csfdock 0.1.2.2
CsfDock
License: MIT
Requires Python: >=3.6.1,<4.0.0

CsfDock
=======

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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 *CsfDock* via pip_ from PyPI_:

.. code:: console

   $ pip install csfdock


Usage
-----

::

    from csfdock.ar2a_v3 import *

Create an Object of the ProjectStart:

::

    a2 = 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/csfdock3.png
   :alt: Image of csfdock


Similarly for Ligand as well

::

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

|Image of csfdock4| 

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 csfdock2| 

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

::

    print(a2)

|Image of csfdock0|

::

    a2.display()

Visualize smiles code and generate 3D structures.

|Image of csfdock6|

::

    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 csfdock5|


.. |Image of csfdock4| image:: ./images/csfdock4.png
.. |Image of csfdock2| image:: ./images/csfdock2.png
.. |Image of csfdock0| image:: ./images/csfdock0.png
.. |Image of csfdock5| image:: ./images/csfdock5.png
.. |Image of csfdock6| image:: ./images/csfdock6.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`_,
*CsfDock* 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/csfdock/issues
.. _pip: https://pip.pypa.io/
.. github-only
.. _Contributor Guide: CONTRIBUTING.rst
.. _Usage: https://csfdock.readthedocs.io/en/latest/usage.html