phievo package
==============

Networks module
---------------

classes_eds2
^^^^^^^^^^^^

.. automodule:: phievo.Networks.classes_eds2
    :members:
    :undoc-members:
    :show-inheritance:

.. automodule:: phievo.Networks.CorePromoter
        :members:
        :undoc-members:
        :show-inheritance:


Mutation
^^^^^^^^
    .. automodule:: phievo.Networks.mutation
        :members:
        :undoc-members:
        :show-inheritance:


TFHill
^^^^^^^^

.. automodule:: phievo.Networks.TFHill
        :members:
        :undoc-members:
        :show-inheritance:

PPI
^^^
.. automodule:: phievo.Networks.PPI
        :members:
        :undoc-members:
        :show-inheritance:

Phosphorylation
^^^^^^^^^^^^^^^
.. automodule:: phievo.Networks.Phosphorylation
        :members:
        :undoc-members:
        :show-inheritance:

Degradation
^^^^^^^^^^^^^^^
.. automodule:: phievo.Networks.Degradation
        :members:
        :undoc-members:
        :show-inheritance:

deriv2
^^^^^^
.. automodule:: phievo.Networks.deriv2
        :members:
        :undoc-members:
        :show-inheritance:

lovelyGraph
^^^^^^^^^^^
.. automodule:: phievo.Networks.lovelyGraph
        :members:
        :undoc-members:
        :show-inheritance:

PlotGraph
---------
Graph
^^^^^
.. automodule:: phievo.Networks.PlotGraph.Graph
        :members:
        :undoc-members:
        :show-inheritance:

Graph components
^^^^^^^^^^^^^^^^
.. automodule:: phievo.Networks.PlotGraph.Components
        :members:
        :undoc-members:
        :show-inheritance:

Layout
^^^^^^
.. automodule:: phievo.Networks.PlotGraph.Layout
        :members:
        :undoc-members:
        :show-inheritance:

Populations
-----------

Default evolution
^^^^^^^^^^^^^^^^^
.. automodule:: phievo.Populations_Types.evolution_gillespie
        :members:
        :undoc-members:
        :show-inheritance:

Pareto evolution
^^^^^^^^^^^^^^^^^
.. automodule:: phievo.Populations_Types.pareto_population
        :members:
        :undoc-members:
        :show-inheritance:

Analysis tools
--------------

Simulation
^^^^^^^^^^
.. automodule:: phievo.AnalysisTools.Simulation
        :members:
        :undoc-members:
        :show-inheritance:

	   
Palette
^^^^^^^
.. automodule:: phievo.AnalysisTools.palette
        :members:
        :undoc-members:
        :show-inheritance:
	   
extra_functions
^^^^^^^^^^^^^^^
.. automodule:: phievo.AnalysisTools.main_functions
        :members:
        :undoc-members:
        :show-inheritance: