Greg, I know all about teething. My 8 month old is pushing out teeth almost every 2 weeks or so. I will continue to test this portion of the code since it seems to be the only open source package wrapped in python that does it mostly correct. openbabel wont even read these SD files with r-groups.
What I did to hack this was to add R1-R9 entries in /rdkit/trunk/Code/GraphMol/atomic_data.cpp with atomic numbers 105-112. I then use the set atomic number functionality in the python wrapped code and change it to one of these series of numbers and then depict. It is not a solid solution, but it works right now. Thanks. Don On 06/14/2011 12:55 PM, Greg Landrum wrote: > Hi Don, > > On Mon, Jun 13, 2011 at 8:58 PM, Donald Keidel<donald.kei...@gmail.com> > wrote: >> Have the following mol file: >> >> RDKit 2D >> >> 7 6 0 0 0 0 0 0 0 0999 V2000 >> 7.9102 -2.4208 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >> 6.4770 -2.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 5.0437 -2.4208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 >> 7.1916 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 5.7583 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 4.3292 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 7.9148 -3.2458 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 >> 2 4 1 0 >> 3 5 1 0 >> 4 1 1 0 >> 5 2 1 0 >> 6 3 1 0 >> 1 7 1 0 >> M RGP 1 7 1 >> V 7 * >> M END >> >> >> When I use RDKit to depict the molecule I get a * in the image where the >> R-group is located. >> >> Is there a way to define what letter or letter with number combination >> is printed for the R-group? A dictionary perhaps? Ideally I would like >> the ability to depict R1 thru R9. > Here's what's going on currently: > By default the rendering code uses atom.GetSymbol() to determine what > should show up in the drawing. > atom.GetSymbol() using the atomic number, unless the atom has the > property "dummyLabel" set. If that property is set, it's used. It > should also be checking for the property "_MolFileRLabel". > > In looking at this I also discovered another problem : there's an > error if you call the depiction code using a molecule with R groups > and the kekulize argument is True. > > I've entered a bug about each of these things. They'll be fixed in the > next release (planned for end of the month). > > It's great (for the RDKit) that someone is really using the R group > stuff in mol files and reporting the problems; this is an > under-utilized/tested piece of the code, so I really appreciate it. > Apologies that you're having to suffer through the teething problems. > > Best, > -greg ------------------------------------------------------------------------------ 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
