.. pywindow documentation master file, created by
   sphinx-quickstart on Thu Jul 19 13:12:27 2018.
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Welcome to ``pywindow``'s documentation!
========================================

GitHub:

    https://github.com/JelfsMaterialsGroup/pywindow - stable release

    https://github.com/marcinmiklitz/pywindow - most up-to-date release

Overview
--------

``pywindow`` is a Python 3 library for the structural analysis of molecular pores.

For quick start head to :ref:`modindex` and see :class:`pywindow.molecular.MolecularSystem`.

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

Installation
------------

Git clone the pywindow repository or download a zipped version.

  .. code-block:: bash

    cd pywindow/

    python setup.py install

Examples
--------

For the specific examples of ``pywindow`` usage see Examples/ directory in the
``pywindow`` Github repository.

Loading input
.............

1. Using file as an input:

  .. code-block:: python

      import pywindow as pw

      molsys = pw.MolecularSystem.load_file(`data/input/PUDXES.xyz`)

2. Using RDKit molecule object as an input:

  .. code-block:: python

      import pywindow as pw
      from rdkit import Chem

      rdkit_mol = Chem.MolFromMol2File("data/input/PUDXES.mol2")

      molsys = pw.MolecularSystem.load_rdkit_mol(rdkit_mol)

3. Using a dictionary (or another :attr:`MoleculeSystem.system`) as input:

  .. code-block:: python

      import pywindow as pw

      molsys = pw.MolecularSystem.load_file(`data/input/PUDXES.xyz`)

      molsys2 = pw.MolecularSystem.load_system(molsys.system)

Pre-processing
..............

If our input requires pre-processing (rebuilding molecules through periodic
boundary and/or force field atom ids deciphering) the following methods allow
that:

1. Rebuilding a periodic system

.. code-block:: python

    rebuild_molsys = molsys.rebuild_system()

2. Deciphering force field atom ids

.. code-block:: python

    molsys.decipher_atom_keys('OPLS')

If the force field is not supported by ``pywindow`` we can use
:func:`pywindow.MolecularSystem.decipher_atom_keys()` to generate a custom
force field deciphering tool.

.. code-block:: python

    some_forcefield = {
                          'ca': 'C',
                          'ni': 'N',
                          'hc': 'H',
                          'ha': 'H'
                      }

    molsys.swap_atom_keys(some_forcefield)


Indices and tables
------------------

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