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