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Pathway

Connected sequence of reactions (analytical abstraction).

Overview

A Pathway is a connected subgraph of the reaction network that performs a coherent metabolic function, such as a biosynthetic pathway, energy cycle, or signaling cascade.

Pathway is an analytical abstraction - it's useful for understanding, generating, and describing reaction networks, but the simulation itself operates directly on Reactions without needing pathway information.

Properties Type Description
reactions list Ordered reactions in the pathway
entry_molecules set Molecules consumed from outside
exit_molecules set Molecules produced for outside
pathway_type PathwayType Linear, branching, cyclic, or signaling
net_stoichiometry dict Net consumption/production

Protocol Definition

from typing import Protocol
from enum import Enum

class PathwayType(Enum):
    LINEAR = "linear"
    BRANCHING = "branching"
    CYCLIC = "cyclic"
    SIGNALING = "signaling"

class Pathway(Entity, Protocol):
    """Connected sequence of reactions."""

    reactions: list[Reaction]
    entry_molecules: set[Molecule]
    exit_molecules: set[Molecule]
    pathway_type: PathwayType

    @property
    def net_stoichiometry(self) -> dict[str, int]:
        """Net input/output across the pathway."""
        ...

Use Cases

  • Understanding: Identify which reactions form glycolysis, TCA cycle, etc.
  • Generation: Create coherent synthetic biologies with sensible pathway structures
  • Analysis: Find bottlenecks, understand metabolic flow
  • Task design: "Diagnose a defect in this pathway"

See Also