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. and Thormann, M. and Pons, M., LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities, J. Chem. Inf. Model., 2005, 45:386-393, doi:10.1021/ci0496797].

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:

master

Belongs to CDK module:

smiles

Keywords:

fingerprint, hologram

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
IBitFingerprint	getBitFingerprint(IAtomContainer iAtomContainer)
ICountFingerprint	getCountFingerprint(IAtomContainer container)
protected List<Map.Entry<String,String>>	getParameters()
Map<String,Integer>	getRawFingerprint(IAtomContainer atomContainer)
int	getSize()

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()

Overrides:

getParameters in class AbstractFingerprinter

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer iAtomContainer)
                                  throws CDKException

Specified by:

getBitFingerprint in interface IFingerprinter

Throws:

CDKException

getRawFingerprint

public Map<String,Integer> getRawFingerprint(IAtomContainer atomContainer)
                                      throws CDKException

Specified by:

getRawFingerprint in interface IFingerprinter

Throws:

CDKException

getSize

public int getSize()

Specified by:

getSize in interface IFingerprinter

getCountFingerprint

public ICountFingerprint getCountFingerprint(IAtomContainer container)
                                      throws CDKException

Specified by:

getCountFingerprint in interface IFingerprinter

Throws:

CDKException