Coevolution of catalysts

Various illustration and computational analogies for a research article about optimization of organic chemistry catalysts using the coevolution approach:

(article data to be added)

Requirements

• rdkit 2020.03.1
• matplotlib 3.1.0
• scikit-learn 1.0.2
• cairosvg 2.7.1
• skunk 1.3.0
• icecream 2.1.3
• map4 (MinHashed Atom-Pair)
• tmap 1.0.6
• tqdm 4.66.1

Reproducing figures from the article

To reproduce the Figure 2B, run the Figure_2B.py script.

To reproduce the Figure 4A, run the Figure_4A.py script.

To reproduce the Figure 4B, run the halides_clustering.py script.

To reproduce the ligands UMAP, run the ligands_mapping_mainfig.py script.

For interactive TSNE map, download the /interactive_HTML_embedding/ folder and open the DNP_TSNE_ECFP6.html file in a browser.

Natural charges calculatd with density functional theory (DFT) are provided in the data/qm/unique_halides_and_bb_vacuum.csv file. Run the qm_nbo_analysis.py script to reproduce the plot of the natural charges.