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. Thanks again for the info and any help. Don On 06/14/2011 01:22 PM, Igor Filippov wrote: > 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
