Reflow list_hybrid_ode

hybrid.pl

@@ -357,23 +357,21 @@ write_hybrid_ode(Stream, Hybrid_original_list) :-
 %
 %
 
-list_hybrid_ode(Stream,Hybrid_original_list) :- % Only MA are converted, need to do others
-  all_items([kind: reaction], Reactions),
+list_hybrid_ode(Stream, Hybrid_original_list) :- % Only MA are converted, need to do others
+  all_items([kind: reaction], List_Reactions),
   forall(
-        member(Reaction,Reactions),
+        member(Reaction, List_Reactions),
         (
-           Reaction =.. [Op,_,_],            
-           Op = (=>)
-         ->
-           convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics),
-           NewReaction =.. [for,NewKinetics,Reaction],
-           write(Stream,NewReaction),write(Stream,'.'),nl(Stream)
-         ;
-           Reaction =.. [Op,_,_], % Otherwise says Singleton variable in branch: Op
-           Reaction =.. [Op,_,SecondPart],
-           convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics),
-           NewReaction =.. [for,NewKinetics,SecondPart],
-           write(Stream,NewReaction),write(Stream,'.'),nl(Stream)
+          Reaction =.. [Op,_,SecondPart],
+          convert_MA(Reaction, List_Reactions, Hybrid_original_list, NewKinetics),
+          (
+            Op = (=>)
+          ->
+            NewReaction =.. [for, NewKinetics, Reaction]
+          ;
+            NewReaction =.. [for, NewKinetics, SecondPart]
+          ),
+          format(Stream, "~w.~n", NewReaction)
         )
   ).
 
@@ -385,7 +383,7 @@ list_hybrid_ode(Stream,Hybrid_original_list) :- % Only MA are converted, need to
 %
 %
 
-convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics) :- 
+convert_MA(Reaction, List_Reactions, Hybrid_original_list, NewKinetics) :- 
   reaction(Reaction, [kinetics: Kinetics,reactants: Reactants,inhibitors: _,  products: _]),
   Kinetics =.. ['MA',K],
   kinetics:eval_kinetics(Reactants, _, product(in('S'*'M', [reactants]), 'M'^'S'), Value),
@@ -393,7 +391,7 @@ convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics) :-
   (
    nb_current(dynamic_parameters,_)
   ->
-   nth1(ReactionNumber,Reactions,Reaction),
+   nth1(ReactionNumber,List_Reactions,Reaction),
    atom_concat('k',ReactionNumber,Kdiff1),
    atom_concat(Kdiff1,'_diff',Kdiff),
    NewPartialKinetics = K * NewValue,
@@ -403,6 +401,21 @@ convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics) :-
    NewKinetics = K * NewValue
   ).
 
+convert_MA2(Reaction, ODESpecies, NewKinetics, Reactants, Products) :-
+  reaction(Reaction, [kinetics: Kinetics,reactants: Reactants,inhibitors: _,  products: Products]),
+  Kinetics =.. ['MA',K],
+  kinetics:eval_kinetics(Reactants, _, product('S'*'M' in [reactants], 'M'^'S'), Value),
+  convert_into_hybrid(Value, ODESpecies, stoch, NewValue),!,
+  NewKinetics = K * NewValue,
+  (
+   nb_current(dynamic_parameters,_)
+  ->
+   true
+  ;
+   assertz(reaction_kinetics(Reaction,NewKinetics))
+  ).
+
+
 
 %! convert_into_hybrid(+Rate, +List_species, +Mode, -NewRate)
 %
@@ -446,6 +459,10 @@ convert_into_hybrid(Molecule, _List_species, _Mode, HybridMolecule) :-
   !.
 
 
+%! prepare_change_list
+%
+%
+
 prepare_change_list(Reactions2,ODESpecies,List) :- % Only MA are converted, need to do others
   findall([Reactants,Products,Kinetics],
          (
@@ -455,20 +472,6 @@ prepare_change_list(Reactions2,ODESpecies,List) :- % Only MA are converted, need
          List
   ).
 
-convert_MA2(Reaction,ODESpecies,NewKinetics,Reactants,Products) :-
-  reaction(Reaction, [kinetics: Kinetics,reactants: Reactants,inhibitors: _,  products: Products]),
-  Kinetics =.. ['MA',K],
-  kinetics:eval_kinetics(Reactants, _, product('S'*'M' in [reactants], 'M'^'S'), Value),
-  convert_into_hybrid(Value, ODESpecies, stoch, NewValue),!,
-  NewKinetics = K * NewValue,
-  (
-   nb_current(dynamic_parameters,_)
-  ->
-   true
-  ;
-   assertz(reaction_kinetics(Reaction,NewKinetics))
-  ).
-
 
 % build_stoechiometry(+Reactant_list, +Product_list, +Species_list, -Stoechiometry)
 %