It's all persistency now!

rate_independence.pl

@@ -434,7 +434,6 @@ add_merge_reaction(M, Reaction1, Reaction2):-
   add_reaction(Kin1*Kin2,Reac,Inhib,Prod,false).
 
 % Dynamic predicate for storing structural information of the graph
-:- dynamic(sur_invariant/1).
 :- dynamic(p_invariant/1).
 :- dynamic(output/1).
 :- dynamic(siphon/1).
@@ -445,7 +444,6 @@ add_merge_reaction(M, Reaction1, Reaction2):-
 test_rate_independence_invariants :-
   biocham_command,
   doc('Tests invariant sufficient conditions for rate independence of the current model for all output species (assuming well-formed kinetics).'),
-  retractall(sur_invariant(_)),
   retractall(p_invariant(_)),
   retractall(output(_)),
   retractall(siphon(_)),
@@ -454,8 +452,6 @@ test_rate_independence_invariants :-
     retract(invariants:base_mol(B)),
     (
       normalize(B, BB),
-      assertz(sur_invariant(BB)),
-      debug(rate, "sur_invariant: ~w", [BB]),
       (
         B = [Out]
       ->
@@ -496,34 +492,17 @@ test_rate_independence_invariants :-
 %! test_rate_independence_invariants(+Output, -Id) is det.
 %
 % check the rate independence of species Output in reaction graph Id
-test_rate_independence_invariants(Output, Id) :-
+test_rate_independence_invariants(Output, _Id) :-
   debug(rate, "Trying for output ~w", [Output]),
   (
-    is_covered_by_p_invariant_with_single_surinv(Output, Output, _)
+    is_persistent(Output),
+    p_invariant(P),
+    member(Output, P)
   ->
-    debug(rate, "~w is the single output of a P-invariant", [Output])
+    format("The output ~w is rate independent.", [Output])
   ;
-    format("Undecided, ~w not isolated in any P-invariant.", [Output]),
+    format("Undecided, ~w not persistent or not covered by any P-invariant.", [Output]),
     fail
-  ),
-  retractall(seen(_)),
-  retractall(visiting(_)),
-  iterate_on_parents(Output, Id),
-  format("The output ~w is rate independent.", [Output]).
-
-
-%! is_covered_by_p_invariant_with_single_surinv(+Species, ?Output, -P) is det.
-%
-% check if Species is covered by a P-invariant P, Output is an Output, and P
-% does not contain any other sur-invariant than Output
-is_covered_by_p_invariant_with_single_surinv(Species, Output, P) :-
-  p_invariant(P),
-  member(Species, P),
-  output(Output),
-  \+ (
-      sur_invariant(S),
-      S \= [Output],
-      ord_subset(S, P)
   ).
 
 
@@ -536,62 +515,6 @@ is_persistent(Species) :-
   \+ member(Species, S),
   !.
 
-is_persistent(Species) :-
-  output(Species).
-
-
-%! iterate_on_parents(+Species, +GraphId) is det.
-%
-% iteratively search if all parents either are presistent or in different P-invariants
-iterate_on_parents(Species, GraphId) :-
-  assertz(seen(Species)),
-  debug(rate, "Searching for ~w parents", [Species]),
-  forall(
-    (
-      item([parent: GraphId, kind: edge, id: EdgeId1, item: (Reaction -> Species)]),
-      \+ (
-          item([parent: GraphId, kind: edge, id: EdgeId2, item: (Species -> Reaction)]),
-          debug(rate, "parent reaction ~w also has ~w as input", [Reaction, Species]),
-          reaction_graphs:get_stoichiometry(EdgeId1, Stoich1),
-          reaction_graphs:get_stoichiometry(EdgeId2, Stoich2),
-          debug(rate, "stoichiometries ~w -> ~w", [Stoich2, Stoich1]),
-          Stoich1 = Stoich2
-        )
-    ),
-    (
-      debug(rate, "parent reaction: ~w", [Reaction]),
-      retractall(visiting(Species-_)),
-      assertz(visiting(Species-[])),
-      forall(
-        item([parent: GraphId, kind: edge, item: (Reactant -> Reaction)]),
-        (
-          debug(rate, "parent: ~w", [Reactant]),
-          visiting(Species-ParentPinvs),
-          (
-            seen(Reactant)
-          ->
-            debug(rate, "parent ~w already seen", [Reactant])
-          ;
-            is_persistent(Reactant)
-          ->
-            debug(rate, "parent ~w persistent", [Reactant])
-          ;
-            is_covered_by_p_invariant_with_single_surinv(Reactant, _, P),
-            \+ member(P, ParentPinvs)
-          ->
-            retract(visiting(Species-ParentPinvs)),
-            assertz(visiting(Species-[P | ParentPinvs])),
-            debug(rate, "parent ~w in P-invariant, iterating", [Reactant]),
-            iterate_on_parents(Reactant, GraphId)
-          ;
-            format("Undecided, ~w needed for an output and non-absorbed.", [Reactant]),
-            fail
-          )
-        )
-      )
-    )
-  ).
-
 
 %! normalize(+Invar, -Normalized) is det.
 %