Package org.openscience.cdk.fingerprint

Interface IFingerprinter

All Known Implementing Classes:

AbstractFingerprinter, AtomPairs2DFingerprinter, CircularFingerprinter, EStateFingerprinter, ExtendedFingerprinter, Fingerprinter, GraphOnlyFingerprinter, HybridizationFingerprinter, KlekotaRothFingerprinter, LingoFingerprinter, MACCSFingerprinter, PubchemFingerprinter, ShortestPathFingerprinter, SignatureFingerprinter, SubstructureFingerprinter

public interface IFingerprinter

Interface for fingerprint calculators.

Author:

egonw

Source code:

main

Belongs to CDK module:

core

Keywords:

fingerprint

Method Summary

Modifier and Type	Method	Description
IBitFingerprint	getBitFingerprint(IAtomContainer container)	Returns the bit fingerprint for the given IAtomContainer.
ICountFingerprint	getCountFingerprint(IAtomContainer container)	Returns the count fingerprint for the given IAtomContainer.
BitSet	getFingerprint(IAtomContainer mol)	Generate a binary fingerprint as a bit.
Map<String,Integer>	getRawFingerprint(IAtomContainer container)	Returns the raw representation of the fingerprint for the given IAtomContainer.
int	getSize()	Returns the size (or length) of the fingerprint.
String	getVersionDescription()	Generate a fingerprint type version description in chemfp's FPS format.

Method Detail

getVersionDescription

String getVersionDescription()

Generate a fingerprint type version description in chemfp's FPS format. We report the library version rather than an individual version per fingerprint, although this is awkward as many fingerprint's don't/won't change between releases and we can not keep compatibility we guarantee we document how the fingerprint was encoded.
Examples:

 #type=CDK-Fingerprinter/2.0 searchDepth=7 pathLimit=2000 hashPseudoAtoms=true
 #type=CDK-CircularFingerprint/2.0 classType=ECFP4
 

Returns:

version description.

getFingerprint

BitSet getFingerprint(IAtomContainer mol)
               throws CDKException

Generate a binary fingerprint as a bit. This method will usually delegate to getBitFingerprint(IAtomContainer) and invoke IBitFingerprint.asBitSet(), it is included for backwards compatibility.

Parameters:

mol - molecule

Returns:

BitSet

Throws:

CDKException - problem generating fingerprint

getBitFingerprint

IBitFingerprint getBitFingerprint(IAtomContainer container)
                           throws CDKException

Returns the bit fingerprint for the given IAtomContainer.

Parameters:

container - IAtomContainer for which the fingerprint should be calculated.

Returns:

the bit fingerprint

Throws:

CDKException - may be thrown if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error

UnsupportedOperationException - if the Fingerprinter can not produce bit fingerprints

getCountFingerprint

ICountFingerprint getCountFingerprint(IAtomContainer container)
                               throws CDKException

Returns the count fingerprint for the given IAtomContainer.

Parameters:

container - IAtomContainer for which the fingerprint should be calculated.

Returns:

the count fingerprint

Throws:

CDKException - if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error.

UnsupportedOperationException - if the Fingerprinter can not produce count fingerprints

getRawFingerprint

Map<String,Integer> getRawFingerprint(IAtomContainer container)
                                     throws CDKException

Returns the raw representation of the fingerprint for the given IAtomContainer. The raw representation contains counts as well as the key strings.

Parameters:

container - IAtomContainer for which the fingerprint should be calculated.

Returns:

the raw fingerprint

Throws:

CDKException

getSize

int getSize()

Returns the size (or length) of the fingerprint.

Returns:

the size of the fingerprint