micom.util
==========

.. py:module:: micom.util

.. autoapi-nested-parse::

   Holds utility functions for other modules.



Attributes
----------

.. autoapisummary::

   micom.util._read_funcs
   micom.util.COMPARTMENT_RE


Functions
---------

.. autoapisummary::

   micom.util.is_active_demand
   micom.util.fix_demands
   micom.util.download_model
   micom.util._read_model
   micom.util.load_model
   micom.util.load_pickle
   micom.util.serialize_models
   micom.util.chr_or_input
   micom.util.clean_ids
   micom.util.compartment_id
   micom.util.join_models
   micom.util.fluxes_from_primals
   micom.util.add_var_from_expression
   micom.util.ex_metabolite
   micom.util.check_modification
   micom.util._format_min_growth
   micom.util._apply_min_growth
   micom.util.adjust_solver_config
   micom.util.reset_min_community_growth


Module Contents
---------------

.. py:data:: _read_funcs

.. py:data:: COMPARTMENT_RE
   :value: '(_{}$)|([^a-zA-Z0-9 :]{}[^a-zA-Z0-9 :]$)'


.. py:function:: is_active_demand(r)

   Check if a reaction is a demand reaction.


.. py:function:: fix_demands(model)

   Check for forced sinks and demands and deactivates them.


.. py:function:: download_model(url, folder='.')

   Download a model.


.. py:function:: _read_model(file)

   Read a model from a local file.


.. py:function:: load_model(filepath)

   Load a cobra model from several file types.


.. py:function:: load_pickle(filename)

   Load a community model from a pickled version.

   :param filename: The file the community is stored in.
   :type filename: str

   :returns: The loaded community model.
   :rtype: micom.Community


.. py:function:: serialize_models(files, dir='.')

   Convert several models to Python pickles.


.. py:function:: chr_or_input(m)

   Return ascii character for the ordinal or the original string.


.. py:function:: clean_ids(id)

   Clean ids up a bit.


.. py:function:: compartment_id(micom_obj)

   Get the compartment id for a cobra object and prune the prefix if needed.


.. py:function:: join_models(model_files, id=None)

   Join several models into one.

   This requires all the models to use the same ID system.

   :param model_files: The files to be joined.
   :type model_files: list of strings
   :param id: The new ID for the model. Will be the ID of the first model if None.
   :type id: str

   :returns: The joined cobra Model.
   :rtype: cobra.Model


.. py:function:: fluxes_from_primals(model, info)

   Extract a list of fluxes from the model primals.


.. py:function:: add_var_from_expression(model, name, expr, lb=None, ub=None)

   Add a variable to a model equaling an expression.


.. py:function:: ex_metabolite(model, rid)

   Get the metabolite from an exchange reaction ID.


.. py:function:: check_modification(community)

   Check whether a community already carries a modification.

   :param community: The community class to check.
   :type community: micom.Community

   :raises ValueError: If the community already carries a modification and adding another
       would not be safe.


.. py:function:: _format_min_growth(min_growth, taxa)

   Format min_growth into a pandas series.

   :param min_growth: The minimum growth rate for each individual in the community. Either
                      a single value applied to all individuals or one value for each.
   :type min_growth: positive float or array-like object.
   :param taxa: The ID for each individual model in the community.
   :type taxa: array-like

   :returns: A pandas Series mapping each individual to its minimum growth rate.
   :rtype: pandas.Series


.. py:function:: _apply_min_growth(community, min_growth, atol=1e-06, rtol=1e-06)

   Set minimum growth constraints on a model.

   Will integrate with the context.


.. py:function:: adjust_solver_config(solver)

   Adjust the optlang solver configuration for larger problems.


.. py:function:: reset_min_community_growth(com)

   Reset the lower bound for the community growth.