import importlib
from sbmltoodejax.biomodels_api import get_content_for_model
from sbmltoodejax.modulegeneration import GenerateModel
from sbmltoodejax.parse import ParseSBMLFile
[docs]
def generate_biomodel(model_idx, model_fp="jax_model.py",
vary_constant_reactants=False, vary_boundary_reactants=False,
deltaT=0.1, atol=1e-6, rtol=1e-12, mxstep=5000000):
"""Calls the `sbmltoodejax.modulegeneration.GenerateModel` for a SBML model hosted on the BioModel website and indexed by the provided `model_idx`.
Args:
model_idx: either an integer, or a valid model id
model_fp (str): filepath for the generated file
deltaT (float, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 0.1.
atol (float, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 1e-6.
rtol (float, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 1e-12.
mxstep (int, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 5000000.
Returns:
model_fp (str): the filepath containing the generated python file
"""
model_xml_body = get_content_for_model(model_idx)
model_data = ParseSBMLFile(model_xml_body)
GenerateModel(model_data, model_fp,
vary_constant_reactants=vary_constant_reactants, vary_boundary_reactants=vary_boundary_reactants,
deltaT=deltaT, atol=atol, rtol=rtol, mxstep=mxstep)
return model_fp
[docs]
def load_biomodel(model_idx, model_fp="jax_model.py",
vary_constant_reactants=False, vary_boundary_reactants=False,
deltaT=0.1, atol=1e-6, rtol=1e-12, mxstep=5000000):
"""Calls the generate_biomodel function for a SBML model hosted on the BioModel website and indexed by the provided `model_idx`,
then loads and returns the generated `model` module and `y0`, `w0`, `c` variables.
Args:
model_idx: either an integer, or a valid model id
model_fp (str): filepath for the generated file
deltaT (float, optional): parameter passed to `generate_biomodel`. Default to 0.1.
atol (float, optional): parameter passed to `generate_biomodel`. Default to 1e-6.
rtol (float, optional): parameter passed to `generate_biomodel`. Default to 1e-12.
mxstep (int, optional): parameter passed to `generate_biomodel`. Default to 5000000.
Returns:
tuple containing
- model (ModelRollout): generated model rollout module
- y0 (jax.numpy.Array): default initial state of y variable(as provided in the SBML file)
- w0 (jax.numpy.Array): default initial state of w variable (as provided in the SBML file)
- c (jax.numpy.Array): default values of constant kinematic parameters c (as provided in the SBML file)
"""
model_fp = generate_biomodel(model_idx, model_fp=model_fp,
vary_constant_reactants=vary_constant_reactants, vary_boundary_reactants=vary_boundary_reactants,
deltaT=deltaT, atol=atol, rtol=rtol, mxstep=mxstep)
spec = importlib.util.spec_from_file_location("JaxModelSpec", model_fp)
module = importlib.util.module_from_spec(spec)
spec.loader.exec_module(module)
model_cls = getattr(module, "ModelRollout")
model = model_cls()
y0 = getattr(module, "y0")
w0 = getattr(module, "w0")
c = getattr(module, "c")
return model, y0, w0, c
