Metadata-Version: 2.1
Name: locuaz
Version: 0.3.1
Summary: Antibody optimization protocol
Author: Patricio Barletta
Author-email: pbarletta@gmail.com
Keywords: molecular,dynamics,antibody,antibodies
Requires-Python: >=3.9.15
Description-Content-Type: text/x-rst
License-File: LICENSE.rst
Requires-Dist: py
Requires-Dist: scipy
Requires-Dist: numpy (<2.0.0,>=1.21.0)
Requires-Dist: attrs
Requires-Dist: chemfiles
Requires-Dist: mdanalysis (>=2.3.0)
Requires-Dist: biobb-common
Requires-Dist: biobb-analysis
Requires-Dist: biobb-model
Requires-Dist: biobb-io
Requires-Dist: biobb-gromacs
Requires-Dist: pdb2pqr
Requires-Dist: gmx-mmpbsa
Requires-Dist: tqdm
Requires-Dist: freesasa
Requires-Dist: pytest
Requires-Dist: cerberus
Provides-Extra: docs
Requires-Dist: sphinx ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme ; extra == 'docs'

========
locuaz
========


.. image:: https://img.shields.io/pypi/v/locuaz.svg
        :target: https://pypi.python.org/pypi/locuaz

.. image:: https://readthedocs.org/projects/locuaz/badge/?version=latest
        :target: https://locuaz.readthedocs.io/en/latest/?version=latest
        :alt: Documentation Status


Looping Uniquely Catered Amino Acid Sequences


* Free software: MIT license
* Documentation: https://locuaz.readthedocs.io.

Install
--------

Check the `Installation <https://locuaz.readthedocs.io/en/latest/installation.html>`_ section on the docs.


Post-Install
-------------
If on MDAnalysis 2.4.3 or older, edit the file ``MDAnalysis/topology/tpr/utils.py`` line 330::
    
  segid = f"seg_{i}_{molblock}"

replace it with::

    segid = molblock[14:] if molblock[:14] == "Protein_chain_" else molblock


On scoring
----------------


Mutators
---------

-  DLPacker is included as a submodule. To download it::

    git submodule init
    git submodule update

Then, in

The first 2 can be copied from the recently downloaded directory (``locuaz/DLPacker``).
The weights have to be `downloaded <https://drive.google.com/file/d/1J4fV9aAr2nssrWN8mQ7Ui-9PVQseE0LQ/view?usp=sharing>`_.
Then, the path to the ``dlpacker`` directory has to be specified in the input config under the
``paths`` key, on the  ``mutator`` option.

Generators
-----------

- ``gmxmmpbsa`` based generators like ``SPM4gmxmmpbsa`` need a residue decomposition file from ``gmxmmpbsa``,
  so the **gmxmmpbsa** script needs to include something along the lines of::

    /
    &decomp
    idecomp=2, dec_verbose=0,
    print_res="within 4"
    /

Credits
-------

- `Biobb <https://mmb.irbbarcelona.org/biobb/documentation/source>`_
- `MDAnalysis <https://github.com/MDAnalysis/mdanalysis>`_
- `FreeSASA <https://github.com/freesasa/freesasa-python>`_


MIT License

Copyright (c) [2023] [Patricio Barletta]

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
