def test_autoname_substituent(self):
h = monosaccharides.Hex
h.add_substituent("phosphate")
iupac.substituents_map_to.pop("phosphate")
t = iupac.to_iupac(h)
r = iupac.from_iupac(t)
self.assertEqual(h, r)
def test_glycan_from_iupac(self):
text = 'a-L-Fucp-(1-6)-[a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)-[a-L-Fucp-(1-3)]b-D-Glcp2NAc-(1-6)-[a-D-Neup5NGc-(2-3)-b-D-Galp-(1-4)-[a-L-Fucp-(1\
-3)]b-D-Glcp2NAc-(1-2)]a-D-Manp-(1-6)-[b-D-Glcp2NAc-(1-4)][b-D-Galp2NAc-(1-4)-b-D-Glcp2NAc-(1-4)-[a-D-Neup5NGc-(2-3)-b-D-Galp-(1-4)-[a-L-Fucp\
-(1-3)]b-D-Glcp2NAc-(1-2)]a-D-Manp-(1-3)]b-D-Manp-(1-4)-b-D-Glcp2NAc-(1-4)]?-D-Glcp2NAc'
reference = common.load("complex_glycan")
self.assertEqual(iupac.from_iupac(text), reference)
def test_monosaccharide_from_iupac(self):
text = "a-L-Fucp"
reference = monosaccharides.Fucose
result = iupac.from_iupac(text)
self.assertEqual(result, reference)
def test_ring_type(self):
for text, start, stop in [("a-D-Hexp", 1, 5), ("a-D-Hexf", 1, 4), ("a-D-Hexo", 0, 0)]:
mono = iupac.from_iupac(text)
self.assertEqual(mono.ring_start, start)
self.assertEqual(mono.ring_end, stop)
def test_special_cases(self):
for text, mass in [('?-D-Neup', 267.095), ('?-D-Neup5Ac', 309.105), ('a-D-Neup5NGc', 325.100)]:
self.assertAlmostEqual(iupac.from_iupac(
iupac.to_iupac(iupac.from_iupac(text))).mass(), mass, 2)
def test_hexa(self):
text = "a-D-HexpA"
result = iupac.from_iupac(text)
self.assertAlmostEqual(result.mass(), 194.042, 2)