strict_catalyst

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

@@ -118,6 +118,7 @@ commands = [
     "list_graphs",
     "list_influences",
     "list_initial_state",
+    "list_input_species",
     "list_isolated_vertices",
     "list_last_state",
     "list_locations",
@@ -178,7 +179,7 @@ commands = [
     "prolog",
     "quit",
     "rate_independence_reduction",
-    "rate_independence_reduction_sources_sinks",
+    "rate_independence_reduction_inputs_sinks",
     "reaction_graph",
     "reaction_model",
     "reduce_model",
@@ -207,7 +208,7 @@ commands = [
     "set_ode_system_name",
     "set_p_m_rate",
     "test_rate_independence",
-    "test_rate_independence_sources_sinks",
+    "test_rate_independence_inputs_sinks",
     "transition",
     "tropicalize",
     "undefined",

graph_properties.pl

@@ -3,12 +3,15 @@
   [
    pathway/2,
    list_source_species/0,
+   list_input_species/0,
    list_sink_species/0,
 				% API
    pathway/3,
+   input_species/1,
    source_species/1,
    sink_species/1,
    is_source/2,
+   is_input/2,
    is_sink/2
   ]
 	 ).
@@ -65,15 +68,21 @@ new_successor((A, PathA), (B, [Reaction|PathA]), Forward):-
 				% Sources and Sinks
 
 
+list_input_species:-
+  biocham_command,
+  doc('Lists the molecular species that are neither a non-strict-catalyst reaction product nor the target of an influence rule in the curent model.Strict catalysts, i.e. catalysts with same stoichiometry in left-hand and right side of reactions, are allowed as inputs.'),
+  input_species(Molecules),
+  writeln(Molecules).
+
 list_source_species:-
   biocham_command,
-  doc('Lists the molecular species that are neither a reaction product, nor the target of an influence rule, in the curent model.'),
+  doc('Lists the molecular species that are neither a reaction product nor the target of an influence rule in the curent model.'),
   source_species(Molecules),
   writeln(Molecules).
 
 list_sink_species:-
   biocham_command,
-  doc('Lists the molecular species that are neither a reactant, nor a (positive) source of an influence rule, in the curent model.'),
+  doc('Lists the molecular species that are neither a reactant nor a positive source of an influence rule in the curent model.'),
   sink_species(Molecules),
   writeln(Molecules).
 
@@ -84,6 +93,10 @@ list_sink_species:-
 
 :-devdoc('Prolog lists of graph sources and sinks.').
 
+input_species(L):-
+  enumerate_molecules(Molecules),
+  realsetof(M, is_input(M, Molecules), L).
+
 source_species(L):-
   enumerate_molecules(Molecules),
   realsetof(M, is_source(M, Molecules), L).
@@ -103,6 +116,15 @@ is_source(M, Molecules):-
      is_target(M,_)
     ).
 
+is_input(M, Molecules):-
+  member(M, Molecules),
+  \+ (
+      is_strict_product(M,_)
+     ),
+  \+ (
+     is_target(M,_)
+    ).
+
 is_sink(M, Molecules):-
   member(M, Molecules),
   \+ (

rate_independence.pl

@@ -3,9 +3,9 @@
   [
     % Commands
    test_rate_independence/0,
-   test_rate_independence_sources_sinks/0,
+   test_rate_independence_inputs_sinks/0,
    test_rate_independence/2,
-   rate_independence_reduction_sources_sinks/0,
+   rate_independence_reduction_inputs_sinks/0,
    rate_independence_reduction/2
   ]
 ).
@@ -49,13 +49,13 @@ test_rate_independence(Inputs, Outputs):-
   rate_independence_reduction(Inputs, Outputs),
   test_rate_independence.
 
-test_rate_independence_sources_sinks :-
+test_rate_independence_inputs_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 (assuming well-formed kinetics).'),
-  source_species(Inputs),
+  doc('Test graphical sufficient conditions for rate independence of the current model for the computation of graph output species from graph input species (assuming well-formed kinetics). The input species are the species that are not a reaction product or a strict catalyst (i.e. with same stoichiometry). The output species are the species that are not reactant.'),
+  input_species(Inputs),
   sink_species(Outputs),
-  write('sources: '), writeln(Inputs),
-  write('sinks: '), writeln(Outputs),
+  write('inputs: '), writeln(Inputs),
+  write('outputs: '), writeln(Outputs),
   test_rate_independence(Inputs, Outputs).
 
 
@@ -70,10 +70,10 @@ rate_independence_reduction(Inputs, Outputs):-
   writeln('Reduced model:'),
   list_model.
 
-rate_independence_reduction_sources_sinks:-
+rate_independence_reduction_inputs_sinks:-
   biocham_command,
-  doc('Reduces the current reaction model while preserving rate independence for computing sink species from source species.'),
-  source_species(Inputs),
+  doc('Reduces the current reaction model while preserving the rate independence property for computing the graph sink species from the input species. Warning: the reduction does not preserve the computation, only the rate independence property which may be true or false.'),
+  input_species(Inputs),
   sink_species(Outputs),
   write('sources: '), writeln(Inputs),
   write('sinks: '), writeln(Outputs),

rate_independence_test.bc

@@ -4,14 +4,14 @@ b => y+c.
 x+y => z.
 c+z => r.
 list_model.
-test_rate_independence_sources_sinks.
+test_rate_independence_inputs_sinks.
 
 clear_model.
 a => b.
 b => c.
 c => b + d.
 list_model.
-test_rate_independence_sources_sinks.
+test_rate_independence_inputs_sinks.
 
 clear_model.
 a => b.
@@ -19,13 +19,13 @@ b => c.
 c => b.
 c => d.
 list_model.
-test_rate_independence_sources_sinks.
+test_rate_independence_inputs_sinks.
 
 clear_model.
 a+b=>b. 
 b+c=>_.
 list_model.
-test_rate_independence_sources_sinks.
+test_rate_independence_inputs_sinks.
 
 clear_model.
 a+b=>c+d.
@@ -34,7 +34,7 @@ c+d=>e.
 e=>c+d.
 e=>f+g.
 list_model.
-test_rate_independence_sources_sinks.
+test_rate_independence_inputs_sinks.
 
 
 clear_model.
@@ -42,7 +42,7 @@ a => b.
 b => a.
 b => c.
 list_model.
-test_rate_independence_sources_sinks.
+test_rate_independence_inputs_sinks.
 
 
 clear_model.
@@ -51,6 +51,6 @@ a=>c.
 b=>d.
 c=>d.
 list_model.
-test_rate_independence_sources_sinks.
+test_rate_independence_inputs_sinks.
 
 

reaction_editor.pl

@@ -24,7 +24,10 @@
     reactions_with_inhibitor/2,
     is_reactant/2,
     is_product/2,
+    is_strict_reactant/2,
+    is_strict_product/2,
     is_catalyst/2,
+    is_strict_catalyst/2,
     is_inhibitor/2,
     find_reaction_prefixed/2,
     is_reaction_model/0,
@@ -243,12 +246,23 @@ is_reactant(S, Reaction):-
   reaction(Reaction, [kinetics: _,reactants: Reactants,inhibitors: _,   products: _]),
   member((_*S), Reactants).
 
+is_strict_reactant(S, Reaction):-
+  item([kind: reaction, item: Reaction]),
+  reaction(Reaction, [kinetics: _,reactants: Reactants,inhibitors: _,   products: Products]),
+  member((M*S), Reactants),
+  \+ member((M*S), Products).
 
 is_product(S, Reaction):-
   item([kind: reaction, item: Reaction]),
   reaction(Reaction, [kinetics: _,reactants: _,inhibitors: _,   products: Products]),
   member((_*S), Products).
 
+is_strict_product(S, Reaction):-
+  item([kind: reaction, item: Reaction]),
+  reaction(Reaction, [kinetics: _,reactants: Reactants,inhibitors: _,   products: Products]),
+  member((M*S), Products),
+  \+ member((M*S), Reactants).
+
 
 is_catalyst(S, Reaction):-
   item([kind: reaction, item: Reaction]),
@@ -256,6 +270,13 @@ is_catalyst(S, Reaction):-
   member((_*S), Reactants),
   member((_*S), Products).
 
+% a strict catalyst has same stoichiometry (cannot be an autocatalyst)
+is_strict_catalyst(S, Reaction):-
+  item([kind: reaction, item: Reaction]),
+  reaction(Reaction, [kinetics: _,reactants: Reactants,inhibitors: _,   products: Products]),
+  member((C*S), Reactants),
+  member((C*S), Products).
+
 
 is_inhibitor(S, Reaction):-
   item([kind: reaction, item: Reaction]),