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Welcome to SwiftPol's documentation!
=========================================================
.. image:: _static/logo.png
   :alt: SwiftPol Logo
   :width: 300px
   :align: center

About SwiftPol
--------------

A polymer sample contains a natural degree of variation in its structure and non-uniformity between its chains, which is often disregarded in MD systems.

SwiftPol uses a statistical approach to build polydisperse polymer systems, allowing for a more realistic representation of polymer systems in MD.

SwiftPol.build.polymer_system takes as an input: 

- The simplified molecular-input line-entry system (SMILES) string of all co-monomers.

- Values of the target average properties of the ensemble: monomer % composition (for copolymers), length, number of chains, blockiness (for blocky copolymers), terminals, residual monomer. 

- Reaction SMARTS which describes the polymerization reaction associated with their polymer chemistry.

...and builds a polydisperse chain ensemble.

.. image:: _static/melt.png
   :alt: Polymer melt
   :width: 300px
   :align: center



above - A 3D representation of a polydisperse polymer system built with SwiftPol. `PolyPly <https://github.com/marrink-lab/polyply_1.0/tree/master/polyply/src>`_ used for generating 3D configuration.


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

   getting_started
   api



Indices and tables
==================

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