Difference between revisions of "Fingerprint (format)"
m (Fingerprint moved to Fingerprint (format): Adding new page / category for fingerprints (for developers))
Revision as of 10:36, 20 February 2007
|Chemical MIME Type||Undefined|
|Open Babel Version||2.0.0 and later|
Constructs and displays fingerprints and (for multiple input objects) the Tanimoto coefficient and whether a superstructure of the first object Options e.g. -xfFP3 -xn128 f<id> fingerprint type N# fold to specified number of bits, 32, 64, 128, etc. h hex output when multiple molecules F displays the available fingerprint types
This format generates molecular fingerprints.
For an intoduction to fingerprint types see http://www.mesaac.com/Fingerprint.htm
A list of available fingerprint types can be obtained by:
The current default type FP2 is is of the Daylight type, indexing a molecule based on the occurrence of linear fragment up to 7 atoms in length. To use a fingerprint type other than the default, use the -xf option, e.g.
babel infile.xxx -ofpt -xfFP3
For a single molecule the fingerprint is output in hexadecimal form (intended mainly for debugging).
With multiple molecules the hexadecimal form is output only if the
-xh option is specified. But in addition the Tanimoto coefficient between the first molecule and each of the subsequent ones is displayed. If the first molecule is a substructure of the target molecule a note saying this is also displayed.
The Tanimoto coefficient is defined as:
Number of bits set in (patternFP & targetFP) / Number of bits in (patternFP | targetFP)
where the boolean operations between the fingerprints are bitwise.
The Tanimoto coefficient has no absolute meaning and depends on the design of the fingerprint.