Source code for sbmlutils.examples.tutorial.minimal_model_comp

"""Example creating composite model."""
from pathlib import Path

from sbmlutils.comp import flatten_sbml
from sbmlutils.cytoscape import visualize_sbml
from sbmlutils.factory import *
from sbmlutils.metadata import *


n_cells = 5
# -------------------------------------------------------------------------------------
model = Model(
    "minimal_model_comp",
    notes="""
    Hierarchical model reusing the minimal model in composite model coupling.
    """,
    packages=[Package.COMP_V1],
)

# create grid of compartments with main species
model.compartments = []
model.species = []
for k in range(n_cells):
    model.compartments.append(
        Compartment(sid=f"cell{k}", value=1.0),
    )
    model.species.append(
        Species(
            sid=f"S{k}",
            # metaId=f"meta_S{k}",
            initialConcentration=10.0 if k == 0 else 0.0,
            compartment=f"cell{k}",
        )
    )

model.parameters = [Parameter("D", 0.01)]

# transport reactions to couple cells
model.reactions = []
for k in range(n_cells - 1):
    model.reactions.append(
        Reaction(
            sid=f"J{k}", equation=f"S{k} <-> S{k+1}", formula=f"D * (S{k}-S{k+1})"
        ),
    )

# -------------------------------------------------------------------------------------
# model coupling
model.external_model_definitions = []
model.replaced_elements = []
model.submodels = []
for k in range(n_cells):
    model.external_model_definitions.append(
        ExternalModelDefinition(
            sid=f"emd{k}", source="minimal_model.xml", modelRef="minimal_model"
        ),
    )
    model.submodels.append(Submodel(sid=f"submodel{k}", modelRef=f"emd{k}"))
    model.replaced_elements.extend(
        [
            # replace compartments
            ReplacedElement(
                sid=f"cell{k}_RE",
                metaId=f"cell{k}_RE",
                elementRef=f"cell{k}",
                submodelRef=f"submodel{k}",
                portRef=f"cell{PORT_SUFFIX}",
            ),
            # replace species
            ReplacedElement(
                sid=f"S{k}_RE",
                metaId=f"S{k}_RE",
                elementRef=f"S{k}",
                submodelRef=f"submodel{k}",
                portRef=f"S1{PORT_SUFFIX}",
            ),
        ]
    )
# -------------------------------------------------------------------------------------


def create(output_dir: Path) -> None:
    """Create model."""

    # create external model
    from sbmlutils.examples.tutorial.minimal_model import model as minimal_model

    sbml_minimal_path = output_dir / f"{minimal_model.sid}.xml"
    create_model(
        model=minimal_model,
        filepath=sbml_minimal_path,
        validation_options=ValidationOptions(units_consistency=False),
    )

    # create comp model
    sbml_path = output_dir / f"{model.sid}.xml"
    sbml_path_flat = output_dir / f"{model.sid}_flat.xml"

    create_model(
        model=model,
        filepath=sbml_path,
        validation_options=ValidationOptions(units_consistency=False),
    )

    # flatten model
    flatten_sbml(sbml_path, sbml_flat_path=sbml_path_flat)

    # visualize all files
    for k, path in enumerate(
        [
            sbml_minimal_path,
            sbml_path,
            sbml_path_flat,
        ]
    ):
        visualize_sbml(sbml_path=path, delete_session=(k == 0))


if __name__ == "__main__":
    from sbmlutils.resources import EXAMPLES_DIR

    create(output_dir=EXAMPLES_DIR)