Re: [Rdkit-discuss] Double Bond Stereochemistry in the RDKit

2018-12-04 Thread Kovas Palunas
Dan! - Kovas From: Dan Nealschneider Date: Tuesday, December 4, 2018 at 10:05 AM To: "col...@gmail.com" Cc: Kovas Palunas , rdkit discuss Subject: Re: [Rdkit-discuss] Double Bond Stereochemistry in the RDKit I've done some in-memory translation of molecules to ROMols, a

Re: [Rdkit-discuss] Double Bond Stereochemistry in the RDKit

2018-12-04 Thread Dan Nealschneider
I've done some in-memory translation of molecules to ROMols, and have used #2 without major problems. I do remember needing to make sure that the stereoatoms are in the correct order - that is, that the first stereoatom is bonded to the beginAtom of the bond. In Python, this is something like: bon

Re: [Rdkit-discuss] Double Bond Stereochemistry in the RDKit

2018-12-04 Thread Brian Cole
Hi Kovas, For your use-case #2 should suffice, "set STEREOCIS/STEREOTRANS tags + manually set stereo atoms". This is what the EnumerateStereoisomers code does: https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/EnumerateStereoisomers.py#L38 As to what is the 'ground truth', that is a more diff

[Rdkit-discuss] Double Bond Stereochemistry in the RDKit

2018-12-03 Thread Kovas Palunas
Hi All, I’m looking for a bit more clarity regarding double bond stereochem in RDKit. Currently, my understanding is that there are 3 ways to currently store this information: 1. STEREOE/STEREOZ tags + stereo atoms on either side of bond set by CIP ranks, as computed when calling MolFromS