Source code for sbmltoodejax.utils

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", 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, deltaT=deltaT, atol=atol, rtol=rtol, mxstep=mxstep) return model_fp
[docs] def load_biomodel(model_idx, model_fp="jax_model.py", 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, 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