Hi Greg, Hi Paolo,
Thank you for that amazingly fast response! Seems like the bug in NAOMI is
the most likely scenario here.
Thank you for the thorough explanation and your time. I'll post new
information on this if anything unexpected comes up.
Kind regards,
Emanuel
Am Mi., 29. Juli 2020 um
Hi Emanuel,
The chirality bit doesn't have anything to do with double bond
stereochemistry.[1] So that's not what's going on here
The RDKit has the ability to pass the mol block provided directly to the
InChI code without interpreting it. I believe that the ChEMBL team is using
that to generate
Hi Emanuel,
the RDKit perceives double bond stereochemistry on read, and encodes on
write, based on 2D coordinates in the molblock,
I put together an example gist here:
https://gist.github.com/ptosco/9ffae8814e84bcf189da7663775748e5
I hope that addresses your question , if not feel free to get
Dear All,
I am currently working with the RDKit generated SDF String that is stored
in the ChEMBL COMPOUND_STRUCTURES table in the ChEMBL database release 26.
My workflow is:
- pull SDF (V2000) from SQL table
- generate internal molecule representation (NAOMI ChemBio tool-kit if
that
