From owner-chemistry@ccl.net Wed Dec 2 16:19:01 2009 From: "Roberto Olivares-Amaya olivares * fas.harvard.edu" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40854-091202141525-31103-+B9LyJaL94XpOt5f2i/kcQ-.-server.ccl.net> X-Original-From: Roberto Olivares-Amaya Content-Type: multipart/alternative; boundary=000feaead813015b770479c22e45 Date: Wed, 2 Dec 2009 12:26:29 -0500 MIME-Version: 1.0 Sent to CCL by: Roberto Olivares-Amaya [olivares%x%fas.harvard.edu] --000feaead813015b770479c22e45 Content-Type: text/plain; charset=ISO-8859-1 Hello: Molgrep, which is part of perlmol is quite successful at doing that given a SMARTS pattern, which could be your specific molecule. We currently work with that with pretty good results. Here is a link to it. http://www.perlmol.org/examples/molgrep/ Roberto -- Roberto Olivares-Amaya Aspuru-Guzik Group Dept. of Chemistry and Chemical Biology Harvard University http://aspuru.chem.harvard.edu On Wed, Dec 2, 2009 at 9:08 AM, Matthias Wirth mawirth[a]gmx.net < owner-chemistry ~ ccl.net> wrote: > > Sent to CCL by: Matthias Wirth [mawirth-$-gmx.net] > Hi Manoj, > > How about having a unique SMILES representation (OpenBabel etc) of your > compounds and using the shell command: > > sort -u mysmiles.smi > > or > > uniq mysmiles.smi > > > Have fun, > > Matthias > > > On Dec 2, 2009, at 5:45 AM, manoj kumar manojrudraraju*gmail.com wrote: > > > Hi All, > > > > Does anyone aware or has developed any tool to retrieve Unique molecules > from a large compound databases. > > > > if not what would be the challenges ahead to develop such script, I wish > to know the math behind such operation and want to develop in python. > > > > Thanks for read and time, > > > > regards > > Manoj > > > > > > > > > > > > - This is automatically added to each message by the mailing script -> > -- Roberto Olivares-Amaya Aspuru-Guzik Group Dept. of Chemistry and Chemical Biology Harvard University http://aspuru.chem.harvard.edu --000feaead813015b770479c22e45 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello:
Molgrep, which is part of perlmol is quite successful at doing th= at given a SMARTS pattern, which could be your specific molecule. We curren= tly work with that with pretty good results.
Here is a link to it.

http://www.perlmol= .org/examples/molgrep/

Roberto
--
Roberto Olivares-Amaya<= br>Aspuru-Guzik Group
Dept. of Chemistry and Chemical Biology
Harvard= University
http://aspuru.chem.harvard.edu
On Wed, Dec 2, 2009 at 9:08 AM, Matthias W= irth mawirth[a]gmx.net <= ;owner-chemistry ~ ccl.net>= wrote:

Sent to CCL by: Matthias Wirth [mawirth-$-gmx.net]
Hi Manoj,

How about having a unique SMILES representation (OpenBabel etc) of your com= pounds and using the shell command:

=A0 =A0 =A0 =A0sort -u mysmiles.smi

or

=A0 =A0 =A0 =A0uniq mysmiles.smi


Have fun,

=A0 =A0 =A0 =A0Matthias


On Dec 2, 2009, at 5:45 AM, manoj kumar manojrudraraju*gmail.com wrote:

> Hi All,
>
> Does anyone aware or has developed any tool to retrieve Unique molecul= es from a large compound databases.
>
> if not what would be the challenges ahead to develop such =A0script, I= wish to know the math behind such operation and want to develop in python.=
>
> Thanks for read and time,
>
> regards
> Manoj
>
>
>
>



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--
Roberto Oli= vares-Amaya
Aspuru-Guzik Group
Dept. of Chemistry and Chemical Biolog= y
Harvard University
http:= //aspuru.chem.harvard.edu
--000feaead813015b770479c22e45--