def test_atoms():
assert atoms.get_maximal_valance(atom_label='C') == 4
assert atoms.get_maximal_valance(atom_label='Aa') == 6
assert atoms.get_atomic_weight(atom_label='C') == 12.01
assert atoms.get_atomic_weight(atom_label='Aa') == 70
assert 0.9 < atoms.get_vdw_radius(atom_label='H') < 1.2
assert 2 < atoms.get_vdw_radius(atom_label='Aa') < 3
assert atoms.is_pi_atom(atom_label='C', valency=3) is True
assert atoms.is_pi_atom(atom_label='C', valency=4) is False
assert atoms.is_pi_atom(atom_label='Aa', valency=9) is False
def remove_bonds_invalid_valancies(species):
"""
Remove invalid valencies for atoms that exceed their maximum valencies e.g.
H should have no more than 1 'bond'
Arguments:
species (autode.species.Species):
"""
for i in species.graph.nodes:
max_valance = get_maximal_valance(atom_label=species.atoms[i].label)
neighbours = list(species.graph.neighbors(i))
if len(neighbours) <= max_valance:
# All is well
continue
logger.warning(f'Atom {i} exceeds its maximal valence removing edges')
# Get the atom indexes sorted by the closest to atom i
closest_atoms = sorted(neighbours,
key=lambda j: species.get_distance(i, j))
# Delete all the bonds to atom(s) j that are above the maximal valance
for j in closest_atoms[max_valance:]:
species.graph.remove_edge(i, j)
return None
def add_bond_rearrangment(bond_rearrangs, reactant, product, fbonds, bbonds):
"""For a possible bond rearrangement, sees if the products are made, and
adds it to the bond rearrang list if it does
Arguments:
bond_rearrangs (list(autode.bond_rearrangements.BondRearrangement)):
list of working bond rearrangments
reactant (molecule object): reactant complex
product (molecule object): product complex
fbonds (list(tuple)): list of bonds to be made
bbonds (list(tuple)): list of bonds to be broken
Returns:
(list(autode.bond_rearrangements.BondRearrangement)):
"""
# Check that the bond rearrangement doesn't exceed standard atom valances
bbond_atoms = [atom for bbond in bbonds for atom in bbond]
for fbond in fbonds:
for atom in fbond:
atom_label = reactant.atoms[atom].label
if (reactant.graph.degree(atom) == get_maximal_valance(atom_label)
and atom not in bbond_atoms):
# If we are here then there is at least one atom that will
# exceed it's maximal valance, therefore
# we don't need to run isomorphism
return bond_rearrangs
rearranged_graph = generate_rearranged_graph(reactant.graph,
fbonds=fbonds,
bbonds=bbonds)
if is_isomorphic(rearranged_graph, product.graph):
ordered_fbonds = []
ordered_bbonds = []
for fbond in fbonds:
if fbond[0] < fbond[1]:
ordered_fbonds.append((fbond[0], fbond[1]))
else:
ordered_fbonds.append((fbond[1], fbond[0]))
for bbond in bbonds:
if bbond[0] < bbond[1]:
ordered_bbonds.append((bbond[0], bbond[1]))
else:
ordered_bbonds.append((bbond[1], bbond[0]))
ordered_fbonds.sort()
ordered_bbonds.sort()
bond_rearrangs.append(
BondRearrangement(forming_bonds=ordered_fbonds,
breaking_bonds=ordered_bbonds))
return bond_rearrangs