org.openscience.cdk.fingerprint

Class Fingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.Fingerprinter

All Implemented Interfaces:

IFingerprinter

Direct Known Subclasses:

ExtendedFingerprinter, GraphOnlyFingerprinter, HybridizationFingerprinter

public class Fingerprinter
extends AbstractFingerprinter
implements IFingerprinter

Generates a fingerprint for a given AtomContainer. Fingerprints are one-dimensional bit arrays, where bits are set according to a the occurrence of a particular structural feature (See for example the Daylight inc. theory manual for more information). Fingerprints allow for a fast screening step to exclude candidates for a substructure search in a database. They are also a means for determining the similarity of chemical structures.

A fingerprint is generated for an AtomContainer with this code:

   Molecule molecule = new Molecule();
   IFingerprinter fingerprinter = new Fingerprinter();
   IBitFingerprint fingerprint = fingerprinter.getBitFingerprint(molecule);
   fingerprint.size(); // returns 1024 by default
   fingerprint.length(); // returns the highest set bit
 

The FingerPrinter assumes that hydrogens are explicitly given! Furthermore, if pseudo atoms or atoms with malformed symbols are present, their atomic number is taken as one more than the last element currently supported in PeriodicTable. Warning: The aromaticity detection for this FingerPrinter relies on AllRingsFinder, which is known to take very long for some molecules with many cycles or special cyclic topologies. Thus, the AllRingsFinder has a built-in timeout of 5 seconds after which it aborts and throws an Exception. If you want your SMILES generated at any expense, you need to create your own AllRingsFinder, set the timeout to a higher value, and assign it to this FingerPrinter. In the vast majority of cases, however, the defaults will be fine.

Another Warning : The daylight manual says: "Fingerprints are not so definite: if a fingerprint indicates a pattern is missing then it certainly is, but it can only indicate a pattern's presence with some probability." In the case of very small molecules, the probability that you get the same fingerprint for different molecules is high.

Author:

steinbeck

Source code:

master

Belongs to CDK module:

standard

Keywords:

fingerprint, similarity

Created on:

2002-02-24

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_SEARCH_DEPTH The default search depth used to create the fingerprints.
static int	DEFAULT_SIZE The default length of created fingerprints.

Constructor Summary

Constructors

Constructor and Description
Fingerprinter() Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
Fingerprinter(int size)
Fingerprinter(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

Methods

Modifier and Type	Method and Description
protected void	encodePaths(IAtomContainer mol, int depth, BitSet fp, int size)
protected int[]	findPathes(IAtomContainer container, int searchDepth) Deprecated. Use encodePaths(IAtomContainer, int, BitSet, int)
IBitFingerprint	getBitFingerprint(IAtomContainer container) Generates a fingerprint of the default size for the given AtomContainer.
IBitFingerprint	getBitFingerprint(IAtomContainer container, AllRingsFinder ringFinder) Generates a fingerprint of the default size for the given AtomContainer.
protected String	getBondSymbol(IBond bond) Gets the bondSymbol attribute of the Fingerprinter class
ICountFingerprint	getCountFingerprint(IAtomContainer container) Returns the count fingerprint for the given IAtomContainer.
protected List<Map.Entry<String,String>>	getParameters() Base classes should override this method to report the parameters they are configured with.
Map<String,Integer>	getRawFingerprint(IAtomContainer iAtomContainer) Returns the raw representation of the fingerprint for the given IAtomContainer.
int	getSearchDepth()
int	getSize() Returns the size (or length) of the fingerprint.
void	setHashPseudoAtoms(boolean value)
void	setPathLimit(int limit)

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

Field Detail

DEFAULT_SIZE

public static final int DEFAULT_SIZE

The default length of created fingerprints.

See Also:

Constant Field Values

DEFAULT_SEARCH_DEPTH

public static final int DEFAULT_SEARCH_DEPTH

The default search depth used to create the fingerprints.

See Also:

Constant Field Values

Constructor Detail

Fingerprinter

public Fingerprinter()

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

Fingerprinter

public Fingerprinter(int size)

Fingerprinter

public Fingerprinter(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 (number of bonds)

Method Detail

getParameters

protected List<Map.Entry<String,String>> getParameters()

Description copied from class: AbstractFingerprinter

Base classes should override this method to report the parameters they are configured with.

Overrides:

getParameters in class AbstractFingerprinter

Returns:

The key=value pairs of configured parameters

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer container,
                                AllRingsFinder ringFinder)
                                  throws CDKException

Generates a fingerprint of the default size for the given AtomContainer.

Parameters:

container - The AtomContainer for which a Fingerprint is generated

ringFinder - An instance of AllRingsFinder

Returns:

A BitSet representing the fingerprint

Throws:

CDKException - if there is a timeout in ring or aromaticity perception

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer container)
                                  throws CDKException

Generates a fingerprint of the default size for the given AtomContainer.

Specified by:

getBitFingerprint in interface IFingerprinter

Parameters:

container - The AtomContainer for which a Fingerprint is generated

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

findPathes

@Deprecated
protected int[] findPathes(IAtomContainer container,
                          int searchDepth)
                    throws CDKException

Deprecated. Use encodePaths(IAtomContainer, int, BitSet, int)

Get all paths of lengths 0 to the specified length. This method will find all paths up to length N starting from each atom in the molecule and return the unique set of such paths.

Parameters:

container - The molecule to search

searchDepth - The maximum path length desired

Returns:

A Map of path strings, keyed on themselves

Throws:

CDKException

encodePaths

protected void encodePaths(IAtomContainer mol,
               int depth,
               BitSet fp,
               int size)
                    throws CDKException

Throws:

CDKException

getBondSymbol

protected String getBondSymbol(IBond bond)

Gets the bondSymbol attribute of the Fingerprinter class

Parameters:

bond - Description of the Parameter

Returns:

The bondSymbol value

setPathLimit

public void setPathLimit(int limit)

setHashPseudoAtoms

public void setHashPseudoAtoms(boolean value)

getSearchDepth

public int getSearchDepth()

getSize

public int getSize()

Description copied from interface: IFingerprinter

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

Description copied from interface: IFingerprinter

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.