Completed ode interface

ode.pl

@@ -18,13 +18,20 @@
     load_ode_system/1,
     add_ode_system/1,
     export_ode_system/1,
+    new_ode_system/1,
     get_current_ode_system/1,
+    set_current_ode_system/1,
+    set_ode_system_name/2,
+    import_ode/2,
+    set_ode_initial_value/2,
+    set_ode_initial_value/3,
+    add_ode/2,
+    import_reactions_from_ode_system/1,
     with_current_ode_system/1,
     all_odes/1,
     ode/2,
-%    export_ode/1,
-    load_ode/1,
-    add_ode/1
+    ode/3,
+    op(1000, fx, init)
   ]).
 
 
@@ -34,7 +41,7 @@
 new_ode_system :-
   biocham_command,
   doc('creates an ODE system.'),
-  add_item([kind: ode_system, key: new_ode_system, id: Id]),
+  new_ode_system(Id),
   set_current_ode_system(Id).
 
 
@@ -50,7 +57,7 @@ set_ode_system_name(Name) :-
   type(Name, name),
   doc('sets the name of the current ODE system.'),
   get_current_ode_system(Id),
-  replace_item(Id, ode_system, Name, Name).
+  set_ode_system_name(Id, Name).
 
 
 list_ode_systems :-
@@ -82,20 +89,8 @@ ode(DX/dt = E) :-
 add_ode(ODE) :-
   ode(ODE),
   !,
-  (
-    ODE = (d(X)/dt = _)
-  ->
-    Item = ODE
-  ;
-    ODE = (DX/dt = E),
-    atom_concat(d, X, DX)
-  ->
-    Item = (d(X)/dt = E)
-  ;
-    throw(error(illformed_ode(ODE)))
-  ),
   get_current_ode_system(Id),
-  add_item([parent: Id, kind: ode, key: X, item: Item]).
+  add_ode(Id, ODE).
 
 
 add_ode(ODEList) :-
@@ -113,22 +108,8 @@ add_ode(ODEList) :-
 import_reactions_from_ode_system :-
   biocham_command,
   doc('adds the reactions that match the current ODE system.'),
-  \+ (
-    ode(X, E),
-    monomial(Monomial, E),
-    \+ (
-      (
-        Monomial = - OppositeMonomial,
-        coefficient_species(OppositeMonomial, Coefficient, Species)
-      ->
-        add_reaction(Coefficient * Species for X => '_')
-      ;
-        coefficient_species(Monomial, Coefficient, Species)
-      ->
-        add_reaction(Coefficient * Species for '_' => X)
-      )
-    )
-  ).
+  get_current_ode_system(Id),
+  import_reactions_from_ode_system(Id).
 
 
 :- grammar(oderef).
@@ -165,8 +146,10 @@ list_ode :-
   doc('
     \\end{example}
   '),
-  get_current_ode_system(Id),
-  list_items([parent: Id, kind: ode]).
+  with_current_ode_system((
+    get_current_ode_system(Id),
+    list_items([parent: Id, kind: ode])
+  )).
 
 
 ode_system :-
@@ -175,7 +158,7 @@ ode_system :-
   delete_ode_system('ode_system'),
   new_ode_system,
   set_ode_system_name('ode_system'),
-  clean_draft_ode,
+  check_draft_ode_cleaned,
   compute_ode,
   simplify_ode,
   put_ode_into_system,
@@ -186,13 +169,9 @@ import_ode(InputFile) :-
   biocham_command,
   type(InputFile, input_file),
   doc('imports a set of ODEs.'),
-  new_ode_system,
-  set_ode_system_name(InputFile),
-  setup_call_cleanup(
-    open(InputFile, read, Stream),
-    read_ode(Stream),
-    close(Stream)
-  ).
+  import_ode(InputFile, Id),
+  set_current_ode_system(Id).
+
 
 init(InitList) :-
   biocham_command,
@@ -242,10 +221,32 @@ export_ode_system(OutputFile) :-
 :- devdoc('\\section{Public API}').
 
 
+new_ode_system(Id) :-
+  add_item([kind: ode_system, key: new_ode_system, id: Id]).
+
+
 get_current_ode_system(Id) :-
   get_selection(current_model, current_ode_system, [Id]).
 
 
+set_current_ode_system(Id) :-
+  set_selection(current_model, current_ode_system, [Id]).
+
+
+set_ode_system_name(Id, Name) :-
+  replace_item(Id, ode_system, Name, Name).
+
+
+import_ode(InputFile, Id) :-
+  new_ode_system(Id),
+  set_ode_system_name(Id, InputFile),
+  setup_call_cleanup(
+    open(InputFile, read, Stream),
+    read_ode(Stream, Id),
+    close(Stream)
+  ).
+
+
 all_odes(ODEs) :-
   get_current_ode_system(Id),
   all_items([parent: Id, kind: ode], ODEs).
@@ -253,6 +254,10 @@ all_odes(ODEs) :-
 
 ode(X, E) :-
   get_current_ode_system(Id),
+  ode(Id, X, E).
+
+
+ode(Id, X, E) :-
   (
     var(X)
   ->
@@ -262,16 +267,65 @@ ode(X, E) :-
   ).
 
 
-:- devdoc('\\section{Private predicates}').
+set_ode_initial_value(Variable, Value) :-
+  get_current_ode_system(Id),
+  set_ode_initial_value(Id, Variable, Value).
 
 
-set_current_ode_system(Id) :-
-  set_selection(current_model, current_ode_system, [Id]).
+set_ode_initial_value(Id, Variable, Value) :-
+  change_item([parent: Id], initial_concentration, Variable, init Variable = Value).
+
+
+add_ode(Id, ODE) :-
+  (
+    ODE = (d(X)/dt = _)
+  ->
+    Item = ODE
+  ;
+    ODE = (DX/dt = E),
+    atom_concat(d, X, DX)
+  ->
+    Item = (d(X)/dt = E)
+  ;
+    throw(error(illformed_ode(ODE)))
+  ),
+  add_item([parent: Id, kind: ode, key: X, item: Item]).
+
+
+import_reactions_from_ode_system(Id) :-
+  \+ (
+    ode(Id, X, E),
+    monomial(Monomial, E),
+    \+ (
+      (
+        Monomial = - OppositeMonomial,
+        coefficient_species(OppositeMonomial, Coefficient, Species)
+      ->
+        add_reaction(Coefficient * Species for X => '_')
+      ;
+        coefficient_species(Monomial, Coefficient, Species)
+      ->
+        add_reaction(Coefficient * Species for '_' => X)
+      )
+    )
+  ).
+
+:- devdoc('\\section{Private predicates}').
 
 
 :- dynamic(draft_ode/2).
 
 
+check_draft_ode_cleaned :-
+  (
+    draft_ode(_, _)
+  ->
+    throw(error(check_draft_ode_cleaned))
+  ;
+    true
+  ).
+
+
 clean_draft_ode :-
   retractall(draft_ode(_, _)).
 
@@ -328,27 +382,13 @@ put_ode_into_system :-
     )
   ).
 
-%export_ode(OutputFile) :-
-%  biocham_command,
-%  type(OutputFile, output_file),
-%  doc('
-%    exports the current Biocham model (reaction rules, initial state, parameters and
-%    macros) in an xppaut .ode file.
-%  '),
-%  automatic_suffix(OutputFile, '.ode', write, FilenameODE),
-%  setup_call_cleanup(
-%    open(FilenameODE, write, Stream),
-%    export_ode_stream(Stream),
-%    close(Stream)
-%  ).
-
 
 delete_single_ode(Name) :-
   get_current_ode_system(Id),
   delete_item([parent: Id, kind: ode, key: Name]).
 
 
-read_ode(Stream) :-
+read_ode(Stream, Id) :-
   repeat,
   read_line_to_codes(Stream, Codes),
   (
@@ -369,11 +409,11 @@ read_ode(Stream) :-
       (
         Expression = (init X = E)
       ->
-        set_ode_initial_value(X, E)
+        set_ode_initial_value(Id, X, E)
       ;
         Expression = (_DX/dt = _E)
       ->
-        add_ode(Expression)
+        add_ode(Id, Expression)
       )
     ->
       fail
@@ -427,11 +467,6 @@ 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).
 
 
@@ -474,52 +509,3 @@ with_current_ode_system(Goal) :-
       )
     )
   ).
-
-%
-%
-%print_ode :-
-%  write('Init \tODE\n'),
-%  \+ (
-%    ode(Molecule, Equation),
-%    get_initial_concentration(Molecule, InitialConcentration),
-%    \+ (
-%      format('~f \td[~w]/dt=~w\n', [InitialConcentration, Molecule, Equation])
-%    )
-%  ).
-%
-%
-%load_ode(InputFile) :-
-%  biocham_command,
-%  type(InputFile, input_file),
-%  doc('
-%    creates a new Biocham model (reaction rules, initial state, parameters and
-%    macros) inferred from an xppaut .ode file (preferably written with
-%    parameters).
-%  '),
-%  external_convert_ode(InputFile, 'external_ode.bc'),
-%  load_biocham('external_ode.bc').
-%
-%
-%add_ode(InputFile) :-
-%  biocham_command,
-%  type(InputFile, input_file),
-%  doc('
-%    adds reaction rules, initial state, parameters and
-%    macros inferred from an xppaut .ode file (preferably written with
-%    parameters).
-%  '),
-%  external_convert_ode(InputFile, 'external_ode.bc'),
-%  add_biocham('external_ode.bc').
-%
-%
-%external_convert_ode(InputFile, OutputFile) :-
-%  setup_call_cleanup(
-%    open('external_load_ode.bc', write, Ode_bc),
-%    (
-%      portray_clause(Ode_bc, load_ode(InputFile)),
-%      portray_clause(Ode_bc, export_biocham(OutputFile)),
-%      portray_clause(Ode_bc, 'quit')
-%    ),
-%    close(Ode_bc)
-%  ),
-%  call_subprocess(path(biocham), ['external_load_ode.bc'], [stdout(pipe(_))]).

odefunction.pl

@@ -21,33 +21,31 @@ add_function(FunctionList) :-
   biocham(present(y,3)),
   biocham(add_function(z=x+y)),
   biocham(list_reactions),
-  biocham(list_ODE),
+  biocham(list_ode),
   doc('
     \\end{example}
   '),
-  setup_call_cleanup(
-	  open('external_ode_function.ode', write, Stream),
-	  export_ode(FunctionList,Stream),
-	  close(Stream)
-      ),
-  add_ode('external_ode_function.ode').
+  new_ode_system(OdeSystem),
+  export_ode(FunctionList, OdeSystem),
+  import_reactions_from_ode_system(OdeSystem),
+  delete_item(OdeSystem).
 
 
-export_ode(_,Stream):-
+export_ode(_, OdeSystem) :-
     enumerate_molecules(L), % useless if item backtracks on Object (not clear to FF)
-    member(Object,L),
+    member(Object, L),
     get_initial_concentration(Object, Concentration),
-    format(Stream, 'init ~a = ~d\n', [Object,Concentration]),
+    set_ode_initial_value(OdeSystem, Object, Concentration),
     fail.
-export_ode(FunctionList,Stream):-
+
+export_ode(FunctionList, OdeSystem) :-
     member(Variable = _, FunctionList),
-    format(Stream, 'init ~a = 0\n', [Variable]),
+    set_ode_initial_value(OdeSystem, Variable, 0),
     fail.
-export_ode(FunctionList,Stream):-
+
+export_ode(FunctionList, OdeSystem) :-
     member(Variable = Value, FunctionList),
-    format(Stream, 'd~a/dt = ~w - ~a\n', [Variable,Value,Variable]),
+    add_ode(OdeSystem, d(Variable)/dt = Value - Variable),
     fail.
-export_ode(_,_).
-
-
 
+export_ode(_,_).

odefunction.plt

@@ -11,4 +11,4 @@ test('add_function'):-
   command(k*[x] for x=>y),
   command(add_function(z=x+y, u=x*y)).
 
-:- end_tests(ode).
+:- end_tests(odefunction).