Difference between revisions of "Fingerprint (format)"

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  </pre>
 
  </pre>
 
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This format generates molecular fingerprints.
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For an intoduction to fingerprint types see http://www.mesaac.com/Fingerprint.htm
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A list of available fingerprint types can be obtained by:
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<pre>
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  babel -F
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</pre>
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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.
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To use a fingerprint type other than the default, use the -xf option, e.g.
 +
 +
<pre>
 +
  babel infile.xxx -ofpt -xfFP3
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</pre>
 +
 +
For a single molecule the fingerprint is output in hexadecimal form
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(intended mainly for debugging).
 +
 +
With multiple molecules the hexadecimal form is output only if the <code>-xh</code> 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:
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  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.
  
 
[[Category:Formats]]
 
[[Category:Formats]]

Revision as of 15:55, 26 January 2006

Filename Extensions fpt
Chemical MIME Type Undefined
Specification URL Unknown
Import {{{import}}}
Export {{{export}}}
Open Babel Version {{{version}}}

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.