def parse(handle):
"""Parse a KEGG pathway map."""
for line in handle:
data, catalysts, reaction = line.split(":")
catalysts = [(catalysts, )]
reactants = {}
before, after = reaction.split("<=>")
compounds = before.split(" + ")
for compound in compounds:
compound = compound.strip()
try:
number, compound = compound.split()
number = -int(number)
except ValueError:
number = -1
reactants[compound] = number
compounds = after.split(" + ")
for compound in compounds:
compound = compound.strip()
try:
number, compound = compound.split()
number = int(number)
except ValueError:
number = +1
reactants[compound] = number
yield Reaction(reactants, catalysts, True, data)
def setUp(self):
self.r_empty = Reaction()
self.r_prod = Reaction({"a": 1})
self.r_dest = Reaction({"a": -1})
self.r_1 = Reaction({"a": -1, "b": 1})
self.r_1i = Reaction({"a": -1, "b": 1, "c": 0})
self.r_2 = Reaction({"b": -1, "c": 1})
self.r_3 = Reaction({"a": -1, "d": 2})
self.r_4 = Reaction({"c": -1, "d": -1, "a": 1, "e": 2})
def test_rev(self):
self.assertEqual(self.r_empty.reverse(), self.r_empty,
"empty reversed not empty")
self.assertEqual(self.r_prod.reverse(), self.r_dest,
"reversed reaction not equal to similar")
self.assertEqual(self.r_4.reverse(),
Reaction({
"c": 1,
"d": 1,
"a": -1,
"e": -2
}), "reversed reaction not equal to similar")
self.assertEqual(self.r_3.reverse().reverse(), self.r_3,
"double reversal not identity")
