def test_2b2f():
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('N', 10, 0, 0), Atom('O', 10.6, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('N', 0.6, 0, 0), Atom('O', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1)], [(2, 3)]], [[(0, 2)], [(1, 3)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 2), (1, 3)], breaking_bonds=[(0, 1), (2, 3)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('H', 10, 0, 0),
Atom('N', 10.6, 0, 0), Atom('O', 20, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('H', 1.2, 0, 0),
Atom('N', 20, 0, 0), Atom('O', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1)], [(2, 3)]], [[(0, 4), (2, 4)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 4), (2, 4)], breaking_bonds=[(0, 1), (2, 3)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('H', 1.2, 0, 0), Atom('O', 10, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('H', 11.2, 0, 0), Atom('O', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1), (1, 2)]], [[(0, 3), (2, 3)], [(1, 3)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 3), (1, 3)], breaking_bonds=[(0, 1), (1, 2)]),
br.BondRearrangement(forming_bonds=[(1, 3), (2, 3)], breaking_bonds=[(0, 1), (1, 2)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('H', 1.2, 0, 0), Atom('O', 10, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('H', 1.2, 0, 0), Atom('O', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1), (1, 2)]], [[(0, 3), (2, 3)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 3), (2, 3)], breaking_bonds=[(0, 1), (1, 2)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('N', 1.2, 0, 0), Atom('C', 10, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('N', 1.2, 0, 0), Atom('C', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [], [], [[[(0, 1)], [(0, 3)]], [[(1, 2)], [(2, 3)]]], [], []) == [br.BondRearrangement(forming_bonds=[(0, 3), (2, 3)], breaking_bonds=[(0, 1), (1, 2)])]
def test_2b1f():
reac = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('C', 0.6, 0, 0),
Atom('O', 1.2, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('C', 10, 0, 0),
Atom('O', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b1f(
reac, prod, [], [[(0, 1)], [(1, 2)]], [[(0, 2)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 2)],
breaking_bonds=[(0, 1), (1, 2)])
]
reac = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('C', 0.6, 0, 0),
Atom('H', 1.2, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('C', 10, 0, 0),
Atom('H', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b1f(
reac, prod, [], [[(0, 1), (1, 2)]], [[(0, 2)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 2)],
breaking_bonds=[(0, 1), (1, 2)])
]
reac = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('H', 0.6, 0, 0),
Atom('H', 1.2, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('H', 0.6, 0, 0),
Atom('H', 10, 0, 0)])
assert br.get_fbonds_bbonds_2b1f(
reac, prod, [], [[(0, 1), (1, 2)]], [], [], [(0, 2)], []) == [
br.BondRearrangement(forming_bonds=[(0, 2)],
breaking_bonds=[(0, 1), (1, 2)])
]
def test_bondrearr_obj():
# Reaction H + H2 -> H2 + H
rearrang = br.BondRearrangement(forming_bonds=[(0, 1)],
breaking_bonds=[(1, 2)])
assert rearrang.n_fbonds == 1
assert rearrang.n_bbonds == 1
assert rearrang.__str__() == '0-1_1-2'
rearrag2 = br.BondRearrangement(forming_bonds=[(0, 1)],
breaking_bonds=[(1, 2)])
assert rearrag2 == rearrang
h2_h_mol = Molecule(name='mol', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 0.0, 0.0, -1.0),
Atom('H', 0.0, 0.0, 1.0)])
active_atom_nl = rearrang.get_active_atom_neighbour_lists(mol=ReactantComplex(h2_h_mol), depth=1)
assert len(active_atom_nl) == 3
assert active_atom_nl == [['H'], ['H'], ['H']]
def test_1b1f():
reac = Molecule(
atoms=[Atom('C', 0, 0, 0),
Atom('H', 0.6, 0, 0),
Atom('H', 10, 0, 0)])
prod = Molecule(
atoms=[Atom('C', 0, 0, 0),
Atom('H', 10, 0, 0),
Atom('H', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_1b1f(reac, prod, [], [[(0, 1)]], [[(1, 2)]],
[], [], []) == [
br.BondRearrangement(forming_bonds=[
(1, 2)
],
breaking_bonds=[
(0, 1)
])
]
reac = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('H', 0.6, 0, 0),
Atom('H', 10, 0, 0)])
prod = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('H', 10, 0, 0),
Atom('H', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_1b1f(reac, prod, [], [], [],
[[[(0, 1)], [(1, 2)]]], [], []) == [
br.BondRearrangement(forming_bonds=[
(1, 2)
],
breaking_bonds=[
(0, 1)
])
]
def test_2b():
reac = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('H', 0.6, 0, 0),
Atom('H', 1.2, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(
atoms=[Atom('H', 0, 0, 0),
Atom('H', 10, 0, 0),
Atom('H', 20, 0, 0)])
# Reactants to products must break two bonds
assert len(
br.get_bond_rearrangs(ReactantComplex(reac),
ProductComplex(prod),
name='2b_test',
save=False)) == 1
assert br.get_fbonds_bbonds_2b(
reac, prod, [], [[(0, 1), (1, 2)]], [], [], [(0, 2)],
[]) == [br.BondRearrangement(breaking_bonds=[(0, 1), (1, 2)])]
def test_get_bond_rearrangs():
# 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',
save=False) == [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)])
os.remove('test_bond_rearrangs.txt')
assert br.get_bond_rearrangs(
ReactantComplex(prod), ProductComplex(reac), name='test2',
save=False) is None
# If reactants and products are identical then the rearrangement is
# undetermined
assert br.get_bond_rearrangs(
ReactantComplex(reac), ProductComplex(reac), name='test3',
save=False) is None
def test_add_bond_rearrang():
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 0.6, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 10, 0, 0)])
assert br.add_bond_rearrangment([], reac, prod, [], [(0, 1)]) == [br.BondRearrangement(breaking_bonds=[(0, 1)])]