Add a present_in_kinetics test and use it to boost check_model

kinetics.pl

@@ -2,7 +2,8 @@
   kinetics,
   [
     kinetics/4,
-    add_coefficient/2
+    add_coefficient/2,
+    present_in_kinetics/2
   ]
 ).
 
@@ -95,6 +96,19 @@ make_sum([RS * RO | Tail], S, O, Expression, Sum) :-
 
 add_coefficient(C, 1 * C).
 
+%! present_in_kinetics(+Molecule, +Kinetics)
+%
+% Test if the Molecule (or whatever actually) is present in the kinetics
+
+present_in_kinetics(Molecule, Molecule) :- !.
+
+present_in_kinetics(Molecule, Kinetics) :-
+  Kinetics =.. [_Functor|Decomposed],
+  present_in_kinetics_sr(Molecule, Decomposed).
+
+present_in_kinetics_sr(Molecule, [Head|Tail]) :-
+  present_in_kinetics(Molecule, Head),!;
+  present_in_kinetics_sr(Molecule, Tail).
 
 
 :-doc('Useful abbreviations for mass action law kinetics (with inhibitors), Michaelis-Menten kinetics, Hill kinetics (with inhibitors).').

models.pl

@@ -85,6 +85,7 @@ Coder: T. Martinez
 :- use_module(arithmetic_rules).
 :- use_module(doc).
 :- use_module(formal_derivation).
+:- use_module(kinetics).
 :- use_module(reaction_rules).
 :- use_module(util).
 
@@ -1373,14 +1374,21 @@ test_wellformed([Molecule|Tail], Expression_raw for Reaction) :-
   ;
     formal_reactant(Molecule, Reaction)
   ->
+    present_in_kinetics(Molecule, Expression),
     test_wf_reactant(Molecule, Expression)
   ;
     formal_inhibitor(Molecule, Reaction)
   ->
+    present_in_kinetics(Molecule, Expression),
     test_wf_inhibitor(Molecule, Expression)
   ;
     !,
-    test_wf_other(Molecule, Expression)
+    (
+      \+(present_in_kinetics(Molecule, Expression)),
+      !
+    ;
+      test_wf_other(Molecule, Expression)
+    )
   ),
   test_wellformed(Tail, Expression for Reaction).