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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