From owner-chemistry@ccl.net Wed Sep 21 10:18:00 2011 From: "Wolf Ihlenfeldt wdi-#-xemistry.com" To: CCL Subject: CCL: ANN: chemfp-1.0 Message-Id: <-45488-110921100748-24065-Zth+j6hYDj9Szpw3PNEBUw{}server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=0016364996dbcdd62b04ad74181f Date: Wed, 21 Sep 2011 16:07:30 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi-*-xemistry.com] --0016364996dbcdd62b04ad74181f Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable An additional note: Since version 3.188, the Cactvs toolkit (www.xemistry.com/academic for free academic/educational downloads) comes with an I/O module for the FPS format, and can both read and write it. The toolkit has support for various fingerprint algorithms, and also supports the PubChem fingerprint encoding in SD-files as well as the native PubChem ASN.1 binary and text formats. On Wed, Sep 21, 2011 at 12:36 AM, Andrew Dalke dalke * dalkescientific.com = < owner-chemistry],[ccl.net> wrote: > > Sent to CCL by: Andrew Dalke [dalke*o*dalkescientific.com] > I've just released version 1.0 of my chemfp project. > > chemfp is a free set of command-line tools, and the underlying Python > software library, for generating cheminformatics fingerprint files > and searching them based on Tanimoto similarity. > > It can use the Open Babel, OEChem, or RDKit chemistry toolkits > to convert structure files into fingerprint files. It also has > a tool to extract fingerprints from fields in an SD file, including > special support for PubChem's CACTVS substructure field. > > The similarity search program does fast Tanimoto searches of > a set of queries against a set of targets, with a user-defined > minimum threshold score and/or a k-nearest neighbors option. > > For more information, follow these links: > > Project home page: http://code.google.com/p/chem-fingerprints/ > Documentation: http://readthedocs.org/docs/chemfp/en/latest/ > Direct download: > http://chem-fingerprints.googlecode.com/files/chemfp-1.0.tar.gz > > Let me know if you find it useful, or if there are any problems. > > Andrew Dalke > dalke+*+dalkescientific.com > > Advertisement: > I develop custom chemistry software and do Python training for > scientists. Are you interested in hiring my services? If you're in > Ireland or England it might even be easy to meet! I'm visiting the > Dublin area until 8 October, then two weeks near Oxford and Cambridge. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi],[xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --0016364996dbcdd62b04ad74181f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
An additional note:

Since version 3.188, the Cactvs toolkit (www.xemistry.com/academic for= free academic/educational downloads) comes with=C2=A0 an I/O module for th= e FPS format, and can both read and write it. The toolkit has support for v= arious fingerprint algorithms, and also supports=C2=A0 the PubChem fingerpr= int encoding in SD-files as well as the native PubChem ASN.1 binary and tex= t formats.

On Wed, Sep 21, 2011 at 12:36 AM, Andrew Dal= ke dalke * dalkescientific.com <= span dir=3D"ltr"><owner-chemi= stry],[ccl.net> wrote:

Sent to CCL by: Andrew Dalke [dalke*o*dalkescientific.com]
I've just released version 1.0 of my chemfp project.

chemfp is a free set of command-line tools, and the underlying Python
software library, for generating cheminformatics fingerprint files
and searching them based on Tanimoto similarity.

It can use the Open Babel, OEChem, or RDKit chemistry toolkits
to convert structure files into fingerprint files. It also has
a tool to extract fingerprints from fields in an SD file, including
special support for PubChem's CACTVS substructure field.

The similarity search program does fast Tanimoto searches of
a set of queries against a set of targets, with a user-defined
minimum threshold score and/or a k-nearest neighbors option.

For more information, follow these links:

=C2=A0Project home page: http://code.google.com/p/chem-fingerprints/ =C2=A0Documentation: http://readthedocs.org/docs/chemfp/en/latest/ =C2=A0Direct download: http://chem-fingerprints.googlec= ode.com/files/chemfp-1.0.tar.gz

Let me know if you find it useful, or if there are any problems.

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Andrew Dalke
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0dalke+*+dalkescientific.com

Advertisement:
=C2=A0I develop custom chemistry software and do Python training for
scientists. Are you interested in hiring my services? If you're in
Ireland or England it might even be easy to meet! I'm visiting the
Dublin area until 8 October, then two weeks near Oxford and Cambridge.



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--
Wolf-D. Ihlenfeldt -=C2= =A0 Xemistry GmbH - w= di],[xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---<= br>xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr.= W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
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--0016364996dbcdd62b04ad74181f--