On Mar 5, 2012, at 3:22 AM, Jochen Schreiber wrote: > i have download the chembl_sdf archive and unpack it. > > The resulting sd file from that archive has 2.5 GB. > > Now i want to create the fs index datei from that sd file with: > > babel -isdf chemble_13.sdf -ofs chembl_13.fs > > This command works but if i want to search with an sd file against the fs > file it doesn't work.
Perhaps chemfp ( http://code.google.com/p/chem-fingerprints/ )might be useful for this case, instead of using OpenBabel directly. I did the following with ChEBI 87, which I downloaded a few hours ago: % ob2fps --id-tag "ChEBI ID" ~/databases/ChEBI_complete.sdf.gz -o chebi.fps.gz ============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. ============================== *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. % gzcat chebi.fps.gz | head -8 #FPS1 #num_bits=1021 #type=OpenBabel-FP2/1 #software=OpenBabel/2.2.3 #source=/Users/dalke/databases/ChEBI_complete.sdf.gz #date=2012-03-05T23:47:50 0000000000000200000000010000000000000000000000000000000000000000100000000000000000020000000000000100000000200002000000000000000000000000000000000000000008800004001000400000000000000000000000000000000000000000000000000000000000000000000000000000000100000100 CHEBI:165 0004000000000200020002010200000000000000000012000100008000000000100040000040000100020008000100000102020000204002000000020002000008000800200000000000a0002a80000400d000400000100840080800000800000100000000000002020000400000080000020100020100200800006300000100 CHEBI:776 # Get the first SD record and use that as the query % gzcat ~/databases/ChEBI_complete.sdf.gz | head -85 | ob2fps --in sdf --id-tag "ChEBI ID" | simsearch --threshold 0.9 chebi.fps #Simsearch/1 #num_bits=1021 #type=Tanimoto k=all threshold=0.9 #software=chemfp/1.1b3 #targets=chebi.fps #target_sources=ChEBI_lite.sdf.gz 25 CHEBI:165 CHEBI:15396 1.00000 CHEBI:15397 1.00000 CHEBI:15410 0.92857 CHEBI:15994 1.00000 CHEBI:16074 1.00000 CHEBI:16985 1.00000 CHEBI:17762 1.00000 CHEBI:179341.00000 CHEBI:28952 1.00000 CHEBI:30154 1.00000 CHEBI:36492 0.92857 CHEBI:36742 0.92857 CHEBI:40611 0.92857 CHEBI:31 0.92857 CHEBI:165 1.00000 CHEBI:4999 1.00000 CHEBI:9577 0.93333 CHEBI:18533 1.00000 CHEBI:36496 0.92857 CHEBI:36612 1.00000 CHEBI:36773 1.00000 CHEBI:50040 0.93333 CHEBI:50043 0.93333 CHEBI:50045 0.93333 CHEBI:50046 0.93333 This says that there are 25 matches to CHEBI:165, which are CHEBI:15396, CHEBI:15397, CHEBI:15410, and more at 1.0 similarity down to CHEBI:50046 at 0.93333 similarity. Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
