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
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
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
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
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