bugcorrection

multistability.pl

@@ -968,9 +968,9 @@ doc('\\end{example}
         true
       ;
         (
-          write('Permutation used: '),
+          write('(using permutation of species: '),
           write(Swaps),
-          write('\n')
+          write(')\n')
         )
       ),
       loop_gauss_system(System),
@@ -982,7 +982,7 @@ doc('\\end{example}
       ;
         (
           conserv_names_to_id(Species_to_change_sign, Species_to_change_sign_id),
-          write('With change of sign for species : '),
+          write('(using change of sign for species : '),
           forall(
             member(S, Species_to_change_sign),
             (
@@ -991,7 +991,7 @@ doc('\\end{example}
             )
           ),
           debug(multistability, "~nDone in ~ws", [Diff_time]),
-          write('\n')
+          write(')\n')
         )
       )
     )
@@ -1005,7 +1005,7 @@ doc('\\end{example}
       ;
         true
       ),
-      write('There may be multistationarity, positive circuit detected'),
+      write('There may be multistationarity, positive circuit detected.'),
       debug(multistability, "~nDone in ~ws", [Diff_time]),
       write('\n')
     )

numerical_simulation.pl

@@ -290,7 +290,8 @@ enumerate_variables(Header: x(VariableIndex)) :-
   VariableMax is VariableCount - 1,
   between(0, VariableMax, VariableIndex),
   variable(Molecule, VariableIndex),
-  format(atom(Header), '~a', [Molecule]).
+%  format(atom(Header), '~a', [Molecule]).
+  format(atom(Header), '~w', [Molecule]).
 
 
 enumerate_nonconstant_parameters(Events, Header: Parameter) :-

toc.org

@@ -18,14 +18,13 @@
 - objects.pl
 ** Aliases
 - aliases.pl
-** Molecules
+** Molecules and initial state
 - molecules.pl
+- initial_state.pl
 ** Parameters
 - parameters.pl
 ** Functions
 - functions.pl
-** Initial state
-- initial_state.pl
 * Reaction Networks
 #** Syntax of reactions and transport rules
 - reaction_rules.pl

tropical.pl

@@ -361,7 +361,7 @@ epsilon_degree(D, A) :-
   (
     D =\= 0
   ->
-    format(atom(A), "ε^~p * ", [D])
+    format(atom(A), "ε^(~p) * ", [D])
   ;
     A = ''
   ).