On 08/12/2011 10:30, Jochen Schreiber wrote: > Hello, > > i have joined all sdf in one (join.sdf). > > Now i want to search: babel join.sdf resultadawd.sdf > -s"B(C1=CC(=CC=C1)N2C(=O)C3CC=C4C(C3C2=O)CC5=C(C4C6=C(C(=CC=C6)F)O)C(=O)C=C(C5=O)Br)(O)O" > > But i became the following output: > > ============================== > *** 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 > > 0 molecules converted > 1 warnings 9 audit log messages
It seems that the first entry in the sdf file is corrupt. This format cannot tolerate misplaced spaces and blank lines. You could post with an attached copy of the file for us to see (don't paste). Incidentally, it would be better to use obabel rather than babel. http://openbabel.org/docs/current/Command-line_tools/babel.html Chris ------------------------------------------------------------------------------ Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
