"""
Model M12a: Extrinsic apoptosis model incorporating the "Direct" MOMP model from
[Cui2008]_.
"""
from pysb import *
from earm import shared
from earm.shared import V
from scipy.constants import N_A
from earm import albeck_modules
from earm import shen_modules
import re
Model()
# Declare monomers
albeck_modules.ligand_to_c8_monomers()
shen_modules.momp_monomers()
albeck_modules.apaf1_to_parp_monomers()
# The specific MOMP model to use
shen_modules.cui_direct(do_pore_transport=True)
# Set initial condition for uncleaved Bid to 20nM, per the paper
Initial(Bid(state='U', bf=None), Parameter('Bid_0', 20e-9 * N_A * V))
albeck_modules.rec_to_bid()
albeck_modules.pore_to_parp()
# Declare common observables
shared.observables()
# Additional observables
Observable('aBax_', Bax(state='A', bf=None))
Observable('Bcl2_', Bcl2(bf=None))
Observable('Bcl2_Bid_', Bcl2(bf=1) % Bid(bf=1))
Observable('Bcl2_Bax_', Bcl2(bf=1) % Bax(bf=1))