Start correction by removing null kinetics

model_correction.pl

+/*
+Implement the automatic correction of models loaded from a sbml file
+Coder: M. Hemery
+*/
+
+:- module(
+  correction,
+  [
+  % Commands
+  correct_model/0
+  % API
+  ]
+).
+
+% Only for separate compilation/linting
+:- use_module(arithmetic_rules).
+:- use_module(doc).
+:- use_module(formal_derivation).
+:- use_module(reaction_rules).
+:- use_module(util).
+
+correct_model :-
+  biocham_command,
+  doc(''),
+  single_model(ModelId),
+  findall(
+    Molecule,
+    identifier_kind(ModelId, Molecule, object),
+    List_Molecule
+  ),
+  reactions_with_species(List_Molecule, List_Reaction),
+  forall(
+    member(Reaction, List_Reaction),
+    remove_null_kinetic(Reaction)
+  ).
+
+%! remove_null_kinetic(+Reaction)
+%
+% Detect and remove reactions with identically null kinetics
+
+remove_null_kinetic(Expression for Reaction) :-
+  (
+    is_null(Expression)
+  ->
+    delete_reaction(Expression for Reaction)
+  ;
+    true
+  ).

toc.org

@@ -52,6 +52,7 @@
 * Importing and Exporting BIOCHAM Models
 ** Biocham files
 - models.pl
+- model_correction.pl
 ** SBML and SBML-qual files
 - sbml_files.pl
 - qual_files.pl