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Corrected typos and improved aesthetics
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timbernat authored Mar 19, 2024
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Expand Up @@ -14,21 +14,21 @@ Source code for [Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shir
## 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 through [Miniforge or Conda](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)); this will greatly accelerate download times.
First, you will need to 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)) 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](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:
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:
```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 .
```
The third command will take **_at least_** a few minutes, and will make the terminal quite bust; remain calm, that's normal!
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 installation fails) are below. These will perform the same install, just much more slowly:
Equivalent commands using just `conda` (in case `mamba` has ot been installed) are below. These will perform the same installation, just much more slowly:
```sh
git clone https://github.com/timbernat/polymerist
cd polymerist
Expand All @@ -37,9 +37,9 @@ 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.
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 environment active, either from the command line or from a [Jupyter Notebook](https://jupyter.org/)!
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](https://jupyter.org/)!


### Copyright
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