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Update README.md
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add citation and disclaimer
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Daniel Schwalbe-Koda authored Jan 10, 2022
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Expand Up @@ -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 <insert HTTPS link>
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/).
Expand All @@ -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:

Expand Down Expand Up @@ -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}
}
```

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