PyPolyBuilder is a python tool that generates MTFs for linear and branched polymers, macromolecules and supramolecular structures
based on predefined BBs. The program considers two main cases: (1) the preparation of MTBs for radial polymers such as dendrimers; and
(2) a general procedure for connecting BBs based on a BB connectivity file. Currently, the output formats are compatible with GROMOS
and GROMACS simulation packages.
The recommended way to install pyPolyBuilder is using pip:
pip install pypolybuilder
Another option is to clone this repository by simply:
git clone https://vitor_horta@bitbucket.org/vitor_horta/pypolybuilder.git
pyPolyBuilder currently supports two building modes: Dendrimer and Polymer.
The required inputs for each mode are detailed in the following subsections.
Also the help command can be used to list all available options:
pypolybuilder --help
The dendrimer building process is based on the following inputs:
--core (Core filename)
--ter (Terminal filename)
--inter (Intermediate filename)
--core (Core filename)
--params (Force Field parameters filename)
--ngen (Number of generations to be built)
Authors of scientific papers including results generated using pyPolyBuilder are encouraged to cite the following paper.
@article{pyPolyBuilder2017,
author = " Vitor A. C. Horta, Mayk Caldas Ramos, Bruno A. C. Horta ",
title = { {Pypolybuilder}: A Python Program for the Creation of Molecular Topologies for Branched Macromolecules, Polymers and Supramolecular Structures },
pages = { PAGENUMBER },
volume = { VOLUMENUMBER },
month = { MONTH },
year = { 2017 },
journal = { JOURNAL }
}