From bae385816a8fad77293a18dff33feefc7459560a Mon Sep 17 00:00:00 2001 From: timbernat <52677403+timbernat@users.noreply.github.com> Date: Tue, 19 Mar 2024 14:50:23 -0600 Subject: [PATCH 1/2] Added graphical abstract and links to publication --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 702c3a1..13b1e3d 100644 --- a/README.md +++ b/README.md @@ -6,12 +6,16 @@ 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, 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. 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: @@ -22,6 +26,8 @@ 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! + 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 From 3a23a40cc37b2af36e10f9e9591e9876f66d95a8 Mon Sep 17 00:00:00 2001 From: timbernat <52677403+timbernat@users.noreply.github.com> Date: Tue, 19 Mar 2024 14:57:11 -0600 Subject: [PATCH 2/2] Corrected typos and improved aesthetics --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 13b1e3d..d665f17 100644 --- a/README.md +++ b/README.md @@ -14,11 +14,11 @@ 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 @@ -26,9 +26,9 @@ 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 @@ -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