Fingerprint (format)

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Filename Extensions fpt
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 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

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 -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.