def test_moma_shlomi_2005(self, toy_model):
if current_solver_name(toy_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = toy_model.objective
reference = {
"b1": 10,
"v1": 10,
"v2": 5,
"v3": 0,
"v4": 0,
"v5": 0,
"v6": 5,
"b2": 5,
"b3": 5
}
expected = {
'b1': 8.8,
'b2': 4.4,
'b3': 4.4,
'v1': 8.8,
'v2': 3.1,
'v3': 1.3,
'v4': 4.4,
'v5': 3.1,
'v6': 0.0
}
with TimeMachine() as tm:
toy_model.reactions.v6.knock_out(tm)
result = moma(toy_model, reference=reference)
for k in reference.keys():
assert abs(expected[k] - result.fluxes[k]) < 0.1, "%s: %f | %f"
assert toy_model.objective is original_objective
def test_shortest_elementary_flux_modes(self, core_model):
if current_solver_name(core_model) == 'glpk':
pytest.skip('sefm not supported for glpk')
sefm = structural.ShortestElementaryFluxModes(core_model)
ems = []
for i, em in enumerate(sefm):
if i > 10:
break
ems.append(em)
assert list(map(len, ems)) == sorted(map(len, ems))
def test_shortest_elementary_flux_modes(self, core_model):
if current_solver_name(core_model) == 'glpk':
pytest.skip('sefm not supported for glpk')
sefm = structural.ShortestElementaryFluxModes(core_model)
ems = []
for i, em in enumerate(sefm):
if i > 10:
break
ems.append(em)
assert list(map(len, ems)) == sorted(map(len, ems))
def test_moma(self, core_model):
if current_solver_name(core_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = moma(core_model, reference=pfba_solution)
distance = sum((abs(solution[v] - pfba_solution[v]) for v in pfba_solution.keys()))
assert abs(0 - distance) < 1e-6, "moma distance without knockouts must be 0 (was %f)" % distance
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("moma_aux_") for v in core_model.solver.variables)
assert not any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
def test_moma(self, core_model):
if current_solver_name(core_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = moma(core_model, reference=pfba_solution)
distance = sum((abs(solution[v] - pfba_solution[v]) for v in pfba_solution.keys()))
assert abs(0 - distance) < 1e-6, "moma distance without knockouts must be 0 (was %f)" % distance
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("moma_aux_") for v in core_model.solver.variables)
assert not any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
def test_moma_shlomi_2005_change_ref_1(self, toy_model):
if current_solver_name(toy_model) == 'glpk':
pytest.skip('glpk does not support qp')
expected = {'b1': 8.8, 'b2': 4.4, 'b3': 4.4, 'v1': 8.8,
'v2': 3.1, 'v3': 1.3, 'v4': 4.4, 'v5': 3.1, 'v6': 0.0}
reference_changed = {"b1": 5, "v1": 5, "v2": 5, "v3": 0, "v4": 0, "v5": 0, "v6": 5, "b2": 5, "b3": 5}
with toy_model:
toy_model.reactions.v6.knock_out()
result_changed = moma(toy_model, reference=reference_changed)
assert np.all([expected != result_changed.fluxes])
assert not any(v.name.startswith("u_") for v in toy_model.solver.variables)
def test_moma_shlomi_2005_change_ref_1(self, toy_model):
if current_solver_name(toy_model) == 'glpk':
pytest.skip('glpk does not support qp')
expected = {'b1': 8.8, 'b2': 4.4, 'b3': 4.4, 'v1': 8.8,
'v2': 3.1, 'v3': 1.3, 'v4': 4.4, 'v5': 3.1, 'v6': 0.0}
reference_changed = {"b1": 5, "v1": 5, "v2": 5, "v3": 0, "v4": 0, "v5": 0, "v6": 5, "b2": 5, "b3": 5}
with toy_model:
toy_model.reactions.v6.knock_out()
result_changed = moma(toy_model, reference=reference_changed)
assert np.all([expected != result_changed.fluxes])
assert not any(v.name.startswith("u_") for v in toy_model.solver.variables)
def test_moma(self, core_model):
if current_solver_name(core_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = moma(core_model, reference=pfba_solution)
distance = sum((abs(solution[v] - pfba_solution[v])
for v in pfba_solution.keys()))
assert abs(
0 - distance
) < 1e-6, "moma distance without knockouts must be 0 (was %f)" % distance
assert core_model.objective is original_objective
def test_moma_shlomi_2005_change_ref(self, toy_model):
if current_solver_name(toy_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = toy_model.objective
reference = {"b1": 10, "v1": 10, "v2": 5, "v3": 0, "v4": 0, "v5": 0, "v6": 5, "b2": 5, "b3": 5}
expected = {'b1': 8.8, 'b2': 4.4, 'b3': 4.4, 'v1': 8.8,
'v2': 3.1, 'v3': 1.3, 'v4': 4.4, 'v5': 3.1, 'v6': 0.0}
with toy_model:
toy_model.reactions.v6.knock_out()
result = moma(toy_model, reference=reference)
for k in reference.keys():
assert abs(expected[k] - result.fluxes[k]) < 0.1, "%s: %f | %f"
assert toy_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("u_") for v in toy_model.solver.variables)
def test_room_shlomi_2005(self, toy_model):
if current_solver_name(toy_model) == "glpk":
pytest.xfail("this test doesn't work with glpk")
original_objective = toy_model.objective
reference = {"b1": 10, "v1": 10, "v2": 5, "v3": 0, "v4": 0, "v5": 0, "v6": 5, "b2": 5, "b3": 5}
expected = {'b1': 10.0, 'b2': 5.0, 'b3': 5.0, 'v1': 10.0,
'v2': 5.0, 'v3': 0.0, 'v4': 5.0, 'v5': 5.0, 'v6': 0.0}
assert not any(v.name.startswith("y_") for v in toy_model.solver.variables)
with toy_model:
toy_model.reactions.v6.knock_out()
result = room(toy_model, reference=reference, delta=0, epsilon=0)
for k in reference.keys():
assert abs(expected[k] - result.fluxes[k]) < 0.1, "%s: %f | %f"
assert toy_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in toy_model.variables)
def test_moma_shlomi_2005_change_ref(self, toy_model):
if current_solver_name(toy_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = toy_model.objective
reference = {"b1": 10, "v1": 10, "v2": 5, "v3": 0, "v4": 0, "v5": 0, "v6": 5, "b2": 5, "b3": 5}
expected = {'b1': 8.8, 'b2': 4.4, 'b3': 4.4, 'v1': 8.8,
'v2': 3.1, 'v3': 1.3, 'v4': 4.4, 'v5': 3.1, 'v6': 0.0}
with toy_model:
toy_model.reactions.v6.knock_out()
result = moma(toy_model, reference=reference)
for k in reference.keys():
assert abs(expected[k] - result.fluxes[k]) < 0.1, "%s: %f | %f"
assert toy_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("u_") for v in toy_model.solver.variables)
def test_room_shlomi_2005(self, toy_model):
if current_solver_name(toy_model) == "glpk":
pytest.xfail("this test doesn't work with glpk")
original_objective = toy_model.objective
reference = {"b1": 10, "v1": 10, "v2": 5, "v3": 0, "v4": 0, "v5": 0, "v6": 5, "b2": 5, "b3": 5}
expected = {'b1': 10.0, 'b2': 5.0, 'b3': 5.0, 'v1': 10.0,
'v2': 5.0, 'v3': 0.0, 'v4': 5.0, 'v5': 5.0, 'v6': 0.0}
assert not any(v.name.startswith("y_") for v in toy_model.solver.variables)
with toy_model:
toy_model.reactions.v6.knock_out()
result = room(toy_model, reference=reference, delta=0, epsilon=0)
for k in reference.keys():
assert abs(expected[k] - result.fluxes[k]) < 0.1, "%s: %f | %f"
assert toy_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in toy_model.variables)
def test_moma_with_cache(self, core_model):
if current_solver_name(core_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = core_model.objective
pfba_solution = pfba(core_model)
essential_reactions = find_essential_reactions(core_model)
cache = ProblemCache(core_model)
for r in core_model.reactions:
if r not in essential_reactions:
with core_model:
r.knock_out()
moma(core_model, reference=pfba_solution, cache=cache)
assert any(v.name.startswith("moma_aux_") for v in core_model.solver.variables)
assert any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
cache.reset()
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("moma_aux_") for v in core_model.solver.variables)
assert not any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
def test_moma_with_cache(self, core_model):
if current_solver_name(core_model) == 'glpk':
pytest.skip('glpk does not support qp')
original_objective = core_model.objective
pfba_solution = pfba(core_model)
essential_reactions = find_essential_reactions(core_model)
cache = ProblemCache(core_model)
for r in core_model.reactions:
if r not in essential_reactions:
with core_model:
r.knock_out()
moma(core_model, reference=pfba_solution, cache=cache)
assert any(v.name.startswith("moma_aux_") for v in core_model.solver.variables)
assert any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
cache.reset()
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("moma_aux_") for v in core_model.solver.variables)
assert not any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
