cobra.io.json

cobra.io.json#

Provide functions for I/O in JSON format.

Attributes#

JSON_SPEC

Functions#

to_json(→ str)

Return the model as a JSON string.

from_json(→ cobra.Model)

Load a cobra model from a JSON string.

save_json_model(→ None)

Write the cobra model to a file in JSON format.

load_json_model(→ cobra.Model)

Load a cobra model from a file in JSON format.

Module Contents#

cobra.io.json.JSON_SPEC = '1'#
cobra.io.json.to_json(model: cobra.Model, sort: bool = False, **kwargs: Any) → str[source]#

Return the model as a JSON string.

Parameters:

  • model (cobra.Model) – The cobra model to represent.

  • sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False).

  • **kwargs (Any) – Keyword arguments passed on to json.dumps.

Returns:

JSON string representation of the cobra model.

Return type:

str

See also

save_json_model

Write directly to a file.

json.dumps

Base function.

cobra.io.json.from_json(document: str) → cobra.Model[source]#

Load a cobra model from a JSON string.

Parameters:

document (str) – The JSON string representation of a cobra model.

Returns:

The cobra model as interpreted from the JSON string.

Return type:

cobra.Model

See also

load_json_model

Load directly from a file.

cobra.io.json.save_json_model(model: cobra.Model, filename: str | pathlib.Path | IO, sort: bool = False, pretty: bool = False, **kwargs: Any) → None[source]#

Write the cobra model to a file in JSON format.

Parameters:

  • model (cobra.Model) – The cobra model to represent.

  • filename (str or file-like) – File path or descriptor that the JSON representation should be written to.

  • sort (bool, optional) – Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False).

  • pretty (bool, optional) – Whether to format the JSON more compactly (default) or in a more verbose but easier to read fashion. Can be partially overwritten by the **kwargs (default False).

  • **kwargs (Any) – Keyword arguments passed to json.dump.

See also

to_json

Return a string representation.

json.dump

Base function.

cobra.io.json.load_json_model(filename: str | pathlib.Path | IO) → cobra.Model[source]#

Load a cobra model from a file in JSON format.

Parameters:

filename (str or file-like) – File path or descriptor that contains the JSON document describing the cobra model.

Returns:

The cobra model as represented in the JSON document.

Return type:

cobra.Model

See also

from_json

Load from a JSON string.