From owner-chemistry@ccl.net Sun May 19 13:24:01 2013
From: "Wolf Ihlenfeldt wdi##xemistry.com" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: compound similarity comparison
Message-Id: <-48715-130519123345-6077-ae/6tO0PX5kVwkFNoljqxg:+:server.ccl.net>
X-Original-From: Wolf Ihlenfeldt <wdi~!~xemistry.com>
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Date: Sun, 19 May 2013 18:33:34 +0200
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Sent to CCL by: Wolf Ihlenfeldt [wdi]![xemistry.com]
For a comprehensive overview on how to this in various toolkits, see

http://ctr.wikia.com/wiki/Chemistry_Toolkit_Rosetta_Wiki

(sample problems 8 and 9). This is a standard feature of about every
chemical information processing toolkit.



On Thu, May 16, 2013 at 3:52 PM, Nicolas Cheron ncheron ~~
fas.harvard.edu <owner-chemistry]-[ccl.net> wrote:
>
> Sent to CCL by: Nicolas Cheron [ncheron.]-[.fas.harvard.edu]
> Hi,
>
> You can also use jcsearch
> http://www.chemaxon.com/jchem/doc/user/Jcsearch.html. If you want to
> look for similarities between InputFile.smi and Database.smi with a
> treshold of 0.1 (threshold is a value between 0 and 1, the closer to 0
> the more similar the structures) you can use this kind of script:
>
> Smiles_Array=(` awk '{ print $1 ; }' InputFile.smi `)
> Smiles_Size=` wc -l InputFile.smi | awk '{ print $1 ; }' `
> x=0
> while [ $x -lt ${Smiles_Size} ]; do
>         echo "#### ${Smiles_Array[$x]} ####" >> Results.smi
>         jcsearch -q "${Smiles_Array[$x]}" Database.smi -t:i:0.1 >> Results.smi
>         echo " " >> Results.smi
> x=`expr $x + 1`
> done
>
>
> Nicolas
>
>
>
> 2013/5/16 Johannes Hachmann jh#%#chemistry.harvard.edu
> <owner-chemistry*ccl.net>:
>>
>> Sent to CCL by: "Johannes Hachmann" [jh+/-chemistry.harvard.edu]
>> Hi Jinming,
>>
>> You are looking for fingerprinting and you can use openbabel for that:
>> http://openbabel.org/wiki/Tutorial:Fingerprints
>>
>> Best wishes
>>
>> Johannes
>>
>> -----------------------------------------------
>> Dr. Johannes Hachmann
>> Research Associate
>> Harvard University
>> Department of Chemistry and Chemical Biology
>> 12 Oxford St, Rm M104A
>> Cambridge, MA 02138
>> -----------------------------------------------
>>
>>
>>
>>> -----Original Message-----
>>> From: owner-chemistry+jh==chemistry.harvard.edu[A]ccl.net [mailto:owner-
>>> chemistry+jh==chemistry.harvard.edu[A]ccl.net] On Behalf Of zhoujinming
>>> zhou_jim#hotmail.com
>>> Sent: Wednesday, 15 May, 2013 21:36
>>> To: Hachmann, Johannes
>>> Subject: CCL: compound similarity comparison
>>>
>>> Dear CCLer
>>>
>>> Does some have the free script for compound similarity comparison using
>>> SMILES format, the one using Java language should be better. Please give
>> some
>>> advice.
>>>
>>> Many Thanks.
>>>
>>> JinMING>
>



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