def _convert_4_atom_3_bond_path(start):
"""
Searches for 4-atom-3-bond [X=X-X=X+] paths starting from the parameter atom.
If a path is found, the starting atom receives an unpaired electron while
the bonds in the delocalization path are "inverted". A unit of charge on the
end atom is neutralized and a lone pair is added.
"""
path = pathfinder.find_butadiene_end_with_charge(start)
if path is not None:
start.radical_electrons += 1
end = path[-1]
end.charge += 1 if end.charge < 0 else -1
end.lone_pairs += 1
# filter bonds from path and convert bond orders:
bonds = path[1::2] # odd
for bond in bonds[::2]: # even
assert isinstance(bond, Bond)
bond.decrement_order()
for bond in bonds[1::2]: # odd bonds
assert isinstance(bond, Bond)
bond.increment_order()
return True
return False
def convert_4_atom_3_bond_path(start):
"""
Searches for 4-atom-3-bond [X=X-X=X+] paths starting from the parameter atom.
If a path is found, the starting atom receives an unpaired electron while
the bonds in the delocalization path are "inverted". A unit of charge on the
end atom is neutralized and a lone pair is added.
"""
path = pathfinder.find_butadiene_end_with_charge(start)
if path is not None:
start.radicalElectrons += 1
end = path[-1]
end.charge += 1 if end.charge < 0 else -1
end.lonePairs += 1
# filter bonds from path and convert bond orders:
bonds = path[1::2]#odd
for bond in bonds[::2]:# even
assert isinstance(bond, Bond)
bond.decrementOrder()
for bond in bonds[1::2]:# odd bonds
assert isinstance(bond, Bond)
bond.incrementOrder()
return True
return False
def test_c8h14o4(self):
inchi = "InChI=1S/C8H14O4S/c1-3-6-13(2,11)7-8(9)4-5-12-10/h3,6H,1,4-5,7H2,2H3,(H-,10,11)"
mol = Molecule().from_inchi(inchi)
start = mol.atoms[0]
path = find_butadiene_end_with_charge(start)
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [1, 3, 6, 13]
self.assertEqual(idx_path, expected_idx_path)
def test_c6h6o6(self):
inchi = "InChI=1S/C6H6O6/c7-6(2-5-12-9)10-3-1-4-11-8/h1,7H,4-5H2"
mol = Molecule().from_inchi(inchi)
start = mol.atoms[2]
path = find_butadiene_end_with_charge(start)
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [3, 10]
self.assertEquals(idx_path, expected_idx_path)
def test_c6h6o4(self):
inchi = "InChI=1S/C6H6O4/c1-2-4-9-6(7)3-5-10-8/h2-3H,1,5H2"
mol = Molecule().from_inchi(inchi)
start = mol.atoms[0]
path = find_butadiene_end_with_charge(start)
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [1, 2, 4, 9]
self.assertEquals(idx_path, expected_idx_path)
def test_co(self):
adjlist = """
1 C u0 p1 c-1 {2,T}
2 O u0 p1 c+1 {1,T}
"""
mol = Molecule().from_adjacency_list(adjlist)
start = mol.atoms[0]
path = find_butadiene_end_with_charge(start)
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [1, 2]
self.assertEquals(idx_path, expected_idx_path)
def test_c2h2o3(self):
adjlist = """
1 C u0 p0 c0 {5,D} {6,S} {7,S}
2 C u0 p0 c0 {3,D} {4,S} {5,S}
3 O u0 p2 c0 {2,D}
4 O u0 p3 c-1 {2,S}
5 O u0 p1 c+1 {1,D} {2,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
start = mol.atoms[0]
path = find_butadiene_end_with_charge(start)
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [1, 5]
self.assertEquals(idx_path, expected_idx_path)
def test_c4h6o(self):
adjlist = """
1 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S}
2 C u0 p1 c-1 {1,S} {3,S} {9,S}
3 C u0 p0 c0 {2,S} {4,S} {10,S} {11,S}
4 C u0 p0 c0 {3,S} {5,T}
5 O u0 p1 c+1 {4,T}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {2,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
start = mol.atoms[3]
path = find_butadiene_end_with_charge(start)
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [4, 5]
self.assertEquals(idx_path, expected_idx_path)
