Add a pruning step on reaction before modifier handling

model_correction.pl

@@ -35,7 +35,7 @@ correct_model :-
     (
       remove_null_kinetic(Reaction),!
     ;
-      split_bidirectional_reaction(Reaction),!
+      split_bidirectional_reaction(List_Molecule, Reaction),!
     ;
       reverse_reaction(Reaction),!
     ;
@@ -61,16 +61,17 @@ remove_null_kinetic(Expression for Reaction) :-
     delete_reaction(Expression for Reaction)
   ).
 
-%! split_bidirectional_reaction(+Reaction)
+%! split_bidirectional_reaction(+List_Mol, +Reaction)
 %
 % Split a bidirection reaction in two
 
-split_bidirectional_reaction(Expression for Reactant => Product) :-
+split_bidirectional_reaction(List_Mol, Expression for Reactant => Product) :-
   (
     ode:substitute_functions(Expression, Expr),
     distribute(Expr, DistExpr),
     DistExpr = Up - Down,
     % test if it is effectively a bidir. reaction
+    member(P, List_Mol),
     models:formal_product(P, Reactant => Product),
     present_in_kinetics(P, Down)
   ->
@@ -106,12 +107,15 @@ reverse_reaction(Expression for Reactant => Product) :-
 correct_modifiers(List_Molecule, Expression_raw for Reaction) :-
   ode:substitute_functions(Expression_raw, Expression),
   detect_modifiers(List_Molecule, Expression, Catalysts, Inhibitors),
+  % purify reaction
+  findall(M, (member(M, List_Molecule), models:formal_catalyst(M, Reaction)), LC),
+  remove_all_catalysts(LC, Reaction, Purified_Reaction),
   (
-    append(Catalysts, Inhibitors, [])
-  ->
-    true
-  ;
-    add_catalysts(Catalysts, Reaction, ReactionTempo),
+    %  append(Catalysts, Inhibitors, [])
+    %->
+    %true
+    %;
+    add_catalysts(Catalysts, Purified_Reaction, ReactionTempo),
     add_inhibitors(Inhibitors, ReactionTempo, NewReaction),
     delete_reaction(Expression_raw for Reaction),
     add_reaction(Expression_raw for NewReaction)
@@ -245,3 +249,29 @@ remove_molecule(P*Molecule+Other, Molecule, Result) :- !,
 
 remove_molecule(Species+Other, Molecule, Without+Other) :-
   remove_molecule(Species, Molecule, Without).
+
+
+%! remove_all_catalysts(+List_Catalyst, +Reaction, -NewReaction)
+%
+%
+
+remove_all_catalysts([], Reaction, Reaction).
+
+remove_all_catalysts([Head|Tail], R/I=>P, RR/I=>PP) :-
+  remove_all_catalysts(Tail, R/I=>P, RT/I=>PT),
+  remove_catalyst(RT, PT, Head, RR, PP).
+
+remove_all_catalysts([Head|Tail], R=>P, RR=>PP) :-
+  remove_all_catalysts(Tail, R=>P, RT=>PT),
+  remove_catalyst(RT, PT, Head, RR, PP).
+
+remove_catalyst(Reac, Prod, Cat, NReac, NProd) :-
+  (
+    remove_molecule(Reac, Cat, TReac),
+    remove_molecule(Prod, Cat, TProd)
+  ->
+    remove_catalyst(TReac, TProd, Cat, NReac, NProd)
+  ;
+    NReac = Reac,
+    NProd = Prod
+  ).