from typing import Dict, Tuple
from collections import namedtuple
from sbmlsim.experiment import SimulationExperiment
from sbmlsim.model import AbstractModel
from sbmlsim.simulation import TimecourseSim
from sbmlsim.simulation.sensitivity import ModelSensitivity
from sbmlsim.task import Task
from ...midazolam import MODEL_PATH
[docs]MolecularWeights = namedtuple("MolecularWeights", "mid mid1oh")
[docs]class MidazolamSimulationExperiment(SimulationExperiment):
"""Base class for all GlucoseSimulationExperiments."""
[docs] def models(self) -> Dict[str, AbstractModel]:
Q_ = self.Q_
models = {
"model": AbstractModel(
source=MODEL_PATH,
language_type=AbstractModel.LanguageType.SBML,
changes={
"KI__MID1OHEX_Vmax": Q_(14.259652024532818, "mmole/min"),
"KI__MID1OHEX_Km": Q_(0.7051197538875393, "mM"),
"ftissue_mid1oh": Q_(99.23248555491428, "liter/min"),
"fup_mid1oh": Q_(0.19507488419734886, "dimensionless"),
},
)
}
return models
[docs] def tasks(self) -> Dict[str, Task]:
if self.simulations():
return {
f"task_{key}": Task(model="model", simulation=key)
for key in self.simulations()
}
else:
return {}
[docs] def simulations(self, simulations=None) -> Dict[str, TimecourseSim]:
if simulations is None:
return simulations
# injecting additional scan dimension for timecourse simulation
# for sim_key, sim in simulations.copy().items():
# if isinstance(sim, TimecourseSim):
# scan = ModelSensitivity.difference_sensitivity_scan(
# model=self._models["model"],
# simulation=sim,
# difference=0.5,
# exclude_filter=exclude_parameters_midazolam,
# )
# simulations[f"{sim_key}_sensitivity"] = scan
# print("Simulation keys:", simulations.keys())
return simulations
@property
[docs] def Mr(self):
return MolecularWeights(
mid=self.Q_(325.768, "g/mole"),
mid1oh=self.Q_(341.8, "g/mole"),
)
[docs]def exclude_parameters_midazolam(pid: str) -> bool:
"""Filter for excluding parameter ids in sensitivity."""
if pid.startswith("Mr_"):
return True
if pid.startswith("conversion_"):
return True
if pid.startswith("F_"):
return True
if pid.startswith("BP_"):
return True
return False