PolyConstruct: a python library for polymer generation

PolyConstruct contains three python tools for generating polymer coordinate and topolgy files for molecular dynamics simulations.

PolyConf is a tool for generating ensembles of polymer conformations by combining monomer coordinate files.

PolyBuild is a tool for generating polymer topology files for simulaton from polymer coordinate files, leveraging the functionality of the gromacs tool pdb2gmx.

PolyTop is a tool for generating polymer topology files from monomer topology files.

PolyConstruct was published in the paper PolyConstruct: adapting biomolecular simulation pipelines for polymers with PolyBuild, PolyConf and PolyTop.

Getting started

Detailed documentation is available at the PolyConstruct ReadTheDocs. This includes installation instructions, tutorials and worked examples, and api documentation for all polyconstruct methods.

There are also detailed tutorials for PolyConf in the folder polyconf_examples, and detailed tutorials for PolyTop in the folder polytop_examples

Quick and dirty installation

From your home directory, clone PolyConstruct from this repository:

cd ~
git clone https://github.com/OMaraLab/polyconstruct.git

Then navigate to ~/polyconstruct

cd polyconstruct

Create a python environment and setup PolyConstruct:

conda create --name polyconstruct python=3.10
conda activate polyconstruct

pip install -r requirements.txt

Then, build the PolyTop, PolyConf and PolyBuild packages:

cd polytop

pip install -e .

cd ../polyconf

pip install -e .

cd ../polybuild

pip install -e .