Package org.openscience.cdk.fingerprint

Class LingoFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.LingoFingerprinter

All Implemented Interfaces:

IFingerprinter

public class LingoFingerprinter
extends AbstractFingerprinter
implements IFingerprinter

An implementation of the LINGO fingerprint [Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45].

While the current implementation converts ring closure symbols to 0's it does not convert 2-letter element symbols to single letters (ala OpenEye).

Author:

Rajarshi Guha

Source code:

main

Belongs to CDK module:

smiles

Keywords:

fingerprint, hologram

Constructor Summary

Constructors

Constructor	Description
LingoFingerprinter()	Initialize the fingerprinter with a default substring length of 4.
LingoFingerprinter(int n)	Initialize the fingerprinter.

Method Summary

Modifier and Type	Method	Description
IBitFingerprint	getBitFingerprint(IAtomContainer iAtomContainer)	Returns the bit fingerprint for the given IAtomContainer.
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 atomContainer)	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, 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

LingoFingerprinter

public LingoFingerprinter()

Initialize the fingerprinter with a default substring length of 4.

LingoFingerprinter

public LingoFingerprinter(int n)

Initialize the fingerprinter.

Parameters:

n - The length of substrings to consider

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 iAtomContainer)
                                  throws CDKException

Description copied from interface: IFingerprinter

Returns the bit fingerprint for the given IAtomContainer.

Specified by:

getBitFingerprint in interface IFingerprinter

Parameters:

iAtomContainer - 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 atomContainer)
                                            throws CDKException

Description copied from interface: IFingerprinter

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:

atomContainer - IAtomContainer for which the fingerprint should be calculated.

Returns:

the raw fingerprint

Throws:

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 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.