def test_predict_with_multiple_solutions(self):
"""Test prediction where multiple solutions exist (TALA)."""
reaction = parse_reaction(
'r5p[c] + xu5p-D[c] <=> g3p[c] + s7p[c]')
formulas = {
'r5p': Formula.parse('C5H9O8P'),
'xu5p-D': Formula.parse('C5H9O8P'),
'g3p': Formula.parse('C3H5O6P'),
's7p': Formula.parse('C7H13O10P'),
}
solutions = list(
mapmaker.predict_compound_pairs(reaction, formulas, self.solver))
self.assertEqual(len(solutions), 2)
# Solution A
self.assertIn({
(Compound('r5p', 'c'), Compound('s7p', 'c')):
Formula.parse('C5O8P'),
(Compound('xu5p-D', 'c'), Compound('g3p', 'c')):
Formula.parse('C3O6P'),
(Compound('xu5p-D', 'c'), Compound('s7p', 'c')):
Formula.parse('C2O2'),
}, solutions)
# Solution B
self.assertIn({
(Compound('xu5p-D', 'c'), Compound('s7p', 'c')):
Formula.parse('C5O8P'),
(Compound('r5p', 'c'), Compound('g3p', 'c')):
Formula.parse('C3O6P'),
(Compound('r5p', 'c'), Compound('s7p', 'c')):
Formula.parse('C2O2'),
}, solutions)
def test_predict_with_multiple_solutions(self):
"""Test prediction where multiple solutions exist (TALA)."""
reaction = parse_reaction(
'r5p[c] + xu5p-D[c] <=> g3p[c] + s7p[c]')
formulas = {
'r5p': Formula.parse('C5H9O8P'),
'xu5p-D': Formula.parse('C5H9O8P'),
'g3p': Formula.parse('C3H5O6P'),
's7p': Formula.parse('C7H13O10P'),
}
solutions = list(
mapmaker.predict_compound_pairs(reaction, formulas, self.solver))
self.assertEqual(len(solutions), 2)
# Solution A
self.assertIn({
(Compound('r5p', 'c'), Compound('s7p', 'c')):
Formula.parse('C5O8P'),
(Compound('xu5p-D', 'c'), Compound('g3p', 'c')):
Formula.parse('C3O6P'),
(Compound('xu5p-D', 'c'), Compound('s7p', 'c')):
Formula.parse('C2O2'),
}, solutions)
# Solution B
self.assertIn({
(Compound('xu5p-D', 'c'), Compound('s7p', 'c')):
Formula.parse('C5O8P'),
(Compound('r5p', 'c'), Compound('g3p', 'c')):
Formula.parse('C3O6P'),
(Compound('r5p', 'c'), Compound('s7p', 'c')):
Formula.parse('C2O2'),
}, solutions)
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')
}
solutions = list(
mapmaker.predict_compound_pairs(reaction, formulas, self.solver))
self.assertEqual(len(solutions), 1)
self.assertEqual(
solutions[0], {
(Compound('atp', 'c'), Compound('adp', 'c')):
Formula.parse('C10N5O10P2'),
(Compound('glc-D', 'c'), Compound('g6p', 'c')):
Formula.parse('C6O6'),
(Compound('atp', 'c'), Compound('g6p', 'c')):
Formula.parse('O3P'),
})
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'),
}
with self.assertRaises(mapmaker.UnbalancedReactionError):
list(mapmaker.predict_compound_pairs(
reaction, formulas, self.solver))
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'),
}
with self.assertRaises(mapmaker.UnbalancedReactionError):
list(mapmaker.predict_compound_pairs(
reaction, formulas, self.solver))
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'),
}
solutions = list(
mapmaker.predict_compound_pairs(reaction, formulas, self.solver))
self.assertEqual(len(solutions), 1)
self.assertEqual(solutions[0], {
(Compound('a', 'c'), Compound('b', 'c')): Formula.parse('C10O6'),
})
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'),
}
solutions = list(
mapmaker.predict_compound_pairs(reaction, formulas, self.solver))
self.assertEqual(len(solutions), 1)
self.assertEqual(solutions[0], {
(Compound('a', 'c'), Compound('b', 'c')): Formula.parse('C10O6'),
})
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')
}
solutions = list(
mapmaker.predict_compound_pairs(reaction, formulas, self.solver))
self.assertEqual(len(solutions), 1)
self.assertEqual(solutions[0], {
(Compound('atp', 'c'), Compound('adp', 'c')):
Formula.parse('C10N5O10P2'),
(Compound('glc-D', 'c'), Compound('g6p', 'c')):
Formula.parse('C6O6'),
(Compound('atp', 'c'), Compound('g6p', 'c')):
Formula.parse('O3P'),
})