Package org.openscience.cdk.fingerprint

Class MACCSFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.MACCSFingerprinter

All Implemented Interfaces:

IFingerprinter

public class MACCSFingerprinter
extends AbstractFingerprinter
implements IFingerprinter

This fingerprinter generates 166 bit MACCS keys. The SMARTS patterns for each of the features was taken from RDKit. However given that there is no official and explicit listing of the original key definitions, the results of this implementation may differ from others. This class assumes that aromaticity perception, atom typing and adding of implicit hydrogens have been performed prior to generating the fingerprint. Note Currently bits 1 and 44 are completely ignored since the RDKit defs do not provide a definition and I can't find an official description of them. Warning - MACCS substructure keys cannot be used for substructure filtering. It is possible for some keys to match substructures and not match the superstructures. Some keys check for hydrogen counts which may not be preserved in a superstructure.

Author:

Rajarshi Guha

Source code:

main

Belongs to CDK module:

fingerprint

Keywords:

fingerprint, similarity

Created on:

2008-07-23

Constructor Summary

Constructors

Constructor	Description
MACCSFingerprinter()
MACCSFingerprinter(IChemObjectBuilder builder)

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.
Map<String,Integer>	getRawFingerprint(IAtomContainer iAtomContainer)	Returns the raw representation of the fingerprint for the given IAtomContainer.
int	getSize()	Returns the size (or length) of the fingerprint.

Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter

getFingerprint, getParameters, getVersionDescription

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter

getFingerprint, getVersionDescription

Constructor Detail

MACCSFingerprinter

public MACCSFingerprinter()

MACCSFingerprinter

public MACCSFingerprinter(IChemObjectBuilder builder)

Method Detail

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer container)
                                  throws CDKException

Returns the bit fingerprint for the given IAtomContainer.

Specified by:

getBitFingerprint in interface IFingerprinter

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

getRawFingerprint

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

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

Specified by:

getRawFingerprint in interface IFingerprinter

Parameters:

iAtomContainer - IAtomContainer for which the fingerprint should be calculated.

Returns:

the raw fingerprint

Throws:

CDKException

getSize

public int getSize()

Returns the size (or length) of the fingerprint.

Specified by:

getSize in interface IFingerprinter

Returns:

the size of the fingerprint

getCountFingerprint

public ICountFingerprint getCountFingerprint(IAtomContainer container)
                                      throws CDKException

Returns the count fingerprint for the given IAtomContainer.

Specified by:

getCountFingerprint in interface IFingerprinter

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.