introducing parameters

rs/__init__.py

@@ -2,7 +2,7 @@ from rs.reaction_system import ReactionSystem
 from rs.context_automaton import ContextAutomaton
 
 from rs.reaction_system_with_concentrations import ReactionSystemWithConcentrations
-from rs.reaction_system_with_concentrations_param import ReactionSystemWithConcentrationsParam
+from rs.reaction_system_with_concentrations_param import ReactionSystemWithConcentrationsParam, ParameterObj
 from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
 
 from rs.extended_context_automaton import ExtendedContextAutomaton

rs/reaction_system_with_concentrations_param.py

@@ -3,17 +3,21 @@ from colour import *
 
 from rs.reaction_system import ReactionSystem
 
-class ParameterSet(object):
+class ParameterObj(object):
 
     def __init__(self, name):
         self.name = name
         
+    def __repr__(self):
+        return "@{0}".format(self.name)
+
 
 class ReactionSystemWithConcentrationsParam(ReactionSystem):
 
     def __init__(self):
 
         self.reactions = []
+        self.parametric_reactions = []
         self.meta_reactions = dict()
         self.permanent_entities = dict()
         self.background_set = []
@@ -85,7 +89,13 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
         if R == [] and not ignore_empty_R:
             raise RuntimeError("No reactants defined")
 
+        #
+        # REACTANTS
+        #
         reactants = []
+        if isinstance(R, ParameterObj):
+            reactants = R
+        else:
             for r in R:
                 self.is_valid_entity_with_concentration(r)
                 self.has_non_zero_concentration(r)
@@ -93,7 +103,14 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
                 reactants.append((self.get_entity_id(entity), level))
                 if self.max_concentration < level:
                     self.max_concentration = level
+        
+        #
+        # INHIBITORS
+        #
         inhibitors = []
+        if isinstance(I, ParameterObj):
+            inhibitors = I
+        else:
             for i in I:
                 self.is_valid_entity_with_concentration(i)
                 self.has_non_zero_concentration(i)
@@ -101,7 +118,14 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
                 inhibitors.append((self.get_entity_id(entity), level))
                 if self.max_concentration < level:
                     self.max_concentration = level
+        
+        #
+        # PRODUCTS
+        #
         products = []
+        if isinstance(P, ParameterObj):
+            products = P
+        else:
             for p in P:
                 self.is_valid_entity_with_concentration(p)
                 self.has_non_zero_concentration(p)
@@ -110,6 +134,10 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
 
         return reactants, inhibitors, products
 
+    def is_parametric_reaction(self, reaction):
+        result = any([isinstance(r_set, ParameterObj) for r_set in reaction])
+        return result
+
     def add_reaction(self, R, I, P):
         """Adds a reaction
         
@@ -119,6 +147,10 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
         if P == []:
             raise RuntimeError("No products defined")
         reaction = self.process_rip(R,I,P)
+        
+        if self.is_parametric_reaction(reaction):
+            self.parametric_reactions.append(reaction)
+        else:
             self.reactions.append(reaction)
 
     def add_reaction_without_reactants(self, R, I, P):
@@ -174,6 +206,14 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
         return s
 
     def state_to_str(self, state):
+        """
+        If state is a parameter, we return
+        the string representation of the whole state
+        which should be the name of the parameter
+        """
+        if isinstance(state, ParameterObj):
+            return str(state)
+        else:
             s = ""
             for ent,level in state:
                 s += self.get_entity_name(ent) + "=" + str(level) + ", "

rs_testing.py

@@ -27,7 +27,7 @@ def trivial_param():
 
     r.add_reaction([("x", 1)], [("c", 1)], [("y", 2)])
     r.add_reaction([("y", 1)], [("c", 1)], [("z", 1)])
-    r.add_reaction([("z", 1)], [("c", 1)], [("final", 1)])
+    r.add_reaction(ParameterObj("P1"), [("c", 1)], [("final", 1)])
 
     c = ContextAutomatonWithConcentrations(r)
     c.add_init_state("0")
@@ -43,7 +43,7 @@ def trivial_param():
         BagDescription.f_TRUE(),
         BagDescription.f_entity("final") >= 1)
 
-    smt_rsc.check_rsltl(formula=f2)
+    smt_rsc.check_rsltl(formula=f2, max_level=5)
 
 
 def example44_param():

smt/smt_checker_rsc_param.py

@@ -14,7 +14,7 @@ from logics import rsLTL_Encoder
 # def simplify(x):
 #     return x
 
-def MAX(a, b):
+def z3_max(a, b):
     return If(a > b, a, b)
 
 class SmtCheckerRSCParam(object):
@@ -31,7 +31,6 @@ class SmtCheckerRSCParam(object):
 
         self.initialise()
     
-    
     def initialise(self):
         """Initialises all the variables used by the checker"""
         
@@ -41,7 +40,6 @@ class SmtCheckerRSCParam(object):
         
         # intermediate products:
         self.v_improd = []
-
         self.v_improd_for_entities = []
 
         self.next_level_to_encode = 0
@@ -55,13 +53,11 @@ class SmtCheckerRSCParam(object):
         
         self.verification_time = None        
 
-
     def reset(self):
         """Reinitialises the state of the checker"""
         
         self.initialise()       
         
-        
     def prepare_all_variables(self):
         """Prepares all the variables"""
 
@@ -70,7 +66,6 @@ class SmtCheckerRSCParam(object):
         self.prepare_intermediate_product_variables()
         self.next_level_to_encode += 1 
         
-        
     def prepare_context_variables(self):
         """Prepares all the context variables"""
 
@@ -82,7 +77,6 @@ class SmtCheckerRSCParam(object):
 
         self.v_ctx.append(variables)
 
-
     def prepare_state_variables(self):
         """Prepares all the state variables"""
 
@@ -95,7 +89,6 @@ class SmtCheckerRSCParam(object):
         
         self.ca_state.append(Int("CA"+str(level)+"_state"))
 
-
     def prepare_intermediate_product_variables(self):
         """
         Prepares the intermediate product variables
@@ -261,17 +254,16 @@ class SmtCheckerRSCParam(object):
         enc = None
 
         if len(elements) == 1:
-            enc = MAX(0, elements[0])
+            enc = z3_max(0, elements[0])
 
         elif len(elements) > 1:
 
             enc = 0
             for i in range(len(elements) - 1):
-                enc = MAX(enc, MAX(elements[i], elements[i + 1]))
+                enc = z3_max(enc, z3_max(elements[i], elements[i + 1]))
 
         return enc
     
-    
     def enc_automaton_trans(self, level):
         """Encodes the transition relation for the context automaton"""