Re: [Rdkit-discuss] problem when drawing a murcko scaffold

Hi Jose Manuel, the problem is just that the scaffold returned by MurckoScaffold.GetScaffoldForMol() has no explicit hydrogens on the imino N: for atom in ms.GetAtoms():     print(atom.GetIdx(), atom.GetAtomicNum(), atom.GetNumExplicitHs(),   atom.GetNumImplicitHs(),

Re: [Rdkit-discuss] Setting custom coordinates for new atoms

Hi Illimar, The problem here is that you are adding atoms to your RWMol, but the Conformer object that you are trying to access with the newly added atom indices is still tied to the original molecule which does not have the newly added atoms, hence your indices are out of bounds. If you

[Rdkit-discuss] Question regarding Chemical Features module on RDKit

Hello, I have a question regarding Chemical Features module on RDKit. I realized that for molecule with SMILES representation "OC1CC1O" from QM9 dataset, using the code fdefName = os.path.join(RDConfig.RDDataDir,'BaseFeatures.fdef') factory = ChemicalFeatures.BuildFeatureFactory(fdefName) mol =

[Rdkit-discuss] problem when drawing a murcko scaffold

Dear all, I noticed a strange behavior when extracting murcko scaffolds from preprocessed molecules with an inhouse standardization protocol. I made a gist to illustrate the problem: https://gist.github.com/jose-manuel/04d69dd3ac52cca74449e73d614df42e This leaves me with several questions: