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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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90
reactics-smt/rs/reaction_system_with_concentrations_param.py
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@@ -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