rs package
This commit is contained in:
Artur Meski
414
rs/reaction_system_with_concentrations.py
Normal file
414
rs/reaction_system_with_concentrations.py
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from sys import exit
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from colour import *
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from rs.reaction_system import ReactionSystem
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class ReactionSystemWithConcentrations(ReactionSystem):
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def __init__(self):
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self.reactions = []
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self.meta_reactions = dict()
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self.permanent_entities = dict()
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self.background_set = []
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self.context_entities = [] # legacy. to be removed
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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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print("\n\nWARNING: no maximal concentration level specified for:", e, "\n\n")
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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 get_max_concentration_level(self, e):
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if e in self.max_conc_per_ent:
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return self.max_conc_per_ent[e]
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else:
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return self.max_concentration
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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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if type(e) is tuple:
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if len(e) == 2 and type(e[1]) is int:
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return True
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if type(e) is list:
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if len(e) == 2 and type(e[1]) is int:
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return True
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print("FATAL. Invalid entity+concentration:")
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print(e)
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exit(1)
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return False
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def get_state_ids(self, state):
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"""Returns entities of the given state without levels"""
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return [e for e,c in state]
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def has_non_zero_concentration(self, elem):
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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, ignore_empty_R=False):
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"""Chcecks concentration levels and converts entities names into their ids"""
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if R == [] and not ignore_empty_R:
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raise RuntimeError("No reactants defined")
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reactants = []
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for r in R:
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self.is_valid_entity_with_concentration(r)
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self.has_non_zero_concentration(r)
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entity,level = r
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reactants.append((self.get_entity_id(entity),level))
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if self.max_concentration < level:
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self.max_concentration = level
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inhibitors = []
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for i in I:
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self.is_valid_entity_with_concentration(i)
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self.has_non_zero_concentration(i)
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entity,level = i
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inhibitors.append((self.get_entity_id(entity),level))
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if self.max_concentration < level:
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self.max_concentration = level
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products = []
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for p in P:
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self.is_valid_entity_with_concentration(p)
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self.has_non_zero_concentration(p)
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entity,level = p
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products.append((self.get_entity_id(entity),level))
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return reactants,inhibitors,products
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def add_reaction(self, R, I, P):
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"""Adds a reaction"""
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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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self.reactions.append(reaction)
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def add_reaction_without_reactants(self, R, I, P):
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"""Adds a reaction"""
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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,ignore_empty_R=True)
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self.reactions.append(reaction)
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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,[],ignore_empty_R=True)
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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", self.get_entity_id(incrementer), reactants, inhibitors))
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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,[],ignore_empty_R=True)
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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", self.get_entity_id(decrementer), reactants, inhibitors))
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def add_permanency(self, ent, I):
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"""Sets entity to be permanent unless it is inhibited"""
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ent_id = self.get_entity_id(ent)
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if ent_id in self.permanent_entities:
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raise RuntimeError("Permanency for {0} already defined.".format(ent))
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inhibitors = self.process_rip([],I,[],ignore_empty_R=True)[1]
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self.permanent_entities[ent_id] = inhibitors
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def set_context_entities(self, entities):
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raise NotImplementedError
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def entities_names_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += entity + ", "
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s = s[:-2]
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return s
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def entities_ids_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += self.get_entity_name(entity) + ", "
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s = s[:-2]
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return s
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def state_to_str(self, state):
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s = ""
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for ent,level in state:
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s += self.get_entity_name(ent) + "=" + str(level) + ", "
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s = s[:-2]
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return s
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def show_background_set(self):
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print(C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
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def show_meta_reactions(self):
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print(C_MARK_INFO + " Meta reactions:")
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for param_ent,reactions in self.meta_reactions.items():
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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(" - [ 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) + "}, I={" + 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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def show_max_concentrations(self):
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print(C_MARK_INFO + " Maximal allowed concentration levels (for optimized translation to RS):")
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for e,max_conc in self.max_conc_per_ent.items():
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print(" - {0:^20} = {1:<6}".format(self.get_entity_name(e),max_conc))
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def show_permanent_entities(self):
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print(C_MARK_INFO + " Permanent entities:")
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for e,inhibitors in self.permanent_entities.items():
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print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ","I={" + self.state_to_str(inhibitors) + "}"))
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def show(self, soft=False):
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self.show_background_set()
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self.show_reactions(soft)
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self.show_permanent_entities()
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self.show_meta_reactions()
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self.show_max_concentrations()
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def get_reactions_by_product(self):
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"""Sorts reactions by their products and returns a dictionary of products"""
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if self.reactions_by_prod != None:
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return self.reactions_by_prod
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producible_entities = set()
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for reaction in self.reactions:
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product_entities = [e for e,c in reaction[2]]
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producible_entities = producible_entities.union(set(product_entities))
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reactions_by_prod = {}
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for p_e in producible_entities:
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reactions_by_prod[p_e] = []
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rcts_for_p_e = reactions_by_prod[p_e]
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for r in self.reactions:
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product_entities = [e for e,c in r[2]]
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if p_e in product_entities:
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reactants = r[0]
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inhibitors = r[1]
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products = [(e,c) for e,c in r[2] if e == p_e]
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prod_conc = products[0][1]
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insert_place = None
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# we need to order the reactions w.r.t. the concentration levels produced (increasing order)
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for i in range(0,len(rcts_for_p_e)):
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checked_conc = rcts_for_p_e[i][2][0][1]
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if prod_conc <= checked_conc:
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insert_place = i
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break
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if insert_place == None: # empty or the is only one element which is smaller than the element being added
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rcts_for_p_e.append((reactants, inhibitors, products)) # we append (to the end)
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else:
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rcts_for_p_e.insert(insert_place,(reactants, inhibitors, products))
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# save in cache
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self.reactions_by_prod = reactions_by_prod
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return reactions_by_prod
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def get_reaction_system(self):
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rs = ReactionSystem()
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for reactants,inhibitors,products in self.reactions:
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new_reactants = []
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new_inhibitors = []
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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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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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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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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,command,reactants,inhibitors in reactions:
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param_ent_name = self.get_entity_name(param_ent)
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new_reactants = []
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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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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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rs.ensure_bg_set_entity(n)
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new_inhibitors.append(n)
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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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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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for ent,inhibitors in self.permanent_entities.items():
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max_c = self.max_concentration
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if ent in self.max_conc_per_ent:
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max_c = self.max_conc_per_ent[ent]
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else:
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print("WARNING:\n\tThere is no maximal concentration level defined for " + self.get_entity_name(ent))
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print("\tThis is a very bad idea -- expect degraded performance\n")
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def e_value(i):
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return self.get_entity_name(ent) + "#" + str(i)
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for value in range(1,max_c+1):
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new_reactants = []
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new_inhibitors = []
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new_products = []
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new_reactants = [e_value(value)]
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for e_inh,conc in inhibitors:
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n = self.get_entity_name(e_inh) + "#" + 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 i in range(1,value+1):
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new_products.append(e_value(i))
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rs.add_reaction(new_reactants,new_inhibitors,new_products)
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return rs
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class ReactionSystemWithAutomaton(object):
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def __init__(self, reaction_system, context_automaton):
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self.rs = reaction_system
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self.ca = context_automaton
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def show(self, soft=False):
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self.rs.show(soft)
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self.ca.show()
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def is_with_concentrations(self):
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if not isinstance(self.rs, ReactionSystemWithConcentrations):
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return False
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if not isinstance(self.ca, ContextAutomatonWithConcentrations):
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return False
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return True
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def sanity_check(self):
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pass
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def get_ordinary_reaction_system_with_automaton(self):
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if not self.is_with_concentrations():
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raise RuntimeError("Not RS/CA with concentrations")
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ors = self.rs.get_reaction_system()
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oca = self.ca.get_automaton_with_flat_contexts(ors)
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return ReactionSystemWithAutomaton(ors, oca)
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# class ReactionSystemWithConcentrationWithAutomaton(ReactionSystemWithAutomaton):
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#
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# def __init__(self, reaction_system, context_automaton):
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# self.rs = reaction_system
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# self.ca = context_automaton
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#
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# def show(self, soft=False):
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# self.rs.show(soft)
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# self.ca.show()
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