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@@ -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) | ||
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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 | ||
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## Installation | ||
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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. | ||
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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. | ||
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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/)! | ||
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A unified set of tools for setting up general organic polymer systems for MD within the OpenFF framework | ||
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### Copyright | ||
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Copyright (c) 2024, Timotej Bernat | ||
Copyright (c) 2024, Timotej Bernat ([email protected]) | ||
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#### Acknowledgements | ||
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