First round of bug correction after previous changes!

aliases.plt

@@ -2,7 +2,7 @@
 
 :- begin_tests(aliases).
 
-test('alias', [true(Reactions == [2 * a => c])]) :-
+test('alias', [true(Reactions == ['MA'(1) for 2 * a => c])]) :-
   clear_model,
   command(a + b => c),
   command(alias(a = b)),

arithmetic_rules.pl

@@ -523,6 +523,9 @@ sign(+ A, 1, A).
 sign(- A, -1, A).
 
 
+
+additive_block('_', []). % Notation of empty set in biocham
+
 additive_block(+ A, [+A]).
 
 additive_block(- A, [-A]).

reaction_editor.pl

@@ -56,7 +56,8 @@ delete_reaction(Reaction):-
   doc('
     removes one reaction rule from the current set of reactions.
   '),
-  delete_item([kind: reaction, item: Reaction]).
+  simplify_reaction(Reaction, ReactionFormated),
+  delete_item([kind: reaction, item: ReactionFormated]).
 
 delete_reaction_named(Name):-
   biocham_command,
@@ -567,7 +568,9 @@ make_reaction(
     ->
       Body = (Reactants <=> RightSolution)
     ;
-      Body = (Reactants + CatalystSolution <=> RightSolution + CatalystSolution)
+      simplify(Reactants + CatalystSolution, Reactants_full),
+      simplify(RightSolution + CatalystSolution, Products_full),
+      Body = (Reactants_full <=> Products_full)
     )
   ;
     (
@@ -575,7 +578,9 @@ make_reaction(
     ->
       Body = (Reactants => RightSolution)
     ;
-      Body = (Reactants + CatalystSolution => RightSolution + CatalystSolution)
+      simplify(Reactants + CatalystSolution, Reactants_full),
+      simplify(RightSolution + CatalystSolution, Products_full),
+      Body = (Reactants_full => Products_full)
     )
   ).
 

reaction_editor.plt

@@ -6,7 +6,7 @@
 
 test(
   'compound',
-  [Reactions == [2 * a + 2 * b => 2 * 'a-b']]
+  [Reactions == ['MA'(1) for 2 * a + 2 * b => 2 * 'a-b']]
 ) :-
   clear_model,
   command(add_reaction(2 * a + 2 * b => 2 * a-b)),
@@ -14,7 +14,7 @@ test(
 
 test(
   'catalyst',
-  [Reactions == [b =[ b + a + c ]=> '_', '_' =[ b + a + c ]=> b]]
+  [Reactions == ['MA'(1) for 2*b+a+c => b+a+c, 'MA'(1) for b+a+c => 2*b+a+c]]
 ) :-
   clear_model,
   add_reaction(a + b + c <=[ b ]=> a + c),
@@ -31,18 +31,16 @@ test(
 
 test(
 'michaelis menten reduction',
-  [true(Reactions == [(2*'MA'(1) for 'S'=['E'+'C']=>'P')])]
+  [Reactions == [2*'MA'(1) for 'S'+'E'+'C'=> 'P'+'E'+'C']]
 ) :-
-
   command(load('library:examples/michaelis-menten/mm.bc')),
   command(delete_reaction('C'=>'E'+'S')),
   command(merge_reactions('E'+'S'=>'C','C'=>'E'+'P')),
-%  command(merge_molecules('E','C')),
   all_items([kind: reaction], Reactions).
 
 test(
 'michaelis menten reduction C',
-  [true(Reactions == [(2*'MA'(1) for 'S'=['E'+'C']=>'P')])]
+  [Reactions == [2*'MA'(1) for 'S'+'E'+'C'=> 'P'+'E'+'C']]
 ) :-
 
   command(load('library:examples/michaelis-menten/mm.bc')),