Public Repository

Last pushed: 3 years ago
Short Description
SDF Toolkit is a set of tools to read and parse molecular data files
Full Description

Raspberry Pi Dockerfile for SDF Toolkit.

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 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 us) that has been written with this toolkit: "add_prop_sdf". This script reads an SDF, adds properties from a CSV file and prints out the new SD file. No GUI here, it's a batch mode program. Also of interest is the script select_sdf which can be use to extract specific records of an SDF. Random selection of records from an SDF can be made with the help of the gen_rnd script.
The SDF_toolkit is freely available under the GNU public license granted by the author. The U.S. Government imposes no license restrictions of its own on the toolkit.

The Dockerfile is located at

/data is exposed as a volume. SDF files can be mounted there, or /SDF_tools contains some sample files.

Note: The toolkit is old; some things have changed in Perl since it was written. Consequently warnings are thrown. I've had no issues from sending them to /dev/null.

A usage example follows, pulling data from a sample file:

$ docker run --rm nimblestratus/rpi-sdf-toolkit /bin/ash -c '(cat /SDF_toolkit/chemfinder.sdf|/SDF_toolkit/extract_prop_sdf -property_name CAS)' 2>/dev/null
Docker Pull Command