ContainerGenerator¶

Composable factory for BioContainers.

Overview¶

ContainerGenerator creates BioContainers by composing simpler generators. Generators are recursively composable: a ContainerGenerator uses MoleculeGenerators and ReactionGenerators internally, and can itself be used by other ContainerGenerators to build deeper hierarchies. This allows complex biological structures to emerge from simple, reusable building blocks.

Properties	Type	Description
molecule_gen	MoleculeGenerator	Source for molecules
reaction_gen	ReactionGenerator	Source for reactions
child_gen	ContainerGenerator	Optional source for child containers

Methods	Description
generate	Generate a container with specified parameters
compose	Combine with another generator to create nested structures

Protocol Definition¶

from typing import Protocol, Optional

class ContainerGenerator(Generator[BioContainer], Protocol):
    """Composable factory for BioContainers."""

    molecule_gen: MoleculeGenerator
    reaction_gen: ReactionGenerator
    child_gen: Optional["ContainerGenerator"]

    def generate(self, n_molecules: int, n_reactions: int,
                 n_children: int = 0, depth: int = 1) -> BioContainer:
        """Generate a container, optionally with nested children."""
        ...

    def compose(self, child_generator: "ContainerGenerator") -> "ContainerGenerator":
        """Return a new generator that uses this for children."""
        ...

Methods¶

generate(n_molecules, n_reactions, n_children, depth) -> BioContainer¶

Creates a container with the specified number of molecules and reactions. If n_children > 0, recursively generates child containers using child_gen (or self if no child_gen specified). The depth parameter limits recursion.

compose(child_generator) -> ContainerGenerator¶

Returns a new ContainerGenerator that uses child_generator to produce its nested containers. This enables building generators for complex hierarchies from simpler ones.

Composability Pattern¶

# Simple generators for different scales
organelle_gen = ContainerGenerator(molecule_gen, reaction_gen)
cell_gen = organelle_gen.compose(organelle_gen)  # cells contain organelles
organ_gen = cell_gen.compose(cell_gen)           # organs contain cells

# Generate a complete organ with nested structure
organ = organ_gen.generate(n_molecules=10, n_reactions=5, n_children=100, depth=3)