Fingerprint (format)

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Revision as of 11:36, 20 February 2007 by Ghutchis (Talk | contribs) (Fingerprint moved to Fingerprint (format): Adding new page / category for fingerprints (for developers))

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Filename Extensions fpt
Chemical MIME Type Undefined
Specification URL Unknown
Import No
Export Yes
Open Babel Version 2.0.0 and later

Options

 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
 

Additional Comments

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:

  babel -F

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.