Re: [Rdkit-discuss] How to determine if atoms are part of the same ring?

On Feb 8, 2017, at 19:22, Markus Metz wrote: > The question to you is: Is there another more elegant way of doing it? May be > I missed something from the python API? I don't quite follow what you are looking for, though I have managed to condense your code somewhat, into:

[Rdkit-discuss] How to determine if atoms are part of the same ring?

Dear RDKit community: I am facing the situation that I would like to attach indices to atoms in a molecule defined by a substructure. The substitution pattern is of importance. Therefore I needed to include the wildcards atoms in my substructure. If I get the atom indices of this substructure,

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

To further help with the work-around: it's safe to sanitize the molecule, but you cannot call Chem.AssignStereochemistry(), which the SMILES parser does when you tell it to sanitize. Here's an example from your gist: In [2]: m3 = Chem.MolFromSmiles('O[C@H]1CC[C@]11CC[C@@](Cl)(Br)CC1',

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

Hi Greg (et al.), Thanks for looking into it. And thanks to Paolo, who gave me a good workaround suggestion – which was to desymmetrise the spirocyclic centre by modifying the isotope on one of the neighbours. This is good for attended processing of single molecules, but not so good for