torchcell.metabolism

Genome-scale metabolic modeling. yeast_GEM wraps the yeast-GEM model (through cobra) and derives its reaction and metabolite graphs; constraints turns a genome-scale model into constraint tensors; flux_layer is a differentiable, enzyme-constrained flux layer; media maps an ontology Media object onto exchange bounds; pathway adds a heterologous pathway to a model as a typed perturbation; and enzyme_kinetics and parameters hold kinetic parameters with their provenance. Nothing is re-exported at the package level, because yeast_GEM imports cobra and downloads the model on first use; import the submodule you need.

betaxanthin

The betaxanthin cassette Cachera transferred into the yeast knockout collection.

Functions

betaxanthin.build_betaxanthin_pathway	Build the cassette as a pathway object against one genome-scale model.
betaxanthin.betaxanthin_demand_ids	Demand reactions whose flux sums to the measured yellow pigment.

constraints

Genome-scale model -> constraint tensors, as pure functions of a GEM.

Classes

constraints.ThermoMode	How the flux layer forms its reaction potential.
constraints.TableCoverage	How much of a parameter table is real, stated rather than assumed.
constraints.ThermoTable	Standard transformed Gibbs energies for one GEM, with provenance.
constraints.CatalyticUnits	The GPR, flattened into AND-terms, as index arrays rather than strings.
constraints.GemTensors	A genome-scale model as tensors: stoichiometry, bounds, GPR, thermodynamics.

Functions

constraints.load_thermo_table	Load \(\Delta_f G'^\circ\) / \(\Delta_r G'^\circ\) from a GEM checkout.
constraints.parse_catalytic_units	Flatten every GPR into AND-terms indexed against rxn_ids.
constraints.independent_balance_rows	Pick a maximal set of linearly independent rows of S.
constraints.null_space_basis	An orthonormal basis \(\mathcal{N}\) of \(\ker S\), so \(S\mathcal{N}=0\).
constraints.build_gem_tensors	Extract every constraint tensor from a cobra model.
constraints.compare_reaction_delta_g	Check the recomputed \(\Delta_r G'^\circ\) against the shipped column.

enzyme_kinetics

Enzyme kinetic parameters (k_cat, K_M) with provenance, from the Open Enzyme Database.

Classes

enzyme_kinetics.KineticKind	Which constant is being resolved.
enzyme_kinetics.KineticSource	Where a value came from.
enzyme_kinetics.KineticRetrieval	Provenance for one retrieved OED slice.
enzyme_kinetics.OedKineticRecord	One OED row, kept verbatim.
enzyme_kinetics.ResolvedKineticParameter	A single parameter chosen for a (protein, substrate) pair, with its audit trail.

Functions

enzyme_kinetics.fetch_oed_records	Page the OED /data endpoint for one organism.
enzyme_kinetics.mirror_oed_slice	Fetch an organism slice, write it with a sha256-pinned provenance record.
enzyme_kinetics.load_mirrored_records	Read the mirror and VERIFY its sha256 before returning anything.
enzyme_kinetics.resolve_parameter	Choose one value from many measurements, by the documented cascade.
enzyme_kinetics.index_by_uniprot	Group rows by UniProt accession, the key the GPR maps yeast genes onto.

flux_layer

A differentiable, enzyme-constrained, thermodynamically-feasible flux layer.

Classes

flux_layer.CompartmentParameters	pH, ionic strength and membrane potential per compartment.
flux_layer.FluxLayerConfig	Every switch the flux layer has, in one place so a run records what it ran.
flux_layer.FluxLayer	Gene tokens in, a feasible flux vector and its feasibility residuals out.

Functions

flux_layer.gene_index_map

Map GEM gene positions onto the model's gene-token positions.

media

Map an ontology Media object onto genome-scale-model exchange bounds.

Classes

media.UptakePolicy	Magnitudes assigned to an uptake bound, by the component's functional role.
media.ExchangeBound	One exchange reaction opened to an uptake magnitude, with its provenance.
media.ComponentResolution	What became of one ontology component on the way to a bound vector.
media.MediaBounds	A medium expressed as exchange bounds for one specific model.
media.MediaBoundsDiff	Exchange-level difference between two bound vectors on the same model.
media.ExchangeIndex	Lookup tables built once from a model's exchange reactions.

Functions

media.build_exchange_index	Index a model's exchange reactions by annotation identifier and by name.
media.resolve_component	Place one ontology component on zero or more exchange reactions.
media.media_to_bounds	Map an ontology Media onto exchange bounds for model.
media.diff_bounds	Exchange-level difference between two bound vectors.

parameters

Kinetic and physical parameters for a GEM, database-first and provenance-tagged.

Classes

parameters.ParameterProvenance	Where one parameter value came from.
parameters.KcatPredictor	A sequence-based turnover predictor.
parameters.PredictorRegistry	The predictors a run is allowed to use, in priority order.
parameters.ParameterTable	One resolved parameter per entity, with a per-entity provenance tag.

Functions

parameters.load_swissprot	Read data/databases/swissprot.tsv, keyed by systematic ORF name.
parameters.molecular_weight_table	Per-gene molecular weight in kDa, from SwissProt.
parameters.uniprot_for_genes	Systematic ORF name -> UniProt accession, the join key into any kinetics database.
parameters.resolve_kcat_table	One \(k_{cat}\) per catalytic unit, database-first.
parameters.load_measured_concentrations	ChEBI id -> measured intracellular concentration in molar, from YMDB.
parameters.concentration_prior	Per-metabolite measured concentration prior, in molar, plus its coverage mask.

pathway

Add a heterologous pathway to a genome-scale model, as a typed perturbation.

Classes

pathway.EvidenceTier	Where a coefficient came from, so a guess can never read as a measurement.
pathway.MetaboliteSpec	A metabolite the genome-scale model does not have yet.
pathway.ReactionSpec	A reaction the genome-scale model does not have yet.
pathway.HeterologousPathway	A named set of metabolites, reactions and genes added to a base strain.

Functions

pathway.apply_pathway

Add a pathway's metabolites, reactions and genes to a genome-scale model.

yeast_GEM

Wrapper around the yeast-GEM metabolic model and its derived graphs.

Classes

yeast_GEM.MemberlessReactionError	A reaction with no metabolites, which neither graph view can represent.
yeast_GEM.YeastGEM	Download, load, and expose the yeast-GEM genome-scale model.

Functions

yeast_GEM.plot_reaction_map	Plot hypergraph for a specific reaction.
yeast_GEM.plot_full_network	Plot the entire metabolic network structure without labels.
yeast_GEM.plot_random_network	Plot a random subgraph of the metabolic network and save it.
yeast_GEM.plot_bipartite_network	Plot a bipartite network visualization of genes to metabolites.
yeast_GEM.sanity_check_metabolic_networks	Print details for a few random reactions as a sanity check.
yeast_GEM.analyze_reactions_without_genes	Analyze reactions without gene associations in the YeastGEM model.
yeast_GEM.test_bipartite_attributes	Test and display the new attributes added to the bipartite graph.