org.openscience.cdk.fingerprint

Class AbstractFingerprinter

java.lang.Object

org.openscience.cdk.fingerprint.AbstractFingerprinter

All Implemented Interfaces:

IFingerprinter

Direct Known Subclasses:

AtomPairs2DFingerprinter, CircularFingerprinter, EStateFingerprinter, Fingerprinter, LingoFingerprinter, MACCSFingerprinter, PubchemFingerprinter, ShortestPathFingerprinter, SignatureFingerprinter, SubstructureFingerprinter

public abstract class AbstractFingerprinter
extends Object
implements IFingerprinter

Constructor Summary

Constructors

Constructor and Description
AbstractFingerprinter()

Method Summary

Modifier and Type	Method and Description
BitSet	getFingerprint(IAtomContainer mol) Generate a binary fingerprint as a bit.
protected List<Map.Entry<String,String>>	getParameters() Base classes should override this method to report the parameters they are configured with.
String	getVersionDescription() Generate a fingerprint type version description in chemfp's FPS format.

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

getBitFingerprint, getCountFingerprint, getRawFingerprint, getSize

Constructor Detail

AbstractFingerprinter

public AbstractFingerprinter()

Method Detail

getParameters

protected List<Map.Entry<String,String>> getParameters()

Base classes should override this method to report the parameters they are configured with.

Returns:

The key=value pairs of configured parameters

getVersionDescription

public final String getVersionDescription()

Description copied from interface: IFingerprinter

Generate a fingerprint type version description in chemfp's FPS format. We report the library version rather than an individual version per fingerprint, although this is awkward as many fingerprint's don't/won't change between releases and we can not keep compatibility we guarantee we document how the fingerprint was encoded.
Examples:

 #type=CDK-Fingerprinter/2.0 searchDepth=7 pathLimit=2000 hashPseudoAtoms=true
 #type=CDK-CircularFingerprint/2.0 classType=ECFP4
 

Specified by:

getVersionDescription in interface IFingerprinter

Returns:

version description.

getFingerprint

public BitSet getFingerprint(IAtomContainer mol)
                      throws CDKException

Generate a binary fingerprint as a bit. This method will usually delegate to IFingerprinter.getBitFingerprint(IAtomContainer) and invoke IBitFingerprint.asBitSet(), it is included for backwards compatibility.

Specified by:

getFingerprint in interface IFingerprinter

Parameters:

mol - molecule

Returns:

BitSet

Throws:

CDKException - problem generating fingerprint