"""
================================================
Toy Injected Glucose Phosphorylation Compartment
================================================
This is a toy example referenced in the documentation.
"""
from vivarium.processes.glucose_phosphorylation import (
GlucosePhosphorylation,
)
from vivarium.processes.injector import Injector
from vivarium.core.experiment import Experiment
from vivarium.core.process import Generator
from vivarium.library.pretty import format_dict
[docs]class InjectedGlcPhosphorylation(Generator):
defaults = {
'glucose_phosphorylation': {
'k_cat': 1e-2,
},
'injector': {
'substrate_rate_map': {
'GLC': 1e-4,
'ATP': 1e-3,
},
},
}
def __init__(self, config):
super(InjectedGlcPhosphorylation, self).__init__(config)
[docs] def generate_processes(self, config):
injector = Injector(self.config['injector'])
glucose_phosphorylation = GlucosePhosphorylation(
self.config['glucose_phosphorylation'])
return {
'injector': injector,
'glucose_phosphorylation': glucose_phosphorylation,
}
[docs] def generate_topology(self, config):
return {
'injector': {
'internal': ('cell', ),
},
'glucose_phosphorylation': {
'cytoplasm': ('cell', ),
'nucleoside_phosphates': ('cell', ),
'global': ('global', ),
},
}