def _load_reactions(sbml_model, model):
new_reactions_ids = []
new_reactions = []
for reaction in sbml_model.getListOfReactions():
if reaction.getId() not in model.reactions:
new_reactions.append(_load_reaction(reaction))
new_reactions_ids.append(reaction.getId())
return (new_reactions_ids, new_reactions)
def _load_cb_parameters(sbml_model, model):
cb_parameters = []
for reaction in sbml_model.getListOfReactions():
if reaction.getId() not in model.reactions:
cb_parameters.append((reaction.getId(),
_get_cb_parameter(reaction, LB_TAG),
_get_cb_parameter(reaction, UB_TAG),
_get_cb_parameter(reaction, OBJ_TAG, default_value=0)))
bounds = map(lambda (r_id, lb, ub, coeff): (r_id, lb, ub), cb_parameters)
coefficients = map(lambda (r_id, lb, ub, coeff): (r_id, coeff), cb_parameters)
return bounds, coefficients
def _load_stoichiometry(sbml_model, model):
inputs = []
for reaction in sbml_model.getListOfReactions():
if reaction.getId() not in model.reactions:
for reactant in reaction.getListOfReactants():
inputs.append((reactant.getSpecies(), reaction.getId(), -reactant.getStoichiometry()))
outputs = []
for reaction in sbml_model.getListOfReactions():
if reaction.getId() not in model.reactions:
for product in reaction.getListOfProducts():
outputs.append((product.getSpecies(), reaction.getId(), product.getStoichiometry()))
return inputs + outputs
def _load_reaction(reaction):
return Reaction(reaction.getId(), reaction.getName(), reaction.getReversible())
