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This commit is contained in:
Artur Meski
2023-07-11 19:48:37 +01:00
parent 8be615b293
commit a1fb5836a5
24 changed files with 965 additions and 727 deletions
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6
reactics-smt/rs/__init__.py
View File

@@ -2,7 +2,11 @@ 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, ParameterObj, is_param
from rs.reaction_system_with_concentrations_param import (
ReactionSystemWithConcentrationsParam,
ParameterObj,
is_param,
)
from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
from rs.extended_context_automaton import ExtendedContextAutomaton

17
reactics-smt/rs/context_automaton.py
View File

@@ -3,7 +3,6 @@ from colour import *
class ContextAutomaton(object):
def __init__(self, reaction_system):
self._states = []
self._transitions = []
@@ -40,7 +39,7 @@ class ContextAutomaton(object):
if name not in self._states:
self._states.append(name)
else:
print("\'%s\' already added. skipping..." % (name,))
print("'%s' already added. skipping..." % (name,))
def add_states(self, states_set):
for st in states_set:
@@ -101,15 +100,14 @@ class ContextAutomaton(object):
if not self.is_valid_context(context_set):
raise RuntimeError(
"one of the entities in the context set is unknown (undefined)!")
"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")
raise RuntimeError('"' + src + '" is an unknown (undefined) state')
if not self.is_state(dst):
raise RuntimeError(
"\"" + dst + "\" is an unknown (undefined) state")
raise RuntimeError('"' + dst + '" is an unknown (undefined) state')
new_context_set = set()
for e in set(context_set):
@@ -118,8 +116,8 @@ class ContextAutomaton(object):
self._prod_entities |= new_context_set
self._transitions.append(
(self.get_state_id(src),
new_context_set, self.get_state_id(dst)))
(self.get_state_id(src), new_context_set, self.get_state_id(dst))
)
def rsset2str(self, elements):
"""Converts the set of entities ids into the string with their names"""
@@ -168,4 +166,5 @@ class ContextAutomaton(object):
self.show_transitions()
self.show_prod_entities()
# EOF

38
reactics-smt/rs/context_automaton_with_concentrations.py
View File

@@ -5,15 +5,13 @@ from rs.context_automaton import ContextAutomaton
class ContextAutomatonWithConcentrations(ContextAutomaton):
def __init__(self, reaction_system):
super(ContextAutomatonWithConcentrations,
self).__init__(reaction_system)
super(ContextAutomatonWithConcentrations, self).__init__(reaction_system)
def is_valid_context(self, context):
if set(
[e for e, lvl in context]).issubset(
self._reaction_system.background_set):
if set([e for e, lvl in context]).issubset(
self._reaction_system.background_set
):
return True
else:
return False
@@ -33,45 +31,38 @@ class ContextAutomatonWithConcentrations(ContextAutomaton):
if not self.is_valid_context(context_set):
raise RuntimeError(
"one of the entities in the context set is unknown (undefined)!")
"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")
raise RuntimeError('"' + src + '" is an unknown (undefined) state')
if not self.is_state(dst):
raise RuntimeError(
"\"" + dst + "\" is an unknown (undefined) state")
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))
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)))
(self.get_state_id(src), new_context_set, self.get_state_id(dst))
)
def get_automaton_with_flat_contexts(self, ordinary_reaction_system):
ca = ContextAutomaton(ordinary_reaction_system)
ca._states = self._states
ca._init_state = self._init_state
for src, ctx, dst in self._transitions:
new_ctx = set()
for ent, conc in ctx:
for i in range(1, conc+1):
n = self._reaction_system.get_entity_name(
ent) + "#" + str(i)
for i in range(1, conc + 1):
n = self._reaction_system.get_entity_name(ent) + "#" + str(i)
ca._reaction_system.ensure_bg_set_entity(n)
new_ctx.add(n)
ca.add_transition(
ca.get_state_name(src),
new_ctx, ca.get_state_name(dst))
ca.add_transition(ca.get_state_name(src), new_ctx, ca.get_state_name(dst))
return ca
@@ -80,4 +71,5 @@ class ContextAutomatonWithConcentrations(ContextAutomaton):
self.show_states()
self.show_transitions()
# EOF

32
reactics-smt/rs/extended_context_automaton.py
View File

@@ -75,23 +75,24 @@ class ExtendedContextAutomaton(ContextAutomaton):
if not self.is_valid_rs_set(ctx_reactants):
raise RuntimeError(
"one of the entities in the reactants set is unknown (undefined)!")
"one of the entities in the reactants set is unknown (undefined)!"
)
if not self.is_valid_rs_set(ctx_inhibitors):
raise RuntimeError(
"one of the entities in the inhibitors set is unknown (undefined)!")
"one of the entities in the inhibitors set is unknown (undefined)!"
)
if not self.is_valid_rs_set(ctx_products):
raise RuntimeError(
"one of the entities in the context set is unknown (undefined)!")
"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")
raise RuntimeError('"' + src + '" is an unknown (undefined) state')
if not self.is_state(dst):
raise RuntimeError(
"\"" + dst + "\" is an unknown (undefined) state")
raise RuntimeError('"' + dst + '" is an unknown (undefined) state')
src_id = self.get_state_id(src)
dst_id = self.get_state_id(dst)
@@ -119,8 +120,15 @@ class ExtendedContextAutomaton(ContextAutomaton):
for src_id, act_id, reaction, dst_id in self._transitions:
str_transition = self.get_state_name(src_id) + " --( "
str_transition += "<" + self.get_actions_str(act_id) + "> | "
str_transition += "( " + self.rsset2str(reaction[0]) + "," + self.rsset2str(
reaction[1]) + "," + self.rsset2str(reaction[2]) + " )"
str_transition += (
"( "
+ self.rsset2str(reaction[0])
+ ","
+ self.rsset2str(reaction[1])
+ ","
+ self.rsset2str(reaction[2])
+ " )"
)
str_transition += " )--> " + self.get_state_name(dst_id)
print(" - " + str_transition)
@@ -130,7 +138,7 @@ class ExtendedContextAutomaton(ContextAutomaton):
if action_name not in self._actions:
self._actions.append(action_name)
else:
print("\'%s\' already added. skipping..." % (action_name,))
print("'%s' already added. skipping..." % (action_name,))
def get_action_id(self, action_name):
"""For an action name returns its id"""
@@ -138,8 +146,7 @@ class ExtendedContextAutomaton(ContextAutomaton):
try:
return self._actions.index(action_name)
except ValueError:
print_error("Undefined context automaton action: " +
repr(action_name))
print_error("Undefined context automaton action: " + repr(action_name))
exit(1)
def get_action_name(self, action_id):
@@ -173,4 +180,5 @@ class ExtendedContextAutomaton(ContextAutomaton):
super(ExtendedContextAutomaton, self).show()
self.show_actions()
# EOF

15
reactics-smt/rs/network_of_context_automata.py
View File

@@ -3,7 +3,6 @@ from colour import *
class NetworkOfContextAutomata(object):
def __init__(self, reaction_system, context_automata):
self.automata = []
self._reaction_system = reaction_system
@@ -44,14 +43,14 @@ class NetworkOfContextAutomata(object):
for automaton in self.automata:
if automaton.reaction_system != self._reaction_system:
print_error(
"Mismatching reaction system used in \"" +
str(automaton.name) + "\"!!!")
'Mismatching reaction system used in "'
+ str(automaton.name)
+ '"!!!'
)
exit(1)
def show_prod_entities(self):
print(
C_MARK_INFO +
" Possible context-products for the network of automata:")
print(C_MARK_INFO + " Possible context-products for the network of automata:")
for entity in self.prod_entities:
print(" - " + self._reaction_system.get_entity_name(entity))
@@ -96,7 +95,8 @@ class NetworkOfContextAutomata(object):
for entity in aut.prod_entities:
self._actions_for_products.setdefault(entity, set())
self._actions_for_products[entity] |= aut.get_actions_producing_entity(
entity)
entity
)
def show(self):
print()
@@ -108,4 +108,5 @@ class NetworkOfContextAutomata(object):
self.show_prod_entities()
self.show_actions()
# EOF

46
reactics-smt/rs/reaction_system.py
View File

@@ -3,9 +3,7 @@ from colour import *
class ReactionSystem(object):
def __init__(self):
self.reactions = []
self.background_set = []
@@ -30,8 +28,7 @@ class ReactionSystem(object):
def assume_not_in_bgset(self, name):
if self.is_in_background_set(name):
raise RuntimeError(
"The entity " + name + " is already on the list")
raise RuntimeError("The entity " + name + " is already on the list")
def add_bg_set_entity(self, name):
self.assume_not_in_bgset(name)
@@ -106,7 +103,6 @@ class ReactionSystem(object):
self.init_contexts.append(integers)
def set_context_entities(self, entities):
for entity in entities:
entity_id = self.get_entity_id(entity)
self.context_entities.append(entity_id)
@@ -131,20 +127,36 @@ class ReactionSystem(object):
def show_reactions(self, soft=False):
print(C_MARK_INFO + " Reactions:")
if soft and len(self.reactions) > 50:
print(" -> there are more than 50 reactions (" +
str(len(self.reactions)) + ")")
print(
" -> there are more than 50 reactions ("
+ str(len(self.reactions))
+ ")"
)
else:
print(
" "*4 + "{0: ^35}{1: ^25}{2: ^15}".format("reactants", " inhibitors", " products"))
" " * 4
+ "{0: ^35}{1: ^25}{2: ^15}".format(
"reactants", " inhibitors", " products"
)
)
for reaction in self.reactions:
# print("\t( R={" + self.state_to_str(reaction[0]) + "}, I={" + self.state_to_str(reaction[1]) + "}, P={" + self.state_to_str(reaction[2]) + "} )")
print(" " + "- {0: ^35}{1: ^25}{2: ^15}".format("{ " + self.state_to_str(reaction[0]) + " }",
" { " + self.state_to_str(reaction[1]) + " }",
" { " + self.state_to_str(reaction[2]) + " }"))
print(
" "
+ "- {0: ^35}{1: ^25}{2: ^15}".format(
"{ " + self.state_to_str(reaction[0]) + " }",
" { " + self.state_to_str(reaction[1]) + " }",
" { " + self.state_to_str(reaction[2]) + " }",
)
)
def show_background_set(self):
print(
C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
C_MARK_INFO
+ " Background set: {"
+ self.entities_names_set_to_str(self.background_set)
+ "}"
)
def show_initial_contexts(self):
if len(self.init_contexts) > 0:
@@ -155,10 +167,12 @@ class ReactionSystem(object):
def show_context_entities(self):
if len(self.context_entities) > 0:
print(
C_MARK_INFO + " Context entities: " + self.entities_ids_set_to_str(self.context_entities))
C_MARK_INFO
+ " Context entities: "
+ self.entities_ids_set_to_str(self.context_entities)
)
def show(self, soft=False):
self.show_background_set()
self.show_initial_contexts()
self.show_reactions(soft)
@@ -181,8 +195,7 @@ class ReactionSystem(object):
reactions_by_prod[prod_entity] = []
for reaction in self.reactions:
if prod_entity in reaction[2]:
reactions_by_prod[prod_entity].append(
[reaction[0], reaction[1]])
reactions_by_prod[prod_entity].append([reaction[0], reaction[1]])
# save in cache
self.reactions_by_prod = reactions_by_prod
@@ -200,4 +213,5 @@ class ReactionSystem(object):
print("Empty background set")
exit(1)
# EOF

3
reactics-smt/rs/reaction_system_with_autnet.py
View File

@@ -1,6 +1,4 @@
class ReactionSystemWithNetworkOfAutomata(object):
def __init__(self, reaction_system, context_automata):
self.rs = reaction_system
self.cas = context_automata
@@ -9,4 +7,5 @@ class ReactionSystemWithNetworkOfAutomata(object):
self.rs.show(soft)
self.cas.show()
# EOF

8
reactics-smt/rs/reaction_system_with_automaton.py
View File

@@ -1,10 +1,11 @@
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,
)
from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
class ReactionSystemWithAutomaton(object):
def __init__(self, reaction_system, context_automaton):
self.rs = reaction_system
self.ca = context_automaton
@@ -15,7 +16,7 @@ class ReactionSystemWithAutomaton(object):
def is_concentr_and_param_compatible(self):
"""
Checks if the underlying RS/CA are compatible
Checks if the underlying RS/CA are compatible
with parameters and concentrations
"""
if not isinstance(self.rs, ReactionSystemWithConcentrationsParam):
@@ -35,7 +36,6 @@ class ReactionSystemWithAutomaton(object):
pass
def get_ordinary_reaction_system_with_automaton(self):
if not self.is_with_concentrations():
raise RuntimeError("Not RS/CA with concentrations")

114
reactics-smt/rs/reaction_system_with_concentrations.py
View File

@@ -5,9 +5,7 @@ from rs.reaction_system import ReactionSystem
class ReactionSystemWithConcentrations(ReactionSystem):
def __init__(self):
self.reactions = []
self.meta_reactions = dict()
self.permanent_entities = dict()
@@ -26,8 +24,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
name = e
print("\nWARNING: no maximal concentration level specified for:", e, "\n")
else:
raise RuntimeError(
"Bad entity type when adding background set element")
raise RuntimeError("Bad entity type when adding background set element")
self.assume_not_in_bgset(name)
self.background_set.append(name)
@@ -41,7 +38,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
self.max_concentration = def_max_conc
def get_max_concentration_level(self, e):
if e in self.max_conc_per_ent:
return self.max_conc_per_ent[e]
else:
@@ -69,8 +65,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def has_non_zero_concentration(self, elem):
if elem[1] < 1:
raise RuntimeError(
"Unexpected concentration level in state: " + str(elem))
raise RuntimeError("Unexpected concentration level in state: " + str(elem))
def process_rip(self, R, I, P, ignore_empty_R=False):
"""Chcecks concentration levels and converts entities names into their ids"""
@@ -123,21 +118,25 @@ class ReactionSystemWithConcentrations(ReactionSystem):
"""Adds a macro/meta reaction for increasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
incr_entity_id = self.get_entity_id(incr_entity)
self.meta_reactions.setdefault(incr_entity_id, [])
self.meta_reactions[incr_entity_id].append(
("inc", self.get_entity_id(incrementer), reactants, inhibitors))
("inc", self.get_entity_id(incrementer), reactants, inhibitors)
)
def add_reaction_dec(self, decr_entity, decrementer, R, I):
"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
decr_entity_id = self.get_entity_id(decr_entity)
self.meta_reactions.setdefault(decr_entity_id, [])
self.meta_reactions[decr_entity_id].append(
("dec", self.get_entity_id(decrementer), reactants, inhibitors))
("dec", self.get_entity_id(decrementer), reactants, inhibitors)
)
def add_permanency(self, ent, I):
"""Sets entity to be permanent unless it is inhibited"""
@@ -145,8 +144,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
ent_id = self.get_entity_id(ent)
if ent_id in self.permanent_entities:
raise RuntimeError(
"Permanency for {0} already defined.".format(ent))
raise RuntimeError("Permanency for {0} already defined.".format(ent))
inhibitors = self.process_rip([], I, [], ignore_empty_R=True)[1]
self.permanent_entities[ent_id] = inhibitors
@@ -177,31 +175,50 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def show_background_set(self):
print(
C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
C_MARK_INFO
+ " Background set: {"
+ self.entities_names_set_to_str(self.background_set)
+ "}"
)
def show_meta_reactions(self):
print(C_MARK_INFO + " Meta reactions:")
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
if r_type == "inc" or r_type == "dec":
print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + " ) Command=( " + self.get_entity_name(
command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
print(
" - [ Type="
+ repr(r_type)
+ " Operand=( "
+ self.get_entity_name(param_ent)
+ " ) Command=( "
+ self.get_entity_name(command)
+ " ) ] -- ( R={"
+ self.state_to_str(reactants)
+ "}, I={"
+ self.state_to_str(inhibitors)
+ "} )"
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
def show_max_concentrations(self):
print(
C_MARK_INFO +
" Maximal allowed concentration levels (for optimized translation to RS):")
C_MARK_INFO
+ " Maximal allowed concentration levels (for optimized translation to RS):"
)
for e, max_conc in self.max_conc_per_ent.items():
print(" - {0:^20} = {1:<6}".format(self.get_entity_name(e), max_conc))
def show_permanent_entities(self):
print(C_MARK_INFO + " Permanent entities:")
for e, inhibitors in self.permanent_entities.items():
print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}"))
print(
" - {0:^20}{1:<6}".format(
self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}",
)
)
def show(self, soft=False):
self.show_background_set()
@@ -220,8 +237,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
for reaction in self.reactions:
product_entities = [e for e, c in reaction[2]]
producible_entities = producible_entities.union(
set(product_entities))
producible_entities = producible_entities.union(set(product_entities))
reactions_by_prod = {}
@@ -242,18 +258,20 @@ class ReactionSystemWithConcentrations(ReactionSystem):
# we need to order the reactions w.r.t. the concentration levels produced (increasing order)
for i in range(0, len(rcts_for_p_e)):
checked_conc = rcts_for_p_e[i][2][0][1]
if prod_conc <= checked_conc:
insert_place = i
break
if insert_place == None: # empty or the is only one element which is smaller than the element being added
if (
insert_place == None
): # empty or the is only one element which is smaller than the element being added
# we append (to the end)
rcts_for_p_e.append((reactants, inhibitors, products))
else:
rcts_for_p_e.insert(
insert_place, (reactants, inhibitors, products))
insert_place, (reactants, inhibitors, products)
)
# save in cache
self.reactions_by_prod = reactions_by_prod
@@ -261,11 +279,9 @@ class ReactionSystemWithConcentrations(ReactionSystem):
return reactions_by_prod
def get_reaction_system(self):
rs = ReactionSystem()
for reactants, inhibitors, products in self.reactions:
new_reactants = []
new_inhibitors = []
new_products = []
@@ -281,7 +297,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
new_inhibitors.append(n)
for ent, conc in products:
for i in range(1, conc+1):
for i in range(1, conc + 1):
n = self.get_entity_name(ent) + "#" + str(i)
rs.ensure_bg_set_entity(n)
new_products.append(n)
@@ -290,7 +306,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
param_ent_name = self.get_entity_name(param_ent)
new_reactants = []
@@ -312,16 +327,15 @@ class ReactionSystemWithConcentrations(ReactionSystem):
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(command))
+ self.get_entity_name(command)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
for l in range(1, max_cmd_c+1):
for l in range(1, max_cmd_c + 1):
cmd_ent = self.get_entity_name(command) + "#" + str(l)
rs.ensure_bg_set_entity(cmd_ent)
if r_type == "inc":
# pre_conc -- predecessor concentration
# succ_conc -- successor concentration concentration
@@ -329,8 +343,8 @@ class ReactionSystemWithConcentrations(ReactionSystem):
pre_conc = param_ent_name + "#" + str(i)
rs.ensure_bg_set_entity(pre_conc)
new_products = []
succ_value = i+l
for j in range(1, succ_value+1):
succ_value = i + l
for j in range(1, succ_value + 1):
if j > self.max_concentration:
break
new_p = param_ent_name + "#" + str(j)
@@ -340,15 +354,16 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
elif r_type == "dec":
for i in range(1, self.max_concentration+1):
for i in range(1, self.max_concentration + 1):
pre_conc = param_ent_name + "#" + str(i)
rs.ensure_bg_set_entity(pre_conc)
new_products = []
succ_value = i-l
for j in range(1, succ_value+1):
succ_value = i - l
for j in range(1, succ_value + 1):
if j > self.max_concentration:
break
new_p = param_ent_name + "#" + str(j)
@@ -358,28 +373,29 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
"Unknown meta-reaction type: " + repr(r_type)
)
for ent, inhibitors in self.permanent_entities.items():
max_c = self.max_concentration
if ent in self.max_conc_per_ent:
max_c = self.max_conc_per_ent[ent]
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(ent))
+ self.get_entity_name(ent)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
def e_value(i):
return self.get_entity_name(ent) + "#" + str(i)
for value in range(1, max_c+1):
for value in range(1, max_c + 1):
new_reactants = []
new_inhibitors = []
new_products = []
@@ -391,7 +407,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.ensure_bg_set_entity(n)
new_inhibitors.append(n)
for i in range(1, value+1):
for i in range(1, value + 1):
new_products.append(e_value(i))
rs.add_reaction(new_reactants, new_inhibitors, new_products)
@@ -400,7 +416,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
class ReactionSystemWithAutomaton(object):
def __init__(self, reaction_system, context_automaton):
self.rs = reaction_system
self.ca = context_automaton
@@ -420,7 +435,6 @@ class ReactionSystemWithAutomaton(object):
pass
def get_ordinary_reaction_system_with_automaton(self):
if not self.is_with_concentrations():
raise RuntimeError("Not RS/CA with concentrations")

90
reactics-smt/rs/reaction_system_with_concentrations_param.py
View File

@@ -5,7 +5,6 @@ from rs.reaction_system import ReactionSystem
class ParameterObj(object):
def __init__(self, name):
self.name = name
@@ -21,9 +20,7 @@ def is_param(some_object):
class ReactionSystemWithConcentrationsParam(ReactionSystem):
def __init__(self):
self.reactions = []
self.parameters = dict()
self.meta_reactions = dict()
@@ -43,8 +40,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
name = e
print("\nWARNING: no maximal concentration level specified for:", e, "\n")
else:
raise RuntimeError(
"Bad entity type when adding background set element")
raise RuntimeError("Bad entity type when adding background set element")
self.assume_not_in_bgset(name)
self.background_set.append(name)
@@ -76,7 +72,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
self.parameters[param_key].idx = len(self.parameters)
def get_max_concentration_level(self, e):
if e in self.max_conc_per_ent:
return self.max_conc_per_ent[e]
else:
@@ -113,17 +108,18 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def terminate_on_invalid_concentration(self, entity, level):
if not self.is_valid_concentration_for_entity(entity, level):
print("FATAL. Invalid entity concentration: {:s}={:d}".format(entity, level))
print(
"FATAL. Invalid entity concentration: {:s}={:d}".format(entity, level)
)
exit(1)
def get_state_ids(self, state):
"""Returns entities of the given state without levels"""
return [self.get_entity_id(e) for e in state]
def has_non_zero_concentration(self, elem):
if elem[1] < 1:
raise RuntimeError(
"Unexpected concentration level in state: " + str(elem))
raise RuntimeError("Unexpected concentration level in state: " + str(elem))
def process_rip(self, R, I, P, ignore_empty_R=False):
"""Chcecks concentration levels and converts entities names into their ids"""
@@ -207,21 +203,25 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
"""Adds a macro/meta reaction for increasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
incr_entity_id = self.get_entity_id(incr_entity)
self.meta_reactions.setdefault(incr_entity_id, [])
self.meta_reactions[incr_entity_id].append(
("inc", self.get_entity_id(incrementer), reactants, inhibitors))
("inc", self.get_entity_id(incrementer), reactants, inhibitors)
)
def add_reaction_dec(self, decr_entity, decrementer, R, I):
"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
reactants, inhibitors, products = self.process_rip(
R, I, [], ignore_empty_R=True)
R, I, [], ignore_empty_R=True
)
decr_entity_id = self.get_entity_id(decr_entity)
self.meta_reactions.setdefault(decr_entity_id, [])
self.meta_reactions[decr_entity_id].append(
("dec", self.get_entity_id(decrementer), reactants, inhibitors))
("dec", self.get_entity_id(decrementer), reactants, inhibitors)
)
def add_permanency(self, ent, I):
"""Sets entity to be permanent unless it is inhibited"""
@@ -229,8 +229,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
ent_id = self.get_entity_id(ent)
if ent_id in self.permanent_entities:
raise RuntimeError(
"Permanency for {0} already defined.".format(ent))
raise RuntimeError("Permanency for {0} already defined.".format(ent))
inhibitors = self.process_rip([], I, [], ignore_empty_R=True)[1]
self.permanent_entities[ent_id] = inhibitors
@@ -269,18 +268,32 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def show_background_set(self):
print(
C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
C_MARK_INFO
+ " Background set: {"
+ self.entities_names_set_to_str(self.background_set)
+ "}"
)
def show_meta_reactions(self):
print(C_MARK_INFO + " Meta reactions:")
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
if r_type == "inc" or r_type == "dec":
print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + " ) Command=( " + self.get_entity_name(
command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
print(
" - [ Type="
+ repr(r_type)
+ " Operand=( "
+ self.get_entity_name(param_ent)
+ " ) Command=( "
+ self.get_entity_name(command)
+ " ) ] -- ( R={"
+ self.state_to_str(reactants)
+ "}, I={"
+ self.state_to_str(inhibitors)
+ "} )"
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
def show_max_concentrations(self):
print(C_MARK_INFO + " Maximal allowed concentration levels:")
@@ -290,8 +303,12 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def show_permanent_entities(self):
print(C_MARK_INFO + " Permanent entities:")
for e, inhibitors in self.permanent_entities.items():
print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}"))
print(
" - {0:^20}{1:<6}".format(
self.get_entity_name(e) + ": ",
"I={" + self.state_to_str(inhibitors) + "}",
)
)
def show(self, soft=False):
self.show_background_set()
@@ -303,7 +320,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def get_producible_entities(self):
"""
Returns the set of entities that appear as products of
Returns the set of entities that appear as products of
reactions.
"""
@@ -311,8 +328,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
for reaction in self.reactions:
product_entities = [e for e, c in reaction[2] if c > 0]
producible_entities = producible_entities.union(
set(product_entities))
producible_entities = producible_entities.union(set(product_entities))
return producible_entities
@@ -324,7 +340,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
rs = ReactionSystem()
for reactants, inhibitors, products in self.reactions:
new_reactants = []
new_inhibitors = []
new_products = []
@@ -349,7 +364,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
for param_ent, reactions in self.meta_reactions.items():
for r_type, command, reactants, inhibitors in reactions:
param_ent_name = self.get_entity_name(param_ent)
new_reactants = []
@@ -371,16 +385,15 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(command))
+ self.get_entity_name(command)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
for l in range(1, max_cmd_c + 1):
cmd_ent = self.get_entity_name(command) + "#" + str(l)
rs.ensure_bg_set_entity(cmd_ent)
if r_type == "inc":
# pre_conc -- predecessor concentration
# succ_conc -- successor concentration concentration
@@ -399,7 +412,8 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
elif r_type == "dec":
for i in range(1, self.max_concentration + 1):
@@ -417,28 +431,29 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
rs.add_reaction(
set(new_reactants + [pre_conc, cmd_ent]),
set(new_inhibitors),
set(new_products))
set(new_products),
)
else:
raise RuntimeError(
"Unknown meta-reaction type: " + repr(r_type))
"Unknown meta-reaction type: " + repr(r_type)
)
for ent, inhibitors in self.permanent_entities.items():
max_c = self.max_concentration
if ent in self.max_conc_per_ent:
max_c = self.max_conc_per_ent[ent]
else:
print(
"WARNING:\n\tThere is no maximal concentration level defined for "
+ self.get_entity_name(ent))
+ self.get_entity_name(ent)
)
print("\tThis is a very bad idea -- expect degraded performance\n")
def e_value(i):
return self.get_entity_name(ent) + "#" + str(i)
for value in range(1, max_c + 1):
new_reactants = []
new_inhibitors = []
new_products = []
@@ -457,4 +472,5 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
return rs
# EOF