Sorting reactions in the increasing order

(per produced entity's concentration level)

rctsys.py

@@ -577,13 +577,32 @@ class ReactionSystemWithConcentrations(ReactionSystem):
 
         for p_e in producible_entities:
             reactions_by_prod[p_e] = []
+            rcts_for_p_e = reactions_by_prod[p_e]
+
             for r in self.reactions:
                 product_entities = [e for e,c in r[2]]
+ 
                 if p_e in product_entities:
                     reactants = r[0]
                     inhibitors = r[1]
                     products = [(e,c) for e,c in r[2] if e == p_e]
-                    reactions_by_prod[p_e].append((reactants, inhibitors, products))
+                    
+                    prod_conc = products[0][1]
+                    insert_place = None
+                    
+                    # we need to order the reactions w.r.t. the concentration levels produced (increasing order)
+                    for i in range(0,len(rcts_for_p_e)):
+                        
+                        checked_conc = rcts_for_p_e[i][2][0][1]
+                        if prod_conc <= checked_conc:
+                            insert_place = i
+                            break
+
+                    if insert_place == None: # empty or the is only one element which is smaller than the element being added
+                        rcts_for_p_e.append((reactants, inhibitors, products)) # we append (to the end)
+                    else:
+                        rcts_for_p_e.insert(insert_place,(reactants, inhibitors, products))
+                    
 
         # save in cache
         self.reactions_by_prod = reactions_by_prod