feat test fixes (6e5ca359) · Commits · 钟慕尧 / deepchem

deepchem/feat/complex_featurizers/complex_atomic_coordinates.py

+10 −1

Original line number	Diff line number	Diff line
		@@ -138,7 +138,7 @@ class AtomicConvFeaturizer(ComplexFeaturizer):
		"""This class computes the featurization that corresponds to AtomicConvModel.

		This class computes featurizations needed for AtomicConvModel.
		Given a two molecular structures, it computes a number of useful
		Given two molecular structures, it computes a number of useful
		geometric features. In particular, for each molecule and the global
		complex, it computes a coordinates matrix of size (N_atoms, 3)
		where N_atoms is the number of atoms. It also computes a
		@@ -153,6 +153,7 @@ class AtomicConvFeaturizer(ComplexFeaturizer):
		returned for each complex. Note that for efficiency, fragments of
		the molecules can be provided rather than the full molecules
		themselves.

		"""

		def __init__(self,
		@@ -180,7 +181,9 @@ class AtomicConvFeaturizer(ComplexFeaturizer):
		this cutoff, the closest `max_num_neighbors` will be used.
		strip_hydrogens: bool (default True)
		Remove hydrogens before computing featurization.

		"""

		self.frag1_num_atoms = frag1_num_atoms
		self.frag2_num_atoms = frag2_num_atoms
		self.complex_num_atoms = complex_num_atoms
		@@ -197,6 +200,7 @@ class AtomicConvFeaturizer(ComplexFeaturizer):
		mol_pdb_file, is_protein=False, sanitize=True, add_hydrogens=False)
		frag2_coords, frag2_mol = load_molecule(
		protein_pdb_file, is_protein=True, sanitize=True, add_hydrogens=False)

		except MoleculeLoadException:
		# Currently handles loading failures by returning None
		# TODO: Is there a better handling procedure?
		@@ -237,6 +241,11 @@ class AtomicConvFeaturizer(ComplexFeaturizer):
		logging.info("Featurizing molecule of size: %d", len(mol.GetAtoms()))
		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))

deepchem/feat/tests/test_atomic_conv_feat.py

+5 −9

Original line number	Diff line number	Diff line
		@@ -4,8 +4,7 @@ Test atomic conv featurizer.

		import os
		import logging
		import numpy as np
		import unittest

		from deepchem.feat import AtomicConvFeaturizer

		logger = logging.getLogger(__name__)
		@@ -37,17 +36,14 @@ def test_atomic_conv_featurization():
		assert frag1_z.shape == (frag1_num_atoms,)

		assert frag2_coords.shape == (frag2_num_atoms, 3)
		##################
		print("len(sorted(list(frag2_neighbor_list.keys())))")
		print(len(sorted(list(frag2_neighbor_list.keys()))))
		print("len(list(range(frag2_num_atoms)))")
		print(len(list(range(frag2_num_atoms))))
		##################

		assert (sorted(list(frag2_neighbor_list.keys())) == list(
		range(frag2_num_atoms)))
		assert frag2_z.shape == (frag2_num_atoms,)

		assert frag2_z.shape == (frag2_num_atoms,)
		assert complex_coords.shape == (complex_num_atoms, 3)

		assert (sorted(list(complex_neighbor_list.keys())) == list(
		range(complex_num_atoms)))

		assert (complex_z.shape == (complex_num_atoms,))

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