Merge remote-tracking branch 'refs/remotes/origin/main'

README.md

@@ -6,23 +6,29 @@ Polymer-Oriented LibrarY of Monomer Expression Rules and In-silico Synthesis Too
 
 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 for [Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shirts, Michael R., "Parameterization of General Organic Polymers within the Open Force Field Framework"](https://pubs.acs.org/doi/10.1021/acs.jcim.3c01691)
+
+![abstract](docs/_static/polymer_param_graphic_TOC.png)
+
 
 ## 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.
+Currently, this package only supports a "dirty" developer install using conda/mamba and `pip`.  
+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 .
 ```
-Equivalent commands using just conda (in case mamba installation fails) are below. These will perform the same install, just much more slowly:
+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 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
@@ -31,9 +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