Architecture Docs

Protocols

Alphabetical listing of all classes in the Alien Biology system, organized by subsystem.

By Subsystem

Subsystem	Classes
Infrastructure	Bio, Entity, Expr, Interpreter, IO
Biology	Atom, Chemistry, Compartment, CompartmentTree, ContainerGenerator, Flow, Generator, Molecule, MoleculeGenerator, Pathway, Reaction, ReactionGenerator, WorldSimulator, WorldState
Execution	Action, Context, Experiment, Measurement, Simulator, State, Step, Task, Test, TestHarness, Timeline, World

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A

• Action — Agent action to perturb the system state
• Atom — Chemical element with symbol, name, and atomic weight

B

• Bio — Loading, hydration, and persistence for biology objects in DAT folders

C

• Chemistry — Container for molecules and reactions forming a chemical system
• Compartment — Nestable container for molecules, reactions, and child containers
• CompartmentTree — Hierarchical topology of compartments with parent-child relationships
• ContainerGenerator — Composable factory for Compartments
• Context — Runtime pegboard for all major subsystems

E

• Entity — Base class for all biology objects
• Experiment — Single world setup with task, agent, scoring
• Expr — Simple functional expressions for operations and declarations

F

• Flow — Membrane transport between parent-child compartments

G

• Generator — Base class for synthetic biology factories

I

• Interpreter — Evaluates Expr trees and handles language dispatch
• IO — Entity I/O: prefix bindings, formatting, parsing, persistence

M

• Measurement — Function to observe system state
• Molecule — Chemical compound composed of atoms with derived formula and weight
• MoleculeGenerator — Factory for synthetic molecules

P

• Pathway — Connected sequence of reactions

R

• Reaction — Transformation between molecules with reactants, products, effectors
• ReactionGenerator — Factory for synthetic reactions

S

• Scenario — Complete runnable unit (chemistry, containers, interface, briefing, constitution)
• Simulator — Execution engine for biology dynamics
• State — Snapshot of molecule concentrations
• Step — Single time advancement applying reactions

T

• Task — Goal specification with scoring criteria
• Test — Batch of experiments across variations
• TestHarness — Execution runner with logging and result aggregation
• Timeline — Sequence of states with intervention hooks

W

• World — Complete runnable setup with system, generators, initial conditions
• WorldSimulator — Multi-compartment simulation engine with reactions and flows
• WorldState — Dense concentration storage for multi-compartment simulations