Cleans the smiles from v1.0.1 from Grambow, C. A., Pattanaik, L. & Green, W. H. Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry. Sci. data 7, 1–8 (2020). Some helpful scripts are also provided.
Some of the scripts utilize helpful functionality from the Reaction Mechanism Generator (RMG) software, such as RMG-Py, RMG-database, and from the Automatic Rate Calculator (ARC). Clone these repositories into the same folder.
The installation instructions for RMG-Py and RMG-database can be found here and involves creating the rmg_env and running make to compile RMG-Py. To install ARC, clone the repo, add ARC to your local path, and create the arc_env; additional detail can be found here. All code in this repo can be run within the arc_env.