Stereochemistry Labelling Done Good

Centres is an Open Source Java library for that allows perception and labelling of stereogenic centres in chemical structures using the Cahn-Ingold-Prelog priority rules.

How to Use

You can use Centres interactively at http://www.simolecule.com/cdkdepict by selecting the annotation "CIP Stereo Label". Alternatively you can download the centres.jar (built on CDK) from the releases page. This JAR can be used to label and test an SD or SMILES file.

java -jar centres.jar input.sdf

To run the benchmark tests pressented by Hanson et al (note limitations below) run the following commands. The files can be downloaded from https://cipvalidationsuite.github.io/ValidationSuite/.

java -jar centres.jar compounds_2d.sdf -e CIP_LABELS
java -jar centres.jar compounds_3d.sdf -e CIP_LABELS
java -jar centres.jar compounds.smi -e 1

Key Features

• Generic library allowing dependency injection of any molecule/atom object representation. Currently supported 'endpoints':
  • Chemistry Development Kit
  • OPSIN
  • JChem
• Perception and labelling of tetrahedral (R/S/r/s) and geometric double bonds (Z/E).
• Implementation of the Cahn-Ingold-Prelog (CIP) priority rules as they appear in Prelog and Helmchen, 1982
• Implementation of the Cahn-Ingold-Prelog (CIP) priority rules as they appear in Nomenclature of Organic Chemistry, IUPAC Recommendations and Preferred Names 2013

Install

jchem and opsin backends do not currently pass the internal validation tests and should be skipped when running tests.

mvn install -pl '!jchem,!opsin'

alternatively skip the tests:

mvn install -DskipTests

License

BSD 2-Clause

Authors

John Mayfield (né May)

Limitations

• Helicene and chirality planes are not supported
• SMILES does not capture axial atropisomerism but this is supported in 2D/3D
• When using CDK the 3D SDfile must find stereocentres with little information available, the current algorithm does not find all centres in the test sets by default. To prevent this a modified version of CDK is used in Centres that captures all possible tetrahedral/double bond stereochemistries.

References

• Robert M. Hanson John Mayfield Mikko J. Vainio Andrey Yerin Dmitry Redkin Sophia Musacchio. Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. Submitted preprint.
• Prelog and Helmchen. Basic Principles of the CIP-System and Proposals for a Revision. Angewandte Chemie International Edition 21 (1982) 567-683
• Perdih and Rmzinger. Stereo-chemistry and Sequence Rules A Proposal for Modification of Cahn-Ingold-Prelog System. Tetrahedron: Asymmetry Vol 5 (1994) 835-861