class AtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID', model=1, chain='A', component_id='C',
component_number=50, name="C1'", symmetry='6_555',
x=-1, y=0, z=0)
def test_has_item_access(self):
self.assertEqual(-1, self.atom.x)
def test_computes_a_unit_id(self):
val = self.atom.unit_id()
ans = "1GID|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def test_computes_its_component_id(self):
val = self.atom.component_unit_id()
ans = "1GID|1|A|C|50||||6_555"
self.assertEqual(val, ans)
def test_can_get_coordinates(self):
val = self.atom.coordinates()
ans = np.array([-1, 0, 0])
np.testing.assert_array_equal(val, ans)
def test_can_get_distance_between_atoms(self):
val = self.atom.distance(Atom(x=1, y=0, z=0))
self.assertEqual(2.0, val)
class AtomTransformationTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID', model=1, chain='A', component_id='C',
component_number=50, name="C1'", symmetry='6_555',
x=-1, y=0, z=2, type='Bob', polymeric=True)
trans = np.array([[1.0, 0.0, 0.0, 0.0],
[0.0, -1.0, 0.0, 97.240],
[0.0, 0.0, -1.0, 0.0],
[0.0, 0.0, 0.0, 1.0]])
self.trans = self.atom.transform(trans)
def test_transform_moves_coordiantes(self):
val = [self.trans.x, self.trans.y, self.trans.z]
ans = [-1.0, 97.240, -2.0]
self.assertEquals(ans, val)
def test_transform_preserves_unit_id(self):
val = self.trans.unit_id()
ans = self.atom.unit_id()
self.assertEquals(ans, val)
def test_perserves_the_type(self):
self.assertEquals('Bob', self.trans.type)
def test_perserves_the_polymeric(self):
self.assertEquals(True, self.trans.polymeric)
class AtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID',
model=1,
chain='A',
component_id='C',
component_number=50,
name="C1'",
symmetry='6_555',
x=-1,
y=0,
z=0)
def test_has_item_access(self):
self.assertEqual(-1, self.atom.x)
def test_computes_a_unit_id(self):
val = self.atom.unit_id()
ans = "1GID|1|A|C|50|C1'|||6_555"
self.assertEqual(val, ans)
def test_computes_its_component_id(self):
val = self.atom.component_unit_id()
ans = "1GID|1|A|C|50||||6_555"
self.assertEqual(val, ans)
def test_can_get_coordinates(self):
val = self.atom.coordinates()
ans = np.array([-1, 0, 0])
np.testing.assert_array_equal(val, ans)
def test_can_get_distance_between_atoms(self):
val = self.atom.distance(Atom(x=1, y=0, z=0))
self.assertEqual(2.0, val)
class AtomTransformationTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='1GID',
model=1,
chain='A',
component_id='C',
component_number=50,
name="C1'",
symmetry='6_555',
x=-1,
y=0,
z=2,
type='Bob',
polymeric=True)
trans = np.array([[1.0, 0.0, 0.0, 0.0], [0.0, -1.0, 0.0, 97.240],
[0.0, 0.0, -1.0, 0.0], [0.0, 0.0, 0.0, 1.0]])
self.trans = self.atom.transform(trans)
def test_transform_moves_coordiantes(self):
val = [self.trans.x, self.trans.y, self.trans.z]
ans = [-1.0, 97.240, -2.0]
self.assertEquals(ans, val)
def test_transform_preserves_unit_id(self):
val = self.trans.unit_id()
ans = self.atom.unit_id()
self.assertEquals(ans, val)
def test_perserves_the_type(self):
self.assertEquals('Bob', self.trans.type)
def test_perserves_the_polymeric(self):
self.assertEquals(True, self.trans.polymeric)
class AlternativeAtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='4OQ8', model=1, chain='A', component_id='SER',
component_number=27, name='CA', alt_id='A',
symmetry='PP')
def test_has_a_unit_id(self):
self.assertEquals('4OQ8|1|A|SER|27|CA|A||PP', self.atom.unit_id())
def test_has_a_component_id(self):
self.assertEquals('4OQ8|1|A|SER|27||A||PP',
self.atom.component_unit_id())
class AlternativeAtomTest(ut.TestCase):
def setUp(self):
self.atom = Atom(pdb='4OQ8',
model=1,
chain='A',
component_id='SER',
component_number=27,
name='CA',
alt_id='A',
symmetry='PP')
def test_has_a_unit_id(self):
self.assertEquals('4OQ8|1|A|SER|27|CA|A||PP', self.atom.unit_id())
def test_has_a_component_id(self):
self.assertEquals('4OQ8|1|A|SER|27||A||PP',
self.atom.component_unit_id())
