=========
m2m's API
=========

Workflow
--------

m2m workflow
++++++++++++

.. automodule::  metage2metabo.m2m.m2m_workflow
    :members:
    :undoc-members:

Reconstruction
++++++++++++++

.. automodule::  metage2metabo.m2m.reconstruction
    :members:
    :undoc-members:

Individual scope
++++++++++++++++

.. automodule::  metage2metabo.m2m.individual_scope
    :members:
    :undoc-members:

Community scope
+++++++++++++++

.. automodule::  metage2metabo.m2m.community_scope
    :members:
    :undoc-members:

Cooperation potential (added-value)
+++++++++++++++++++++++++++++++++++

.. automodule::  metage2metabo.m2m.community_addedvalue
    :members:
    :undoc-members:

Minimal community
+++++++++++++++++

.. automodule::  metage2metabo.m2m.minimal_community
    :members:
    :undoc-members:

SBML Management
---------------

.. automodule::  metage2metabo.sbml_management
    :members:
    :undoc-members:

Utils
-----

.. automodule::  metage2metabo.utils
    :members:
    :undoc-members:

m2m_analysis
------------

m2m_analysis workflow
+++++++++++++++++++++

.. automodule::  metage2metabo.m2m_analysis.m2m_analysis_workflow
    :members:
    :undoc-members:

Enumeration of Minimal communities
++++++++++++++++++++++++++++++++++

.. automodule::  metage2metabo.m2m_analysis.enumeration
    :members:
    :undoc-members:

Creation of graph solution
++++++++++++++++++++++++++

.. automodule::  metage2metabo.m2m_analysis.solution_graph
    :members:
    :undoc-members:

Compression of graph
++++++++++++++++++++

.. automodule::  metage2metabo.m2m_analysis.graph_compression
    :members:
    :undoc-members:

taxonomy
++++++++++++++++++++

.. automodule::  metage2metabo.m2m_analysis.taxonomy
    :members:
    :undoc-members:

Main
-----

.. automodule::  metage2metabo.__main__
    :members:
    :undoc-members: