export_ode_system

models.pl

@@ -20,6 +20,7 @@
     single_model/1,
     add_item/1,
     replace_item/4,
+    change_item/4,
     set_annotation/3,
     get_annotation/3,
     delete_annotation/2,
@@ -787,6 +788,17 @@ replace_item(Id, Kind, Key, Item) :-
   put_item(Parent, Kind, Key, Item, Id).
 
 
+change_item(Options, Kind, Key, Item) :-
+  catch(
+    (
+      find_item([kind: Kind, key: Key, id: Id | Options]),
+      replace_item(Id, Kind, Key, Item)
+    ),
+    error(unknown_item),
+    add_item([kind: Kind, key: Key, item: Item | Options])
+  ).
+
+
 create_item_id(Id) :-
   count(item_id, Id).
 

numerical_simulation.pl

@@ -28,9 +28,10 @@ numerical_simulation(Time) :-
   biocham_command,
   type(Time, time),
   doc('performs a numerical simulation up to a given time.'),
-  ode_system,
-  make_ode_system,
-  solve(Time).
+  with_current_ode_system((
+    numerical_simulation:make_ode_system,
+    numerical_simulation:solve(Time)
+  )).
 
 
 make_ode_system :-

ode.pl

@@ -14,7 +14,12 @@
     ode_system/0,
     import_ode/1,
     import_reactions_from_ode_system/0,
+    (init)/1,
+    load_ode_system/1,
+    add_ode_system/1,
+    export_ode_system/1,
     get_current_ode_system/1,
+    with_current_ode_system/1,
     all_odes/1,
     ode/2,
     op(1000, fx, init)
@@ -185,6 +190,50 @@ import_ode(InputFile) :-
     close(Stream)
   ).
 
+init(InitList) :-
+  biocham_command,
+  type(InitList, '*'(name = arithmetic_expression)),
+  doc('sets the initial value of a variable in the current set of ODEs.'),
+  \+ (
+    member(Variable = Value, InitList),
+    \+ (
+      set_ode_initial_value(Variable, Value)
+    )
+  ).
+
+
+load_ode_system(InputFile) :-
+  biocham_command,
+  type(InputFile, input_file),
+  doc('
+    acts as \\command{load_biocham/1} but importing a model from an ODE system.
+  '),
+  load_all('ode', InputFile).
+
+
+add_ode_system(InputFile) :-
+  biocham_command,
+  type(InputFile, input_file),
+  doc('
+    acts as \\command{add_biocham/1} but importing a model from an ODE system.
+  '),
+  load_all('ode', InputFile).
+
+
+export_ode_system(OutputFile) :-
+  biocham_command,
+  type(OutputFile, output_file),
+  doc('exports the current ODE system.'),
+  with_current_ode_system((
+    setup_call_cleanup(
+      open(OutputFile, write, Stream),
+      with_output_to(
+        Stream,
+        print_ode_system
+      ),
+      close(Stream)
+    )
+  )).
 
 :- devdoc('\\section{Public API}').
 
@@ -269,7 +318,9 @@ put_ode_into_system :-
   \+ (
     draft_ode(X, Expression),
     \+ (
-      add_ode(d(X)/dt = Expression)
+      add_ode(d(X)/dt = Expression),
+      get_initial_concentration(X, Concentration),
+      set_ode_initial_value(X, Concentration)
     )
   ).
 
@@ -280,7 +331,6 @@ delete_single_ode(Name) :-
 
 
 read_ode(Stream) :-
-  get_current_ode_system(Id),
   repeat,
   read_line_to_codes(Stream, Codes),
   (
@@ -299,9 +349,9 @@ read_ode(Stream) :-
       !
     ;
       (
-        Expression = (init X = _E)
+        Expression = (init X = E)
       ->
-        add_item([parent: Id, kind: initial_concentration, key: X, item: Expression])
+        set_ode_initial_value(X, E)
       ;
         Expression = (_DX/dt = _E)
       ->
@@ -358,6 +408,55 @@ coefficient_species(Coefficient * Species, Coefficient, Species) :-
 
 coefficient_species(Species, 1, Species).
 
+
+set_ode_initial_value(Variable, Value) :-
+  get_current_ode_system(Id),
+  change_item([parent: Id], initial_concentration, Variable, init Variable = Value).
+
+
+models:add_file_suffix('ode', add_ode_system_file).
+
+
+add_ode_system_file(InputFile) :-
+  import_ode(InputFile),
+  import_reactions_from_ode_system,
+  get_current_ode_system(Id),
+  delete_item(Id).
+
+
+print_ode_system :-
+  get_current_ode_system(Id),
+  \+ (
+    item([parent: Id, kind: initial_concentration, item: (init X = E)]),
+    \+ (
+      format('init ~p = ~p\n', [X, E])
+    )
+  ),
+  \+ (
+    item([parent: Id, kind: ode, item: (d(X)/dt = E)]),
+    \+ (
+      format('d~p/dt = ~p\n', [X, E])
+    )
+  ),
+  format('done\n').
+
+
+with_current_ode_system(Goal) :-
+  (
+    get_current_ode_system(_)
+  ->
+    Goal
+  ;
+    setup_call_cleanup(
+      ode_system,
+      Goal,
+      (
+        get_current_ode_system(Id),
+        delete_item(Id)
+      )
+    )
+  ).
+
 %
 %
 %print_ode :-

ode.plt

@@ -40,4 +40,11 @@ test(
   all_items([kind: reaction], Reactions).
 
 
+test('export_ode_system', [true(Lines == ['init b = 0', 'init a = 1', 'db/dt = a', 'da/dt = -a', 'done'])]) :-
+  clear_model,
+  command(a => b),
+  command(present(a)),
+  export_ode_system('test.ode'),
+  list_file_lines('test.ode', Lines).
+
 :- end_tests(ode).

parameters.pl

@@ -12,21 +12,12 @@
 
 set_parameter(ParameterList) :-
   biocham_command(*),
-  type(ParameterList, '*'(parameter = number)),
+  type(ParameterList, '*'(parameter = arithmetic_expression)),
   doc('sets the value of parameters.'),
   \+ (
     member(Parameter = Value, ParameterList),
     \+ (
-      catch(
-        (
-          find_item([kind: parameter, key: Parameter, id: Id]),
-          replace_item(Id, parameter, Parameter, parameter(Parameter = Value))
-        ),
-        error(unknown_item),
-        add_item([
-          kind: parameter, key: Parameter, item: parameter(Parameter = Value)
-        ])
-      )
+      change_item([], parameter, Parameter, parameter(Parameter = Value))
     )
   ).
 

util.pl

@@ -14,7 +14,10 @@
     indent/2,
     view_image/1,
     set_image_viewer_driver/1,
-    open_file/1,
+    list_file_lines/2,
+    list_stream_lines/2,
+    file_line_by_line/2,
+    stream_line_by_line/2,
     term_morphism/3,
     substitute/4,
     call_subprocess/3
@@ -159,6 +162,43 @@ set_image_viewer_driver(Driver) :-
   nb_setval(image_viewer_driver, Driver).
 
 
+list_file_lines(Filename, List) :-
+  findall(
+    Line,
+    file_line_by_line(Filename, Line),
+    List
+  ).
+
+
+list_stream_lines(Stream, List) :-
+  findall(
+    Line,
+    stream_line_by_line(Stream, Line),
+    List
+  ).
+
+
+file_line_by_line(Filename, Line) :-
+  setup_call_cleanup(
+    open(Filename, read, Stream),
+    stream_line_by_line(Stream, Line),
+    close(Stream)
+  ).
+
+
+stream_line_by_line(Stream, Line) :-
+  repeat,
+  read_line_to_codes(Stream, Codes),
+  (
+    Codes = end_of_file
+  ->
+    !,
+    fail
+  ;
+    atom_codes(Line, Codes)
+  ).
+
+
 term_morphism(F, TermIn, TermOut) :-
   functor(TermIn, Functor, Arity),
   functor(TermOut, Functor, Arity),