[Rdkit-discuss] sanifix

Hi All, I have been trying to use sanifix4.py to get around the "Can't kekulize mol" problem but without success. I have a library of compounds with O=c1cccnn1 fragment unable to kekulize (example:CCC(N)Cc1cc(=O)[nH]nc1c2ccco2). It has been a few years since this script came ut. I just wonder if

Re: [Rdkit-discuss] Reaction changing bonds but not charges

That works, thanks! I'll be sure to include an explicit +0 when converting when I need the product to be neutral. On Mon, Oct 9, 2017 at 11:15 AM, Chris Earnshaw wrote: > Hi > > I don't think the reaction SMARTS does specify a change in the > charges. The N and O have to

Re: [Rdkit-discuss] Reaction changing bonds but not charges

Hi I don't think the reaction SMARTS does specify a change in the charges. The N and O have to be charged in order to match the reactant pattern but they won't be altered by the transformation. If you specify that the product atoms are explicitly neutral I think you'll get the result you want -

[Rdkit-discuss] Reaction changing bonds but not charges

Hi, I am using rdChemReactions to perform substructure transformations as defined by configurable reaction smarts. When I create the reaction and run a mol through it that I expect to be transformed by the indicated reaction smarts, I see that the bonds have been changed according to the smarts,

[Rdkit-discuss] 2017.09.1 RDKit release

Many thanks to all for this new RDKit release. I have used commercial software in my past, and I am more and more impressed by the capabilities of RDKit and other open source software. Please keep up the good work! Regards, Jim Metz -Original Message- From:

Re: [Rdkit-discuss] UFF atom type errors

Hello Greg, The only thought I had was that these atom types just didn’t exist in the UFF forcefield and therefore I was just out of luck for compounds with boron (borax) and such. If there are indeed plausible atom types and rdkit is just not picking them, then that is another issue all