[Rdkit-discuss] Build matching 3D structure

Hello I'm having a hard time trying to build a 3D structure for a new molecule (new) based on a reference molecule (ref). In this case, ref is a substructure of new, and I want the coordinates of their matching atoms to be exactly the same. I have tried using:

[Rdkit-discuss] Manganese ion as a radical?

Dear rdkit community, I’m not quite sure if this is more of an rdkit or a chemistry related question. I’d like to understand why a manganese ion has 3 radical electrons when interpreted by rdkit. I have not seen radicals in any other metal ion so far. The code to get the depiction looks

Re: [Rdkit-discuss] Define identical atoms in SMARTS pattern

Thanks you to David, Ivan, and Hao for the very useful answers. Best regards, Jan > On 24 Jul 2020, at 15.51, Jan Halborg Jensen wrote: > > Is there a way to find a [C]([#X])[#X] pattern, where X=X, that finds C(C)C, > C(O)O, C(F)F, etc., but not C(C)O, etc.? > > Best regards, Jan > >