Re: [Rdkit-discuss] How to generate bioisosters?

Hi Greg, I got it to work with my function “get_amide_biosters(smiles)” which I am happy to share once I clean it up a bit . Sorry I was not clear. both get_amide_biosters("CC(NC)=O") and get_amide_biosters("CC(OC)=O") provide the same recursive smiles: >>

Re: [Rdkit-discuss] How to generate bioisosters?

On Tue, Feb 6, 2018 at 10:42 AM, Alexis Parenty < alexis.parenty.h...@gmail.com> wrote: > I will try your approach and will nest all the result smiles into a > unique recursive smiles. > I'm not quite sure what you mean here, but it sounds unlikely to work. I think you may need to do a SMILES

Re: [Rdkit-discuss] Finding possible reaction products

One option is to construct a library of reaction SMARTS for common chemical reactions. Another, more exhaustive, approach is enumerate all possible connectivity matrices and convert them to molecules See DOI: 10.1039/C7SC03628K and https://github.com/jensengroup/xyz2mol I am working on

Re: [Rdkit-discuss] How to generate bioisosters?

Hi Greg, Thanks a lot for your response, it helps a lot. I indeed notice it was more difficult with two attachment point (I got it working with acid bioisosters, one attachment point but could not make my head around with two). I will try your approach and will nest all the result smiles into a

[Rdkit-discuss] Finding possible reaction products

Hi all! I was wondering what is the best approach to generating all the possible products for a given set of reactants using RDkit. My goal is to be able to find all possible products and then carry out a Nuged Elastic Band calculation to estimate the rate constants of those reactions. I would