tcren package
=============

Structure I/O
-------------

tcren.structure.model module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.structure.model
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tcren.structure.io module
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.structure.io
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Annotation
----------

tcren.annotation.arda_adapter module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.annotation.arda_adapter
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tcren.annotation.chains module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.annotation.chains
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tcren.annotation.cgene module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.annotation.cgene
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MHC mapping
-----------

tcren.mhc.imgt module
~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.mhc.imgt
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tcren.mhc.reference module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.mhc.reference
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tcren.mhc.mapper module
~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.mhc.mapper
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tcren.mhc.domains module
~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.mhc.domains
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tcren.mhc.regions module
~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.mhc.regions
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tcren.mhc.linker module
~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.mhc.linker
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tcren.mhc.pseudo module
~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.mhc.pseudo
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Contacts
--------

tcren.contacts.geometry module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.contacts.geometry
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tcren.contacts.definitions module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.contacts.definitions
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tcren.contacts.table module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.contacts.table
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tcren.contactmap module
~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.contactmap
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Potentials
----------

tcren.potential.model module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.potential.model
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tcren.potential.derive module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.potential.derive
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Scoring
-------

tcren.scoring module
~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.scoring
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tcren.pipeline module
~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.pipeline
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tcren.refine package
~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.refine
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.. automodule:: tcren.refine.substitute
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Data paths
----------

tcren.paths module
~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.paths
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Analysis
--------

tcren.analysis module
~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.analysis
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Orientation
-----------

tcren.orient.align module
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.orient.align
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tcren.orient.frame module
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.orient.frame
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tcren.orient.exceptions module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.orient.exceptions
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tcren.orient.chains module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.orient.chains
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tcren.orient.pipeline module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.orient.pipeline
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tcren.orient.docking module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: tcren.orient.docking
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Command line
------------

tcren.cli module
~~~~~~~~~~~~~~~~~

.. automodule:: tcren.cli
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