def test_labels(self):
""" just checks for exceptions """
featurizer = MDFeaturizer(pdbfile)
featurizer.add_angles([[1, 2, 3], [4, 5, 6]])
featurizer.add_backbone_torsions()
featurizer.add_contacts([[0, 1], [0, 3]])
featurizer.add_distances([[0, 1], [0, 3]])
featurizer.add_inverse_distances([[0, 1], [0, 3]])
cs = CustomFeature(lambda x: x - 1)
cs.dimension = lambda: 3
featurizer.add_custom_feature(cs)
featurizer.describe()
def test_labels(self):
""" just checks for exceptions """
featurizer = MDFeaturizer(pdbfile)
featurizer.add_angles([[1, 2, 3], [4, 5, 6]])
featurizer.add_backbone_torsions()
featurizer.add_contacts([[0, 1], [0, 3]])
featurizer.add_distances([[0, 1], [0, 3]])
featurizer.add_inverse_distances([[0, 1], [0, 3]])
cs = CustomFeature(lambda x: x - 1, dim=3)
featurizer.add_custom_feature(cs)
featurizer.add_minrmsd_to_ref(pdbfile)
featurizer.add_residue_mindist()
featurizer.add_group_mindist([[0, 1], [0, 2]])
featurizer.describe()
def testAddFeaturesWithDuplicates(self):
"""this tests adds multiple features twice (eg. same indices) and
checks whether they are rejected or not"""
featurizer = MDFeaturizer(pdbfile)
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
self.assertEqual(len(featurizer.active_features), 1)
featurizer.add_backbone_torsions()
self.assertEqual(len(featurizer.active_features), 2)
featurizer.add_backbone_torsions()
self.assertEqual(len(featurizer.active_features), 2)
featurizer.add_contacts([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 3)
featurizer.add_contacts([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 3)
# try to fool it with ca selection
ca = featurizer.select_Ca()
ca = featurizer.pairs(ca)
featurizer.add_distances(ca)
self.assertEqual(len(featurizer.active_features), 4)
featurizer.add_distances_ca()
self.assertEqual(len(featurizer.active_features), 4)
featurizer.add_inverse_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 5)
featurizer.add_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 6)
featurizer.add_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 6)
def my_func(x):
return x - 1
def foo(x):
return x - 1
my_feature = CustomFeature(my_func)
my_feature.dimension = 3
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), 7)
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), 7)
# since myfunc and foo are different functions, it should be added
foo_feat = CustomFeature(foo, dim=3)
featurizer.add_custom_feature(foo_feat)
self.assertEqual(len(featurizer.active_features), 8)
def testAddFeaturesWithDuplicates(self):
"""this tests adds multiple features twice (eg. same indices) and
checks whether they are rejected or not"""
featurizer = MDFeaturizer(pdbfile)
expected_active = 1
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_contacts([[0, 1], [0, 3]])
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_contacts([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), expected_active)
# try to fool it with ca selection
ca = featurizer.select_Ca()
ca = featurizer.pairs(ca, excluded_neighbors=0)
featurizer.add_distances(ca)
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_distances_ca(excluded_neighbors=0)
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_inverse_distances([[0, 1], [0, 3]])
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_distances([[0, 1], [0, 3]])
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), expected_active)
def my_func(x):
return x - 1
def foo(x):
return x - 1
expected_active += 1
my_feature = CustomFeature(my_func)
my_feature.dimension = 3
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), expected_active)
# since myfunc and foo are different functions, it should be added
expected_active += 1
foo_feat = CustomFeature(foo, dim=3)
featurizer.add_custom_feature(foo_feat)
self.assertEqual(len(featurizer.active_features), expected_active)
expected_active += 1
ref = mdtraj.load(xtcfile, top=pdbfile)
featurizer.add_minrmsd_to_ref(ref)
featurizer.add_minrmsd_to_ref(ref)
self.assertEquals(len(featurizer.active_features), expected_active)
expected_active += 1
featurizer.add_minrmsd_to_ref(pdbfile)
featurizer.add_minrmsd_to_ref(pdbfile)
self.assertEquals(len(featurizer.active_features), expected_active)
expected_active += 1
featurizer.add_residue_mindist()
featurizer.add_residue_mindist()
self.assertEquals(len(featurizer.active_features), expected_active)
expected_active += 1
featurizer.add_group_mindist([[0, 1], [0, 2]])
featurizer.add_group_mindist([[0, 1], [0, 2]])
self.assertEquals(len(featurizer.active_features), expected_active)