com.chemaxon.descriptors.metrics

Enum BinaryMetrics

java.lang.Object

java.lang.Enum<BinaryMetrics>

com.chemaxon.descriptors.metrics.BinaryMetrics

All Implemented Interfaces:

BinaryVectorComparator, MetricMetadata, java.io.Serializable, java.lang.Comparable<BinaryMetrics>

@Beta
 @PublicAPI
public enum BinaryMetrics
extends java.lang.Enum<BinaryMetrics>
implements BinaryVectorComparator

Simple metrics suitable for finite length binary vectors.

Please note that this enum is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.

Author:

Gabor Imre

Nested Class Summary

Nested classes/interfaces inherited from interface com.chemaxon.descriptors.metrics.BinaryVectorComparator

BinaryVectorComparator.Util

Enum Constant Summary

Enum Constants

Enum Constant and Description
BINARY_COMMONPART Commonly set bits.
BINARY_COMMONPART_NORMALIZED Common set bit ratio.
BINARY_DICE Dice's similarity measure.
BINARY_EUCLIDEAN Euclidean distance.
BINARY_EUCLIDEAN_NORMALIZED Normalized Euclidean distance.
BINARY_TANIMOTO Tanimoto coefficient.
MANHATTAN Manhattan distance.
MANHATTAN_NORMALIZED Normalized Manhattan metric.
PETKE Petke or Braun-Blanquet similarity.
SIMPSON Simpson similarity.

Method Summary

Modifier and Type	Method and Description
static BinaryMetrics	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static BinaryMetrics[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.chemaxon.descriptors.metrics.BinaryVectorComparator

calculateBinaryVectorDissimilarity, calculateBinaryVectorSimilarity, getLowerBoundForBinaryVectors, getUnguardedDissimilarityCalculator, getUpperBoundForBinaryVectors

Methods inherited from interface com.chemaxon.descriptors.metrics.MetricMetadata

isDissimilarityZeroIFFEquals, isMetricSpace, isNonNegative, isSymmetric, isTriangeInequalityHolds

Enum Constant Detail

MANHATTAN

public static final BinaryMetrics MANHATTAN

Manhattan distance.

Binary positions with different values.

See Also:

http://en.wikipedia.org/wiki/Taxicab_geometry

MANHATTAN_NORMALIZED

public static final BinaryMetrics MANHATTAN_NORMALIZED

Normalized Manhattan metric.

The similarity/dissimilarity values range of the MANHATTAN normalized to the unit interval (0.0 - 1.0, including bounds).

BINARY_EUCLIDEAN

public static final BinaryMetrics BINARY_EUCLIDEAN

Euclidean distance.

Square root of the sums of the difference squares.

See Also:

http://en.wikipedia.org/wiki/Euclidean_distance

BINARY_EUCLIDEAN_NORMALIZED

public static final BinaryMetrics BINARY_EUCLIDEAN_NORMALIZED

Normalized Euclidean distance.

The similarity/dissimilarity values range of the BINARY_EUCLIDEAN normalized to the unit interval (0.0 - 1.0, including bounds).

BINARY_COMMONPART

public static final BinaryMetrics BINARY_COMMONPART

Commonly set bits.

The count of bit positions which contains set bits is considered as the similarity value. Please note that this comparison yields non-zero and non-maximal dissimilarity for equal, non-empty descriptors.

BINARY_COMMONPART_NORMALIZED

public static final BinaryMetrics BINARY_COMMONPART_NORMALIZED

Common set bit ratio.

The similarity/dissimilarity values range of the BINARY_COMMONPART normalized to the unit interval (0.0 - 1.0, including bounds).

BINARY_DICE

public static final BinaryMetrics BINARY_DICE

Dice's similarity measure.

Similarity coefficient is twice the common part divided by the sum of components.

When comparing all-zero binary fingerprint we return minimal similarity/maximal dissimilarity.

See Also:

http://en.wikipedia.org/wiki/Dice%27s_coefficient

BINARY_TANIMOTO

public static final BinaryMetrics BINARY_TANIMOTO

Tanimoto coefficient.

When comparing all-zero binary fingerprint we return minimal similarity/maximal dissimilarity in the current implementation.

Please note that the triangle inequality holds for the Tanimoto distance; see Lipkus, AlanH.: A proof of the triangle inequality for the Tanimoto distance (Journal of Mathematical Chemistry, 1999, volume 26, pages 263-265)

See Also:

http://en.wikipedia.org/wiki/Jaccard_index

PETKE

public static final BinaryMetrics PETKE

Petke or Braun-Blanquet similarity.

Similarity is calculated by |Q & T| / max(|Q|, |T|).

When comparing all-zero binary fingerprint we return minimal similarity/maximal dissimilarity in the current implementation.

See Also:

"Sastry et al., J. Chem. Inf. Model. 2010, 50, 771-784", "ISBN 978-3-662-44342-2, page 332."

SIMPSON

public static final BinaryMetrics SIMPSON

Simpson similarity.

Similarity is calculated by |Q & T| / min(|Q|, |T|).

When comparing all-zero binary fingerprint we return minimal similarity/maximal dissimilarity in the current implementation.

See Also:

"ISBN 978-3-662-44342-2, page 332."

Method Detail

values

public static BinaryMetrics[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (BinaryMetrics c : BinaryMetrics.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static BinaryMetrics valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null