def test_room_with_reaction_filter(self):
original_objective = self.model.objective
pfba_solution = pfba(self.model)
solution = room(self.model, reference=pfba_solution,
reactions=['EX_o2_LPAREN_e_RPAREN_', 'EX_glc_LPAREN_e_RPAREN_'])
self.assertEqual(len(solution.fluxes), 2)
self.assertIs(self.model.objective, original_objective)
def test_room_with_reaction_filter(self):
original_objective = self.model.objective
pfba_solution = pfba(self.model)
solution = room(self.model, reference=pfba_solution,
reactions=['EX_o2_LPAREN_e_RPAREN_', 'EX_glc_LPAREN_e_RPAREN_'])
self.assertEqual(len(solution.fluxes), 2)
self.assertIs(self.model.objective, original_objective)
def test_room_shlomi_2005(self):
reference = {
"b1": -10,
"v1": 10,
"v2": 5,
"v3": 0,
"v4": 0,
"v5": 0,
"v6": 5,
"b2": 5,
"b3": 5
}
TOY_MODEL_PAPIN_2004.solver = self.model.solver.interface
with TimeMachine() as tm:
TOY_MODEL_PAPIN_2004.reactions.v6.knock_out(tm)
result = room(TOY_MODEL_PAPIN_2004,
reference=reference,
delta=0,
epsilon=0)
self.assertEquals(
result.fluxes, {
'b1': 10.0,
'b2': 5.0,
'b3': 5.0,
'v1': 5.0,
'v2': 5.0,
'v3': 0.0,
'v4': 5.0,
'v5': 5.0,
'v6': 0.0
})
def test_room_shlomi_2005(self, toy_model):
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
}
with TimeMachine() as tm:
toy_model.reactions.v6.knock_out(tm)
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 is original_objective
def test_room(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = room(core_model, reference=pfba_solution)
assert abs(0 - solution.objective_value) < 1e-6, \
"room objective without knockouts must be 0 (was %f)" % solution.objective_value
assert core_model.objective is original_objective
def test_room(self):
original_objective = self.model.objective
pfba_solution = pfba(self.model)
solution = room(self.model, reference=pfba_solution)
self.assertAlmostEqual(0, solution.objective_value,
delta=1e-6,
msg="room objective without knockouts must be 0 (was %f)" % solution.objective_value)
self.assertIs(self.model.objective, original_objective)
def test_room_with_reaction_filter(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = room(core_model, reference=pfba_solution,
reactions=['EX_o2_LPAREN_e_RPAREN_', 'EX_glc_LPAREN_e_RPAREN_'])
assert len(solution.fluxes) == 2
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in core_model.solver.variables)
def test_room_with_reaction_filter(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = room(core_model, reference=pfba_solution,
reactions=['EX_o2_LPAREN_e_RPAREN_', 'EX_glc_LPAREN_e_RPAREN_'])
assert len(solution.fluxes) == 2
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in core_model.solver.variables)
def test_room(self):
original_objective = self.model.objective
pfba_solution = pfba(self.model)
solution = room(self.model, reference=pfba_solution)
self.assertAlmostEqual(0, solution.objective_value,
delta=1e-6,
msg="room objective without knockouts must be 0 (was %f)" % solution.objective_value)
self.assertIs(self.model.objective, original_objective)
def test_room_with_reaction_filter(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = room(
core_model,
reference=pfba_solution,
reactions=['EX_o2_LPAREN_e_RPAREN_', 'EX_glc_LPAREN_e_RPAREN_'])
assert len(solution.fluxes) == 2
assert core_model.objective is original_objective
def test_room(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = room(core_model, reference=pfba_solution)
assert abs(0 - solution.objective_value) < 1e-6, \
"room objective without knockouts must be 0 (was %f)" % solution.objective_value
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in core_model.solver.variables)
assert not any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
def test_room(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
solution = room(core_model, reference=pfba_solution)
assert abs(0 - solution.objective_value) < 1e-6, \
"room objective without knockouts must be 0 (was %f)" % solution.objective_value
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in core_model.solver.variables)
assert not any(c.name.startswith("moma_const_") for c in core_model.solver.constraints)
def test_room_shlomi_2005(self):
reference = {"b1": -10, "v1": 10, "v2": 5, "v3": 0, "v4": 0, "v5": 0, "v6": 5, "b2": 5, "b3": 5}
TOY_MODEL_PAPIN_2004.solver = self.model.solver.interface
with TimeMachine() as tm:
TOY_MODEL_PAPIN_2004.reactions.v6.knock_out(tm)
result = room(TOY_MODEL_PAPIN_2004, reference=reference, delta=0, epsilon=0)
self.assertEquals(
result.fluxes,
{'b1': 10.0, 'b2': 5.0, 'b3': 5.0, 'v1': 5.0, 'v2': 5.0, 'v3': 0.0, 'v4': 5.0, 'v5': 5.0, 'v6': 0.0})
def test_room_shlomi_2005(self):
original_objective = self.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}
TOY_MODEL_PAPIN_2003.solver = self.model.solver.interface
with TimeMachine() as tm:
TOY_MODEL_PAPIN_2003.reactions.v6.knock_out(tm)
result = room(TOY_MODEL_PAPIN_2003, reference=reference, delta=0, epsilon=0)
for k in reference.keys():
self.assertAlmostEqual(expected[k], result.fluxes[k], delta=0.1, msg="%s: %f | %f")
self.assertIs(self.model.objective, original_objective)
def test_room_shlomi_2005(self):
original_objective = self.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}
TOY_MODEL_PAPIN_2003.solver = self.model.solver.interface
with TimeMachine() as tm:
TOY_MODEL_PAPIN_2003.reactions.v6.knock_out(tm)
result = room(TOY_MODEL_PAPIN_2003, reference=reference, delta=0, epsilon=0)
for k in reference.keys():
self.assertAlmostEqual(expected[k], result.fluxes[k], delta=0.1, msg="%s: %f | %f")
self.assertIs(self.model.objective, original_objective)
def test_room_with_cache(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
essential_reactions = find_essential_reactions(core_model)
cache = ProblemCache(core_model)
infeasible = 0
for r in core_model.reactions:
if r not in essential_reactions:
with core_model:
r.knock_out()
try:
room(core_model, reference=pfba_solution, cache=cache)
assert any(v.name.startswith("y_") for v in core_model.solver.variables)
assert any(c.name.startswith("room_const_") for c in core_model.solver.constraints)
except OptimizationError: # TODO: room shouldn't return infeasible for non-essential reactions
infeasible += 1
continue
assert infeasible < len(core_model.reactions)
cache.reset()
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in core_model.solver.variables)
assert not any(c.name.startswith("room_const_") for c in core_model.solver.constraints)
def test_room_with_cache(self, core_model):
original_objective = core_model.objective
pfba_solution = pfba(core_model)
essential_reactions = find_essential_reactions(core_model)
cache = ProblemCache(core_model)
infeasible = 0
for r in core_model.reactions:
if r not in essential_reactions:
with core_model:
r.knock_out()
try:
room(core_model, reference=pfba_solution, cache=cache)
assert any(v.name.startswith("y_") for v in core_model.solver.variables)
assert any(c.name.startswith("room_const_") for c in core_model.solver.constraints)
except OptimizationError: # TODO: room shouldn't return infeasible for non-essential reactions
infeasible += 1
continue
assert infeasible < len(core_model.reactions)
cache.reset()
assert core_model.objective.expression == original_objective.expression
assert not any(v.name.startswith("y_") for v in core_model.solver.variables)
assert not any(c.name.startswith("room_const_") for c in core_model.solver.constraints)
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_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)
