def test_consistent_atom_order(self):
"""Test that the atom order is preserved whether starting from SMILES or from xyz"""
spc1 = ARCSpecies(label='spc1', smiles='CCCO')
xyz1 = spc1.get_xyz()
for adj, coord in zip(spc1.mol.toAdjacencyList().splitlines(), xyz1.splitlines()):
if adj and coord:
self.assertEqual(adj.split()[1], coord.split()[0])
xyz2 = """C -0.37147383 -0.54225753 0.07779977
C 0.99011397 0.11006088 -0.10715587
H -0.33990169 -1.22256017 0.93731544
H -0.60100180 -1.16814809 -0.79292035
H 1.26213386 0.70273091 0.77209458
O 1.96607463 -0.90691160 -0.28642183
H 0.99631715 0.75813344 -0.98936747
H -1.27803075 1.09840370 1.16400304
C -1.46891192 0.48768649 0.27579733
H -2.43580767 -0.00829320 0.40610628
H -1.54270451 1.15356356 -0.58992943
H 2.82319256 -0.46240839 -0.40178723"""
spc2 = ARCSpecies(label='spc2', xyz=xyz2)
for adj, coord in zip(spc2.mol.toAdjacencyList().splitlines(), xyz2.splitlines()):
if adj and coord:
self.assertEqual(adj.split()[1], coord.split()[0])
n3_xyz = str("""N -1.1997440839 -0.1610052059 0.0274738287
H -1.4016624407 -0.6229695533 -0.8487034080
H -0.0000018759 1.2861082773 0.5926077870
N 0.0000008520 0.5651072858 -0.1124621525
H -1.1294692206 -0.8709078271 0.7537518889
N 1.1997613019 -0.1609980472 0.0274604887
H 1.1294795781 -0.8708998550 0.7537444446
H 1.4015274689 -0.6230592706 -0.8487058662""")
spc3 = ARCSpecies(label=str('N3'), xyz=n3_xyz, multiplicity=1, smiles=str('NNN'))
self.assertEqual(spc3.mol.atoms[1].symbol, 'H')
spc3.generate_conformers()
self.assertEqual(len(spc3.conformers), 5)
xyz4 = """O -1.48027320 0.36597456 0.41386552
C -0.49770656 -0.40253648 -0.26500019
C 0.86215119 0.24734211 -0.11510338
H -0.77970114 -0.46128090 -1.32025907
H -0.49643724 -1.41548311 0.14879346
H 0.84619526 1.26924854 -0.50799415
H 1.14377239 0.31659216 0.94076336
H 1.62810781 -0.32407050 -0.64676910
H -1.22610851 0.40421362 1.35170355"""
spc4 = ARCSpecies(label='CCO', smiles='CCO', xyz=xyz4) # define from xyz for consistent atom order
for atom1, atom2 in zip(spc4.mol.atoms, spc4.mol_list[0].atoms):
self.assertEqual(atom1.symbol, atom2.symbol)
def test_save_conformers_file(self):
"""test the save_conformers_file function"""
project = 'arc_project_for_testing_delete_after_usage'
project_directory = os.path.join(arc_path, 'Projects', project)
label = 'butanol'
spc1 = ARCSpecies(label=label, smiles='CCCCO')
spc1.generate_conformers(n_confs=3)
self.assertIn(len(spc1.conformers), [2, 3])
plotter.save_conformers_file(project_directory=project_directory, label=spc1.label,
xyzs=spc1.conformers, level_of_theory='APFD/def2tzvp',
multiplicity=spc1.multiplicity, charge=spc1.charge, is_ts=False,
energies=spc1.conformer_energies)
conf_file_path = os.path.join(project_directory, 'output', 'Species', label, 'geometry', 'conformers',
'conformers_before_optimization.txt')
self.assertTrue(os.path.isfile(conf_file_path))
def test_conformers(self):
"""Test conformer generation"""
self.spc1.conformers = list()
self.spc1.conformer_energies = list()
self.assertEqual(len(self.spc1.conformers), len(self.spc1.conformer_energies))
self.spc1.generate_conformers()
self.assertIn(len(self.spc1.conformers), [2, 3])
self.assertEqual(len(self.spc1.conformers), len(self.spc1.conformer_energies))
self.spc2.conformers = list()
self.spc2.generate_conformers()
self.assertEqual(len(self.spc2.conformers), 1)
self.spc3.conformers = list()
self.spc3.generate_conformers()
self.assertEqual(len(self.spc3.conformers), 1)
self.spc4.conformers = list()
self.spc4.generate_conformers()
self.assertIn(len(self.spc4.conformers), [3, 4, 5])
self.spc5.conformers = list()
self.spc5.generate_conformers()
self.assertEqual(len(self.spc5.conformers), 3)
self.spc6.conformers = list()
self.spc6.generate_conformers()
self.assertEqual(len(self.spc6.conformers), 4)
self.spc8.conformers = list()
self.spc8.generate_conformers()
self.assertEqual(len(self.spc8.conformers), 4)
self.spc9.conformers = list()
self.spc9.generate_conformers()
self.assertEqual(len(self.spc9.conformers), 1)
self.spc10.conformers = list()
self.spc10.generate_conformers(confs_to_dft=1)
self.assertEqual(len(self.spc10.conformers), 1)
self.spc10.conformers = list()
self.spc10.generate_conformers(confs_to_dft=2)
self.assertEqual(len(self.spc10.conformers), 2)
self.spc10.conformers = list()
self.spc10.generate_conformers(confs_to_dft=3)
self.assertEqual(len(self.spc10.conformers), 3)
self.spc11.conformers = list()
self.spc11.generate_conformers(confs_to_dft=1)
self.assertEqual(len(self.spc11.conformers), 2) # has more confs due to chiral center
self.spc11.conformers = list()
self.spc11.generate_conformers(confs_to_dft=2)
self.assertEqual(len(self.spc11.conformers), 3)
self.spc11.conformers = list()
self.spc11.generate_conformers(confs_to_dft=3)
self.assertIn(len(self.spc11.conformers), [3, 4])
xyz12 = """C 0.00000000 0.00000000 0.00000000
H 1.07008000 -0.14173100 0.00385900
H -0.65776100 -0.85584100 -0.00777700
H -0.41231900 0.99757300 0.00391900"""
spc12 = ARCSpecies(label='CH3', smiles='[CH3]', xyz=xyz12)
spc12.generate_conformers()
self.assertEqual(len(spc12.conformers), 2)
self.assertEqual(len(spc12.conformer_energies), 2)
