This reaction database is generated by manuscript "Comprehensive exploration of graphically defined reaction spaces."
The additional data files are provided on FigShare. RGD1CHNO_AMsmiles.csv contains atom-mapped SMILES, activation energies, and enthalpies of formation for each reaction; RGD1_CHNO.h5 contains the geometry information and energies; DFT_reaction_info.csv is supplied to reproduce figures in the article; RandP_smiles.txt is a dictionary to map the reactant and product smiles appear in RGD1_CHNO.h5 to a molecule index (molX); RGD1_RPs.h5 provides xtb and DFT optimized geometries of each individual reactant/product molecules.
- Usage of python code
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parse_data.py: This script parses all of the model reactions stored in a HDF5 file which can be freely downloaded from figshare.
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make_stat_plots.py: This script parses the a csv file of reaction features and makes bar plots of different reaction features as DE_break_dist.pdf
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draw_violin.py: This script parses csv files of reaction features and DFT energies and makes violin plots of the activation energy distribution of different reaction types as reaction_stat.pdf
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