Hello everybody, i have a problem with similarity search on a fs-File.
babel Compound_000000001_000025000.fs result.sdf -s"O([C@H](C[N+](C)(C)C)CC(=O)[O-])C(=O)C 1" -at0.85 This works great. The fs is created on the Compound_000000001_000025000.sdf from the PubChem Compound Database. But i want to do the search on all the fs Files. So i first create an sdf file which contains all information from the sdf-Files. From this big sdf File i create the fs File (babel join.sdf -ofs join.fs). But if i do: babel join.fs result.sdf -s"O([C@H](C[N+](C)(C)C)CC(=O)[O-])C(=O)C 1" -at0.85 It won't work. This is the output: ============================== *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Invalid bond specification, atom numbers or bond order are wrong. ============================== *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Invalid bond specification, atom numbers or bond order are wrong. ============================== *** Open Babel Warning in ReadMolecule WARNING: Problems reading a MDL file Invalid bond specification, atom numbers or bond order are wrong. 39 molecules converted 122 warnings 1042 audit log messages 4 debugging messages With more several warnings before. The search on the big sdf File work: babel join.sdf result.sdf -s"O([C@H](C[N+](C)(C)C)CC(=O)[O-])C(=O)C 1" -at0.85 I hope you could help me because i don't know why this happen. WIth best, Jochen Schreiber ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
