Package org.openscience.cdk.fingerprint

Interface Summary

Interface	Description
IBitFingerprint	Interface for bit fingerprint representations.
ICountFingerprint	Interface for count fingerprint representations.
IFingerprinter	Interface for fingerprint calculators.

Class Summary

Class	Description
AbstractFingerprinter
AtomPairs2DFingerprinter	Generates an atom pair 2D fingerprint as implemented in PaDEL given an IAtomContainer, that extends the Fingerprinter.
BitSetFingerprint
CircularFingerprinter	Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6 fingerprints, which are partially described by Rogers et al.
CircularFingerprinter.FP
EStateFingerprinter	This fingerprinter generates 79 bit fingerprints using the E-State fragments.
ExtendedFingerprinter	Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional bits describing ring features.
Fingerprinter	Generates a fingerprint for a given AtomContainer.
FingerprinterTool	Tool with helper methods for IFingerprint.
GraphOnlyFingerprinter	Specialized version of the Fingerprinter which does not take bond orders into account.
HybridizationFingerprinter	Generates a fingerprint for a given IAtomContainer.
IntArrayCountFingerprint
IntArrayFingerprint
KlekotaRothFingerprinter	SMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity (Klekota, Justin and Roth, Frederick P.. Bioinformatics. 2008. 24).
LingoFingerprinter	An implementation of the LINGO fingerprint (Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45).
MACCSFingerprinter	This fingerprinter generates 166 bit MACCS keys.
PubchemFingerprinter	Generates a Pubchem fingerprint for a molecule.
RandomNumber	Generates pseudorandom numbers using the MersenneTwister method from commons-math.
ShortestPathFingerprinter	Generates a fingerprint for a given IAtomContainer.
ShortestPathWalker
SignatureFingerprinter	An implementation of a AtomSignature-based fingerprint.
SimpleAtomCanonicalizer	This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
SimpleAtomComparator	This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
StandardSubstructureSets	Default sets of atom containers aimed for use with the substructure.
SubstructureFingerprinter	IFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from.