def setUp(self):
self._model = NativeModel({
'name':
'Test model',
'biomass':
'rxn_1',
'reactions': [{
'id': 'rxn_1',
'name': 'Reaction 1',
'equation': '|A_\u2206[e]| => |B[c]|',
'genes': ['gene_1', 'gene_2']
}, {
'id': 'rxn_2_\u03c0',
'name': 'Reaction 2',
'equation': '|B[c]| <=> |C[e]|',
'genes': 'gene_3 or (gene_4 and gene_5)'
}, {
'id': 'rxn_3',
'equation': 'D[c] => E[c]'
}],
'compounds': [{
'id': 'A_\u2206',
'name': 'Compound A',
'charge': 0
}, {
'id': 'B',
'name': 'Compound B',
'formula': 'H2O',
'charge': -1
}, {
'id': 'C',
'charge': -1,
'formula': 'O2'
}],
'media': [{
'compartment': 'e',
'compounds': [{
'id': 'A_\u2206'
}, {
'id': 'C'
}]
}],
'limits': [{
'reaction': 'rxn_2_\u03c0',
'upper': 100
}]
})
self._infeasible_model = NativeModel({
'biomass':
'rxn_1',
'reactions': [{
'id': 'rxn_1',
'equation': 'A[c] => B[c]'
}],
'limits': [{
'reaction': 'rxn_1',
'fixed': 10
}]
})
def setUp(self):
self._model_dir = tempfile.mkdtemp()
path = os.path.join(self._model_dir, 'model.yaml')
with codecs.open(path, 'w', 'utf-8') as f:
f.write('''---
name: Test model
biomass: rxn_1
reactions:
- id: rxn_1
equation: '|A_\u2206[e]| => |B[c]|'
genes:
- gene_1
- gene_2
- id: rxn_2_\u03c0
equation: '|B[c]| => |C[e]|'
genes: 'gene_3 or (gene_4 and gene_5)'
compounds:
- id: A_\u2206
- id: B
- id: C
media:
- compartment: e
compounds:
- id: A_\u2206
- id: C
limits:
- reaction: rxn_2_\u03c0
upper: 100
''')
self._model = NativeModel(self._model_dir)
def setUp(self):
self._model_dir = tempfile.mkdtemp()
with open(os.path.join(self._model_dir, 'model.yaml'), 'w') as f:
f.write('\n'.join([
'---',
'reactions:',
' - id: rxn_1',
' equation: A[e] <=> B[c]',
' genes: gene_1 and gene_2',
' - id: rxn_2',
' equation: A[e] => C[c]',
' genes: gene_3',
' - id: rxn_3',
' equation: A[e] => D[e]',
' - id: rxn_4',
' equation: C[c] => D[e]',
' genes: [gene_4, gene_5, gene_6]',
'compounds:',
' - id: A',
' - id: B',
' - id: C',
' - id: D',
'media:',
' - compartment: e',
' compounds:',
' - id: A',
' reaction: rxn_5',
' - id: D',
' reaction: rxn_6',
'model:',
' - reactions:',
' - rxn_3',
' - rxn_4',
]))
self._model = NativeModel(self._model_dir)
def setUp(self):
self._model_dir = tempfile.mkdtemp()
with open(os.path.join(self._model_dir, 'model.yaml'), 'w') as f:
f.write('\n'.join([
'---',
'reactions:',
' - id: rxn_1',
' equation: A[e] => B[c]',
' - id: rxn_2',
' equation: B[c] => C[e]',
' - id: rxn_3',
' equation: A[e] + (6) B[c] <=> (6) C[e] + (6) D[c]',
'compounds:',
' - id: A',
' formula: C6H12O6',
' charge: 1',
' - id: B',
' formula: O2',
' charge: 1',
' - id: C',
' formula: CO2',
' charge: -1',
' - id: D',
' formula: H2O',
]))
self._model = NativeModel.load_model_from_path(self._model_dir)
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)