def test_attack_cost():
subst_centers = get_substitution_centres(reactant=reac_complex,
bond_rearrangement=bond_rearr,
shift_factor=2)
atoms = [
Atom('F', -2.99674, -0.35248, 0.17493),
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)
]
ideal_complex = ReactantComplex(f, ch3cl)
ideal_complex.set_atoms(atoms)
attack_cost = substitution.attack_cost(reac_complex,
subst_centers,
attacking_mol_idx=0)
ideal_attack_cost = substitution.attack_cost(ideal_complex,
subst_centers,
attacking_mol_idx=0)
# The cost function should be larger for the randomly located reaction
# complex compared to the ideal
assert attack_cost > ideal_attack_cost
def test_attack_cost():
subst_centers = substitution.get_substitution_centres(reactant=reac_complex,
bond_rearrangement=bond_rearr,
shift_factor=2)
ideal_complex = ReactantComplex(f, ch3cl)
ideal_complex.set_atoms(atoms=xyz_file_to_atoms(os.path.join(here, 'data', 'sn2_reac_complex.xyz')))
attack_cost = substitution.attack_cost(reac_complex, subst_centers, attacking_mol_idx=0)
ideal_attack_cost = substitution.attack_cost(ideal_complex, subst_centers, attacking_mol_idx=0)
# The cost function should be larger for the randomly located reaction complex compared to the ideal
assert attack_cost > ideal_attack_cost
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_subst_centre():
subst_centers = substitution.get_substitution_centres(
reactant=reac_complex, bond_rearrangement=bond_rearr, shift_factor=2)
# Only one atom gets attacked in an SN2
assert len(subst_centers) == 1
sc = subst_centers[0]
assert type(sc) is substitution.SubstitutionCentre
assert reac_complex.atoms[sc.a_atom].label == 'F'
assert reac_complex.atoms[sc.c_atom].label == 'C'
assert reac_complex.atoms[sc.x_atom].label == 'Cl'
# The attacking flouride ion doesn't have any nearest neighbours
assert len(sc.a_atom_nn) == 0
# The attacking atom to substitution centre atom ideal bond length
# should be ~ 3 Å
assert type(sc.r0_ac) is float
assert 2.0 < sc.r0_ac < 5.0
def translate_rotate_reactant(reactant,
bond_rearrangement,
shift_factor,
n_iters=10):
"""
Shift a molecule in the reactant complex so that the attacking atoms
(a_atoms) are pointing towards the attacked atoms (l_atoms)
Arguments:
reactant (autode.complex.ReactantComplex):
bond_rearrangement (autode.bond_rearrangement.BondRearrangement):
shift_factor (float):
n_iters (int): Number of iterations of translation/rotation to perform
to (hopefully) find the global minima
"""
if not hasattr(reactant, 'molecules'):
logger.warning('Cannot rotate/translate component, not a Complex')
return
if len(reactant.molecules) < 2:
logger.info('Reactant molecule does not need to be translated or '
'rotated')
return
logger.info('Rotating/translating into a reactive conformation... running')
# This function can add dummy atoms for e.g. SN2' reactions where there
# is not a A -- C -- Xattern for the substitution centre
subst_centres = get_substitution_centres(reactant,
bond_rearrangement,
shift_factor=shift_factor)
if all(sc.a_atom in reactant.get_atom_indexes(mol_index=0)
for sc in subst_centres):
attacking_mol = 0
else:
attacking_mol = 1
# Disable the logger to prevent rotation/translations printing
logger.disabled = True
# Find the global minimum for inplace rotation, translation and rotation
min_cost, opt_x = None, None
for _ in range(n_iters):
res = minimize(get_cost_rotate_translate,
x0=np.random.random(11),
method='BFGS',
tol=0.1,
args=(reactant, subst_centres, attacking_mol))
if min_cost is None or res.fun < min_cost:
min_cost = res.fun
opt_x = res.x
# Renable the logger
logger.disabled = False
logger.info(f'Minimum cost for translating/rotating is {min_cost:.3f}')
# Translate/rotation the attacking molecule optimally
reactant.rotate_mol(axis=opt_x[:3],
theta=opt_x[3],
mol_index=attacking_mol)
reactant.translate_mol(vec=opt_x[4:7], mol_index=attacking_mol)
reactant.rotate_mol(axis=opt_x[7:10],
theta=opt_x[10],
mol_index=attacking_mol)
logger.info(' ... done')
reactant.print_xyz_file()
# Remove any dummy atoms that may have been added
# in alt_substitution_centres
reactant.atoms = [atom for atom in reactant.atoms if atom.label != 'D']
return None