org.openscience.cdk.similarity

Class Tanimoto

java.lang.Object

org.openscience.cdk.similarity.Tanimoto

@TestClass(value="org.openscience.cdk.similarity.TanimotoTest")
public class Tanimoto
extends Object

Calculates the Tanimoto coefficient for a given pair of two fingerprint bitsets or real valued feature vectors. The Tanimoto coefficient is one way to quantitatively measure the "distance" or similarity of two chemical structures.

You can use the FingerPrinter class to retrieve two fingerprint bitsets. We assume that you have two structures stored in cdk.Molecule objects. A tanimoto coefficient can then be calculated like:

   BitSet fingerprint1 = Fingerprinter.getFingerprint(molecule1);
   BitSet fingerprint2 = Fingerprinter.getFingerprint(molecule2);
   float tanimoto_coefficient = Tanimoto.calculate(fingerprint1, fingerprint2);
  

The FingerPrinter assumes that hydrogens are explicitely given, if this is desired!

Note that the continuous Tanimoto coefficient does not lead to a metric space

Author:

steinbeck

Keywords:

jaccard, similarity, tanimoto

Created on:

2005-10-19

Constructor Summary

Constructors

Constructor and Description
Tanimoto()

Method Summary

Methods

Modifier and Type	Method and Description
static float	calculate(BitSet bitset1, BitSet bitset2) Evaluates Tanimoto coefficient for two bit sets.
static float	calculate(double[] features1, double[] features2) Evaluates the continuous Tanimoto coefficient for two real valued vectors.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Tanimoto

public Tanimoto()

Method Detail

calculate

@TestMethod(value="testTanimoto1,testTanimoto2")
public static float calculate(BitSet bitset1,
                              BitSet bitset2)
                       throws CDKException

Evaluates Tanimoto coefficient for two bit sets.

Parameters:

bitset1 - A bitset (such as a fingerprint) for the first molecule

bitset2 - A bitset (such as a fingerprint) for the second molecule

Returns:

The Tanimoto coefficient

Throws:

CDKException - if bitsets are not of the same length

calculate

@TestMethod(value="testTanimoto3")
public static float calculate(double[] features1,
                              double[] features2)
                       throws CDKException

Evaluates the continuous Tanimoto coefficient for two real valued vectors.

Parameters:

features1 - The first feature vector

features2 - The second feature vector

Returns:

The continuous Tanimoto coefficient

Throws:

CDKException - if the features are not of the same length