Fingerprint (format)

From Open Babel
Jump to: navigation, search
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
  s  describe each set bit
  u  describe each unset bit
 

Additional Comments

This format generates molecular fingerprints.

For an introduction to fingerprint types see http://www.mesaac.com/Fingerprint.htm

A list of available fingerprint types can be obtained by:

  babel -L fingerprints

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.


In Fingerprint FP4 each bit corresponds to a particular chemical feature, which are specified as SMARTS patterns in SMARTS_InteLigand.txt. Use the -xs option to output a tab separated list of the features in a molecule. For instance a well-known molecule gives

Primary_carbon: Carboxylic_acid: Carboxylic_ester: Carboxylic_acid_derivative: Vinylogous_carbonyl_or_carboxyl_derivative: Vinylogous_ester: Aromatic: Conjugated_double_bond: C_ONS_bond: 1,3-Tautomerizable: Rotatable_bond: CH-acidic: