jklustor-all-api-0.0.7-20140619012755 (ChemAxon)

A B C D E F G H I L M N P R S T U V W X

A

AbstractShapeComparator<T extends ShapeDescriptor> - Class in com.chemaxon.descriptors.alignment
 
AbstractShapeComparator(DescriptorGenerator<T>) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
AbstractShapeGenerator<D extends ShapeDescriptor,P extends AbstractShapeGeneratorParameter> - Class in com.chemaxon.descriptors.alignment
 
AbstractShapeGenerator(P) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
AbstractShapeGeneratorParameter - Class in com.chemaxon.descriptors.alignment
Helper class without the requested getDescriptorGenerator method.
AbstractShapeGeneratorParameter(AtomTyping) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
 
adaptiveSPHEX(int, int, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
Sphere exclusion clustering with sphere radius inference.
addChildCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Add a cluster to another cluster as a child cluster.
addDataPoint(double, double) - Method in class com.chemaxon.clustering.util.Util.StringScatterPlot
Add new point to put.
addMolecule(Molecule) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add a new structure.
addMolecules(Collection<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add multiple structures.
addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Allocate a new cluster.
addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Allocate a new cluster.
addPropertyChangeListener(PropertyChangeListener) - Method in interface com.chemaxon.calculations.common.CancelObserver
Add a listener for cancellation.
addPropertyChangeListener(PropertyChangeListener) - Method in class com.chemaxon.calculations.common.ProgressObservers.CancelObserverImpl
 
addStructuresToCluster(Collection<Integer>, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Add multiple structures to a cluster.
addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Set a structure to be a part of a cluster as a leaf.
addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Add a structure to a cluster as an immediate leaf.
appendLongAsBinaryString(StringBuilder, long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Convert 64 bit long to binary string.
AtomTyping - Enum in com.chemaxon.descriptors.alignment
Settings for shape associated atom typing.
atomTypizer(EcfpAtomTypizers) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Set atom typizer to use.

B

BaseShapeComparatorParameter - Class in com.chemaxon.descriptors.alignment
 
BaseShapeComparatorParameter(FlexibilityMode, ShapeFunction, Optional<Integer>) - Constructor for class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
BinaryMetrics - Enum in com.chemaxon.descriptors.metrics
Simple metrics suitable for finite length binary vectors.
BinaryVectorComparator - Interface in com.chemaxon.descriptors.metrics
Basic functionality for finite binary vector based calculations.
BinaryVectorComparator.Util - Class in com.chemaxon.descriptors.metrics
Simple consistency check utility.
BinaryVectorComparator.Util() - Constructor for class com.chemaxon.descriptors.metrics.BinaryVectorComparator.Util
 
BinaryVectorDescriptor - Interface in com.chemaxon.descriptors.common
BinaryVectorDescriptor is a Descriptor which holds a fixed length binary fingerprint.
BinaryVectors - Class in com.chemaxon.descriptors.common
Utility methods related to bit string descriptors.
BinaryVectors.Endianness - Enum in com.chemaxon.descriptors.common
Order of components in packed representations.
bitsPerPattern(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Set bits per pattern.
bondCount(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Set bond count to consider.
build() - Method in interface com.chemaxon.apidiscovery.interfaces.ParameterBuilder
Constructs an immutable instance of T.
build(IDBasedHierarchy) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder
Build the assigner.
build() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Build immutable clustering representation.
build(IDBasedAssignerBuilder) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Build an immutable snapshot of the clustering.
build() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Build the immutable clustering representation.
build(DescriptorGenerator<D>, DescriptorComparator<D>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Build immutable input descriptor.
build() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Build immutable parameter object.
build() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
 
BuilderClass - Annotation Type in com.chemaxon.apidiscovery.annotations
This annotation gives information about the associated ParameterBuilder for this class.
BvGenerator - Interface in com.chemaxon.descriptors.vectors.binary
Generator for generic binary vector descriptors.
BvParameters - Class in com.chemaxon.descriptors.vectors.binary
Parameters for generic binary vector descriptor.
BvParameters(BvParameters.Builder) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters
Constructor based on a builder.
BvParameters() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters
Construct with default values.
BvParameters.Builder - Class in com.chemaxon.descriptors.vectors.binary
Builder for BvParameters.
BvParameters.Builder() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Constructor with default settings.
BvParameters.Builder(BvParameters) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Construct to represent the state of a parameter object instance.
BvParameters.ConstructBvGenerator - Interface in com.chemaxon.descriptors.vectors.binary
Interface representing BvGenerator implementation constructor
BvParameters.StringFormat - Enum in com.chemaxon.descriptors.vectors.binary
Fingerprint textual representation.
BYTES_IN_INT - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
Number of bytes in an int.
BYTES_IN_LONG - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
Number of bytes in a long.

C

calculateBinaryVectorDissimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
Calculate represented dissimilarity score from binary vector parameters.
calculateBinaryVectorDissimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
calculateBinaryVectorSimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
Calculate represented similarity score from binary vector parameters.
calculateBinaryVectorSimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
calculateDarkness() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
Calculate the darkness of this fingerprint.
calculateDissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateDissimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateDissimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors.
calculateDissimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors in serialized form.
calculateFloatVectorDissimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Calculate dissimilarity.
calculateFloatVectorSimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Calculate similarity.
calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateSimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateSimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors.
calculateSimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors in serialized form.
cancel() - Method in class com.chemaxon.calculations.common.ProgressObservers.CancelObserverImpl
Sign cancelling.
CancelObserver - Interface in com.chemaxon.calculations.common
Callback to propagate cancel requests into long running tasks.
canHandle(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory
Returns true if this factory can handle the given xml.
Cfp - Interface in com.chemaxon.descriptors.fingerprints.cfp
Folded fixed length bit string representation of the CFP descriptor.
CfpComparator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Comparator for Cfp descriptor representation.
CfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Calculates CFP (fixed length folded binary verctor representation) descriptors.
CfpParameters - Class in com.chemaxon.descriptors.fingerprints.cfp
CFP parameters class.
CfpParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Constructor using the default settings.
CfpParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.cfp
Builder class for the immutable parameter object.
CfpParameters.Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Constructor with default settings.
CfpParameters.Builder(CfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Constructor based on a parameter object.
CfpParameters.ConstructCfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Interface representing CFP generator constructor.
CfpTableReader - Class in com.chemaxon.descriptors.fingerprints.cfp
MDTable reader for CFP.
CfpTableReader() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
 
CfpTableReader.Factory - Interface in com.chemaxon.descriptors.fingerprints.cfp
Factory class.
checkBitCounts(int, int, int, int) - Static method in class com.chemaxon.descriptors.metrics.BinaryVectorComparator.Util
Check that descriptor comparison parameters are consistent.
checkVectors(float[], float[]) - Static method in class com.chemaxon.descriptors.metrics.FloatVectorComparator.Util
Ensure that compared vectors are not null, empty and matches.
Cluster<T> - Interface in com.chemaxon.clustering.common
Cluster represents a group of structures.
cluster(DissimilarityInput, LanceWilliamsMerge, ProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
Invoke clustering.
clusterLevel(IDBasedHierarchicCluster) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder.IDBAssignerImpl
 
clusterLevel(T) - Method in interface com.chemaxon.clustering.common.LevelAssigner
Level associated to a hierarchic cluster.
clusterOf(T) - Method in interface com.chemaxon.clustering.common.HierarchicClustering
Identify the lowest level cluster containing the given item.
clusterOf(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Look up immediate parent of a structure present in the clustering.
clusterOf(Integer) - Method in interface com.chemaxon.clustering.common.IDBasedHierarchy
Identify the lowest level cluster containing the given item.
clusterOf(T) - Method in interface com.chemaxon.clustering.common.SingleLevelClustering
Identify the cluster containing the given item.
clusters() - Method in interface com.chemaxon.clustering.common.HierarchicCluster
Access further grouping of the represented elements.
clusters() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicCluster
 
clusters() - Method in interface com.chemaxon.clustering.common.SingleLevelClustering
Represented cluster.
coeffQuery(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Set query coefficient.
coeffTarget(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Set target coefficient.
com.chemaxon.apidiscovery - package com.chemaxon.apidiscovery
API Discovery framework.
com.chemaxon.apidiscovery.annotations - package com.chemaxon.apidiscovery.annotations
Annotations used by the API Discovery framework.
com.chemaxon.apidiscovery.interfaces - package com.chemaxon.apidiscovery.interfaces
Interfaces introduced for the API Discovery framework.
com.chemaxon.apidiscovery.util - package com.chemaxon.apidiscovery.util
Various utilities.
com.chemaxon.calculations.common - package com.chemaxon.calculations.common
Common components of Calculator APIs.
com.chemaxon.clustering.common - package com.chemaxon.clustering.common
Common components of clustering related APIs.
com.chemaxon.clustering.singlelinkage - package com.chemaxon.clustering.singlelinkage
Single linkage clustering algorithm.
com.chemaxon.clustering.sphex - package com.chemaxon.clustering.sphex
Sphere exclusion clustering algorithm.
com.chemaxon.clustering.util - package com.chemaxon.clustering.util
Clustering related utilities.
com.chemaxon.clustering.wards - package com.chemaxon.clustering.wards
Ward's minimum variance implemented as a generic agglomerative hierarchical clustering algorithm.
com.chemaxon.descriptors.alignment - package com.chemaxon.descriptors.alignment
3D flexible alignment based molecular shape similarity calculation.
com.chemaxon.descriptors.common - package com.chemaxon.descriptors.common
Base interfaces for Descriptors API.
com.chemaxon.descriptors.db - package com.chemaxon.descriptors.db
Interfaces for database import/export.
com.chemaxon.descriptors.fingerprints.cfp - package com.chemaxon.descriptors.fingerprints.cfp
API of the Chemaxon hashed fingerprint family molecular descriptors.
com.chemaxon.descriptors.fingerprints.ecfp - package com.chemaxon.descriptors.fingerprints.ecfp
API of the ECFP fingerprint family molecular descriptors.
com.chemaxon.descriptors.fingerprints.pf2d - package com.chemaxon.descriptors.fingerprints.pf2d
API of the 2D pharmacophore fingerprint family molecular descriptors.
com.chemaxon.descriptors.metrics - package com.chemaxon.descriptors.metrics
Common descriptor comparison metrics.
com.chemaxon.descriptors.vectors - package com.chemaxon.descriptors.vectors
Generic vector descriptors.
com.chemaxon.descriptors.vectors.binary - package com.chemaxon.descriptors.vectors.binary
Generic binary vector descriptors.
com.chemaxon.descriptors.vectors.floats - package com.chemaxon.descriptors.vectors.floats
Generic floating point vector descriptors.
compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
compare(T, T) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
 
compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
 
compare(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors.
compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Compare two descriptors in serialized form.
ComparisonResult - Interface in com.chemaxon.descriptors.common
Result of a descriptor comparison.
constructBvGenerator(BvParameters) - Method in interface com.chemaxon.descriptors.vectors.binary.BvParameters.ConstructBvGenerator
Construct new instance
constructCfpGenerator(CfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.ConstructCfpGenerator
Constructor invocation.
constructEcfpGenerator(EcfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.ConstructEcfpGenerator
Constructor invocation.
constructFvGenerator(FvParameters) - Method in interface com.chemaxon.descriptors.vectors.floats.FvParameters.ConstructFvGenerator
Construct new instance
constructPfGenerator(PfParameters) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.ConstructPfGenerator
Constructor invocation.
countNumberOfClusters(HierarchicClustering<?, ? extends HierarchicCluster<?>>) - Static method in class com.chemaxon.clustering.util.Util
Count the number of clusters in a clustering.
create() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
Invoke creator method.
createForgivingNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a forgiving observer which wont enforce API contracts.
createForgivingNullObserver(ProgressObservers.PollingCanceller) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a forgiving cancellable observer which wont enforce API contracts.
createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.binary.BvParameters
Construct a builder for this parameter class, initialized to default.
createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Construct a builder for this parameter class, initialized to default.
createNewReader(String) - Static method in class com.chemaxon.descriptors.db.MDTableReader
Create an MDTableReader from the xml configuration string.
createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
Create a PfTableReader from the xml configuration string.
createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader
Create a PfTableReader from the xml configuration string.
createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
Create a PfTableReader from the xml configuration string.
createNoCancelObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a cancel observer which wont cancel execution.
createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a SubProgressObserver which ignores observed data.
createReader(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory
Generates reader object.
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader.Factory
 
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader.Factory
 
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader.Factory
 
createUnitPathAssigner(IDBasedHierarchy) - Static method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder
Utility method to build a path length assigner based on a hierarchy.
Creator - Annotation Type in com.chemaxon.apidiscovery.annotations
Creator methods produce instances of specific classes.
CreatorWrapper<T> - Class in com.chemaxon.apidiscovery
CreatorWrapper acts as a type- and instance -dependent service loader.
CreatorWrapper(Object, Method, Object) - Constructor for class com.chemaxon.apidiscovery.CreatorWrapper
Construct a wrapper.

D

DEFAULT_BITS_TO_SET_FOR_PATTERNS - Static variable in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
The number of bits used to code each pattern in the hashed binary vector representation.
DEFAULT_CFP_LENGTH - Static variable in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Default length (bit count) for CFP - folded binary fingerprint representation.
DEFAULT_CFP_MAX_PATTERN_LENGTH - Static variable in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
The maximum length of consecutive bonds in the linear paths that are considered during the fragmentation of the molecule.
DEFAULT_CONFCOUNT - Static variable in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
DEFAULT_ECFP_ATOMTYPIZER - Static variable in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Default ECFP atom typizer to use.
DEFAULT_ECFP_DIAMETER - Static variable in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Default diameter to use.
DEFAULT_ECFP_LENGTH - Static variable in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Default length (bit count) for ECFP - folded binary fingerprint representation.
DEFAULT_ENDIANNESS - Static variable in class com.chemaxon.descriptors.vectors.binary.BvParameters
Default endianness of packing operations.
DEFAULT_FLEXIBILITY_MODE - Static variable in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
DEFAULT_LENGTH - Static variable in class com.chemaxon.descriptors.vectors.binary.BvParameters
Default length (bit count).
DEFAULT_LENGTH - Static variable in class com.chemaxon.descriptors.vectors.floats.FvParameters
Default length (dimensions).
DEFAULT_NUMERIC_REPRESENTATION - Static variable in class com.chemaxon.descriptors.vectors.floats.FvParameters
Default numeric representation.
DEFAULT_SCALED_MAX - Static variable in class com.chemaxon.descriptors.vectors.floats.FvParameters
Default max value for scaling.
DEFAULT_SCALED_MIN - Static variable in class com.chemaxon.descriptors.vectors.floats.FvParameters
Default min value for scaling.
DEFAULT_SHAPE_FUNCTION - Static variable in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
DEFAULT_SPARSE_COMPRESSION - Static variable in class com.chemaxon.descriptors.vectors.floats.FvParameters
Default compression.
DEFAULT_STRING_FORMAT - Static variable in class com.chemaxon.descriptors.vectors.binary.BvParameters
Default String format.
Description - Annotation Type in com.chemaxon.apidiscovery.annotations
The annotated element has a description contained in this annotation.
Descriptor - Interface in com.chemaxon.descriptors.common
Descriptor represents a molecular descriptor calculated by a specific DescriptorGenerator instance for a specific structure.
DescriptorComparator<D extends Descriptor> - Interface in com.chemaxon.descriptors.common
Common functionality for descriptor comparison.
DescriptorGenerator<B extends Descriptor> - Interface in com.chemaxon.descriptors.common
DescriptorGenerator implements molecule to descriptor calculation functionality.
DescriptorParameters - Interface in com.chemaxon.descriptors.common
Descriptor calculator parameters base interface.
detachToRootCluster(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Remove a cluster from its current parent cluster.
diameter(int) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Sets diameter.
dijk(int, int, int, double, double, double) - Method in interface com.chemaxon.clustering.wards.LanceWilliamsMerge
Returns the distance of cluster k and the cluster resulted from merging cluster i and j.
dijk(int, int, int, double, double, double) - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage
 
dijk(int, int, int, double, double, double) - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage
 
dijk(int, int, int, double, double, double) - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.SingleLinkage
 
dijk(int, int, int, double, double, double) - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.Wards
 
Discovery - Class in com.chemaxon.apidiscovery
Utility methods for parameter discovery.
dissimilarity(int, int) - Method in interface com.chemaxon.clustering.common.DissimilarityInput
Dissimilarity/distance between an ordered pair of input items.
dissimilarity(int, int) - Method in class com.chemaxon.clustering.common.MolInput
 
DissimilarityInput - Interface in com.chemaxon.clustering.common
DissimilarityInput represents an input set for similarity based clustering algorithm.
done() - Method in interface com.chemaxon.calculations.common.SubProgressObserver
Notifies that the represented task is finished and no further work will be done.
DRShapeDescriptor - Interface in com.chemaxon.descriptors.alignment
Descriptor (serialized data) for the Distance range assisted shape alignment comparison.
DRShapeMetrics - Enum in com.chemaxon.descriptors.alignment
Metrics for distance range assisted shape comparison.

E

Ecfc - Interface in com.chemaxon.descriptors.fingerprints.ecfp
List of identifiers occurrence counts representation of XCFX descriptor family.
Ecfl - Interface in com.chemaxon.descriptors.fingerprints.ecfp
List of unique identifiers representation of XCFC descriptor family.
Ecfp - Interface in com.chemaxon.descriptors.fingerprints.ecfp
Folded fixed length bit string representation of the ECFP descriptor family.
EcfpAtomTypizers - Enum in com.chemaxon.descriptors.fingerprints.ecfp
Predefined atom typing settings for ECFP fingerprint family.
EcfpComparator - Interface in com.chemaxon.descriptors.fingerprints.ecfp
Comparator for Ecfp descriptor representation.
EcfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.ecfp
Calculates ECFP (fixed length folded binary vector representation) descriptors.
EcfpParameters - Class in com.chemaxon.descriptors.fingerprints.ecfp
ECFP parameters class.
EcfpParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Constructor using the default settings.
EcfpParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.ecfp
Builder class for the immutable parameter object.
EcfpParameters.Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Constructor with default settings.
EcfpParameters.Builder(EcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Constructor based on a parameter object.
EcfpParameters.ConstructEcfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.ecfp
Interface representing ECFP generator constructor.
EcfpTableReader - Class in com.chemaxon.descriptors.fingerprints.ecfp
MDTable reader for ECFP/FCFP.
EcfpTableReader() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader
 
EcfpTableReader.Factory - Interface in com.chemaxon.descriptors.fingerprints.ecfp
Factory class.
endianness(BinaryVectors.Endianness) - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Set endianness of packing operations.
ensureBinaryString(String, int) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Ensure that a String contains a valid binary representation.
equals(Object) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
equals(Object) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
 

F

FIRED_PROPERTY_NAME - Static variable in interface com.chemaxon.calculations.common.CancelObserver
Name of property stored in fired property change listener upon cancellation.
fixedSPHEX(double, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
Sphere exclusion clustering with defined sphere radius.
flexibilityMode(FlexibilityMode) - Method in interface com.chemaxon.descriptors.alignment.FlexibilityModeParameterBuilder
 
FlexibilityModeParameterBuilder - Interface in com.chemaxon.descriptors.alignment
 
FloatVectorComparator - Interface in com.chemaxon.descriptors.metrics
Float vector based calculations.
FloatVectorComparator.Util - Class in com.chemaxon.descriptors.metrics
Various utility methods related to float vector comparation.
FloatVectorDescriptor - Interface in com.chemaxon.descriptors.common
FloatVectorDescriptor is a Descriptor which holds a float vector fingerprint.
FloatVectorMetrics - Enum in com.chemaxon.descriptors.metrics
Simple metrics for float vectors.
fromBitSet(BitSet) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator
Create a descriptor from a BitSet representation.
fromByteArray(byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Builds a descriptor from its byte array representation.
fromFloats(float[]) - Method in interface com.chemaxon.descriptors.vectors.floats.FvGenerator
Create a descriptor from a custom representation.
fromString(String) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
fromString(String) - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Builds a descriptor from its string representation.
FvGenerator - Interface in com.chemaxon.descriptors.vectors.floats
Generator for generic binary vector descriptors.
FvParameters - Class in com.chemaxon.descriptors.vectors.floats
Parameters for generic float vector descriptor.
FvParameters(FvParameters.Builder) - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters
Constructor based on a builder.
FvParameters() - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters
Construct with default values.
FvParameters.Builder - Class in com.chemaxon.descriptors.vectors.floats
Builder for FvParameters.
FvParameters.Builder() - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Constructor with default settings.
FvParameters.Builder(FvParameters) - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Construct to represent the state of a parameter object instance.
FvParameters.ConstructFvGenerator - Interface in com.chemaxon.descriptors.vectors.floats
Interface representing BvGenerator implementation constructor
FvParameters.NumericRepresentation - Enum in com.chemaxon.descriptors.vectors.floats
Representation of the vector coordinates.
FvParameters.SparseCompression - Enum in com.chemaxon.descriptors.vectors.floats
Optimization for sparse vectors.

G

generateDescriptor(Molecule) - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Calculates the associated descriptor for the given Molecule.
generateDescriptor(Molecule) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
 
generateDescriptor(Molecule) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
 
generateDescriptor(Molecule) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
 
get() - Method in class com.chemaxon.apidiscovery.InstanceWrapper
Get the actual wrapped instance.
getAlignedQuery() - Method in interface com.chemaxon.descriptors.alignment.ShapeComparisonResult
 
getAlignedTarget() - Method in interface com.chemaxon.descriptors.alignment.ShapeComparisonResult
 
getAllLeaves(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Return the IDs of all immediate and transitive leaves.
getAPIFieldName() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
API field name.
getAtomTyping() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
 
getAtomTypizer() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Atom typizer to use.
getBareDescriptor(D) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
getBareDescriptor(B) - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Get bare-only form of a descriptor.
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
Creates a new Comparator instance according to the given metric.
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
Creates a new Comparator instance according to the given metric.
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator
Creates a new Comparator instance according to the given metric.
getBinaryVectorComparator(BinaryMetrics) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
Creates a new comparator instance according to the given metric.
getBinaryVectorComparator(BinaryMetrics) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader
Creates a new comparator instance according to the given metric.
getBitsPerPattern() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Bits set for each pattern.
getBondCount() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Max pattern length considered (bond count).
getBooleanValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of a boolean field.
getBuilder() - Method in class com.chemaxon.apidiscovery.InstanceWrapper
Get an associated builder for the given instance if exists.
getBuilderOrParameterObject() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
Get the parameter object or its mutable builder if exists.
getChildClusters(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Return the IDs of child cluster IDs.
getClusterCountsForLevels() - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder.IDBAssignerImpl
 
getClusterCountsForLevels() - Method in interface com.chemaxon.clustering.common.LevelAssigner
Cluster counts resulted from partitioning at associated distinct cluster levels.
getClusterID() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicCluster
Associated cluster ID, unique among a clustering.
getClusterLevel(int) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder
Get the current associated level for a cluster.
getClusterRepresentant(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Retrieve cluster representant ID.
getCoeffQuery() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
Query side coefficient.
getCoeffTarget() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
Target side coefficient.
getCurrentValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Current value.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Gets the default comparator object.
getDefaultComparator() - Method in class com.chemaxon.descriptors.db.MDTableReader
Gets default comparator.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
 
getDefaultComparator() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
Gets default comparator.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
 
getDefaultComparator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader
Gets default comparator.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
 
getDefaultComparator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
Gets default comparator.
getDescription() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
 
getDescription() - Method in class com.chemaxon.apidiscovery.InstanceWrapper
Represented instance description - from its description annotation.
getDescription() - Method in interface com.chemaxon.apidiscovery.interfaces.Validator
Description of this validator.
getDescription() - Method in class com.chemaxon.apidiscovery.Validators.MultiplyOf32
 
getDescription() - Method in class com.chemaxon.apidiscovery.Validators.NonNegativeDouble
 
getDescription() - Method in class com.chemaxon.apidiscovery.Validators.NonNegativeInteger
 
getDescription() - Method in class com.chemaxon.apidiscovery.Validators.NoValidator
 
getDescription() - Method in class com.chemaxon.apidiscovery.Validators.PositiveInteger
 
getDescription() - Method in class com.chemaxon.apidiscovery.Validators.UnitInterval
 
getDescriptionAnnotation(Object) - Static method in class com.chemaxon.apidiscovery.Discovery
Retrieve the description annotation on an object.
getDescriptionAnnotation() - Method in class com.chemaxon.apidiscovery.InstanceWrapper
Represented instances description annotation.
getDescriptorGenerator() - Method in interface com.chemaxon.descriptors.alignment.DRShapeDescriptor
 
getDescriptorGenerator() - Method in interface com.chemaxon.descriptors.alignment.ShapeDescriptor
 
getDescriptorGenerator() - Method in interface com.chemaxon.descriptors.common.Descriptor
Get associated DescriptorGenerator.
getDescriptorGenerator() - Method in interface com.chemaxon.descriptors.common.DescriptorParameters
Return the represented descriptor generator.
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
 
getDetailedDescription() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Detailed description.
getDiameter() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
The maximum diameter of the circular neighborhoods.
getDissimilarity() - Method in interface com.chemaxon.descriptors.common.ComparisonResult
Dissimilarity score of the comparison.
getDistinctClusterLevels() - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder.IDBAssignerImpl
 
getDistinctClusterLevels() - Method in interface com.chemaxon.clustering.common.LevelAssigner
Distinct cluster levels represented by this assigner.
getDoubleValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of a double field.
getEndianness() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
Endianness of packing operations.
getEnumValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of an enum field.
getEuclideanNorm() - Method in interface com.chemaxon.descriptors.common.FloatVectorDescriptor
Euclidean norm of the represented vector.
getFlexibilityMode() - Method in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
getFloatMetricsComparator(FloatVectorMetrics) - Method in interface com.chemaxon.descriptors.vectors.floats.FvGenerator
Get comparator.
getFloatVectorComparator(FloatVectorMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
Creates a new comparator instance according to the given metric.
getFloatVectorComparator(FloatVectorMetrics) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
Creates a new comparator instance according to the given metric.
getFP() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
Get integer array representation of this fingerprint.
getFP() - Method in interface com.chemaxon.descriptors.common.FloatVectorDescriptor
Gets the float array representation of the fingerprint.
getFpAsLongs() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
Get long array representation of this fingerprint.
getGuardObject() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
getGuardObject() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Gets the guard object.
getImmediateLeaves(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Return the IDs of immediate leaves.
getIntValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of an int field.
getLeafLevel(int) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder
Get the current associated level for a leaf.
getLength() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Returns represented fingerprint length (bit count) setting.
getLength() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Returns represented fingerprint length (bit count) setting.
getLength() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
Returns represented fingerprint length (bit count) setting.
getLength() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Returns represented fingerprint length (bit count) setting.
getLowerBound() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
getLowerBound() - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Get lower bound for the similarity/dissimilarity values if such one can be determined.
getLowerBoundForBinaryVectors(int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
Possible lowest value of similarity/dissimilarity scores.
getLowerBoundForBinaryVectors(int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
getLowerBoundForFloatVectors() - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Possible lowest value of similarity/dissimilarity scores.
getManhattanNorm() - Method in interface com.chemaxon.descriptors.common.FloatVectorDescriptor
Manhattan norm of the represented vector.
getMaxClusterID() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
Maximal ClusterID present in this clustering.
getMaxClusterID() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchy
Maximal ClusterID present in this clustering.
getMaximumNorm() - Method in interface com.chemaxon.descriptors.common.FloatVectorDescriptor
Maximum norm of the represented vector.
getMaxLeafID() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
Maximal leaf ID referenced in this clustering.
getMaxLeafID() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchy
Maximal lead ID referenced in this clustering.
getMessageForInvalid() - Method in interface com.chemaxon.apidiscovery.interfaces.ValidateResult
Get description in case of an invalid parameter value.
getMessageForInvalid() - Method in class com.chemaxon.apidiscovery.Validators.InvalidResult
 
getMetricMetadata() - Method in interface com.chemaxon.clustering.common.DissimilarityInput
Metadata about the underlying metric.
getMetricMetadata() - Method in class com.chemaxon.clustering.common.MolInput
 
getMetricMetadata() - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Metadata about this metric.
getMolecule(int) - Method in class com.chemaxon.clustering.common.MolInput
Retrieve a structure.
getName() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
 
getName() - Method in class com.chemaxon.apidiscovery.InstanceWrapper
Represented instance name - from its Description annotation.
getName() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Name.
getNodeType() - Method in enum com.chemaxon.descriptors.alignment.ShapeFunction
 
getNumericRepresentation() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Numeric representation.
getOrder() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
Order stored in creator annotation.
getOrder() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Order stored in parameter annotation.
getParameterClass() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Return enum class for enum field.
getParameters() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
getParameters() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Gets the parameter class.
getParentClusterID(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Looks up a clusters parent cluster ID.
getPreferredAssigner() - Method in interface com.chemaxon.clustering.common.HierarchicClustering
Preferred assigner.
getPreferredAssigner() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
 
getScaledMax() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Max value for scaled fixed point representations.
getScaledMin() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Min value for scaled fixed point representations.
getShapeData() - Method in interface com.chemaxon.descriptors.alignment.ShapeDescriptor
 
getShapeFunction() - Method in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
getShortName() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
 
getShortName() - Method in class com.chemaxon.apidiscovery.InstanceWrapper
Represented instance short name - from its Description annotation.
getShortName() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Short name.
getSimilarity() - Method in interface com.chemaxon.descriptors.common.ComparisonResult
Similarity score of the comparison.
getSparseCompression() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Sparse compression.
getStringFormat() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
Returns represented string format.
getStringValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of a String field.
getStructureImmediateParentCluster(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Look up structure's immediate parent cluster ID.
getTryCount() - Method in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
Creates a new Comparator instance according to the given Tversky metric parameters.
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
Creates a new Comparator instance according to the given Tversky metric parameters.
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator
Creates a new Comparator instance according to the given Tversky metric parameters.
getType() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Type.
getUpperBound() - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Get upper bound for the similarity/dissimilarity values if such one can be determined.
getUpperBoundForBinaryVectors(int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
Possible highest value of similarity/dissimilarity scores.
getUpperBoundForBinaryVectors(int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
getUpperBoundForFloatVectors() - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Possible highest value of similarity/dissimilarity scores.
getXmlConfig() - Method in class com.chemaxon.descriptors.db.MDTableReader
Gets configuration string.
getXmlConfig() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
The XML configuration string.

H

hashCode() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
hashCode() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
 
hasParent(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Check if a cluster has parent cluster id set.
HierarchicCluster<T> - Interface in com.chemaxon.clustering.common
Represents a group (cluster) of structures, possibly divided into further non overlapping clusters.
HierarchicClustering<T,C extends HierarchicCluster<T>> - Interface in com.chemaxon.clustering.common
A grouping of structures into disjunct hierarchical groups.
HierarchicClustering.Alignment - Enum in com.chemaxon.clustering.common
Level interpretation.
hierarchicIndexOf(T, HierarchicClustering<T, ? extends HierarchicCluster<T>>) - Static method in class com.chemaxon.clustering.util.Util
Consruct a hierarchic index for a given member of a clustering.
hierarchyToString(IDBasedHierarchicClustering, IDBasedAssigner, List<String>, int) - Static method in class com.chemaxon.clustering.util.Util
Render a minimalist dendrogram from a String.

I

IDBasedAssigner - Interface in com.chemaxon.clustering.common
Assign levels to IDBasedHierarchicClustering.
IDBasedAssignerBuilder - Class in com.chemaxon.clustering.common
An ID based cluster level assigner builder.
IDBasedAssignerBuilder() - Constructor for class com.chemaxon.clustering.common.IDBasedAssignerBuilder
 
IDBasedAssignerBuilder.IDBAssignerImpl - Class in com.chemaxon.clustering.common
Implementation for level assigner.
IDBasedAssignerBuilder.IDBAssignerImpl(IDBasedHierarchy, IDBasedAssignerBuilder) - Constructor for class com.chemaxon.clustering.common.IDBasedAssignerBuilder.IDBAssignerImpl
Construct immutable assigner/
IDBasedClusterBuilder - Class in com.chemaxon.clustering.common
Builder for ID based non-hierarchic clustering.
IDBasedClusterBuilder() - Constructor for class com.chemaxon.clustering.common.IDBasedClusterBuilder
Instantiate an empty builder.
IDBasedHierarchicCluster - Interface in com.chemaxon.clustering.common
A Hierarchic cluster over integers, preferably IDs; having associated integral ClusterID.
IDBasedHierarchicClusterBuidler - Class in com.chemaxon.clustering.common
Builder for integer ID based hierarchic cluster building.
IDBasedHierarchicClusterBuidler(HierarchicClustering.Alignment) - Constructor for class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
New builder instance.
IDBasedHierarchicClustering - Interface in com.chemaxon.clustering.common
A Hierarchic clustering over integers, preferably IDs.
IDBasedHierarchy - Interface in com.chemaxon.clustering.common
Instances represent the structure of an ID based hierarchic clustering.
IDBasedSingleLevelClustering - Interface in com.chemaxon.clustering.common
A SingleLevelClustering of clusters containing Integer IDs.
initializeBuilderIfExists(T) - Static method in class com.chemaxon.apidiscovery.Discovery
Create initial Builder if possible.
InstanceWrapper<T> - Class in com.chemaxon.apidiscovery
Wrapper for Instances.
InstanceWrapper(T) - Constructor for class com.chemaxon.apidiscovery.InstanceWrapper
Create a wrapper for an instance
intsToString(int[], String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Convert array of integers to a String.
isCancelled() - Method in interface com.chemaxon.calculations.common.CancelObserver
Returns whether cancellation of current operation has been requested.
isCancelled() - Method in class com.chemaxon.calculations.common.ProgressObservers.CancelObserverImpl
 
isCancelled() - Method in interface com.chemaxon.calculations.common.ProgressObservers.PollingCanceller
Returns true when cancelled.
isClusterRepresentantSet(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Check if cluster representant is present.
isDissimilarityZeroIFFEquals() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata
Zero dissimilarity and identity.
isDissimilarityZeroIFFEquals() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
isDoubleValid(double) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Check if a value for a double field is valid.
isEmpty() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Check if the tree is empty.
isMetricSpace() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata
Metric space.
isMetricSpace() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
isNonNegative() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata
Non negativeness of the dissimilarity values.
isNonNegative() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
isParametrized(Object) - Static method in class com.chemaxon.apidiscovery.Discovery
Check if an object is parametrized.
isRepresentantFound(Collection<? extends HierarchicCluster<Integer>>, Collection<Integer>, int) - Static method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Utility method to check representant presence.
isServiceAvailable(Class<S>) - Static method in class com.chemaxon.apidiscovery.util.ServiceUtil
Check if a specific service is defined and implementation can be loaded.
isSymmetric() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata
Symmetry.
isSymmetric() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
isTriangeInequalityHolds() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata
Triangle inequality.
isTriangeInequalityHolds() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
isValid() - Method in interface com.chemaxon.apidiscovery.interfaces.ValidateResult
Check if the validated value is valid.
isValid() - Method in class com.chemaxon.apidiscovery.Validators.InvalidResult
 

L

LanceWilliamsAlgorithm - Class in com.chemaxon.clustering.wards
Agglomerative hierarchical clustering implementation for Lance-Williams algorithm family.
LanceWilliamsAlgorithm() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
 
LanceWilliamsMerge - Interface in com.chemaxon.clustering.wards
Instances represent a cluster distance update for agglomerative clusterings.
LanceWilliamsMerges - Class in com.chemaxon.clustering.wards
Singleton instances of various cluster merge operations.
LanceWilliamsMerges() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges
 
LanceWilliamsMerges.AverageLinkage - Class in com.chemaxon.clustering.wards
Average linkage clustering, also known as UPGMA.
LanceWilliamsMerges.AverageLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage
 
LanceWilliamsMerges.CompleteLinkage - Class in com.chemaxon.clustering.wards
Complete linkage clustering, also known as farthest neighbor clustering.
LanceWilliamsMerges.CompleteLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage
 
LanceWilliamsMerges.SingleLinkage - Class in com.chemaxon.clustering.wards
Single linkage clustering also known as nearest neighbor clustering.
LanceWilliamsMerges.SingleLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.SingleLinkage
 
LanceWilliamsMerges.Wards - Class in com.chemaxon.clustering.wards
Ward's minimum variance clustering.
LanceWilliamsMerges.Wards() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.Wards
 
leafLevel(Integer) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder.IDBAssignerImpl
 
leafLevel(L) - Method in interface com.chemaxon.clustering.common.LevelAssigner
Level associated to a leaf object.
leaves() - Method in interface com.chemaxon.clustering.common.HierarchicCluster
Access leaves associated to this node.
length(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Set fingerprint length, the bit count of the folded binary fingerprint representation.
length(int) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Set fingerprint length, the bit count of the folded binary fingerprint representation.
length(int) - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Set fingerprint length.
length(int) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Set fingerprint length.
LevelAssigner<L,T extends HierarchicCluster<L>> - Interface in com.chemaxon.clustering.common
Assigns levels for clusters and leaves.
linearEuclideanDissimilarityInput(double[]) - Static method in class com.chemaxon.clustering.util.Util
Construct a DissimilarityInput over a set of 1D values.
listCreators(Object, Class<T>) - Static method in class com.chemaxon.apidiscovery.Discovery
CreatorWrapper acts as a type-dependent service loader.
listInstances(Class<T>) - Static method in class com.chemaxon.apidiscovery.Discovery
Collect instances of a specific type.
listParameters(Object) - Static method in class com.chemaxon.apidiscovery.Discovery
Retrieve parameters for a mutable parameter object.
loadService(Class<S>, boolean) - Static method in class com.chemaxon.apidiscovery.util.ServiceUtil
Load and instantiate an implementation for a given service interface.
LOG2_BYTES_IN_INT - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
Log2 of BinaryVectors.BYTES_IN_INT.
LOG2_BYTES_IN_LONG - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
Log2 of BinaryVectors.BYTES_IN_LONG.
longsToBinaryString(long[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Convert array of longs to a binary String.
longsToString(long[], String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Convert array of longs to a String.

M

maxDepth(HierarchicClustering<?, ? extends HierarchicCluster<?>>) - Static method in class com.chemaxon.clustering.util.Util
Find max depth.
maxLevel() - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder.IDBAssignerImpl
 
maxLevel() - Method in interface com.chemaxon.clustering.common.LevelAssigner
Maximal level associated.
MDReaderFactory - Interface in com.chemaxon.descriptors.db
Factory class for MDTableReader.
MDTableReader<D extends Descriptor> - Class in com.chemaxon.descriptors.db
Deserialize fingerprint from MDTable (JChem).
MDTableReader() - Constructor for class com.chemaxon.descriptors.db.MDTableReader
 
members() - Method in interface com.chemaxon.clustering.common.Cluster
Represented members of this cluster.
MetricMetadata - Interface in com.chemaxon.descriptors.metrics
Metric Metadata contains info about a specific metric.
MolInput<D extends Descriptor> - Class in com.chemaxon.clustering.common
Dissimilarity input implementation over Molecule objects and descriptors.
MolInput(List<? extends Molecule>, DescriptorGenerator<D>, DescriptorComparator<D>) - Constructor for class com.chemaxon.clustering.common.MolInput
Construct over Molecules.
MolInputBuilder - Class in com.chemaxon.clustering.common
Convenience class to compose input from molecules to a clustering algorithm.
MolInputBuilder() - Constructor for class com.chemaxon.clustering.common.MolInputBuilder
Construct an empty builder.
MolInputBuilder(Collection<? extends Molecule>) - Constructor for class com.chemaxon.clustering.common.MolInputBuilder
Construct a builder with stored structures.

N

numericRepresentation(FvParameters.NumericRepresentation) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Set numeric representation of vector coordinates.

P

packBytesToInt(byte, byte, byte, byte) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Pack four 8 bit bytes into a 32 bit int.
packBytesToInt(byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Pack four 8 bit bytes into a 32 bit int.
packBytesToInts(byte[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Pack array of bytes into an array of ints.
packBytesToLong(byte, byte, byte, byte, byte, byte, byte, byte) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Pack eight 8 bit bytes into a 64 bit long.
packBytesToLong(byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Pack eight 8 bit bytes into a 64 bit long.
packBytesToLongs(byte[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Pack array of bytes into an array of longs.
packIntsToLong(int, int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Pack two 32 bit integers into a 64 bit long.
packIntsToLongs(int[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Pack array of ints into an array of longs.
Parameter - Annotation Type in com.chemaxon.apidiscovery.annotations
Parameter field to be exposed to the user interface.
ParameterBuilder<T> - Interface in com.chemaxon.apidiscovery.interfaces
This interface represents a builder.
parameters - Variable in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
ParameterWrapper - Class in com.chemaxon.apidiscovery
Wraps a parameter which can be set or get on an object.
ParameterWrapper(Object, Field) - Constructor for class com.chemaxon.apidiscovery.ParameterWrapper
Create a for a parameter field of a mutable object.
ParameterWrapper.ParameterType - Enum in com.chemaxon.apidiscovery
Wrapped parameter types.
Parametrized - Annotation Type in com.chemaxon.apidiscovery.annotations
Indicated that the annotated class has mutable parameters which can be handled by API discovery framework.
parent() - Method in interface com.chemaxon.clustering.common.HierarchicCluster
Get parent for non roots.
parent() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicCluster
 
parseBinaryStringAsLong(String) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Parse a binary String as a 64 bit long.
parseBinaryStringAsLongs(String, int, BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Parse a binary string of '0' and '1' characters into a packed long array.
parseInts(String, int, String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Parse an String containing integer values.
parseLongs(String, int, String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Parse an String containing long values.
parseParameterValue(String) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Parse parameter value from a String.
partition(double) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder.IDBAssignerImpl
 
partition(double) - Method in interface com.chemaxon.clustering.common.LevelAssigner
Create a partition of the associated hierarchic clustering at a specified level.
PfComparator - Interface in com.chemaxon.descriptors.fingerprints.pf2d
Comparator for PharmacophoreFP descriptor representation.
PfGenerator - Interface in com.chemaxon.descriptors.fingerprints.pf2d
Generates 2D pharmacophore fingerprints.
PfParameters - Class in com.chemaxon.descriptors.fingerprints.pf2d
Pharmacophore FP parameters class.
PfParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
Constructor using the default settings.
PfParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.pf2d
Builder class for the immutable parameter object.
PfParameters.Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Constructor with default settings.
PfParameters.Builder(PfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Constructor based on a parameter object.
PfParameters.ConstructPfGenerator - Interface in com.chemaxon.descriptors.fingerprints.pf2d
Interface representing PF generator constructor.
PfTableReader - Class in com.chemaxon.descriptors.fingerprints.pf2d
MDTable reader for 2D pharmacophore fingerprints.
PfTableReader() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
 
PfTableReader.Factory - Interface in com.chemaxon.descriptors.fingerprints.pf2d
Factory class.
PharmacophoreFP - Interface in com.chemaxon.descriptors.fingerprints.pf2d
2D pharmacophore fingerprint representation.
PostOrderDfsVisitor<T> - Interface in com.chemaxon.clustering.util
Function passed for DFS post order traversal.
preferredAlignment() - Method in interface com.chemaxon.clustering.common.HierarchicClustering
Preferred alignment of the represented clustering.
preferredAlignment() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchy
Preferred alignment of the represented clustering.
ProgressObserver - Interface in com.chemaxon.calculations.common
Observer for reporting the progress of long running tasks.
ProgressObservers - Class in com.chemaxon.calculations.common
Utility functions for the creation of ProgressObservers.
ProgressObservers.CancelObserverImpl - Class in com.chemaxon.calculations.common
Implementation of CancelObserver.
ProgressObservers.CancelObserverImpl() - Constructor for class com.chemaxon.calculations.common.ProgressObservers.CancelObserverImpl
Constructor for a cancellable observer implementation.
ProgressObservers.CancelObserverImpl(ProgressObservers.PollingCanceller) - Constructor for class com.chemaxon.calculations.common.ProgressObservers.CancelObserverImpl
Constructor with an underlying polling source.
ProgressObservers.PollingCanceller - Interface in com.chemaxon.calculations.common
Interface exposing only a polling method to delegate cancel status events.

R

read(byte[]) - Method in class com.chemaxon.descriptors.db.MDTableReader
Generates a descriptor from a byte array.
readFromDB(byte[]) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
Read fingerprint from database.
RECOMMENDED_VALUE - Static variable in class com.chemaxon.apidiscovery.Validators.UnitInterval
The recommended valui in case of reject.
removePropertyChangeListener(PropertyChangeListener) - Method in interface com.chemaxon.calculations.common.CancelObserver
Remove a listener.
removePropertyChangeListener(PropertyChangeListener) - Method in class com.chemaxon.calculations.common.ProgressObservers.CancelObserverImpl
 
removeStructure(int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Remove a structure from its respective cluster.
removeStructure(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Remove a structure from its current parent cluster.
representant() - Method in interface com.chemaxon.clustering.common.Cluster
Cluster representant member.
roots() - Method in interface com.chemaxon.clustering.common.HierarchicClustering
Highest level cluster(s).
roots() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchy
Roots of the clustering.

S

scaledMax(double) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Set upper bound for coordinate values used by fixed point backed representation.
scaledMin(double) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Set lower bound for coordinate values used by fixed point backed representation.
selectInstance(Class<T>, String) - Static method in class com.chemaxon.apidiscovery.Discovery
Look up an instance by its short name.
ServiceUtil - Class in com.chemaxon.apidiscovery.util
Utility class to ease service location.
setBooleanValue(boolean) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Set value of a boolean field.
setClusterLevel(int, double) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder
Set the level of a specific cluster.
setClusterRepresentant(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Set cluster representant ID.
setDoubleValue(double) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Set value of a double field.
setIntValue(int) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Set int value of a int field.
setLeafLevel(int, double) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder
Set the level of a specific leaf node.
setStringValue(String) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Set String value of a String field.
setValue(Object) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Set value.
ShapeComparator<T extends ShapeDescriptor> - Interface in com.chemaxon.descriptors.alignment
 
ShapeComparatorException - Exception in com.chemaxon.descriptors.alignment
 
ShapeComparatorException(Throwable) - Constructor for exception com.chemaxon.descriptors.alignment.ShapeComparatorException
 
ShapeComparisonResult - Interface in com.chemaxon.descriptors.alignment
Flexible alignment based shape descriptor calculation
ShapeDescriptor - Interface in com.chemaxon.descriptors.alignment
 
ShapeFunction - Enum in com.chemaxon.descriptors.alignment
 
ShapeGeneratorException - Exception in com.chemaxon.descriptors.alignment
 
ShapeGeneratorException(Throwable) - Constructor for exception com.chemaxon.descriptors.alignment.ShapeGeneratorException
 
ShapeMetrics - Enum in com.chemaxon.descriptors.alignment
 
simpleSingleLinkageClustering(DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.singlelinkage.SingleLinkage
Single linkage clustering implementation.
SingleLevelClustering<T,C extends Cluster<T>> - Interface in com.chemaxon.clustering.common
A grouping of structures into disjunct groups.
SingleLinkage - Class in com.chemaxon.clustering.singlelinkage
Single linkage similarity clustering algorithm.
size() - Method in interface com.chemaxon.clustering.common.DissimilarityInput
Item count to be considered.
size() - Method in class com.chemaxon.clustering.common.MolInput
 
size() - Method in class com.chemaxon.clustering.common.MolInputBuilder
Added structure count.
skipChildTraversal(IDBasedHierarchicCluster, int) - Method in interface com.chemaxon.clustering.util.PostOrderDfsVisitor
Decide if a cluster's children should be traversed.
sparseCompression(FvParameters.SparseCompression) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Set compression of sparse vectors.
SphereExclusion - Class in com.chemaxon.clustering.sphex
Core functionality related to sphere exclusion clustering.
sphexCentroids(double, int, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
Identify SphereExclusion clustering based centroids for a given set.
sphexClassify(int[], DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
Classify input items into clusters determined by nearest centroids.
sqrDist(float[], float[]) - Static method in class com.chemaxon.descriptors.metrics.FloatVectorComparator.Util
Calculates squared Euclidean distance.
stringFormat(BvParameters.StringFormat) - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Set String format.
SubProgressObserver - Interface in com.chemaxon.calculations.common
Observer for reporting the progress of subtasks.
subTask(String, long) - Method in interface com.chemaxon.calculations.common.ProgressObserver
Follow the processing of a specific amount of work units by a separate observer.
suggestValid() - Method in interface com.chemaxon.apidiscovery.interfaces.ValidateResult
Suggest a valid value if possible.
suggestValid() - Method in class com.chemaxon.apidiscovery.Validators.InvalidResult
 
switchToDeterminate(long) - Method in interface com.chemaxon.calculations.common.ProgressObserver
Notifies that the remaining amount of work units to complete this task is known.

T

toByteArray(D) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
toByteArray() - Method in interface com.chemaxon.descriptors.alignment.ShapeDescriptor
 
toByteArray(B) - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Creates the byte array representation of a descriptor object.
toDetailedString(IDBasedSingleLevelClustering) - Static method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Utility method to create a detailed string representation of a clustering.
toDetailedString() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Create a detailed multiline String representation of the builder state.
toDetailedString(IDBasedHierarchicClustering) - Static method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Utility method to create a detailed string representation of a clustering.
toHistogramString() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFP
Converts the fingerprint into a human readable string.
toJsonMixed(IDBasedHierarchicClustering) - Static method in class com.chemaxon.clustering.util.Util
Provide a JSON-like representation for Web GUI widget display.
toString(int, int, boolean, boolean) - Method in class com.chemaxon.clustering.util.Util.StringScatterPlot
Create a multiline representation of the given plot.
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage
 
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage
 
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.SingleLinkage
 
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.Wards
 
toString(D) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
toString() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
toString(B) - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Creates the String representation of a descriptor object.
toString() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
 
toString() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
 
toString() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
 
toString() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
 
toString() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
 
toString() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
 
toStringRepresentation() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Create String representation of the represented value.
traversePostOrderDFS(PostOrderDfsVisitor<T>, IDBasedHierarchicClustering) - Static method in class com.chemaxon.clustering.util.Util
Invoke recursive DFS post order traversal on a hierarchy.
TverskyParameters - Class in com.chemaxon.descriptors.metrics
Parameters for Tversky index.
TverskyParameters(TverskyParameters.Builder) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters
Instantiate with builder's actual state.
TverskyParameters() - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters
Instantiate with default values.
TverskyParameters.Builder - Class in com.chemaxon.descriptors.metrics
Builder for parameter object.
TverskyParameters.Builder() - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate builder with default values.
TverskyParameters.Builder(TverskyParameters) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate builder based on an actual parameter instance.

U

unitPathAssigner() - Method in interface com.chemaxon.clustering.common.HierarchicClustering
Assigner which consider parent-child edges as unit length.
unitPathAssigner() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
 
UnitPathAssigner - Class in com.chemaxon.clustering.common
Assigning unit distance based on path length from leaves/roots.
UnitPathAssigner() - Constructor for class com.chemaxon.clustering.common.UnitPathAssigner
 
unpackBytesFromInt(int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Unpack four 8 bit bytes from a 32 bit int.
unpackBytesFromInt(int, byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Unpack four 8 bit bytes from a 32 bit int.
unpackBytesFromInts(int[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Unpack array of ints into an array of bytes.
unpackBytesFromLong(long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Unpack eight 8 bit bytes from a 64 bit long.
unpackBytesFromLong(long, byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Unpack eight 8 bit bytes from a 64 bit long.
unpackBytesFromLongs(long[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Unpack array of longs into an array of bytes.
unpackInt0FromLong(long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Unpack first 32 bit integer from a 64 bit long according to the represented endianness.
unpackInt1FromLong(long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Unpack second 32 bit integer from a 64 bit long according to the represented endianness.
unpackIntsFromLongs(long[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors
Unpack array of longs into an array of ints.
updateRepresentant(int, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Set/update the cluster representant structure.
Util - Class in com.chemaxon.clustering.util
Clustering related utility methods.
Util.StringScatterPlot - Class in com.chemaxon.clustering.util
ASCII scatter plot.
Util.StringScatterPlot() - Constructor for class com.chemaxon.clustering.util.Util.StringScatterPlot
Construct an empty scatter plot.

V

ValidateResult<T> - Interface in com.chemaxon.apidiscovery.interfaces
Result of a parameter validation.
validateValue(T) - Method in interface com.chemaxon.apidiscovery.interfaces.Validator
Validate parameter value.
validateValue(Integer) - Method in class com.chemaxon.apidiscovery.Validators.MultiplyOf32
 
validateValue(Double) - Method in class com.chemaxon.apidiscovery.Validators.NonNegativeDouble
 
validateValue(Integer) - Method in class com.chemaxon.apidiscovery.Validators.NonNegativeInteger
 
validateValue(Object) - Method in class com.chemaxon.apidiscovery.Validators.NoValidator
 
validateValue(Integer) - Method in class com.chemaxon.apidiscovery.Validators.PositiveInteger
 
validateValue(Double) - Method in class com.chemaxon.apidiscovery.Validators.UnitInterval
 
Validator<T> - Interface in com.chemaxon.apidiscovery.interfaces
Validator for a parameter.
Validators - Class in com.chemaxon.apidiscovery
Validator related utilities.
Validators.InvalidResult<T> - Class in com.chemaxon.apidiscovery
An invalid result.
Validators.InvalidResult(String, T) - Constructor for class com.chemaxon.apidiscovery.Validators.InvalidResult
Construct an invalid result with suggested valid value.
Validators.InvalidResult(String) - Constructor for class com.chemaxon.apidiscovery.Validators.InvalidResult
Construct an invalid result without suggestion.
Validators.MultiplyOf32 - Class in com.chemaxon.apidiscovery
Ensure that parameter is multiply of 32.
Validators.MultiplyOf32() - Constructor for class com.chemaxon.apidiscovery.Validators.MultiplyOf32
 
Validators.NonNegativeDouble - Class in com.chemaxon.apidiscovery
Validator accepts only non negative doubles (also 0).
Validators.NonNegativeDouble() - Constructor for class com.chemaxon.apidiscovery.Validators.NonNegativeDouble
 
Validators.NonNegativeInteger - Class in com.chemaxon.apidiscovery
Validator accepts only non negative integers (zero and greater).
Validators.NonNegativeInteger() - Constructor for class com.chemaxon.apidiscovery.Validators.NonNegativeInteger
 
Validators.NoValidator<T> - Class in com.chemaxon.apidiscovery
A validator always result as valid.
Validators.NoValidator() - Constructor for class com.chemaxon.apidiscovery.Validators.NoValidator
 
Validators.PositiveInteger - Class in com.chemaxon.apidiscovery
Validator accepts only positive integers (1 or greater; excluding 0).
Validators.PositiveInteger() - Constructor for class com.chemaxon.apidiscovery.Validators.PositiveInteger
 
Validators.UnitInterval - Class in com.chemaxon.apidiscovery
Validator accepts double values in the unit interval (0.0 - 1.0, inclusive).
Validators.UnitInterval() - Constructor for class com.chemaxon.apidiscovery.Validators.UnitInterval
 
VALIDRESULT - Static variable in class com.chemaxon.apidiscovery.Validators
A valid result.
valueOf(String) - Static method in enum com.chemaxon.apidiscovery.ParameterWrapper.ParameterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.clustering.common.HierarchicClustering.Alignment
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.AtomTyping
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.DRShapeMetrics
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.ShapeFunction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.ShapeMetrics
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.fingerprints.ecfp.EcfpAtomTypizers
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.metrics.BinaryMetrics
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.metrics.FloatVectorMetrics
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.vectors.binary.BvParameters.StringFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.NumericRepresentation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.SparseCompression
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.chemaxon.apidiscovery.ParameterWrapper.ParameterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.clustering.common.HierarchicClustering.Alignment
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.AtomTyping
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.DRShapeMetrics
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.ShapeFunction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.ShapeMetrics
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.fingerprints.ecfp.EcfpAtomTypizers
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.metrics.BinaryMetrics
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.metrics.FloatVectorMetrics
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.vectors.binary.BvParameters.StringFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.NumericRepresentation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.SparseCompression
Returns an array containing the constants of this enum type, in the order they are declared.
visit(IDBasedHierarchicCluster, List<T>, int) - Method in interface com.chemaxon.clustering.util.PostOrderDfsVisitor
Visit a cluster.
vLength(float[]) - Static method in class com.chemaxon.descriptors.metrics.FloatVectorComparator.Util
Calculates length (magnitude) of vector.

W

worked(long) - Method in interface com.chemaxon.calculations.common.ProgressObserver
Notifies that a given number of work units has been completed.

X

xmlConfig(String) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Sets configuration xml string.
xmlConfig(Optional<String>) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Sets configuration xml string.

A B C D E F G H I L M N P R S T U V W X

jklustor-all-api-0.0.7-20140619012755 (ChemAxon)