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 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 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())
def test_can_build_problematic_id(self):
atom = Atom(pdb='3V27',
model=1,
chain='A',
component_id='G',
component_number=94,
component_index=1,
insertion_code='A',
x=None, y=None, z=None,
group='ATOM',
type='OP1',
name='P',
symmetry='1_555',
polymeric=False)
val = atom.component_unit_id()
ans = '3V27|1|A|G|94|||A'
self.assertEquals(ans, val)
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())
def test_can_build_problematic_id(self):
atom = Atom(pdb='3V27',
model=1,
chain='A',
component_id='G',
component_number=94,
component_index=1,
insertion_code='A',
x=None,
y=None,
z=None,
group='ATOM',
type='OP1',
name='P',
symmetry='1_555',
polymeric=False)
val = atom.component_unit_id()
ans = '3V27|1|A|G|94|||A'
self.assertEquals(ans, val)
