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