class TestAtom(unittest.TestCase):
"""
Test atom class.
"""
def setUp(self):
"""
Instantiates a pair of atom objects for tests.
"""
self.empty_atom = Atom()
self.trial_atom = Atom()
self.trial_atom.atomname = "C"
self.trial_atom.coordinates = Point(coords=np.array([1, 2, 3]))
self.trial_atom.charge = 0.0
self.trial_atom.element = "C"
self.trial_atom.residue = "CYS"
# TODO(bramsundar): Fill in a non-junk value for chain.
self.trial_atom.chain = "FF"
self.trial_atom.indices_of_atoms_connecting = [4, 5, 6]
def test_copy_of(self):
"""
TestAtom: Verify that copy_of preserves atom information.
"""
copy_atom = self.trial_atom.copy_of()
assert copy_atom.atomname == "C"
assert np.array_equal(copy_atom.coordinates.as_array(), np.array([1, 2, 3]))
assert copy_atom.charge == 0
assert copy_atom.element == "C"
assert copy_atom.residue == "CYS"
assert copy_atom.chain == "FF"
assert copy_atom.indices_of_atoms_connecting == [4, 5, 6]
def test_create_pdb_line(self):
"""
TestAtom: Verify that PDB Line is in correct format.
"""
# TODO(bramsundar): Add a more nontrivial test after looking into
# PDB standard.
line = self.trial_atom.create_pdb_line(1)
assert type(line) == str
def test_number_of_neighors(self):
"""
TestAtom: Verify that the number of neighbors is computed correctly.
"""
assert self.empty_atom.number_of_neighbors() == 0
assert self.trial_atom.number_of_neighbors() == 3
class TestAtom(unittest.TestCase):
"""
Test atom class.
"""
def setUp(self):
"""
Instantiates a pair of atom objects for tests.
"""
self.empty_atom = Atom()
self.trial_atom = Atom()
self.trial_atom.atomname = "C"
self.trial_atom.coordinates = Point(coords=np.array([1, 2, 3]))
self.trial_atom.charge = 0.
self.trial_atom.element = "C"
self.trial_atom.residue = "CYS"
# TODO(bramsundar): Fill in a non-junk value for chain.
self.trial_atom.chain = "FF"
self.trial_atom.indices_of_atoms_connecting = [4, 5, 6]
def test_copy_of(self):
"""
TestAtom: Verify that copy_of preserves atom information.
"""
copy_atom = self.trial_atom.copy_of()
assert copy_atom.atomname == "C"
assert np.array_equal(copy_atom.coordinates.as_array(),
np.array([1, 2, 3]))
assert copy_atom.charge == 0
assert copy_atom.element == "C"
assert copy_atom.residue == "CYS"
assert copy_atom.chain == "FF"
assert copy_atom.indices_of_atoms_connecting == [4, 5, 6]
def test_create_pdb_line(self):
"""
TestAtom: Verify that PDB Line is in correct format.
"""
# TODO(bramsundar): Add a more nontrivial test after looking into
# PDB standard.
line = self.trial_atom.create_pdb_line(1)
assert type(line) == str
def test_number_of_neighors(self):
"""
TestAtom: Verify that the number of neighbors is computed correctly.
"""
assert self.empty_atom.number_of_neighbors() == 0
assert self.trial_atom.number_of_neighbors() == 3
