def setUp(cls):
"""A method that is run before each unit test in this class"""
spc = Species().from_smiles('CCO')
log = GaussianLog(
os.path.join(os.path.dirname(__file__), 'data', 'ethylene.log'))
spc.conformer = log.load_conformer()[0]
coords, numbers, masses = log.load_geometry()
spc.conformer.coordinates = coords, 'angstroms'
spc.conformer.number = numbers
spc.conformer.mass = masses, 'amu'
cls.thermo_job = ThermoJob(species=spc, thermo_class='NASA')
def test_get_str_xyz(self):
"""Test generating an xyz string from the species.conformer object"""
log = GaussianLog(
os.path.join(os.path.dirname(__file__), 'data', 'ethylene_G3.log'))
conformer = log.load_conformer()[0]
coords, number, mass = log.load_geometry()
conformer.coordinates, conformer.number, conformer.mass = (
coords, "angstroms"), number, (mass, "amu")
spc1 = Species(smiles='C=C')
spc1.conformer = conformer
xyz_str = get_str_xyz(spc1)
expected_xyz_str = """C 0.00545100 0.00000000 0.00339700
H 0.00118700 0.00000000 1.08823200
H 0.97742900 0.00000000 -0.47841600
C -1.12745800 0.00000000 -0.70256500
H -1.12319800 0.00000000 -1.78740100
H -2.09943900 0.00000000 -0.22075700"""
self.assertEqual(xyz_str, expected_xyz_str)