I don't know about reading but openbabel can certainly write out SD files with R-groups as atomic aliases. Those SD files are then displayed correctly in most molecular editors I've tested (Symyx Draw, MolSketch, ChemDraw).
Igor On Tue, 2011-06-14 at 16:22 -0400, Donald Keidel wrote: > 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 ------------------------------------------------------------------------------ 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
