:truck: move data (fea42a67) · Commits · 钟慕尧 / deepchem

deepchem/feat/tests/3ws9_ligand.sdf→deepchem/feat/tests/data/3ws9_ligand.sdf

+0 −0

File moved.

+0 −0

File moved.

+6 −6

Original line number	Diff line number	Diff line
		@@ -27,8 +27,8 @@ class TestHelperFunctions(unittest.TestCase):
		# TODO test more formats for ligand
		current_dir = os.path.dirname(os.path.realpath(__file__))
		self.protein_file = os.path.join(current_dir,
		'3ws9_protein_fixer_rdkit.pdb')
		self.ligand_file = os.path.join(current_dir, '3ws9_ligand.sdf')
		'data', '3ws9_protein_fixer_rdkit.pdb')
		self.ligand_file = os.path.join(current_dir, 'data', '3ws9_ligand.sdf')

		def test_load_molecule(self):
		# adding hydrogens and charges is tested in dc.utils
		@@ -194,13 +194,13 @@ class TestPiInteractions(unittest.TestCase):

		# load and sanitize two real molecules
		_, self.prot = rgf.load_molecule(
		os.path.join(current_dir, '3ws9_protein_fixer_rdkit.pdb'),
		os.path.join(current_dir, 'data', '3ws9_protein_fixer_rdkit.pdb'),
		add_hydrogens=False,
		calc_charges=False,
		sanitize=True)

		_, self.lig = rgf.load_molecule(
		os.path.join(current_dir, '3ws9_ligand.sdf'),
		os.path.join(current_dir, 'data', '3ws9_ligand.sdf'),
		add_hydrogens=False,
		calc_charges=False,
		sanitize=True)
		@@ -320,8 +320,8 @@ class TestFeaturizationFunctions(unittest.TestCase):
		def setUp(self):
		current_dir = os.path.dirname(os.path.realpath(__file__))
		self.protein_file = os.path.join(current_dir,
		'3ws9_protein_fixer_rdkit.pdb')
		self.ligand_file = os.path.join(current_dir, '3ws9_ligand.sdf')
		'data', '3ws9_protein_fixer_rdkit.pdb')
		self.ligand_file = os.path.join(current_dir, 'data', '3ws9_ligand.sdf')

		def test_compute_all_ecfp(self):
		_, mol = rgf.load_molecule(self.ligand_file)

deleted100644 → 0

+0 −43

Original line number	Diff line number	Diff line
		"""
		Tests for importing .sdf files
		"""
		__author__ = "Joseph Gomes"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import os
		import unittest
		import tempfile
		import shutil
		import deepchem as dc


		class TestFeaturizedSamples(unittest.TestCase):
		"""
		Test Featurized Samples class.
		"""

		def random_test_train_valid_test_split_from_sdf(self):
		"""Test of singletask CoulombMatrixEig regression on .sdf file."""
		splittype = "random"
		input_transforms = []
		output_transforms = ["normalize"]
		model_params = {}
		tasks = ["atomization_energy"]
		task_type = "regression"
		task_types = {task: task_type for task in tasks}
		current_dir = os.path.dirname(os.path.abspath(__file__))
		input_file = os.path.join(current_dir, "data/water.sdf")

		featurizer = dc.feat.CoulombMatrixEig(6, remove_hydrogens=False)
		loader = dc.data.SDFLoader(tasks=tasks, featurizer=featurizer)

		dataset = loader.featurize(input_file)

		# Splits featurized samples into train/test
		splitter = dc.splits.RandomSplitter()
		train_dataset, valid_dataset, test_dataset = \
		splitter.train_valid_test_split(dataset)
		assert len(train_dataset) == 8
		assert len(valid_dataset) == 1
		assert len(test_dataset) == 1

+2 −2

Original line number	Diff line number	Diff line
		@@ -10,9 +10,9 @@ class TestFragmentUtil(unittest.TestCase):
		# TODO test more formats for ligand
		current_dir = os.path.dirname(os.path.realpath(__file__))
		self.protein_file = os.path.join(
		current_dir, '../../feat/tests/3ws9_protein_fixer_rdkit.pdb')
		current_dir, '../../feat/tests/data/3ws9_protein_fixer_rdkit.pdb')
		self.ligand_file = os.path.join(current_dir,
		'../../feat/tests/3ws9_ligand.sdf')
		'../../feat/tests/data/3ws9_ligand.sdf')

		def test_get_contact_atom_indices(self):
		complexes = rdkit_util.load_complex([self.protein_file, self.ligand_file])