def check_bond_dissociation_energy_and_isomorphic_and_rings(
self, bond_list, bbond_list):
energy = 0.0
reactant_graph = self.reac_mol_graph
atoms = [
Atom(atomic_symbol=reactant_graph.atoms[i].label)
for i in range(reactant_graph.n_atoms)
]
product = Species(atoms)
graph = nx.Graph()
for i in range(reactant_graph.n_atoms):
graph.add_node(i,
atom_label=reactant_graph.atoms[i].label,
stereo=False)
if bond_list is not None:
[
graph.add_edge(bond[0], bond[1], pi=False, active=False)
for bond in bond_list
]
product.graph = graph
# Filter the isomorphic
if is_isomorphic(reactant_graph.graph, product.graph):
return False
elif self.check_four_and_three_membered_rings(product.graph):
return False
else:
# Filter the bond dissociation energy
num = sum([bb[2] for bb in bbond_list])
for break_bond in bbond_list:
first_atom = reactant_graph.atoms[break_bond[0]].label
second_atom = reactant_graph.atoms[break_bond[1]].label
bond_type = break_bond[2]
supported_element = ['C', 'N', 'H', 'O', 'S', 'Cl', 'Si']
if first_atom not in supported_element or second_atom not in supported_element:
# use 100 instead
energy += 100
else:
# consider if break double bond (2-->1 not break 2) then the bond dissociation use double bond energy - single bond energy
if num >= 3 and bond_type >= 2:
try:
energy += props.bond_dissociation_energy[
first_atom, second_atom, bond_type]
energy -= props.bond_dissociation_energy[
first_atom, second_atom, bond_type - 1]
except:
energy += props.bond_dissociation_energy[
second_atom, first_atom, bond_type]
energy -= props.bond_dissociation_energy[
second_atom, first_atom, bond_type - 1]
else:
try:
energy += props.bond_dissociation_energy[
first_atom, second_atom, bond_type]
except:
energy += props.bond_dissociation_energy[
second_atom, first_atom, bond_type]
if energy / _constants.CAL2J > self.bond_dissociation_cutoff:
return False
else:
return True
