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 based upon concepts introduced in "Parameterization of General Organic Polymers within the Open Force Field Framework" (Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shirts, Michael R.)
Currently, this package only supports a "dirty" pip installation from a clone of this GitHub repo.
First, you will need to install some iteration of the conda environment manager. Possible builds (in decreasing order of recommendation) are:
- The very-rapid
mambapackage manager; installable either through Miniforge or Conda - The lightweight Miniconda Distribution
- The bulky Anaconda Distribution Once you install one of these (or if you already have one installed on your system), you may proceed with on of the installation modes.
For nominal use, polymerist can be installed 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/release-build.yml
mamba activate polymerist-env
pip install .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/release-build.yml
conda activate polymerist-env
pip install .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!
Those developing for polymerist may like to have an editable local installation, in which they can make changes to the source code and test behavior changes in real-time.
In this case, one requires an "editable build" which does NOT live in the site_packages dir of the created env. This type of installation proceeds as follows:
git clone https://github.com/timbernat/polymerist
cd polymerist
mamba env create -n polymerist-dev -f devtools/conda-envs/dev-build.yml
mamba activate polymerist-dev
pip install -e . --config-settings editable_mode=strictThe --config-settings editable_mode flag in the final line allows this install to "play nicely" with PyLance, making auto-completion and navigation to source code much easier for VSCode users.
It is optional, and can be removed if this compatibility is not desired.
Copyright (c) 2024, Timotej Bernat ([email protected])
Project based on the Computational Molecular Science Python Cookiecutter version 1.1.