posgen 0.1.1.3
PosGen
License: MIT
Requires Python: >=3.8.13,<4.0.0

POSGEN
=======

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|Read the Docs| |Tests| |Codecov|

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   :target: https://posgen.readthedocs.io/
   :alt: Read the documentation at https://posgen.readthedocs.io/
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A simple package for making custome scoring function in smina, visulaization of molecules, ligand and memebrane using py3dmol.

An implementation of regression for optimizing scoring function and $\alpha$ and $\beta$ from experimental data.


Features
--------

* Visualize Receptor, lipids and ligands 
* Automate docking using  smina                                
* Calculate RMSD and plot RMSD Matrix                                 
* Develop Custom Scoring Functions
* Optimize $\alpha$ and $\beta$
* and many more..

Requirements
------------

* TODO


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

You can install *posgen* via pip_ from PyPI_:

.. code:: console

   $ pip install posgen


Usage
-----

::

    from posgen import posgen

Create an Object of the ProjectStart:

::

    a2 = posgen.ProjectStart() 

Can set your project directory as follow which may not be same as the
runing notebook.Creates a relative paths for files inside the project
directory

::

    a2.SetFolders(".") 

Adding a receptor into the project is as easy as following:

::

    a2.LoadReceptor("membrane")
    a2.SimpleView

.. figure:: ./images/posgen3.png
   :alt: Image of posgen


Similarly for Ligand as well

::

    a2.LoadLigand("./DATA/Conformer3D_CID_139199449.sdf") 

|Image of posgen4| 

For docking visualization of grid box around active
site is important. Here we can just give an input to create a grid and
visualize it.

::

    a2.LoadBox([7.623, 3.103, -18.483], [30.0, 50, 20]) 

Whole view of the molecules loaded into the project instance can be
visualize as following:

::

    a2.ShowMolecules() 

|Image of posgen2| 

View the detail information of the project instace
using print() method on the instance variable.

::

    print(a2)

|Image of posgen0|

::

    a2.display()

Visualize smiles code and generate 3D structures.

|Image of posgen6|

::

    df =rmsd_matrix(poses,verbose=False, plot=True, save=True, annot=True, key="latest_calculation")


View the RMSDs of the ligands docked in matrix view.

|Image of posgen5|


.. |Image of posgen4| image:: ./images/posgen4.png
.. |Image of posgen2| image:: ./images/posgen2.png
.. |Image of posgen0| image:: ./images/posgen0.png
.. |Image of posgen5| image:: ./images/posgen5.png
.. |Image of posgen6| image:: ./images/posgen6.png

Please see the `Command-line Reference <Usage_>`_ for details.


Contributing
------------

Contributions are very welcome.
To learn more, see the `Contributor Guide`_.


License
-------

Distributed under the terms of the `MIT license`_,
*PosGen* is free and open source software.


Issues
------

If you encounter any problems,
please `file an issue`_ along with a detailed description.


.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _MIT license: https://opensource.org/licenses/MIT
.. _PyPI: https://pypi.org/
.. _file an issue: https://github.com/takshan/posgen/issues
.. _pip: https://pip.pypa.io/
.. github-only
.. _Contributor Guide: CONTRIBUTING.rst
.. _Usage: https://posgen.readthedocs.io/en/latest/usage.html