def test_reactions_in_group_become_blocked_if_one_is_removed(
self, core_model):
essential_reactions = core_model.essential_reactions()
coupled_reactions = structural.find_coupled_reactions_nullspace(
core_model)
for group in coupled_reactions:
representative = pick_one(group)
if representative not in essential_reactions:
with TimeMachine() as tm:
assert core_model == representative.model
tm(do=partial(core_model.remove_reactions,
[representative],
delete=False),
undo=partial(core_model.add_reactions,
[representative]))
# # FIXME: Hack because of optlang queue issues with GLPK
# core_model.solver.update()
assert representative not in core_model.reactions
assert representative.forward_variable not in core_model.solver.variables
assert representative.reverse_variable not in core_model.solver.variables
assert representative not in core_model.reactions
assert representative.model is None
blocked_reactions = find_blocked_reactions(core_model)
assert all(r in blocked_reactions for r in group
if r != representative)
assert representative in core_model.reactions
coupled_reactions = structural.find_coupled_reactions(core_model)
for group in coupled_reactions:
representative = pick_one(group)
if representative not in essential_reactions:
with TimeMachine() as tm:
fwd_var_name = representative.forward_variable.name
rev_var_name = representative.reverse_variable.name
assert core_model == representative.model
tm(do=partial(core_model.remove_reactions,
[representative],
delete=False),
undo=partial(core_model.add_reactions,
[representative]))
# # FIXME: Hack because of optlang queue issues with GLPK
# core_model.solver.update()
assert representative not in core_model.reactions
assert fwd_var_name not in core_model.solver.variables
assert rev_var_name not in core_model.solver.variables
assert representative not in core_model.reactions
assert representative.model is None
blocked_reactions = find_blocked_reactions(core_model)
assert representative not in core_model.reactions
assert all(r in blocked_reactions for r in group
if r != representative)
assert representative in core_model.reactions
def test_find_blocked_reactions(self):
self.model.reactions.PGK.knock_out(
) # there are no blocked reactions in EcoliCore
blocked_reactions = find_blocked_reactions(self.model)
self.assertEqual(
blocked_reactions,
[self.model.reactions.GAPD, self.model.reactions.PGK])
def test_reactions_in_group_become_blocked_if_one_is_removed(self, core_model):
essential_reactions = find_essential_reactions(core_model)
coupled_reactions = structural.find_coupled_reactions_nullspace(core_model)
for group in coupled_reactions:
representative = pick_one(group)
if representative not in essential_reactions:
with core_model:
assert core_model == representative.model
core_model.remove_reactions([representative])
# # FIXME: Hack because of optlang queue issues with GLPK
# core_model.solver.update()
assert representative not in core_model.reactions
assert representative.forward_variable not in core_model.solver.variables
assert representative.reverse_variable not in core_model.solver.variables
assert representative not in core_model.reactions
assert representative.model is None
blocked_reactions = find_blocked_reactions(core_model)
assert all(r in blocked_reactions for r in group if r != representative)
assert representative in core_model.reactions
coupled_reactions = structural.find_coupled_reactions(core_model)
for group in coupled_reactions:
representative = pick_one(group)
if representative not in essential_reactions:
with core_model:
fwd_var_name = representative.forward_variable.name
rev_var_name = representative.reverse_variable.name
assert core_model == representative.model
core_model.remove_reactions([representative])
# # FIXME: Hack because of optlang queue issues with GLPK
# core_model.solver.update()
assert representative not in core_model.reactions
assert fwd_var_name not in core_model.solver.variables
assert rev_var_name not in core_model.solver.variables
assert representative not in core_model.reactions
assert representative.model is None
blocked_reactions = find_blocked_reactions(core_model)
assert representative not in core_model.reactions
assert all(r in blocked_reactions for r in group if r != representative)
assert representative in core_model.reactions
def test_find_blocked_reactions(core_model):
core_model.reactions.PGK.knock_out()
blocked_reactions = find_blocked_reactions(core_model)
assert blocked_reactions == {core_model.reactions.GAPD, core_model.reactions.PGK}
def test_find_blocked_reactions(self):
self.model.reactions.PGK.knock_out() # there are no blocked reactions in EcoliCore
blocked_reactions = find_blocked_reactions(self.model)
self.assertEqual(blocked_reactions, [self.model.reactions.GAPD, self.model.reactions.PGK])
def test_find_blocked_reactions(core_model):
core_model.reactions.PGK.knock_out()
blocked_reactions = find_blocked_reactions(core_model)
assert blocked_reactions == {core_model.reactions.GAPD, core_model.reactions.PGK}