chemaxon.descriptors

Class SimilarityCalculatorFactory

java.lang.Object

chemaxon.descriptors.SimilarityCalculatorFactory

@PublicAPI
public class SimilarityCalculatorFactory
extends java.lang.Object

This factory creates a similarity calculator object according to the user defined parameters. A series of fingerprint similarity calculation can be performed with the user defined metrics of this object after defining the query structure.

Example Usage:
 SimilarityCalculator sc = SimilarityCalculatorFactory.create("TVERSKY;0.33;0.99");
 The filed separator ";" is used as defined in SimilarityCalculatorFactory.SEPARATOR.
 int[] query = precalculated fingerprint; bitstring represented as int array.
 sc.setQueryFingerprint(query);

 // here can be a loop that iterates on target fingerprints
 int[] target = precalculated fingerprint; bitstring represented as int array.
 float similarity = sc.getSimilarity(target);
 float disssimilarity = sc.getDissimilarity(target);
 // target loop ends
 

Since:

JChem 5.2.2.

Author:

Adrian Kalaszi

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SimilarityCalculatorFactory.Representation

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	SEPARATOR This character is used to separate fields of the parameter string.

Method Summary

Modifier and Type	Method and Description
static SimilarityCalculator<int[]>	create(java.lang.String params) Creates a similarity calculator object according to the user defined parameters.
static SimilarityCalculator<int[]>	create(java.lang.String params, int from, int to) Creates a similarity calculator object according to the user defined parameters.
static java.text.NumberFormat	getNumberFormat()
static float	parse(java.lang.String number)

Methods inherited from class java.lang.Object

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

Field Detail

SEPARATOR

public static java.lang.String SEPARATOR

This character is used to separate fields of the parameter string.

Method Detail

create

public static SimilarityCalculator<int[]> create(java.lang.String params)
                                          throws java.text.ParseException

Creates a similarity calculator object according to the user defined parameters. The query fingerprint can be set using the setQueryFingerprint method of the returned object.

Parameters:

params - Define similarity function type and its possible parameters. There is a brief and a detailed notation. Use only one of them at the same time. The fields are separated with ";" by default but this SEPARATOR can be changed. Everything is case insensitive.

 Brief: (sequence sensitive)
 - At first position there must the metrics name stand:
    TANIMOTO, TVERSKY, DICE, EUCLIDEAN, NORMALIZED_EUCLIDEAN, SUBSTRUCTURE, SUPERSTRUCTURE, DEFAULT
    the default metrics type is now Tanimoto.
 - At the third and fourth position the alpha parameter for query and beta for target is expeceted
   if Tversky index is selected.If not given, default parameter values are 1-1 resulting in TANIMOTO metric.
 -e.g.: TVERSKY;0.33;0.99 or DICE
 Detailed: (sequence insensitive)
 - Metrics name is given using the the prefix: "metrics=" (without quotation mark)
    TANIMOTO, TVERSKY, DICE, EUCLIDEAN, NORMALIZED_EUCLIDEAN, SUBSTRUCTURE, SUPERSTRUCTURE
 - to set Tversky weight for query use tverskyWeightForQuery=
 - to set Tversky weight for target use tverskyWeightForTarget=
   If the weight was not given, the default "1" is used.
 -e.g. metrics=TVERSKY;tverskyWeightForQuery=0.33;tverskyWeightForTarget=0.99
 

Returns:

SimilarityCalculator that is paramtrized according to the given metrics.

Throws:

java.text.ParseException - if input string error

create

public static SimilarityCalculator<int[]> create(java.lang.String params,
                                                 int from,
                                                 int to)
                                          throws java.text.ParseException

Creates a similarity calculator object according to the user defined parameters. The query fingerprint can be set at using the setQueryFingerprint method of the returning object.

Parameters:

params - Defines similarity function type and its possible parameters. See: create( String params )

from - The starting position from which the integer array is examined (inclusive)

to - The ending position to which the integer array is examined (exclusive)

Returns:

SimilarityCalculator that is paramtrized according to the given metrics.

Throws:

java.text.ParseException - if input string error

parse

public static float parse(java.lang.String number)
                   throws java.text.ParseException

Throws:

java.text.ParseException

getNumberFormat

public static java.text.NumberFormat getNumberFormat()