Exemplo n.º 1
0
def test_check_solvent():

    r = Reactant(name='r', solvent_name='water')
    p = Product(name='p')

    with pytest.raises(SolventsDontMatch):
        _ = reaction.Reaction(r, p)

    p = Product(name='p', solvent_name='water')
    reaction_check = reaction.Reaction(r, p)
    assert reaction_check.solvent.name == 'water'
Exemplo n.º 2
0
def test_free_energy_profile():

    # Use a spoofed Gaussian09 and XTB install
    Config.lcode = 'xtb'

    Config.hcode = 'g09'
    Config.G09.path = here

    Config.ts_template_folder_path = os.getcwd()

    method = get_hmethod()
    assert method.name == 'g09'

    rxn = reaction.Reaction(Reactant(name='F-', smiles='[F-]'),
                            Reactant(name='CH3Cl', smiles='ClC'),
                            Product(name='Cl-', smiles='[Cl-]'),
                            Product(name='CH3F', smiles='CF'),
                            name='sn2',
                            solvent_name='water')

    # Don't run the calculation without a working XTB install
    if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
        return

    rxn.calculate_reaction_profile(free_energy=True)

    # Allow ~0.5 kcal mol-1 either side of the true value

    dg_ts = rxn.calc_delta_g_ddagger()
    assert 17 < dg_ts * Constants.ha2kcalmol < 18

    dg_r = rxn.calc_delta_g()
    assert -13.2 < dg_r * Constants.ha2kcalmol < -12.3

    dh_ts = rxn.calc_delta_h_ddagger()
    assert 9.2 < dh_ts * Constants.ha2kcalmol < 10.3

    dh_r = rxn.calc_delta_h()
    assert -13.6 < dh_r * Constants.ha2kcalmol < -12.6

    # Should be able to plot an enthalpy profile
    plot_reaction_profile([rxn], units=KcalMol, name='enthalpy', enthalpy=True)
    assert os.path.exists('enthalpy_reaction_profile.png')
    os.remove('enthalpy_reaction_profile.png')

    # Reset the configuration to the default values
    Config.hcode = None
    Config.G09.path = None
    Config.lcode = None
    Config.XTB.path = None
Exemplo n.º 3
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def test_detection():

    # F- + H2CCHCH2Cl -> FCH2CHCH2 + Cl-
    reaction = Reaction(Reactant(name='F-', charge=-1, atoms=[Atom('F')]),
                        Reactant(name='alkeneCl', smiles='C=CCCl'),
                        Product(name='alkeneF', smiles='C=CCF'),
                        Product(name='Cl-', charge=-1, atoms=[Atom('Cl')]))

    assert reaction.type == Substitution

    reactant, product = get_complexes(reaction)

    bond_rearrs = get_bond_rearrangs(reactant, product, name='SN2')

    # autodE should find both direct SN2 and SN2' pathways
    assert len(bond_rearrs) == 2
    os.remove('SN2_bond_rearrangs.txt')
Exemplo n.º 4
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def test_swap_reacs_prods():

    reactant = Reactant(name='r')
    product = Product(name='p')

    swapped_reaction = reaction.Reaction(reactant, product)
    assert swapped_reaction.reacs[0].name == 'r'
    assert swapped_reaction.prods[0].name == 'p'

    swapped_reaction.switch_reactants_products()
    assert swapped_reaction.reacs[0].name == 'p'
    assert swapped_reaction.prods[0].name == 'r'
Exemplo n.º 5
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def test_single_points():

    # Spoof ORCA install
    Config.ORCA.path = here

    rxn = reaction.Reaction(Reactant(smiles='O'), Product(smiles='O'))

    # calculate_single_points should be pretty tolerant.. not raising
    # exceptions if the energy is already None
    rxn.calculate_single_points()
    assert rxn.reacs[0].energy is None

    overlapping_h2 = Reactant(atoms=[Atom('H'), Atom('H')])
    overlapping_h2.energy = -1
    rxn.reacs = [overlapping_h2]

    # Shouldn't calculate a single point for a molecule that is not
    # 'reasonable'
    rxn.calculate_single_points()
    assert rxn.reacs[0].energy == -1

    Config.ORCA.path = None
Exemplo n.º 6
0
from autode.reactions import Reaction
from autode.species import Reactant, Product
from autode.input_output import xyz_file_to_atoms
from autode.config import Config
from time import time
import os

here = os.path.dirname(os.path.abspath(__file__))
data_path = os.path.join(here, 'data', 'benchmark')

# Leave unchanged for comparable timings
Config.n_cores = 8

sn2 = Reaction(Reactant(name='F-', smiles='[F-]'),
               Reactant(name='CH3Cl', smiles='ClC'),
               Product(name='Cl-', smiles='[Cl-]'),
               Product(name='CH3F', smiles='CF'),
               solvent_name='water',
               name='sn2')

cope = Reaction(Reactant(name='diene1', smiles='C=C[C@H](C)[C@@H](C)C=C'),
                Product(name='diene2', smiles='C/C=C/CC/C=C/C'),
                name='cope_rearrangement')

da = Reaction(Reactant(name='butadiene', smiles='C=CC=C'),
              Reactant(name='ethene', smiles='C=C'),
              Product(name='cyclohexene', smiles='C1C=CCCC1'),
              name='diels_alder')

h_shift = Reaction(Reactant(name='radical1', smiles='CC[C]([H])[H]'),
                   Product(name='radical2', smiles='C[C]([H])C'),