import function definitions from SBML

modules/sbml/sbml.pl

@@ -35,6 +35,10 @@
     parameter_getValue/2,
     rule_getVariable/2,
     rule_getMath/2,
+    function_getName/2,
+    function_getBody/2,
+    function_getNumArguments/2,
+    function_getArgument/3,
     is_assignment/1,
     compartment_getId/2,
     compartment_getVolume/2

modules/sbml/sbml_swiprolog.c

@@ -67,6 +67,11 @@ PL_get_rule(term_t rule_term, Rule_t **rule) {
     return PL_get_pointer(rule_term, (void **) rule);
 }
 
+int
+PL_get_function(term_t function_term, FunctionDefinition_t **function) {
+    return PL_get_pointer(function_term, (void **) function);
+}
+
 int
 PL_unify_sbmlDocument_or_free(term_t document_term, SBMLDocument_t *document) {
     int result = PL_unify_pointer(document_term, document);
@@ -176,6 +181,16 @@ pl_model_getListOfRules(term_t model_term, term_t listOfRules_term) {
     PL_succeed;
 }
 
+static foreign_t
+pl_model_getListOfFunctions(term_t model_term, term_t listOfFunctions_term) {
+    Model_t *model;
+    ListOf_t *listOfFunctions;
+    PL_check(PL_get_model(model_term, &model));
+    PL_check(listOfFunctions = Model_getListOfFunctionDefinitions(model));
+    PL_check(PL_unify_pointer(listOfFunctions_term, listOfFunctions));
+    PL_succeed;
+}
+
 static foreign_t
 pl_model_getSpeciesById(
     term_t model_term, term_t id_term, term_t species_term
@@ -482,6 +497,48 @@ pl_rule_getMath(term_t rule_term, term_t formula_term) {
     PL_succeed;
 }
 
+static foreign_t
+pl_function_getName(term_t function_term, term_t formula_term) {
+    FunctionDefinition_t *function;
+    const char *name;
+    PL_check(PL_get_function(function_term, &function));
+    PL_check(name = FunctionDefinition_getId(function));
+    PL_check(PL_unify_atom_chars(formula_term, name));
+    PL_succeed;
+}
+
+static foreign_t
+pl_function_getBody(term_t function_term, term_t formula_term) {
+    FunctionDefinition_t *function;
+    const char *formula;
+    PL_check(PL_get_function(function_term, &function));
+    PL_check(formula = SBML_formulaToString(FunctionDefinition_getBody(function)));
+    PL_check(PL_unify_atom_chars(formula_term, formula));
+    PL_succeed;
+}
+
+static foreign_t
+pl_function_getNumArguments(term_t function_term, term_t num_term) {
+    FunctionDefinition_t *function;
+    unsigned int n;
+    PL_check(PL_get_function(function_term, &function));
+    PL_check(n = FunctionDefinition_getNumArguments(function));
+    PL_check(PL_unify_integer(num_term, n));
+    PL_succeed;
+}
+
+static foreign_t
+pl_function_getArgument(term_t function_term, term_t num_term, term_t arg_term) {
+    FunctionDefinition_t *function;
+    const char *argument;
+    int num;
+    PL_check(PL_get_function(function_term, &function));
+    PL_check(PL_get_integer(num_term, &num));
+    PL_check(argument = SBML_formulaToString(FunctionDefinition_getArgument(function, num)));
+    PL_check(PL_unify_atom_chars(arg_term, argument));
+    PL_succeed;
+}
+
 static foreign_t
 pl_is_assignment(term_t rule_term) {
     Rule_t *rule;
@@ -521,6 +578,7 @@ PL_extension sbml_predicates[] = {
     { "model_getListOfCompartments", 2, (pl_function_t) pl_model_getListOfCompartments, 0 },
     { "model_getListOfParameters", 2, (pl_function_t) pl_model_getListOfParameters, 0 },
     { "model_getListOfRules", 2, (pl_function_t) pl_model_getListOfRules, 0 },
+    { "model_getListOfFunctions", 2, (pl_function_t) pl_model_getListOfFunctions, 0 },
     { "model_getSpeciesById", 3, (pl_function_t) pl_model_getSpeciesById, 0 },
     { "listOf_get", 3, (pl_function_t) pl_listOf_get, 0 },
     { "listOf_size", 2, (pl_function_t) pl_listOf_size, 0 },
@@ -550,6 +608,10 @@ PL_extension sbml_predicates[] = {
     { "parameter_getValue", 2, (pl_function_t) pl_parameter_getValue, 0 },
     { "rule_getVariable", 2, (pl_function_t) pl_rule_getVariable, 0 },
     { "rule_getMath", 2, (pl_function_t) pl_rule_getMath, 0 },
+    { "function_getName", 2, (pl_function_t) pl_function_getName, 0 },
+    { "function_getBody", 2, (pl_function_t) pl_function_getBody, 0 },
+    { "function_getNumArguments", 2, (pl_function_t) pl_function_getNumArguments, 0 },
+    { "function_getArgument", 3, (pl_function_t) pl_function_getArgument, 0 },
     { "compartment_getId", 2, (pl_function_t) pl_compartment_getId, 0 },
     { "compartment_getVolume", 2, (pl_function_t) pl_compartment_getVolume, 0 },
     { "is_assignment", 1, (pl_function_t) pl_is_assignment, 0 },

modules/sbml/sbml_utils.pl

@@ -5,6 +5,7 @@
     model_reaction/2,
     model_species/2,
     model_assignment_rule/2,
+    model_function/2,
     reaction_reactant/2,
     reaction_modifier/2,
     reaction_product/2,
@@ -14,6 +15,7 @@
     species_has_only_substance_units/1,
     parameter_id_and_value/3,
     rule_var_and_math/3,
+    function_name_args_body/4,
     model_compartment/2,
     model_parameter/2,
     compartment_volume/3,
@@ -55,6 +57,11 @@ model_assignment_rule(Model, Rule) :-
   is_assignment(Rule).
 
 
+model_function(Model, Function) :-
+  model_getListOfFunctions(Model, ListOfFunctions),
+  member_listof(Function, ListOfFunctions).
+
+
 reaction_reactant(Reaction, Reactant) :-
   reaction_getListOfReactants(Reaction, ListOfReactants),
   member_listof(Reactant, ListOfReactants).
@@ -126,6 +133,21 @@ rule_var_and_math(Rule, Variable, Math) :-
   sbml_atom_to_term(MathAtom, Math).
 
 
+function_name_args_body(Function, Name, Args, Body) :-
+  function_getName(Function, Name),
+  function_getBody(Function, BodyAtom),
+  sbml_atom_to_term(BodyAtom, Body),
+  function_getNumArguments(Function, NumArgs),
+  findall(
+    Arg,
+    (
+      between(0, NumArgs, Index),
+      function_getArgument(Function, Index, Arg)
+    ),
+    Args
+  ).
+
+
 sbml_atom_to_term(Atom, Term) :-
   read_term_from_atom(Atom, STerm, [variable_names(Names)]),
   name_variables_and_anonymous(STerm, Names),

sbml_files.pl

@@ -76,6 +76,7 @@ add_sbml_model(Model) :-
   add_compartments(Model),
   add_global_parameters(Model),
   add_assignment_rules(Model),
+  add_function_definitions(Model),
   add_species(Model),
   add_reactions(Model).
 
@@ -167,6 +168,17 @@ add_assignment_rules(Model) :-
   ).
 
 
+add_function_definitions(Model) :-
+  forall(
+    model_function(Model, Function),
+    (
+      function_name_args_body(Function, Name, Args, Body),
+      Func =.. [Name | Args],
+      function([Func = Body])
+    )
+  ).
+
+
 global_local_parameters([], _Rid, Kinetics, Kinetics).
 
 global_local_parameters([Parameter | LocalParameters], Rid, LKinetics, GKinetics) :-