Rxn-INSIGHT: Fast Chemical Reaction Analysis Using Bond-Electron Matrices

Rxn-INSIGHT is an open-source algorithm, written in python, to classify and name chemical reactions, and suggest reaction conditions based on similarity and popularity.

1. Installation

Rxn-INSIGHT relies on NumPy, Pandas, RDKit, RDChiral, and RXNMapper.

A virtual environment can be installed with Anaconda as follows:

conda env create -f environment.yml
conda activate rxn-insight

To add the rxn-insight environment to Jupyter Notebook:

python -m ipykernel install --user --name=rxn-insight

2. Usage

Basic Usage

from rxn_insight.reaction import Reaction
r = "c1ccccc1I.C=CC(=O)OC>>COC(=O)/C=C/c1ccccc1"  # Define a Reaction SMILES identifier
rxn = Reaction(r)
ri = rxn.get_reaction_info()

The reaction info contains most of the information:

{'REACTION': 'C=CC(=O)OC.Ic1ccccc1>>COC(=O)/C=C/c1ccccc1', 
 'MAPPED_REACTION': '[CH3:1][O:2][C:3](=[O:4])[CH:5]=[CH2:6].I[c:7]1[cH:8][cH:9][cH:10][cH:11][cH:12]1>>[CH3:1][O:2][C:3](=[O:4])/[CH:5]=[CH:6]/[c:7]1[cH:8][cH:9][cH:10][cH:11][cH:12]1', 
 'N_REACTANTS': 2, 
 'N_PRODUCTS': 1, 
 'FG_REACTANTS': ('Aromatic halide', 'Vinyl'), 
 'FG_PRODUCTS': (), 
 'PARTICIPATING_RINGS_REACTANTS': ('c1ccccc1',), 
 'PARTICIPATING_RINGS_PRODUCTS': ('c1ccccc1',), 
 'ALL_RINGS_PRODUCTS': ('c1ccccc1',), 
 'BY-PRODUCTS': ('HI',), 
 'CLASS': 'C-C Coupling', 
 'TAG': '55becfded1a3842d5a03bbf3e1610411c659aff0806930400c4db2ef61f9c87f', 
 'SOLVENT': ('',), 
 'REAGENT': ('',), 
 'CATALYST': ('',), 
 'REF': '', 
 'NAME': 'Heck terminal vinyl', 
 'SCAFFOLD': 'c1ccccc1'}

Similarity Search

A similarity search can be performed when a database with similar reactions is provided as a pandas DataFrame (df in this case). Another Pandas DataFrame is returned.

df_nbs = rxn.find_neighbors(df, fp="MACCS", concatenate=True, threshold=0.5, broaden=True, full_search=False)

Condition Suggestion

Reaction conditions can be suggested when a Pandas DataFrame is provided.

rxn.suggest_conditions(df)
suggested_solvents = rxn.suggested_solvent
suggested_catalysts = rxn.suggested_catalyst
suggested_reagents = rxn.suggested_reagent

3. Datasets

The complete USPTO dataset that is analyzed by Rxn-INSIGHT, as described in the manuscript, can be found on Zenodo: https://doi.org/10.5281/zenodo.10171745. The gzip file should be downloaded and placed in the folder data/.

4. Reference