def test_merge(self):
model = native.NativeModel()
model.compounds.update([
entry.DictCompoundEntry({
'id': 'g6p_c',
'name': 'G6P'
}),
entry.DictCompoundEntry({
'id': 'g6p_e',
'name': 'G6P'
})
])
model.reactions.update([
entry.DictReactionEntry({
'id':
'TP_g6p',
'equation':
parse_reaction('g6p_c[c] <=> g6p_e[e]')
})
])
exchange_compound = Compound('g6p_e', 'e')
model.exchange[exchange_compound] = (exchange_compound, 'EX_g6p_e',
-10, 0)
sbml.merge_equivalent_compounds(model)
self.assertEqual({entry.id for entry in model.compounds}, {'g6p'})
self.assertEqual(model.reactions['TP_g6p'].equation,
parse_reaction('g6p[c] <=> g6p[e]'))
new_exchange_compound = Compound('g6p', 'e')
self.assertEqual(model.exchange[new_exchange_compound],
(new_exchange_compound, 'EX_g6p_e', -10, 0))
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_create_compound_dict_entry_copy(self):
props = {'id': 'test_compound', 'name': 'Test compound'}
e = entry.DictCompoundEntry(props)
e2 = entry.DictCompoundEntry(e)
self.assertIsInstance(e2, entry.CompoundEntry)
self.assertEqual(e2.id, 'test_compound')
self.assertEqual(e2.name, 'Test compound')
def test_use_compound_dict_entry_setters(self):
e = entry.DictCompoundEntry({}, id='new_id')
e.formula = 'CO2'
e.name = 'Compound 1'
e.charge = 5
self.assertEqual(e.formula, 'CO2')
self.assertEqual(e.properties['formula'], 'CO2')
self.assertEqual(e.name, 'Compound 1')
self.assertEqual(e.charge, 5)
def test_write_compounds_with_properties(self):
stream = StringIO()
compounds = [
entry.DictCompoundEntry({
'id': 'c1',
'name': 'Compound 1',
'charge': 2
}),
entry.DictCompoundEntry({
'id': 'c2',
'name': 'Compound 2',
'formula': 'H2O'
})
]
self.writer.write_compounds(stream, compounds, properties={'name'})
self.assertEqual(yaml.safe_load(stream.getvalue()),
[{
'id': 'c1',
'name': 'Compound 1'
}, {
'id': 'c2',
'name': 'Compound 2'
}])
def test_convert_compound_entry(self):
compound = entry.DictCompoundEntry({
'id': 'c1',
'name': 'Compound 1',
'charge': 2,
'formula': None,
'custom': 'ABC'
})
d = self.writer.convert_compound_entry(compound)
self.assertIsInstance(d, OrderedDict)
self.assertEqual(d['id'], 'c1')
self.assertEqual(d['name'], 'Compound 1')
self.assertEqual(d['charge'], 2)
self.assertEqual(d['custom'], 'ABC')
self.assertNotIn('formula', d)
def test_create_compound_dict_entry(self):
props = {
'id': 'test_compound',
'name': 'Test compound',
'formula': 'H2O',
'charge': 1,
'custom': 'ABC'
}
e = entry.DictCompoundEntry(props)
self.assertIsInstance(e, entry.CompoundEntry)
self.assertEqual(e.id, 'test_compound')
self.assertEqual(e.name, 'Test compound')
self.assertEqual(e.formula, 'H2O')
self.assertEqual(e.charge, 1)
self.assertEqual(e.properties.get('custom'), 'ABC')
def test_create_reaction_entry_from_compound_entry(self):
e = entry.DictCompoundEntry({'id': 'compound_1', 'name': 'Compound 1'})
with self.assertRaises(ValueError):
e2 = entry.DictReactionEntry(e)
def test_create_compound_dict_entry_with_id_override(self):
props = {'id': 'old_id', 'name': 'Compound 1', 'formula': 'CO2'}
e = entry.DictCompoundEntry(props, id='new_id')
self.assertEqual(e.id, 'new_id')
self.assertEqual(e.properties['id'], 'new_id')
def test_create_compound_dict_entry_without_id(self):
props = {'name': 'Compound 1', 'formula': 'CO2'}
with self.assertRaises(ValueError):
e = entry.DictCompoundEntry(props)