Hey Dan, I just tried redownloading the sdf from here: http://dtp.nci.nih.gov/branches/dscb/natprod_explanation2.html
and I get this file http://dtp.nci.nih.gov/branches/dscb/natprod_ii_aug11.sdf which seems to be the same one as before. Is this indeed the latest one? I just want to make sure somethings not screwy with my OpenBabel installation. Thanks, David On Wed, Sep 7, 2011 at 10:28 AM, Daniel Zaharevitz [via Open Babel] < ml-node+3796738-45934757-258...@n4.nabble.com> wrote: > > On Aug 11, 2011, at 2:21 PM, David Flicker wrote: > > Thanks for all the help. > > I redownloaded the Diversity Set II, the Natural Products Set II, and the > FDA approved oncology drugs sets from the DTP website. It seems that only > the Natural Products one has a bad SDF and returns the bond count error. > > > It took longer than I thought, but the updated sdf file for the natural > products should now be in place. Let me know if you have problems. Babel > converts all to smiles fine for me. > > DanZ > > > > > However, both of the FDA approved SDF's cause OpenBabel to crash on > molecule number 747972 for no apparent reason. I have submitted a bug > report to SourceForge. > > Cheers, > > David > > On Thu, Aug 11, 2011 at 5:05 AM, Daniel Zaharevitz <[hidden > email]<http://user/SendEmail.jtp?type=node&node=3796738&i=0> > > wrote: > >> >> On Aug 10, 2011, at 8:24 PM, Geoff Hutchison wrote: >> >> > >> > On Aug 10, 2011, at 7:36 PM, Craig A. James wrote: >> > >> >> Sometimes you get this problem if your file has a mixture of Windows >> (CRLF) line endings and Unix/Linix (LF only) line endings. The files look >> fine in a text editor, but actually have extra line endings that the editor >> suppresses. >> > >> > In practice, Open Babel has a line-ending filter which works fairly well >> at finding such mixtures of line endings. But I agree with Craig that the >> file as posted in the e-mail is not a valid SD file. >> >> >> If you didn't get it directly from the DTP site ( >> http://dtp.nci.nih.gov/branches/dscb/natprod_explanation2.html), try >> downloading again. I know we have fixed some things in the past and if you >> got an old version, the problem might already be fixed. On the other hand, >> there are a lot of weird things that happen to EOL on download. If the file >> needs fixing let me know, although it might take a bit before I can work on >> it. Today is the first day in a new office building and it will take a while >> to get everything back up and running. >> >> DanZ >> >> >> /******************************************** >> * Daniel Zaharevitz >> * Chief, Information Technology Branch >> * Developmental Therapeutics Program >> * National Cancer Institute >> * [hidden email] <http://user/SendEmail.jtp?type=node&node=3796738&i=1> >> * >> ********************************************/ >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> user administration capabilities and model configuration. Take >> the hassle out of deploying and managing Subversion and the >> tools developers use with it. >> http://p.sf.net/sfu/wandisco-dev2dev >> _______________________________________________ >> OpenBabel-discuss mailing list >> [hidden email] <http://user/SendEmail.jtp?type=node&node=3796738&i=2> >> >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. > > http://p.sf.net/sfu/wandisco-dev2dev_______________________________________________ > OpenBabel-discuss mailing list > [hidden email] <http://user/SendEmail.jtp?type=node&node=3796738&i=3> > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > /******************************************** > * Daniel Zaharevitz > * Chief, Information Technology Branch > * Developmental Therapeutics Program > * National Cancer Institute > * [hidden email] <http://user/SendEmail.jtp?type=node&node=3796738&i=4> > * > ********************************************/ > > > > > > ------------------------------------------------------------------------------ > > Using storage to extend the benefits of virtualization and iSCSI > Virtualization increases hardware utilization and delivers a new level of > agility. 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