Fingerprint Types Supported in Open Babel


What Fingerprint Types are Supported in Open Babel?



You can get a list of fingerprint types supported in Open Babel by running the "babel -L fingerprints" command:

fyicenter$ babel -L fingerprints 

FP2    Indexes linear fragments up to 7 atoms.
FP3    SMARTS patterns specified in the file patterns.txt
FP4    SMARTS patterns specified in the file SMARTS_InteLigand.txt
MACCS    SMARTS patterns specified in the file MACCS.txt

FP2 is the default fingerprint type used in "babel" command. It is described in Open Babel documentation as:

FP2, a path-based fingerprint which indexes small molecule fragments based on linear segments of up to 7 atoms (somewhat similar to the Daylight fingerprints):

A molecule structure is analyzed to identify linear fragments of length from 1-7 atoms. Single atom fragments of C, N, and O are ignored. A fragment is terminated when the atoms form a ring.

For each of these fragments the atoms, bonding and whether they constitute a complete ring is recorded and saved in a set so that there is only one of each fragment type. Chemically identical versions, (i.e. ones with the atoms listed in reverse order and rings listed starting at different atoms) are identified and only a single canonical fragment is retained.

Each remaining fragment is assigned a hash number from 0 to 1020 which is used to set a bit in a 1024 bit vector


Substructure Search with Fingerprints

"babel -o fpt ..." Command - Similarity Search

Similarity Search with Open Babel

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2020-12-15, 898🔥, 0💬