How to generate fingerprint?

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How to generate fingerprint?

nilesh_tawari
I want to know how to get various binary fingerprints for all molecules in sdf file using Open Babel.
Thanks
-nilesh
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Re: How to generate fingerprint?

Chris Morley-3
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.

Chris



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