def setUpClass(cls):
cls.lot_get = LevelOfTheory(method='CCSD(T)-F12',
basis='cc-pVTZ-F12',
software='Molpro')
cls.lot_fit = LevelOfTheory(method='wB97M-V',
basis='def2-TZVPD',
software='Q-Chem')
cls.lot_nonexisting = LevelOfTheory('notamethod')
cls.bac = BAC(cls.lot_get)
cls.tmp_melius_params = {
'atom_corr': {
'H': 1.0,
'C': 2.0,
'N': 3.0,
'O': 4.0,
'S': 5.0,
'F': 6.0,
'Cl': 7.0,
'Br': 8.0
},
'bond_corr_length': {
'H': 1.0,
'C': 2.0,
'N': 3.0,
'O': 4.0,
'S': 5.0,
'F': 6.0,
'Cl': 7.0,
'Br': 8.0
},
'bond_corr_neighbor': {
'H': 1.0,
'C': 2.0,
'N': 3.0,
'O': 4.0,
'S': 5.0,
'F': 6.0,
'Cl': 7.0,
'Br': 8.0
},
'mol_corr': 1.0
}
cls.tmp_petersson_params = {
'C-H': 1.0,
'C-C': 2.0,
'C=C': 3.0,
'C-O': 4.0
}
# Set molecule, bonds, nums, and coords for testing Petersson and Melius BACs
cls.multiplicity = 1
smi = 'C=C(OSC=S)C#CC1C(=O)N=CNC1SSC(O)C#N'
mol = Molecule(smiles=smi, multiplicity=cls.multiplicity)
cls.bonds = Counter(
f'{b.atom1.element.symbol}{BOND_SYMBOLS[b.order]}{b.atom2.element.symbol}'
for b in mol.get_all_edges())
pybel_mol = pybel.readstring('smi', smi)
pybel_mol.addh()
pybel_mol.make3D()
mol_3d = _pybel_to_rmg(pybel_mol)
cls.nums = [atom.number for atom in mol_3d.atoms]
cls.coords = np.array([atom.coords for atom in mol_3d.atoms])
def setUpClass(cls):
cls.model_chem_get = 'ccsd(t)-f12/cc-pvtz-f12'
cls.model_chem_fit = 'wb97m-v/def2-tzvpd'
cls.model_chem_nonexisting = 'notamethod/notabasis'
cls.bac = BAC(cls.model_chem_get)
cls.tmp_melius_params = {
'atom_corr': {'H': 1.0, 'C': 2.0, 'N': 3.0, 'O': 4.0, 'S': 5.0, 'F': 6.0, 'Cl': 7.0, 'Br': 8.0},
'bond_corr_length': {'H': 1.0, 'C': 2.0, 'N': 3.0, 'O': 4.0, 'S': 5.0, 'F': 6.0, 'Cl': 7.0, 'Br': 8.0},
'bond_corr_neighbor': {'H': 1.0, 'C': 2.0, 'N': 3.0, 'O': 4.0, 'S': 5.0, 'F': 6.0, 'Cl': 7.0, 'Br': 8.0},
'mol_corr': 1.0
}
cls.tmp_petersson_params = {'C-H': 1.0, 'C-C': 2.0, 'C=C': 3.0, 'C-O': 4.0}
# Set molecule, bonds, nums, and coords for testing Petersson and Melius BACs
cls.multiplicity = 1
smi = 'C=C(OSC=S)C#CC1C(=O)N=CNC1SSC(O)C#N'
mol = Molecule(smiles=smi, multiplicity=cls.multiplicity)
cls.bonds = Counter(
f'{b.atom1.element.symbol}{BOND_SYMBOLS[b.order]}{b.atom2.element.symbol}' for b in mol.get_all_edges()
)
pybel_mol = pybel.readstring('smi', smi)
pybel_mol.addh()
pybel_mol.make3D()
mol_3d = _pybel_to_rmg(pybel_mol)
cls.nums = [atom.number for atom in mol_3d.atoms]
cls.coords = np.array([atom.coords for atom in mol_3d.atoms])
