tools-cell2mol

In this repository we provide the code to deploy an online service for the interpretation of crystallographic unit cells using cell2mol_.

Contents

• 1   How to cite
• 2   Contributors
• 3   Prerequisites
• 4   Running the tool locally
• 5   Known errors

1   How to cite

Vela, S.; Laplaza, R.; Cho, Y.; Corminboeuf, C. cell2mol: encoding chemistry to interpret crystallographic data. Npj Comput. Mater. 2022. 8. 188; doi: 10.1038/s41524-022-00874-9

2   Contributors

Developed by LCMD members at EPFL under the supervision of Prof. Corminboeuf:

• Sergi Vela, Yuri Cho, Ruben Laplaza (EPFL) [cell2mol development]
• Liam Marsh, Osvaldo Hernandez-Cuellar (EPFL) [tools-cell2mol development]

3   Prerequisites

• docker >= v18.09
• tools-barebone >= 1.0.0

4   Running the tool locally

Download the tools-cell2mol repository.

In the main directory, build the docker container by executing:

sudo docker-compose build

this has to be done only the first time or when changing the tools-cell2mol version.

To run tools-cell2mol locally, you can execute:

sudo docker-compose up

in the main directory, and then connect to http://localhost:8090 (or the direction docker indicates you in case you have more than one container running) with your browser.

5   Known errors

Few chemical patterns tend to be poorly interpreted by cell2mol, because of inconsistencies in either cell2mol itself, or in xyz2mol.

cell2mol determines the bond order between atoms based on their connectivity, typical atomic valence electrons of the atoms involved, and the most plausible total charge of the molecule. cell2mol is inevitably incorrect if there is an extra electron or radical chemical species. Other known ligands with wrong interpretations are the triiodide (I3-), and azide (N3-) ions. Future development of cell2mol will aim a fixing those errors. If users identify other common misinterpretations, please contact the authors.