reste 1 seul exemple d'indecision mais mon systeme de reecriture me laisse perplexe

rate_independence.pl

@@ -205,95 +205,164 @@ simplify(Molecules):-
   simpl(M),
   !.
 
+
+
+% Elimination of reaction catalyst M not produced in other reaction
 % 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\=[],
+  delete(Reactions, Reaction1, Reactions2),
 
-  reaction(Reaction1, _, _, _, Products1),
-  forall(
-	 member(Reaction2, Reactions2),
-	 (
-	  \+ (is_reactant(X, Reaction1), is_reactant(X, Reaction2)),
-	  \+ reaction(Reaction2, _, Products1, _, _)
-	 )
-	),
-  !,
-  delete_reaction(Reaction1),
+  (
+   Reactions=[Reaction1] % M catalyst not produced elsewhere
+  ->
+   delete_reaction(Reaction1),
+   reaction(Reaction1, Kinetics1, Reactants1, Inhibitors1, Products1),
+   member((C*M), Reactants1),
+   delete(Reactants1, (C*M), Reac1),
+   member((D*M), Products1),
+   delete(Products1, (D*M), Prod1),
+   (
+    C<D
+   ->
+    E is D-C,
+    add_reaction(Kinetics1, Reac1, Inhibitors1, [(E*M) | Prod1], false)
+   ;
+    C>D
+   ->
+    E is C-D,
+    add_reaction(Kinetics1, [(E*M) | Reac1], Inhibitors1, Prod1, false)
+   ;
+    add_reaction(Kinetics1, Reac1, Inhibitors1, Prod1, false)
+   )
   
-  forall(
-	 member(Reaction2, Reactions2),
-	 (
-	  delete_reaction(Reaction2),
-	  add_merge_reactions(M, Reaction1, Reaction2)
+  ; % M isolated
+
+   reaction(Reaction1, _, _, _, Products1),
+   forall(
+	  member(Reaction2, Reactions2),
+	  (
+	   \+ (is_reactant(X, Reaction1), is_reactant(X, Reaction2)),
+	   \+ reaction(Reaction2, _, Products1, _, _)
+	  )
+	 ),
+   !,
+   delete_reaction(Reaction1),
+   
+   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 a 1<=>3 M (4<)=>2 b rewritten a (<)=> b
-% WOULD NEED TO BE GENERALIZED TO alpha <=> beta <=> gamma in alpha<=>gamma FOR ELIMINATING ISOLATED beta
+% Elimination of M in 2 loops alpha 1<=>3 M (4<)=>2 gamma rewritten alpha (<)=> gamma
+% GENERALIZED TO alpha 1<=>3 beta+M (4<)=>2 gamma in alpha<=>gamma ELIMINATING M ISOLATED AND KEEPING REACTIONS WITH BETA
 simpl(M):-
-  reactions_with_reactant([M], [Reaction1, Reaction2]), 
+  reactions_with_reactant([M], [Reaction1, Reaction2]), % M isolated
   reactions_with_product([M], [Reaction3 | Reactions]),
   (
-   Reactions=[Reaction4]
+   Reactions=[Reaction4] 
   ->
-   reaction(Reaction4, _, Reactants4, _, [S*M])
+   reaction(Reaction4, Kinetics4, Reactants4, Inhibitors4, Products4),
+   member((S*M), Products4),
+   delete(Products4, (S*M), Beta)
   ;
    Reactions=[]
   ),
-  reaction(Reaction1, _, [S*M], _, Products1),
-  reaction(Reaction2, _, [S*M], _, Products2),
-  reaction(Reaction3, _, Reactants3, _, [S*M]),
 
+  
+  reaction(Reaction1, Kinetics1, Reactants1, Inhibitors1, Products1),
+  member((S*M), Reactants1),
+
+  reaction(Reaction2, Kinetics2, Reactants2, Inhibitors2, Products2),
+  member((S*M), Reactants2),
+  
+  reaction(Reaction3, Kinetics3, Reactants3, Inhibitors3, Products3),
+  member((S*M), Products3),
+
+  delete(Reactants1, (S*M), Beta),
+  delete(Reactants2, (S*M), Beta),
+  delete(Products3, (S*M), Beta),
+  
   (
-   Products1=Reactants3
-  ->
-   add_merge_reactions(M, Reaction3, Reaction2),
+   Beta=[]
+
+  -> % merge reactions
    (
-    Reactions=[]
+    Products1=Reactants3
    ->
-    true
-   ;
-    Products2=Reactants4,
-    add_merge_reactions(M, Reaction4, Reaction1),
-    delete_reaction(Reaction4)
+    add_merge_reactions(M, Reaction3, Reaction2),
+    (
+     Reactions=[]
+    ->
+     true
+    ;
+     Products2=Reactants4,
+     add_merge_reactions(M, Reaction4, Reaction1),
+     delete_reaction(Reaction4)
+    )
+   ; % 1 and 2 exchanged by pattern matching
+    Products2=Reactants3,
+    add_merge_reactions(M, Reaction3, Reaction1),
+    (
+     Reactions=[]
+    ->
+     true
+    ;
+     Products1=Reactants4,
+     add_merge_reactions(M, Reaction4, Reaction2),
+     delete_reaction(Reaction4)
+    )
    )
-  ;
-   Products2=Reactants3,
-   add_merge_reactions(M, Reaction3, Reaction1),
+  
+  ; % eliminate M from reactions
+   (Products1=Reactants3 ; Products2=Reactants3),
+   add_reaction(Kinetics1, Beta, Inhibitors1, Products1, false),
+   add_reaction(Kinetics2, Beta, Inhibitors2, Products2, false),
+   add_reaction(Kinetics3, Reactants3, Inhibitors3, Beta, false),
    (
     Reactions=[]
    ->
     true
    ;
-    Products1=Reactants4,
-    add_merge_reactions(M, Reaction4, Reaction2),
+    (
+     Products1=Reactants3
+    ->
+     Products2=Reactants4
+    ;
+     Products1=Reactants4
+    ),
+    add_reaction(Kinetics4, Reactants4, Inhibitors4, Beta, false),
     delete_reaction(Reaction4)
    )
-  ),   
+  ),
+  
   delete_reaction(Reaction1),
   delete_reaction(Reaction2),
   delete_reaction(Reaction3).
+   
 
 
 add_merge_reactions(M, Reaction1, Reaction2):-
   reaction(Reaction1, Kinetics1, Reactants1, Inhibitors1, Products1),
-  subtract(Reactants1, [_*M], Reac1),
-  subtract(Products1, [_*M], Prod1),
-  subtract(Inhibitors1, [M], Inhib1),
+  delete(Reactants1, (_*M), Reac1),
+  delete(Products1, (_*M), Prod1),
+  delete(Inhibitors1, M, Inhib1),
 
   reaction(Reaction2, Kinetics2, Reactants2, Inhibitors2, Products2),
-  subtract(Reactants2, [_*M], Reac2),
-  subtract(Products2, [_*M], Prod2),
-  subtract(Inhibitors2, [M], Inhib2),
+  delete(Reactants2, (_*M), Reac2),
+  delete(Products2, (_*M), Prod2),
+  delete(Inhibitors2, M, Inhib2),
 
-  kinetics(Reac1, Inhib1, Kinetics1, Kin1),
+  kinetics(Reac1, Inhib1, Kinetics1, Kin1), % M remains in kinetics
   kinetics(Reac2, Inhib2, Kinetics2, Kin2),
   append(Reac1, Reac2, Reac),
   append(Prod1, Prod2, Prod),

rate_independence_test.bc

+prolog('writeln("%%%%%%%% WRONG ANSWER %%%%%%%%%")').
+
+prolog('writeln("%%%%%%%% UNDECIDED %%%%%%%%%")').
+
+
+clear_model.
+a+b=>c+d.
+c+d=>a+b.
+c+d=>e.
+e=>c+f.
+list_model.
+test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: composite loop leakage with and-fork")'). prolog('writeln("============")').
+
+
+clear_model.
+MA(k1) for a+b => b.
+MA(k2) for b+c=>d.
+list_model.
+test_rate_independence_inputs_sinks. % no
+prolog('writeln("ANSWER YES: irrelevant input")'). prolog('writeln("============")').
+
+
+
+prolog('writeln("%%%%%%% CORRECT ANSWER %%%%%%%%")').
+
+
+clear_model.
+MA(k1) for a+b => b.
+MA(k2) for b+c=>d.
+list_model.
+test_rate_independence({b,c}, {d}). % no
+prolog('writeln("ANSWER YES: declared irrelevant input")'). prolog('writeln("============")').
+
+
+clear_model.
+a+b=>c+d.
+c+d=>a+b.
+c+d=>e.
+list_model.
+test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: composite loop leakage with or-fork")'). prolog('writeln("============")').
+
+
+clear_model.
+a+b=>c+d.
+c+d=>a+b.
+c+d=>e.
+e=>c+d.
+e=>f+g.
+list_model.
+test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: composite double loop leakage with composite or-fork")'). prolog('writeln("============")').
+
+
 clear_model.
 a => x+c.
 b => y+c.
@@ -26,54 +81,66 @@ list_model.
 test_rate_independence_inputs_sinks.
 prolog('writeln("ANSWER YES: loop leakage with and-fork")'). prolog('writeln("============")').
 
+
 clear_model.
 a => b.
 b => c.
+b => d.
 c => a.
-c => d.
+c => e.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: loop leakage with or-fork")'). prolog('writeln("============")').
+prolog('writeln("ANSWER NO: loop double leakage with or-forks")'). prolog('writeln("============")').
+
 
 
 clear_model.
 a => b.
-b => a.
-b => c.
+b => c+d.
+c => a+e.
 list_model.
-test_rate_independence_inputs_sinks. %
-prolog('writeln("ANSWER YES: loop leakage with or-fork")'). prolog('writeln("============")').
+test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER NO: loop double leakage with and-fork")'). prolog('writeln("============")').
 
 
 clear_model.
-a+b=>c+d.
-c+d=>a+b.
-c+d=>e.
+a => b.
+b => c+d.
+c => a.
+c => e.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: composite loop leakage with or-fork")'). prolog('writeln("============")').
+prolog('writeln("ANSWER NO: loop double leakage with and-or-fork")'). prolog('writeln("============")').
 
 
 clear_model.
-a+b=>c+d.
-c+d=>a+b.
-c+d=>e.
-e=>c+d.
-e=>f+g.
+a => b.
+b => a.
+b => c.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: composite loop leakage with or-fork")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: short loop leakage with or-fork")'). prolog('writeln("============")').
+
+
+clear_model.
+a => b.
+b => c.
+c => a.
+c => d.
+list_model.
+test_rate_independence_inputs_sinks.
+prolog('writeln("ANSWER YES: loop leakage with or-fork")'). prolog('writeln("============")').
 
 
 
 clear_model.
 a+b=>c+d.
-c+d=>a+b.
 c+d=>e.
 e=>c+f.
 list_model.
 test_rate_independence_inputs_sinks.
-prolog('writeln("ANSWER YES: composite loop leakage with and-fork")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: partial loop leakage with or-fork")'). prolog('writeln("============")').
+
 
 
 clear_model.
@@ -85,12 +152,13 @@ test_rate_independence_inputs_sinks. % yes
 prolog('writeln("ANSWER YES: closing and-fork with or-join")'). prolog('writeln("============")').
 
 
+
 clear_model.
 a=>b+c.
 b+c=>d.
 list_model.
 test_rate_independence_inputs_sinks. % yes
-prolog('writeln("ANSWER NO: closing and-fork with and-join")'). prolog('writeln("============")').
+prolog('writeln("ANSWER YES: closing and-fork with and-join")'). prolog('writeln("============")').
 
 
 clear_model.
@@ -141,12 +209,4 @@ test_rate_independence_inputs_sinks. % no
 prolog('writeln("ANSWER NO: output in loop equilibriuem")'). prolog('writeln("============")').
 
 
-clear_model.
-MA(k1) for a+b => b.
-MA(k2) for b+c=>d.
-list_model.
-test_rate_independence_inputs_sinks. % no
-prolog('writeln("ANSWER YES: irrelevant input")'). prolog('writeln("============")').
-
-