"babel -H fpt" - Fingerprint Help Information

Q

How to get help information on Open Babel Fingerprints?

✍: FYIcenter.com

A

You can use the "babel -H fpt" command to get help information on Open Babel Fingerprints:

fyicenter$ babel -H fpt 

fpt  Fingerprint format
Generate or display molecular fingerprints.
This format constructs and displays fingerprints and (for multiple input
objects) the Tanimoto coefficient and whether a superstructure of the first
object.

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, for example::

  babel infile.xxx -o fpt -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 object 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.

Use the ``-xs`` option to describe the bits that are set in the fingerprint.
The output depends on the fingerprint type. For Fingerprint FP4, each bit
corresponds to a particular chemical feature, which are specified as SMARTS
patterns in :file:`SMARTS_InteLigand.txt`, and the output is a tab-separated
list of the features of 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:

For the path-based fingerprint FP2, the output from the ``-xs`` option is
instead a list of the chemical fragments used to set bits, e.g.::

 $ obabel -:"CCC(=O)Cl" -o fpt -xs -xf FP2
 >
 0 6 1 6 <670>
 0 6 1 6 1 6 <260>
 0 8 2 6 <623>
 ...etc

where the first digit is 0 for linear fragments but is a bond order
for cyclic fragments. The remaining digits indicate the atomic number
and bond order alternatively. Note that a bond order of 5 is used for
aromatic bonds. For example, bit 623 above is the linear fragment O=C
(8 for oxygen, 2 for double bond and 6 for carbon).

Write 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
 o  hex output only
 s  describe each set bit
 u  describe each unset bit

This format is Write-only

 

Using Fastsearch Fingerprint Index

"babel" - FP2 Fingerprint Fragment Ends at Ring

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2020-11-22, 166👍, 0💬