com.chemaxon.descriptors.fingerprints.maccs

Interface MaccsGenerator

All Superinterfaces:

BinaryVectorMetricFactory<MaccsComparator>, DescriptorGenerator<BinaryVectorDescriptor>, DescriptorSerializer<BinaryVectorDescriptor>, Guarded, MetricFactory<MaccsComparator>, Serializable

public interface MaccsGenerator
extends DescriptorGenerator<BinaryVectorDescriptor>, BinaryVectorMetricFactory<MaccsComparator>

Interface to define the MACCS fingerprint generator

Nested Class Summary

Nested classes/interfaces inherited from interface com.chemaxon.descriptors.common.Guarded

Guarded.EnsureThat, Guarded.New

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

BinaryVectorMetricFactory.ToLinenote<C>

Method Summary

Modifier and Type	Method and Description
BinaryLongComparisonContextFactory	comparisonContextFactory() Get an unguarded context factory.
Maccs	generateDescriptor(Molecule m) Calculates the associated descriptor for the given Molecule.
MaccsComparator	getBinaryMetricsComparator(BinaryMetrics metrics) Deprecated. Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
MaccsComparator	getDefaultComparator() Deprecated.
MaccsParameters	getParameters() Gets the parameter object.
MaccsComparator	getTverskyComparator(double coeffQuery, double coeffTarget) Deprecated. Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
MaccsComparator	getTverskyComparator(TverskyParameters tverskyParamaters) Deprecated. Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)

Methods inherited from interface com.chemaxon.descriptors.common.DescriptorGenerator

defaultComparison, getBareDescriptor

Methods inherited from interface com.chemaxon.descriptors.common.DescriptorSerializer

fromByteArray, fromString, serializerIsEqualWith, toByteArray, toString

Methods inherited from interface com.chemaxon.descriptors.common.Guarded

getGuardObject

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

forBinaryMetrics, forTversky, forTverskyCoefficients

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

comparisonLinenote, defaultComparison

Method Detail

getDefaultComparator

@Deprecated
MaccsComparator getDefaultComparator()

Deprecated.

Description copied from interface: DescriptorGenerator

Gets the default comparator object.

Specified by:

getDefaultComparator in interface DescriptorGenerator<BinaryVectorDescriptor>

Returns:

default comparator

getBinaryMetricsComparator

@Deprecated
MaccsComparator getBinaryMetricsComparator(BinaryMetrics metrics)

Deprecated. Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)

Creates a new Comparator instance according to the given binary metric parameters.

Parameters:

metrics - the binary metric for the output comparator

Returns:

the comparator

getTverskyComparator

@Deprecated
MaccsComparator getTverskyComparator(TverskyParameters tverskyParamaters)

Deprecated. Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)

Creates a new Comparator instance according to the given Tversky metric parameters.

Parameters:

tverskyParamaters - the Tversky metric parameters

Returns:

the comparator

getTverskyComparator

@Deprecated
MaccsComparator getTverskyComparator(double coeffQuery,
                                                 double coeffTarget)

Deprecated. Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)

Creates a new Comparator instance according to the given Tversky metric parameters.

Parameters:

coeffQuery - Query side coefficient

coeffTarget - Target side coefficient

Returns:

a comparator object

comparisonContextFactory

BinaryLongComparisonContextFactory comparisonContextFactory()

Description copied from interface: DescriptorGenerator

Get an unguarded context factory. Implementations are supposed to provide space/processing efficient unguarded representation if applicable. Otherwise it is possible to expose byte [] serialization based unguarded representation.

Implementations are expected to provide additional factory methods for unguarded and plain descriptor comparators for implemented metrics.

Specified by:

comparisonContextFactory in interface DescriptorGenerator<BinaryVectorDescriptor>

Returns:

an unguarded context factory

generateDescriptor

Maccs generateDescriptor(Molecule m)

Description copied from interface: DescriptorGenerator

Calculates the associated descriptor for the given Molecule.

Note that different descriptors/application scenarios might need different structure standardization. Currently structure standardization is generally not in the scope of the responsibilities of DescriptorGenerator to the possible maximal extent.

Since the returned descriptor might contain additional data (reference to input Molecule, etc) if it is stored for later comparison it is recommended to use the bare-only representation returned by DescriptorGenerator.getBareDescriptor(com.chemaxon.descriptors.common.Descriptor).

Specified by:

generateDescriptor in interface DescriptorGenerator<BinaryVectorDescriptor>

Parameters:

m - Input molecule

Returns:

The calculated descriptor. If the implementation discriminates between rich and bare types then the rich type is returned, otherwise the bare type. Note that the bare type is always available using DescriptorGenerator.getBareDescriptor(com.chemaxon.descriptors.common.Descriptor) on either the rich or the bare representation.

getParameters

MaccsParameters getParameters()

Description copied from interface: DescriptorGenerator

Gets the parameter object.

Specified by:

getParameters in interface DescriptorGenerator<BinaryVectorDescriptor>

Returns:

paramater obj