Cleaning up rs/

rs/__init__.py

@@ -10,3 +10,5 @@ from rs.extended_context_automaton import ExtendedContextAutomaton
 from rs.network_of_context_automata import NetworkOfContextAutomata
 from rs.reaction_system_with_automaton import ReactionSystemWithAutomaton
 from rs.reaction_system_with_autnet import ReactionSystemWithNetworkOfAutomata
+
+# EOF

rs/context_automaton.py

@@ -162,3 +162,4 @@ class ContextAutomaton(object):
         self.show_transitions()
         self.show_prod_entities()
 
+# EOF

rs/context_automaton_with_concentrations.py

@@ -67,3 +67,4 @@ class ContextAutomatonWithConcentrations(ContextAutomaton):
         self.show_states()
         self.show_transitions()
 
+# EOF

rs/extended_context_automaton.py

@@ -165,3 +165,4 @@ class ExtendedContextAutomaton(ContextAutomaton):
         super(ExtendedContextAutomaton, self).show()
         self.show_actions()
 
+# EOF 

rs/network_of_context_automata.py

@@ -102,3 +102,4 @@ class NetworkOfContextAutomata(object):
         self.show_prod_entities()
         self.show_actions()
 
+# EOF 

rs/reaction_system.py

@@ -192,3 +192,5 @@ class ReactionSystem(object):
         if self.background_set == []:
             print("Empty background set")
             exit(1)
+
+# EOF

rs/reaction_system_with_autnet.py

@@ -9,3 +9,4 @@ class ReactionSystemWithNetworkOfAutomata(object):
         self.rs.show(soft)
         self.cas.show()
 
+# EOF

rs/reaction_system_with_concentrations.py

@@ -402,12 +402,5 @@ class ReactionSystemWithAutomaton(object):
         return ReactionSystemWithAutomaton(ors, oca)
         
 
-# class ReactionSystemWithConcentrationWithAutomaton(ReactionSystemWithAutomaton):
+# EOF
-#
+
-#     def __init__(self, reaction_system, context_automaton):
-#         self.rs = reaction_system
-#         self.ca = context_automaton
-#
-#     def show(self, soft=False):
-#         self.rs.show(soft)
-#         self.ca.show()

rs/reaction_system_with_concentrations_param.py

@@ -97,7 +97,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
 
     def get_state_ids(self, state):
         """Returns entities of the given state without levels"""
-        # return [e for e,c in state]
         return [self.get_entity_id(e) for e in state]
 
     def has_non_zero_concentration(self, elem):
@@ -425,59 +424,4 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
 
         return rs
 
-
+# EOF
-# class ReactionSystemWithAutomaton(object):
-#
-#     def __init__(self, reaction_system, context_automaton):
-#         self.rs = reaction_system
-#         self.ca = context_automaton
-#
-#     def show(self, soft=False):
-#         self.rs.show(soft)
-#         self.ca.show()
-#
-#     def is_concentr_and_param_compatible(self):
-#         """
-#         Checks if the underlying RS/CA are compatible
-#         with parameters and concentrations
-#         """
-#         if not isinstance(self.rs, ReactionSystemWithConcentrationsParam):
-#             return False
-#         if not isinstance(self.ca, ContextAutomatonWithConcentrations):
-#             return False
-#         return True
-#
-#     def is_with_concentrations(self):
-#         """
-#         Checks if the underlying RS and CA provide
-#         concentration levels
-#         """
-#         if not isinstance(self.rs, ReactionSystemWithConcentrations):
-#             return False
-#         if not isinstance(self.ca, ContextAutomatonWithConcentrations):
-#             return False
-#         return True
-#
-#     def sanity_check(self):
-#         pass
-#
-#     def get_ordinary_reaction_system_with_automaton(self):
-#
-#         if not self.is_with_concentrations():
-#             raise RuntimeError("Not RS/CA with concentrations")
-#
-#         ors = self.rs.get_reaction_system()
-#         oca = self.ca.get_automaton_with_flat_contexts(ors)
-#
-#         return ReactionSystemWithAutomaton(ors, oca)
-#
-
-# class ReactionSystemWithConcentrationWithAutomaton(ReactionSystemWithAutomaton):
-#
-#     def __init__(self, reaction_system, context_automaton):
-#         self.rs = reaction_system
-#         self.ca = context_automaton
-#
-#     def show(self, soft=False):
-#         self.rs.show(soft)
-#         self.ca.show()