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.

If you use PolyConstruct, please cite the following paper:

Munaweera, R.; Quinn, A.; Morrow, L.; Morris, R. A.; O’Mara, M. L. PolyConstruct : Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild , PolyConf , and PolyTop. J. Chem. Inf. Model. 2025, acs.jcim.4c02375. https://doi.org/10.1021/acs.jcim.4c02375.

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 is a series of detailed tutorials for PolyConf in the folder polyconf_examples, and for PolyTop in the folder polytop_examples. A set of example input and output files for PolyBuild are presented in the folder polybuild_examples/RTP_entries

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 .