.. include:: /include/links.rst

.. _combined_modules:

=========================================================
Creating new polymers from different modules
=========================================================

Another important functionality of PySoftK_ is the possibility to create different polymer architectures by combining different modules. 

Let's create a patterned polymer by permuting four monomers using the :mod:`pysoftk.topologies.diblock` function.

First, we need to import the corresponding modules from PySoftK_ to allow us to read and join the monomers
using RDKit_.

.. literalinclude:: scripts/combined_func.py
   :lines: 1-7

Then, we can create the alphabetic permutations and define the monomers whose SMILES codes have been inputted  using  RDKit_ :

.. literalinclude:: scripts/combined_func.py
  :lines: 6-8

Once the monomers have been created, the PySoftK_ function can be used to create the patterned
polymer:
	 
.. literalinclude:: scripts/combined_func.py
  :lines: 11-18

The newly created polymer topology can be **used** as an initial monomer for futher modelling.
In this case, we use the linear polymer function (:mod:`pysoftk.linear\_polymer.super\_monomer`)
uses the previous patterned polymer as initial monomer and creates a new linear polymer
of two-unit repetition. 

.. literalinclude:: scripts/combined_func.py
  :lines: 20-25

The final script is:

.. literalinclude:: scripts/combined_func.py

By using common visualization software (such as VMD_), the built structure **combined_func.py** can be displayed as shown:

.. figure:: images/abcd_pol.png
   :align: center
   :figclass: align-center

Creating a patterned-linear polymer using different modules of PySoftK_.