add notebook ASSB with outputs

Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/biocham/biocham

about.pl

@@ -8,7 +8,7 @@
     about/0
   ]).
 
-version('4.1.6').
+version('4.1.7').
 
 copyright(
   'Copyright (C) 2003-2018 Inria, EPI Lifeware, Saclay-Île de France, France'

ode.pl

@@ -1077,8 +1077,7 @@ ode_add_expression_to_molecule(NewExpression, Molecule) :-
   (
     retract(assoc(Molecule, Expression))
   ->
-    true
+    asserta(assoc(Molecule, Expression + NewExpression))
   ;
-    Expression = 0
-  ),
-  asserta(assoc(Molecule, Expression + NewExpression)).
+    asserta(assoc(Molecule, NewExpression))
+  ).

reaction_editor.pl

@@ -471,11 +471,12 @@ factorize_solution([], []).
 
 factorize_solution([Coefficient * Object | Tail], SimplifiedSolution) :-
   collect_object(Tail, Object, TailCoefficient, Others),
-  simplify(Coefficient + TailCoefficient, SimplifiedCoefficient),
+  % simplify(Coefficient + TailCoefficient, SimplifiedCoefficient),
+  SimplifiedCoefficient is Coefficient + TailCoefficient,
   (
     SimplifiedCoefficient = 0
   ->
-    simplify_solution(Others, SimplifiedCoefficient)
+    simplify_solution(Others, SimplifiedSolution)
   ;
     SimplifiedSolution = [SimplifiedCoefficient * Object | SimplifiedTail],
     simplify_solution(Others, SimplifiedTail)
@@ -598,13 +599,17 @@ make_reaction(
 
 
 compute_ode_for_reactions :-
-  \+ (
-    item([kind: reaction, item: Item]),
-    reaction(Item, Kinetics, Reactants, Inhibitors, Products),
-    \+ (
+  forall(
+    (
+      item([kind: reaction, item: Item]),
+      reaction(Item, Kinetics, Reactants, Inhibitors, Products)
+    ),
+    (
       kinetics(Reactants, Inhibitors, Kinetics, KineticsExpression),
-      add_molecules(Reactants, -KineticsExpression),
-      add_molecules(Products, KineticsExpression)
+      maplist(negate_coefficient, Reactants, NegatedReactants),
+      append(NegatedReactants, Products, StoichiometricSolution),
+      simplify_solution(StoichiometricSolution, SimplifiedSolution),
+      add_molecules(SimplifiedSolution, KineticsExpression)
     )
   ).
 
@@ -620,3 +625,6 @@ add_molecules(Molecules, Kinetics) :-
 
 add_molecule(Coefficient * Molecule, Kinetics) :-
   ode_add_expression_to_molecule(Coefficient * Kinetics, Molecule).
+
+
+negate_coefficient(C*X, (-C)*X).