MoleculeGenerator¶

Factory for synthetic molecules.

Overview¶

MoleculeGenerator produces BioMolecules with configurable properties. Different named instances can match specific distributions (e.g., KEGG-like) or generate purely synthetic molecules.

Methods	Description
generate_primitive	Generate a bdepth=0 molecule
generate_at_depth	Generate molecule at specific biosynthetic depth
generate_name	Generate alien molecule name

Protocol Definition¶

from typing import Protocol

class MoleculeGenerator(Generator[BioMolecule], Protocol):
    """Factory for synthetic molecules."""

    def generate_primitive(self) -> BioMolecule:
        """Generate a bdepth=0 molecule."""
        ...

    def generate_at_depth(self, bdepth: int) -> BioMolecule:
        """Generate molecule at specific biosynthetic depth."""
        ...

    def generate_name(self) -> str:
        """Generate alien molecule name."""
        ...

Methods¶

generate_primitive() -> BioMolecule¶

Generates a bdepth=0 primitive molecule from alien atoms.

generate_at_depth(bdepth) -> BioMolecule¶

Generates a molecule at the specified biosynthetic depth.

generate_name() -> str¶

Generates an alien name using Markov chain or diffusion model.

Configurable Properties¶

Implementations can parameterize: - Atom count distributions per bdepth - Functional group frequencies - Molecular weight distributions - Naming patterns (Markov, diffusion, etc.)