.. _api-reference:

API Reference
=============

This page gathers the full autodoc output for every Python module that
ships with **generate_InitCond**, including the lightweight helpers
inside the :py:mod:`analysis` package.

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   :local:
   :depth: 1


Core pipeline utilities
-----------------------

fix_datafiles                     
~~~~~~~~~~~~~

.. automodule:: fix_datafiles
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LT_writer
~~~~~~~~~

.. automodule:: LT_writer
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writePackmolInput
~~~~~~~~~~~~~~~~~

.. automodule:: writePackmolInput
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writeSysLT
~~~~~~~~~~

.. automodule:: writeSysLT
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updateColVar
~~~~~~~~~~~~

.. automodule:: updateColVar
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updateInput
~~~~~~~~~~~

.. automodule:: updateInput
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Analysis helpers
----------------

plot_PE
~~~~~~~

.. automodule:: analysis.plot_PE
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plot_BSF
~~~~~~~~

.. automodule:: analysis.plot_BSF
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plot_SD
~~~~~~~

.. automodule:: analysis.plot_SD
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plot_cSize
~~~~~~~~~~

.. automodule:: analysis.plot_cSize
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plot_radialDist
~~~~~~~~~~~~~~~

.. automodule:: analysis.plot_radialDist
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plot_pair_bonds
~~~~~~~~~~~~~~~~~

.. automodule:: analysis.plot_pair_bonds
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plot_cSizeBSF
~~~~~~~~~~~~~

.. automodule:: analysis.plot_cSizeBSF
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plot_sticker_dist
~~~~~~~~~~~~~~~~~

.. automodule:: analysis.plot_sticker_dist
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plot_neighCount
~~~~~~~~~~~~~~~

.. automodule:: analysis.plot_neighCount
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