On 8/10/11 1:29 PM, DavidFlicker wrote: > Hello, > > I just downloaded the NCI Natural Products Set II sdf file and I cannot get > OpenBabel to convert it to any format. > > I get this error: > ============================== > *** Open Babel Warning in OpenBabel::MDLFormat::ReadMolecule > WARNING: Problems reading a MDL file > Cannot read atom and bond count > Expected standard 6 character atom and bond count > > This is what the first entry in the sdf looks like:
If there are really blank lines after the atom block and the bond block, then it's an invalid SDF. You might try posting it as an attachment if you're not sure. Sometimes email programs throw in extra blank lines. 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. Craig > 757 > CML DOM 02221007322D > > 30 32 0 0 0 0 0 0 0 0999 V2000 > -1.7627 -1.5440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -0.7617 -1.2290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 0.8432 2.0199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.4812 1.6519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.2052 1.6519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.4812 0.9149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.2052 0.9149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.8432 0.5459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.4327 0.5459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.0577 0.9079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.6867 0.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.8432 -0.1900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.4327 -0.1900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.6867 -0.1900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.5832 -0.8800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.6857 -0.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.1567 -0.8800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3967 -0.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.2957 -0.5420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -2.9367 -0.1723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.3847 1.9919 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -1.0252 1.6214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.1567 -1.6400 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.4841 -2.0099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.1249 -1.6399 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.4841 -2.7499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.8432 2.7099 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1.4841 3.0799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.1062 2.0119 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 2.7467 1.6413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > > 1 18 2 0 0 0 0 > 17 2 1 1 0 0 0 > 3 5 2 0 0 0 0 > 3 4 1 0 0 0 0 > 3 27 1 0 0 0 0 > 4 6 2 0 0 0 0 > 4 29 1 0 0 0 0 > 5 7 1 0 0 0 0 > 5 21 1 0 0 0 0 > 6 8 1 0 0 0 0 > 7 8 2 0 0 0 0 > 7 9 1 0 0 0 0 > 8 12 1 0 0 0 0 > 9 10 2 0 0 0 0 > 9 13 1 0 0 0 0 > 10 11 1 0 0 0 0 > 11 14 2 0 0 0 0 > 12 15 1 0 0 0 0 > 13 16 2 0 0 0 0 > 13 17 1 0 0 0 0 > 14 18 1 0 0 0 0 > 14 19 1 0 0 0 0 > 15 17 1 0 0 0 0 > 16 18 1 0 0 0 0 > 17 23 1 6 0 0 0 > 19 20 1 0 0 0 0 > 21 22 1 0 0 0 0 > 23 24 1 0 0 0 0 > 24 25 2 0 0 0 0 > 24 26 1 0 0 0 0 > 27 28 1 0 0 0 0 > 29 30 1 0 0 0 0 > > M END > > I've tried copying in different, known-to-work, count lines but to no avail. > > http://forums.openbabel.org/file/n3734151/npset_ii.sdf npset_ii.sdf > > Thanks for any help. > > Cheers, > > David > > -- > View this message in context: > http://forums.openbabel.org/SDF-conversion-error-tp3734151p3734151.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > uberSVN's rich system and user administration capabilities and model > configuration take the hassle out of deploying and managing Subversion and > the tools developers use with it. Learn more about uberSVN and get a free > download at: http://p.sf.net/sfu/wandisco-dev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > 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 OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
