test_rate_independence_sources_sinks

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

@@ -206,6 +206,7 @@ commands = [
     "set_ode_system_name",
     "set_p_m_rate",
     "test_rate_independence",
+    "test_rate_independence_sources_sinks",
     "transition",
     "tropicalize",
     "undefined",

graph_properties.pl

@@ -103,7 +103,7 @@ is_sink(M, Molecules):-
       is_reactant(M,_)
      ),
   \+ (
-     is_source(M,_)
+     is_influence_source(M,_)
      ).
 
 

rate_independence.pl

@@ -3,6 +3,7 @@
   [
     % Commands
    test_rate_independence/0,
+   test_rate_independence_sources_sinks/0,
    test_rate_independence/2,
    rate_independence_reduction/2
   ]
@@ -36,6 +37,13 @@ test_rate_independence :-
 
 				% to generalize to influence models too
 
+test_rate_independence_sources_sinks :-
+  biocham_command,
+  doc('Test graphical sufficient conditions for rate independence of the current model for the computation of graph sink species from graph source species.'),
+  source_species(Inputs),
+  sink_species(Outputs),
+  test_rate_independence(Inputs, Outputs).
+
 % Test rate independence for given inputs and outputs by performing rate-independence preserving reduction
 test_rate_independence(Inputs, Outputs):-
   biocham_command,
@@ -44,7 +52,8 @@ test_rate_independence(Inputs, Outputs):-
   doc('Checks whether the current reaction model is rate independent
      for computing the given set of molecular species \\argument{Outputs} from \\argument{Inputs}.
      Warning: this command destroys the current model by applying the \\command{rate_independence_reduction}.'),
-  rate_independence_check(Inputs, Outputs).
+  rate_independence_reduction(Inputs, Outputs),
+  test_rate_independence.
 
 % Performs a model reduction which preserves the rate independence property for given inputs and outputs
 rate_independence_reduction(Inputs, Outputs):-
@@ -141,10 +150,6 @@ dfs_no_loop(GraphId, Vertex) :-
   assertz(seen(Vertex)).
 
 
-% Graph rewriting for checking rate independence with respect to Inputs and Outputs
-rate_independence_check(Inputs, Outputs):-
-  simplify(Inputs, Outputs),
-  check_rate_independence.
 
 % Compression of species with no outgoing fork and trivial loops
 simplify(Inputs, Outputs):-