def test_reaction_mass_balance(read_only_model):
"""
Expect all reactions to be mass balanced.
This will exclude biomass, exchange and demand reactions as they are
unbalanced by definition. It will also fail all reactions where at
least one metabolite does not have a formula defined.
In steady state, for each metabolite the sum of influx equals the sum
of outflux. Hence the net masses of both sides of any model reaction have
to be equal. Reactions where at least one metabolite does not have a
charge are not considered to be balanced, even though the remaining
metabolites participating in the reaction might be.
"""
ann = test_reaction_mass_balance.annotation
internal_rxns = con_helpers.get_internals(read_only_model)
ann["data"] = get_ids(
consistency.find_mass_unbalanced_reactions(internal_rxns)
)
ann["metric"] = len(ann["data"]) / len(internal_rxns)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) reactions are mass unbalanced with at least
one of the metabolites not having a formula or the overall mass not
equal to 0: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_reaction_mass_balance(model):
"""
Expect all reactions to be mass balanced.
This will exclude biomass, exchange and demand reactions as they are
unbalanced by definition. It will also fail all reactions where at
least one metabolite does not have a formula defined.
In steady state, for each metabolite the sum of influx equals the sum
of efflux. Hence the net masses of both sides of any model reaction have
to be equal. Reactions where at least one metabolite does not have a
formula are not considered to be balanced, even though the remaining
metabolites participating in the reaction might be.
Implementation:
For each reaction that isn't a boundary or biomass reaction check if each
metabolite has a non-zero elements attribute and if so calculate if the
overall element balance of reactants and products is equal to zero.
"""
ann = test_reaction_mass_balance.annotation
internal_rxns = con_helpers.get_internals(model)
ann["data"] = get_ids(
consistency.find_mass_unbalanced_reactions(internal_rxns))
ann["metric"] = len(ann["data"]) / len(internal_rxns)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) reactions are mass unbalanced with at least
one of the metabolites not having a formula or the overall mass not
equal to 0: {}""".format(len(ann["data"]), ann["metric"],
truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_reaction_mass_balance(model):
"""
Expect all reactions to be mass balanced.
This will exclude biomass, exchange and demand reactions as they are
unbalanced by definition. It will also fail all reactions where at
least one metabolite does not have a formula defined.
In steady state, for each metabolite the sum of influx equals the sum
of efflux. Hence the net masses of both sides of any model reaction have
to be equal. Reactions where at least one metabolite does not have a
formula are not considered to be balanced, even though the remaining
metabolites participating in the reaction might be.
Implementation:
For each reaction that isn't a boundary or biomass reaction check if each
metabolite has a non-zero elements attribute and if so calculate if the
overall element balance of reactants and products is equal to zero.
"""
ann = test_reaction_mass_balance.annotation
internal_rxns = con_helpers.get_internals(model)
ann["data"] = get_ids(
consistency.find_mass_unbalanced_reactions(internal_rxns)
)
ann["metric"] = len(ann["data"]) / len(internal_rxns)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) reactions are mass unbalanced with at least
one of the metabolites not having a formula or the overall mass not
equal to 0: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_find_mass_unbalanced_reactions(model, num):
"""Expect all reactions to be mass balanced."""
internal_rxns = con_helpers.get_internals(model)
reactions = consistency.find_mass_unbalanced_reactions(internal_rxns)
assert len(reactions) == num
def test_find_mass_unbalanced_reactions(model, num):
"""Expect all reactions to be mass balanced."""
internal_rxns = con_helpers.get_internals(model)
reactions = consistency.find_mass_unbalanced_reactions(internal_rxns)
assert len(reactions) == num