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"""Implements the Reaction class."""
from SpeciesReference import SpeciesReference
from math import *
class Reaction:
"""A reaction is comprised of an identifier, name, reactants, products,
mass action indicator, and propensity function.
Member data:
- self.reactants: List of SpeciesReference.
- self.products: List of SpeciesReference."""
def __init__(self, model, reactants, products, propensityExpression):
self.model = model
# A list of SpeciesReference.
self.reactants = reactants
# A list of SpeciesReference.
self.products = products
# The string that defines the propensity function.
self.propensityExpression = propensityExpression
def propensity(self):
return self.propensityFunction(self.model)
def initialize(self):
self.count = 0
# Decorate the expression here so that we don't have to do it when
# the reaction fires. Note that we can't do this in the constructor
# because the propensity expression may depend on parameters that would
# not yet have been defined.
e = self.model.decorate(self.propensityExpression)
self.propensityFunction = lambda m: eval(e)
def fire(self):
self.count += 1
for x in self.reactants:
self.model.species[x.species].amount -= x.stoichiometry
for x in self.products:
self.model.species[x.species].amount += x.stoichiometry
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