Hey, i have testet it again:
babel join.sdf joinout.sdf -s"CN" ============================== *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Cannot read atom and bond count Expected standard 6 character atom and bond count 3396 molecules converted 1 warnings 54338 audit log messages obabel isn't install on the server. With 90% Tanimoto: babel join.sdf joinout.sdf -s"CN" -at0.9 ============================== *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Cannot read atom and bond count Expected standard 6 character atom and bond count 3396 molecules converted 1 warnings 54338 audit log messages The joinout.sdf has always 19MB so i think there are always the 3396 inside. The same if i try: babel join.sdf joinout.sdf -s"CN" -at5 Any Idea? Am 12.12.2011 um 16:31 schrieb Geoffrey Hutchison: >> I create the joined.sdf as follows: cat *.sdf > joined.txt and then mv >> joined.txt joined.sdf > > It's hard to know, but I suspect your *.sdf don't necessarily have the > correct $$$ and newline to separate one SDF from another. > > If you don't try to filter, how many molecules does babel find? > > % obabel joined.sdf -O joined.smi > > How many molecules are reported? > > Best regards, > -Geoff ------------------------------------------------------------------------------ Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
