[Rdkit-discuss] double bond stereochemistry question

2017-08-11 Thread Tyler Backman
I am trying to write a series of dehydratase reactions with RDKit that create specific double bond stereochemistry, but I have found that if I install one double bond, it often reverses the stereochemistry on other bonds, if they are present. For example, I create the following molecule which

Re: [Rdkit-discuss] Building RDKit from source

2017-10-03 Thread Tyler Backman
This might also be of interest, I have a Dockerfile here which builds RDKit, including the postgresql cartridge: https://github.com/JBEI/clusterCAD/blob/master/debian-cheminformatics/Dockerfile Sincerely, Tyler Backman On Tue, Oct 3, 2017 at 2:45 AM, Greg Landrum <greg.land...@gmail.com>

Re: [Rdkit-discuss] suggestions for comprehensive searchable database of natural products

2017-11-28 Thread Tyler Backman
Hi Jim, MiBIG is a useful database of natural product gene clusters and structures, which you can download in JSON format here, and use pretty easily from within Python: https://mibig.secondarymetabolites.org/repository.html This also includes pathway and organism information. Secondly, our

[Rdkit-discuss] Some compounds don't match themselves after converting to isomeric SMILES and back?

2018-06-07 Thread Tyler Backman
this with a version of Rapamycin I constructed de-novo using SMARTS reactions for each enzyme. This one also had an identical isomeric SMILES to the selleckchem one, but matched 39 out of 65 atoms with itself, vs 19 out of 65 for the selleckchem structure. Sincerely, Tyler Backman