def find_exchange_rxns(model):
u"""
Return a list of exchange reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines exchange reactions as:
-- reactions that 'define the extracellular environment'
-- 'unbalanced, extra-organism reactions that represent the supply to or
removal of metabolites from the extra-organism "space"'
-- reactions with a formula such as: 'met_e -> ' or ' -> met_e' or
'met_e <=> '
Exchange reactions differ from demand reactions in that the metabolites
are removed from or added to the extracellular environment only. With this
the uptake or secretion of a metabolite is modeled, respectively.
References
----------
.. [1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for
generating a high-quality genome-scale metabolic reconstruction.
Nature protocols. Nature Publishing Group.
http://doi.org/10.1038/nprot.2009.203
"""
try:
extracellular = find_compartment_id_in_model(model, 'e')
except KeyError:
extracellular = None
return find_boundary_types(model, 'exchange', extracellular)
def extend_exchanges(model, cpd_ids, ex):
model_exchanges = set(find_boundary_types(model, 'exchange', external_compartment=ex))
new_ex_ids = set()
for cpd in cpd_ids:
cpd = model.metabolites.get_by_id(cpd)
if str(cpd.compartment) != ex:
continue
else:
if bool(set(cpd.reactions) & model_exchanges) == False:
try:
new_id = 'EX_' + cpd.id
model.add_boundary(cpd, type='exchange', reaction_id=new_id, lb=-1000.0, ub=1000.0)
new_ex_ids |= set([new_id])
except ValueError:
pass
return new_ex_ids
def find_demand_reactions(model):
u"""
Return a list of demand reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines demand reactions as:
-- 'unbalanced network reactions that allow the accumulation of a compound'
-- reactions that are chiefly added during the gap-filling process
-- as a means of dealing with 'compounds that are known to be produced by
the organism [..] (i) for which no information is available about their
fractional distribution to the biomass or (ii) which may only be produced
in some environmental conditions
-- reactions with a formula such as: 'met_c -> '
Demand reactions differ from exchange reactions in that the metabolites
are not removed from the extracellular environment, but from any of the
organism's compartments.
References
----------
.. [1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for
generating a high-quality genome-scale metabolic reconstruction.
Nature protocols. Nature Publishing Group.
http://doi.org/10.1038/nprot.2009.203
"""
try:
extracellular = find_compartment_id_in_model(model, 'e')
except KeyError:
extracellular = None
return find_boundary_types(model, 'demand', extracellular)
def find_sink_reactions(model):
u"""
Return a list of sink reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines sink reactions as:
-- 'similar to demand reactions' but reversible, thus able to supply the
model with metabolites
-- reactions that are chiefly added during the gap-filling process
-- as a means of dealing with 'compounds that are produced by nonmetabolic
cellular processes but that need to be metabolized'
-- reactions with a formula such as: 'met_c <-> '
Sink reactions differ from exchange reactions in that the metabolites
are not removed from the extracellular environment, but from any of the
organism's compartments.
References
----------
.. [1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for
generating a high-quality genome-scale metabolic reconstruction.
Nature protocols. Nature Publishing Group.
http://doi.org/10.1038/nprot.2009.203
"""
try:
extracellular = find_compartment_id_in_model(model, 'e')
except KeyError:
extracellular = None
return find_boundary_types(model, 'sink', extracellular)
def demands(self):
"""Demand reactions in model.
Irreversible reactions that accumulate or consume a metabolite in
the inside of the model.
"""
return find_boundary_types(self, "demand", None)
def exchanges(self):
"""Exchange reactions in model.
Reactions that exchange mass with the exterior. Uses annotations
and heuristics to exclude non-exchanges such as sink reactions.
"""
return find_boundary_types(self, "exchange", None)
def sinks(self):
"""Sink reactions in model.
Reversible reactions that accumulate or consume a metabolite in
the inside of the model.
"""
return find_boundary_types(self, "sink", None)
def test_exchange(self, model):
ex = model.exchanges
assert all(r.id.startswith("EX_") for r in ex)
ex = medium.find_boundary_types(model, "exchange", "e")
assert all(r.id.startswith("EX_") for r in ex)
def test_no_boundary_reactions(self, empty_model):
assert medium.find_boundary_types(empty_model, 'e', None) == []
def test_exchange(self, model):
ex = model.exchanges
assert all(r.id.startswith("EX_") for r in ex)
ex = medium.find_boundary_types(model, "exchange", "e")
assert all(r.id.startswith("EX_") for r in ex)
def test_no_boundary_reactions(self, empty_model):
assert medium.find_boundary_types(empty_model, 'e', None) == []
def test_no_boundary_reactions(empty_model: Model) -> None:
"""Test proper identification of no boundary reactions."""
assert find_boundary_types(empty_model, "e", None) == []
def test_find_boundary_types_exchange(model: Model) -> None:
"""Test boundary type identification for exchanges."""
ex = model.exchanges
assert all(r.id.startswith("EX_") for r in ex)
ex = find_boundary_types(model, "exchange", "e")
assert all(r.id.startswith("EX_") for r in ex)
