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working on Blood-Glucose example

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Artur Meski
2016-03-01 21:25:34 +01:00
parent 0137a20867
commit 3f3690c861
8 changed files with 1891 additions and 18 deletions
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(3,3,0.368922)
(1,1,0.010178999999999994)
(1,1,0.009978000000000015)

22
rctsys.py
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@@ -430,10 +430,10 @@ class ReactionSystemWithConcentrations(ReactionSystem):
if elem[1] < 1: if elem[1] < 1:
raise RuntimeError("Unexpected concentration level in state: " + str(elem)) raise RuntimeError("Unexpected concentration level in state: " + str(elem))
def check_rip(self, R, I, P): def check_rip(self, R, I, P, ignore_empty_R=False):
"""Chcecks concentration levels and converts entities names into their ids""" """Chcecks concentration levels and converts entities names into their ids"""
if R == []: if R == [] and not ignore_empty_R:
raise RuntimeError("No reactants defined") raise RuntimeError("No reactants defined")
reactants = [] reactants = []
@@ -469,10 +469,18 @@ class ReactionSystemWithConcentrations(ReactionSystem):
reaction = self.check_rip(R,I,P) reaction = self.check_rip(R,I,P)
self.reactions.append(reaction) self.reactions.append(reaction)
def add_reaction_without_reactants(self, R, I, P):
"""Adds a reaction"""
if P == []:
raise RuntimeError("No products defined")
reaction = self.check_rip(R,I,P,ignore_empty_R=True)
self.reactions.append(reaction)
def add_reaction_inc(self, incr_entity, incrementer, R, I): def add_reaction_inc(self, incr_entity, incrementer, R, I):
"""Adds a macro/meta reaction for increasing the value of incr_entity""" """Adds a macro/meta reaction for increasing the value of incr_entity"""
reactants,inhibitors,products = self.check_rip(R,I,[]) reactants,inhibitors,products = self.check_rip(R,I,[],ignore_empty_R=True)
incr_entity_id = self.get_entity_id(incr_entity) incr_entity_id = self.get_entity_id(incr_entity)
self.meta_reactions.setdefault(incr_entity_id,[]) self.meta_reactions.setdefault(incr_entity_id,[])
self.meta_reactions[incr_entity_id].append(("inc", self.get_entity_id(incrementer), reactants, inhibitors)) self.meta_reactions[incr_entity_id].append(("inc", self.get_entity_id(incrementer), reactants, inhibitors))
@@ -480,7 +488,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
def add_reaction_dec(self, decr_entity, decrementer, R, I): def add_reaction_dec(self, decr_entity, decrementer, R, I):
"""Adds a macro/meta reaction for decreasing the value of incr_entity""" """Adds a macro/meta reaction for decreasing the value of incr_entity"""
reactants,inhibitors,products = self.check_rip(R,I,[]) reactants,inhibitors,products = self.check_rip(R,I,[],ignore_empty_R=True)
decr_entity_id = self.get_entity_id(decr_entity) decr_entity_id = self.get_entity_id(decr_entity)
self.meta_reactions.setdefault(decr_entity_id,[]) self.meta_reactions.setdefault(decr_entity_id,[])
self.meta_reactions[decr_entity_id].append(("dec", self.get_entity_id(decrementer), reactants, inhibitors)) self.meta_reactions[decr_entity_id].append(("dec", self.get_entity_id(decrementer), reactants, inhibitors))
@@ -522,10 +530,16 @@ class ReactionSystemWithConcentrations(ReactionSystem):
else: 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("[*] Maximal allowed concentration levels (for optimized translation to RS):")
for e,max_conc in self.max_conc_per_ent.items():
print("\t - {0:>20} = {1:<6}".format(self.get_entity_name(e),max_conc))
def show(self, soft=False): def show(self, soft=False):
self.show_background_set() self.show_background_set()
self.show_reactions(soft) self.show_reactions(soft)
self.show_meta_reactions() self.show_meta_reactions()
self.show_max_concentrations()
def get_reactions_by_product(self): def get_reactions_by_product(self):
"""Sorts reactions by their products and returns a dictionary of products""" """Sorts reactions by their products and returns a dictionary of products"""

40
rs_examples.py
View File

@@ -388,26 +388,44 @@ def chain_reaction(print_system=False):
f.write(log_str) f.write(log_str)
f.close() f.close()
def blood_glucose_regulation(): def blood_glucose_regulation(print_system=True):
r = ReactionSystemWithConcentrations() r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("inc_insulin",1)) r.add_bg_set_entity(("inc_insulin",1))
r.add_bg_set_entity(("dec_insulin",1)) r.add_bg_set_entity(("dec_insulin",1))
r.add_bg_set_entity(("inc_glycemia",1)) r.add_bg_set_entity(("inc_glycemia",1))
r.add_bg_set_entities(("inc_")) r.add_bg_set_entity(("dec_glycemia",1))
r.add_bg_set_entity(("inc_glucagon",1))
r.add_bg_set_entities([(sugar,1),(aspartame,1),(glycemia,3),(glucagon,1),(insulin,2)]) r.add_bg_set_entities([("sugar",1),("aspartame",1),("glycemia",3),("glucagon",1),("insulin",2)])
# r.add_reaction([],[],[]) # r.add_reaction([],[],[])
r.add_reaction([(sugar,1)],[],[(inc_insulin,1),(inc_glycemia,1)]) r.add_reaction([("sugar",1)],[],[("inc_insulin",1),("inc_glycemia",1)])
r.add_reaction([],[],[]) r.add_reaction([("aspartame",1)],[],[("insulin",1)])
r.add_reaction([],[],[]) r.add_reaction_without_reactants([],[("glycemia",1)],[("insulin",1)])
r.add_reaction([("glycemia",3)],[],[("insulin",1)])
r.add_reaction([("insulin",2)],[],[("dec_glycemia",1)])
r.add_reaction([("insulin",1),("glycemia",3)],[],[("dec_glycemia",1)])
r.add_reaction([("insulin",1)],[("glycemia",2)],[("dec_glycemia",1)])
r.add_reaction([("glucagon",1)],[],[("glycemia",1)])
# inc/dec:
r.add_reaction_inc("glycemia", "inc_glycemia", [],[("glycemia",3),("dec_glycemia",1)])
r.add_reaction_inc("glycemia", "dec_glycemia", [],[("glycemia",1),("inc_glycemia",1)])
# potrzebne sa reakcje, ktore utrzymaja okresolna molekule na tym samym poziomie
# -> przed podtrzymaniem trzeba sie upewnic, ze jednak jakas reakcja nie chce zmienic tego poziomu
# moje:
r.add_reaction([("sugar",1)],[],[("sugar",1)])
c = ContextAutomatonWithConcentrations(r) c = ContextAutomatonWithConcentrations(r)
c.add_init_state("init") c.add_init_state("0")
c.add_state("working") c.add_state("1")
c.add_transition("init", [("e_1",1),("inc",1)], "working") c.add_transition("0", [("sugar",1)], "1")
c.add_transition("working", [("inc",1)], "working") c.add_transition("1", [], "1")
# c.add_transition("1", [("sugar",1)], "1")
rc = ReactionSystemWithAutomaton(r,c) rc = ReactionSystemWithAutomaton(r,c)

3
rssmt.py
View File

@@ -29,7 +29,8 @@ rsmc_banner = """
def process(): def process():
# rs_examples.run_counter_exp() # rs_examples.run_counter_exp()
rs_examples.chain_reaction(print_system=True) # rs_examples.chain_reaction(print_system=True)
rs_examples.blood_glucose_regulation()
################################################################## ##################################################################