Re: [Rdkit-discuss] Changes in morgan fingerprint code?

2023-01-16 Thread Francois Berenger
Dear Eric, Sure, if fingerprints are not stable over time, some people who check things very carefully (as you did) will have some surprises. This being said, you should probably be using InChI keys, if you want a hash for each molecule. Regards, F. On 13/01/2023 06:37, Eric Jonas wrote: H

Re: [Rdkit-discuss] Changes in morgan fingerprint code?

2023-01-13 Thread Ling Chan
Yes, if you don't care about stereochemistry, you need to do a Chem.RemoveStereochemistry() prior to your comparison. But if you do care about stereochemistry, "CC=CC(C)(O)CF" and "C/C=C/[C@](C)(O)CF" are indeed different molecular specifications. As for fingerprints, I believe that most fingerpri

Re: [Rdkit-discuss] Changes in morgan fingerprint code?

2023-01-13 Thread Rocco Moretti
> > Just as an FYI: the best easy way, by far, to keep track of whether or not > you've seen a particular molecule is to use the SMILES. > Though as a caveat with SMILES, be aware of issues about partial chirality and E/Z isomerization specification. "CC=CC(C)(O)CF" is not the same SMILES as "C/C=

Re: [Rdkit-discuss] Changes in morgan fingerprint code?

2023-01-12 Thread Greg Landrum
Hi Eric, That would be due to the fix for this bug: https://github.com/rdkit/rdkit/issues/5036 If you were generating the fingerprints on "normal" (i.e. hydrogen-suppressed) graphs, you wouldn't notice this one, but the fact that you add the Hs before generating the fingerprint causes you to notic

[Rdkit-discuss] Changes in morgan fingerprint code?

2023-01-12 Thread Eric Jonas
Hello! I use the crc of morgan fingerprints as a quick-and-dirty way to keep track of different molecules, but now I realize it might have been too quick and dirty! In particular, there appears to have been a change in the morgan code sometime between 2021.09.02 and 2022.03.05. The following code p