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Added dirty install instructions to README
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timbernat authored Mar 19, 2024
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Expand Up @@ -4,12 +4,41 @@ Polymer-Oriented LibrarY of Monomer Expression Rules and In-silico Synthesis Too
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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


## 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 ([email protected])


#### Acknowledgements
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