[Rdkit-discuss] Apologies for the delays processing pull requests

Dear all, There's something of a backlog of unprocessed pull requests for the RDKit. Putting (what I hope were) the final touches on the release ended up being a time consuming slog and didn't leave me much time for looking at PRs. I'm sorry for this; it's great to have the contributions coming

[Rdkit-discuss] 2018.03.1 RDKit release

I'm pleased to announce that the next version of the RDKit - 2018.03 - is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_1 Binaries have been uploaded to anaconda.org

Re: [Rdkit-discuss] Any known papers on reverse engineering fingerprints into structures?

> > > which could of course also be changed to something expensive to > calculate. > Yes, that could be possible. Abstractly, let the first 20 bytes of each > fingerprint be a salt, and use something like bcrypt so each fingerprint > test requires that the query structure be re-fingerprinted for

Re: [Rdkit-discuss] Any known papers on reverse engineering fingerprints into structures?

Thanks Andrew, very interesting and useful script! Unfortunately it doesn't work on circular/ECFP-like fingerprints. It has the requirement that the fingerprint be a substructure fingerprint as you described. It seems the evolutionary/genetic algorithm approach is the current state-of-the-art for

[Rdkit-discuss] ScaffoldTree rdkit

Hi, I am trying to generate scaffold tree using rdkit for a data set. I could not find any information here http://www.rdkit.org/Python_Docs/rdkit.Chem.Scaffolds.ScaffoldTree-module.html There is an old thread about this https://sourceforge.net/p/rdkit/mailman/message/34137965/ Could

Re: [Rdkit-discuss] Any known papers on reverse engineering fingerprints into structures?

On Apr 23, 2018, at 14:54, Brian Cole wrote: > Unfortunately it doesn't work on circular/ECFP-like fingerprints. To be fair, you didn't mention that was a requirement. ;) > It has the requirement that the fingerprint be a substructure fingerprint as > you described. Could

Re: [Rdkit-discuss] ScaffoldTree rdkit

Hi Abhik, That's something that ended up being included in the documentation that shouldn't be there (it's leftovers from a quick attempt I made a while ago to re-implement the scaffold tree algorithm in Python). -greg On Mon, Apr 23, 2018 at 3:13 PM, abhik wrote: > Hi, > >

Re: [Rdkit-discuss] Any known papers on reverse engineering fingerprints into structures?

Hi, Another option is to use generative models that uses fingerprints as input (ex: https://arxiv.org/abs/1701.01329, https://pubs.acs.org/doi/10.1021/acs.molpharmaceut.7b00346). If you use as a scoring function of the generated molecules the Tanimoto Distance to a given fingerprint, you can often

Re: [Rdkit-discuss] Any known papers on reverse engineering fingerprints into structures?

Hi all, I’ve just had the attached from Roger Sayle, which might be of interest. Dave Hi Andrew and Dave, John (Mayfield) has just pointed me at the very interesting discussion raging on sourceforge. Alas, I've no idea how to post/tweet/snapchat a reply, but thought I'd at least contribute this

Re: [Rdkit-discuss] Any known papers on reverse engineering fingerprints into structures?

Hi All, I remember reading Dave’s patent when I was writing my CoG program around 2002. I had to write my own fingerprinting algorithm, based on Daylight fingerprints, called Fingal, which I could use to decode the fingerprints back into the structure(s) represented by it. I also had to