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"""Implements the Model class."""
import math
import re
import string
class Model:
"""The model describes the parameters, compartments, species, and
reactions."""
def __init__(self, startingTime):
"""
Make an empty model.
Member data. For each, the keys are the identifiers.
- species: A dictionary of species.
- reactions: A dictionary of reactions.
- timeEvents: A dictionary of time events.
- triggerEvents: A dictionary of trigger events.
- parameters: A dictionary of parameters. Note that the compartment
volumes are grouped with the parameters.
"""
# The simulation starting time.
self.startingTime = float(startingTime)
self.time = None
self.species = {}
self.reactions = {}
self.timeEvents = {}
self.triggerEvents = {}
self.parameters = {}
self.isInitialized = False
def initialize(self):
"""Initialize the species populations, reaction counts, events,
and parameters."""
self.isInitialized = True
self.time = self.startingTime
for id in self.species:
self.species[id].initialize()
for id in self.reactions:
self.reactions[id].initialize()
for id in self.timeEvents:
self.timeEvents[id].initialize()
for id in self.triggerEvents:
self.triggerEvents[id].initialize()
for id in self.parameters:
self.parameters[id].initialize()
def decorate(self, expression):
# All species and parameters must be added for decoration to work.
assert self.isInitialized
return re.sub('([a-zA-z]|_)[a-zA-Z0-9_]*', self.decorateIdentifierTime,
expression)
def decorateExceptTime(self, expression):
"""Decorate for a binary function of the model and the time."""
# All species and parameters must be added for decoration to work.
assert self.isInitialized
return re.sub('([a-zA-z]|_)[a-zA-Z0-9_]*', self.decorateIdentifier,
expression)
def decorateIdentifier(self, matchObject):
"""Change parameters and species to the variable name, assuming that
the Model variable is 'm'."""
mo = matchObject.group()
# Special case: the e in 1e-5 is not a parameter.
n = matchObject.start()
if mo == 'e' and n != 0 and matchObject.string[n-1] in\
['.'] + list(string.digits):
return mo
if mo in self.parameters:
return "m.parameters['" + mo + "'].value"
elif mo in self.species:
return "m.species['" + mo + "'].amount"
else:
return mo
def decorateIdentifierTime(self, matchObject):
"""Change parameters and species to the variable name, assuming that
the Model variable is 'm'."""
if matchObject.group() == 't':
return 'm.time'
else:
return self.decorateIdentifier(matchObject)
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