Subject: Announce: The Perl SDF Toolkit

From: Bruno Bienfait <[email-masked]>
Date: Fri, 02 Jul 1999 16:30:37 -0400

Dear CCL'ers,

I am making freely available my SDF toolkit, which I (and other
people in my Lab) have found useful when working with SD files,
especially large ones (such as the NCI Open Database).

SDF or Structure Data File is a common file format developped by
Molecular Design Limited to handle a list of molecular structures
associated with properties.

The purpose of this SDF toolkit is to provide functions to read and parse
SDFs, filter, and add/remove properties.  It can also read comma separated
value (CSV) tables which contain new fields to be added to the SDF file.
A typical application would be to add to an existing SD file calculated
Log P values or biological data exported from a spreadsheet.  The new SDF
can thereafter be displayed with the new data fields with e.g. ChemFinder,
the CACTVS system browser csbr, and probably many other programs.

The SDF toolkit is written in Perl 5, a free, widely available, scripting
language.

One useful application (at least for me) that has been written with this
toolkit: "add_prop_sdf".  This script reads an SDF, adds properties from a
comma separated values (CSV) file and prints out the new SDF file. Also of
interest may be the script "select_sdf" which can be used to extract
specific records from an SDF.

The SDF_toolkit is freely available under the GNU public license.

The toolkit can be downloaded, and more information found, at:

http://cactus.cit.nih.gov/SDF_toolkit/

Bruno Bienfait

--
[ Bruno Bienfait, Ph. D.            Laboratory of Medicinal Chemistry ]
[                                   National Cancer Institute         ]
[ Email : [email-masked]      National Institutes of Health     ]
[ Phone : (301) 402-3111            Building 37, Room 5B20            ]
[ Fax   : (301) 496-5839            Bethesda Maryland 20892 , USA     ]
[ WWW   : http://www.brunob.org                                       ]