RDChiral: An RDKit Wrapper for Handling Stereochemistry
in Retrosynthetic Template Extraction and Application
Posted on 2019-06-12 - 22:43
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.
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Coley, Connor
W.; Green, William H.; Jensen, Klavs F. (2019). RDChiral: An RDKit Wrapper for Handling Stereochemistry
in Retrosynthetic Template Extraction and Application. ACS Publications. Collection. https://doi.org/10.1021/acs.jcim.9b00286
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AUTHORS (3)
CC
Connor
W. Coley
WG
William H. Green
KJ
Klavs F. Jensen
CATEGORIES
- Space Science
- Medicine
- Genetics
- Molecular Biology
- Biotechnology
- Evolutionary Biology
- Chemical Sciences not elsewhere classified
- Biological Sciences not elsewhere classified
- Information Systems not elsewhere classified
- Mathematical Sciences not elsewhere classified
- Inorganic Chemistry
- Science Policy
- Plant Biology
KEYWORDS
retrosynthetic transformationsretrosynthetic template extraction algorithmopen-source Python wrappersynthesis planningapplication noteopen-source implementationRDChiralchiral tetrahedral centersretrosynthetic reaction templatesRDKit WrapperSMARTS patternsRetrosynthetic Template Extractionatom-mapped reaction SMILES stringsstereochemical informationSMARTS strings