From f52323f14bd6c65baf17f319001886414456575f Mon Sep 17 00:00:00 2001 From: Norwid Behrnd Date: Thu, 21 Jul 2022 18:51:12 +0200 Subject: [PATCH 1/2] edit, remove overly long lines in the documentation --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 4fbc058..5cf451a 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ # Convert Cartesian coordinates to one or more molecular graphs -Given Cartesian coordinates in the form of a `.xyz` file, the code constructs a list of one or more molecular graphs. In cases where there are several possible resonance forms xyz2mol returns a list of all, otherwise just a list of one. +Given Cartesian coordinates in the form of a `.xyz` file, the code constructs a +list of one or more molecular graphs. In cases where there are several possible +resonance forms xyz2mol returns a list of all, otherwise just a list of one. This code is based on the work of DOI: [10.1002/bkcs.10334](http://dx.doi.org/10.1002/bkcs.10334) @@ -17,7 +19,8 @@ Depends on `rdkit`, `numpy`, and `networkx`. Easiest to setup via anaconda/conda `conda install -c conda-forge xyz2mol` -Setup for a standalone enviroment is avaliable via `Makefile`. To setup and test simply clone the project and make. +Setup for a standalone enviroment is avaliable via `Makefile`. To setup and test +simply clone the project and make. git clone https://github.com/jensengroup/xyz2mol @@ -26,7 +29,8 @@ and then run the following the the `xyz2mol` folder make make test -Note, it is also possible to run the code without the `networkx` dependencies, but is slower. +Note, it is also possible to run the code without the `networkx` dependencies, +but is slower. ## Example usage From b061977d333d3a897af2feb31786688483945b55 Mon Sep 17 00:00:00 2001 From: Norwid Behrnd Date: Thu, 21 Jul 2022 18:56:23 +0200 Subject: [PATCH 2/2] add, link to Jan Jensen's presentation of xyz2mol --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 5cf451a..bf79c05 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,11 @@ DOI: [10.1002/bkcs.10334](http://dx.doi.org/10.1002/bkcs.10334) Bull. Korean Chem. Soc. 2015, Vol. 36, 1769-1777 +At the 2020 RDKit Virtual UGM, Jan H. Jensen presented the tool with his talk +"Dealing with organometallic molecules in RDKit" +([slides](https://github.com/rdkit/UGM_2020/blob/master/Presentations/JanJensen.pdf), +[video recording](https://www.youtube.com/watch?v=HD6IpXMVKeo)). + ## Setup Depends on `rdkit`, `numpy`, and `networkx`. Easiest to setup via anaconda/conda: