def test_get_bond_rearrangs():
if os.path.exists('test_bond_rearrangs.txt'):
os.remove('test_bond_rearrangs.txt')
# ethane --> Ch3 + Ch3
reac = Molecule(smiles='CC')
prod = Molecule(atoms=[Atom('C', -8.3, 1.4, 0.0),
Atom('C', 12, 1.7, -0.0),
Atom('H', -8.6, 0.5, -0.5),
Atom('H', -8.6, 2.3, -0.4),
Atom('H', -8.6, 1.3, 1),
Atom('H', 12.3, 1.7, -1.0),
Atom('H', 12.4, 0.8, 0.4),
Atom('H', 12.3, 2.5, 0.5)])
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='test') == [br.BondRearrangement(breaking_bonds=[(0, 1)])]
# Rerunning the get function should read test_bond_rearrangs.txt, so modify it, swapping 0 and 1 in the breaking
# bond then reopen
with open('test_bond_rearrangs.txt', 'w') as rearr_file:
print('fbond\n'
'bbonds\n'
'1 0\n'
'end', file=rearr_file)
rearr = br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='test')[0]
assert rearr == BondRearrangement(breaking_bonds=[(1, 0)])
assert br.get_bond_rearrangs(ReactantComplex(prod), ProductComplex(reac), name='test2') is None
# If reactants and products are identical then the rearrangement is undetermined
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(reac), name='test3') is None
os.remove('test_bond_rearrangs.txt')
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_calculate_reaction_profile_energies():
test_reac = Reactant(name='test', smiles='C')
test_reac.energy = -1
test_prod = Product(name='test', smiles='C')
test_prod.energy = -1.03187251
tsguess = TSguess(atoms=test_reac.atoms, reactant=ReactantComplex(test_reac), product=ProductComplex())
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
ts.energy = -0.96812749
reaction = Reaction(test_reac, test_prod)
reaction.ts = ts
energies = plotting.calculate_reaction_profile_energies(reactions=[reaction],
units=KcalMol)
# Energies have been set to ∆E = -20 and ∆E‡ = 20 kcal mol-1 respectively
assert energies[0] == 0
assert 19 < energies[1] < 21
assert -21 < energies[2] < -19
# Copying the reaction should give relative energies [0, 20, -20, 0, -40]
energies = plotting.calculate_reaction_profile_energies(reactions=[reaction, deepcopy(reaction)],
units=KcalMol)
# Energies have been set to ∆E = -20 and ∆E‡ = 20 kcal mol-1 respectively
assert energies[0] == 0
assert -0.1 < energies[3] < 0.1
assert -41 < energies[4] < -39
def test_graph_no_other_bonds():
reac = Reactant(name='r',
atoms=xyz_file_to_atoms('h_shift_correct_ts_mode.xyz'))
br = BondRearrangement(breaking_bonds=[(1, 10)],
forming_bonds=[(5, 10)])
calc = Calculation(name='h_shift',
molecule=reac,
method=orca,
keywords=orca.keywords.opt_ts,
n_cores=1)
calc.output.filename = 'h_shift_correct_ts_mode.out'
calc.output.file_lines = open('h_shift_correct_ts_mode.out', 'r').readlines()
f_ts = Species(name='f_displaced', charge=0, mult=1,
atoms=get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=1.0))
b_ts = Species(name='b_displaced', charge=0, mult=1,
atoms=get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=-1.0))
assert not imag_mode_generates_other_bonds(ts=reac,
f_species=f_ts,
b_species=b_ts,
bond_rearrangement=br)
def test_reaction_warnings():
test_reac = Reactant(name='test', smiles='C')
test_reac.energy = -1
test_prod = Product(name='test', smiles='C')
test_prod.energy = -1.03187251
tsguess = TSguess(atoms=test_reac.atoms,
reactant=ReactantComplex(test_reac),
product=ProductComplex())
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
ts.energy = -0.98
ts.imaginary_frequencies = [-100]
reaction = Reaction(test_reac, test_prod)
reaction.ts = None
# Should be some warning with no TS
assert len(
plotting.get_reaction_profile_warnings(reactions=[reaction])) > 10
# Should be no warnings with a TS that exists and has an energy and one
# imaginary freq
reaction.ts = ts
warnings = plotting.get_reaction_profile_warnings(reactions=[reaction])
assert 'None' in warnings
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_plot_reaction_profile():
r = Reactant(name='reactant', smiles='C')
p = Product(name='product', smiles='C')
tsguess = TSguess(atoms=r.atoms,
reactant=ReactantComplex(r),
product=ProductComplex(p))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
reaction = Reaction(r, p)
reaction.ts = ts
plotting.plot_reaction_profile(reactions=[reaction],
units=KjMol,
name='test')
assert os.path.exists('test_reaction_profile.png')
os.remove('test_reaction_profile.png')
with pytest.raises(AssertionError):
plotting.plot_reaction_profile(reactions=[reaction],
units=KjMol,
name='test',
free_energy=True,
enthalpy=True)
return None
def test_ts_conformer(tmpdir):
os.chdir(tmpdir)
ch3cl = Reactant(charge=0,
mult=1,
atoms=[
Atom('Cl', 1.63664, 0.02010, -0.05829),
Atom('C', -0.14524, -0.00136, 0.00498),
Atom('H', -0.52169, -0.54637, -0.86809),
Atom('H', -0.45804, -0.50420, 0.92747),
Atom('H', -0.51166, 1.03181, -0.00597)
])
f = Reactant(charge=-1, mult=1, atoms=[Atom('F', 4.0, 0.0, 0.0)])
ch3f = Product(charge=0,
mult=1,
atoms=[
Atom('C', -0.05250, 0.00047, -0.00636),
Atom('F', 1.31229, -0.01702, 0.16350),
Atom('H', -0.54993, -0.04452, 0.97526),
Atom('H', -0.34815, 0.92748, -0.52199),
Atom('H', -0.36172, -0.86651, -0.61030)
])
cl = Reactant(charge=-1, mult=1, atoms=[Atom('Cl', 4.0, 0.0, 0.0)])
f_ch3cl_tsguess = TSguess(reactant=ReactantComplex(f, ch3cl),
product=ProductComplex(ch3f, cl),
atoms=[
Atom('F', -2.66092, -0.01426, 0.09700),
Atom('Cl', 1.46795, 0.05788, -0.06166),
Atom('C', -0.66317, -0.01826, 0.02488),
Atom('H', -0.78315, -0.58679, -0.88975),
Atom('H', -0.70611, -0.54149, 0.97313),
Atom('H', -0.80305, 1.05409, 0.00503)
])
f_ch3cl_tsguess.bond_rearrangement = BondRearrangement(breaking_bonds=[
(2, 1)
],
forming_bonds=[(0,
2)])
f_ch3cl_ts = TransitionState(ts_guess=f_ch3cl_tsguess)
atoms = conf_gen.get_simanl_atoms(
species=f_ch3cl_ts, dist_consts=get_distance_constraints(f_ch3cl_ts))
regen = Molecule(name='regenerated_ts', charge=-1, mult=1, atoms=atoms)
# regen.print_xyz_file()
# Ensure the making/breaking bonds retain their length
regen_coords = regen.get_coordinates()
assert are_coords_reasonable(regen_coords) is True
assert 1.9 < np.linalg.norm(regen_coords[0] - regen_coords[2]) < 2.1
assert 2.0 < np.linalg.norm(regen_coords[1] - regen_coords[2]) < 2.2
os.chdir(here)
def test_n_membered_rings():
h2o = Molecule(atoms=[Atom('O'), Atom('H', x=-1), Atom('H', x=1)])
bond_rearr = BondRearrangement(forming_bonds=[(1, 2)])
# Forming bond over H-H should give a single 3-membered ring
assert bond_rearr.n_membered_rings(h2o) == [3]
bond_rearr = BondRearrangement(breaking_bonds=[(0, 1)])
assert bond_rearr.n_membered_rings(h2o) == []
# Breaking an O-H and forming a H-H should not make any rings
bond_rearr = BondRearrangement(breaking_bonds=[(0, 2)],
forming_bonds=[(1, 2)])
assert bond_rearr.n_membered_rings(h2o) == [3]
def test_reactant_complex_truncation():
# Non-sensical bond rearrangement
bond_rearr = BondRearrangement(forming_bonds=[(0, 1)], breaking_bonds=[(0, 5)])
methane_dimer = ReactantComplex(methane, methane)
# Should not truncate methane dimer at all
truncated = get_truncated_complex(methane_dimer, bond_rearr)
assert truncated.n_atoms == 10
def test_product_complex_truncation():
# H atom transfer from methane to ethene
bond_rearr = BondRearrangement(breaking_bonds=[(0, 1)], forming_bonds=[(1, 5)])
methane_ethene = ReactantComplex(methane, ethene, name='product_complex')
# Should retain all atoms
truncated = get_truncated_complex(methane_ethene, bond_rearr)
assert truncated.n_atoms == 11
def test_enone_truncation():
enone = Reactant(name='enone', smiles='CC(O)=CC(=O)OC')
reactant = ReactantComplex(enone)
bond_rearr = BondRearrangement(breaking_bonds=[(2, 11)],
forming_bonds=[(11, 5)])
truncated = get_truncated_complex(reactant, bond_rearr)
assert truncated.n_atoms == 10
assert truncated.graph.number_of_edges() == 9
def test_reac_to_prods():
rearrang = BondRearrangement([(0, 4)], [(3, 4)])
prod_graph = mol_graphs.reac_graph_to_prod_graph(g, rearrang)
expected_edges = [(0, 1), (1, 2), (2, 0), (0, 3), (0, 4)]
expected_graph = nx.Graph()
for edge in expected_edges:
expected_graph.add_edge(*edge)
assert mol_graphs.is_isomorphic(expected_graph, prod_graph)
def test_has_correct_mode_no_calc():
bond_rearr = BondRearrangement(breaking_bonds=[(2, 1)],
forming_bonds=[(0, 2)])
calc = Calculation(molecule=ts,
method=method,
keywords=method.keywords.opt_ts,
name='tmp')
# Calculation has no output so should not have the correct mode
assert not imag_mode_has_correct_displacement(
calc, bond_rearrangement=bond_rearr)
def test_large_truncation():
mol = ReactantComplex(
Reactant(name='product', atoms=xyz_file_to_atoms('product.xyz')))
bond_rearr = BondRearrangement(breaking_bonds=[(7, 8), (14, 18)])
assert mol.n_atoms == 50
truncated = get_truncated_complex(r_complex=mol,
bond_rearrangement=bond_rearr)
assert truncated.n_atoms == 27
assert truncated.graph.number_of_edges() == 28
def test_prune_small_rings3():
# Square H4 "molecule"
h4 = Molecule(atoms=[
Atom('H'),
Atom('H', x=0.5),
Atom('H', y=0.5),
Atom('H', x=0.5, y=0.5)
])
make_graph(h4, allow_invalid_valancies=True)
# Some unphysical bond rearrangements
three_mem = BondRearrangement(forming_bonds=[(0, 3)],
breaking_bonds=[(1, 2)])
four_mem = BondRearrangement(forming_bonds=[(0, 1)],
breaking_bonds=[(1, 2)])
bond_rearrs = [three_mem, four_mem]
ade.Config.skip_small_ring_tss = True
br.prune_small_ring_rearrs(bond_rearrs, h4)
# Should not prune if there are different ring sizes
assert len(bond_rearrs) == 2
def test_two_component_truncation():
propylbromide = Reactant(name='RBr', atoms=xyz_file_to_atoms('RBr.xyz'))
chloride = Reactant(name='Cl', smiles='[Cl-]')
mol = ReactantComplex(chloride, propylbromide)
bond_rearr = BondRearrangement(forming_bonds=[(0, 3)],
breaking_bonds=[(3, 4)])
truncated = get_truncated_complex(r_complex=mol,
bond_rearrangement=bond_rearr)
# Should truncate to ethylbromide + Cl-
assert truncated.n_atoms == 9
def test_core_strip():
bond_rearr = BondRearrangement()
bond_rearr.active_atoms = [0]
stripped = get_truncated_complex(methane, bond_rearr)
# Should not strip any atoms if the carbon is designated as active
assert stripped.n_atoms == 5
stripped = get_truncated_complex(ethene, bond_rearr)
assert stripped.n_atoms == 6
bond_rearr.active_atoms = [1]
# Propene should strip to ethene if the terminal C=C is the active atom
stripped = get_truncated_complex(propene, bond_rearr)
assert stripped.n_atoms == 6
assert is_isomorphic(stripped.graph, ethene.graph)
# But-1-ene should strip to ethene if the terminal C=C is the active atom
stripped = get_truncated_complex(but1ene, bond_rearr)
assert stripped.n_atoms == 6
assert is_isomorphic(stripped.graph, ethene.graph)
# Benzene shouldn't be truncated at all
stripped = get_truncated_complex(benzene, bond_rearr)
assert stripped.n_atoms == 12
bond_rearr.active_atoms = [0]
# Ethanol with the terminal C as the active atom should not replace the OH
# with a H
stripped = get_truncated_complex(ethanol, bond_rearr)
assert stripped.n_atoms == 9
# Ether with the terminal C as the active atom should replace the OMe with
# OH
stripped = get_truncated_complex(methlyethylether, bond_rearr)
assert stripped.n_atoms == 9
assert is_isomorphic(stripped.graph, ethanol.graph)
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
def test_more_forming_than_breaking():
h_a = Reactant(atoms=[Atom('H')], name='h_a')
h_b = Reactant(atoms=[Atom('H')], name='h_b')
h2_sep = Complex(h_a, h_b)
h2 = Product(atoms=[Atom('H'), Atom('H', x=1)], name='h2')
rxn = Reaction(h_a, h_b, h2)
bond_rearr = BondRearrangement(forming_bonds=[(0, 1)], breaking_bonds=None)
assert bond_rearr.n_fbonds > bond_rearr.n_bbonds
# Number of bonds in the product needs to be the same or fewer than
# the reactant currently. Will need more get_ts_guess_function_and_params
# if this is to be supproted
with pytest.raises(NotImplementedError):
_ = get_ts(reaction=rxn, reactant=h2_sep, bond_rearr=bond_rearr)
def test_correct_imag_mode():
os.chdir(os.path.join(here, 'data'))
bond_rearrangement = BondRearrangement(breaking_bonds=[(4, 1), (4, 18)],
forming_bonds=[(1, 18)])
g09 = G09()
g09.available = True
calc = Calculation(name='tmp',
molecule=ReactantComplex(
Reactant(smiles='CC(C)(C)C1C=CC=C1')),
method=g09,
keywords=Config.G09.keywords.opt_ts)
calc.output.filename = 'correct_ts_mode_g09.log'
calc.output.set_lines()
f_displaced_atoms = get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=1.0)
f_species = Species(name='f_displaced',
atoms=f_displaced_atoms,
charge=0,
mult=1) # Charge & mult are placeholders
b_displaced_atoms = get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=-1.0)
b_species = Species(name='b_displaced',
atoms=b_displaced_atoms,
charge=0,
mult=1)
# With the correct mode no other bonds are made
assert not imag_mode_generates_other_bonds(
ts=calc.molecule,
f_species=f_species,
b_species=b_species,
bond_rearrangement=bond_rearrangement)
calc.output.filename = 'incorrect_ts_mode_g09.log'
calc.output.set_lines()
assert not imag_mode_has_correct_displacement(calc, bond_rearrangement)
os.chdir(here)
def test_plot_reaction_profile():
# only tests the file is created with the right name
os.chdir(os.path.join(here, 'data'))
r = Reactant(name='reactant', smiles='C')
p = Product(name='product', smiles='C')
tsguess = TSguess(atoms=r.atoms, reactant=ReactantComplex(r), product=ProductComplex(p))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
reaction = Reaction(r, p)
reaction.ts = ts
plotting.plot_reaction_profile(reactions=[reaction], units=KjMol, name='test_reaction')
assert os.path.exists('test_reaction_reaction_profile.png')
os.remove('test_reaction_reaction_profile.png')
os.chdir(here)
def test_plot_reaction_profile():
r = Reactant(name='reactant', smiles='C')
p = Product(name='product', smiles='C')
tsguess = TSguess(atoms=r.atoms,
reactant=ReactantComplex(r),
product=ProductComplex(p))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
reaction = Reaction(r, p)
reaction.ts = ts
plotting.plot_reaction_profile(reactions=[reaction],
units=KjMol,
name='test_reaction')
assert os.path.exists('test_reaction_reaction_profile.png')
os.remove('test_reaction_reaction_profile.png')
def has_correct_mode(name, fbonds, bbonds):
reac = Reactant(name='r', atoms=xyz_file_to_atoms(f'{name}.xyz'))
calc = Calculation(name=name,
molecule=reac,
method=orca,
keywords=orca.keywords.opt_ts,
n_cores=1)
calc.output.filename = f'{name}.out'
calc.output.file_lines = open(f'{name}.out', 'r').readlines()
bond_rearr = BondRearrangement(breaking_bonds=bbonds,
forming_bonds=fbonds)
# Don't require all bonds to be breaking/making in a 'could be ts' function
return imag_mode_has_correct_displacement(calc, bond_rearr,
delta_threshold=0.05,
req_all=False)
def test_ts_template():
# Spoof XTB install
Config.XTB.path = here
Config.ts_template_folder_path = os.path.join(here, 'data', 'ts_guess')
bond_rearr = BondRearrangement(breaking_bonds=[(2, 1)],
forming_bonds=[(0, 2)])
reac_shift = reac_complex.copy()
reac_shift.set_atoms(atoms=[
Atom('F', -3.0587, -0.8998, -0.2180),
Atom('Cl', 0.3842, 0.86572, -1.65507),
Atom('C', -1.3741, -0.0391, -0.9719),
Atom('H', -1.9151, -0.0163, -1.9121),
Atom('H', -1.6295, 0.6929, -0.2173),
Atom('H', -0.9389, -0.9786, -0.6534)
])
reac_shift.print_xyz_file()
templates = get_ts_templates()
assert len(templates) == 1
assert templates[0].graph.number_of_nodes() == 6
tsg_template = get_template_ts_guess(reac_shift,
product_complex,
name='template',
bond_rearr=bond_rearr,
method=XTB(),
dist_thresh=4.0)
# Reset the folder path to the default
Config.ts_template_folder_path = None
assert tsg_template is not None
def test_prune_small_rings():
# Cope rearrangement reactant
cope_r = Molecule(atoms=[
Atom('C', -1.58954, 1.52916, -0.43451),
Atom('C', -1.46263, 0.23506, 0.39601),
Atom('C', -0.57752, 2.62322, -0.15485),
Atom('H', -2.59004, 1.96603, -0.22830),
Atom('H', -1.55607, 1.26799, -1.51381),
Atom('C', 0.40039, 2.56394, 0.75883),
Atom('C', -0.24032, -0.62491, 0.13974),
Atom('H', -2.34641, -0.39922, 0.17008),
Atom('H', -1.50638, 0.49516, 1.47520),
Atom('C', 0.72280, -0.36227, -0.75367),
Atom('H', -0.66513, 3.53229, -0.74242),
Atom('H', 0.55469, 1.70002, 1.39347),
Atom('H', 1.07048, 3.40870, 0.88117),
Atom('H', -0.14975, -1.53366, 0.72733),
Atom('H', 0.70779, 0.51623, -1.38684),
Atom('H', 1.55578, -1.04956, -0.86026)
])
six_mem = BondRearrangement(forming_bonds=[(5, 9)],
breaking_bonds=[(1, 0)])
assert six_mem.n_membered_rings(mol=cope_r) == [6]
four_mem = BondRearrangement(forming_bonds=[(0, 9)],
breaking_bonds=[(1, 0)])
assert four_mem.n_membered_rings(cope_r) == [4]
ade.Config.skip_small_ring_tss = False
bond_rearrs = [six_mem, four_mem]
br.prune_small_ring_rearrs(possible_brs=bond_rearrs, mol=cope_r)
# Should not prune if Config.skip_small_ring_tss = False
assert len(bond_rearrs) == 2
ade.Config.skip_small_ring_tss = True
br.prune_small_ring_rearrs(possible_brs=bond_rearrs, mol=cope_r)
# should remove the 4-membered ring
assert len(bond_rearrs) == 1
from autode import Reactant, Product, Reaction
from autode.bond_rearrangement import BondRearrangement
from autode.transition_states.locate_tss import get_ts
r = Reactant('cope_r.xyz')
p = Product('cope_p.xyz')
reaction = Reaction(r, p, name='cope')
# Define the bond rearrangement as tuples for each forming and breaking bond
bond_rearr = BondRearrangement(forming_bonds=[(5, 9)], breaking_bonds=[(0, 1)])
ts = get_ts(reaction, r, bond_rearr)
print(ts.imaginary_frequencies)
])
cl = Product(charge=-1, mult=1, atoms=[Atom('Cl', 4.0, 0.0, 0.0)])
product_complex = ProductComplex(ch3f, cl)
tsguess = TSguess(reactant=reac_complex,
product=product_complex,
atoms=[
Atom('F', -2.66092, -0.01426, 0.09700),
Atom('Cl', 1.46795, 0.05788, -0.06166),
Atom('C', -0.66317, -0.01826, 0.02488),
Atom('H', -0.78315, -0.58679, -0.88975),
Atom('H', -0.70611, -0.54149, 0.97313),
Atom('H', -0.80305, 1.05409, 0.00503)
])
tsguess.bond_rearrangement = BondRearrangement(breaking_bonds=[(2, 1)],
forming_bonds=[(0, 2)])
ts = TransitionState(ts_guess=tsguess)
@testutils.work_in_zipped_dir(os.path.join(here, 'data', 'ts.zip'))
def test_ts_guess_class():
# Force ORCA to appear available
Config.hcode = 'orca'
Config.ORCA.path = here
assert tsguess.reactant.n_atoms == 6
assert tsguess.product.n_atoms == 6
# C -- Cl distance should be long