rdkit.Chem.rdCIPLabeler module

Module containing a function to assign stereochemical labels based on an accurate CIP rules implementation. This algoritm is a port of https://github.com/SiMolecule/centres, which was originally written by John Mayfield. The original algorithm is described in:

Hanson, R. M., Musacchio, S., Mayfield, J. W., Vainio, M. J., Yerin, A., Redkin, D. Algorithmic Analysis of Cahn–Ingold–Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. J. Chem. Inf. Model. 2018, 58, 1755-1765.

rdkit.Chem.rdCIPLabeler.AssignCIPLabels((Mol)mol[, (AtomPairsParameters)atomsToLabel=None[, (AtomPairsParameters)bondsToLabel=None[, (int)maxRecursiveIterations=0]]]) → None :

New implementation of Stereo assignment using a true CIP ranking. On return: The molecule to contains CIP flags Errors: when maxRecursiveIterations is exceeded, throws a MaxIterationsExceeded error ARGUMENTS:

  • mol: the molecule

  • atomsToLabel: (optional) list of atoms to label

  • bondsToLabel: (optional) list of bonds to label

  • maxRecursiveIterations: (optional) protects against pseudo-infinite

recursion for highly symmetrical structures.

A value of 1,250,000 take about 1 second. Most structures requires less than 10,000iterations. A peptide with MW~3000 took about 100 iterations, and a 20,000 mw protein took about 600 iterations

(0 = default - no limit)

C++ signature :

void AssignCIPLabels(RDKit::ROMol {lvalue} [,boost::python::api::object=None [,boost::python::api::object=None [,unsigned int=0]]])