def test_check_final_xyz_isomorphism(self):
"""Test the check_final_xyz_isomorphism() method"""
xyz1 = """C -1.9681540 0.0333440 -0.0059220
C -0.6684360 -0.7562450 0.0092140
C 0.5595480 0.1456260 -0.0036480
O 0.4958540 1.3585920 0.0068500
N 1.7440770 -0.5331650 -0.0224050
H -2.8220500 -0.6418490 0.0045680
H -2.0324190 0.6893210 0.8584580
H -2.0300690 0.6574940 -0.8939330
H -0.6121640 -1.4252590 -0.8518010
H -0.6152180 -1.3931710 0.8949150
H 1.7901420 -1.5328370 0.0516350
H 2.6086580 -0.0266360 0.0403330"""
spc1 = ARCSpecies(label='propanamide1', smiles='CCC(=O)N', xyz=xyz1)
spc1.final_xyz = spc1.conformers[0]
is_isomorphic1 = spc1.check_final_xyz_isomorphism()
self.assertTrue(is_isomorphic1)
xyz2 = """C 0.6937910 -0.8316510 0.0000000
O 0.2043990 -1.9431180 0.0000000
N 0.0000000 0.3473430 0.0000000
C -1.4529360 0.3420060 0.0000000
C 0.6724520 1.6302410 0.0000000
H 1.7967050 -0.6569720 0.0000000
H -1.7909050 -0.7040620 0.0000000
H -1.8465330 0.8552430 0.8979440
H -1.8465330 0.8552430 -0.8979440
H 1.7641260 1.4761740 0.0000000
H 0.4040540 2.2221690 -0.8962980
H 0.4040540 2.2221690 0.8962980""" # dimethylformamide, O=CN(C)C
spc2 = ARCSpecies(label='propanamide2', smiles='CCC(=O)N', xyz=xyz1) # define w/ the correct xyz
spc2.final_xyz = xyz2 # set .final_xyz to the incorrect isomer
spc2.conf_is_isomorphic = True # set to True so that isomorphism is strictly enforced
is_isomorphic2 = spc2.check_final_xyz_isomorphism()
self.assertFalse(is_isomorphic2)
is_isomorphic3 = spc2.check_final_xyz_isomorphism(allow_nonisomorphic_2d=True)
self.assertTrue(is_isomorphic3)
spc2.conf_is_isomorphic = False # set to False so that isomorphism is not strictly enforced
is_isomorphic4 = spc2.check_final_xyz_isomorphism()
self.assertTrue(is_isomorphic4)
def test_save_geo(self):
"""Test saving the geometry files for a species"""
spc = ARCSpecies(label='methylamine',
smiles='CN',
multiplicity=1,
charge=0)
spc.final_xyz = str_to_xyz(
"""N -0.74566988 -0.11773792 0.00000000
C 0.70395487 0.03951260 0.00000000
H 1.12173564 -0.45689176 -0.87930074
H 1.06080468 1.07995075 0.00000000
H 1.12173564 -0.45689176 0.87930074
H -1.16115119 0.31478894 0.81506145
H -1.16115119 0.31478894 -0.81506145""")
spc.opt_level = 'opt/level'
project = 'arc_project_for_testing_delete_after_usage'
project_directory = os.path.join(arc_path, 'Projects', project)
xyz_path = os.path.join(project_directory, 'output', 'Species',
spc.label, 'geometry', 'methylamine.xyz')
gjf_path = os.path.join(project_directory, 'output', 'Species',
spc.label, 'geometry', 'methylamine.gjf')
plotter.save_geo(species=spc, project_directory=project_directory)
xyz_data = """7
methylamine optimized at opt/level
N -0.74566988 -0.11773792 0.00000000
C 0.70395487 0.03951260 0.00000000
H 1.12173564 -0.45689176 -0.87930074
H 1.06080468 1.07995075 0.00000000
H 1.12173564 -0.45689176 0.87930074
H -1.16115119 0.31478894 0.81506145
H -1.16115119 0.31478894 -0.81506145
"""
gjf_data = """# hf/3-21g
methylamine optimized at opt/level
0 1
N -0.74566988 -0.11773792 0.00000000
C 0.70395487 0.03951260 0.00000000
H 1.12173564 -0.45689176 -0.87930074
H 1.06080468 1.07995075 0.00000000
H 1.12173564 -0.45689176 0.87930074
H -1.16115119 0.31478894 0.81506145
H -1.16115119 0.31478894 -0.81506145
"""
with open(xyz_path, 'r') as f:
data = f.read()
self.assertEqual(data, xyz_data)
with open(gjf_path, 'r') as f:
data = f.read()
self.assertEqual(data, gjf_data)
def test_symmetry(self):
"""Test external symmetry and chirality determination"""
allene = ARCSpecies(label=str('allene'), smiles=str('C=C=C'), multiplicity=1, charge=0)
allene.final_xyz = """C -1.01646 0.10640 -0.91445
H -1.39000 1.03728 -1.16672
C 0.00000 0.00000 0.00000
C 1.01653 -0.10640 0.91438
H -1.40975 -0.74420 -1.35206
H 0.79874 -0.20864 1.92036
H 2.00101 -0.08444 0.59842"""
allene.determine_symmetry()
self.assertEqual(allene.optical_isomers, 1)
self.assertEqual(allene.external_symmetry, 4)
ammonia = ARCSpecies(label=str('ammonia'), smiles=str('N'), multiplicity=1, charge=0)
ammonia.final_xyz = """N 0.06617 0.20024 0.13886
H -0.62578 -0.34119 0.63709
H -0.32018 0.51306 -0.74036
H 0.87976 -0.37219 -0.03564"""
ammonia.determine_symmetry()
self.assertEqual(ammonia.optical_isomers, 1)
self.assertEqual(ammonia.external_symmetry, 3)
methane = ARCSpecies(label=str('methane'), smiles=str('C'), multiplicity=1, charge=0)
methane.final_xyz = """C 0.00000 0.00000 0.00000
H -0.29717 0.97009 -0.39841
H 1.08773 -0.06879 0.01517
H -0.38523 -0.10991 1.01373
H -0.40533 -0.79140 -0.63049"""
methane.determine_symmetry()
self.assertEqual(methane.optical_isomers, 1)
self.assertEqual(methane.external_symmetry, 12)
chiral = ARCSpecies(label=str('chiral'), smiles=str('C(C)(O)(N)'), multiplicity=1, charge=0)
chiral.final_xyz = """C -0.49341625 0.37828349 0.00442108
H -1.56331545 0.39193350 0.01003359
N 0.01167132 1.06479568 1.20212111
H 1.01157784 1.05203730 1.19687531
H -0.30960193 2.01178202 1.20391932
O -0.03399634 -0.97590449 0.00184366
H -0.36384913 -1.42423238 -0.78033350
C 0.02253835 1.09779040 -1.25561654
H -0.34510997 0.59808430 -2.12741255
H -0.32122209 2.11106387 -1.25369100
H 1.09243518 1.08414066 -1.26122530"""
chiral.determine_symmetry()
self.assertEqual(chiral.optical_isomers, 2)
self.assertEqual(chiral.external_symmetry, 1)
s8 = ARCSpecies(label=str('s8'), smiles=str('S1SSSSSSS1'), multiplicity=1, charge=0)
s8.final_xyz = """S 2.38341 0.12608 0.09413
S 1.45489 1.88955 -0.13515
S -0.07226 2.09247 1.14966
S -1.81072 1.52327 0.32608
S -2.23488 -0.39181 0.74645
S -1.60342 -1.62383 -0.70542
S 0.22079 -2.35820 -0.30909
S 1.66220 -1.25754 -1.16665"""
s8.determine_symmetry()
self.assertEqual(s8.optical_isomers, 1)
self.assertEqual(s8.external_symmetry, 8)
water = ARCSpecies(label=str('H2O'), smiles=str('O'), multiplicity=1, charge=0)
water.final_xyz = """O 0.19927 0.29049 -0.11186
H 0.50770 -0.61852 -0.09124
H -0.70697 0.32803 0.20310"""
water.determine_symmetry()
self.assertEqual(water.optical_isomers, 1)
self.assertEqual(water.external_symmetry, 2)
