black formatting
This commit is contained in:
Artur Meski
@@ -5,9 +5,7 @@ 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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@@ -26,8 +24,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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name = e
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print("\nWARNING: no maximal concentration level specified for:", e, "\n")
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else:
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raise RuntimeError(
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"Bad entity type when adding background set element")
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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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@@ -41,7 +38,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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@@ -69,8 +65,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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(
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"Unexpected concentration level in state: " + str(elem))
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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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@@ -123,21 +118,25 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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(
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R, I, [], ignore_empty_R=True)
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R, I, [], ignore_empty_R=True
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)
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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(
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("inc", self.get_entity_id(incrementer), reactants, inhibitors))
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("inc", self.get_entity_id(incrementer), reactants, inhibitors)
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)
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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(
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R, I, [], ignore_empty_R=True)
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R, I, [], ignore_empty_R=True
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)
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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(
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("dec", self.get_entity_id(decrementer), reactants, inhibitors))
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("dec", self.get_entity_id(decrementer), reactants, inhibitors)
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)
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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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@@ -145,8 +144,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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(
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"Permanency for {0} already defined.".format(ent))
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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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@@ -177,31 +175,50 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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def show_background_set(self):
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print(
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C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
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C_MARK_INFO
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+ " Background set: {"
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+ self.entities_names_set_to_str(self.background_set)
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+ "}"
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)
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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) + " ) Command=( " + self.get_entity_name(
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command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
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print(
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" - [ Type="
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+ repr(r_type)
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+ " Operand=( "
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+ self.get_entity_name(param_ent)
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+ " ) Command=( "
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+ self.get_entity_name(command)
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+ " ) ] -- ( R={"
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+ self.state_to_str(reactants)
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+ "}, I={"
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+ self.state_to_str(inhibitors)
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+ "} )"
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)
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else:
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raise RuntimeError(
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"Unknown meta-reaction type: " + repr(r_type))
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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(
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C_MARK_INFO +
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" Maximal allowed concentration levels (for optimized translation to RS):")
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C_MARK_INFO
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+ " Maximal allowed concentration levels (for optimized translation to RS):"
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)
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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) + ": ",
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"I={" + self.state_to_str(inhibitors) + "}"))
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print(
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" - {0:^20}{1:<6}".format(
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self.get_entity_name(e) + ": ",
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"I={" + self.state_to_str(inhibitors) + "}",
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)
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)
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def show(self, soft=False):
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self.show_background_set()
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@@ -220,8 +237,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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(
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set(product_entities))
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producible_entities = producible_entities.union(set(product_entities))
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reactions_by_prod = {}
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@@ -242,18 +258,20 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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if (
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insert_place == None
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): # empty or the is only one element which is smaller than the element being added
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# we append (to the end)
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rcts_for_p_e.append((reactants, inhibitors, products))
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else:
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rcts_for_p_e.insert(
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insert_place, (reactants, inhibitors, products))
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insert_place, (reactants, inhibitors, products)
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)
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# save in cache
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self.reactions_by_prod = reactions_by_prod
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@@ -261,11 +279,9 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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@@ -281,7 +297,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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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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@@ -290,7 +306,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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@@ -312,16 +327,15 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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else:
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print(
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"WARNING:\n\tThere is no maximal concentration level defined for "
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+ self.get_entity_name(command))
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+ self.get_entity_name(command)
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)
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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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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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@@ -329,8 +343,8 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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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:
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break
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new_p = param_ent_name + "#" + str(j)
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@@ -340,15 +354,16 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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rs.add_reaction(
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set(new_reactants + [pre_conc, cmd_ent]),
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set(new_inhibitors),
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set(new_products))
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set(new_products),
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)
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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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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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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:
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break
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new_p = param_ent_name + "#" + str(j)
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@@ -358,28 +373,29 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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rs.add_reaction(
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set(new_reactants + [pre_conc, cmd_ent]),
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set(new_inhibitors),
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set(new_products))
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set(new_products),
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)
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else:
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raise RuntimeError(
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"Unknown meta-reaction type: " + repr(r_type))
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"Unknown meta-reaction type: " + repr(r_type)
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)
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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(
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"WARNING:\n\tThere is no maximal concentration level defined for "
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+ self.get_entity_name(ent))
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+ self.get_entity_name(ent)
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)
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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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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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@@ -391,7 +407,7 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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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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@@ -400,7 +416,6 @@ class ReactionSystemWithConcentrations(ReactionSystem):
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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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@@ -420,7 +435,6 @@ class ReactionSystemWithAutomaton(object):
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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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