Hi,
and this is not what i want.
I must do an evaluation. This is my task. And i need to use open babel and
other tools for the similarity search.
So now the question again:
How could i perform the similarity search with babel on chembl?
babel /bioinf/MuDiSAR/db/chembl/chembl_13.sdf search/babelchemblresult.sdf
-s"${smi}" -at0.85
This command works (especially very fast) but the result does not contain any
entries.
Is it because the chembl_13.sdf contains no SMILES strings?
Or is there a other way to search with babel in chembl (convert the sdf to an
specific format)?
Jochen
Am 07.03.2012 um 10:09 schrieb Björn Grüning:
> Hi,
>
> you can't. FPS is a new format from the chemfp project. You have to use
> chemfp. There is a nice script called simsearch, that assist you with
> the searching.
>
> Kind regards,
> Bjoern
>
>> Hello,
>>
>> ok i think this works:
>>
>> ob2fps /bioinf/MuDiSAR/db/chembl/chembl_13.sdf -o chembl_13.fps
>> ==============================
>> *** Open Babel Warning in Expand
>> Alias -N was not chemically interpreted
>>
>> ==============================
>> *** Open Babel Warning in Expand
>> Alias -N was not chemically interpreted
>>
>>
>> cat chembl_13.fps
>> #FPS1
>> #num_bits=1021
>> #software=OpenBabel/2.3.1
>> #type=OpenBabel-FP2/1
>> #source=/bioinf/MuDiSAR/db/chembl/chembl_13.sdf
>> #date=2012-03-07T07:24:20
>> 00260000004008a00b0006001000000c000000100000004000000080010800001800508383000003300e2538000100000102000008208000000000020000001008001c0000001880012000001a90001600b0034000003008c2080800800a20000c200020000000001000000080000000000e0104000110000072000100000100
>> Record1
>> 200600c2043806c04b04860a0e42430e5150049060000808812320c0022404001c0470830950883b588f2438280fd0c10102605000a0690604f28896710206100c210d0ae8101aa000a2610022c9009d00d885400490300df08808708009509e081018200048000040c00008ba5c0400100605d40a43100101ba80410a600004
>> Record2
>>
>> But i have one question: How can i start the sim search with babel. In my
>> case i do:
>>
>> babel /bioinf/MuDiSAR/db/chembl/chembl_13.sdf search/babelchemblresult.sdf
>> -s"${smi}" -at0.85
>>
>> where smi is the smiles string / query
>>
>> with best
>>
>> jochen schreiber
>> ------------------------------------------------------------------------------
>> Virtualization & Cloud Management Using Capacity Planning
>> Cloud computing makes use of virtualization - but cloud computing
>> also focuses on allowing computing to be delivered as a service.
>> http://www.accelacomm.com/jaw/sfnl/114/51521223/
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>
> --
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
>
> Tel.: +49 761 203-4872
> Fax.: +49 761 203-97769
> E-Mail: [email protected]
> Web: http://www.pharmaceutical-bioinformatics.org/
>
------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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