Frustratometer Functions
========================

Overview
--------
The ``frustratometer`` package includes several submodules each designed to handle different aspects of the frustration analysis pipeline. Below are the main modules and their descriptions.

Protein Database Handling
-------------------------
.. automodule:: frustratometer.pdb
    :synopsis: Module for handling protein data bank (PDB) operations.
    :members:
    :undoc-members:
    :member-order: bysource
    

Protein Family Analysis
-----------------------
.. automodule:: frustratometer.pfam
    :synopsis: Tools for working with protein families (Pfam) data.
    :members:
    :undoc-members:
    :member-order: bysource
    

Sequence Alignment
------------------
.. automodule:: frustratometer.align
    :synopsis: Utilities for sequence alignment.
    :members:
    :undoc-members:
    :member-order: bysource
    

MSA Filtering
--------------
.. automodule:: frustratometer.filter
    :synopsis: Methods for filtering and refining data sets.
    :members:
    :undoc-members:
    :member-order: bysource

Mapping Utilities
-----------------
.. automodule:: frustratometer.map
    :synopsis: Functions for mapping pfam sequences to pdb structures.
    :members:
    :undoc-members:
    :member-order: bysource
    

Direct Coupling Analysis
------------------------
.. automodule:: frustratometer.dca
    :synopsis: Functions for building and analyzing direct coupling models.
    :members:
    :undoc-members:

    .. automodule:: frustratometer.dca.pydca
        :synopsis: Wrappers for pyDCA.
        :members:
        :undoc-members:
        :member-order: bysource
        

    .. automodule:: frustratometer.dca.matlab
        :synopsis: Wrappers for matlab DCA functions.
        :members:
        :undoc-members:
        :member-order: bysource
        

Frustration Analysis
--------------------
.. automodule:: frustratometer.frustration
    :synopsis: Methods for analysis of frustration.
    :members:
    :undoc-members:
    :member-order: bysource
    

Utility Functions
-----------------
.. automodule:: frustratometer.utils
    :synopsis: Helper functions and utilities supporting the main modules.
    :members:
    :undoc-members:
    :member-order: bysource