RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application

J Chem Inf Model. 2019 Jun 24;59(6):2529-2537. doi: 10.1021/acs.jcim.9b00286. Epub 2019 Jun 13.


There is a renewed interest in computer-aided synthesis planning, where the vast majority of approaches require the application of retrosynthetic reaction templates. Here we introduce RDChiral, an open-source Python wrapper for RDKit designed to provide consistent handling of stereochemical information in applying retrosynthetic transformations encoded as SMARTS strings. RDChiral is designed to enforce the introduction, destruction, retention, and inversion of chiral tetrahedral centers as well as the cis/trans configuration of double bonds. We also introduce an open-source implementation of a retrosynthetic template extraction algorithm to generate SMARTS patterns from atom-mapped reaction SMILES strings. In this application note, we describe the implementation of these two pieces of code and illustrate their use through many examples.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chemical Phenomena
  • Cheminformatics
  • Small Molecule Libraries / chemistry*
  • Software*
  • Stereoisomerism


  • Small Molecule Libraries