Dear Evgueni,
> I have enclosed SDF file with some structures and file with problems. > The main things is that SDMolSupplier cannot read structure #11 which any > other tool will read without any problems and in some structures some cycles > ROMol will consider wrong as aromatic (see structures 3,4,5 for example) - > see Problems.doc for details. > > Any suggestions? I have not looked at all the structures with problems, but I don't see anything here that's overly alarming. The aromaticity cases you refer to as "wrong" match the RDKit definition of aromaticity : the ring c1nc(=O)cc[nH]1 is conjugated and has 6 pi electrons (0 from the C with the extracyclic double bond to O, 2 from the NH, 1 from the other atoms), so it's considered aromatic. Structure 11 contains the substructure CN1=C[NH]N=C1, which contains a 4-coordinate neutral nitrogen in a non-aromatic ring. This is not considered a valid valence state for the N, so the RDKit won't process the molecule. Best Regards, -greg
