Re: [Rdkit-discuss] Bond-type perception.
On Apr 4, 2011, at 11:28 PM, Greg Landrum wrote: 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 Moreover, I'd be happy to donate bond perception code to RDKit, but these things only really work well when you have 3D coordinates. (I've tried many implementations.) But I can't quite figure out how you'd want to perceive bond types without any obvious information. Cheers, -Geoff -- 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 Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Bond-type perception.
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? Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Bond-type perception.
Dear Jacco, On Mon, Apr 4, 2011 at 6:48 PM, Jacco van de Streek vandestr...@avmatsim.de 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 Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
