com.chemaxon.descriptors.fingerprints.ecfp

Interface EcfpGenerator

All Superinterfaces:

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

@Beta
 @PublicAPI
public interface EcfpGenerator
extends DescriptorGenerator<BinaryVectorDescriptor>, BinaryVectorMetricFactory<EcfpComparator>

Calculates ECFP (fixed length folded binary vector representation) descriptors.

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

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.
Ecfp	generateDescriptor(Molecule m) Calculates the associated descriptor for the given Molecule.
EcfpComparator	getBinaryMetricsComparator(BinaryMetrics metrics) Deprecated. Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
EcfpComparator	getDefaultComparator() Deprecated.
EcfpParameters	getParameters() Gets the parameter object.
EcfpComparator	getTverskyComparator(double coeffQuery, double coeffTarget) Deprecated. Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
EcfpComparator	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
EcfpComparator getDefaultComparator()

Deprecated.

Description copied from interface: DescriptorGenerator

Gets the default comparator object.

Specified by:

getDefaultComparator in interface DescriptorGenerator<BinaryVectorDescriptor>

Returns:

default comparator

getBinaryMetricsComparator

@Deprecated
EcfpComparator getBinaryMetricsComparator(BinaryMetrics metrics)

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

Creates a new Comparator instance according to the given metric.

Parameters:

metrics - binary metric

Returns:

a comparator object

getTverskyComparator

@Deprecated
EcfpComparator 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 - parameters for the comparator

Returns:

a comparator object

getTverskyComparator

@Deprecated
EcfpComparator 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

Ecfp 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

EcfpParameters getParameters()

Description copied from interface: DescriptorGenerator

Gets the parameter object.

Specified by:

getParameters in interface DescriptorGenerator<BinaryVectorDescriptor>

Returns:

paramater obj