On 14/06/2011 22:50, Donald Keidel wrote: > Igor, > > Thank you for information regarding openbabel writing of SDF with > r-groups. I tested 5 different methods in which chemists create SD > files with r-groups and with all 5 openbabel would report errors when > converting from sdf to sdf. I might be doing something wrong, but the > command I was using was something like the following: babel -isdf > <filename> -osdf<new_filename>. I know this is not the openbabel list, > so I will try not to write much more other than the following: > > When you were writing r-groups with openbabel I assume you created an > openbabel molecule object and then added the r-groups and then finally > wrote them out to file. Did you do this with pybel? If so can you > provide me with some sample code to illustrate how you did this. As you > can tell above I have only experimented with openbabel on the command > line and not using pybel.
SD files have many less obvious features, some of which are in use and which are not. It would be helpful to me if you were able to send me the files with different r-group representations which you feel OpenBabel (or RDKit) should be able read and I will try to extend OpenBabel's capabilities. At present it has reasonable support for reading and writing the alias A line, but not the others, as you have found. Sorry for hijacking this list! Chris ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
