From d88240cbed05986cb4100bb87dd8c77e642b3717 Mon Sep 17 00:00:00 2001
From: mlehner <marc.lehner@phys.chem.ethz.ch>
Date: Mon, 9 Oct 2023 20:31:01 +0200
Subject: [PATCH] update readme

---
 README.md           |  8 ++++----
 environment.yml     |  2 +-
 min_environment.yml | 31 +++++++++++++++++++++++++++++++
 3 files changed, 36 insertions(+), 5 deletions(-)
 create mode 100644 min_environment.yml

diff --git a/README.md b/README.md
index 13470d5..95d4a52 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-Welcome to Serenityff-Charge
+Welcome to DASH
 ==============================
 
 [//]: # (Badges)
@@ -17,7 +17,7 @@ Description
 
    Additionally, this repository contains all tools and functions needed to generate a new decision tree for partial charge assignmend, based on the attention data of a graph neural network, cabable of predicting the partial charges of a molecule.
 
-   This repository contains code for the publication by M. Lehner et al. DOI: [arXiv:2305.15981](https://doi.org/10.48550/arXiv.2305.15981)
+   This repository contains code for the publication by M. Lehner et al. DOI: [arXiv:2305.15981](https://doi.org/10.48550/arXiv.2305.15981) and [10.1021/acs.jcim.3c00800](https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c00800)
 
 
 Content
@@ -61,8 +61,8 @@ Installation
 
    ```bash
     conda env create -f environment.yml
-    conda activate serenityff-charge
+    conda activate dash
     python setup.py install
    ```
 
-This will create a conda enviroment with the correct packages and install the openff plugin for partial charge assignment in openff.
+This will create a conda enviroment with the correct packages and install the openff plugin for partial charge assignment in openff. If you plan on only using the DASH tree and not developing new trees you can also use the file `min_environment.yml` instead, which does not contain any pytorch and pytorch geometric libraries.
diff --git a/environment.yml b/environment.yml
index c97fcfb..83d694b 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,4 +1,4 @@
-name: sff
+name: dash
 channels:
   - defaults
   - conda-forge
diff --git a/min_environment.yml b/min_environment.yml
new file mode 100644
index 0000000..f516d37
--- /dev/null
+++ b/min_environment.yml
@@ -0,0 +1,31 @@
+name: dash
+channels:
+  - defaults
+  - conda-forge
+  - pytorch
+  - pyg
+dependencies:
+  - sphinx_rtd_theme
+  - python
+  - numpy
+  - m2r
+  - conda-build
+  - typing
+  - mpmath
+  - scipy
+  - nbsphinx
+  - pytest
+  - numba
+  - sympy
+  - pandas
+  - sphinx
+  - rdkit
+  - openff-toolkit=0.10.0
+  - codecov
+  - pandoc
+  - pytest-cov
+  - pytables
+  - pip
+  - pre-commit
+  - ipykernel
+  - py3dmol