a) The parameter of the -s option has to be a SMILES string (or a
filename) The ${...} syntax is not recognised.
b) It is better to use obabel rather than babel because it is safer and
more versatile. The syntax difference is very small ( -O before output
filename).
So this works for me:
obabel chembl_02.sdf -ofs
obabel chembl_02.fs -O result.sdf -s"c1cccc(C#N)c1C#N" -at0.85
Instead of the SMILES you may prefer to have the pattern molecule in a
file (with any format).
Chris
On 07/03/2012 09:31, Jochen Schreiber wrote:
> Hi,
>
> and this is not what i want.
> I must do an evaluation. This is my task. And i need to use open babel and
> other tools for the similarity search.
>
> So now the question again:
> How could i perform the similarity search with babel on chembl?
>
> babel /bioinf/MuDiSAR/db/chembl/chembl_13.sdf search/babelchemblresult.sdf
> -s"${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/
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>> --
>> 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: bjoern.gruen...@pharmazie.uni-freiburg.de
>> 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/
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
------------------------------------------------------------------------------
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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