def get_bonds(self):
test_conf = Conformer()
test_conf.rmg_molecule = self.rmg_molecule
try:
test_conf._rdkit_molecule = self._pseudo_geometry
except:
self.get_rdkit_mol()
test_conf._rdkit_molecule = self._pseudo_geometry
test_conf._ase_molecule = self.ase_molecule
return test_conf.get_bonds()
class TestConformer(unittest.TestCase):
def setUp(self):
self.conformer = Conformer(smiles='CC')
def test_rmg_molecules(self):
self.assertIsInstance(self.conformer.rmg_molecule, RMGMolecule)
def test_rdkit_mol(self):
autotst_rdkit = self.conformer.get_rdkit_mol()
self.assertIsInstance(autotst_rdkit, Mol)
def test_ase_mol(self):
autotst_ase_mol = self.conformer.get_ase_mol()
self.assertIsInstance(autotst_ase_mol, Atoms)
def test_get_molecules(self):
autotst_rdkit, autotst_ase_mol = self.conformer.get_molecules()
self.assertIsInstance(autotst_rdkit, Mol)
self.assertIsInstance(autotst_ase_mol, Atoms)
def test_get_bonds(self):
bonds = self.conformer.get_bonds()
self.assertIsInstance(bonds, list)
self.assertIsInstance(bonds[0], Bond)
self.assertEquals(len(bonds), 7)
def test_get_angles(self):
angles = self.conformer.get_angles()
self.assertIsInstance(angles, list)
self.assertIsInstance(angles[0], Angle)
self.assertEquals(len(angles), 12)
def test_get_torsions(self):
torsions = self.conformer.get_torsions()
self.assertIsInstance(torsions, list)
self.assertIsInstance(torsions[0], Torsion)
self.assertEquals(len(torsions), 1)
def test_get_cistrans(self):
cistrans = self.conformer.get_cistrans()
self.assertIsInstance(cistrans, list)
self.assertEquals(len(cistrans), 0)
def test_get_chiralcenters(self):
chiralcenters = self.conformer.get_chiral_centers()
self.assertIsInstance(chiralcenters, list)
self.assertEquals(len(chiralcenters), 0)
def test_get_geometries(self):
geometries = self.conformer.get_geometries()
self.assertIsInstance(geometries, tuple)
self.assertIsInstance(geometries[0], list)
self.assertIsInstance(geometries[0][0], Bond)
self.assertIsInstance(geometries[1], list)
self.assertIsInstance(geometries[1][0], Angle)
self.assertIsInstance(geometries[2], list)
self.assertIsInstance(geometries[2][0], Torsion)
self.assertIsInstance(geometries[3], list)
self.assertIsInstance(geometries[4], list)
def test_calculate_symmetry_number(self):
self.assertEquals(self.conformer.calculate_symmetry_number(), 1)
os.remove("./CC.symm")
class TestConformer(unittest.TestCase):
def setUp(self):
self.conformer = Conformer(smiles='CC')
def test_rmg_molecules(self):
self.assertIsInstance(self.conformer.rmg_molecule, RMGMolecule)
def test_rdkit_mol(self):
autotst_rdkit = self.conformer.get_rdkit_mol()
self.assertIsInstance(autotst_rdkit, Mol)
def test_ase_mol(self):
autotst_ase_mol = self.conformer.get_ase_mol()
self.assertIsInstance(autotst_ase_mol, Atoms)
def test_get_molecules(self):
autotst_rdkit, autotst_ase_mol = self.conformer.get_molecules()
self.assertIsInstance(autotst_rdkit, Mol)
self.assertIsInstance(autotst_ase_mol, Atoms)
def test_get_bonds(self):
bonds = self.conformer.get_bonds()
self.assertIsInstance(bonds, list)
self.assertIsInstance(bonds[0], Bond)
self.assertEquals(len(bonds), 7)
def test_get_angles(self):
angles = self.conformer.get_angles()
self.assertIsInstance(angles, list)
self.assertIsInstance(angles[0], Angle)
self.assertEquals(len(angles), 12)
def test_get_torsions(self):
torsions = self.conformer.get_torsions()
self.assertIsInstance(torsions, list)
self.assertIsInstance(torsions[0], Torsion)
self.assertEquals(len(torsions), 1)
def test_get_cistrans(self):
cistrans = self.conformer.get_cistrans()
self.assertIsInstance(cistrans, list)
self.assertEquals(len(cistrans), 0)
def test_get_chiralcenters(self):
chiralcenters = self.conformer.get_chiral_centers()
self.assertIsInstance(chiralcenters, list)
self.assertEquals(len(chiralcenters), 0)
def test_get_geometries(self):
geometries = self.conformer.get_geometries()
self.assertIsInstance(geometries, tuple)
self.assertIsInstance(geometries[0], list)
self.assertIsInstance(geometries[0][0], Bond)
self.assertIsInstance(geometries[1], list)
self.assertIsInstance(geometries[1][0], Angle)
self.assertIsInstance(geometries[2], list)
self.assertIsInstance(geometries[2][0], Torsion)
self.assertIsInstance(geometries[3], list)
self.assertIsInstance(geometries[4], list)
def test_calculate_symmetry_number(self):
species_to_test = {
"CC": 18.0,
}
self.assertEquals(self.conformer.calculate_symmetry_number(), 18.0)
def test_get_xyz_block(self):
xyz_block = self.conformer.get_xyz_block()
positions = self.conformer.ase_molecule.arrays["positions"]
for n in range(len(positions)):
self.assertTrue((np.array([
float(x) for x in xyz_block.split('\n')[n].split()[1:]
]) == positions[n]).all())
