import_reac/infl => load and add

ode.pl

@@ -15,8 +15,10 @@
     list_ode/0,
     ode_system/0,
     import_ode/1,
-    import_reactions_from_ode_system/0,
-    import_influences_from_ode_system/0,
+    load_reactions_from_ode_system/0,
+    load_influences_from_ode_system/0,
+    add_reactions_from_ode_system/0,
+    add_influences_from_ode_system/0,
     (init)/1,
 %    load_ode_system/1,
     load_reactions_from_ode/1,
@@ -339,19 +341,19 @@ init(InitList) :-
     )
   ).
 
-import_reactions_from_ode_system :-
+add_reactions_from_ode_system :-
   biocham_command,
   doc('adds a set of reactions equivalent to the current ODE system.'),
   get_current_ode_system(Id),
   !,
   retractall(flag_influences),
   import_reactions_from_ode_system(Id).
-import_reactions_from_ode_system :-
+add_reactions_from_ode_system :-
   print_message(warning,'there is no current ode system').
 
 
 
-import_influences_from_ode_system :-
+add_influences_from_ode_system :-
   biocham_command,
   doc('adds a set of influences equivalent to the current ODE system.'),
   get_current_ode_system(Id),
@@ -359,10 +361,27 @@ import_influences_from_ode_system :-
   (assertz(flag_influences);retractall(flag_influences)),
   import_influences_from_ode_system(Id),
   retractall(flag_influences).
-import_influences_from_ode_system :-
+add_influences_from_ode_system :-
   print_message(warning,'there is no current ode system').
 
 
+load_reactions_from_ode_system :-
+  biocham_command,
+  doc('Replaces the current reactions with those from
+    \\command{add_reactions_from_ode_system/0}.'),
+  delete_reactions,
+  add_reactions_from_ode_system.
+
+
+load_influences_from_ode_system :-
+  biocham_command,
+  doc('Replaces the current reactions with those from
+    \\command{add_influences_from_ode_system/0}.'),
+  delete_reactions,
+  add_influences_from_ode_system.
+
+
+
 
 
 :- devdoc('\\section{Public API}').
@@ -591,6 +610,13 @@ non_decomposable_term_in_additive_normal_form(Coefficient, Term, Coefficient * T
   integer(Coefficient),
   !.
 
+non_decomposable_term_in_additive_normal_form(-1, NCoeff * Term, Coefficient *
+  Term) :-
+    number(Coefficient),
+    Coefficient < 0,
+    !,
+    NCoeff is -Coefficient.
+
 non_decomposable_term_in_additive_normal_form(1, Term, Term).
 
 
@@ -1027,11 +1053,13 @@ models:add_file_suffix('ode', add_ode_system_file).
 
 add_ode_system_file(InputFile) :-
   import_ode(InputFile),
-  (flag_influences
-   ->
-       import_influences_from_ode_system
-   ;
-   import_reactions_from_ode_system),
+  (
+    flag_influences
+  ->
+    add_influences_from_ode_system
+  ;
+    add_reactions_from_ode_system
+  ),
   get_current_ode_system(Id),
   delete_item(Id).
 

ode.plt

@@ -42,7 +42,7 @@ done
   all_items([parent: Id], ODEs).
 
 test(
-  'import_reactions_from_ode_system',
+  'add_reactions_from_ode_system',
   [true(Reactions == [v*a/(a+k) for a => b])]
 ) :-
   clear_model,
@@ -51,7 +51,9 @@ test(
   add_ode(db/dt = v*a/(a+k)),
   add_ode(dc/dt = 1),
   delete_ode([c]),
-  import_reactions_from_ode_system,
+  add_reactions_from_ode_system,
+  all_items([kind: reaction], Reactions),
+  load_reactions_from_ode_system,
   all_items([kind: reaction], Reactions).
 
 

reaction_editor.pl

@@ -6,6 +6,7 @@
     list_reactions/0,
     list_rules/0,
     delete_reaction/1,
+    delete_reactions/0,
     delete_reaction_named/1,
     delete_reaction_prefixed/1,
     merge_reactions/2,
@@ -37,14 +38,14 @@ add_reaction(Reaction) :-
   type(Reaction, reaction),
   doc('
     adds reaction rules to the current set of reactions.
-    This command is implicit: reaction rules are directly added when reading them.
-  '),
+  This command is implicit: reaction rules are directly added when reading them.
+'),
+\+ (
+  reaction_named(Reaction, Name, Kinetics, Reactants, Inhibitors, Products),
   \+ (
-    reaction_named(Reaction, Name, Kinetics, Reactants, Inhibitors, Products),
-    \+ (
-      add_reaction(Name, Kinetics, Reactants, Inhibitors, Products, false)
-    )
-  ).
+    add_reaction(Name, Kinetics, Reactants, Inhibitors, Products, false)
+  )
+).
 
 :- doc('\\begin{remark}In Biocham v4, a reaction network is represented by a multiset of reactions. Reactions can thus be added in multiple copies in which case their reaction rates are summed.\\end{remark}').
 
@@ -66,12 +67,19 @@ delete_reaction_named(Name):-
     removes  reaction rules by their name from the current set of reactions.
   '),
   Item=(Name--_),
-\+ (
+  \+ (
     item([kind:reaction, id: Id, item:Item]),
-\+ (
-    delete_item(Id)
-)
-).
+    \+ (
+      delete_item(Id)
+    )
+  ).
+
+
+delete_reactions :-
+  biocham_command,
+  doc('Removes all reaction rules from the current model.'),
+  forall(item([kind: reaction, id: Id]), delete_item(Id)).
+
 
 delete_reaction_prefixed(Prefix):-
   biocham_command,
@@ -80,25 +88,25 @@ delete_reaction_prefixed(Prefix):-
     removes the reaction rules that match a name prefix.
   '),
   Item=(Name--_),
-\+ (
+  \+ (
     item([kind:reaction, id: Id, item:Item]),
     atom_concat(Prefix,_,Name),
-\+ (
-    delete_item(Id)
-)
-).
+    \+ (
+      delete_item(Id)
+    )
+  ).
 
 
 find_reaction_prefixed(Prefix,Name):-
-    biocham_command,
-    type(Prefix, name),
-    type(Name, name),
-    devdoc('
+  biocham_command,
+  type(Prefix, name),
+  type(Name, name),
+  devdoc('
     Name is the name of a reaction prefixed by Prefix.
-    '),
-    Item=(Name--_),
-    item([kind:reaction, id: _Id, item:Item]),
-    atom_concat(Prefix,_,Name).
+  '),
+  Item=(Name--_),
+  item([kind:reaction, id: _Id, item:Item]),
+  atom_concat(Prefix,_,Name).
 
 
 merge_reactions(Reaction1, Reaction2):-