Dear All,

I have hit what I think is a problem with stereochemistry perception/handling 
for certain types of pseudochiral and/or spirocyclic systems.
Basically I am observing that some types of input tetrahedral stereochemical 
information gets lost when an RDKit molecule is generated.
But I only realised this because I was wanting to generate conformers and was 
seeing stereochemical scrambling...

Anyway, an example with pictures will probably explain things better:

Any help/advice appreciated.

Kind regards


PLEASE READ: This email is confidential and may be privileged. It is intended 
for the named addressee(s) only and access to it by anyone else is 
unauthorised. If you are not an addressee, any disclosure or copying of the 
contents of this email or any action taken (or not taken) in reliance on it is 
unauthorised and may be unlawful. If you have received this email in error, 
please notify the sender or Email is not a secure 
method of communication and the Company cannot accept responsibility for the 
accuracy or completeness of this message or any attachment(s). Please check 
this email for virus infection for which the Company accepts no responsibility. 
If verification of this email is sought then please request a hard copy. Unless 
otherwise stated, any views or opinions presented are solely those of the 
author and do not represent those of the Company.

The Vernalis Group of Companies
100 Berkshire Place
Wharfedale Road
Winnersh, Berkshire
RG41 5RD, England
Tel: +44 (0)118 938 0000

To access trading company registration and address details, please go to the 
Vernalis website at and click on the "Company address and 
registration details" link at the bottom of the page..
Check out the vibrant tech community on one of the world's most
engaging tech sites,!
Rdkit-discuss mailing list

Reply via email to