Crate gapsmith_db 

Loaders for gapseq’s reference-data tables in dat/.

Every loader is self-contained: pass in a path (or the DataRoot for the batch loader), get back a plain Rust value. No implicit paths, no globals.

The parsers are tolerant of the exact minor variations seen in real gapseq dat/ files (some tables have 13 columns, others 14; MNXref prefixes blocks of #-comments). Row validation errors carry line numbers so the culprit can be found quickly.

Re-exports

pub use biomass::BiomassTemplate;

pub use biomass::BiomassComponent;

pub use biomass::BiomassGroup;

pub use biomass::BiomassError;

pub use common::DbError;

pub use complex::ComplexSubunitEntry;

pub use complex::ComplexSubunitTable;

pub use exception::ExceptionRow;

pub use medium_rules::MediumRule;

pub use mnxref::MnxrefSeed;

pub use mnxref::MnxrefSeedOther;

pub use pathway::PathwayRow;

pub use pathway::PathwayTable;

pub use pathway::PwySource;

pub use seed::SeedCpdRow;

pub use seed::SeedRxnRow;

pub use seed::load_seed_metabolites;

pub use seed::load_seed_reactions;

pub use stoich_hash::rxn_stoich_hash;

pub use stoich_parse::parse_stoichiometry;

pub use stoich_parse::StoichTerm;

pub use stoich_parse::StoichParseError;

pub use subex::SubexRow;

pub use tcdb::TcdbSubstrateRow;

Modules

biomass

Biomass JSON template loader.

common

Shared error type plus tiny helpers used across loaders.

complex

dat/complex_subunit_dict.tsv loader.

exception

dat/exception.tbl loader — enzymes with known false-friends, requiring stricter identity cutoffs (see src/analyse_alignments.R:108–143).

medium_rules

dat/medium_prediction_rules.tsv loader.

mnxref

MNXref cross-reference loaders.

pathway

Pathway table loader — handles meta_pwy.tbl, kegg_pwy.tbl, seed_pwy.tbl, custom_pwy.tbl.

seed

SEED reaction and metabolite table loaders.

stoich_hash

Stoichiometric hash — port of src/generate_rxn_stoich_hash.R.

stoich_parse

Parser for SEED stoichiometry strings.

subex

dat/subex.tbl loader.

tcdb

dat/tcdb_substrates.tbl loader.

Structs

DataRoot

The full set of reference tables gapseq consults. Fields are populated lazily as the relevant loaders are called; DataRoot::load loads everything at once.