Re: [Rdkit-discuss] reproduce this method to obtain graph using RDkit

For what it's worth, the RDKit allows you to get the adjacency matrix for a molecule with the function Chem.GetAdjacencyMatrix (from python) or MolOps::getAdjacencyMatrix (from c++). -greg On Wednesday, 3 February 2016, Maciek Wójcikowski wrote: > So my initial guess was

Re: [Rdkit-discuss] RDKit Valences

Jan answers the question perfectly below (thanks Jan!) It's certainly possible to modify the RDKit's default valence table as Jan describes. It requires a bit of testing to make sure that things like 3D coordinate generation still work. Given that some of us are not particularly fond of general

Re: [Rdkit-discuss] how to replace a bond and preserve chirality

Hi Dave, Thanks for the suggestion about mutating the atom in-place then pruning the rest of the R-group away. This will work, but it's inelegant and slow. Here's why. I'm trying to construct an R-group table for each core, for up to 3 R-groups, of a data set. For that, I need to know the

Re: [Rdkit-discuss] how to replace a bond and preserve chirality

HI Andrew, I don't have a solution for RDKit, because I don't know if you can do this sort of thing. But when I've tackled this in OEChem, I've changed the atomic number of the substituent atom to something else (I always use Xe, because I know that will never be anything other than a marker