def setUp(self):
self.model = native.NativeModel()
self.model.reactions.update([
entry.DictReactionEntry({
'id': 'EX_g6p',
'equation': parse_reaction('g6p[e] <=>')
}),
entry.DictReactionEntry({
'id': 'EX_glc-D',
'equation': parse_reaction('glc-D[e] <=>')
}),
entry.DictReactionEntry({
'id': 'SINK_glc-D',
'equation': parse_reaction('glc-D[c] <=>')
}),
entry.DictReactionEntry({
'id':
'rxn_1',
'equation':
parse_reaction('g6p[c] <=> glc-D[c]')
}),
entry.DictReactionEntry({
'id':
'TP_glc-D',
'equation':
parse_reaction('glc-D[c] <=> glc-D[e]')
})
])
def test_write_reactions(self):
stream = StringIO()
reactions = [
entry.DictReactionEntry({
'id': 'r1',
'name': 'Reaction 1',
'equation': Reaction(Direction.Both, {})
}),
entry.DictReactionEntry({
'id':
'r2',
'name':
'Reaction 2',
'equation':
Reaction(Direction.Forward, {
Compound('c1', 'c'): -1,
Compound('c2', 'c'): 2
})
})
]
self.writer.write_reactions(stream, reactions)
# The reaction equation for r1 is invalid (no compounds) and is
# therefore skipped.
self.assertEqual(yaml.safe_load(stream.getvalue()),
[{
'id': 'r1',
'name': 'Reaction 1'
}, {
'id': 'r2',
'name': 'Reaction 2',
'equation': 'c1[c] => (2) c2[c]'
}])
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_use_reaction_dict_entry_setters(self):
e = entry.DictReactionEntry({}, id='reaction_1')
e.name = 'Reaction 1'
e.equation = 'A => B'
e.genes = 'gene_1 and gene_2'
self.assertEqual(e.name, 'Reaction 1')
self.assertEqual(e.equation, 'A => B')
self.assertEqual(e.genes, 'gene_1 and gene_2')
self.assertEqual(e.properties['genes'], 'gene_1 and gene_2')
def test_convert_reaction_entry(self):
equation = Reaction(Direction.Both, {
Compound('c1', 'c'): -1,
Compound('c2', 'c'): 1
})
reaction = entry.DictReactionEntry({
'id': 'rxn01234',
'name': 'Test reaction',
'equation': equation,
'custom_property': -34,
'another_custom_property': None
})
d = self.writer.convert_reaction_entry(reaction)
self.assertIsInstance(d, OrderedDict)
self.assertEqual(d['id'], 'rxn01234')
self.assertEqual(d['name'], 'Test reaction')
self.assertEqual(d['equation'], equation)
self.assertEqual(d['custom_property'], -34)
self.assertNotIn('another_custom_property', d)
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_reaction_entry(self):
props = {'id': 'reaction_1', 'name': 'Reaction 1'}
e = entry.DictReactionEntry(props)
self.assertIsInstance(e, entry.ReactionEntry)
self.assertEqual(e.id, 'reaction_1')
self.assertEqual(e.name, 'Reaction 1')