encours

rate_independence.pl

@@ -177,6 +177,7 @@ simplify(Inputs, Outputs):-
   \+ simplify(Molecules).
 
 simplify(Inputs, Outputs):-
+writeln('--------- iterate ---------'), list_model, 
   simplify(Inputs, Outputs).
   
 
@@ -204,24 +205,37 @@ simplify(Molecules):-
   simpl(M),
   !.
 
-% Elimination of species M if no outgoing fork
-% rewritten by merging reactions
-% alpha_i => beta_i + M  and M + gamma => delta is rewritten alpha_i + gamma => beta_i + delta
+% Elimination of species M isolated in reactions alpha_i => beta_i + M  and M + gamma => delta 
+% if forall i  alpha_i\cap\gamma=\emptyset and \alpha_i \= \delta
+% by merging reactions resulting in alpha_i + gamma => beta_i + delta
 simpl(M):-
   reactions_with_reactant([M], [Reaction1]), 
   reactions_with_product([M], Reactions), 
   subtract(Reactions, [Reaction1], Reactions2),
   Reactions2\=[],
+
+  reaction(Reaction1, _, _, _, Products1),
+  forall(
+	 member(Reaction2, Reactions2),
+	 (
+	  \+ (is_reactant(X, Reaction1), is_reactant(X, Reaction2)),
+	  \+ reaction(Reaction2, _, Products1, _, _)
+	 )
+	),
   !,
   delete_reaction(Reaction1),
   
-  member(Reaction2, Reactions2),
-  delete_reaction(Reaction2),
-  add_merge_reactions(M, Reaction1, Reaction2).
+  forall(
+	 member(Reaction2, Reactions2),
+	 (
+	  delete_reaction(Reaction2),
+	  add_merge_reactions(M, Reaction1, Reaction2)
+	 )
+	).
 
 % Todo: accept reversible reactions with syntax <=>
 
-% Elimination of M in 2 loops alpha 1<=>3 M (4<)=>2 gamma rewritten alpha (<)=> gamma
+% Elimination of M in 2 loops a 1<=>3 M (4<)=>2 b rewritten a (<)=> b
 simpl(M):-
   reactions_with_reactant([M], [Reaction1, Reaction2]), 
   reactions_with_product([M], [Reaction3 | Reactions]),

rate_independence_test.bc

@@ -5,6 +5,7 @@ x+y => z.
 c+z => r.
 list_model.
 test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: max = sum-min")'). prolog('writeln("============")').
 
 clear_model.
 a => b.
@@ -12,6 +13,7 @@ b => c.
 c => b + d.
 list_model.
 test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: loop leakage")'). prolog('writeln("============")').
 
 clear_model.
 a => b.
@@ -20,12 +22,24 @@ c => b.
 c => d.
 list_model.
 test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: loop leakage")'). prolog('writeln("============")').
 
 clear_model.
 a+b=>b. 
-b+c=>_.
+b+c=>d.
 list_model.
 test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: irrelevant fork")'). prolog('writeln("============")').
+
+
+clear_model.
+a => b.
+b => a.
+b => c.
+list_model.
+test_rate_independence_inputs_sinks. %
+prolog('writeln("ANSWER YES: loop leakage")'). prolog('writeln("============")').
+
 
 clear_model.
 a+b=>c+d.
@@ -35,14 +49,7 @@ e=>c+d.
 e=>f+g.
 list_model.
 test_rate_independence_inputs_sinks.
-
-
-clear_model.
-a => b.
-b => a.
-b => c.
-list_model.
-test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: composite loop leakage")'). prolog('writeln("============")').
 
 
 clear_model.
@@ -51,6 +58,45 @@ a=>c.
 b=>d.
 c=>d.
 list_model.
-test_rate_independence_inputs_sinks.
+test_rate_independence_inputs_sinks. % yes
+prolog('writeln("ANSWER YES: closing or-fork with or-join")'). prolog('writeln("============")').
+
+
+clear_model.
+MA(k1) for A => B.
+MA(k2) for A + B => C.
+list_model.
+test_rate_independence_inputs_sinks. % no
+prolog('writeln("ANSWER NO: closing or-fork with and-join")'). prolog('writeln("============")').
+
+
+% loop and fork
+clear_model.
+MA(1) for A=>B.
+MA(2) for B=>C.
+MA(5) for B=>D.
+MA(6) for D=>B.
+list_model.
+test_rate_independence_inputs_sinks. % no
+prolog('writeln("ANSWER NO: parasite loop and fork")'). prolog('writeln("============")').
+
+
+clear_model.
+MA(k1) for a => b.
+MA(k2) for b => a.
+MA(k3) for b => c.
+MA(k4) for c => b.
+list_model.
+test_rate_independence({a},{c}). % no
+prolog('writeln("ANSWER NO: loop equilibrium output")'). prolog('writeln("============")').
+
+
+clear_model.
+MA(k1) for a+b => b.
+MA(k2) for b+c=>d.
+list_model.
+test_rate_independence({a},{c}). % no
+prolog('writeln("ANSWER NO")'). prolog('writeln("============")').
+
 
 

reaction_editor.pl

@@ -183,7 +183,7 @@ list_reactions_with_reactant(ObjectSet):-
   reactions_with_reactant(ObjectSet, Reactions),
   forall(member(R,Reactions), writeln(R)).
 
-% setof with composite goals is bugged !
+
 reactions_with_reactant(ObjectSet, Reactions):-
   realsetof(Reaction, reaction_editor:reactant(ObjectSet, Reaction), Reactions).