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 <zahar...@mail.nih.gov>
> 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
> * zahar...@mail.nih.gov
> *
> ********************************************/
>
>
>
>
>
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