From d0e3916bec6ffba52a153fb2d55b993b5623a9a3 Mon Sep 17 00:00:00 2001 From: Josh Horton Date: Wed, 31 May 2023 10:47:00 +0100 Subject: [PATCH] update the readme with reviewer feedback --- README.md | 53 ++++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 44 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 9e4b0ee..a67a2fa 100644 --- a/README.md +++ b/README.md @@ -19,20 +19,50 @@ Detailed usage examples can be found in the OpenFF Toolkit repository. Each force field is currently available in two forms -- both with and without bond constraints to hydrogen. The default version of each force field (i.e. de-1.0.0.offxml) is suitable for typical molecular dynamics simulations with constrained bonds to hydrogen. The "unconstrained" version of each force field (i.e. de_unconstrained-1.0.0.offxml) should be used when single-point energies are a major concern (e.g. geometry optimizations) and when comparing the force field to QM data. -| Filename | DOI | FF line | Release Date | Major format changes? | -|---------------------------------------|------|------------|--------------|-----------------------| -| `de-force-1.0.0.offxml` | TODO | DE-Force-1 | Feb 17, 2023 | No | -| `de-force_unconstrained-1.0.0.offxml` | TODO | DE-Force-1 | Feb 17, 2023 | No | +| Filename | DOI | FF line | Release Date | Major format changes? | +|---------------------------------------|--|------------|--------------|-----------------------| +| `de-force-1.0.0.offxml` | https://doi.org/10.26434/chemrxiv-2023-28r9s | DE-Force-1 | Feb 17, 2023 | No | +| `de-force_unconstrained-1.0.0.offxml` | https://doi.org/10.26434/chemrxiv-2023-28r9s | DE-Force-1 | Feb 17, 2023 | No | -## Installation +# Installation +## Installation of virtual environment + +``de-forcefields`` packages are published via [conda-forge](https://conda-forge.org/) and are simple to install via the [conda](https://docs.conda.io/en/latest/) package manager. +If you don't have the conda package manager installed already you can follow the [guide](https://conda.io/projects/conda/en/latest/user-guide/install/index.html#installation) provided by conda to get started. +Before installing the package we recommend using a virtual environment to avoid dependency conflicts with other packages. You can then create a new environment and install `de-forcefields` via: ```shell -conda install -c conda-forge de-forcefields +conda create -c conda-forge --name deforce de-forcefields +``` + +The environment must then be activated before the software can be used: + +```shell +conda activate deforce +``` + +To deactivate the environment use: + +```shell +conda deactivate +``` + +Finally, the environment can be removed via: + +```shell +conda remove -n deforce --all ``` +## Installing via conda -## Use +The package can also be installed into an existing virtual environment via: + +```shell +conda install -c conda-forge de-forcefields +``` + +# Use Installing this package exposes an entry point that makes the `deforcefields/offxml/` directory easily accessible by other packages in the same Python installation. If the [OpenFF Toolkit](https://github.com/openforcefield/openff-toolkit) is installed, it will automatically detect and use this entry point: @@ -55,7 +85,7 @@ Otherwise, the entry point can be accessed by querying the `openforcefield.smirn Force fields in the `DE-Force-1` lines are descended from [OpenFF-2.0.0 Sage](https://doi.org/10.5281/zenodo.5214478). -## General versioning guidelines +# General versioning guidelines Force fields moving forward will be called `name-X.Y.Z` @@ -64,5 +94,10 @@ Force fields moving forward will be called `name-X.Y.Z` * `Z` is a bugfix version -- e.g. something we've caught and corrected. -## Versions +# Versions - `DE-Force-1` : Proof of concept general transferable Double Exponential force field fit using [Sage training data](https://doi.org/10.26434/chemrxiv-2022-n2z1c-v2). + + +# Copyright + +Copyright (c) 2023 Josh Horton \ No newline at end of file