timbernat / polymerist

Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools

Polymer-Oriented LibrarY of Monomer Expression Rules and In-silico Synthesis Tools

A unified set of tools for monomer template generation, topology building, force-field parameterization, and MD simulations of general organic polymer systems within the OpenFF framework

Source code for Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shirts, Michael R., "Parameterization of General Organic Polymers within the Open Force Field Framework"

Installation

Currently, this package only supports a "dirty" developer install using conda/mamba and pip.
First, you will need to install the conda environment manager (either the lightweight Miniconda Distribution (recommended) or the bulkier Anaconda Distribution) if you don't already have it. Further, it is highly recommended (but optional) that you also have the mamba package manager installed (either through Miniforge or Conda); this will greatly accelerate download times.

Once mamba is installed, you can proceed with the dirty polymerist install into a safe virtual environment (named "polymerist-env" here). To install, execute the following set of commands in a command line interface (CLI) in whichever directory you'd like the dev installation to live:

git clone https://github.com/timbernat/polymerist
cd polymerist
mamba env create -n polymerist-env -f devtools/conda-envs/polymerist-env.yml
mamba activate polymerist-env
pip install -e .

The third command will take at least a few minutes, and will make the CLI terminal quite busy; remain calm, that's normal!

Equivalent commands using just conda (in case mamba has not been installed) are below. These will perform the same installation, just much more slowly:

git clone https://github.com/timbernat/polymerist
cd polymerist
conda env create -n polymerist-env -f devtools/conda-envs/polymerist-env.yml
conda activate polymerist-env
pip install -e .

As an optional last step, it is recommended that you correctly set up paths to your OpenEye License, if you have access to one. Portions of conformer-generation and partial-charge assignment in polymerist will work more effectively with the OpenEye toolkit installed and licensed, but 'polymerist' is set up to not require these closed-source dependencies.

From here, you should be able to run polymerist-dependent scripts in the polymerist-env virtual environment active, either from the command line or from a Jupyter Notebook!

Copyright

Copyright (c) 2024, Timotej Bernat ([email protected])

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.