Package org.openscience.cdk.fingerprint

Class AtomPairs2DFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter

All Implemented Interfaces:

IFingerprinter

public class AtomPairs2DFingerprinter
extends AbstractFingerprinter
implements IFingerprinter

Generates an atom pair 2D fingerprint as implemented in PaDEL given an IAtomContainer, that extends the Fingerprinter.

Author:

Lyle Burgoon (lyle.d.burgoon@usace.army.mil)

See Also:

Fingerprinter

Source code:

main

Belongs to CDK module:

fingerprint

Keywords:

fingerprint, similarity

Created on:

2018-02-05

Constructor Summary

Constructors

Constructor	Description
AtomPairs2DFingerprinter()

Method Summary

Modifier and Type	Method	Description
IBitFingerprint	getBitFingerprint(IAtomContainer container)	Returns the bit fingerprint for the given IAtomContainer.
ICountFingerprint	getCountFingerprint(IAtomContainer mol)	Returns the count fingerprint for the given IAtomContainer.
Map<String,Integer>	getRawFingerprint(IAtomContainer mol)	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

AtomPairs2DFingerprinter

public AtomPairs2DFingerprinter()

Method Detail

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

getBitFingerprint

public IBitFingerprint getBitFingerprint(IAtomContainer container)
                                  throws CDKException

Description copied from interface: IFingerprinter

Returns the bit fingerprint for the given IAtomContainer.

Specified by:

getBitFingerprint in interface IFingerprinter

Parameters:

container - 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 mol)
                                            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:

mol - IAtomContainer for which the fingerprint should be calculated.

Returns:

the raw fingerprint

Throws:

CDKException

getCountFingerprint

public ICountFingerprint getCountFingerprint(IAtomContainer mol)
                                      throws CDKException

Description copied from interface: IFingerprinter

Returns the count fingerprint for the given IAtomContainer.

Specified by:

getCountFingerprint in interface IFingerprinter

Parameters:

mol - 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.