conservations handled, doc added, real command

lemon.pl

@@ -15,6 +15,7 @@
 
 % :- use_module(doc).
 :- use_module(counters).
+:- use_module(invariants).
 
 
 %! export_lemon_graph(+OutputFile) is det.
@@ -22,6 +23,12 @@
 % exports the current influence graph to OutputFile (adding '.lgf' extension
 % if needed)
 export_lemon_graph(OutputFile) :-
+  biocham_command,
+  doc('exports the current influence graph to \\argument{OutputFile} in Lemon
+    graph format (\\url{http://lemon.cs.elte.hu/trac/lemon}) (adding ".lgf"
+    extension if needed). Computes the conservation laws of the model in order
+    to do so.'),
+  type(OutputFile, output_file),
   automatic_suffix(OutputFile, '.lgf', write, FilenameLgf),
   setup_call_cleanup(
     open(FilenameLgf, write, Stream),
@@ -34,6 +41,7 @@ export_lemon_graph(OutputFile) :-
 %
 % exports the current influence graph to the given Stream
 export_lemon_stream(Stream) :-
+  with_output_to(atom(_), invariants:find_pinvar),
   setup_call_cleanup(
     new_graph(GraphId),
     (
@@ -53,8 +61,6 @@ export_lemon_stream(Stream) :-
 %! export_lemon_stream(+Id, +Stream) is det.
 %
 % exports the graph associated to Id to the stream Stream
-%
-% @tbd export conservation laws
 export_lemon_stream(Id, Stream) :-
   write(Stream, '@nodes\nlabel\tspecies\n'),
   set_counter(species, 0),
@@ -93,7 +99,18 @@ export_lemon_stream(Id, Stream) :-
     )
   ),
   % TODO conservation laws
-  write(Stream, '@attributes\n').
+  write(Stream, '@attributes\nconserv '),
+  findall(
+    Conserv,
+    (
+      invariants:base_mol(List),
+      atomic_list_concat(List, ',', Conserv)
+    ),
+    ConservList
+  ),
+  atomic_list_concat(ConservList,';', ConservAtom),
+  write(Stream, ConservAtom),
+  write(Stream, ';\n').
 
 
 %! reactions(-Reaction, -Uid) is nondet.

toc.org

@@ -45,6 +45,7 @@
 - influence_editor.pl
 ** Influence graph
 - influence_graphs.pl
+- lemon.pl
 * Events
 - events.pl
 * Importing and Exporting BIOCHAM Models