org.openscience.cdk.fingerprint

Class ExtendedFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.Fingerprinter

org.openscience.cdk.fingerprint.ExtendedFingerprinter

All Implemented Interfaces:

IFingerprinter

public class ExtendedFingerprinter
extends Fingerprinter
implements IFingerprinter

Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional bits describing ring features.

Author:

shk3

See Also:

Fingerprinter

Source code:

master

Belongs to CDK module:

fingerprint

Keywords:

fingerprint, similarity

Created on:

2006-01-13

Field Summary

Fields inherited from class org.openscience.cdk.fingerprint.Fingerprinter

DEFAULT_SEARCH_DEPTH, DEFAULT_SIZE

Constructor Summary

Constructors

Constructor and Description
ExtendedFingerprinter() Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
ExtendedFingerprinter(int size)
ExtendedFingerprinter(int size, int searchDepth) Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.

Method Summary

Modifier and Type	Method and Description
IBitFingerprint	getBitFingerprint(IAtomContainer container) Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
IBitFingerprint	getBitFingerprint(IAtomContainer atomContainer, IRingSet ringSet, List<IRingSet> rslist) Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
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.Fingerprinter

encodePaths, findPathes, getBitFingerprint, getBondSymbol, getParameters, getSearchDepth, setHashPseudoAtoms, setPathLimit

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

getFingerprint, 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

ExtendedFingerprinter

public ExtendedFingerprinter()

Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.

ExtendedFingerprinter

public ExtendedFingerprinter(int size)

ExtendedFingerprinter

public ExtendedFingerprinter(int size,
                             int searchDepth)

Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.

Parameters:

size - The desired size of the fingerprint

searchDepth - The desired depth of search

Method Detail

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer container)
                                  throws CDKException

Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics. It contains the informations from getBitFingerprint() and bits which tell if the structure has 0 rings, 1 or less rings, 2 or less rings ... 10 or less rings (referring to smallest set of smallest rings) and bits which tell if there is a fused ring system with 1,2...8 or more rings in it

Specified by:

getBitFingerprint in interface IFingerprinter

Overrides:

getBitFingerprint in class Fingerprinter

Parameters:

container - The AtomContainer for which a Fingerprint is generated

Returns:

a bit fingerprint for the given IAtomContainer.

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

Overrides:

getRawFingerprint in class Fingerprinter

Parameters:

iAtomContainer - IAtomContainer for which the fingerprint should be calculated.

Returns:

the raw fingerprint

Throws:

CDKException

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer,
                                         IRingSet ringSet,
                                         List<IRingSet> rslist)
                                  throws CDKException

Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics. It contains the informations from getBitFingerprint() and bits which tell if the structure has 0 rings, 1 or less rings, 2 or less rings ... 10 or less rings and bits which tell if there is a fused ring system with 1,2...8 or more rings in it. The RingSet used is passed via rs parameter. This must be a smallesSetOfSmallestRings. The List must be a list of all ring systems in the molecule.

Parameters:

atomContainer - The AtomContainer for which a Fingerprint is generated

ringSet - An SSSR RingSet of ac (if not available, use getExtendedFingerprint(AtomContainer ac), which does the calculation)

rslist - A list of all ring systems in ac

Returns:

a BitSet representing the fingerprint

Throws:

CDKException - for example if input can not be cloned.

getSize

public int getSize()

Returns the size (or length) of the fingerprint.

Specified by:

getSize in interface IFingerprinter

Overrides:

getSize in class Fingerprinter

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

Overrides:

getCountFingerprint in class Fingerprinter

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.