Re: [Rdkit-discuss] UFF atom type errors

CHEMBL1796997 is Helium and the same molecule that throws the first UFFTYPER warnings. Originally I had searched my sdf file only for He1 and found no hits. >From the original Goddard paper in 1992, there is only He4+4 atomtype >described explicitly. I can reason based on the error that

Re: [Rdkit-discuss] Implicit Hydrogens On Aromatic Hetereoatoms

Greg, That fixed it! Thanks so much, that makes a lot more sense now. -Chris On Fri, Oct 6, 2017 at 1:25 AM, Greg Landrum wrote: > Hi Chris, > > There's an additional step performed during sanitization that recognizes > that the implicit H needs to be on the N. The

Re: [Rdkit-discuss] nitrogen valence issues

The rdkit sdf files were washed with MOE and then read into rdkitagain for 3D structure generation. As there are only a dozen problem cases out of 1.5 million compounds, I just removed them from my main file and downloaded the mol files from chembl and double check the structures.

Re: [Rdkit-discuss] UFF atom type errors

Hello, Can you provide a small sdf contains molecules that have this issue ? thanks in advance, BR, Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA

Re: [Rdkit-discuss] UFF atom type errors

Yeah, those atom types that you are seeing are the names of the UFF atom types that the RDKit assigns. If an atom has a hybridization/charge-state that's not recognized, you'll get those parameterization errors. If you're aware of a better way to handle this (or a way to sensibly guess