Re: [Rdkit-discuss] Chembience

2018-10-31 Thread Markus Sitzmann
Hello, I have releases Chembience 0.2.6 - it switches Python from 3.6 to 3.7 and updates RDKit to 2018.09.1. Just to mention it, the Docker images of all previous releases are also still available from Dockerhub. https://github.com/chembience/chembience/releases/tag/v0.2.6

Re: [Rdkit-discuss] Sometimes one sanitization is not enough?

2018-10-31 Thread Ivan Tubert-Brohman
Hi Greg, Thanks for the detailed explanation. You are right that this is not a real molecule; it came from applying a user-supplied reaction SMARTS. (The reaction SMARTS was not the best-written perhaps, but that's tangential...). I normally sanitize the products and skip those that fail the

Re: [Rdkit-discuss] Adding certain atomic indexes to functional groups

2018-10-31 Thread Noki Lee
Thanks, I'll check it out. Until now, it works pretty well! By the way, I'm curious about the RWmol. What does it do and what is the difference between GetMol() and EditableMol()? On Tue, Oct 30, 2018 at 4:36 PM Greg Landrum wrote: > Hi, > > I think this gist does what you're looking for: >

Re: [Rdkit-discuss] Sometimes one sanitization is not enough?

2018-10-31 Thread Greg Landrum
Hi Ivan, Short answer: I would not normally expect a second sanitization to fail if the first succeeds, but your input SMILES is very odd and triggers a bug. This is an interesting edge case for the sanitization code because it includes a weird mix of aromatic and aliphatic atoms and bonds, I do