Crate gapsmith_core 

Core types for gapsmith.

Every other crate depends on this one. Kept deliberately small: only the in-memory representation of a metabolic model plus the supporting ID, stoichiometry, and GPR types. No I/O, no solvers, no databases.

Overview

Model is the central type — an analogue of cobrar’s ModelOrg S4 class. It bundles:

• Compartments (cytosol c0, extracellular e0, periplasm p0).
• Metabolites (compound id + compartment + chemical formula).
• Reactions (id, name, bounds, objective coefficient, GPR, EC list, gapseq-specific gs.origin provenance tag, SEED curation status).
• A sparse StoichMatrix in CSC layout (sprs under the hood), one column per reaction, one row per metabolite.
• A ModelAnnot bundle of provenance metadata that travels with the model through CBOR / SBML round-trips.

ID newtypes

CpdId, RxnId, GeneId wrap Arc<str>. Cloning is cheap and the types are mutually incompatible so a metabolite id can’t accidentally be used where a reaction id is expected.

Serialisation

Every public type derives Serialize + Deserialize. CBOR (via ciborium) is the primary storage format; JSON works too. See the gapsmith-io crate for the round-trip helpers.

Re-exports

pub use compartment::Compartment;

pub use compartment::CompartmentId;

pub use gpr::Gpr;

pub use gpr::GprParseError;

pub use id::CpdId;

pub use id::GeneId;

pub use id::RxnId;

pub use metabolite::Metabolite;

pub use model::Model;

pub use model::ModelAnnot;

pub use model::ModelError;

pub use reaction::Reaction;

pub use reaction::Reversibility;

pub use reaction::SeedStatus;

pub use stoich::StoichMatrix;

Modules

compartment

Compartment identifiers.

gpr

Gene-protein-reaction (GPR) Boolean expressions.

id

Newtype wrappers for the three identifier namespaces used throughout gapseq.

metabolite

Metabolite metadata.

model

In-memory metabolic model.

reaction

Reaction metadata.

stoich

Sparse stoichiometric matrix.