locuaz 0.7.5.4
Antibody optimization protocol
Requires Python: >=3.10
Keywords: molecular, dynamics, antibody, antibodies

========
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

.. image:: https://zenodo.org/badge/502907107.svg
        :target: https://zenodo.org/doi/10.5281/zenodo.10937388

Looping Uniquely Catered Amino Acid Sequences

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

Install
--------

Create a conda environment YAML file named, for example, ``usr_deps.yaml``::

    name: locuaz
    channels:
      - conda-forge
    dependencies:
      - conda-forge::python>=3.10
      - conda-forge::ambertools>=22.0.0
      - conda-forge::tensorflow
      - conda-forge::openbabel
      - conda-forge::pygraphviz

by running:

.. code-block:: console

    mamba env create -f usr_deps.yaml

Then, activate the environment and install the protocol through pip:

.. code-block:: console

    pip install locuaz

Check the `Installation`_ section on the docs for more info.


Post-Install
-------------

Using DLPacker based mutators
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

If you wish to used *DLPacker* based *Mutators* (``dlp`` and ``dlpr``), DLPacker weights have to be downloaded.
Get them `here <https://drive.google.com/file/d/1J4fV9aAr2nssrWN8mQ7Ui-9PVQseE0LQ/view?usp=sharing>`_
or `here`_. These weights have to be extracted to a dedicated folder and its path has to be specified in the
input config under the ``paths`` key, on the  ``mutator`` option. Check the `docs`_ for more info.


Running
-------

After that, running *locauz* is as simple as:


.. code-block:: console

    # Activate your environment
    mamba activate locuaz
    # Point locuaz to your config file
    locuaz config.yaml

Check the `tutorials`_ for info on how to write this config file.

.. _tutorials: https://locuaz.readthedocs.io/en/latest/tutorialsimple.html

Citing
-------



Credits
-------

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

.. _docs: https://locuaz.readthedocs.io/en/latest/mutators.html
.. _Installation: https://locuaz.readthedocs.io/en/latest/installation.html


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.