diff --git a/README.md b/README.md index ef9dd5f..702c3a1 100644 --- a/README.md +++ b/README.md @@ -4,12 +4,41 @@ Polymer-Oriented LibrarY of Monomer Expression Rules and In-silico Synthesis Too [![GitHub Actions Build Status](https://github.com/timbernat/polymerist/workflows/CI/badge.svg)](https://github.com/timbernat/polymerist/actions?query=workflow%3ACI) [![codecov](https://codecov.io/gh/timbernat/polymerist/main/graph/badge.svg)](https://codecov.io/gh/timbernat/polymerist/branch/main) +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 + + +## Installation + +Currently, this package only supports a "dirty" developer install using conda/mamba and `pip`. +First, install the `conda` environment manager (either the lightweight [Miniconda Distribution](https://docs.anaconda.com/free/miniconda/miniconda-install/) (recommended) or the bulkier [Anaconda Distribution](https://www.anaconda.com/download)). +Further, it is highly recommended (but optional) that you install the mamba package manager (either thru [Miniforge or Conda](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)); 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 the CLI in whichever directory you'd like the dev installation to live: +```sh +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 . +``` +Equivalent commands using just conda (in case mamba installation fails) are below. These will perform the same install, just much more slowly: +```sh +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](https://docs.eyesopen.com/toolkits/python/quickstart-python/license.html), 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 the package 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 environment active, either from the command line or from a [Jupyter Notebook](https://jupyter.org/)! -A unified set of tools for setting up general organic polymer systems for MD within the OpenFF framework ### Copyright -Copyright (c) 2024, Timotej Bernat +Copyright (c) 2024, Timotej Bernat (timotej.bernat@colorado.edu) #### Acknowledgements