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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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46
reactics-smt/rs/reaction_system.py
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@@ -3,9 +3,7 @@ from colour import *
class ReactionSystem(object):
def __init__(self):
self.reactions = []
self.background_set = []
@@ -30,8 +28,7 @@ class ReactionSystem(object):
def assume_not_in_bgset(self, name):
if self.is_in_background_set(name):
raise RuntimeError(
"The entity " + name + " is already on the list")
raise RuntimeError("The entity " + name + " is already on the list")
def add_bg_set_entity(self, name):
self.assume_not_in_bgset(name)
@@ -106,7 +103,6 @@ class ReactionSystem(object):
self.init_contexts.append(integers)
def set_context_entities(self, entities):
for entity in entities:
entity_id = self.get_entity_id(entity)
self.context_entities.append(entity_id)
@@ -131,20 +127,36 @@ class ReactionSystem(object):
def show_reactions(self, soft=False):
print(C_MARK_INFO + " Reactions:")
if soft and len(self.reactions) > 50:
print(" -> there are more than 50 reactions (" +
str(len(self.reactions)) + ")")
print(
" -> there are more than 50 reactions ("
+ str(len(self.reactions))
+ ")"
)
else:
print(
" "*4 + "{0: ^35}{1: ^25}{2: ^15}".format("reactants", " inhibitors", " products"))
" " * 4
+ "{0: ^35}{1: ^25}{2: ^15}".format(
"reactants", " inhibitors", " products"
)
)
for reaction in self.reactions:
# print("\t( R={" + self.state_to_str(reaction[0]) + "}, I={" + self.state_to_str(reaction[1]) + "}, P={" + self.state_to_str(reaction[2]) + "} )")
print(" " + "- {0: ^35}{1: ^25}{2: ^15}".format("{ " + self.state_to_str(reaction[0]) + " }",
" { " + self.state_to_str(reaction[1]) + " }",
" { " + self.state_to_str(reaction[2]) + " }"))
print(
" "
+ "- {0: ^35}{1: ^25}{2: ^15}".format(
"{ " + self.state_to_str(reaction[0]) + " }",
" { " + self.state_to_str(reaction[1]) + " }",
" { " + self.state_to_str(reaction[2]) + " }",
)
)
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_initial_contexts(self):
if len(self.init_contexts) > 0:
@@ -155,10 +167,12 @@ class ReactionSystem(object):
def show_context_entities(self):
if len(self.context_entities) > 0:
print(
C_MARK_INFO + " Context entities: " + self.entities_ids_set_to_str(self.context_entities))
C_MARK_INFO
+ " Context entities: "
+ self.entities_ids_set_to_str(self.context_entities)
)
def show(self, soft=False):
self.show_background_set()
self.show_initial_contexts()
self.show_reactions(soft)
@@ -181,8 +195,7 @@ class ReactionSystem(object):
reactions_by_prod[prod_entity] = []
for reaction in self.reactions:
if prod_entity in reaction[2]:
reactions_by_prod[prod_entity].append(
[reaction[0], reaction[1]])
reactions_by_prod[prod_entity].append([reaction[0], reaction[1]])
# save in cache
self.reactions_by_prod = reactions_by_prod
@@ -200,4 +213,5 @@ class ReactionSystem(object):
print("Empty background set")
exit(1)
# EOF