Hello,
ok i think this works:
ob2fps /bioinf/MuDiSAR/db/chembl/chembl_13.sdf -o chembl_13.fps
==============================
*** Open Babel Warning in Expand
Alias -N was not chemically interpreted
==============================
*** Open Babel Warning in Expand
Alias -N was not chemically interpreted
cat chembl_13.fps
#FPS1
#num_bits=1021
#software=OpenBabel/2.3.1
#type=OpenBabel-FP2/1
#source=/bioinf/MuDiSAR/db/chembl/chembl_13.sdf
#date=2012-03-07T07:24:20
00260000004008a00b0006001000000c000000100000004000000080010800001800508383000003300e2538000100000102000008208000000000020000001008001c0000001880012000001a90001600b0034000003008c2080800800a20000c200020000000001000000080000000000e0104000110000072000100000100
Record1
200600c2043806c04b04860a0e42430e5150049060000808812320c0022404001c0470830950883b588f2438280fd0c10102605000a0690604f28896710206100c210d0ae8101aa000a2610022c9009d00d885400490300df08808708009509e081018200048000040c00008ba5c0400100605d40a43100101ba80410a600004
Record2
But i have one question: How can i start the sim search with babel. In my case
i do:
babel /bioinf/MuDiSAR/db/chembl/chembl_13.sdf search/babelchemblresult.sdf
-s"${smi}" -at0.85
where smi is the smiles string / query
with best
jochen schreiber
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