memote.experimental
¶
Modules related to reading and writing experimental files.
Subpackages¶
Submodules¶
Package Contents¶
Classes¶
ExperimentConfiguration |
Represent an experimental configuration. |
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class
memote.experimental.
ExperimentConfiguration
(filename, **kwargs)[source]¶ Bases:
object
Represent an experimental configuration.
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load
(self, model)¶ Load all information from an experimental configuration file.
Parameters: - model : cobra.Model
The metabolic model under investigation.
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validate
(self)¶ Validate the configuration file.
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load_medium
(self, model)¶ Load and validate all media.
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load_essentiality
(self, model)¶ Load and validate all data files.
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load_growth
(self, model)¶ Load and validate all data files.
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get_path
(self, obj, default)¶ Return a relative or absolute path to experimental data.
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get_minimal_growth_rate
(self, model, threshold=0.1)¶ Calculate min growth default value or return input value.
This value is used to determine if a model is capable of growth under certain experimental conditions.
Parameters: - model : cobra.Model
- threshold : float, optional
If no input is provided by the user the default value is set to a coefficient threshold times the growth under default constraints (default: 0.1).
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