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CosolvKit: a versatile tool for cosolvent MD preparation and analysis
========================================

**CosolvKit** is one of the most **generalizable** and **flexible** **open-source** cosolvent systems preparation tool. It is developed on top of the **OpenMM** echosystem and allows the user to specify every kind of cosolvent molecule(s) in the form of SMILES strings at desired concentrations (M) - or specific number of copies.
It exposes a user friendly interface that ensures reproducibility through the files config.json, cosolvents.json and forcefields.json that define all the setup options. At the same time, CosolvKit has also a powerful python API that ensures high **flexibility** and ease of use.


.. important:: \This pre-print in ChemRxiv describes the original design, implementation, and features of CosolvKit:\
      *CosolvKit: a versatile tool for cosolvent MD preparation and analysis.*
      Niccolo Bruciaferri ,Jerome Eberhardt ,Manuel A. Llanos ,Johannes R. Loeffler ,
      Matthew Holcomb ,Monica L. Fernandez-Quintero ,Diogo Santos-Martins ,Andrew B. Ward ,Stefano Forli.  
        
      DOI: `https://doi.org/10.26434/chemrxiv-2024-rmsnj`

   If using CosolvKit in your work, please cite this pre-print.

Availability
------------
CosolvKit can be easily installed with all its dependencies using `pip` or `conda` package managers.

All **source code** is available under the `LGPL License, version 2.1+ <https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html>`_ from `github.com/forlilab/cosolvkit <https://github.com/forlilab/cosolvkit>`_ and the Python Package index `https://pypi.org/project/cosolvkit <pypi.org/project/cosolvkit>`_.

Participating
-------------
Please report bugs or enhancement requests through the `Issue Tracker <https://github.com/forlilab/cosolvkit/issues>`_.

CosolvKit is **open source** and welcomes your contributions. `Fork the repository on GitHub <https://github.com/forlilab/cosolvkit>`_ and submit a pull request.


Welcome to cosolvkit's documentation!
=====================================

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   modules

Indices and tables
********************

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: Manual

   installation
   citations
   changes

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: Tutorials

   get_started
   cmdline
   api

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: Python Documentation

   cosolvkit