code: def repair(self, rebuild_index=True, rebuild_relationships=True):
          
          if rebuild_index:  # DictList indexes
              self.reactions._generate_index()
              self.metabolites._generate_index()
              self.genes._generate_index()
              self.groups._generate_index()
          if rebuild_relationships:
              for met in self.metabolites:
                  met._reaction.clear()
              for gene in self.genes:
                  gene._reaction.clear()
              for rxn in self.reactions:
                  for met in rxn._metabolites:
                      met._reaction.add(rxn)
                  for gene in rxn._genes:
                      gene._reaction.add(rxn)
  
          # point _model to self
          for l in (self.reactions, self.genes, self.metabolites, self.groups):
              for e in l:
                  e._model = self
docs: Update all indexes and pointers in a model
  
          Parameters
          ----------
          rebuild_index : bool
              rebuild the indices kept in reactions, metabolites and genes
          rebuild_relationships : bool
               reset all associations between genes, metabolites, model and
               then re-add them.