I changed the CML reader/writer a while back to be compatible with MarvinSketch and not depend on everyone using the "dictRef". Looks like the molecule is read correctly though and it's the selection which is messed up?
J On 12 Apr 2013, at 06:37, Egon Willighagen <[email protected]> wrote: > Hi all, > > I was just digitizing the ACS New Orleans meeting drug disclosures > liveblogged by Carmen Drahl using Bioclipse and posting them on > Twitter with drawing, InChI, and InChIKey... I even created a > WikiPedia page for one of them. All went well, and I placed the > matching CML. > > But then I used the "gist" manager to read them back in: > gist.download(5369422) > > And then it shows that the wedge bond information is messed up (see > the attached screenshot). I double checked the CML and that looks > fine, so the problem seems to be in the wedge bond info reading. I > will follow up on this as soon as possible! > > This is a very nasty bug and should not have happened. I will figure > out when it happened and what the exact trouble is. > > The screenshot shows the downloaded "gist" and one of the opened > structures, with spurious wedge bonds. Selecting one shows it in the > Outline and in the Properties view that it is for b32 (and b33 is the > other wrong one), and also that in the file it is just one b31 bond. > > Well, more soon, I hope! > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > <cmlProblem.png>------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
