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Table 3 The molecular fingerprints in CDK

From: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

 

Bit version

Count version

CDK version

Default Size

CircularFingerprinter [35, 86]

\(\checkmark\)

\(\checkmark\)

v2.0

1024/\(2^{32}\)*

EStateFingerprinter [87]

\(\checkmark\)

 

v1.2.0

79

ExtendedFingerprinter

\(\checkmark\)

 

v1.0

\(1024\)

Fingerprinter

\(\checkmark\)

 

v1.0

\(1024\)

GraphOnlyFingerprinter

\(\checkmark\)

 

v1.0

\(1024\)

HybridizationFingerprinter

\(\checkmark\)

 

v1.4.0

\(1024\)

KlekotaRothFingerprinter [88]

\(\checkmark\)

 

v1.4.6

4860

LingoFingerprinter [89]

\(\checkmark\)

 

v2.0

NA\(^{\dagger }\)

MACCSFingerprinter

\(\checkmark\)

 

v1.2.0

166

PubchemFingerprinter [90]

\(\checkmark\)

 

v1.4.0

881

ShortestPathFingerprinter

\(\checkmark\)

 

v2.0

1024

SignatureFingerprinter [44]

\(\checkmark\)

\(\checkmark\)

v2.0

\(2^{32}\)

SubstructureFingerprinter

\(\checkmark\)

 

v1.0

307

  1. Listed are the currently available molecular fingerprint in CDK with information about whether they come as a bit and/or count version, what CDK version they were introduced in, their default size, and relevant references, where applicable
  2. * For the CircularFingerprinter the bit version is folded to 1024 whereas the count version is unfolded
  3. \(^\dagger\) The LingoFingerprinter does not have a default size