org.openscience.cdk.fingerprint

Class ExtendedFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.ExtendedFingerprinter

All Implemented Interfaces:

IFingerprinter

public class ExtendedFingerprinter
extends Object
implements IFingerprinter

Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional (25) bits describing ring features and isotopic masses. JWM Comment: It's better to actually just hash the rings over the entire length simply using a different seed. The original version of the class used non-unique SSSR which of course doesn't work for substructure screening so this fingerprint can only be used for similarity.

Author:

shk3

See Also:

Fingerprinter

Source code:

master

Belongs to CDK module:

fingerprint

Keywords:

fingerprint, similarity

Created on:

2006-01-13

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.
BitSet	getFingerprint(IAtomContainer mol) Generate a binary fingerprint as a bit.
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.
String	getVersionDescription() Generate a fingerprint type version description in chemfp's FPS format.
void	setHashPseudoAtoms(boolean hashPseudoAtoms) Set the hashPseudoAtoms for the base daylight/path fingerprint.
void	setPathLimit(int pathLimit) Set the pathLimit for the base daylight/path fingerprint.

Methods inherited from class java.lang.Object

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

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

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

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 - A 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

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.

getVersionDescription

public String getVersionDescription()

Description copied from interface: IFingerprinter

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
 

Specified by:

getVersionDescription in interface IFingerprinter

Returns:

version description.

getFingerprint

public BitSet getFingerprint(IAtomContainer mol)
                      throws CDKException

Description copied from interface: IFingerprinter

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

Specified by:

getFingerprint in interface IFingerprinter

Parameters:

mol - molecule

Returns:

BitSet

Throws:

CDKException - problem generating fingerprint

setPathLimit

public void setPathLimit(int pathLimit)

Set the pathLimit for the base daylight/path fingerprint. If too many paths are generated from a single atom an exception is thrown.

Parameters:

pathLimit - the number of paths to generate from a node

See Also:

Fingerprinter

setHashPseudoAtoms

public void setHashPseudoAtoms(boolean hashPseudoAtoms)

Set the hashPseudoAtoms for the base daylight/path fingerprint. This indicates whether pseudo-atoms should be hashed, for substructure screening this is not desirable - but this fingerprint uses SSSR so can't be used for substructure screening regardless.

Parameters:

hashPseudoAtoms - the number of paths to generate from a node

See Also:

Fingerprinter