``pdb_prot_align`` documentation
===================================================

``pdb_prot_align`` is a program written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_ to align proteins to `Protein Data Bank (PDB) <https://www.rcsb.org/>`_ structures.

Making such alignments can be useful when you want to relate the evolutionary information in a protein alignment to the structure of a protein.
However, the alignments are often difficult because the sequential numbering of sequences used in bioinformatics can differ from the numbering of the protein structure file.
The goal of ``pdb_prot_align`` is to simplify reconciliation of this numbering. 

You may want to simply run ``pdb_prot_align`` via its :ref:`cli`.
However, if you prefer to work within Python you can use the :mod:`pdb_prot_align` package, including the top-level :func:`pdb_prot_align.main.run` that mimics the :ref:`cli`.

As described in the :ref:`examples`, there are also utilities to make it easy to visualize the results in the context of the protein structures using `pymol <https://pymol.org/>`_ or `nglview <https://github.com/arose/nglview>`_.

Contents
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.. toctree::
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   self

.. toctree::
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   installation
   cli
   examples
   pdb_prot_align
   package_index
   acknowledgments