7.1.3. cobrame.io package

7.1.3.1. Submodules

7.1.3.2. cobrame.io.dict module

cobrame.io.dict.get_numeric_from_string(string)[source]
Parameters:string (str) – String representation of numeric expression
Returns:Numeric representation of string
Return type:float or sympy expression
cobrame.io.dict.get_sympy_expression(value)[source]

Return sympy expression from json string using sympify

mu is assumed to be positive but using sympify does not apply this assumption. The mu symbol produced from sympify is replaced with cobrame’s mu value to ensure the expression can be used in the model.

Parameters:value (str) – String representation of mu containing expression
Returns:Numeric representation of string with cobrame’s mu symbol substituted
Return type:sympy expression
cobrame.io.dict.me_model_from_dict(obj)[source]

Load ME-model from its dictionary representation. This will return a full MEModel object identical to the one saved.

Parameters:obj (dict) – Dictionary representation of ME-model
Returns:Full COBRAme ME-model
Return type:MEModel
cobrame.io.dict.me_model_to_dict(model)[source]

Create dictionary representation of full ME-model

Parameters:model (MEModel) –
Returns:Dictionary representation of ME-model
Return type:dict

7.1.3.3. cobrame.io.json module

cobrame.io.json.get_schema()[source]

Load JSON schema for ME-model JSON saving/loading

Returns:JSONSCHEMA
Return type:dict
cobrame.io.json.load_json_me_model(file_name)[source]

Load a full JSON version of the ME-model. Loading a model in this format will return a ME-model identical to the one saved, which retains all ME-model functionality.

Parameters:file_name (str or file-like object) – Filename of the JSON output or an open json file
Returns:A full ME-model
Return type:cobrame.core.model.MEModel
cobrame.io.json.load_reduced_json_me_model(file_name)[source]

Load a stripped-down JSON version of the ME-model. This will exclude all of ME-Model information except the reaction stoichiometry information and the reaction bounds. Saving/loading a model in this format will thus occur much quicker, but limit the ability to edit the model and use most of its features.

Parameters:file_name (str or file-like object) – Filename of the JSON ME-model
Returns:COBRA Model representation of the ME-model. This will not include all of the functionality of a MEModel but will solve identically compared to the full model.
Return type:cobra.core.model.Model
cobrame.io.json.save_json_me_model(model, file_name)[source]

Save a full JSON version of the ME-model. Saving/loading a model in this format can then be loaded to return a ME-model identical to the one saved, which retains all ME-model functionality.

Parameters:
  • model (cobrame.core.model.MEModel) – A full ME-model
  • file_name (str or file-like object) – Filename of the JSON output or an open json file
cobrame.io.json.save_reduced_json_me_model(me0, file_name)[source]

Save a stripped-down JSON version of the ME-model. This will exclude all of ME-Model information except the reaction stoichiometry information and the reaction bounds. Saving/loading a model in this format will thus occur much quicker, but limit the ability to edit the model and use most of its features.

Parameters:

7.1.3.4. Module contents