Model adapter (Python)

geckopy objects in geckopy.adapter.

Functions

Function	Summary
ComplexParams
EvotuneParams	Hyperparameters for kcat tuning against experimental data.
generate_template_toml	Generate a commented TOML template for a new ecModel project.
KcatAssignmentParams	How kcats are assigned from the kcat source files (collect_kcats).
KcatStageParams	One [[kcat_assignment.stage]]: decides each reaction that is still
KeggParams
MatlabParams	Settings that only GECKO (MATLAB) reads; geckopy ignores them.
ModelAdapter	Holds the organism-specific parameters and overridable
ModelParameters	Top-level parameters for an ecModel adapter.
OkpParams	OpenKineticsPredictor settings (used by submit/fetch_open_kinetics_predictor).
resolve_adapter	Return the adapter to use, falling back to model.adapter.
resolve_param	Return an explicit value, else fall back to adapter.params.<attr>.
SourceGroupRule	One trust-tier entry in EvotuneParams.source_groups.
SpontaneousParams	Which reactions proceed without an enzyme.
UniprotParams

Reference

ComplexParams

EvotuneParams

Hyperparameters for kcat tuning against experimental data.

Sources not matched by any source_groups entry fall back to the *_default fields (matching MATLAB's noKcatSource behaviour: sigma0logDefault etc. apply to every kcat first, then only ones with a recognised source get overridden by their group's value).

generate_template_toml

generate_template_toml(*, project_name: str='my-ecmodel')

Generate a commented TOML template for a new ecModel project.

Every section of the schema is emitted, evotune kcat tuning hyperparameters included; optional fields are commented out at their defaults, so the template doubles as the reference for what can be set.

Parameters

project_name

Name written into the template's header comment.

Returns

str

The full TOML template text, ending in a newline.

KcatAssignmentParams

How kcats are assigned from the kcat source files (collect_kcats).

KcatStageParams

One [[kcat_assignment.stage]]: decides each reaction that is still

open, by the first listed source with a value (select) or by all listed sources with a value, weighted by their reliability (combine).

KeggParams

MatlabParams

Settings that only GECKO (MATLAB) reads; geckopy ignores them.

They let one model_adapter.toml configure both tools.

ModelAdapter

Holds the organism-specific parameters and overridable

helpers for one ecModel project.

Most users don't subclass this directly: they make a folder with a model_adapter.toml and call ModelAdapter.from_folder(folder).

Subclass only when a particular organism needs custom logic (e.g. an unusual way to identify spontaneous reactions, or a bespoke gene-id mapping that the default UniProt-table-driven one can't handle).

ModelParameters

Top-level parameters for an ecModel adapter.

OkpParams

OpenKineticsPredictor settings (used by submit/fetch_open_kinetics_predictor).

The API key is intentionally NOT here (it is a secret): provide it as a function argument, the OKP_API_KEY environment variable, or the file <path>/data/okpApiKey.txt.

resolve_adapter

resolve_adapter(model, adapter: Optional['ModelAdapter']=None, *, purpose: str='this function')

Return the adapter to use, falling back to model.adapter.

Parameters

model

Any object that may have an .adapter attribute (a cobra Model, an EcModel, ...). getattr is used so plain cobra.Model doesn't trip on the missing attribute.

adapter

An explicitly-passed adapter. If non-None, returned as-is (takes priority over model.adapter).

purpose

Short description of why the calling function needs an adapter; included in the error message when none can be resolved. Example: "to read params.enzyme_comp".

Returns

ModelAdapter

Either adapter (if given) or model.adapter.

Raises

ValueError

If both adapter and model.adapter are None. The message tells the caller how to fix it.

resolve_param

resolve_param(model, explicit, attr: str, *, adapter: Optional['ModelAdapter']=None, purpose: str='this function')

Return an explicit value, else fall back to adapter.params.<attr>.

Lets a function take the single parameter it needs directly, only requiring a full ModelAdapter when the value is not supplied.

Parameters

model

Any object that may have an .adapter attribute, used as the fallback source when adapter is not given.

explicit

The caller-supplied value. If not None, it is returned as-is and no adapter is consulted at all.

attr

Name of the attribute to read off adapter.params when explicit is None.

adapter

An explicitly-passed adapter, used instead of model.adapter when resolving the fallback value.

purpose

Short description of why the calling function needs the value; forwarded to resolve_adapter for its error message.

Returns

```explicitif given, otherwisegetattr(adapter.params, attr)``.` :

SourceGroupRule

One trust-tier entry in EvotuneParams.source_groups.

ec.source holds literal strings like "dlkcat", "brenda", and -- for OpenKineticsPredictor kcats -- the raw predictor method name (e.g. "CataPro"), not a generic "okp" tag. A rule matches a given ec.source value if it's listed in sources, or (when match_okp is True) if it equals the project's configured OKP method (OkpParams.method).

SpontaneousParams

Which reactions proceed without an enzyme.

Both rules may be given; a reaction is spontaneous if either matches. GECKO (MATLAB) reads the same keys, so a project needs no code for this.

UniprotParams