[Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

Dear RDKit community, I'm trying to use RDKit to read in Corina generated stereoisomers (from a Mol file), assign chiral tags and stereochemistry to the structure and output the canonical smiles string for each isomer of a given molecule (in Python), when I do this, half the canonical smiles

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

Maybe when you have a toolkit as blazingly fast as RDKit it captures the chirality of N center before it has time to interconvert -P. On Wed, Aug 19, 2015 at 10:17 PM, John M john.wilkinson...@gmail.com wrote: More odd is the carbon stereocentre with two methyls... Generally trivalent

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

Hi Rob, The results below are quite strange. As John has already pointed out: there really shouldn't be chirality present on either the N+ or the C that has two methyls attached. I tried to reproduce the problem by running corina myself using the same command-line options you provided (from