org.pistoiaalliance.helm.HELMSimilarityLibrary

Class Similarity

java.lang.Object

org.pistoiaalliance.helm.HELMSimilarityLibrary.Similarity

public class Similarity
extends Object

Similarity class calculates the Tanimoto value of two hashed bitstring fingerprints.

Author:

bueltel

Constructor Summary

Constructors

Constructor and Description
Similarity()

Method Summary

Modifier and Type	Method and Description
static double	calculateSimilarity(BitSet helmBitFingerprintI, BitSet helmBitFingerprintJ) Method calculates the similarity (tanimoto coefficient) of two bitset fingerprints.
static double	calculateSimilarity(org.helm.notation2.parser.notation.HELM2Notation notation1, org.helm.notation2.parser.notation.HELM2Notation notation2) Method calculates the similarity (tanimoto coefficient) of two HELM notations
static double	calculateSimilarityNatAnalogs(org.helm.notation2.parser.notation.HELM2Notation notation1, org.helm.notation2.parser.notation.HELM2Notation notation2) Method calculates the similarity (tanimoto coefficient) of two HELM notations and takes the natural analogs of modified monomers into account.

Methods inherited from class java.lang.Object

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

Constructor Detail

Similarity

public Similarity()

Method Detail

calculateSimilarity

public static double calculateSimilarity(org.helm.notation2.parser.notation.HELM2Notation notation1,
                                         org.helm.notation2.parser.notation.HELM2Notation notation2)
                                  throws Exception

Method calculates the similarity (tanimoto coefficient) of two HELM notations

Parameters:

notation1 - the first HELM notation

notation2 - the second HELM notation

Returns:

double tanimoto coefficient

Throws:

Exception - if anything goes wrong

calculateSimilarityNatAnalogs

public static double calculateSimilarityNatAnalogs(org.helm.notation2.parser.notation.HELM2Notation notation1,
                                                   org.helm.notation2.parser.notation.HELM2Notation notation2)
                                            throws Exception

Method calculates the similarity (tanimoto coefficient) of two HELM notations and takes the natural analogs of modified monomers into account.

Parameters:

notation1 - the first HELM notation

notation2 - the second HELM notation

Returns:

double tanimoto coefficient

Throws:

Exception - if anything goes wrong

calculateSimilarity

public static double calculateSimilarity(BitSet helmBitFingerprintI,
                                         BitSet helmBitFingerprintJ)

Method calculates the similarity (tanimoto coefficient) of two bitset fingerprints.

Parameters:

helmBitFingerprintI - the first bit set fingerprint

helmBitFingerprintJ - the second bit set fingerprint

Returns:

double tanimoto coefficient