org.openscience.cdk.fingerprint

Class ShortestPathFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.ShortestPathFingerprinter

All Implemented Interfaces:

Serializable, IFingerprinter

public class ShortestPathFingerprinter
extends AbstractFingerprinter
implements IFingerprinter, Serializable

Generates a fingerprint for a given IAtomContainer. 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:
 It is recommended to use atomtyped container before generating the fingerprints.

 For example: AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer);

   AtomContainer molecule = new AtomContainer();
   AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer);
   IFingerprinter fingerprinter = new ShortestPathFingerprinter();
   IBitFingerprint fingerprint = fingerprinter.getFingerprint(molecule);
   fingerprint.fingerprintLength(); // returns 1024 by default
   fingerprint.length(); // returns the highest set bit
 

The FingerPrinter calculates fingerprint based on the Shortest Paths between two atoms. It also takes into account ring system, charges etc while generating a fingerprint.

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.

Author:

Syed Asad Rahman (2012)

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

fingerprint

Keywords:

fingerprint, similarity

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_SIZE The default length of created fingerprints.

Constructor Summary

Constructors

Constructor and Description
ShortestPathFingerprinter() Creates a fingerprint generator of length DEFAULT_SIZE
ShortestPathFingerprinter(int fingerprintLength) Constructs a fingerprint generator that creates fingerprints of the given fingerprintLength, using a generation algorithm with shortest paths.

Method Summary

Methods

Modifier and Type	Method and Description
IBitFingerprint	getBitFingerprint(IAtomContainer ac) Generates a shortest path based BitSet fingerprint for the given AtomContainer.
ICountFingerprint	getCountFingerprint(IAtomContainer iac) Returns the count fingerprint for the given IAtomContainer.
Map<String,Integer>	getRawFingerprint(IAtomContainer ac) 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

Field Detail

DEFAULT_SIZE

public static final int DEFAULT_SIZE

The default length of created fingerprints.

See Also:

Constant Field Values

Constructor Detail

ShortestPathFingerprinter

public ShortestPathFingerprinter()

Creates a fingerprint generator of length DEFAULT_SIZE

ShortestPathFingerprinter

public ShortestPathFingerprinter(int fingerprintLength)

Constructs a fingerprint generator that creates fingerprints of the given fingerprintLength, using a generation algorithm with shortest paths.

Parameters:

fingerprintLength - The desired fingerprintLength of the fingerprint

Method Detail

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer ac)
                                  throws CDKException

Generates a shortest path based BitSet fingerprint for the given AtomContainer.

Specified by:

getBitFingerprint in interface IFingerprinter

Parameters:

ac - The AtomContainer for which a fingerprint is generated

Returns:

A BitSet representing the fingerprint

Throws:

CDKException - if there error in aromaticity perception or other CDK functions

getRawFingerprint

public Map<String,Integer> getRawFingerprint(IAtomContainer ac)
                                      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:

ac - The AtomContainer for which a fingerprint is generated

Returns:

Map of raw fingerprint paths/features

Throws:

UnsupportedOperationException - method is not supported

CDKException

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 iac)
                                      throws CDKException

Description copied from interface: IFingerprinter

Returns the count fingerprint for the given IAtomContainer.

Specified by:

getCountFingerprint in interface IFingerprinter

Parameters:

iac - 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.