def test_acrolein(self):
mol = Molecule().from_smiles("C=CC=O") # Acrolein
start, end = mol.atoms[0], mol.atoms[3]
path = find_butadiene(start, end)
self.assertIsNotNone(path)
start, end = mol.atoms[0], mol.atoms[4] # wrong end
path = find_butadiene(start, end)
self.assertIsNone(path)
start, end = mol.atoms[-1], mol.atoms[3] # wrong start
path = find_butadiene(start, end)
self.assertIsNone(path)
def _fix_butadiene_path(start, end):
"""
Searches for a 1,3-butadiene path between the start and end atom.
Adds an unpaired electron to start and end atom, and "inverts" the bonds
in between them.
"""
path = pathfinder.find_butadiene(start, end)
if path is not None:
start.radical_electrons += 1
end.radical_electrons += 1
# filter bonds from path and convert bond orders:
bonds = path[1::2] # odd elements
for bond in bonds[::2]: # even bonds
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 fix_butadiene_path(start, end):
"""
Searches for a 1,3-butadiene path between the start and end atom.
Adds an unpaired electron to start and end atom, and "inverts" the bonds
in between them.
"""
path = pathfinder.find_butadiene(start, end)
if path is not None:
start.radicalElectrons += 1
end.radicalElectrons += 1
# filter bonds from path and convert bond orders:
bonds = path[1::2]#odd elements
for bond in bonds[::2]:# even bonds
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_13cyclohexadiene(self):
adjlist = """
1 C u0 p0 c0 {2,D} {6,S} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {4,D} {9,S}
4 C u0 p0 c0 {3,D} {5,S} {10,S}
5 C u0 p0 c0 {4,S} {6,S} {11,S} {12,S}
6 C u0 p0 c0 {1,S} {5,S} {13,S} {14,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {5,S}
13 H u0 p0 c0 {6,S}
14 H u0 p0 c0 {6,S}
"""
mol = Molecule().from_adjacency_list(adjlist) # 1,3-cyclohexadiene
start, end = mol.atoms[0], mol.atoms[3]
path = find_butadiene(start, end)
self.assertIsNotNone(path)
def test_135hexatriene(self):
mol = Molecule().from_smiles("C=CC=CC=C") # 1,3,5-hexatriene
start, end = mol.atoms[0], mol.atoms[5]
path = find_butadiene(start, end)
self.assertIsNotNone(path)
def test_c4h4(self):
mol = Molecule().from_smiles("C=C=C=C") # C4H4
start, end = mol.atoms[0], mol.atoms[3]
path = find_butadiene(start, end)
self.assertIsNotNone(path)
def test_benzene(self):
mol = Molecule().from_smiles("C1=CC=CC=C1") # benzene
start, end = mol.atoms[0], mol.atoms[5]
path = find_butadiene(start, end)
self.assertIsNotNone(path)
