def generate_lone_pair_multiple_bond_resonance_structures(mol):
"""
Generate all of the resonance structures formed by lone electron pair - multiple bond shifts in 3-atom systems.
Examples: aniline (Nc1ccccc1), azide, [:NH2]C=[::O] <=> [NH2+]=C[:::O-]
(where ':' denotes a lone pair, '.' denotes a radical, '-' not in [] denotes a single bond, '-'/'+' denote charge)
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Molecule)
cython.declare(atom=Atom, atom1=Atom, atom2=Atom, atom3=Atom, bond12=Bond, bond23=Bond)
cython.declare(v1=Vertex, v2=Vertex)
structures = []
for atom in mol.vertices:
if atom.lone_pairs >= 1:
paths = pathfinder.find_lone_pair_multiple_bond_paths(atom)
for atom1, atom2, atom3, bond12, bond23 in paths:
# Adjust to (potentially) new resonance structure
atom1.decrement_lone_pairs()
atom3.increment_lone_pairs()
bond12.increment_order()
bond23.decrement_order()
atom1.update_charge()
atom3.update_charge()
# Make a copy of structure
structure = mol.copy(deep=True)
# Restore current structure
atom1.increment_lone_pairs()
atom3.decrement_lone_pairs()
bond12.decrement_order()
bond23.increment_order()
atom1.update_charge()
atom3.update_charge()
try:
structure.update_atomtypes(log_species=False)
except AtomTypeError:
pass # Don't append resonance structure if it creates an undefined atomtype
else:
structures.append(structure)
return structures
def test_h2nnoo(self):
smiles = "N[N+]([O-])=O"
mol = Molecule().from_smiles(smiles)
paths = find_lone_pair_multiple_bond_paths(mol.atoms[0])
self.assertTrue(paths)
def test_sn2(self):
smiles = "OS(O)=[N+]=[N-]"
mol = Molecule().from_smiles(smiles)
paths = find_lone_pair_multiple_bond_paths(mol.atoms[2])
self.assertTrue(paths)
def test_hn3(self):
smiles = "[NH-][N+]#N"
mol = Molecule().from_smiles(smiles)
paths = find_lone_pair_multiple_bond_paths(mol.atoms[0])
self.assertTrue(paths)
def test_n2ob(self):
smiles = "N#[N+][O-]"
mol = Molecule().from_smiles(smiles)
paths = find_lone_pair_multiple_bond_paths(mol.atoms[2])
self.assertTrue(paths)
def test_n2oa(self):
smiles = "[N-]=[N+]=O"
mol = Molecule().from_smiles(smiles)
paths = find_lone_pair_multiple_bond_paths(mol.atoms[0])
self.assertTrue(paths)
def test_nh2cho(self):
smiles = 'NC=O'
mol = Molecule().from_smiles(smiles)
paths = find_lone_pair_multiple_bond_paths(mol.atoms[0])
self.assertTrue(paths)
