def _testformula(self, num):
smile1, sum_forms = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
for i, mol in enumerate(mols):
self.assertTrue(i < len(sum_forms))
self.assertEqual(str(mol.get_formula_dict()), sum_forms[i])
def _testformula(self, num):
def create_st_sum(st):
symbols = [a.symbol for a in (st.references[0], st.references[-1])]
symbols.sort()
return tuple(symbols + [st.value == st.SAME_SIDE and 1 or -1])
# round 1
smile1 = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts1 = [create_st_sum(st) for st in mol.stereochemistry]
# round 2
mol.stereochemistry = []
mol.detect_stereochemistry_from_coords()
sts2 = [create_st_sum(st) for st in mol.stereochemistry]
for stsum in sts2:
if not stsum in sts1:
# not necessarily an error, we must count changes
changes = 0
for (v1, v2) in zip(stsum, sts1[0]):
if v1 != v2:
changes += 1
self.assertEqual(changes % 2, 0)
else:
self.assertEqual((stsum in sts1), True)
def _testformula(self, num):
smile1, charges = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
comp_charges = [mol.charge for mol in mols]
comp_charges.sort()
charges = list(charges)
charges.sort()
self.assertEqual(comp_charges, charges)
def test2(self):
"""test reactions with some empty parts"""
c = smiles.converter()
reacts = c.read_text("C=C.[H][H]>>CC")
self.assertEqual(len(reacts), 1)
react = reacts[0]
self.assertEqual(len(react.reagents), 0)
self.assertEqual(len(react.reactants), 2)
self.assertEqual(len(react.products), 1)
def _testformula(self, num):
smile1, match_pair_num, exposed_vs_num = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
mate, nrex = mol.get_maximum_matching()
self.assertEqual(nrex, exposed_vs_num)
self.assertEqual(len([v for v, m in mate.items() if m != 0]),
2 * match_pair_num)
def _testformula(self, num):
smile1, directions = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts = [
st.value == st.SAME_SIDE and 1 or -1 for st in mol.stereochemistry
]
sts.sort()
sts = tuple(sts)
self.assertEqual(sts, directions)
def _testformula(self, num):
smile1, (explicit_hs, occupied_v, free_v) = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
ns = [v for v in mol.vertices if v.symbol == 'N']
self.assertEqual(len(ns), 1)
n = ns[0]
self.assertEqual(n.explicit_hydrogens, explicit_hs)
self.assertEqual(n.free_valency, free_v)
self.assertEqual(n.occupied_valency, occupied_v)
def test1(self):
"""tests handling of reactions by the SMILES reader on a preparation of methyl-formate"""
c = smiles.converter()
reacts = c.read_text("O=CO.CO>[H+]>O=COC.O")
self.assertEqual(reacts, c.result)
self.assertEqual(c.last_status, c.STATUS_OK)
self.assertEqual(len(reacts), 1)
react = reacts[0]
self.assertEqual(len(react.reactants), 2)
self.assertEqual(len(react.reactants[0].molecule.atoms), 3)
self.assertEqual(len(react.reactants[1].molecule.atoms), 2)
self.assertEqual(len(react.reagents[0].molecule.atoms), 1)
self.assertEqual(len(react.products[0].molecule.atoms), 4)
self.assertEqual(len(react.products[1].molecule.atoms), 1)
self.assertEqual(str(react.products[0].molecule.get_formula_dict()),
"C2H4O2")
def _testformula(self, num):
def create_st_sum(st):
symbols = [a.symbol for a in (st.references[0], st.references[-1])]
symbols.sort()
return tuple(symbols + [st.value == st.SAME_SIDE and 1 or -1])
# round 1
smile1 = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts1 = [create_st_sum(st) for st in mol.stereochemistry]
# round 2
smile2 = conv.mols_to_text([mol])
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts2 = [create_st_sum(st) for st in mol.stereochemistry]
for stsum in sts2:
self.assertEqual((stsum in sts1), True)
def test_empty_smiles(self):
conv = smiles.converter()
for text in ("", " "):
mols = conv.read_text("")
self.assertEqual(mols, [])