

		assert complex_neighbor_list[0] == [1, 2, 14, 3]
		assert (complex_z.shape == (complex_num_atoms,))

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