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Semi-working version of parametric MC for rsLTL

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This commit is contained in:
Artur Meski
2017-09-17 12:24:07 +01:00
parent f7cfeb43c1
commit 9297a7caf7
4 changed files with 188 additions and 117 deletions
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23
rs/reaction_system_with_concentrations_param.py
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@@ -14,6 +14,8 @@ class ParameterObj(object):
def is_param(some_object):
if isinstance(some_object, ParameterObj):
return True
else:
return False
class ReactionSystemWithConcentrationsParam(ReactionSystem):
@@ -21,7 +23,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
self.reactions = []
self.parameters = dict()
self.parametric_reactions = []
# self.parametric_reactions = []
self.meta_reactions = dict()
self.permanent_entities = dict()
self.background_set = []
@@ -170,10 +172,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
raise RuntimeError("No products defined")
reaction = self.process_rip(R,I,P)
if self.is_parametric_reaction(reaction):
self.parametric_reactions.append(reaction)
else:
self.reactions.append(reaction)
self.reactions.append(reaction)
def add_reaction_without_reactants(self, R, I, P):
"""Adds a reaction"""
@@ -254,18 +253,6 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
" ) Command=( " + self.get_entity_name(command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
def show_param_reactions(self, soft=False):
print(C_MARK_INFO + " Parametric reactions:")
if soft and len(self.parametric_reactions) > 50:
print(" -> there are more than 50 reactions (" + str(len(self.parametric_reactions)) + ")")
else:
print(" "*4 + "{0: ^35}{1: ^25}{2: ^15}".format("reactants"," inhibitors"," products"))
for reactants,inhibitors,products in self.parametric_reactions:
print(" " + "- {0: ^35}{1: ^25}{2: ^15}".format(
"{ " + self.state_to_str(reactants) + " }",
" { " + self.state_to_str(inhibitors) + " }",
" { " + self.state_to_str(products) + " }"))
def show_max_concentrations(self):
print(C_MARK_INFO + " Maximal allowed concentration levels:")
@@ -280,7 +267,7 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
def show(self, soft=False):
self.show_background_set()
self.show_reactions(soft)
self.show_param_reactions(soft)
# self.show_param_reactions(soft)
self.show_permanent_entities()
self.show_meta_reactions()
self.show_max_concentrations()