def _init_from_smiles(self, reaction_smiles):
"""
Initialise from a SMILES string of the whole reaction e.g.
CC(C)=O.[C-]#N>>CC([O-])(C#N)C
for the addition of cyanide to acetone
Arguments:
reaction_smiles (str):
"""
try:
reacs_smiles, prods_smiles = reaction_smiles.split('>>')
except ValueError:
raise UnbalancedReaction('Could not decompose to reacs & prods')
# Add all the reactants and products with interpretable names
for i, reac_smiles in enumerate(reacs_smiles.split('.')):
reac = Reactant(smiles=reac_smiles)
reac.name = f'r{i}_{reac.formula()}'
self.reacs.append(reac)
for i, prod_smiles in enumerate(prods_smiles.split('.')):
prod = Product(smiles=prod_smiles)
prod.name = f'p{i}_{prod.formula()}'
self.prods.append(prod)
return None
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_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_find_tss():
Config.num_conformers = 1
# Spoof ORCA install
Config.ORCA.path = here
# Don't run the calculation without a working XTB install
if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
return
if os.path.exists('/dev/shm'):
Config.ll_tmp_dir = '/dev/shm'
Config.XTB.path = shutil.which('xtb')
Config.ORCA.implicit_solvation_type = cpcm
Config.make_ts_template = False
Config.num_complex_sphere_points = 2
Config.num_complex_random_rotations = 1
# SN2 example
flouride = Reactant(name='F-', smiles='[F-]')
methyl_chloride = Reactant(name='CH3Cl', smiles='ClC')
chloride = Product(name='Cl-', smiles='[Cl-]')
methyl_flouride = Product(name='CH3F', smiles='CF')
reaction = Reaction(flouride,
methyl_chloride,
chloride,
methyl_flouride,
name='sn2',
solvent_name='water')
# Will work in data/locate_ts/transition_states
reaction.locate_transition_state()
assert reaction.ts is not None
os.chdir('transition_states')
assert reaction.ts.is_true_ts()
os.chdir('..')
reaction.ts.save_ts_template(folder_path=os.getcwd())
assert os.path.exists('template0.txt')
# There should now be a saved template
templates = get_ts_templates(folder_path=os.getcwd())
assert len(templates) == 1
template = templates[0]
assert template.solvent.name == 'water'
assert template.mult == 1
assert template.charge == -1
assert template.graph.number_of_nodes() == 6
# Reset the configuration
Config.ll_tmp_dir = None
def test_isomorphic_reactant_product():
r_water = Reactant(name='h2o', smiles='O')
r_methane = Reactant(name='methane', smiles='C')
p_water = Product(name='h2o', smiles='O')
p_methane = Product(name='methane', smiles='C')
# Reaction where the reactant and product complexes are isomorphic
# should return no TS
reaction = Reaction(r_water, r_methane, p_water, p_methane)
reaction.locate_transition_state()
assert reaction.ts is None
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 _init_from_smiles(self, reaction_smiles):
"""
Initialise from a SMILES string of the whole reaction e.g.
CC(C)=O.[C-]#N>>CC([O-])(C#N)C
for the addition of cyanide to acetone
Arguments:
reaction_smiles (str):
"""
try:
reacs_smiles, prods_smiles = reaction_smiles.split('>>')
except ValueError:
raise UnbalancedReaction('Could not decompose to reacs & prods')
def name(smiles):
"""A more readable string as a name"""
return ''.join([a for a in smiles if a.isalpha()])
# Add all the reactants and products
for reac_smiles in reacs_smiles.split('.'):
self.reacs.append(Reactant(name=name(reac_smiles),
smiles=reac_smiles))
for prod_smiles in prods_smiles.split('.'):
self.prods.append(Product(name=name(prod_smiles),
smiles=prod_smiles))
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_2dpes_properties():
pes = pes_2d.PES2d(reactant=Reactant(smiles='O'),
product=Product(),
r1s=np.linspace(4.0, 1.5, 9),
r1_idxs=(0, 2),
r2s=np.linspace(1.78, 4.0, 8),
r2_idxs=(1, 2))
assert not pes.products_made()
def test_bonds():
h1 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=0.0)
h2 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=0.7)
h3 = Atom(atomic_symbol='H', x=0.0, y=0.0, z=1.7)
hydrogen = Reactant(name='H2', atoms=[h1, h2], charge=0, mult=1)
h = Reactant(name='H', atoms=[h3], charge=0, mult=2)
reac = ReactantComplex(hydrogen, h)
prod_h2 = Product(name='H2', atoms=[h1, h2], charge=0, mult=1)
prod_h = Product(name='H', atoms=[h3], charge=0, mult=2)
fbond = FormingBond(atom_indexes=(1, 2), species=reac)
bbond = BreakingBond(atom_indexes=(0, 1), species=reac, reaction=Reaction(hydrogen, h, prod_h2, prod_h))
assert fbond.curr_dist == 1.0
assert 0.6 < fbond.final_dist < 0.8
assert 2.0 < bbond.final_dist < 2.5
assert bbond.curr_dist == 0.7
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 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_fb_rp_isomorphic():
reac = ReactantComplex(f, ch3cl)
prod = ProductComplex(ch3f, cl)
assert f_b_isomorphic_to_r_p(forwards=prod,
backwards=reac,
reactant=reac,
product=prod)
assert f_b_isomorphic_to_r_p(forwards=reac,
backwards=prod,
reactant=reac,
product=prod)
assert not f_b_isomorphic_to_r_p(
forwards=reac, backwards=reac, reactant=reac, product=prod)
# Check for e.g. failed optimisation of the forwards displaced complex
mol_no_atoms = Product()
assert not f_b_isomorphic_to_r_p(
forwards=mol_no_atoms, backwards=reac, reactant=reac, product=prod)
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)])
reac_complex = ReactantComplex(f, ch3cl)
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 = Product(charge=-1, mult=1, atoms=[Atom('Cl', 4.0, 0.0, 0.0)])
product_complex = ProductComplex(ch3f, cl)
@testutils.work_in_zipped_dir(os.path.join(here, 'data', 'ts_guess.zip'))
def test_ts_template_save():
ts_graph = reac_complex.graph.copy()
# Add the F-C bond as active
ts_graph.add_edge(0, 2, active=True)
def test_get_ts_guess_2dscan():
ch3cl_f = Reactant(name='CH3Cl_F-',
charge=-1,
mult=1,
atoms=[
Atom('F', -4.14292, -0.24015, 0.07872),
Atom('Cl', 1.63463, 0.09787, -0.02490),
Atom('C', -0.14523, -0.00817, 0.00208),
Atom('H', -0.47498, -0.59594, -0.86199),
Atom('H', -0.45432, -0.49900, 0.93234),
Atom('H', -0.56010, 1.00533, -0.04754)
])
ch3f_cl = Product(name='CH3Cl_F-',
charge=-1,
mult=1,
atoms=[
Atom('F', 1.63463, 0.09787, -0.02490),
Atom('Cl', -4.14292, -0.24015, 0.07872),
Atom('C', -0.14523, -0.00817, 0.00208),
Atom('H', -0.47498, -0.59594, -0.86199),
Atom('H', -0.45432, -0.49900, 0.93234),
Atom('H', -0.56010, 1.00533, -0.04754)
])
# H H
# F- C--Cl -> F--C Cl-
# H H H H
pes = pes_2d.PES2d(reactant=ReactantComplex(ch3cl_f),
product=ProductComplex(ch3f_cl),
r1s=np.linspace(4.0, 1.5, 9),
r1_idxs=(0, 2),
r2s=np.linspace(1.78, 4.0, 8),
r2_idxs=(1, 2))
pes.calculate(name='SN2_PES', method=xtb, keywords=xtb.keywords.low_opt)
assert pes.species[0, 1] is not None
assert -13.13 < pes.species[0, 1].energy < -13.11
assert pes.species.shape == (9, 8)
assert pes.rs.shape == (9, 8)
assert type(pes.rs[0, 1]) == tuple
assert pes.rs[1, 1] == (np.linspace(4.0, 1.5,
9)[1], np.linspace(1.78, 4.0, 8)[1])
# Fitting the surface with a 2D polynomial up to order 3 in r1 and r2 i.e.
# r1^3r2^3
pes.fit(polynomial_order=3)
assert pes.coeff_mat is not None
assert pes.coeff_mat.shape == (4, 4) # Includes r1^0 etc.
pes.print_plot(name='pes_plot')
assert os.path.exists('pes_plot.png')
os.remove('pes_plot.png')
# Products should be made on this surface
assert pes.products_made()
# Get the TS guess from this surface calling all the above functions
reactant = ReactantComplex(ch3cl_f)
fbond = FormingBond(atom_indexes=(0, 2), species=reactant)
fbond.final_dist = 1.5
bbond = BreakingBond(atom_indexes=(1, 2),
species=reactant,
reaction=Reaction(ch3cl_f, ch3f_cl))
bbond.final_dist = 4.0
ts_guess = pes_2d.get_ts_guess_2d(reactant=reactant,
product=ProductComplex(ch3f_cl),
bond1=fbond,
bond2=bbond,
polynomial_order=3,
name='SN2_PES',
method=xtb,
keywords=xtb.keywords.low_opt,
dr=0.3)
assert ts_guess is not None
assert ts_guess.n_atoms == 6
assert ts_guess.energy is None
assert 1.9 < ts_guess.get_distance(0, 2) < 2.1
assert 1.9 < ts_guess.get_distance(1, 2) < 2.0
def test_find_tss():
os.chdir(os.path.join(here, 'data', 'locate_ts'))
Config.num_conformers = 1
# Spoof ORCA install
Config.ORCA.path = here
# Don't run the calculation without a working XTB install
if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
return
Config.XTB.path = shutil.which('xtb')
Config.ORCA.implicit_solvation_type = 'cpcm'
Config.make_ts_template = False
Config.num_complex_sphere_points = 2
Config.num_complex_random_rotations = 1
# SN2 example
flouride = Reactant(name='F-', smiles='[F-]')
methyl_chloride = Reactant(name='CH3Cl', smiles='ClC')
chloride = Product(name='Cl-', smiles='[Cl-]')
methyl_flouride = Product(name='CH3F', smiles='CF')
reaction = Reaction(flouride,
methyl_chloride,
chloride,
methyl_flouride,
name='sn2',
solvent_name='water')
# Will work in data/locate_ts/transition_states
reaction.locate_transition_state()
assert reaction.ts is not None
os.chdir(os.path.join(here, 'data', 'locate_ts', 'transition_states'))
for filename in os.listdir(os.getcwd()):
if filename.endswith(('.inp', '.png')):
os.remove(filename)
assert reaction.ts.is_true_ts()
reaction.ts.save_ts_template(folder_path=os.getcwd())
assert os.path.exists('template0.obj')
# There should now be a saved template
templates = get_ts_templates(folder_path=os.getcwd())
assert len(templates) == 1
template = templates[0]
assert template.solvent.name == 'water'
assert template.mult == 1
assert template.charge == -1
assert template.graph.number_of_nodes() == 6
# Tidy the generated files
os.remove('template0.obj')
os.chdir(here)