class AtomTest(ut.TestCase):
def setUp(self):
self.atoms = [
Atom(name='N9', x=3.0, y=3.0, z=3.0),
Atom(name='C4', x=2.0, y=2.0, z=2.0),
Atom(name='N3', x=1.0, y=1.0, z=1.0),
Atom(name='C3', x=0.0, y=0.0, z=0.0),
]
self.component = Component(self.atoms)
def test_it_can_get_atoms_by_name(self):
val = list(self.component.atoms(name=['N3', 'C4']))
ans = [self.atoms[1], self.atoms[2]]
self.assertEquals(ans, val)
def test_it_can_get_atoms_by_defined_names(self):
self.component.centers.define('example', ['N9', 'C3'])
val = list(self.component.atoms(name='example'))
ans = [self.atoms[0], self.atoms[-1]]
self.assertEquals(ans, val)
class BasicTest(ut.TestCase):
def setUp(self):
self.atoms = [
Atom(type='C', name='a1', polymeric='A', component_number=3,
x=0.0, y=0.0, z=0.0),
Atom(type='C', name='a2', polymeric='B', component_number=2,
x=0.0, y=0.0, z=0.0),
Atom(type='N', name='b1', polymeric='C', component_number=1,
x=0.0, y=0.0, z=0.0),
Atom(type='N', name='c2', polymeric='C', component_number=0,
x=0.0, y=0.0, z=0.0)
]
self.component = Component(self.atoms, type='rna', pdb='1GID', model=1,
chain='A', sequence='C', number=50,
symmetry='6_555')
def test_has_item_access(self):
val = self.component.type
ans = 'rna'
self.assertEqual(val, ans)
def test_length_is_number_atoms(self):
val = len(self.component)
ans = 4
self.assertEqual(val, ans)
def test_computes_unit_id(self):
val = self.component.unit_id()
ans = "1GID|1|A|C|50||||6_555"
self.assertEquals(val, ans)
def test_can_get_filtered_atoms(self):
val = list(self.component.atoms(type='C'))
ans = self.atoms[0:2]
self.assertEquals(val, ans)
def test_can_filter_using_a_list(self):
val = list(self.component.atoms(polymeric=['A', 'C']))
ans = [self.atoms[0], self.atoms[2], self.atoms[3]]
self.assertEquals(val, ans)
def test_can_filter_using_a_function(self):
val = list(self.component.atoms(polymeric=lambda a: a == 'C'))
ans = self.atoms[2:4]
self.assertEquals(val, ans)
def test_can_filter_by_several_attributes(self):
val = list(self.component.atoms(type='C', polymeric='B'))
ans = [self.atoms[1]]
self.assertEquals(val, ans)
def test_can_check_is_complete(self):
val = self.component.is_complete(['a1', 'a2', 'b1'])
self.assertTrue(val)
def test_can_check_is_not_complete(self):
val = self.component.is_complete(['a1', 'a2', 'g3'])
self.assertFalse(val)
def test_can_check_is_complete_using_custom_key(self):
val = self.component.is_complete([1, 2], key='component_number')
self.assertTrue(val)
def test_can_check_is_not_complete_using_custom_key(self):
val = self.component.is_complete([1, 2, 10], key='component_number')
self.assertFalse(val)
def test_knows_is_equal_to_itself(self):
self.assertTrue(self.component == self.component)
def test_knows_is_equal_to_equivelant_component(self):
self.assertTrue(self.component == self.component.select())
class InferHydrogenTest(ut.TestCase):
def setUp(self):
some_atoms = [
Atom(insertion_code='?', component_id='G', name='P',
symmetry='1_555', component_number='118', chain='B', y=54.015,
x=47.242, model='1', z=51.393, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='OP1',
symmetry='1_555', component_number='118', chain='B', y=53.619,
x=45.943, model='1', z=50.812, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='OP2',
symmetry='1_555', component_number='118', chain='B', y=55.016,
x=48.096, model='1', z=50.668, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O5'",
symmetry='1_555', component_number='118', chain='B', y=54.52,
x=47.009, model='1', z=52.887, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C5'",
symmetry='1_555', component_number='118', chain='B', y=53.848,
x=46.12, model='1', z=53.764, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C4'",
symmetry='1_555', component_number='118', chain='B', y=54.529,
x=46.123, model='1', z=55.11, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O4'",
symmetry='1_555', component_number='118', chain='B', y=54.338,
x=47.426, model='1', z=55.73, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C3'",
symmetry='1_555', component_number='118', chain='B', y=56.037,
x=45.94, model='1', z=55.051, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O3'",
symmetry='1_555', component_number='118', chain='B', y=56.374,
x=44.553, model='1', z=54.993, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C2'",
symmetry='1_555', component_number='118', chain='B', y=56.495,
x=46.647, model='1', z=56.326, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="O2'",
symmetry='1_555', component_number='118', chain='B', y=56.349,
x=45.878, model='1', z=57.494, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name="C1'",
symmetry='1_555', component_number='118', chain='B', y=55.528,
x=47.827, model='1', z=56.387, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N9',
symmetry='1_555', component_number='118', chain='B', y=56.026,
x=49.033, model='1', z=55.738, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C8',
symmetry='1_555', component_number='118', chain='B', y=55.785,
x=49.442, model='1', z=54.455, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N7',
symmetry='1_555', component_number='118', chain='B', y=56.371,
x=50.566, model='1', z=54.161, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C5',
symmetry='1_555', component_number='118', chain='B', y=57.031,
x=50.913, model='1', z=55.323, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C6',
symmetry='1_555', component_number='118', chain='B', y=57.827,
x=52.019, model='1', z=55.608, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='O6',
symmetry='1_555', component_number='118', chain='B', y=58.131,
x=52.969, model='1', z=54.873, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N1',
symmetry='1_555', component_number='118', chain='B', y=58.301,
x=51.975, model='1', z=56.907, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C2',
symmetry='1_555', component_number='118', chain='B', y=58.033,
x=50.991, model='1', z=57.814, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N2',
symmetry='1_555', component_number='118', chain='B', y=58.557,
x=51.138, model='1', z=59.032, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='N3',
symmetry='1_555', component_number='118', chain='B', y=57.299,
x=49.949, model='1', z=57.556, pdb='1GID'),
Atom(insertion_code='?', component_id='G', name='C4',
symmetry='1_555', component_number='118', chain='B', y=56.828,
x=49.974, model='1', z=56.301, pdb='1GID')
]
self.res = Component(some_atoms, type='rna', pdb='1GID', model=1,
chain='A', sequence='G', number=50,
symmetry='6_555')
def test_has_no_hydrogens_initially(self):
atoms = list(self.res.atoms(name=['H1', 'H8', 'H9', '1H2', '2H2']))
self.assertEqual(len(atoms), 0)
def test_hydrogen_infers_on_residue(self):
self.res.infer_hydrogens()
atoms = list(self.res.atoms(name=['H1', 'H8', 'H9', '1H2', '2H2']))
self.assertEqual(len(atoms), 5)
def test_infers_correct_location(self):
raise SkipTest()
