insuffisance des regles de reecritures

biocham_jupyter/guinbextension/src/config/workflows/commands.py

@@ -211,6 +211,7 @@ commands = [
     "set_p_m_rate",
     "test_rate_independence",
     "test_rate_independence_inputs_sinks",
+    "test_rate_independence_invariants",
     "transition",
     "tropicalize",
     "undefined",

rate_independence.pl

@@ -166,7 +166,14 @@ dfs_no_loop(GraphId, Vertex) :-
   ),
   assertz(seen(Vertex)).
 
+
 :- dynamic(removableInputs/0).
+:- dynamic(restrictionOnTrivialReaction/0).
+restrictionOnTrivialReaction.
+:- dynamic(noIsolatedReactant/0).
+noIsolatedReactant.
+:- dynamic(noBetaEmpty/0).
+noBetaEmpty. % incorrect otherwise on eliminating d in loop a+b<=>c+d=>e=>c+b
 
 % Elimination of trivial reactions and isolated species with no outgoing fork
 simplify(Inputs, Outputs):-
@@ -200,11 +207,12 @@ trivial_loop(Molecules):-
   delete_reaction(Reaction1),
   delete_reaction(Reaction2).
 
+
 % Elimination of trivial reactions with products=reactants apart from inputs and outputs
 trivial_reaction(Molecules):-
   item([kind:reaction, id: Id, item: Reaction]),
   reaction(Reaction, _Kinetics, Reactants, _Inhibitors, Reactants),
-  forall(member((_*X), Reactants), member(X, Molecules)),
+  (restrictionOnTrivialReaction -> forall(member((_*X), Reactants), member(X, Molecules)); true),
 write('--> removing trivial reaction '), writeln(Reaction),
   delete_item(Id).
 
@@ -219,7 +227,6 @@ same_reaction:-
 write('--> removing double reaction '), writeln(Reaction2),
   delete_item(Id2).
 
-:- dynamic(noIsolatedReactant).
 
 % Isolated reactant in one reaction
 % to do? eliminates d in c+d=>e=>c+output and does not conclude to rate independence
@@ -259,10 +266,9 @@ eliminate(M):-
 
 
   
-% Warning: Now restricted to GAMMA EMPTY and SAME STOICHIOMETRY 
-% Elimination of species M isolated in reactions alpha_i =>2 beta_i + M  and M (+ gamma) =>1 delta 
-% if forall i  alpha_i\cap\delta=\emptyset and \alpha_i\cap\gamma \= \empty
-% by merging reactions resulting in alpha_i (+ gamma) => beta_i + delta
+% Elimination of species M isolated in reactions alpha_i =>2 beta_i + M  and M  =>1 gamma
+% if forall i  alpha_i\cap\gamma=\emptyset 
+% by merging reactions resulting in alpha_i => beta_i + gamma
 eliminate(M):-
   reactions_with_reactant([M], [Reaction1]), 
   reaction(Reaction1, _, [C*M], _, _Products1), % gamma empty
@@ -291,7 +297,6 @@ write('--> eliminating '), write(M), write(' reactant only in '), write(Reaction
 
 				% Todo: accept reversible reactions with syntax <=>
 
-:- dynamic(noBetaEmpty).
 
 
 
@@ -380,7 +385,7 @@ eliminate(M):-
   delete(Products1, (C*M), Beta),
   delete(Products4, (C*M), Beta),
 
-  (noBetaEmpty -> Beta=[]),
+  (noBetaEmpty -> Beta=[]; true),
     
   write('--> eliminating '), write(M), write(' in double loop '), write(Reaction1),
   write(' <--> '),write(Reaction2), write(Reaction3), write(' <--> '), writeln(Reaction4),

rate_independence_test.bc

 
 
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+prolog("writeln(' Cas problematiques en tete qui montrent l insuffisance des reecritures')").
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 prolog("writeln(' ')").
 clear_model.
+a+b=>c+d.
+c+d=>a+b.
 c+d=>e.
 e=>c+f.
 search_conservations.
 test_rate_independence_inputs_sinks.
-prolog('writeln("The model is rate independent: composite loop leakage with and-fork")').
+prolog('writeln("The model is rate independent: composite loop with and-fork")').
+
 
 prolog("writeln(' ')").
 clear_model.
+a+b=>c+d.
+c+d=>a+b.
 c+d=>e.
-e=>c+f+d.
+e=>c.
+e=>f.
 search_conservations.
 test_rate_independence_inputs_sinks.
-prolog('writeln("Undecided since no: second loop creates synthesis ")').
+prolog('writeln("Undecided, since no: composite loop with or-fork ")').
+
+
+prolog("writeln(' ')").
+clear_model.
+a+b=>c+d.
+c+d=>a+b.
+c+d=>e.
+search_conservations.
+test_rate_independence_inputs_sinks.
+prolog('writeln("The model is rate independent: composite loop leakage with or-fork")').
+
+
+prolog("writeln(' ')").
+clear_model.
+a+b=>c+d.
+c+d=>a+b.
+c+d=>e.
+e=>c+f.
+search_conservations.
+test_rate_independence_inputs_sinks.
+prolog('writeln("The model is rate independent: composite loop leakage with and-fork")').
 
 
 prolog("writeln(' ')").
@@ -24,11 +53,40 @@ clear_model.
 a+b=>c+d.
 c+d=>a+b.
 c+d=>e.
+e=>c+d.
+e=>f+g.
+search_conservations.
+test_rate_independence_inputs_sinks.
+prolog('writeln("The model is rate independent: composite double loop leakage with composite or-fork")').
+
+
+prolog("writeln(' ')").
+clear_model.
+MA(k1) for a+b => b.
+MA(k2) for b+c=>d.
+search_conservations.
+test_rate_independence({b,c}, {d}). % no
+prolog('writeln("The model is rate independent: without input a")').
+
+
+prolog("writeln('%%%%%%%%%%%%%%%%%%%%%%')").
+
+prolog("writeln(' ')").
+clear_model.
+c+d=>e.
 e=>c+f.
 search_conservations.
 test_rate_independence_inputs_sinks.
 prolog('writeln("The model is rate independent: composite loop leakage with and-fork")').
 
+prolog("writeln(' ')").
+clear_model.
+c+d=>e.
+e=>c+f+d.
+search_conservations.
+test_rate_independence_inputs_sinks.
+prolog('writeln("Undecided since no: second loop creates synthesis ")').
+
 
 
 prolog("writeln(' ')").
@@ -76,25 +134,6 @@ test_rate_independence_inputs_sinks. % no
 prolog('writeln("The model is rate independent: trivial loop leakage")').
 
 
-prolog("writeln(' ')").
-clear_model.
-MA(k1) for a+b => b.
-MA(k2) for b+c=>d.
-search_conservations.
-test_rate_independence({b,c}, {d}). % no
-prolog('writeln("The model is rate independent: without input a")').
-
-prolog("writeln(' ')").
-clear_model.
-a+b=>c+d.
-c+d=>a+b.
-c+d=>e.
-e=>c+d.
-e=>f+g.
-search_conservations.
-test_rate_independence_inputs_sinks.
-prolog('writeln("The model is rate independent: composite double loop leakage with composite or-fork")').
-
 prolog("writeln(' ')").
 clear_model.
 a+b=>c+d.
@@ -210,15 +249,6 @@ prolog('writeln("Undecided since no: subtle multiple steady states ")').
 
 
 
-prolog("writeln(' ')").
-clear_model.
-a+b=>c+d.
-c+d=>a+b.
-c+d=>e.
-search_conservations.
-test_rate_independence_inputs_sinks.
-prolog('writeln("The model is rate independent: composite loop leakage with or-fork")').
-
 
 
 prolog("writeln(' ')").