Read Me

SDF or Structures Data File is a common file format developed by Molecular Design Limited  to handle a list of molecular structures with associated properties. The file format has been published (Dalby et al., J. Chem. Inf. Comput. Sci. 1992, 32: 244-255).

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 SD file. A typical application is to add calculated Log P values or biological data exported from a spreadsheet.



The home page of the SDF toolkit is here: 
http://cactus.nci.nih.gov/SDF_toolkit/

The sourceforge archive contains the latest release of the toolkit. The SDF toolkit contains many tools. Some of them are very easy to use whereas others are more complicated. Unfortunately, almost no documentation is provided. There is however a pdf file  (sdf_toolkit_cookbook.pdf) in the docs directory. It is by far an unfinished document. It is distributed as it is in the hope that despite its unfinished state it could be useful.


All tools are written in Perl. The tools are located in the bin directory. The tools need a library that is located in the lib directory. The simplest way to run a tool is to enter a command such as:

perl -I lib bin/grep_sdf

All tools have a built-in help.

perl -I lib bin/grep_sdf -h


The SDF toolkit is not really under active devellopement. Features and bug fixes are added from time to time when needed by the author.


Bruno Bienfait, April 2010