def toSMILES(self):
cutting_label_list = []
for vertex in self.vertices:
if isinstance(vertex, CuttingLabel):
cutting_label_list.append(vertex.symbol)
SMILES_before = self.copy(deep=True)
final_vertices = []
for ind, atom in enumerate(SMILES_before.atoms):
element_symbol = atom.symbol
if isinstance(atom, CuttingLabel):
substi_name = 'Si'
substi = Atom(element=substi_name)
substi.label = element_symbol
for bondedAtom, bond in atom.edges.iteritems():
new_bond = Bond(bondedAtom, substi, order=bond.order)
bondedAtom.edges[substi] = new_bond
del bondedAtom.edges[atom]
substi.edges[bondedAtom] = new_bond
substi.radicalElectrons = 3
final_vertices.append(substi)
else:
final_vertices.append(atom)
SMILES_before.vertices = final_vertices
mol_repr = Molecule()
mol_repr.atoms = SMILES_before.vertices
SMILES_after = mol_repr.toSMILES()
import re
smiles = re.sub('\[Si\]', '', SMILES_after)
return smiles
