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reference to the presentation of xyz2mol #35

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reference to the presentation of xyz2mol #35

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edit, remove overly long lines in the documentation
nbehrnd Jul 21, 2022
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nbehrnd Jul 21, 2022
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# 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)
Expand All @@ -11,13 +13,19 @@ 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:

`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

Expand All @@ -26,7 +34,8 @@ 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
Expand Down