:orphan: true

.. _pwchem-convert-structure:

###############################################################
Convert structure
###############################################################
This protocol converts the format of the files stored for a set of Small Molecules, an Atom Structure or a Molecular
dynamics system (either coordinates, topology or trajectory files).

In order to do the conversions, we use `RDKit <https://github.com/rdkit/rdkit>`_ or `OpenBabel <https://github.com/openbabel/openbabel>`_ 
for small molecules, `Biopython <https://biopython.org/>`_ for Atom Structures and `Parmed <https://parmed.github.io/ParmEd/html/index.html>`_
and `MDTraj <https://www.mdtraj.org/1.9.8.dev0/index.html>`_ for Molecular Dynamics systems.

Input
----------------------------------------
.. include:: ../../../../templates/plugins/input-help.rst

.. image:: ../../../../../_static/images/plugins/pwchem/general/convert-structure/form_1.png
   :alt: Convert structure form 1
   :height: 400
   :align: center

|

.. image:: ../../../../../_static/images/plugins/pwchem/general/convert-structure/form_2.png
   :alt: Convert structure form 2
   :height: 400
   :align: center

|

The result of this protocol is object equal to the one in the input, but this time the files inside this object are in
the desired format.

.. |testCommand| replace:: pwchem.tests.tests_general.TestConverter
.. include:: ../../../../templates/plugins/protocol-test.rst