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Reaction Systems with Concentrations. Context Automaton class.

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This commit is contained in:
Artur Meski
2016-02-14 20:25:07 +01:00
parent 6aaca2ba27
commit 9245546d3d
3 changed files with 88 additions and 41 deletions
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119
rctsys.py
View File

@@ -18,56 +18,56 @@ from sys import exit
class ContextAutomaton(object):
def __init__(self, reaction_system):
self.__states = []
self.__transitions = []
self.__init_state = None
self.__reaction_system = reaction_system
self._states = []
self._transitions = []
self._init_state = None
self._reaction_system = reaction_system
@property
def states(self):
return self.__states
return self._states
@property
def transitions(self):
return self.__transitions
return self._transitions
def add_state(self, name):
if name not in self.__states:
self.__states.append(name)
if name not in self._states:
self._states.append(name)
else:
print("\'%s\' already added. skipping..." % (name,))
def add_init_state(self, name):
self.add_state(name)
self.__init_state = self.__states.index(name)
self._init_state = self._states.index(name)
def get_init_state_name(self):
if self.__init_state == None:
if self._init_state == None:
return None
return self.__states[self.__init_state]
return self._states[self._init_state]
def is_state(self, name):
if name in self.__states:
if name in self._states:
return True
else:
return False
def get_state_id(self, name):
try:
return self.__states.index(name)
return self._states.index(name)
except ValueError:
print("Undefined context automaton state: " + repr(name))
exit(1)
def get_init_state_id(self):
return self.__init_state
return self._init_state
def print_states(self):
for state in self.__states:
for state in self._states:
print(state)
def is_valid_context(self, context):
if set(context).issubset(self.__reaction_system.background_set):
if set(context).issubset(self._reaction_system.background_set):
return True
else:
return False
@@ -84,12 +84,12 @@ class ContextAutomaton(object):
if not self.is_state(dst):
raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
new_context_set = set()
for e in set(context_set):
new_context_set.add(self.__reaction_system.get_entity_id(e))
self.__transitions.append((self.get_state_id(src),new_context_set,self.get_state_id(dst)))
new_context_set.add(self._reaction_system.get_entity_id(e))
self._transitions.append((self.get_state_id(src),new_context_set,self.get_state_id(dst)))
def context2str(self, ctx):
"""Converts the set of entities ids into the string with their names"""
@@ -97,13 +97,13 @@ class ContextAutomaton(object):
return "0"
s = "{"
for c in ctx:
s += " " + self.__reaction_system.get_entity_name(c)
s += " " + self._reaction_system.get_entity_name(c)
s += " }"
return s
def show_transitions(self):
print("[*] Context automaton transitions:")
for transition in self.__transitions:
for transition in self._transitions:
str_transition = str(transition[0]) + " --( "
str_transition += self.context2str(transition[1])
str_transition += " )--> " + str(transition[2])
@@ -112,7 +112,7 @@ class ContextAutomaton(object):
def show_states(self):
init_state_name = self.get_init_state_name()
print("[*] Context automaton states:")
for state in self.__states:
for state in self._states:
print("\t- " + state, end="")
if state == init_state_name:
print(" [init]")
@@ -124,6 +124,48 @@ class ContextAutomaton(object):
self.show_transitions()
class ContextAutomatonWithConcentrations(ContextAutomaton):
def __init__(self, reaction_system):
self._states = []
self._transitions = []
self._init_state = None
self._reaction_system = reaction_system
def is_valid_context(self, context):
if set([e for e,lvl in context]).issubset(self._reaction_system.background_set):
return True
else:
return False
def context2str(self, ctx):
if len(ctx) == 0:
return "0"
s = "{"
for ent,lvl in ctx:
s += " " + str((self._reaction_system.get_entity_name(ent),lvl))
s += " }"
return s
def add_transition(self, src, context_set, dst):
if not type(context_set) is set and not type(context_set) is list:
print("Contexts set must be of type set or list")
if not self.is_valid_context(context_set):
raise RuntimeError("one of the entities in the context set is unknown (undefined)!")
if not self.is_state(src):
raise RuntimeError("\"" + src + "\" is an unknown (undefined) state")
if not self.is_state(dst):
raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
new_context_set = set()
for ent,lvl in set(context_set):
new_context_set.add((self._reaction_system.get_entity_id(ent),lvl))
self._transitions.append((self.get_state_id(src),new_context_set,self.get_state_id(dst)))
class ReactionSystem(object):
def __init__(self):
@@ -309,19 +351,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
self.reactions_by_prod = None
def get_entity_id(self, name):
try:
return self.background_set.index(name)
except ValueError:
print("Undefined background set entity: " + repr(name))
exit(1)
def get_state_ids(self, state):
ids = []
for entity in state:
ids.append(self.get_entity_id(entity))
return ids
def is_valid_entity_with_concentration(self, e):
"""Sanity check for entities with concentration"""
@@ -383,10 +412,10 @@ class ReactionSystemWithConcentrations(ReactionSystem):
s = s[:-2]
return s
def states_to_str(self, state):
def state_to_str(self, state):
s = ""
for entity,level in state:
s += str((self.get_entity_name(entity),level)) + ", "
for ent,level in state:
s += str((self.get_entity_name(ent),level)) + ", "
s = s[:-2]
return s
@@ -432,3 +461,15 @@ class ReactionSystemWithAutomaton(object):
self.rs.show(soft)
self.ca.show()
#
# 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()

1
rs_examples.py
View File

@@ -261,4 +261,3 @@ def drs_mutex_property1(k):
state.extend([[] for i in range(k)])
return state

9
rssmt.py
View File

@@ -6,7 +6,7 @@
"""
from rctsys import ReactionSystem,ReactionSystemWithConcentrations
from rctsys import ReactionSystem,ReactionSystemWithConcentrations,ContextAutomatonWithConcentrations
from smtchecker import SmtChecker
from smtcheckerpgrs import SmtCheckerPGRS
from smtcheckerdistribrs import SmtCheckerDistribRS
@@ -69,6 +69,13 @@ def main():
r.add_reaction([("a",1)],[("b",2)],[("c",1)])
r.show()
c = ContextAutomatonWithConcentrations(r)
c.add_init_state("1")
c.add_transition("1", [("c",1)], "1")
c.add_transition("1", [("d",2)], "1")
c.show()
if __name__ == "__main__":
try: