Incrementation & decrementation by a specified value.
This commit is contained in:
Artur Meski
8
mkplotdat.sh
Executable file
8
mkplotdat.sh
Executable file
@@ -0,0 +1,8 @@
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#!/bin/sh
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if [ "$1" = "" ];then
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echo "Usage: $0 <input file>"
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exit 1
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fi
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f="$1"
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cat $f | tr -d '()' | tr ',' '\t'
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151
rctsys.py
151
rctsys.py
@@ -185,7 +185,7 @@ class ContextAutomatonWithConcentrations(ContextAutomaton):
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for ent,conc in ctx:
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for i in range(1,conc+1):
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n = self._reaction_system.get_entity_name(ent) + "_" + str(i)
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n = self._reaction_system.get_entity_name(ent) + "#" + str(i)
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ca._reaction_system.ensure_bg_set_entity(n)
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new_ctx.add(n)
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@@ -207,19 +207,21 @@ class ReactionSystem(object):
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self.init_contexts = []
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self.context_entities = []
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def add_bg_set_entity(self, name):
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if not self.is_in_background_set(name):
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self.background_set.append(name)
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else:
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def assume_not_in_bgset(self, name):
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if self.is_in_background_set(name):
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raise RuntimeError("The entity " + name + " is already on the list")
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def add_bg_set_entity(self, name):
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self.assume_not_in_bgset(name)
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self.background_set.append(name)
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def ensure_bg_set_entity(self, name):
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if not self.is_in_background_set(name):
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self.background_set.append(name)
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def add_bg_set_entities(self, names):
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for name in names:
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self.add_bg_set_entity(name)
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def add_bg_set_entities(self, elements):
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for e in elements:
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self.add_bg_set_entity(e)
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def is_in_background_set(self, entity):
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"""Checks if the given name is valid wrt the background set="""
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@@ -250,7 +252,7 @@ class ReactionSystem(object):
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"""Adds a reaction"""
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if R == [] or P == []:
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raise RuntimeError("No reactants of products defined")
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raise RuntimeError("No reactants or products defined")
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reactants = []
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for entity in R:
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@@ -380,6 +382,28 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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self.reactions_by_prod = None
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self.max_concentration = 0
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self.max_conc_per_ent = dict()
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def add_bg_set_entity(self, e):
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name = ""
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def_max_conc = -1
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if type(e) is tuple and len(e) == 2:
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name,def_max_conc = e
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elif type(e) is str:
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name = e
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else:
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raise RuntimeError("Bad entity type when adding background set element")
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self.assume_not_in_bgset(name)
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self.background_set.append(name)
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if def_max_conc != -1:
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ent_id = self.get_entity_id(name)
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self.max_conc_per_ent.setdefault(ent_id, 0)
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if self.max_conc_per_ent[ent_id] < def_max_conc:
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self.max_conc_per_ent[ent_id] = def_max_conc
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if self.max_concentration < def_max_conc:
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self.max_concentration = def_max_conc
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def is_valid_entity_with_concentration(self, e):
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"""Sanity check for entities with concentration"""
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@@ -406,7 +430,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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if elem[1] < 1:
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raise RuntimeError("Unexpected concentration level in state: " + str(elem))
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def process_rip(self, R, I, P):
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def check_rip(self, R, I, P):
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"""Chcecks concentration levels and converts entities names into their ids"""
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if R == []:
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@@ -442,24 +466,24 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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if P == []:
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raise RuntimeError("No products defined")
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reaction = self.process_rip(R,I,P)
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reaction = self.check_rip(R,I,P)
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self.reactions.append(reaction)
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def add_reaction_inc(self, incr_entity, R, I):
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def add_reaction_inc(self, incr_entity, incrementer, R, I):
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"""Adds a macro/meta reaction for increasing the value of incr_entity"""
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reactants,inhibitors,products = self.process_rip(R,I,[])
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reactants,inhibitors,products = self.check_rip(R,I,[])
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incr_entity_id = self.get_entity_id(incr_entity)
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self.meta_reactions.setdefault(incr_entity_id,[])
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self.meta_reactions[incr_entity_id].append(("inc", reactants, inhibitors))
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self.meta_reactions[incr_entity_id].append(("inc", self.get_entity_id(incrementer), reactants, inhibitors))
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def add_reaction_dec(self, incr_entity, R, I):
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def add_reaction_dec(self, decr_entity, decrementer, R, I):
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"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
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reactants,inhibitors,products = self.process_rip(R,I,[])
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reactants,inhibitors,products = self.check_rip(R,I,[])
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decr_entity_id = self.get_entity_id(decr_entity)
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self.meta_reactions.setdefault(decr_entity_id,[])
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self.meta_reactions[decr_entity_id].append(("dec", reactants, inhibitors))
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self.meta_reactions[decr_entity_id].append(("dec", self.get_entity_id(decrementer), reactants, inhibitors))
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def set_context_entities(self, entities):
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raise NotImplementedError
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@@ -491,10 +515,10 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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def show_meta_reactions(self):
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print("[*] Meta reactions:")
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for param_ent,reactions in self.meta_reactions.items():
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for r_type,reactants,inhibitors in reactions:
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for r_type,command,reactants,inhibitors in reactions:
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if r_type == "inc" or r_type == "dec":
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print("\t - [ Type=" + repr(r_type) + " Parameter=( " + self.get_entity_name(param_ent) + \
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" ) ] -- ( R={" + self.state_to_str(reactants) + "}, \tI={" + self.state_to_str(inhibitors) + "} )")
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print("\t - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + \
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" ) Command=( " + self.get_entity_name(command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, \tI={" + self.state_to_str(inhibitors) + "} )")
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else:
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raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
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@@ -543,25 +567,25 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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new_products = []
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for ent,conc in reactants:
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n = self.get_entity_name(ent) + "_" + str(conc)
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n = self.get_entity_name(ent) + "#" + str(conc)
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rs.ensure_bg_set_entity(n)
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new_reactants.append(n)
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for ent,conc in inhibitors:
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n = self.get_entity_name(ent) + "_" + str(conc)
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n = self.get_entity_name(ent) + "#" + str(conc)
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rs.ensure_bg_set_entity(n)
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new_inhibitors.append(n)
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for ent,conc in products:
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for i in range(1,conc+1):
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n = self.get_entity_name(ent) + "_" + str(i)
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n = self.get_entity_name(ent) + "#" + str(i)
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rs.ensure_bg_set_entity(n)
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new_products.append(n)
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rs.add_reaction(new_reactants,new_inhibitors,new_products)
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for param_ent,reactions in self.meta_reactions.items():
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for r_type,reactants,inhibitors in reactions:
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for r_type,command,reactants,inhibitors in reactions:
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param_ent_name = self.get_entity_name(param_ent)
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@@ -569,46 +593,61 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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new_inhibitors = []
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for ent,conc in reactants:
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n = self.get_entity_name(ent) + "_" + str(conc)
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n = self.get_entity_name(ent) + "#" + str(conc)
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rs.ensure_bg_set_entity(n)
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new_reactants.append(n)
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for ent,conc in inhibitors:
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n = self.get_entity_name(ent) + "_" + str(conc)
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n = self.get_entity_name(ent) + "#" + str(conc)
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rs.ensure_bg_set_entity(n)
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new_inhibitors.append(n)
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if r_type == "inc":
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# pre_conc -- predecessor concentration
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# succ_conc -- successor concentration concentration
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for i in range(1,self.max_concentration):
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pre_conc = param_ent_name + "_" + str(i)
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rs.ensure_bg_set_entity(pre_conc)
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new_products = []
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succ_value = i+1
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for j in range(1,succ_value+1):
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new_p = param_ent_name + "_" + str(j)
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rs.ensure_bg_set_entity(new_p)
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new_products.append(new_p)
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rs.add_reaction(new_reactants + [pre_conc], new_inhibitors, new_products)
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elif r_type == "dec":
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for i in range(1,self.max_concentration):
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pre_conc = param_ent_name + "_" + str(i+1)
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rs.ensure_bg_set_entity(pre_conc)
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new_products = []
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succ_value = i
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for j in range(1,succ_value+1):
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new_p = param_ent_name + "_" + str(j)
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rs.ensure_bg_set_entity(new_p)
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new_products.append(new_p)
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rs.add_reaction(new_reactants + [pre_conc], new_inhibitors, new_products)
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max_cmd_c = self.max_concentration
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if command in self.max_conc_per_ent:
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max_cmd_c = self.max_conc_per_ent[command]
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else:
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raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
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print("WARNING:\n\tThere is no maximal concentration level defined for " + self.get_entity_name(command))
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print("\tThis is a very bad idea -- expect degraded performance\n")
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for l in range(1,max_cmd_c+1):
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cmd_ent = self.get_entity_name(command) + "#" + str(l)
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rs.ensure_bg_set_entity(cmd_ent)
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if r_type == "inc":
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# pre_conc -- predecessor concentration
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# succ_conc -- successor concentration concentration
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for i in range(1,self.max_concentration):
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pre_conc = param_ent_name + "#" + str(i)
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rs.ensure_bg_set_entity(pre_conc)
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new_products = []
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succ_value = i+l
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for j in range(1,succ_value+1):
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if j > self.max_concentration: break
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new_p = param_ent_name + "#" + str(j)
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rs.ensure_bg_set_entity(new_p)
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new_products.append(new_p)
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if new_products != []:
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rs.add_reaction(set(new_reactants + [pre_conc,cmd_ent]), set(new_inhibitors), set(new_products))
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elif r_type == "dec":
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for i in range(1,self.max_concentration+1):
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pre_conc = param_ent_name + "#" + str(i)
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rs.ensure_bg_set_entity(pre_conc)
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new_products = []
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succ_value = i-l
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for j in range(1,succ_value+1):
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if j > self.max_concentration: break
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new_p = param_ent_name + "#" + str(j)
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rs.ensure_bg_set_entity(new_p)
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new_products.append(new_p)
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if new_products != []:
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rs.add_reaction(set(new_reactants + [pre_conc,cmd_ent]), set(new_inhibitors), set(new_products))
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else:
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raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
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return rs
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@@ -323,15 +323,16 @@ def chain_reaction(print_system=False):
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exit(1)
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r = ReactionSystemWithConcentrations()
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r.add_bg_set_entity("inc")
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r.add_bg_set_entity("dec")
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r.add_bg_set_entity(("inc",1))
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r.add_bg_set_entity(("dec",1))
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for i in range(1,chainLen+1):
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r.add_bg_set_entity("e_" + str(i))
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for i in range(1,chainLen+1):
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ent = "e_" + str(i)
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r.add_reaction_inc(ent, [(ent, 1),("inc",1)],[(ent,maxConc)])
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r.add_reaction_inc(ent, "inc", [(ent, 1)],[(ent,maxConc)])
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r.add_reaction_dec(ent, "dec", [(ent, 1)],[])
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if i < chainLen:
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r.add_reaction([(ent,maxConc)],[],[("e_"+str(i+1),1)])
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@@ -350,15 +351,17 @@ def chain_reaction(print_system=False):
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if verify_rsc:
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smt_rsc = SmtCheckerRSC(rc)
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smt_rsc.check_reachability([('e_'+str(chainLen),maxConc)],max_level=maxConc*chainLen+10)
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# smt_rsc.show_encoding([('e_'+str(1),1)],print_time=True,max_level=maxConc*chainLen+10)
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prop = [('e_'+str(chainLen),maxConc)]
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smt_rsc.check_reachability(prop,max_level=maxConc*chainLen+10)
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# smt_rsc.show_encoding(prop,print_time=True,max_level=maxConc*chainLen+10)
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if not verify_rsc:
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else:
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orc = rc.get_ordinary_reaction_system_with_automaton()
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if print_system:
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print("\nTranslated:")
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orc.show()
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smt_tr_rs = SmtCheckerPGRS(orc)
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smt_tr_rs.check_reachability(['e_'+str(chainLen)+"_"+str(maxConc)])
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smt_tr_rs.check_reachability(['e_'+str(chainLen)+"#"+str(maxConc)])
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# print("Reaction System with Concentrations:", smt_rsc.get_verification_time())
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# print("Reaction System from translating RSC:", smt_tr_rs.get_verification_time())
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2
rssmt.py
2
rssmt.py
@@ -29,7 +29,7 @@ rsmc_banner = """
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def process():
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# rs_examples.run_counter_exp()
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rs_examples.chain_reaction()
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rs_examples.chain_reaction(print_system=True)
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##################################################################
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@@ -8,8 +8,8 @@ from sys import stdout
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from itertools import chain
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import resource
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# def simplify(x):
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# return x
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def simplify(x):
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return x
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class SmtCheckerRSC(object):
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@@ -114,7 +114,10 @@ class SmtCheckerRSC(object):
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# -------- meta reactions ---------------------------------------------------
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for r_type,reactants,inhibitors in meta_reactions:
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for r_type,command_entity,reactants,inhibitors in meta_reactions:
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# command entity is e.g. 'inc' for incrementation operation
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# (inc,W) gives us the value W by which the given entity's value should be incremented
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enc_reactants = True
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enc_inhibitors = True
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@@ -122,17 +125,47 @@ class SmtCheckerRSC(object):
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for reactant,concentration in reactants:
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enc_reactants = simplify(And(enc_reactants,
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Or(self.v[level][reactant] >= concentration, self.v_ctx[level][reactant] >= concentration)))
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# command entity needs to be present (with concentration level > 0) in order to perform the operation
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enc_reactants = simplify(And(enc_reactants,
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Or(self.v[level][command_entity] > 0, self.v_ctx[level][command_entity] > 0)))
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for inhibitor,concentration in inhibitors:
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enc_inhibitors = simplify(And(enc_inhibitors,
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And(self.v[level][inhibitor] < concentration, self.v_ctx[level][inhibitor] < concentration)))
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if r_type == "inc":
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# if r_type == "inc":
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# # depending on if the value of the command entity is greater in the context or in the current RS state
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# # we choose to increment by the greater value from v or v_ctx (this is because we take the max value).
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# enc_products = Or(
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# And(self.v_ctx[level][command_entity] >= self.v[level][command_entity],
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# self.v[level+1][prod_entity] == If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity])+self.v_ctx[level][command_entity]),
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# And(self.v[level][command_entity] > self.v_ctx[level][command_entity],
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# self.v[level+1][prod_entity] == If(self.v[level][prod_entity]>self.v_ctx[level][command_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity])+self.v[level][command_entity]))
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#
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# elif r_type == "dec":
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# # same happens here, but we decrement with the maximum value encoded at v or v_ctx.
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# enc_products = Or(
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# And(self.v_ctx[level][command_entity] >= self.v[level][command_entity],
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# self.v[level+1][prod_entity] == If(self.v[level][prod_entity]>self.v_ctx[level][command_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity])-self.v_ctx[level][command_entity]),
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# And(self.v[level][command_entity] > self.v_ctx[level][command_entity],
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# self.v[level+1][prod_entity] == If(self.v[level][prod_entity]>self.v_ctx[level][command_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity])-self.v[level][command_entity]))
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#
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# if r_type == "inc":
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# enc_products = self.v[level+1][prod_entity] == self.v[level][prod_entity]+1
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#
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# elif r_type == "dec":
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# enc_products = self.v[level+1][prod_entity] == self.v[level][prod_entity]-1
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enc_products = self.v[level+1][prod_entity] == self.v[level][prod_entity]+1
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if r_type == "inc":
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enc_products = self.v[level+1][prod_entity] == \
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If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) + \
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If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity])
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elif r_type == "dec":
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|
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enc_products = self.v[level+1][prod_entity] == self.v[level][prod_entity]-1
|
||||
enc_products = self.v[level+1][prod_entity] == \
|
||||
If(self.v[level][prod_entity]>self.v_ctx[level][prod_entity],self.v[level][prod_entity],self.v_ctx[level][prod_entity]) - \
|
||||
If(self.v[level][command_entity]>self.v_ctx[level][command_entity],self.v[level][command_entity],self.v_ctx[level][command_entity])
|
||||
|
||||
else:
|
||||
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
|
||||
@@ -355,7 +388,8 @@ class SmtCheckerRSC(object):
|
||||
self.solver.push()
|
||||
|
||||
s = self.enc_min_state(current_level,state)
|
||||
print(s)
|
||||
print("Test: ", s)
|
||||
|
||||
self.solver.add(s)
|
||||
|
||||
result = self.solver.check()
|
||||
|
||||
Reference in New Issue
Block a user