def __init__(self,
reactions=None,
essential_reactions=None,
use_nullspace_simplification=True,
*args,
**kwargs):
super(ReactionKnockoutOptimization, self).__init__(*args, **kwargs)
if reactions is None:
self.reactions = set([r.id for r in self.model.reactions])
else:
self.reactions = reactions
logger.debug("Computing essential reactions...")
if essential_reactions is None:
self.essential_reactions = set(
r.id
for r in find_essential_reactions(self.model, processes=1))
else:
self.essential_reactions = set([
r.id for r in find_essential_reactions(self.model, processes=1)
])
self.essential_reactions.update(essential_reactions)
if use_nullspace_simplification:
ns = nullspace(create_stoichiometric_array(self.model))
dead_ends = set(find_blocked_reactions_nullspace(self.model,
ns=ns))
exchanges = set(self.model.boundary)
reactions = [
r for r in self.model.reactions
if (r not in exchanges) and (r not in dead_ends) and (
r.id not in self.essential_reactions)
]
groups = find_coupled_reactions_nullspace(self.model, ns=ns)
groups_keys = [
set(group) for group in groups
if any(r.id in reactions for r in group)
]
reduced_set = reduce_reaction_set(reactions, groups_keys)
to_keep = [r.id for r in reduced_set]
else:
groups = None
to_keep = set(r.id for r in self.model.reactions)
to_keep.difference_update(r.id for r in self.model.boundary)
to_keep.difference_update(self.essential_reactions)
to_keep = list(to_keep)
self.representation = to_keep
self._target_type = REACTION_KNOCKOUT_TYPE
self._decoder = decoders.ReactionSetDecoder(self.representation,
self.model,
groups=groups)
self._evaluator = evaluators.KnockoutEvaluator(
model=self.model,
decoder=self._decoder,
objective_function=self.objective_function,
simulation_method=self._simulation_method,
simulation_kwargs=self._simulation_kwargs)
def test_coupled_reactions(self, core_model):
# If a reaction is essential, all coupled reactions are essential
essential_reactions = find_essential_reactions(core_model)
coupled_reactions = structural.find_coupled_reactions_nullspace(core_model)
for essential_reaction in essential_reactions:
for group in coupled_reactions:
assert isinstance(group, dict)
if essential_reaction in group:
assert all(group_reaction in essential_reactions for group_reaction in group)
def test_coupled_reactions(self, core_model):
# If a reaction is essential, all coupled reactions are essential
essential_reactions = find_essential_reactions(core_model)
coupled_reactions = structural.find_coupled_reactions_nullspace(core_model)
for essential_reaction in essential_reactions:
for group in coupled_reactions:
assert isinstance(group, dict)
if essential_reaction in group:
assert all(group_reaction in essential_reactions for group_reaction in group)
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 __init__(self, reactions=None, essential_reactions=None, use_nullspace_simplification=True, *args, **kwargs):
super(ReactionKnockoutOptimization, self).__init__(*args, **kwargs)
if reactions is None:
self.reactions = set([r.id for r in self.model.reactions])
else:
self.reactions = reactions
logger.debug("Computing essential reactions...")
if essential_reactions is None:
self.essential_reactions = set(r.id for r in find_essential_reactions(self.model, processes=1))
else:
self.essential_reactions = set([r.id for r in find_essential_reactions(self.model, processes=1)])
self.essential_reactions.update(essential_reactions)
if use_nullspace_simplification:
ns = nullspace(create_stoichiometric_array(self.model))
dead_ends = set(find_blocked_reactions_nullspace(self.model, ns=ns))
exchanges = set(self.model.boundary)
reactions = [
r for r in self.model.reactions
if (r not in exchanges) and (
r not in dead_ends) and (
r.id not in self.essential_reactions)
]
groups = find_coupled_reactions_nullspace(self.model, ns=ns)
groups_keys = [set(group) for group in groups if any(r.id in reactions for r in group)]
reduced_set = reduce_reaction_set(reactions, groups_keys)
to_keep = [r.id for r in reduced_set]
else:
groups = None
to_keep = set(r.id for r in self.model.reactions)
to_keep.difference_update(r.id for r in self.model.boundary)
to_keep.difference_update(self.essential_reactions)
to_keep = list(to_keep)
self.representation = to_keep
self._target_type = REACTION_KNOCKOUT_TYPE
self._decoder = decoders.ReactionSetDecoder(self.representation, self.model, groups=groups)
self._evaluator = evaluators.KnockoutEvaluator(model=self.model,
decoder=self._decoder,
objective_function=self.objective_function,
simulation_method=self._simulation_method,
simulation_kwargs=self._simulation_kwargs)
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 _reduce_to_nullspace(self, reactions):
self.reaction_groups = find_coupled_reactions_nullspace(self._model)
reaction_groups_keys = [set(group) for group in self.reaction_groups]
reduced_reactions = reduce_reaction_set(reactions,
reaction_groups_keys)
return reduced_reactions
def _reduce_to_nullspace(self, reactions):
reaction_groups = find_coupled_reactions_nullspace(self._model)
reduced_reactions = reduce_reaction_set(reactions, reaction_groups)
return reduced_reactions
