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_reaction_formula_none_return(self):
reaction = parse_reaction('A[e] + (6) B[c] <=> (6) C[e] + (6) D[c]')
compound_formula = {
'A': Formula.parse('C6H12O6'),
'B': Formula.parse('O2'),
'C': Formula.parse('CO2'),
}
result = balancecheck.reaction_formula(reaction, compound_formula)
self.assertIsNone(result)
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_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_write_compounds(self):
stream = StringIO()
compounds = [
entry.DictCompoundEntry({
'id': 'c1',
'name': 'Compound 1',
'charge': 2,
'custom': 34.5
}),
entry.DictCompoundEntry({
'id': 'c2',
'name': 'Compound 2',
'formula': Formula.parse('H2O')
})
]
self.writer.write_compounds(stream, compounds)
self.assertEqual(yaml.safe_load(stream.getvalue()), [
{
'id': 'c1',
'name': 'Compound 1',
'charge': 2,
'custom': 34.5
},
{
'id': 'c2',
'name': 'Compound 2',
'formula': 'H2O'
}
])
def test_formula_substitute_non_positive(self):
f = Formula.parse('CH3(CH2)nCOOH')
with self.assertRaises(ValueError):
f.substitute(lambda v: {'n': -5}.get(v.symbol, v))
with self.assertRaises(ValueError):
f.substitute(lambda v: {'n': 0}.get(v.symbol, v))
def test_weighted_formula(self):
weighted = mapmaker._weighted_formula(
Formula.parse('C1H2N3S4R'), mapmaker.default_weight)
self.assertEqual(set(weighted), {
(Atom.C, 1, 1),
# H is discarded
(Atom.N, 3, 0.4),
(Atom.S, 4, 1),
(Radical('R'), 1, 40.0)
})
def test_formula_balance(self):
d = {reaction.id: value for reaction, value in
balancecheck.formula_balance(self._model)}
self.assertEqual(d['rxn_1'][0], Formula.parse('C6H12O6'))
self.assertEqual(d['rxn_1'][1], Formula.parse('O2'))
self.assertEqual(d['rxn_2'][0], Formula.parse('O2'))
self.assertEqual(d['rxn_2'][1], Formula.parse('CO2'))
self.assertEqual(d['rxn_3'][0], Formula.parse('C6H12O18'))
self.assertEqual(d['rxn_3'][1], Formula.parse('C6H12O18'))
def setUp(self):
self.dest = tempfile.mkdtemp()
self.model = NativeModel({
'id': 'test_mode',
'name': 'Test model',
})
# Compounds
self.model.compounds.add_entry(CompoundEntry({
'id': 'cpd_1',
'formula': Formula.parse('CO2')
}))
self.model.compounds.add_entry(CompoundEntry({
'id': 'cpd_2',
}))
self.model.compounds.add_entry(CompoundEntry({
'id': 'cpd_3',
}))
# Compartments
self.model.compartments.add_entry(CompartmentEntry({
'id': 'c'
}))
self.model.compartments.add_entry(CompartmentEntry({
'id': 'e'
}))
# Reactions
self.model.reactions.add_entry(ReactionEntry({
'id': 'rxn_1',
'equation': parse_reaction('(2) cpd_1[c] <=> cpd_2[e] + cpd_3[c]'),
'genes': boolean.Expression('g_1 and (g_2 or g_3)'),
'subsystem': 'Some subsystem'
}))
self.model.reactions.add_entry(ReactionEntry({
'id': 'rxn_2',
'equation': parse_reaction(
'(0.234) cpd_1[c] + (1.34) cpd_2[c] => cpd_3[c]'),
'subsystem': 'Biomass'
}))
self.model.biomass_reaction = 'rxn_2'
self.model.limits['rxn_1'] = 'rxn_1', Decimal(-42), Decimal(1000)
self.model.exchange[Compound('cpd_2', 'e')] = (
Compound('cpd_2', 'e'), 'EX_cpd_2', -10, 0)
def test_reaction_formula_normal_return(self):
reaction = parse_reaction('A[e] + (6) B[c] <=> (6) C[e] + (6) D[c]')
compound_formula = {
'A': Formula.parse('C6H12O6'),
'B': Formula.parse('O2'),
'C': Formula.parse('CO2'),
'D': Formula.parse('H2O')
}
left_form, right_form = balancecheck.reaction_formula(
reaction, compound_formula)
self.assertEqual(left_form, Formula.parse('C6H12O18'))
self.assertEqual(right_form, Formula.parse('C6H12O18'))
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'),
}
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_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_formula_parse_with_wide_count(self):
f = Formula.parse('C6H10O2')
self.assertEqual(f, Formula({Atom.C: 6, Atom.H: 10, Atom.O: 2}))
def test_formula_parse_with_numbered_radical(self):
f = Formula.parse('C2H4NO2(R1)')
self.assertEqual(f, Formula({Atom('C'): 2, Atom('H'): 4, Atom('N'): 1,
Atom('O'): 2, Radical('R1'): 1}))
def test_formula_parse_with_wide_counted_subgroup(self):
f = Formula.parse('C2(CH)10NO2')
self.assertEqual(f, Formula({Atom('C'): 2, Atom('N'): 1, Atom('O'): 2,
Formula({Atom('C'): 1, Atom('H'): 1}): 10}))
def test_formula_is_not_variable(self):
f = Formula.parse('C6H12O6')
self.assertFalse(f.is_variable())
def test_formula_balance_missing_on_both_sides(self):
f1, f2 = Formula.balance(Formula.parse('C3H6OH'),
Formula.parse('CH6O2'))
self.assertEqual(f1, Formula({Atom.O: 1}))
self.assertEqual(f2, Formula({Atom.C: 2, Atom.H: 1}))
def test_formula_parse_with_wide_element(self):
f = Formula.parse('ZnO')
self.assertEqual(f, Formula({Atom.Zn: 1, Atom.O: 1}))
def test_formula_parse_with_two_identical_counted_subgroups(self):
f = Formula.parse('C2H6O2(CH)2(CH)2')
self.assertEqual(f, Formula({
Atom.C: 2, Atom.H: 6, Atom.O: 2,
Formula({Atom.C: 1, Atom.H: 1}): 4}))
def test_formula_parse_with_wide_counted_subgroup(self):
f = Formula.parse('C2(CH)10NO2')
self.assertEqual(f, Formula({
Atom.C: 2, Atom.N: 1, Atom.O: 2,
Formula({Atom.C: 1, Atom.H: 1}): 10}))
def test_formula_balance_subgroups_cancel_out(self):
f1, f2 = Formula.balance(Formula.parse('H2(CH2)n'), Formula.parse('CH3O(CH2)n'))
self.assertEqual(f1, Formula({Atom('C'): 1, Atom('H'): 1, Atom('O'): 1}))
self.assertEqual(f2, Formula())
def test_formula_balance_missing_on_both_sides(self):
f1, f2 = Formula.balance(Formula.parse('C3H6OH'), Formula.parse('CH6O2'))
self.assertEqual(f1, Formula({Atom('O'): 1}))
self.assertEqual(f2, Formula({Atom('C'): 2, Atom('H'): 1}))
def test_formula_balance_missing_on_one_side(self):
f1, f2 = Formula.balance(Formula.parse('H2O'), Formula.parse('OH'))
self.assertEqual(f1, Formula())
self.assertEqual(f2, Formula({Atom('H'): 1}))
def test_formula_is_variable(self):
f = Formula.parse('C2H4NO2R(C2H2NOR)n')
self.assertTrue(f.is_variable())
def test_formula_is_variable(self):
f = Formula.parse('C2H4NO2R(C2H2NOR)n')
self.assertTrue(f.is_variable())
def test_formula_parse_with_final_digit(self):
f = Formula.parse('H2O2')
self.assertEqual(f, Formula({Atom('H'): 2, Atom('O'): 2}))
def test_formula_parse_with_implicit_final_digit(self):
f = Formula.parse('H2O')
self.assertEqual(f, Formula({Atom.H: 2, Atom.O: 1}))
def test_formula_parse_with_implicitly_counted_subgroup(self):
f = Formula.parse('C2H6O2(CH)')
self.assertEqual(f, Formula({Atom('C'): 2, Atom('H'): 6, Atom('O'): 2,
Formula({Atom('C'): 1, Atom('H'): 1}): 1}))
def test_formula_balance_subgroups_cancel_out(self):
f1, f2 = Formula.balance(Formula.parse('H2(CH2)n'),
Formula.parse('CH3O(CH2)n'))
self.assertEqual(f1, Formula({Atom.C: 1, Atom.H: 1, Atom.O: 1}))
self.assertEqual(f2, Formula())
def test_formula_parse_with_two_distinct_counted_subgroups(self):
f = Formula.parse('C2H6O2(CH)2(CH2)2')
self.assertEqual(f, Formula({Atom('C'): 2, Atom('H'): 6, Atom('O'): 2,
Formula({Atom('C'): 1, Atom('H'): 1}): 2,
Formula({Atom('C'): 1, Atom('H'): 2}): 2}))
def test_formula_parse_with_implicit_final_digit(self):
f = Formula.parse('H2O')
self.assertEqual(f, Formula({Atom('H'): 2, Atom('O'): 1}))
def test_formula_parse_with_radical(self):
f = Formula.parse('C2H4NO2R')
self.assertEqual(f, Formula({
Atom.C: 2, Atom.H: 4, Atom.N: 1, Atom.O: 2, Radical('R'): 1}))
def test_formula_parse_with_implicit_digit(self):
f = Formula.parse('C2H5NO2')
self.assertEqual(f, Formula({Atom('C'): 2, Atom('H'): 5, Atom('N'): 1, Atom('O'): 2}))
def test_formula_parse_with_wide_element(self):
f = Formula.parse('ZnO')
self.assertEqual(f, Formula({Atom('Zn'): 1, Atom('O'): 1}))
def test_formula_is_not_variable(self):
f = Formula.parse('C6H12O6')
self.assertFalse(f.is_variable())
def test_formula_parse_with_wide_count(self):
f = Formula.parse('C6H10O2')
self.assertEqual(f, Formula({Atom('C'): 6, Atom('H'): 10, Atom('O'): 2}))
def test_formula_balance_missing_on_one_side(self):
f1, f2 = Formula.balance(Formula.parse('H2O'), Formula.parse('OH'))
self.assertEqual(f1, Formula())
self.assertEqual(f2, Formula({Atom.H: 1}))
def test_formula_parse_error(self):
with self.assertRaises(ParseError):
Formula.parse('H2O. ABC')
