Dear Jacco, On Mon, Apr 4, 2011 at 6:48 PM, Jacco van de Streek <[email protected]> wrote: > Dear Greg, > > we have started using RDKit today. We would like to use RDKit to > perceive bond types, even for topological molecules without 3D > coordinates. We tried to do this by creating an RWMol object for methane > consisting of one carbon and four hydrogen atoms, with four C-H bonds > all of type Bond::UNSPECIFIED. The atoms do not have 3D coordinates, so > this is a topological model. We then called sanitizeMol() and > constructed an ROMol from the RWMol. When we then wrote the smiles > representation of the ROMol to screen, however, the bond types were > still Bond::UNSPECIFIED. > > Any thoughts?
I'm not quite sure what you're trying to do. Aside from recognizing aromaticity, the RDKit does not do any bond perception; it assumes that bond types are set properly in the input molecules. So if you want to build methane, you need to set the four C-H bonds to type Bond::SINGLE. Best Regards, -greg ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
