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by starred repositories"],"sub_categories":[],"readme":".. image:: https://raw.githubusercontent.com/AstraZeneca/jazzy/master/docs/_static/jazzy.png\n  :width: 400\n  :alt: Jazzy\n\n|PyPI| |Status| |Python Version| |License|\n\n|Read the Docs| |Tests| |Codecov|\n\n|pre-commit| |Black|\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/jazzy.svg\n   :target: https://pypi.org/project/jazzy/\n   :alt: PyPI\n.. |Status| image:: https://img.shields.io/pypi/status/jazzy.svg\n   :target: https://pypi.org/project/jazzy/\n   :alt: Status\n.. |Python Version| image:: https://img.shields.io/pypi/pyversions/jazzy\n   :target: https://pypi.org/project/jazzy\n   :alt: Python Version\n.. |License| image:: https://img.shields.io/pypi/l/jazzy\n   :target: https://opensource.org/licenses/Apache-2.0\n   :alt: License\n.. |Read the Docs| image:: https://img.shields.io/readthedocs/jazzy/latest.svg?label=Read%20the%20Docs\n   :target: https://jazzy.readthedocs.io/\n   :alt: Read the documentation at https://jazzy.readthedocs.io/\n.. |Tests| image:: https://github.com/AstraZeneca/jazzy/workflows/Tests/badge.svg\n   :target: https://github.com/AstraZeneca/jazzy/actions?workflow=Tests\n   :alt: Tests\n.. |Codecov| image:: https://codecov.io/gh/AstraZeneca/jazzy/branch/master/graph/badge.svg?token=4HCWYH61S5\n   :target: https://codecov.io/gh/AstraZeneca/jazzy\n   :alt: Codecov\n.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit\u0026logoColor=white\n   :target: https://github.com/pre-commit/pre-commit\n   :alt: pre-commit\n.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\n   :target: https://github.com/psf/black\n   :alt: Black\n\nFull Author List\n----------------\n* Eike Caldeweyher\n* Gian Marco Ghiandoni\n\n\nIntroduction\n------------\n*Jazzy* is an efficient computational tool for the calculation of hydration free energies and hydrogen-bond acceptor and donor strengths.\nA publication describing the implementation, fitting, and validation of *Jazzy* can be found at `doi.org/10.1038/s41598-023-30089-x`_.\n\n| If you are using *Jazzy* in your research, please remember to cite our publication as:\n| *Ghiandoni, G.M., Caldeweyher, E. Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules. Sci Rep 13, 4143 (2023)*\n\n\nFeatures\n--------\n\n* Hydration free energies\n* Hydrogen-bond strengths\n* Visualisation functions (SVG)\n* Application programming interface\n* Command-line interface\n\n\nInstallation via PyPI\n---------------------\n\nYou can install *Jazzy* via pip_ from PyPI_:\n\n.. code:: console\n\n   $ pip install jazzy\n\n\nInstallation via Poetry (for development)\n-----------------------------------------\n\nRequirements to install *Jazzy* from the code repository:\n\n- `poetry`_\n- `pyenv`_ or `conda`_\n- python\u003e=3.6\n\nFirst check that ``poetry`` is running (v1.4.1 at March 2023)\n\n.. code:: console\n\n   $ poetry --version\n   Poetry version v1.4.1\n\nCreate a virtual environment (via ``pyenv`` or ``conda``) and activate it. Afterwards, clone the *Jazzy* project from GitHub and install it using ``poetry``.\n\n.. code:: console\n\n   $ git clone git@github.com:AstraZeneca/jazzy.git\n   $ cd jazzy\n   $ poetry install\n\nIf you wish to replicate our parameter fitting (see ``data/optuna_fitting`` and ``optimisation``), you need to install the specific version of ``optuna``.\nAt the time of the study, we used ``optuna==2.3.0``. You can install that manually using ``pip`` or ``poetry``.\n\n.. code:: console\n\n   $ poetry install --with optuna\n   $ pip freeze | grep optuna\n   optuna==2.3.0\n\nUsage and Cookbook\n------------------\n\nPlease see the `Usage \u003cUsage_\u003e`_ and `Cookbook \u003cCookbook_\u003e`_ sections for details.\n\n\nContributing\n------------\n\nJazzy is an open project in every shape and form, thus feedback on how to improve its documentation or functionalities is always welcome.\nTo learn more, see the `Contributor Guide`_.\n\n\nLicense\n-------\n\nDistributed under the terms of the `Apache 2.0 license`_,\n*Jazzy* is free and open source software.\n\n\nIssues\n------\n\nIf you encounter any problems,\nplease `file an issue`_ along with a detailed description.\n\n\nCredits\n-------\n\nThis project was generated from `@cjolowicz`_'s `Hypermodern Python Cookiecutter`_ template.\n\n.. _@cjolowicz: https://github.com/cjolowicz\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _Apache 2.0 license: https://opensource.org/licenses/Apache-2.0\n.. _poetry: https://python-poetry.org/docs/#installation\n.. _pyenv: https://github.com/pyenv/pyenv#installation\n.. _conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html\n.. _PyPI: https://pypi.org/\n.. _Hypermodern Python Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python\n.. _file an issue: https://github.com/AstraZeneca/jazzy/issues\n.. _pip: https://pip.pypa.io/\n.. _doi.org/10.1038/s41598-023-30089-x: https://doi.org/10.1038/s41598-023-30089-x\n.. github-only\n.. _Contributor Guide: contributing.rst\n.. _Cookbook: https://jazzy.readthedocs.io/en/latest/cookbook.html\n.. _Usage: https://jazzy.readthedocs.io/en/latest/usage.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAstraZeneca%2Fjazzy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FAstraZeneca%2Fjazzy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAstraZeneca%2Fjazzy/lists"}