com.chemaxon.descriptors.fingerprints.pf2d

Interface PfGenerator

All Superinterfaces:

DescriptorGenerator<FloatVectorDescriptor>, DescriptorSerializer<FloatVectorDescriptor>, FloatVectorMetricFactory<PfComparator>, Guarded, MetricFactory<PfComparator>, Serializable

@PublicAPI
public interface PfGenerator
extends DescriptorGenerator<FloatVectorDescriptor>, FloatVectorMetricFactory<PfComparator>

Generates 2D pharmacophore fingerprints.

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.FloatVectorMetricFactory

FloatVectorMetricFactory.ToLinenote<C>

Method Summary

Modifier and Type	Method and Description
FloatVectorComparisonContextFactory	comparisonContextFactory() Get an unguarded context factory.
PharmacophoreFP	generateDescriptor(Molecule m) Calculates the associated descriptor for the given Molecule.
PfComparator	getDefaultComparator() Deprecated.
PfComparator	getFloatVectorComparator(FloatVectorMetrics metrics) Deprecated. Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)
PfParameters	getParameters() Gets the parameter object.

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.FloatVectorMetricFactory

forFloatMetrics, forTversky, forTverskyCoefficients

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

comparisonLinenote, defaultComparison

Method Detail

getDefaultComparator

@Deprecated
PfComparator getDefaultComparator()

Deprecated.

Description copied from interface: DescriptorGenerator

Gets the default comparator object.

Specified by:

getDefaultComparator in interface DescriptorGenerator<FloatVectorDescriptor>

Returns:

default comparator

getFloatVectorComparator

@Deprecated
PfComparator getFloatVectorComparator(FloatVectorMetrics metrics)

Deprecated. Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)

Creates a new comparator instance according to the given metric.

Parameters:

metrics - float vector metric

Returns:

a comparator object

comparisonContextFactory

FloatVectorComparisonContextFactory 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<FloatVectorDescriptor>

Returns:

an unguarded context factory

generateDescriptor

PharmacophoreFP 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<FloatVectorDescriptor>

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

PfParameters getParameters()

Description copied from interface: DescriptorGenerator

Gets the parameter object.

Specified by:

getParameters in interface DescriptorGenerator<FloatVectorDescriptor>

Returns:

paramater obj