extract_reaction_template

Extract reaction templates from chemical reaction data.

Requirements

Java: 1.8
ChemAxon API: 18.18.0

Installation

Refer to the link below.

• ChemAxon

Usage

1. Donwload USPTO reaction data extracted by Lowe.
2. Get reaction smiles and remove duplicate reaction.

tail -n +2 1976_Sep2016_USPTOgrants_smiles.rsmi | awk -F '\t' '{print $1}' | sort | uniq > 1976_Sep2016_USPTOgrants_smiles_uniq.smi

3. Extract reaction templates.

javac src/main/ExtractReactionTemplate.java
java src/main/ExtractReactionTemplate -f smarts -i 1976_Sep2016_USPTOgrants_smiles_uniq.smi -o PATH_TO_DIRECTORY

The output file contains;

• product
• row reaction
• reaction template including the reaction center atoms
• reaction template including the reaction center atoms and 1-neighbor atoms

Example

javac src/main/ExtractReactionTemplate.java
java src/main/ExtractReactionTemplate -f smarts -i sample.smi -o sample.txt

Information

• Reaction Mapping
• SMILES

Reference

Shoichi Ishida , Kei Terayama, Ryosuke Kojima, Kiyosei Takasu, Yasushi Okuno
Prediction and Interpretable Visualization of Retrosynthetic Reactions Using Graph Convolutional Networks
Journal of Chemical Information and Modeling. [DOI: 10.1021/acs.jcim.9b00538]