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])