CoDIAC
=============================
.. toctree::
	:maxdepth: 2
	:caption: Contents:

	Examples/Examples
	Dependencies
	Installation



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


Overview
--------

.. figure:: CoDIAC_OverView.pdf
    :class: with-border

    An overview of the key aspects of CoDIAC. The modules and pipeline for :ref:`setting up the reference files<reference>`.
    The :ref:`structure analysis modules<structure>` that fetch all structure files (whether PDB of AlphaFold) from the 
    reference file, convert to adjacency files of contacts, and allow for region of interest contact analysis
    between domains (intraprotein) or between a protein and a ligand (interprotein). Additional layers, such as 
    other annotations of proteins and domains :ref:`PTM and Mutations<annotations>` allow fetching on the reference file of PTMs and mutations within the regions of interest
    and the :ref:`Jalview tools<jalview>` allow for the integration of any feature types and calculation of annotation tracks 
    for visualization.

.. _reference:

Reference Setup
---------------
   
.. toctree::
	:maxdepth: 2
	:caption: Contents:

    UniProt
    PDB
    AlphaFold
    InterPro
    IntegrateStructure_Reference
	include_readme.rst
	

.. _structure:

Structure Analysis
------------------
.. toctree::
	:maxdepth: 2
	:caption: Contents:

    contactMap
    AdjacencyFiles


.. _annotations:

Annotation tools
----------------
.. toctree::
	:maxdepth: 2
	:caption: Contents: 
    
    Mutations
    PTM

.. _jalview:

Jalview and Feature tools
-------------------------
.. toctree::
	:maxdepth: 2
	:caption: Contents: 
    
    jalviewFunctions
    translateFeatures