class TestCustomFeature(unittest.TestCase):
def setUp(self):
self.feat = MDFeaturizer(pdbfile)
self.traj = mdtraj.load(xtcfile, top=pdbfile)
self.pairs = [[0, 1], [0, 2], [1, 2]] #some distances
self.means = [.5, .75, 1.0] #bogus means
self.U = np.array([[0, 1], [1, 0], [
1, 1
]]) #bogus transformation, projects from 3 distances to 2 components
def test_some_feature(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
Y_custom_feature = self.feat.transform(self.traj)
# Directly call the function
Y_function = some_call_to_mdtraj_some_operations_some_linalg(
self.traj, self.pairs, self.means, self.U)
assert np.allclose(Y_custom_feature, Y_function)
def test_describe(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
self.feat.describe()
def test_dimensionality(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
assert self.feat.dimension() == self.U.shape[1]
class TestCustomFeature(unittest.TestCase):
def setUp(self):
self.feat = MDFeaturizer(pdbfile)
self.traj = mdtraj.load(xtcfile, top=pdbfile)
self.pairs = [[0, 1], [0, 2], [1, 2]] #some distances
self.means = [.5, .75, 1.0] #bogus means
self.U = np.array([[0, 1], [1, 0], [
1, 1
]]) #bogus transformation, projects from 3 distances to 2 components
def test_some_feature(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
Y_custom_feature = self.feat.transform(self.traj)
# Directly call the function
Y_function = some_call_to_mdtraj_some_operations_some_linalg(
self.traj, self.pairs, self.means, self.U)
assert np.allclose(Y_custom_feature, Y_function)
def test_describe(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_describe_given(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg,
self.U.shape[1],
self.pairs,
self.means,
self.U,
description=['foo'] * self.U.shape[1])
desc = self.feat.describe()
self.assertIn('foo', desc)
self.assertEqual(len(desc), self.feat.dimension())
def test_describe_given_str(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg,
self.U.shape[1],
self.pairs,
self.means,
self.U,
description='test')
desc = self.feat.describe()
self.assertIn('test', desc)
self.assertEqual(len(desc), self.feat.dimension())
def test_describe_given_wrong(self):
""" either a list matching input dim, or 1 element iterable allowed"""
with self.assertRaises(ValueError) as cm:
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg,
self.U.shape[1] + 1,
self.pairs,
self.means,
self.U,
description=['ff', 'ff'])
def test_describe_1_element_expand(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg,
self.U.shape[1] + 1,
self.pairs,
self.means,
self.U,
description=['test'])
desc = self.feat.describe()
self.assertEqual(desc, ['test'] * 3)
def test_dimensionality(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
assert self.feat.dimension() == self.U.shape[1]