:mod:`memote.experimental`
==========================

.. py:module:: memote.experimental

.. autoapi-nested-parse::

   Modules related to reading and writing experimental files.
















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Subpackages
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.. toctree::
   :titlesonly:
   :maxdepth: 3

   schemata/index.rst


Submodules
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.. toctree::
   :titlesonly:
   :maxdepth: 1

   checks/index.rst
   config/index.rst
   essentiality/index.rst
   experiment/index.rst
   experimental_base/index.rst
   growth/index.rst
   medium/index.rst
   tabular/index.rst


Package Contents
----------------

Classes
~~~~~~~

.. autoapisummary::

   memote.experimental.ExperimentConfiguration



.. py:class:: ExperimentConfiguration(filename, **kwargs)

   Bases: :class:`object`

   Represent an experimental configuration.
















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   .. method:: load(self, model)

      Load all information from an experimental configuration file.


      :Parameters:

          **model** : cobra.Model
              The metabolic model under investigation.














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   .. method:: validate(self)

      Validate the configuration file.
















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   .. method:: load_medium(self, model)

      Load and validate all media.
















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   .. method:: load_essentiality(self, model)

      Load and validate all data files.
















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   .. method:: load_growth(self, model)

      Load and validate all data files.
















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   .. method:: get_path(self, obj, default)

      Return a relative or absolute path to experimental data.
















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   .. method:: 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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