def test_translate_rotate():
reactant = ReactantComplex(
Reactant(name='F-', charge=-1, atoms=[Atom('F')]),
Reactant(name='alkeneCl', atoms=xyz_file_to_atoms('alkene.xyz')))
assert len(reactant.molecules) == 2
# Initially the geometry is not sensible
assert reactant.get_distance(0, 2) < 1.0
# SN2' bond rearrangement
bond_rearr = BondRearrangement(forming_bonds=[(0, 1)],
breaking_bonds=[(3, 4)])
translate_rotate_reactant(reactant, bond_rearr, shift_factor=1.5)
assert len(reactant.atoms) == 10
os.remove('complex.xyz')
# The geometry should now be sensible
for i in range(1, 10):
assert reactant.get_distance(0, i) > 2.0
# Should be closer to the end carbon than the middle
assert reactant.get_distance(0, 1) < reactant.get_distance(0, 2)
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
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')
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'
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'
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
def test_subst():
reactant = Reactant(name='sn2_r', atoms=xyz_file_to_atoms('reactant.xyz'))
# SN2' bond rearrangement
bond_rearr = BondRearrangement(forming_bonds=[(0, 1)],
breaking_bonds=[(3, 4)])
subst_centers = get_substitution_centres(reactant,
bond_rearr,
shift_factor=1.0)
assert len(subst_centers) == 1
# get_substitution_centres should add a dummy atom so the ACX angle is
# defined
assert len(reactant.atoms) == 11
or minor release
"""
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')