ReactionGenerator¶

Factory for synthetic reactions.

Overview¶

ReactionGenerator produces BioReactions with configurable kinetics and stoichiometry. Different named instances can match specific distributions (e.g., KEGG-like) or generate purely synthetic reactions.

Methods	Description
generate_anabolic	Generate anabolic reaction from given inputs
generate_catabolic	Generate catabolic reaction breaking down input
generate_energy	Generate energy carrier reaction

Protocol Definition¶

from typing import Protocol

class ReactionGenerator(Generator[BioReaction], Protocol):
    """Factory for synthetic reactions."""

    def generate_anabolic(self, inputs: list[BioMolecule]) -> BioReaction:
        """Generate anabolic reaction from given inputs."""
        ...

    def generate_catabolic(self, input: BioMolecule) -> BioReaction:
        """Generate catabolic reaction breaking down input."""
        ...

    def generate_energy(self) -> BioReaction:
        """Generate energy carrier reaction."""
        ...

Methods¶

generate_anabolic(inputs) -> BioReaction¶

Generates a reaction that builds a higher-depth molecule from inputs.

generate_catabolic(input) -> BioReaction¶

Generates a reaction that breaks down a molecule into simpler products.

generate_energy() -> BioReaction¶

Generates an energy carrier reaction (alien ATP/NADH analog).

Configurable Properties¶

Implementations can parameterize: - (n_reactants, n_products) template frequencies - Delta-depth patterns per reaction class - Activation energy and delta-G distributions - Effector role frequencies