def test_reaction_class():
h1 = reaction.Reactant(name='h1', atoms=[Atom('H', 0.0, 0.0, 0.0)])
hh_product = reaction.Product(name='hh', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 0.7, 0.0, 0.0)])
# h + h > mol
hh_reac = reaction.Reaction(h1, h2, hh_product, name='h2_assoc')
h1.energy = 2
h2.energy = 3
hh_product.energy = 1
# Only swap to dissociation in invoking locate_ts()
assert hh_reac.type == reaction_types.Addition
assert len(hh_reac.prods) == 1
assert len(hh_reac.reacs) == 2
assert hh_reac.ts is None
assert hh_reac.tss is None
assert hh_reac.name == 'h2_assoc'
assert hh_reac.calc_delta_e() == -4
h1 = reaction.Reactant(name='h1', atoms=[Atom('H')])
hh_reactant = reaction.Reactant(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
hh_product = reaction.Product(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
# h + mol > mol + h
h_sub = reaction.Reaction(h1, hh_reactant, h2_product, hh_product,
solvent_name='water')
assert h_sub.type == reaction_types.Substitution
assert h_sub.name == 'reaction'
assert h_sub.solvent.name == 'water'
assert h_sub.solvent.smiles == 'O'
def test_bad_balance():
hh_product = reaction.Product(name='hh',
atoms=[Atom('H'),
Atom('H', x=1.0)])
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, hh_product)
h_minus = reaction.Reactant(name='h1_minus', atoms=[Atom('H')], charge=-1)
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, h_minus, hh_product)
h1_water = reaction.Reactant(name='h1',
atoms=[Atom('H')],
solvent_name='water')
h2_water = reaction.Reactant(name='h2',
atoms=[Atom('H', x=1.0)],
solvent_name='water')
hh_thf = reaction.Product(name='hh',
atoms=[Atom('H'), Atom('H', x=1.0)],
solvent_name='thf')
with pytest.raises(SolventsDontMatch):
reaction.Reaction(h1_water, h2_water, hh_thf)
with pytest.raises(NotImplementedError):
hh_triplet = reaction.Product(name='hh_trip',
atoms=[Atom('H'),
Atom('H', x=0.7)],
mult=3)
reaction.Reaction(h1, h2, hh_triplet)
def test_bad_balance():
hh_product = reaction.Product(
name='hh', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 1.0, 0.0, 0.0)])
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, hh_product)
h_minus = reaction.Reactant(name='h1_minus',
atoms=[Atom('H', 0.0, 0.0, 0.0)],
charge=-1)
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, h_minus, hh_product)
h1_water = reaction.Reactant(name='h1',
atoms=[Atom('H', 0.0, 0.0, 0.0)],
solvent_name='water')
h2_water = reaction.Reactant(name='h2',
atoms=[Atom('H', 1.0, 0.0, 0.0)],
solvent_name='water')
hh_thf = reaction.Product(
name='hh',
atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 1.0, 0.0, 0.0)],
solvent_name='thf')
with pytest.raises(SolventsDontMatch):
reaction.Reaction(h1_water, h2_water, hh_thf)
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_from_smiles():
# Chemdraw can generate a reaction with reactants and products
addition = reaction.Reaction(smiles='CC(C)=O.[C-]#N>>CC([O-])(C#N)C')
assert len(addition.reacs) == 2
assert len(addition.prods) == 1
# Should be readable-ish names
for reac in addition.reacs:
assert reac.name != 'molecule'
with pytest.raises(UnbalancedReaction):
_ = reaction.Reaction('CC(C)=O.[C-]#N')
def test_calc_delta_e():
r1 = reaction.Reactant(name='h', atoms=[Atom('H', 0.0, 0.0, 0.0)])
r1.energy = -0.5
r2 = reaction.Reactant(name='h', atoms=[Atom('H', 0.0, 0.0, 0.0)])
r2.energy = -0.5
tsguess = TSguess(atoms=None,
reactant=ReactantComplex(r1),
product=ProductComplex(r2))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
ts.energy = -0.8
p = reaction.Product(
name='hh', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 1.0, 0.0, 0.0)])
p.energy = -1.0
reac = reaction.Reaction(r1, r2, p)
reac.ts = ts
assert -1E-6 < reac.calc_delta_e() < 1E-6
assert 0.2 - 1E-6 < reac.calc_delta_e_ddagger() < 0.2 + 1E-6
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_unavail_properties():
ha = reaction.Reactant(name='ha', atoms=[Atom('H')])
hb = reaction.Product(name='hb', atoms=[Atom('H')])
rxn = reaction.Reaction(ha, hb)
delta = reaction.calc_delta_with_cont(left=[ha], right=[hb], cont='h_cont')
assert delta is None
# Should not raise an exception(?)
rxn.find_lowest_energy_ts_conformer()
rxn.calculate_thermochemical_cont(free_energy=False, enthalpy=False)
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_reaction_identical_reac_prods():
os.chdir(os.path.join(here, 'data'))
hh_reactant = reaction.Reactant(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
hh_product = reaction.Product(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
h2_reaction = reaction.Reaction(hh_reactant, hh_product)
h2_reaction.locate_transition_state()
assert h2_reaction.ts is None
shutil.rmtree('transition_states')
os.chdir(here)
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_check_rearrangement():
# Linear H3 -> Trigonal H3
make_graph(species=trig_h3, allow_invalid_valancies=True)
reac = reaction.Reaction(lin_h3, trig_h3)
