From 28713e0c3e6f77c45c98869f1e7ad6627eb207df Mon Sep 17 00:00:00 2001 From: Daniel Schwalbe-Koda Date: Mon, 10 Jan 2022 12:25:05 -0500 Subject: [PATCH] Update README.md add citation and disclaimer --- README.md | 29 ++++++++++++++++++++++++++--- 1 file changed, 26 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index f2849d0..8d4cb78 100644 --- a/README.md +++ b/README.md @@ -29,10 +29,11 @@ conda activate VOID Zeo++ and its interface to pymatgen are required to use the Voronoi sampler. The following instructions for their installation are based off the original instructions at the [pymatgen documentation](https://pymatgen.org/pymatgen.io.zeopp.html#zeo-installation-steps). -The original code retrieval with `svn checkout –username anonsvn https://code.lbl.gov/svn/voro/trunk` (password anonsvn) no longer works. Instead, use these repositories for [Voro++](https://github.com/chr1shr/voro) and [Zeo++](https://github.com/richardjgowers/zeoplusplus). +The original code retrieval with `svn checkout –username anonsvn https://code.lbl.gov/svn/voro/trunk` (password anonsvn) no longer works. Instead, we suggest using these mirrors for [Voro++](https://github.com/chr1shr/voro) and [Zeo++](https://github.com/richardjgowers/zeoplusplus): ```bash -git clone +git clone https://github.com/chr1shr/voro.git +git clone https://github.com/richardjgowers/zeoplusplus.git ``` Please note that there may be differences between the Zeo++ code in the Github repository and the stable version available for download in [this link](http://www.maciejharanczyk.info/Zeopp/). @@ -54,7 +55,7 @@ Run `make dylib` within the Zeo++ directory. Navigate to `cython_wrapper/` in the Zeo++ directory and edit `setup_alt.py` to point the variables `includedirs` and `libdirs` to the correct Voro++ directory. Run `python setup_alt.py develop` to install Zeo++ python bindings. -If you have problems compiling this library, please try contacting the Zeo++ developers. +If you have problems compiling this library, please try contacting the Zeo++ developers. We do not offer support for compilation of Zeo++, Voro++ or other dependencies. Finally, install the `VOID` package by navigating to the VOID directory and running: @@ -82,3 +83,25 @@ Further examples can be seen in the [examples](examples/README.md) folder. ## Nomenclature The nomenclature of the variables in this software follows (mostly) the [traditional molecular docking terminology](https://en.wikipedia.org/wiki/Docking_(molecular)) + +## Citing + +The publication describing the algorithm and the software is the following: + + +D. Schwalbe-Koda and R. Gómez-Bombarelli. _J. Phys. Chem. C_ **125** (5), 3009–3017 (2021). DOI [10.1021/acs.jpcc.0c10108](https://doi.org/10.1021/acs.jpcc.0c10108) + +If you use this software, please cite the paper above. The bibtex for the citation is the following: + +``` +@article{schwalbe2021supramolecular, + title={Supramolecular recognition in crystalline nanocavities through Monte Carlo and Voronoi network algorithms}, + author={Schwalbe-Koda, Daniel and G{\'o}mez-Bombarelli, Rafael}, + journal={The Journal of Physical Chemistry C}, + volume={125}, + number={5}, + pages={3009--3017}, + year={2021}, + publisher={ACS Publications} +} +```