Merge convert_into_hybrid 1 and 2 in a single predicate

hybrid.pl

@@ -389,7 +389,7 @@ convert_MA(Reaction,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),
-  convert_into_hybrid(Value,Hybrid_original_list,NewValue),!,
+  convert_into_hybrid(Value, Hybrid_original_list, std, NewValue),!,
   (
    nb_current(dynamic_parameters,_)
   ->
@@ -404,33 +404,41 @@ convert_MA(Reaction,Reactions,Hybrid_original_list,NewKinetics) :-
   ).
 
 
-%! convert_into_hybrid(+Rate, +List_species, -NewRate)
+%! convert_into_hybrid(+Rate, +List_species, +Mode, -NewRate)
 %
 % Rewrite the reaction rate using the species_total function
+% When Mode = stoch, Species outside Liste_species are convert to Species_stoch
+% and are otherwise untouched
 
-convert_into_hybrid(Value * 1, List_species, NewValue) :-
-  convert_into_hybrid(Value, List_species, NewValue).
+convert_into_hybrid(Value * 1, List_species, Mode, NewValue) :-
+  convert_into_hybrid(Value, List_species, Mode, NewValue).
 
-convert_into_hybrid(Value ^ 1, List_species, NewValue) :-
-  convert_into_hybrid(Value, List_species, NewValue).
+convert_into_hybrid(Value ^ 1, List_species, Mode, NewValue) :-
+  convert_into_hybrid(Value, List_species, Mode, NewValue).
 
-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, List_species, Mode, NewValue1 * NewValue2) :-
+  convert_into_hybrid(Value1, List_species, Mode, NewValue1),
+  convert_into_hybrid(Value2, List_species, Mode, 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, List_species, Mode, NewValue1 ^ NewValue2) :-
+  convert_into_hybrid(Value1, List_species, Mode, NewValue1),
+  convert_into_hybrid(Value2, List_species, Mode, NewValue2).
 
-convert_into_hybrid(Number, _, Number) :-
+convert_into_hybrid(Number, _, _Mode, Number) :-
   number(Number),
   !.
 
-convert_into_hybrid(Molecule, List_species, Molecule) :-
-  \+(member(Molecule, List_species)),
-  !.
+convert_into_hybrid(Molecule, List_species, Mode, Out_Molecule) :-
+  \+(member(Molecule, List_species)),!,
+  (
+    Mode = stoch
+  ->
+    species_to_stoch(Molecule, Out_Molecule)
+  ;
+    Out_Molecule = Molecule
+  ).
 
-convert_into_hybrid(Molecule, List_species, HybridMolecule) :-
+convert_into_hybrid(Molecule, _List_species, _Mode, HybridMolecule) :-
   get_option(stochastic_conversion, Rate),
   nb_getval(volume,Volume),
   species_to_total(Molecule, Molecule_total),
@@ -451,7 +459,7 @@ 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_hybrid2(Value,ODESpecies,NewValue),!,
+  convert_into_hybrid(Value, ODESpecies, stoch, NewValue),!,
   NewKinetics = K * NewValue,
   (
    nb_current(dynamic_parameters,_)
@@ -461,42 +469,6 @@ convert_MA2(Reaction,ODESpecies,NewKinetics,Reactants,Products) :-
    assertz(reaction_kinetics(Reaction,NewKinetics))
   ).
 
-convert_into_hybrid2(Value * 1, ODESpecies,NewValue) :-
-  convert_into_hybrid2(Value,ODESpecies,NewValue).
-
-convert_into_hybrid2(Value ^ 1, ODESpecies,NewValue) :-
-  convert_into_hybrid2(Value,ODESpecies,NewValue).
-
-convert_into_hybrid2(Value1 * Value2, ODESpecies,NewValue1 * NewValue2) :-
-  convert_into_hybrid2(Value1,ODESpecies,NewValue1),
-  convert_into_hybrid2(Value2,ODESpecies,NewValue2).
-
-convert_into_hybrid2(Value1 ^ Value2, ODESpecies,NewValue1 ^ NewValue2) :-
-  convert_into_hybrid2(Value1,ODESpecies,NewValue1),
-  convert_into_hybrid2(Value2,ODESpecies,NewValue2).
-
-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),
-  !.
-
-convert_into_hybrid2(Molecule,Hybrid_original_list,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),
-  !.
 
 % build_stoechiometry(+Reactant_list, +Product_list, +Species_list, -Stoechiometry)
 %
@@ -1183,8 +1155,6 @@ hybrid_dynamic_simulation(InputFile,OutFilename,Volume,Time,PropTresh,PartTresh)
              )
            ),
           Reactants_by_rules),
-  writeln(Reactants1),
-  writeln(Reactants_by_rules),
   
   build_constraints_by_rules(Reactants_by_rules, SortedReactants, 1, [], Hybrid_reactants_list),  
   build_constraints_list(Hybrid_reactants_list, Constraints_list),