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ABIO biology

Molecules, reactions, chemistry, compartments and the simulators over them.

The generator and pathway pages this index used to carry were retired 2026-10-07 (T068): MoleculeGenerator, ReactionGenerator, ContainerGenerator, the Generator protocol and Pathway are M1 design-era classes that no survivor of M47.7 / T056 implements. World construction is the suite subsystem's skeletons and drafter heads now (see ABIO Suite Runtime), and the reaction-network views that replaced Pathway's role live in infra/graph_ops.py. The "(Rust)" markers are gone with them: rust/ is a stub nothing in the package calls.

Atoms and Molecules

Chemical elements and compounds in the alien biology. - ABIO Atom - Chemical element with symbol, name, and atomic weight. Immutable value objects shared across molecules. - ABIO Molecule - Chemical compound composed of atoms. Has biosynthetic depth, derived formula (symbol), and molecular weight.

Reactions

Transformations between molecules. - ABIO Reaction - Transformation with reactants, products, effectors, and rate functions.

Chemistry

Container for molecules and reactions forming a chemical system. - ABIO Chemistry - Entity that groups molecules and reactions together. Provides validation, state management, and simulation support.

Compartments

Nestable biological structures from organelles to organisms. All are Entity subclasses. - ABIO Compartment - Nestable Entity for molecules, reactions, and child containers. Kind labels: organism, organ, cell, organelle.

Simulation

Multi-compartment simulation with reactions within compartments and flows across membranes. - ABIO WorldState - Dense concentration storage: [num_compartments × num_molecules] array. GPU-friendly, O(1) access. - ABIO CompartmentTree - Hierarchical topology of compartments. Stores parent-child relationships, separated from concentrations. - ABIO Flow - Transport between compartments: TransportFlux, amount-conserving between any two compartment pools, applied in one rationed pass. - ABIO WorldSimulator - Multi-compartment simulation engine. Applies reactions within compartments, flows across membranes.