def test_predict_compound_pairs(self):
"""Test prediction of HEX1 reaction."""
reaction = parse_reaction(
'atp[c] + glc-D[c] => adp[c] + g6p[c] + h[c]')
formulas = {
'atp': Formula.parse('C10H12N5O13P3'),
'adp': Formula.parse('C10H12N5O10P2'),
'glc-D': Formula.parse('C6H12O6'),
'g6p': Formula.parse('C6H11O9P'),
'h': Formula.parse('H'),
}
transfer, balance = findprimarypairs.predict_compound_pairs(
reaction, formulas)
self.assertEqual(balance, {})
self.assertEqual(transfer, {
((Compound('atp', 'c'), 1), (Compound('adp', 'c'), 1)):
Formula.parse('C10H12N5O10P2'),
((Compound('glc-D', 'c'), 1), (Compound('g6p', 'c'), 1)):
Formula.parse('C6H11O6'),
((Compound('atp', 'c'), 1), (Compound('g6p', 'c'), 1)):
Formula.parse('O3P'),
((Compound('glc-D', 'c'), 1), (Compound('h', 'c'), 1)):
Formula.parse('H'),
})
def test_predict_compound_pairs_multiple(self):
"""Test prediction of reaction with multiple instances."""
reaction = parse_reaction(
'a[c] <=> (2) b[c] + c[c]')
formulas = {
'a': Formula.parse('C10H13O6'),
'b': Formula.parse('C5H6O3'),
'c': Formula.parse('H'),
}
transfer, balance = findprimarypairs.predict_compound_pairs(
reaction, formulas)
self.assertEqual(balance, {})
self.assertEqual(transfer, {
((Compound('a', 'c'), 1), (Compound('b', 'c'), 1)):
Formula.parse('C5H6O3'),
((Compound('a', 'c'), 1), (Compound('b', 'c'), 2)):
Formula.parse('C5H6O3'),
((Compound('a', 'c'), 1), (Compound('c', 'c'), 1)):
Formula.parse('H'),
})
def test_predict_compound_pairs_unbalanced(self):
"""Test prediction of (non-sense) unbalanced reaction."""
reaction = parse_reaction(
'a[c] <=> b[c] + c[c]')
formulas = {
'a': Formula.parse('C10H12'),
'b': Formula.parse('C9H11'),
'c': Formula.parse('CO2'),
}
transfer, balance = findprimarypairs.predict_compound_pairs(
reaction, formulas)
self.assertEqual(balance, {
(Compound('a', 'c'), 1): Formula.parse('H'),
(Compound('c', 'c'), 1): Formula.parse('O2'),
})
self.assertEqual(transfer, {
((Compound('a', 'c'), 1), (Compound('b', 'c'), 1)):
Formula.parse('C9H11'),
((Compound('a', 'c'), 1), (Compound('c', 'c'), 1)):
Formula.parse('C'),
})
def test_predict_compound_pairs_ambig(self):
"""Test prediction of (non-sense) ambiguous reaction."""
reaction = parse_reaction('a[c] + b[c] => c[c] + d[c]')
formulas = {
'a': Formula.parse('C10H10'),
'b': Formula.parse('C10H10'),
'c': Formula.parse('C10H10'),
'd': Formula.parse('C10H10')
}
transfer, balance, ambiguous_pairs = findprimarypairs.predict_compound_pairs(
reaction, formulas)
all_perm = set(set(permutations(list(ambiguous_pairs)[0])))
ambig = list(ambiguous_pairs)[0]
self.assertEqual(balance, {})
self.assertEqual(
transfer, {
((Compound('b', 'c'), 1), (Compound('d', 'c'), 1)):
Formula.parse('C10H10'),
((Compound('a', 'c'), 1), (Compound('c', 'c'), 1)):
Formula.parse('C10H10')
})
self.assertEqual(ambig, ambig if ambig in all_perm else set())