org.openscience.cdk.fingerprint

Class EStateFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.EStateFingerprinter

All Implemented Interfaces:

IFingerprinter

public class EStateFingerprinter
extends AbstractFingerprinter
implements IFingerprinter

This fingerprinter generates 79 bit fingerprints using the E-State fragments.

The E-State fragments are those described in [Hall, L.H. and Kier, L.B. , Electrotopological State Indices for Atom Types: A Novel Combination of Electronic, Topological, and Valence State Information, Journal of Chemical Information and Computer Science, 1995, 35:1039-1045, doi:10.1021/ci00028a014] and the SMARTS patterns were taken from RDKit. Note that this fingerprint simply indicates the presence or occurrence of the fragments. If you need counts of the fragments take a look at KierHallSmartsDescriptor, which also lists the substructures corresponding to each bit position.

This class assumes that aromaticity perception and atom typing have been performed prior to generating the fingerprint. Warning - ESTATE 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:

Rajarhi Guha

Source code:

master

Belongs to CDK module:

fingerprint

Keywords:

fingerprint, similarity, estate

Created on:

2008-07-23

Constructor Summary

Constructors

Constructor and Description
EStateFingerprinter()

Method Summary

Methods

Modifier and Type	Method and Description
IBitFingerprint	getBitFingerprint(IAtomContainer atomContainer) 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

EStateFingerprinter

public EStateFingerprinter()

Method Detail

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
                                  throws CDKException

Returns the bit fingerprint for the given IAtomContainer.

Specified by:

getBitFingerprint in interface IFingerprinter

Parameters:

atomContainer - 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.