better species ignore list for equilibration

tropical.pl

@@ -215,6 +215,11 @@ subst_deg_and_vars(A ^ N, Vars, Ai, NN * AA) :-
   !,
   subst_deg_and_vars(A, Vars, Ai, AA).
 
+subst_deg_and_vars(N, _Vars, _Ai, D) :-
+  number(N),
+  !,
+  get_degree(N, D).
+
 subst_deg_and_vars(K, _Vars, _Ai, D) :-
   degree(K, D),
   !.
@@ -425,7 +430,7 @@ ignore_unbalanced([H | T], [H | TT]) :-
 
 :- initial(option(tropical_epsilon: 0.1)).
 :- initial(option(tropical_max_degree: 3)).
-:- initial(option(tropical_partial: 0)).
+:- initial(option(tropical_ignore: {})).
 :- initial(option(tropical_denominator: 0)).
 
 :- biocham_silent(clear_model).
@@ -456,12 +461,11 @@ tropicalize :-
     'Max absolute value of the degree in epsilon as a power of 2'
   ),
   option(
-    tropical_partial,
-    number,
+    tropical_ignore,
+    {object},
     Partial,
-    'Number of a variable (as displayed by \\command{list_molecules/0} plus 1)
-      to ignore for equilibration (0 to ignore none, -1 to ignore all
-      unbalanced)'
+    'set of species to ignore for equilibration ({} to ignore none, {-1} to
+     ignore all unbalanced)'
   ),
   option(
     tropical_denominator,
@@ -501,18 +505,26 @@ tropicalize :-
     get_equilibrations(Vars, Ai, E, _DE),
     debug(tropical, "equilibrations: ~w", [E]),
     (
-      Partial == 0
+      Partial == [{}]
     ->
       Equils = E
     ;
-      Partial == -1
+      Partial == [-1]
     ->
       ignore_unbalanced(E, Equils),
       write(E),nl,
       write(Equils),nl
     ;
-      format("Ignoring equilibration for ~wth variable\n", [Partial]),
-      nth1(Partial, E, _, Equils)
+      format("Ignoring equilibration for ~w\n", [Partial]),
+      findall(
+        Eq,
+        (
+          nth0(N, E, Eq),
+          nth0(N, Vars, V),
+          \+ member(V, Partial)
+        ),
+        Equils
+      )
     ),
     debug(tropical, "equilibrations: ~w~n", [Equils]),
     equilibrate_rec(Equils),