def __add_enzyme(self, reaction, cmpt_id):
'''Adds enzyme to reaction in given compartment.'''
sbo_term = sbml_utils.SBO_TERMS[sbml_utils.PROTEIN]
modifier = sbml_utils.get_species(self.__model, cmpt_id,
sbml_utils.get_unique_id(),
sbo_term)
ref = reaction.createModifier()
ref.setSpecies(modifier.getId())
ref.setSBOTerm(sbml_utils.SBO_TERMS[sbml_utils.ENZYME])
return modifier
def __get_func_def(self, formula, parameters, num_reacts, num_prods):
'''Gets existing or creates new functionDefinition from given
parameters.'''
if formula in self.__formula_to_id:
formula_id = self.__formula_to_id[formula]
function_definition = \
self.__model.getFunctionDefinition(formula_id)
else:
function_definition = self.__model.createFunctionDefinition()
function_definition.setId(sbml_utils.get_unique_id())
function_definition.setName(_get_func_name(num_reacts, num_prods))
function_definition.setMath(_get_math(formula, parameters))
self.__formula_to_id[formula] = function_definition.getId()
return function_definition