Rewrite and comment the convert_into_hybrid stuff

hybrid.pl

@@ -342,7 +342,9 @@ build_reactants([Species|SpTail], ODESpecies, [Reactant|ReacTail]) :-
   build_reactants(SpTail, ODESpecies, ReacTail).
   
 
-% write_hybrid_ode(+Stream, +Hybrid_list)
+%! write_hybrid_ode(+Stream, +Hybrid_list)
+%
+% write the ode model in the output file
 
 write_hybrid_ode(Stream, Hybrid_original_list) :-
   list_hybrid_ode(Stream, Hybrid_original_list),
@@ -351,6 +353,10 @@ write_hybrid_ode(Stream, Hybrid_original_list) :-
   with_output_to(Stream, models:list_model_events),
   with_output_to(Stream, models:list_model_macros(function)).
 
+%! list_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),
   forall(
@@ -375,10 +381,14 @@ list_hybrid_ode(Stream,Hybrid_original_list) :- % Only MA are converted, need to
 /*  Can try to get the kinetics function in BIOCHAM 4  directly and translate, but i didn't know how
    Also can direclty adapt the kinetics with the hybrid species list, but need to translate the kinetics first if needed */
 
+%! convert_MA()
+%
+%
+
 convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics) :- 
   reaction(Reaction, [kinetics: Kinetics,reactants: Reactants,inhibitors: _,  products: _]),
   Kinetics =.. ['MA',K],
-  kinetics:eval_kinetics(Reactants, _, product('S'*'M' in [reactants], 'M'^'S'), Value),
+  kinetics:eval_kinetics(Reactants, _, product(in('S'*'M', [reactants]), 'M'^'S'), Value),
   convert_into_hybrid(Value,Hybrid_original_list,NewValue),!,
   (
    nb_current(dynamic_parameters,_)
@@ -393,42 +403,41 @@ convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics) :-
    NewKinetics = K * NewValue
   ).
 
-convert_into_hybrid(Value * 1, ODESpecies,NewValue) :-
-  convert_into_hybrid(Value,ODESpecies,NewValue).
 
-convert_into_hybrid(Value ^ 1, ODESpecies,NewValue) :-
-  convert_into_hybrid(Value,ODESpecies,NewValue).
+%! convert_into_hybrid(+Rate, +List_species, -NewRate)
+%
+% Rewrite the reaction rate using the species_total function
+
+convert_into_hybrid(Value * 1, List_species, NewValue) :-
+  convert_into_hybrid(Value, List_species, NewValue).
 
+convert_into_hybrid(Value ^ 1, List_species, NewValue) :-
+  convert_into_hybrid(Value, List_species, NewValue).
 
-convert_into_hybrid(Value1 * Value2, Hybrid_original_list,NewValue1 * NewValue2) :-
-  convert_into_hybrid(Value1,Hybrid_original_list,NewValue1),
-  convert_into_hybrid(Value2,Hybrid_original_list,NewValue2).
+convert_into_hybrid(Value1 * Value2, List_species, NewValue1 * NewValue2) :-
+  convert_into_hybrid(Value1, List_species, NewValue1),
+  convert_into_hybrid(Value2, List_species, NewValue2).
 
-convert_into_hybrid(Value1 ^ Value2, Hybrid_original_list,NewValue1 ^ NewValue2) :-
-  convert_into_hybrid(Value1,Hybrid_original_list,NewValue1),
-  convert_into_hybrid(Value2,Hybrid_original_list,NewValue2).
+convert_into_hybrid(Value1 ^ Value2, List_species, NewValue1 ^ NewValue2) :-
+  convert_into_hybrid(Value1, List_species, NewValue1),
+  convert_into_hybrid(Value2, List_species, NewValue2).
 
-convert_into_hybrid(Number,_,Number) :-
+convert_into_hybrid(Number, _, Number) :-
   number(Number),
   !.
 
-convert_into_hybrid(Molecule,Hybrid_original_list,Molecule) :-
-  \+(member(Molecule,Hybrid_original_list)),
+convert_into_hybrid(Molecule, List_species, Molecule) :-
+  \+(member(Molecule, List_species)),
   !.
 
-convert_into_hybrid(Molecule,Hybrid_original_list,HybridMolecule) :-
+convert_into_hybrid(Molecule, List_species, HybridMolecule) :-
   get_option(stochastic_conversion, Rate),
   nb_getval(volume,Volume),
-  member(Molecule,Hybrid_original_list),
   species_to_total(Molecule, Molecule_total),
-  atom_concat('(',Molecule_total,Molecule1),
-  atom_concat(Molecule1,'/(',Molecule2),
-  atom_concat(Molecule2,Rate,Molecule3),
-  atom_concat(Molecule3,'*',Molecule4),
-  atom_concat(Molecule4,Volume,Molecule5),
-  atom_concat(Molecule5,'))',HybridMolecule),
+  atomic_list_concat(['(',Molecule_total,'/(',Rate,'*',Volume,'))'], HybridMolecule),
   !.
 
+
 prepare_change_list(Reactions2,ODESpecies,List) :- % Only MA are converted, need to do others
   findall([Reactants,Products,Kinetics],
          (
@@ -470,6 +479,7 @@ convert_into_hybrid2(Number,_,Number) :-
   number(Number),
   !.
 
+% this is the part that differentiate it from convert_into_hybrid
 convert_into_hybrid2(Molecule,ODESpecies,StochMolecule) :-
   \+(member(Molecule,ODESpecies)),
   species_to_stoch(Molecule,StochMolecule),