def write_fluxes_to_objectives(
fluxes: np_series,
objective_value: float,
rpsbml: rpSBML,
objective_id: str,
logger: Logger = getLogger(__name__)) -> None:
"""
Write Cobra results to the reactions of pathway with id pathway_id in rpsbml object.
Parameters
----------
fluxes: np_series
Fluxes.
objective_value: float
Value of the objective.
rpsbml: rpSBML
rpSBML object of which reactions will be updated with results
objective_id: str
The id of the objective to optimise
"""
rpsbml.logger.debug(
'Set the objective ' + str(objective_id) \
+ ' a flux_value of ' + str(objective_value)
)
# get the objective
obj = rpsbml.getObjective(objective_id, objective_value)
rpsbml.updateBRSynth(obj, 'flux_value', str(objective_value))
Bigg_Reaction_Prefix = 'R_'
for flux_obj in obj.getListOfFluxObjectives():
rxn_id = flux_obj.getReaction()
if rxn_id.startswith(Bigg_Reaction_Prefix):
rxn_id = rxn_id[2:]
flux = fluxes.get(rxn_id)
# sometimes flux cannot be returned
if flux is None:
rpsbml.logger.warning(
f'Cannot retrieve reaction ID {str(rxn_id)} flux from cobrapy... setting to 0.0'
)
flux = 0.0
rpsbml.logger.debug(
'Set the reaction ' + str(rxn_id) \
+ ' a flux_value of ' + str(flux)
)
rpsbml.updateBRSynth(flux_obj, 'flux_value', str(flux))
def write_fluxes_to_reactions(
fluxes: np_series,
rpsbml: rpSBML,
pathway_id: str,
sim_type: str,
logger: Logger = getLogger(__name__)) -> None:
"""
Write Cobra results to the reactions of pathway with id pathway_id in rpsbml object.
Parameters
----------
fluxes: np_series
Fluxes.
rpsbml: rpSBML
rpSBML object of which reactions will be updated with results
pathway_id: str
The id of the pathway within reactions will be updated
objective_id: str
The id of the objective to optimise
"""
rp_pathway = rpsbml.getGroup(pathway_id)
for member in rp_pathway.getListOfMembers():
rxn = rpsbml.getModel().getReaction(member.getIdRef())
if rxn is None:
logger.error(
'Cannot retreive the following reaction: ' \
+ str(member.getIdRef())
)
#return False
continue
flux = fluxes.get(rxn.getId())
logger.debug(
'Set the reaction ' + str(member.getIdRef()) \
+ ' a ' + str('fba_' + str(sim_type)) \
+ ' of ' + str(flux))
rpsbml.updateBRSynth(rxn, 'fba_' + str(sim_type), str(flux))
