On 28/09/2010 13:27, nilesh_tawari wrote:
> I want to know how to get various binary fingerprints for all molecules in
> sdf file using Open Babel.
From the commandline (or the equivalent in the GUI)
babel infile.sdf outfile.fpt -xh -xf FP2
This provides fingerprints for all the molecules in hexadecimal, with
some extra information. In v2.3.0 (about to be released) -xo option
will output just the fingerprint. The fingerprint types that are
available are FP2 (fragment based), FP4 and MACCS (structure keys).
Get more information from
babel -L fpt
or the plugin menu in the GUI.
If you need the fingerprints in binary, look at FastSearch format.