Hello,
this sounds great. But i NEED Open Babel. This is not my decision.
Any other ideas why this not work?
With best
Jochen Schreiber
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.
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