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

preprint
submitted on 04.04.2019 and posted on 05.04.2019 by Connor W. Coley, William H. Green, Klavs F. Jensen
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 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 tetrahedral centers as well as the cis/trans chirality 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 manuscript, we describe the implementation of these two pieces of code and illustrate their use through many examples.

The two .json.gz files can be generated from the open source USPTO data available at https://figshare.com/articles/Chemical_reactions_from_US_patents_1976-Sep2016_/5104873 using the code contained in the rdchiral GitHub repository. They are placed here for convenience if you would prefer to copy them into the templates/data subfolder instead of creating them from the source .rsmi file.

Funding

ARO W911NF-16- 2-0023

NSF GRFP 1122374

History

Email Address of Submitting Author

ccoley@mit.edu

Institution

MIT

Country

United States

ORCID For Submitting Author

0000-0002-8271-8723

Declaration of Conflict of Interest

No conflict of interest

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