def test_determine_family(self):
"""Test the determine_family() function."""
rxn = ARCReaction(r_species=[ARCSpecies(label='CH2CH2CH3', smiles='[CH2]CC')],
p_species=[ARCSpecies(label='CH3CHCH3', smiles='C[CH]C')])
self.assertIsNone(rxn.family)
rmgdb.determine_family(rxn, db=None)
self.assertEqual(rxn.family.label, 'intra_H_migration')
rxn = ARCReaction(r_species=[ARCSpecies(label='C2H6', smiles='CC'),
ARCSpecies(label='OH', smiles='[OH]')],
p_species=[ARCSpecies(label='water', smiles='O'),
ARCSpecies(label='C2H5', smiles='[CH2]C')])
self.assertIsNone(rxn.family)
rmgdb.determine_family(rxn, db=self.rmgdb)
self.assertEqual(rxn.family.label, 'H_Abstraction')
r_1 = ARCSpecies(label='C3H6O', smiles='CCC=O')
r_2 = ARCSpecies(label='C4H9O', smiles='[CH2]C(C)CO')
p_1 = ARCSpecies(label='C3H5O', smiles='CC=C[O]') # This is the "wrong" resonance structure on purpose.
p_2 = ARCSpecies(label='C4H10O', smiles='CC(C)CO')
rxn = ARCReaction(reactants=['C3H6O', 'C4H9O'], products=['C3H5O', 'C4H10O'],
r_species=[r_1, r_2], p_species=[p_1, p_2])
self.assertIsNone(rxn.family)
rmgdb.determine_family(rxn, db=self.rmgdb)
self.assertEqual(rxn.family.label, 'H_Abstraction')
def test_parse_xyz_from_file(self):
"""Test parsing xyz from a file"""
path1 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.gjf')
path2 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.xyz')
path3 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'AIBN.gjf')
path4 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'molpro.in')
path5 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'qchem.in')
path6 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'qchem_output.out')
path7 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'TS.gjf')
xyz1 = parser.parse_xyz_from_file(path1)
xyz2 = parser.parse_xyz_from_file(path2)
xyz3 = parser.parse_xyz_from_file(path3)
xyz4 = parser.parse_xyz_from_file(path4)
xyz5 = parser.parse_xyz_from_file(path5)
xyz6 = parser.parse_xyz_from_file(path6)
xyz7 = parser.parse_xyz_from_file(path7)
self.assertEqual(xyz1.rstrip(), xyz2.rstrip())
self.assertTrue(
'C 1.40511900 0.21728200 0.07675200' in xyz1)
self.assertTrue(
'O -0.79314200 1.04818800 0.18134200' in xyz1)
self.assertTrue(
'H -0.43701200 -1.34990600 0.92900600' in xyz2)
self.assertTrue(
'C 2.12217963 -0.66843078 1.04808732' in
xyz3)
self.assertTrue(
'N 2.41731872 -1.07916417 2.08039935' in
xyz3)
spc3 = ARCSpecies(label='AIBN', xyz=xyz3)
self.assertEqual(len(spc3.mol.atoms), 24)
self.assertTrue(
'S -0.4204682221 -0.3909949822 0.0245352116'
in xyz4)
self.assertTrue(
'N -1.99742564 0.38106573 0.09139807' in
xyz5)
self.assertTrue(
'N -1.17538406 0.34366165 0.03265021' in xyz6)
self.assertEqual(len(xyz7.strip().splitlines()), 34)
def test_process_conformers_file(self):
"""Test processing ARC conformer files"""
path1 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'conformers_before_optimization.txt')
path2 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'conformers_after_optimization.txt')
path3 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'conformers_file.txt')
xyzs, energies = parser.process_conformers_file(path1)
self.assertEqual(len(xyzs), 3)
self.assertEqual(len(energies), 3)
self.assertTrue(all([e is None for e in energies]))
spc1 = ARCSpecies(label='tst1', xyz=xyzs[0])
self.assertEqual(len(spc1.conformers), 1)
xyzs, energies = parser.process_conformers_file(path2)
self.assertEqual(len(xyzs), 3)
self.assertEqual(len(energies), 3)
self.assertEqual(energies, [0.0, 10.271, 10.288])
spc2 = ARCSpecies(label='tst2', xyz=xyzs[:2])
self.assertEqual(len(spc2.conformers), 2)
self.assertEqual(len(spc2.conformer_energies), 2)
xyzs, energies = parser.process_conformers_file(path3)
self.assertEqual(len(xyzs), 4)
self.assertEqual(len(energies), 4)
self.assertEqual(energies, [0.0, 0.005, None, 0.005])
spc3 = ARCSpecies(label='tst3', xyz=xyzs)
self.assertEqual(len(spc3.conformers), 4)
self.assertEqual(len(spc3.conformer_energies), 4)
spc4 = ARCSpecies(label='tst4', xyz=path1)
self.assertEqual(len(spc4.conformers), 3)
self.assertTrue(all([e is None for e in spc4.conformer_energies]))
spc5 = ARCSpecies(label='tst5', xyz=path2)
self.assertEqual(len(spc5.conformers), 3)
self.assertTrue(all([e is not None for e in spc5.conformer_energies]))
spc6 = ARCSpecies(label='tst6', xyz=path3)
self.assertEqual(len(spc6.conformers), 4)
def test_parse_xyz_from_file(self):
"""Test parsing xyz from a file"""
path1 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.gjf')
path2 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'CH3C(O)O.xyz')
path3 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'AIBN.gjf')
path4 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'molpro.in')
path5 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'qchem.in')
path6 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'qchem_output.out')
path7 = os.path.join(arc_path, 'arc', 'testing', 'xyz', 'TS.gjf')
path8 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'formaldehyde_coords.xyz')
path9 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'optim_traj_terachem.xyz') # test trajectories
path10 = os.path.join(arc_path, 'arc', 'testing', 'xyz',
'ethane_minimize_terachem_output.out')
path11 = os.path.join(arc_path, 'arc', 'testing',
'orca_example_opt.log')
xyz1 = parser.parse_xyz_from_file(path1)
xyz2 = parser.parse_xyz_from_file(path2)
xyz3 = parser.parse_xyz_from_file(path3)
xyz4 = parser.parse_xyz_from_file(path4)
xyz5 = parser.parse_xyz_from_file(path5)
xyz6 = parser.parse_xyz_from_file(path6)
xyz7 = parser.parse_xyz_from_file(path7)
xyz8 = parser.parse_xyz_from_file(path8)
xyz9 = parser.parse_xyz_from_file(path9)
xyz10 = parser.parse_xyz_from_file(path10)
xyz11 = parser.parse_xyz_from_file(path11)
self.assertEqual(xyz1, xyz2)
xyz1_str = xyz_to_str(xyz1)
xyz2_str = xyz_to_str(xyz2)
xyz3_str = xyz_to_str(xyz3)
xyz4_str = xyz_to_str(xyz4)
xyz5_str = xyz_to_str(xyz5)
xyz6_str = xyz_to_str(xyz6)
xyz9_str = xyz_to_str(xyz9)
xyz11_str = xyz_to_str(xyz11)
self.assertTrue(
'C 1.40511900 0.21728200 0.07675200' in xyz1_str)
self.assertTrue(
'O -0.79314200 1.04818800 0.18134200' in xyz1_str)
self.assertTrue(
'H -0.43701200 -1.34990600 0.92900600' in xyz2_str)
self.assertTrue(
'C 2.12217963 -0.66843078 1.04808732' in xyz3_str)
self.assertTrue(
'N 2.41731872 -1.07916417 2.08039935' in xyz3_str)
spc3 = ARCSpecies(label='AIBN', xyz=xyz3)
self.assertEqual(len(spc3.mol.atoms), 24)
self.assertTrue(
'S -0.42046822 -0.39099498 0.02453521' in xyz4_str)
self.assertTrue(
'N -1.99742564 0.38106573 0.09139807' in xyz5_str)
self.assertTrue(
'N -1.17538406 0.34366165 0.03265021' in xyz6_str)
self.assertEqual(len(xyz7['symbols']), 34)
self.assertEqual(len(xyz8['symbols']), 4)
expected_xyz_9 = """N -0.67665958 0.74524340 -0.41319355
H -1.26179357 1.52577220 -0.13687665
H 0.28392722 1.06723640 -0.44163375
N -0.75345799 -0.33268278 0.51180786
H -0.97153041 -0.02416219 1.45398654
H -1.48669570 -0.95874053 0.20627423
N 2.28178508 -0.42455356 0.14404399
H 1.32677989 -0.80557411 0.33156013"""
self.assertEqual(xyz9_str, expected_xyz_9)
self.assertIsNone(xyz10)
expected_xyz_11 = """C 0.00917900 -0.00000000 -0.00000000
O 1.20814900 -0.00000000 0.00000000
H -0.59436200 0.94730400 0.00000000
H -0.59436200 -0.94730400 0.00000000"""
self.assertEqual(xyz11_str, expected_xyz_11)