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https://github.com/AstraZeneca/jazzy

Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules.
https://github.com/AstraZeneca/jazzy

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Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules.

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README 

        
.. image:: https://raw.githubusercontent.com/AstraZeneca/jazzy/master/docs/_static/jazzy.png

  :width: 400

  :alt: Jazzy



|PyPI| |Status| |Python Version| |License|



|Read the Docs| |Tests| |Codecov|



|pre-commit| |Black|



.. |PyPI| image:: https://img.shields.io/pypi/v/jazzy.svg

   :target: https://pypi.org/project/jazzy/

   :alt: PyPI

.. |Status| image:: https://img.shields.io/pypi/status/jazzy.svg

   :target: https://pypi.org/project/jazzy/

   :alt: Status

.. |Python Version| image:: https://img.shields.io/pypi/pyversions/jazzy

   :target: https://pypi.org/project/jazzy

   :alt: Python Version

.. |License| image:: https://img.shields.io/pypi/l/jazzy

   :target: https://opensource.org/licenses/Apache-2.0

   :alt: License

.. |Read the Docs| image:: https://img.shields.io/readthedocs/jazzy/latest.svg?label=Read%20the%20Docs

   :target: https://jazzy.readthedocs.io/

   :alt: Read the documentation at https://jazzy.readthedocs.io/

.. |Tests| image:: https://github.com/AstraZeneca/jazzy/workflows/Tests/badge.svg

   :target: https://github.com/AstraZeneca/jazzy/actions?workflow=Tests

   :alt: Tests

.. |Codecov| image:: https://codecov.io/gh/AstraZeneca/jazzy/branch/master/graph/badge.svg?token=4HCWYH61S5

   :target: https://codecov.io/gh/AstraZeneca/jazzy

   :alt: Codecov

.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white

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.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg

   :target: https://github.com/psf/black

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Full Author List

----------------

* Eike Caldeweyher

* Gian Marco Ghiandoni



Introduction

------------

*Jazzy* is an efficient computational tool for the calculation of hydration free energies and hydrogen-bond acceptor and donor strengths.

A publication describing the implementation, fitting, and validation of *Jazzy* can be found at `doi.org/10.1038/s41598-023-30089-x`_.



| If you are using *Jazzy* in your research, please remember to cite our publication as:

| *Ghiandoni, G.M., Caldeweyher, E. Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules. Sci Rep 13, 4143 (2023)*



Features

--------



* Hydration free energies

* Hydrogen-bond strengths

* Visualisation functions (SVG)

* Application programming interface

* Command-line interface



Installation via PyPI

---------------------



You can install *Jazzy* via pip_ from PyPI_:



.. code:: console



   $ pip install jazzy



Installation via Poetry (for development)

-----------------------------------------



Requirements to install *Jazzy* from the code repository:



- `poetry`_

- `pyenv`_ or `conda`_

- python>=3.6



First check that ``poetry`` is running (v1.4.1 at March 2023)



.. code:: console



   $ poetry --version

   Poetry version v1.4.1



Create a virtual environment (via ``pyenv`` or ``conda``) and activate it. Afterwards, clone the *Jazzy* project from GitHub and install it using ``poetry``.



.. code:: console



   $ git clone [email protected]:AstraZeneca/jazzy.git

   $ cd jazzy

   $ poetry install



If you wish to replicate our parameter fitting (see ``data/optuna_fitting`` and ``optimisation``), you need to install the specific version of ``optuna``.

At the time of the study, we used ``optuna==2.3.0``. You can install that manually using ``pip`` or ``poetry``.



.. code:: console



   $ poetry install --with optuna

   $ pip freeze | grep optuna

   optuna==2.3.0



Usage and Cookbook

------------------



Please see the `Usage `_ and `Cookbook `_ sections for details.



Contributing

------------



Jazzy is an open project in every shape and form, thus feedback on how to improve its documentation or functionalities is always welcome.

To learn more, see the `Contributor Guide`_.



License

-------



Distributed under the terms of the `Apache 2.0 license`_,

*Jazzy* is free and open source software.



Issues

------



If you encounter any problems,

please `file an issue`_ along with a detailed description.



Credits

-------



This project was generated from `@cjolowicz`_'s `Hypermodern Python Cookiecutter`_ template.



.. _@cjolowicz: https://github.com/cjolowicz

.. _Cookiecutter: https://github.com/audreyr/cookiecutter

.. _Apache 2.0 license: https://opensource.org/licenses/Apache-2.0

.. _poetry: https://python-poetry.org/docs/#installation

.. _pyenv: https://github.com/pyenv/pyenv#installation

.. _conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html

.. _PyPI: https://pypi.org/

.. _Hypermodern Python Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python

.. _file an issue: https://github.com/AstraZeneca/jazzy/issues

.. _pip: https://pip.pypa.io/

.. _doi.org/10.1038/s41598-023-30089-x: https://doi.org/10.1038/s41598-023-30089-x

.. github-only

.. _Contributor Guide: contributing.rst

.. _Cookbook: https://jazzy.readthedocs.io/en/latest/cookbook.html

.. _Usage: https://jazzy.readthedocs.io/en/latest/usage.html