Skip navigation links
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 

A

a0() - Method in interface com.chemaxon.overlap.cli.util.images.Range
Lower end, inclusive.
a1() - Method in interface com.chemaxon.overlap.cli.util.images.Range
Higher end, exclusive
absentids - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo
Structures which associated ID is absent.
absentmols - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo
Absent molecule count.
AbstractSerialization<S extends D,D> - Class in com.chemaxon.overlap.persistence.serialization
Deserializer conform serialization delegating serialization/deserialization to custom implementations.
AbstractSerialization(Class<D>) - Constructor for class com.chemaxon.overlap.persistence.serialization.AbstractSerialization
Construct.
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
 
accept(T) - Method in interface com.chemaxon.calculations.io.Sink
Deprecated.
 
accept(R) - Method in class com.chemaxon.overlap.partialresult.OneKeeperPartialResultHolder
 
accept(R) - Method in interface com.chemaxon.overlap.partialresult.PartialResultConsumer
Accepts the result.
accept(R) - Method in class com.chemaxon.overlap.partialresult.SimplePartialResultHolder
 
ACCEPTED - Static variable in annotation type com.chemaxon.overlap.wui.application.Status
202 Accepted.
acceptIfNeeded(Supplier<R>) - Method in class com.chemaxon.overlap.partialresult.OneKeeperPartialResultHolder
Accepts only if previous result has been taken before.
acceptIfNeeded(Supplier<R>) - Method in interface com.chemaxon.overlap.partialresult.PartialResultConsumer
Optionally accepts a partial result.
acceptIfNeeded(Supplier<R>) - Method in class com.chemaxon.overlap.partialresult.SimplePartialResultHolder
 
accomodate(RangeSpec) - Method in interface com.chemaxon.overlap.cli.util.images.RangeSpec
Accomodate a child range specification.
accomodate(int) - Method in interface com.chemaxon.overlap.cli.util.images.RangeSpec
Accomodate a child range.
adaptiveSPHEX(int, int, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
Sphere exclusion clustering with sphere radius inference.
add(double) - Method in class com.chemaxon.calculations.util.Histo
Add a value to the histogram.
add(SubPane) - Method in class com.chemaxon.overlap.cli.util.images.HFlowPane
 
add(SubPane) - Method in class com.chemaxon.overlap.cli.util.images.VFlowPane
 
add(T) - Method in class com.chemaxon.overlap.cli.util.pages.PagedBuilder
Add an item.
add(int, String) - Method in class com.chemaxon.overlap.io.CompactStringStorage.Builder
 
add(int, T) - Method in interface com.chemaxon.overlap.io.MasterStorages.MasterStorageBuilder
Add next represented data.
add(double) - Method in class com.chemaxon.overlap.result.impl.LinearHistogramBuilder
Add a new value.
add(Function<String, T>) - Method in class com.chemaxon.overlap.service.task.TaskService
Generates a new id, and adds Task.
add(long) - Method in class com.chemaxon.overlap.wui.dto.SizeInfoDto
Add to the represented size.
add(Object) - Method in class com.chemaxon.overlap.wui.res.StatRes
Add statistics representation.
addAdditionalData(String, Object) - Method in class com.chemaxon.overlap.cli.prof.Prof
Add additional data to be included in the output.
addAll(InputStream, String, int, int, StandardizerWrapper, SubProgressObserver, ExecutorService, MoleculeCallback) - Method in interface com.chemaxon.overlap.io.Updater
Read all molecules from a structure file into the similarity subsystem.
addAll(InputStream, String, int, int, StandardizerWrapper, SubProgressObserver, ExecutorService, MoleculeCallback) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 
addCell(String) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder
Add single line cell.
addCell(int, String) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder
 
addCell(Collection<String>) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder
Add multi line cell.
addCell(int, Collection<String>) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder
 
addChildCluster(int) - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec
Add child cluster.
addChildCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Add a cluster to another cluster as a child cluster.
addColumn(Class<T>, String) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Add a column.
addColumn(Class<T>, String, List<T>) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Adds a column that uses the provided list to store the elements.
addColumn(String) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Add an Object column.
addColumn(Class<T>, String) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
addColumn(Class<T>, String, List<T>) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
addColumn(String) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
addDataPoint(double, double) - Method in class com.chemaxon.clustering.util.Util.StringScatterPlot
Add new point to put.
addDeferredAttribute(String, Class<T>, T) - Method in interface com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerialization
Specify a named attribute.
addDeferredAttribute(String, Class<T>, T) - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl
 
addDelayedSingleOutput(PipelineStep, String, String, Class<T>, Consumer<Consumer<T>>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addDelayedSingleOutput(PipelineStep, String, String, Class<T>, Consumer<Consumer<T>>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Register an output with a single value.
addDescriptor(D) - Method in interface com.chemaxon.overlap.io.Updater
Add a single descriptor to the similarity subsystem.
addDescriptor(D) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 
addDetail(String, long) - Method in class com.chemaxon.overlap.wui.dto.SizeInfoDto
Add a named size component.
addDoneListener(Consumer<ProgressObserver>) - Method in class com.chemaxon.calculations.common.ListenableObserver
 
addDoneListener(Consumer<ProgressObservable>) - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
 
addDoneListener(Consumer<ProgressObservable>) - Method in interface com.chemaxon.calculations.common.ProgressObservable
 
addDoubleColumn(String) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Add a Double column.
addDoubleColumn(String) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
addDtoChoice(String, String, Supplier<D>, Function<D, T>) - Method in interface com.chemaxon.apidiscovery.linenote.LinenoteBuilder
Add a choice for a single parametrization.
addEnumChoice(Class<E>, Function<E, T>) - Method in interface com.chemaxon.apidiscovery.linenote.LinenoteBuilder
Add a choice for each enum instances.
addErrorReportListener(Sink<ErrorReport>) - Static method in class com.chemaxon.overlap.wui.resources.exceptions.WuiExceptionMapper
Add a listener for mapped error reports.
addExtProbe(String, Supplier<? extends Object>) - Method in class com.chemaxon.overlap.cli.prof.Prof
Add additional probe.
addFragment(RgFrag) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton
Add fragment.
addImmediateLeaf(int) - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec
Add a leaf to this cluster.
addImmediateLeafWithLevel(int, double) - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec
Add a leaf to this cluster.
addImmediateLeaves(Integer...) - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec
Add multiple leaves to the represented cluster.
addIntegerColumn(String) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Add an integer column.
addIntegerColumn(String) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
addIteratorOutput(PipelineStep, String, String, Class<T>, Supplier<Iterator<T>>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addIteratorOutput(PipelineStep, String, String, Class<T>, Supplier<Iterator<T>>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Register an output with an iterator of values.
additionalResourceDirectory(String) - Method in class com.chemaxon.screen.desktop.JettyStarter
Specify additional resource directory.
addLoadingTaskWithObserver(String, String, Errors.CheckedConsumer<SubProgressObserver>) - Method in class com.chemaxon.overlap.wui.StartupHandler
The observer will be closed automaticly.
addMasterStorageBuilder(PipelineStep, String, String, Class<T>, MasterStorages.MasterStorageBuilder<T>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addMasterStorageBuilder(PipelineStep, String, String, Class<T>, MasterStorages.MasterStorageBuilder<T>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Add a MasterStorage building node.
addMissing(int) - Method in class com.chemaxon.overlap.io.CompactStringStorage.Builder
 
addMissing(int) - Method in class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorBuilder
Report master index for which no client index is associated.
addMissing(int) - Method in interface com.chemaxon.overlap.io.MasterStorages.MasterStorageBuilder
Add missing data.
addMolecule(Molecule) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add a new structure.
addMolecule(Molecule) - Method in interface com.chemaxon.overlap.io.Updater
Add a single molecule to the similarity subsystem.
addMolecule(Molecule) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
 
addMolecules(Collection<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add multiple structures.
addMolecules(Iterator<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add multiple structures.
addMolecules(Iterator<? extends Molecule>, StandardizerWrapper) - Method in class com.chemaxon.clustering.common.MolInputBuilder
Add multiple structures with preprocessing.
addMultiDtoChoices(String, List<String>, List<Supplier<D>>, Function<D, T>) - Method in interface com.chemaxon.apidiscovery.linenote.LinenoteBuilder
Add multiple choices with multiple parameterizations.
addMultiple(LinearHistogramBuilder) - Method in class com.chemaxon.overlap.result.impl.LinearHistogramBuilder
Add multiple values represented by a histogram builder.
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.
addOk(int, int) - Method in class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorBuilder
Report new master-client mapping.
addOverlayCell(int, int, int, int, SubPane) - Method in class com.chemaxon.overlap.cli.util.images.GridPane
Set an overlay cell.
addRepeatedInput(PipelineStep, String, String, Class<T>, Consumer<T>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addRepeatedInput(PipelineStep, String, String, Class<T>, Consumer<T>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Register an input which accepts repeated values.
addResult(String, String, int) - Method in class com.chemaxon.screen.Column
 
addRow() - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Add new empty row.
addRow() - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
addRowBuilder() - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Row builder.
addRowBuilder() - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
addSimilarities(int, List<SimilarityResult>) - Method in class com.chemaxon.overlap.result.impl.KnnResultsBuilder
Add dissimilarities.
addSimpleChoice(String, String, Supplier<T>) - Method in interface com.chemaxon.apidiscovery.linenote.LinenoteBuilder
Add a no-parameter choice.
addSingleInput(PipelineStep, String, String, Class<T>, Consumer<T>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addSingleInput(PipelineStep, String, String, Class<T>, Consumer<T>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Register an input with a single value.
addSingleShotOutput(PipelineStep, String, String, Class<T>, Supplier<T>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addSingleShotOutput(PipelineStep, String, String, Class<T>, Supplier<T>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Register an output with a single value.
addSingleSimilarity(int, SimilarityResult) - Method in class com.chemaxon.overlap.result.impl.KnnResultsBuilder
Add a single similarity.
addStatefulMetricOutput(PipelineStep, String, String, Supplier<Long>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addStatefulMetricOutput(PipelineStep, String, String, Supplier<Long>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Register a secondary output providing metrics.
addStatelessTransformation(PipelineStep, String, String, Class<U>, String, String, Class<V>, Function<U, V>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addStatelessTransformation(PipelineStep, String, String, Class<U>, String, String, Class<V>, Function<U, V>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Add stateless transformation.
addStep(PipelineStep) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
addStep(PipelineStep) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
 
addStringColumn(String) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Add a String column.
addStringColumn(String) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
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.
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.CloneCxnMolecule
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
Append linenote spec.
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.Connect
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolExporter
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolImporter
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.GetMoleculeName
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.GetSdfProperty
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.Mark
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.ToLines
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.ToSdfs
 
addToLinenote(LinenoteBuilder<PipelineStep>) - Static method in class com.chemaxon.overlap.cli.util.pipeline.TransformMolecule
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.CloneCxnMolecule
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.Connect
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolExporter
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolImporter
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.GetMoleculeName
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.GetSdfProperty
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.Mark
 
addToPipeline(PipelineContext) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineStep
Wire step into the pipeline.
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.ToLines
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.ToSdfs
 
addToPipeline(PipelineContext) - Method in class com.chemaxon.overlap.cli.util.pipeline.TransformMolecule
 
addWorkedListener(Consumer<ProgressObserver>) - Method in class com.chemaxon.calculations.common.ListenableObserver
 
addZAttachment(Molecule, int, int, int) - Static method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
 
align(List<String>, CharLayout.HA) - Static method in class com.chemaxon.calculations.util.CharLayout
Align lines.
Align - Enum in com.chemaxon.overlap.cli.util.images
1D alignment.
AllAbsentMasterMoleculeStorage - Class in com.chemaxon.overlap.io
All absent MasterMoleculeStorage implementation.
AllAbsentMasterMoleculeStorage(int) - Constructor for class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
Create.
allAbsentMasterMoleculeStorage(int) - Static method in class com.chemaxon.overlap.io.MasterStorages
All absent MMS.
allAtoms() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
 
AllButFirstToken - Class in com.chemaxon.overlap.splits
Return everything except the first token.
AllButFirstToken() - Constructor for class com.chemaxon.overlap.splits.AllButFirstToken
 
allNeighborCount - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
 
allneighborcount - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo
All neighbor count stored.
allPass() - Static method in class com.chemaxon.overlap.servlets.SelfKnnFilters
Create filter passing everything.
allSingleAtomExtensions() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton
All single atom based growth candidates.
alwaysThrottle() - Static method in class com.chemaxon.calculations.common.AutoThrottles
Printout always requested.
and(StandardizerWrapper) - Method in class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk
 
and(StandardizerWrapper) - Method in class com.chemaxon.clustering.framework.RemoveSidechainsSc
 
and(StandardizerWrapper) - Method in interface com.chemaxon.overlap.io.StandardizerWrapper
Create a new wrapper representing an additional step.
angleDeg(V3D) - Method in class com.chemaxon.calculations.util.V3D
Calculates the angle closed by two vectors in degrees.
angleRad(V3D) - Method in class com.chemaxon.calculations.util.V3D
Calculates the angle closed by two vectors in radians.
anyCancelled(CancelObserver...) - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a cancel observer which cancels when any of the specified observer is cancelled.
append(List<StringBuilder>, StringBuilder) - Static method in class com.chemaxon.calculations.util.CharLayout
Append rows to a StringBuilder target.
append(int, Map<String, String>) - Method in class com.chemaxon.screen.Column
 
appendLongAsBinaryString(StringBuilder, long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness
Convert 64 bit long to binary string.
appendToLastCell(Collection<String>) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder
Append multiple lines to the last cells content.
appentToLastCell(String) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder
Append a line to the last cells content.
Application - Class in com.chemaxon.overlap.wui.application
JAX-RS configuration.
Application() - Constructor for class com.chemaxon.overlap.wui.application.Application
 
Application.AdditionalApplicationClassesProvider - Interface in com.chemaxon.overlap.wui.application
Service for injecting further Application classes.
apply(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.BinaryLongFpExtractor
 
apply(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.FloatsExtractor
 
apply(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledBytesFvExtractor
 
apply(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledShortsFvExtractor
 
apply(T) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.SerializingUnguardedExtractor
 
apply(BinaryVectorMetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory.ToLinenote
 
apply(FloatVectorMetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.FloatVectorMetricFactory.ToLinenote
 
apply(MetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.MetricFactory.ToLinenote
 
apply(String) - Method in class com.chemaxon.overlap.cli.util.importing.ParseCustomToDescriptor
 
apply(String) - Method in class com.chemaxon.overlap.cli.util.importing.ParseCustomToUnguarded
 
apply(StructureRecord) - Method in class com.chemaxon.overlap.cli.util.importing.ParseStructureRecordToUnguarded
 
apply(StructureRecord) - Method in class com.chemaxon.overlap.cli.util.importing.ParseStructureRecordToUnguardedWithMol
 
apply(Double) - Method in class com.chemaxon.overlap.servlets.ScalarFilter
 
apply(String) - Method in class com.chemaxon.overlap.splits.AllButFirstToken
 
apply(String) - Method in class com.chemaxon.overlap.splits.FirstToken
 
apply(String) - Method in class com.chemaxon.overlap.splits.Identity
 
apply(String) - Method in class com.chemaxon.overlap.splits.SecondToken
 
Area - Interface in com.chemaxon.overlap.cli.util.images
A rectangular area.
areAllAbsent() - Method in interface com.chemaxon.overlap.io.MasterStorage
Check for all absent.
AreaSpec - Interface in com.chemaxon.overlap.cli.util.images
Rectangular area size requirement.
areaSpec() - Method in class com.chemaxon.overlap.cli.util.images.BorderedPane
 
areaSpec() - Method in class com.chemaxon.overlap.cli.util.images.GridPane
 
areaSpec() - Method in class com.chemaxon.overlap.cli.util.images.HFlowPane
 
areaSpec() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
 
areaSpec() - Method in interface com.chemaxon.overlap.cli.util.images.SubPane
Requested area specification.
areaSpec() - Method in class com.chemaxon.overlap.cli.util.images.VFlowPane
 
areQueryIdsShown() - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder
 
areQueryIdsShown() - Method in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
 
areTargetIdsShown() - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder
 
areTargetIdsShown() - Method in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
 
argumentGuardedWith(Object) - Method in class com.chemaxon.descriptors.common.reflect.SingleArgumentTransformingInvocationHandler
Convenience factory.
aromatizeBasic() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
aromatizeBasic() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap basic aromatization.
aromatizeGeneral() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
aromatizeGeneral() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap general aromatization.
aromatizeLoose() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
aromatizeLoose() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap loose aromatization.
arrayAwareToString(Object) - Static method in class com.chemaxon.calculations.util.ToStrings
Array aware toString.
arrayAwareToString(Object) - Static method in class com.chemaxon.overlap.io.Util
Array aware toString.
arrayToSet(String) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.BitArrayToBitSet
 
asInstanceOf(Class<MI>, AI) - Static method in class com.chemaxon.descriptors.common.reflect.Reflect
Hide actual implementation and type parameters by proxying to a marker interface.
asList() - Method in interface com.chemaxon.calculations.util.cellfield.Column
Column as List.
asList() - Method in class com.chemaxon.calculations.util.cellfield.impl.ColumnImpl
 
asString - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryUsageDesc
 
asString - Variable in class com.chemaxon.overlap.wui.dto.MemoryUsageDescDto
 
AsyncCall<R> - Class in com.chemaxon.overlap.service.async
Represents an async call from rest with an id.
AsyncCall(String, ExecutableTask<R>, Future<R>) - Constructor for class com.chemaxon.overlap.service.async.AsyncCall
 
AsyncCallDto<T> - Class in com.chemaxon.overlap.wui.dto
Status of an asynchronous call.
AsyncCallDto() - Constructor for class com.chemaxon.overlap.wui.dto.AsyncCallDto
 
AsyncCallIdNotFoundException(String) - Constructor for exception com.chemaxon.overlap.service.async.AsyncCallService.AsyncCallIdNotFoundException
 
AsyncCallPresenter - Class in com.chemaxon.overlap.presenter
Presentation layer for AsyncCalls.
AsyncCallPresenter() - Constructor for class com.chemaxon.overlap.presenter.AsyncCallPresenter
 
AsyncCallService - Class in com.chemaxon.overlap.service.async
 
AsyncCallService() - Constructor for class com.chemaxon.overlap.service.async.AsyncCallService
 
AsyncCallService(IdGenerator) - Constructor for class com.chemaxon.overlap.service.async.AsyncCallService
 
AsyncCallService.AsyncCallIdNotFoundException - Exception in com.chemaxon.overlap.service.async
 
AsyncResult<T> - Interface in com.chemaxon.overlap.result
Result handler for long running asynchronous calculations where partial return values are provided.
atnoArray(Molecule) - Static method in class com.chemaxon.calculations.util.MU
Extract atno array.
atom1 - Variable in class com.chemaxon.calculations.util.MU.BondList
Bond end atom 1.
atom2 - Variable in class com.chemaxon.calculations.util.MU.BondList
Bond end atom 2.
atomCoordinates3d(Molecule) - Static method in class com.chemaxon.calculations.util.MU
Extract 3D atom coordinates.
atomlabels - Variable in class com.chemaxon.overlap.wui.dto.PmapperResponse
Textual pharmacophore mapping for atoms.
atoms - Variable in class com.chemaxon.overlap.wui.dto.PmapperFeature
Atom indices assigned this feature.
AtomTyping - Enum in com.chemaxon.descriptors.alignment
Settings for shape associated atom typing.
atomTyping(AtomTyping) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter.Builder
 
atomTyping(AtomTyping) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter.Builder
 
atomTypizer(EcfpAtomTypizers) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Set atom typizer to use.
atomTypizer(EcfpAtomTypizers) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Set atom typizer to use.
attachedAtoms() - Method in interface com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroup
Indices of attached atoms.
attachedAtoms() - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
 
Attachment - Class in com.chemaxon.virtuallib.sc.model.sdf
Represents an attachment point.
Attachment(int, int, int, int) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.Attachment
 
attachmentAtoms() - Method in interface com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroup
Indices of attachment pseudo atoms.
attachmentAtoms() - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
 
AttachmentGroup - Interface in com.chemaxon.virtuallib.sc.model.sdf
Group of attachments.
AttachmentGroupImpl - Class in com.chemaxon.virtuallib.sc.model.sdf
Implementation.
AttachmentGroupImpl(Collection<Attachment>) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
Construct.
attachmentIndices() - Method in interface com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroup
Atachment indices represented by this collection.
attachmentIndices() - Method in class com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroupImpl
 
autoflush(boolean) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
 
autoGzip(InputStream) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Detect gzipped InputStream.
autogzip(boolean) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
 
AutoThrottle - Interface in com.chemaxon.calculations.common
Throttles interactive periodic events.
AutoThrottles - Class in com.chemaxon.calculations.common
Helper class for AutoThrottle creation.
available() - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
 
availableMetrics(DescRes) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
List of available metrics.
availableProcessors - Variable in class com.chemaxon.overlap.cli.prof.Memstat
Available processors.
AverageLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage
 
avgInvocationTimeInMs - Variable in class com.chemaxon.calculations.common.TimerStatistics
Average time of a single invocation in ms.
awaitCompletion(Long) - Method in class com.chemaxon.overlap.service.async.AsyncCall
Waits if necessary for at most the given time for the call to complete.
awaitCompletionAndGetResult() - Method in class com.chemaxon.overlap.service.async.AsyncCall
Waits if necessary for at most the given time for the call to complete and returns it's result.
awaitCompletionAndGetResult(Long) - Method in class com.chemaxon.overlap.service.async.AsyncCall
Waits if necessary for at most the given time for the call to complete, and then retrieves its result, if available.
awaitCompletionWithTimeoutAndConvertToDto(AsyncCall<?>, Long) - Method in class com.chemaxon.overlap.presenter.AsyncCallPresenter
with partial result
awaitCompletionWithTimeoutAndConvertToDto(AsyncCall<?>, Long, boolean) - Method in class com.chemaxon.overlap.presenter.AsyncCallPresenter
Waits if necessary for at most the given time for the call to complete, and then retrieves its result as dto.

B

base64img - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityTargetInfo
Base64 encoded png image of the target molecule if requested, otherwise null.
base64img - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest
true when Base64 encoded target images are requested.
base64img - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
 
BaseShapeComparatorParameter - Class in com.chemaxon.descriptors.alignment
 
BaseShapeComparatorParameter(AlignmentProperties.FlexibilityMode, ShapeFunction, Optional<Integer>) - Constructor for class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
BatchedPagedProcessor - Class in com.chemaxon.overlap.concurrent
Lightweight wrapper to provide batched paged processing.
BemisMurckoClustering - Class in com.chemaxon.clustering.framework
Convenience utilities for using Bemis-Murcko clustering.
bemisMurckoFrameworkAssociation() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
bestEffortConvert(Molecule) - Static method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
Convert Molecule to String multiple formats.
binary - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest
Use binary format by invoking MolExporter#exportToBinFormat(chemaxon.struc.Molecule, java.lang.String) and base64 encoding the result.
binary - Variable in class com.chemaxon.overlap.wui.dto.ConversionResult
Is binary format requested.
BinaryLongCommonpart - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded comparator for BinaryMetrics.BINARY_COMMONPART.
BinaryLongCommonpart(int) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpart
Construct.
BinaryLongCommonpartNormalized - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
BinaryLongCommonpartNormalized(int) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpartNormalized
Construct.
BinaryLongComparisonContextFactory - Class in com.chemaxon.descriptors.common.comparison.impl
Factory for packed long [] binary fingerprints.
BinaryLongComparisonContextFactory(int, DescriptorSerializer<BinaryVectorDescriptor>) - Constructor for class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
Instantiate.
BinaryLongDice - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded comparator for BinaryMetrics.BINARY_DICE.
BinaryLongDice() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongDice
 
BinaryLongEuclidean - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded comparator for BinaryMetrics.BINARY_EUCLIDEAN.
BinaryLongEuclidean() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclidean
 
BinaryLongEuclideanNormalized - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
BinaryLongEuclideanNormalized(int) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclideanNormalized
Construct.
BinaryLongFpExtractor - Class in com.chemaxon.descriptors.common.unguarded.impl.extractors
Extract packed long [] binary fp from a BinaryVectorDescriptor.
BinaryLongFpExtractor(int, Object) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.extractors.BinaryLongFpExtractor
Construct.
BinaryLongManhattan - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded Manhattan comparator for binary fingerprints represented as long [].
BinaryLongManhattan() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattan
 
BinaryLongManhattanNormalized - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded normalized Manhattan comparator for binary fingerprints represented as long [].
BinaryLongManhattanNormalized(int) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattanNormalized
Construct.
BinaryLongPetke - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded Petke comparator for binary fingerprints represented as long [].
BinaryLongPetke() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongPetke
 
BinaryLongSimpson - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded Simpson comparator for binary fingerprints represented as long [].
BinaryLongSimpson() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongSimpson
 
BinaryLongTanimoto - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Unguarded Tanimoto comparator for binary fingerprints represented as long [].
BinaryLongTanimoto() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTanimoto
 
BinaryLongTversky - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
Parametrized Tversky comparator for binary fingerprints represented as long [].
BinaryLongTversky(double, double) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTversky
Construct new instance.
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.
BinaryVectorComparisonContextFactory<T extends Serializable> - Interface in com.chemaxon.descriptors.common.comparison
Comparison context factory for binary vector descriptors.
BinaryVectorDescriptor - Interface in com.chemaxon.descriptors.common
BinaryVectorDescriptor is a Descriptor which holds a fixed length binary fingerprint.
BinaryVectorDescriptorComparator - Class in com.chemaxon.descriptors.common.binary
DescriptorComparator for binary vectors.
BinaryVectorDescriptorComparator(DescriptorSerializer<BinaryVectorDescriptor>, BinaryVectorComparator, int, UnguardedContext<BinaryVectorDescriptor, ?>) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
Create an instance.
BinaryVectorDescriptorImpl - Class in com.chemaxon.descriptors.common.binary
Binary vector fingerprint representation.
BinaryVectorDescriptorImpl(BitSet, Object, int, BinaryVectors.Endianness) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
Constructor.
BinaryVectorDescriptorImpl(int[], Object, int, BinaryVectors.Endianness) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
Constructor.
BinaryVectorDescriptorImpl(int[], Object, int) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
BinaryVectorDescriptorImpl(long[], Object, int, BinaryVectors.Endianness) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
Construct from a long array representation.
BinaryVectorDescriptorImpl(long[], Object, int) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
BinaryVectorDescriptorImpl(byte[], Object, int, BinaryVectors.Endianness) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
Construct from serialized form.
BinaryVectorDescriptorImpl(byte[], Object, int) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
BinaryVectorDescriptorImpl(String, Object, int, BinaryVectors.Endianness) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
Construct from decimal String representation.
BinaryVectorDescriptorSerializer - Class in com.chemaxon.descriptors.common.binary
Serializer for BinaryVectorDescriptor.
BinaryVectorDescriptorSerializer(Object, int, BinaryVectors.Endianness) - Constructor for class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer
Construct.
BinaryVectorMetricFactory<C> - Interface in com.chemaxon.descriptors.metrics
Represents available metrics for binary vector based descriptors.
BinaryVectorMetricFactory.ToLinenote<C> - Class in com.chemaxon.descriptors.metrics
Utility for creating a default linenote.
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.
bincount - Variable in class com.chemaxon.overlap.wui.dto.Histogram
Bin count.
bins - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionRequest
 
bins - Variable in class com.chemaxon.overlap.wui.dto.Histogram
Histogram bins.
binValues(int[]) - Method in interface com.chemaxon.overlap.result.LinearHistogram
Write bin values to an array,
binwidth - Variable in class com.chemaxon.overlap.wui.dto.Histogram
Bin width.
BitArrayToBitSet - Class in com.chemaxon.descriptors.fingerprints.maccs.cli
 
BitArrayToBitSet() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.cli.BitArrayToBitSet
 
bitSetToDescriptor(Object, BitSet) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.Utils
This method reads the fingerprint from a file in Bitset form and gives back it in as Maccs
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.
bondList(Molecule) - Static method in class com.chemaxon.calculations.util.MU
Extract a bondlist.
BondList(Molecule) - Constructor for class com.chemaxon.calculations.util.MU.BondList
 
border(String, int) - Method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer
Specify border.
borderColor(String) - Method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer
Draw border.
BorderedPane - Class in com.chemaxon.overlap.cli.util.images
Delegates a pane with added borders.
BorderedPane(SubPane, int, int, int, int) - Constructor for class com.chemaxon.overlap.cli.util.images.BorderedPane
 
BorderedPane(SubPane, int) - Constructor for class com.chemaxon.overlap.cli.util.images.BorderedPane
 
BppManagerMBean - Interface in com.chemaxon.overlap.concurrent
MBean for managing batched paged processor.
BppParameters - Class in com.chemaxon.overlap.concurrent.impl
Parameters object for batched paged processor.
BppParameters(int, int, SubProgressObserver, ExecutorService) - Constructor for class com.chemaxon.overlap.concurrent.impl.BppParameters
 
BppParameters(BppParameters) - Constructor for class com.chemaxon.overlap.concurrent.impl.BppParameters
 
BruteForcePagedSimilarity<D extends Descriptor> - Class in com.chemaxon.overlap.bruteforce
Brute force paged similarity search.
BruteForcePagedSimilarity(DescriptorComparator<D>, List<ImmutableList<D>>, List<D>) - Constructor for class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Construct new immutable reference.
buffer(int) - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
 
buffer(int) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
 
buffer(int) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
 
BufferedImageRenderer - Class in com.chemaxon.overlap.cli.util.images
Renderer implementation to paint on a BufferedImage.
BufferedImageRenderer(int, int) - Constructor for class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
Size of image in pixels.
BufferedImageRendering - Class in com.chemaxon.overlap.cli.util.images
Render a layout to a BufferedImage.
BufferedImageRendering(boolean) - Constructor for class com.chemaxon.overlap.cli.util.images.BufferedImageRendering
Construct.
build() - Method in interface com.chemaxon.apidiscovery.interfaces.ParameterBuilder
Constructs an immutable instance of T.
build() - Method in interface com.chemaxon.apidiscovery.linenote.LinenoteBuilder
Create factory.
build() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
Build immutable clustering representation.
build() - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec
Build represented hierarchy.
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.alignment.drshape.DRShapeComparatorParameter.Builder
 
build() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter.Builder
 
build() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter.Builder
 
build() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter.Builder
 
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.ecfp.ThreadLocalizedEcfpParameters.Builder
Build immutable representation.
build() - Method in class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
Build a new instance of MaccsParameters.
build() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
 
build() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
 
build() - Method in class com.chemaxon.overlap.cli.util.pages.PagedBuilder
Build immutable representation.
build() - Method in class com.chemaxon.overlap.io.CompactStringStorage.Builder
 
build() - Method in class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorBuilder
Build serializable, immutable projector.
build() - Method in class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorMcb
Build serializable, immutable projector.
build() - Method in interface com.chemaxon.overlap.io.MasterStorages.MasterStorageBuilder
Build immutable, serializable storage from the current state.
build() - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
Create immutable representation.
build() - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
Create the master storage from the current state.
build() - Method in class com.chemaxon.overlap.result.impl.KnnResultsBuilder
Build.
build() - Method in class com.chemaxon.overlap.result.impl.LinearHistogramBuilder
Build histogram.
build(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder
Build scaffold extension.
builder() - Static method in class com.chemaxon.apidiscovery.linenote.Linenotes
Create line notes builder.
builder() - Static method in class com.chemaxon.calculations.util.CharLayout
Construct an empty builder.
builder(String) - Static method in class com.chemaxon.calculations.util.CharLayout
Construct an empty builder initialized from a multiline.
Builder() - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter.Builder
Instantiates a Builder for ShapeComparatorParameters building with default values.
Builder(DRShapeComparatorParameter) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter.Builder
 
Builder() - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter.Builder
 
Builder(DRShapeGeneratorParameter) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter.Builder
 
Builder() - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter.Builder
Instantiates a Builder for ShapeComparatorParameters building with default values.
Builder(ShapeComparatorParameter) - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter.Builder
 
Builder() - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter.Builder
 
Builder(ShapeGeneratorParameter) - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter.Builder
 
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Constructor with default settings.
Builder(CfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
Constructor based on a parameter object.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Constructor with default settings.
Builder(EcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Constructor based on a parameter object.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Construct.
Builder(ThreadLocalizedEcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Construct from the state of a ThreadLocalizedEcfpParameters.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
Constructor mandated by descriptors API contracts.
Builder(MaccsParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
Constructor mandated by descriptors API contracts.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Constructor with default settings.
Builder(PfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
Constructor based on a parameter object.
Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
Constructor with default settings.
Builder(ThreadLocalizedPfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder
Constructor based on a parameter object.
Builder() - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate builder with default values.
Builder(double, double) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate with weights.
Builder(TverskyParameters) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
Instantiate builder based on an actual parameter instance.
Builder() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Constructor with default settings.
Builder(BvParameters) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Construct to represent the state of a parameter object instance.
Builder() - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Constructor with default settings.
Builder(FvParameters) - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
Construct to represent the state of a parameter object instance.
Builder(int, int) - Constructor for class com.chemaxon.overlap.io.CompactStringStorage.Builder
Construct.
BuilderClass - Annotation Type in com.chemaxon.apidiscovery.annotations
This annotation gives information about the associated ParameterBuilder for this class.
builderToString(List<StringBuilder>) - Static method in class com.chemaxon.calculations.util.CharLayout
Collapse builder contents to a String.
BuildStorage - Class in com.chemaxon.overlap.cli
Build serialized descriptors storage from molecules.
BuildStorageStat - Class in com.chemaxon.overlap.cli
Statistics for BuildStorage execution.
BuildStorageStat() - Constructor for class com.chemaxon.overlap.cli.BuildStorageStat
 
BvGenerator - Interface in com.chemaxon.descriptors.vectors.binary
Generator for generic binary vector descriptors.
BvGeneratorImpl - Class in com.chemaxon.descriptors.vectors.binary
Implementation for binary vectors.
BvGeneratorImpl.Service - Class in com.chemaxon.descriptors.vectors.binary
Class wrapping constructor for DI.
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.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.
byAtom(int) - Method in interface com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroup
Retrieve attachment by its pseudo atom index.
byAtom(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
 
byCompatibleCountDecreasing() - Static method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.ScoredExtension
 
byGainDecreasing() - Static method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.ScoredExtension
 
byIndex(int) - Method in interface com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroup
Retrieve attachment by its index.
byIndex(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroupImpl
 
byteDiffSumToDouble(long) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
Scale the sum of differences of bytes into double.
byteDiffSumToDouble(long) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
byteDomainToDouble(double) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
Scale byte domain representation to the original.
byteDomainToDouble(double) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
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.
bytesFromFloats(float[]) - Static method in class com.chemaxon.descriptors.common.realvector.Util
Serialize floats to byte array.
bytesFromShorts(short[]) - Static method in class com.chemaxon.descriptors.common.realvector.Util
Serialize shorts to byte array.
byteSqrDiffSumToDouble(long) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
Scale the square sum of differences of bytes into double.
byteSqrDiffSumToDouble(long) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
bytesToFloats(byte[]) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
bytesToFloats(byte[]) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
byteToFloat(byte) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
Scale byte representation to float.
byteToFloat(byte) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 

C

calcSpec - Variable in class com.chemaxon.overlap.cli.util.prop.CliParam
Parameter for extractor.
calcType - Variable in class com.chemaxon.overlap.cli.util.prop.CliParam
Extractor type.
calculate(DescRes, DissimilarityDistributionRequest, ProgressObserver) - Method in class com.chemaxon.overlap.service.CalculateDissimilarityDistributionService
 
calculate(DescRes, DissimilarityDistributionRequest, ExecutionMonitoring<DissimilarityDistributionResult>) - Method in class com.chemaxon.overlap.service.CalculateDissimilarityDistributionService
 
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
 
calculateByDescriptor(DescRes, String, String, double, double, int) - Method in class com.chemaxon.overlap.service.CalculateDissimilarityDistributionService
 
calculateDarkness() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
 
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(BinaryVectorDescriptor, BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
calculateDissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
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.
calculateDissimilarity(FloatVectorDescriptor, FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
calculateDissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
calculateDissimilarity(FloatVectorDescriptor, FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
calculateDissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
calculateDissimilarityDistribution(T, double, double, int, SubProgressObserver, PartialResultConsumer<LinearHistogram>, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Calculate dissimilarity distribution.
calculateDissimilarityDistribution(DescRes, String, String, double, double, int) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Calculate dissimilarity distribution for a query molecule.
calculateDissimilarityDistributionByDescriptor(DescRes, String, String, double, double, int) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Calculate dissimilarity distribution for a query molecule.
calculateDissimilarityDistributionByDescriptorPost(DescRes, String, String, double, double, int) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Calculate dissimilarity distribution for a query molecule.
calculateDissimilarityDistributionPost(DescRes, String, String, double, double, int) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Calculate dissimilarity distributon for a query molecule.
calculateDissimilarityDistributionPostBody(DescRes, DissimilarityDistributionRequest) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Calculate dissimilarity distributon for a query molecule.
calculateDissimilarityDistributionPostBodyAsync(DescRes, DissimilarityDistributionRequest, Long) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Launch asynchronous dissimilarity distribution calculation.
CalculateDissimilarityDistributionService - Class in com.chemaxon.overlap.service
 
CalculateDissimilarityDistributionService() - Constructor for class com.chemaxon.overlap.service.CalculateDissimilarityDistributionService
 
calculateDissimilarityMatrix(DissimilarityInput, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
Distance matrix calculation.
calculateFloatVectorDissimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Calculate dissimilarity.
calculateFloatVectorSimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
Deprecated.
In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
calculateFullMatrix(List<T>, SubProgressObserver, ExecutorService, boolean) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Calculate full dissimilarity matrix.
calculateImplicitHSubstitutionCount(RgFrag, IntMatch) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
Implicit H count.
CalculateOverlap - Class in com.chemaxon.overlap.cli
Calculate overlap between two sets.
CalculateOverlap.OverlapResult<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.overlap.cli
Data object for compared sets.
CalculateOverlapParameters - Class in com.chemaxon.overlap.cli
Command line arguments.
CalculateOverlapParameters() - Constructor for class com.chemaxon.overlap.cli.CalculateOverlapParameters
 
CalculateOverlapParameters.NoSplitter - Class in com.chemaxon.overlap.cli
Helper class to avoid splitting multi arity cli arguments on commas.
CalculateOverlapStat - Class in com.chemaxon.overlap.cli
Statistics for CalculateOverlap execution.
CalculateOverlapStat() - Constructor for class com.chemaxon.overlap.cli.CalculateOverlapStat
 
calculateSelfKnn(int, int, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Brute force find kNN among the contents of the represented descriptors.
CalculateSelfOverlap - Class in com.chemaxon.overlap.cli
Calculate self overlap.
CalculateSelfOverlap.SelfOverlap<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.overlap.cli
Data object for self overlap.
calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateSimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
calculateSimilarity(BinaryVectorDescriptor, BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
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.
calculateSimilarity(FloatVectorDescriptor, FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
calculateSimilarity(FloatVectorDescriptor, FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
call() - Method in class com.chemaxon.overlap.storage.SerializeTask
 
cancel() - Method in class com.chemaxon.calculations.common.CancelObserverImpl
Sign cancelling.
cancel() - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
 
cancel() - Method in interface com.chemaxon.calculations.common.ProgressObservable
Sets the cancelled state.
cancel(String) - Method in class com.chemaxon.overlap.service.async.AsyncCallService
 
cancel(String) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalAsyncCallsResource
Sets the cancel request state.
cancelled - Variable in class com.chemaxon.overlap.wui.dto.TaskDto
Set when task execution is cancelled.
CancelObserver - Interface in com.chemaxon.calculations.common
Callback to propagate cancel requests into long running tasks.
CancelObserverImpl - Class in com.chemaxon.calculations.common
Implementation of CancelObserver.
CancelObserverImpl() - Constructor for class com.chemaxon.calculations.common.CancelObserverImpl
Constructor for a cancellable observer implementation.
CancelObserverImpl(CancelObserver) - Constructor for class com.chemaxon.calculations.common.CancelObserverImpl
Constructor with an underlying polling source.
canHandle(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory
Returns true if this factory can handle the given xml.
canHandle(String) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl.CfpReaderFactoryImpl
 
canHandle(String) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl.EcfpReaderFactoryImpl
 
canHandle(String) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl.PfReaderFactoryImpl
 
canonicalSmiles() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
canonicalSmilesBasedFrameworks(Function<Molecule, T>, StandardizerWrapper...) - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
CellField - Interface in com.chemaxon.calculations.util.cellfield
CellField is a dynamic data structure containing columns of different data types.
CellFieldImpl - Class in com.chemaxon.calculations.util.cellfield.impl
Naive CellField implementation backed up by column storage ArrayLists.
CellFieldImpl() - Constructor for class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
CellFieldImpl.ConstructWrapper - Class in com.chemaxon.calculations.util.cellfield.impl
Implementation for DI interface.
CellFields - Class in com.chemaxon.calculations.util.cellfield
Utility methods for CellField API.
CellFields.ConstructNewCellFieldImpl - Interface in com.chemaxon.calculations.util.cellfield
Interface used for DI.
cellSize - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
 
cfgxml(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.TransformMolecule
 
Cfp - Interface in com.chemaxon.descriptors.fingerprints.cfp
Folded fixed length bit string representation of the CFP descriptor.
CfpBsWrapper - Class in com.chemaxon.descriptors.alternates
Wrapper for CFP with binary string representation.
CfpBsWrapper(String) - Constructor for class com.chemaxon.descriptors.alternates.CfpBsWrapper
Construct new instance.
CfpComparator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Comparator for Cfp descriptor representation.
CfpDsWrapper - Class in com.chemaxon.descriptors.alternates
Wrapper for CFP with default decimal String representation.
CfpDsWrapper(String) - Constructor for class com.chemaxon.descriptors.alternates.CfpDsWrapper
Construct new instance.
CfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Calculates CFP (fixed length folded binary vector 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.ConstructCfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
Interface representing CFP generator constructor.
CfpReaderFactoryImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl.CfpReaderFactoryImpl
 
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.
CfpTableReaderImpl - Class in com.chemaxon.descriptors.fingerprints.cfp
CfpTableReader implementation.
CfpTableReaderImpl(String) - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl
 
CfpTableReaderImpl.CfpReaderFactoryImpl - Class in com.chemaxon.descriptors.fingerprints.cfp
Factory implementation for CfpTableReader.
chainOf(StandardizerWrapper...) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Create a chained wrapper.
CharIterator - Class in com.chemaxon.overlap.cli.util.pipeline
Non synchronized buffering over a Reader.
CharIterator(Reader, int) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.CharIterator
 
CharLayout - Class in com.chemaxon.calculations.util
Simple utilities for character based multiline layouts.
CharLayout.HA - Enum in com.chemaxon.calculations.util
Possible horizontal alignments.
charset(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
 
charset(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
 
checkBitCounts(int, int, int, int) - Static method in class com.chemaxon.descriptors.metrics.BinaryVectorComparator.Util
Check that descriptor comparison parameters are consistent.
ChemTermPropertyExtractor<T> - Class in com.chemaxon.overlap.cli.util.prop.impl
Extractor for Chemical Terms
ChemTermPropertyExtractorFactory - Class in com.chemaxon.overlap.cli.util.prop.impl
Extractor factory for ChemTermPropertyExtractor.
ChemTermPropertyExtractorFactory() - Constructor for class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractorFactory
 
ChoiceDescriptor - Interface in com.chemaxon.apidiscovery.linenote
Represents a factory method with its parameterization.
choiceDescriptors() - Method in interface com.chemaxon.apidiscovery.linenote.Linenote
Available choices.
ChoiceParameterDescriptor<T> - Interface in com.chemaxon.apidiscovery.linenote
Parameter for a choice.
ChoiceParameterType - Enum in com.chemaxon.apidiscovery.linenote
Parameter types.
choiceParameterValue(ChoiceParameterDescriptor<T>) - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceParameterValueProvider
Provide parameter value for choice parameter descriptor.
ChoiceParameterValueProvider - Interface in com.chemaxon.apidiscovery.linenote
Provide parameter value for choice parameter descriptor.
choices - Variable in class com.chemaxon.overlap.wui.dto.LinenoteDto
Choices represented.
ChoiceValueParameterParser<T> - Interface in com.chemaxon.apidiscovery.linenote
Value parameter parser.
clean2d - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest
Invoke Clean2D (Cleaner#clean(chemaxon.struc.MoleculeGraph, int)) on the imported structure.
Clean2dWrapper - Class in com.chemaxon.descriptors.alternates
Wrap Clean2D.
Clean2dWrapper(String) - Constructor for class com.chemaxon.descriptors.alternates.Clean2dWrapper
Construct.
clearMoleculeProperties() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
cliArguments - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat
CLI arguments.
cliArguments - Variable in class com.chemaxon.overlap.cli.BuildStorageStat
CLI arguments.
cliArguments - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
CLI arguments.
cliArguments - Variable in class com.chemaxon.overlap.cli.CreateMmsStat
CLI arguments.
cliArguments - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
CLI arguments.
cliArguments - Variable in class com.chemaxon.overlap.cli.SearchStorageStat
CLI arguments.
CliEntry<PT> - Interface in com.chemaxon.overlap.cli.invocation
Entry point of a CLI.
CliEntry2<PT,ST> - Interface in com.chemaxon.overlap.cli.invocation
Entry point of a CLI which can collect execution statistics.
CliInvocation - Class in com.chemaxon.overlap.cli.invocation
Utilities to handle command line interface invocations.
CliInvocationEnv - Interface in com.chemaxon.overlap.cli.invocation
Environment of an invocation.
CliInvocationEnv2<ST> - Interface in com.chemaxon.overlap.cli.invocation
Environment of an invocation when statistics is possibly specified.
CliInvocationSpec<PT> - Interface in com.chemaxon.overlap.cli.invocation
Specify command line invocation.
CliInvocationSpec2<PT,ST> - Interface in com.chemaxon.overlap.cli.invocation
Environment of a profiling/execution statistics aware CLI invocation.
CliParam - Class in com.chemaxon.overlap.cli.util.prop
Command line parameter DTO for property extractor specification.
CliParam.Converter - Class in com.chemaxon.overlap.cli.util.prop
Expose parser for JCommander.
cliParameters - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat
CLI parameters parsed.
cliParameters - Variable in class com.chemaxon.overlap.cli.BuildStorageStat
CLI parameters parsed.
cliParameters - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
CLI parameters parsed.
cliParameters - Variable in class com.chemaxon.overlap.cli.CreateMmsStat
CLI parameters parsed.
cliParameters - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
CLI parameters parsed.
cliParameters - Variable in class com.chemaxon.overlap.cli.SearchStorageStat
CLI parameters parsed.
CliUtil - Class in com.chemaxon.overlap.cli.util
CLI related utilities for overlap-examples.
clone() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder
Clone.
CloneCxnMolecule - Class in com.chemaxon.overlap.cli.util.pipeline
Clone Molecule object for subsequent modifications.
CloneCxnMolecule() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.CloneCxnMolecule
 
cloneMolecule(Molecule) - Method in class com.chemaxon.overlap.cli.util.pipeline.CloneCxnMolecule
 
close() - Method in interface com.chemaxon.calculations.common.ProgressObserver
close() - Method in interface com.chemaxon.calculations.io.CloseableIterator
 
close() - Method in interface com.chemaxon.calculations.io.CloseableSink
Close sink, cleanup if required.
close() - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
close() - Method in class com.chemaxon.calculations.util.CloseableLineIterator
 
close() - Method in class com.chemaxon.overlap.cli.prof.Prof
 
close() - Method in class com.chemaxon.overlap.cli.util.MultiInputCloseableIterator
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.Connect
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.Mark
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.OutputStreamStatCollector
 
close() - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineStep
Close the step.
close() - Method in interface com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerialization
Close the underlying resource and write retained index data.
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
 
close() - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
 
close() - Method in class com.chemaxon.overlap.io.StructureRecordIterator
 
close() - Method in class com.chemaxon.overlap.service.async.AsyncCallService
 
CloseableAbstractIterator<T> - Class in com.chemaxon.calculations.io
Guava AbstractIterator based CloseableIterator extension.
CloseableAbstractIterator() - Constructor for class com.chemaxon.calculations.io.CloseableAbstractIterator
 
CloseableIterator<T> - Interface in com.chemaxon.calculations.io
Closeable iterator.
CloseableIterators - Class in com.chemaxon.calculations.io
Utility class.
CloseableLineIterator - Class in com.chemaxon.calculations.util
Closeable LineIterator wrapper.
CloseableLineIterator(Reader) - Constructor for class com.chemaxon.calculations.util.CloseableLineIterator
Construct.
CloseableSink<T> - Interface in com.chemaxon.calculations.io
Closeable sink accepting values.
CloseableSinks - Class in com.chemaxon.calculations.io
Utilities.
CloseableStringSink - Interface in com.chemaxon.calculations.io
Convenience interface.
Cluster<T> - Interface in com.chemaxon.clustering.common
Cluster represents a group of structures.
cluster(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
A spec for a clusterId.
cluster(DissimilarityInput, LanceWilliamsMerge, ProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
Invoke clustering.
cluster(double[][], LanceWilliamsMerge, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
Invoke clustering.
clusterLevel(T) - Method in interface com.chemaxon.clustering.common.LevelAssigner
Level associated to a hierarchic cluster.
clusterLevelFunction() - Method in interface com.chemaxon.clustering.common.LevelAssigner
CLuster level association.
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(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.
CmdlineContext - Interface in com.chemaxon.calculations.util
Represents contexts of command line applications.
CmdlineContext.ExitWithNonZeroStatus - Exception in com.chemaxon.calculations.util
Expected exception when CmdlineContext.exit(int) invoked with non-zero status.
CmdlineContext.ExitWithZeroStatus - Exception in com.chemaxon.calculations.util
Expected exception when CmdlineContext.exit(int) invoked with zero status.
CmdlineUtils - Class in com.chemaxon.calculations.util
Command line related utilities.
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.
collectContextNames() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Collect applicable names.
collectionCount - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.GarbageCollector
 
collectionCount - Variable in class com.chemaxon.overlap.wui.dto.GarbageCollectorInfoDto
 
collectionTime - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.GarbageCollector
 
collectionTime - Variable in class com.chemaxon.overlap.wui.dto.GarbageCollectorInfoDto
 
collectionUsage - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryPool
Collection usage of the pool or null when collection usage not supported.
collectionUsage - Variable in class com.chemaxon.overlap.wui.dto.MemoryPoolInfoDto
Collection usage of the pool or null when collection usage not supported.
collectionUsageUsed - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryPool
Collection usage of the pool or -1 when usage not supported.
collectionUsageUsed - Variable in class com.chemaxon.overlap.wui.dto.MemoryPoolInfoDto
Collection usage of the pool or -1 when usage not supported.
CollectStorage - Class in com.chemaxon.overlap.cli.util.pipeline
Collect a master property storage.
CollectStorage() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
 
colorScaleLabelHeight - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
 
colorScaleLabelText - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
 
Column<T> - Interface in com.chemaxon.calculations.util.cellfield
Column represents a specific column (property) of a specific cell field.
Column - Class in com.chemaxon.screen
 
Column(String) - Constructor for class com.chemaxon.screen.Column
 
ColumnImpl<T> - Class in com.chemaxon.calculations.util.cellfield.impl
Implementation for Column.
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.linenote - package com.chemaxon.apidiscovery.linenote
Linear parameter notation utilities.
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.calculations.io - package com.chemaxon.calculations.io
 
com.chemaxon.calculations.io.formats - package com.chemaxon.calculations.io.formats
 
com.chemaxon.calculations.logging.moleculeawarelog - package com.chemaxon.calculations.logging.moleculeawarelog
 
com.chemaxon.calculations.util - package com.chemaxon.calculations.util
Various utilities used in calculations, descriptors, clustering and overlap analysis.
com.chemaxon.calculations.util.cellfield - package com.chemaxon.calculations.util.cellfield
Simple cell field api.
com.chemaxon.calculations.util.cellfield.impl - package com.chemaxon.calculations.util.cellfield.impl
Cellfield utility implementations.
com.chemaxon.clustering.common - package com.chemaxon.clustering.common
Common components of clustering related APIs.
com.chemaxon.clustering.framework - package com.chemaxon.clustering.framework
Hierarchic structural framework based clustering.
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.alignment.drshape - package com.chemaxon.descriptors.alignment.drshape
 
com.chemaxon.descriptors.alignment.shape - package com.chemaxon.descriptors.alignment.shape
 
com.chemaxon.descriptors.alternates - package com.chemaxon.descriptors.alternates
Alternate implementations allowing integration testing.
com.chemaxon.descriptors.alternates.cli - package com.chemaxon.descriptors.alternates.cli
 
com.chemaxon.descriptors.common - package com.chemaxon.descriptors.common
Unguarded descriptor handling.
com.chemaxon.descriptors.common.binary - package com.chemaxon.descriptors.common.binary
Default implementation and utilities for binary vector (bit string) descriptors.
com.chemaxon.descriptors.common.comparison - package com.chemaxon.descriptors.common.comparison
 
com.chemaxon.descriptors.common.comparison.impl - package com.chemaxon.descriptors.common.comparison.impl
 
com.chemaxon.descriptors.common.realvector - package com.chemaxon.descriptors.common.realvector
Default implementation for real vector descriptors.
com.chemaxon.descriptors.common.reflect - package com.chemaxon.descriptors.common.reflect
 
com.chemaxon.descriptors.common.unguarded - package com.chemaxon.descriptors.common.unguarded
Interfaces for Descriptors API unguarded representations.
com.chemaxon.descriptors.common.unguarded.impl - package com.chemaxon.descriptors.common.unguarded.impl
Unguarded descriptor handling implementations.
com.chemaxon.descriptors.common.unguarded.impl.calc - package com.chemaxon.descriptors.common.unguarded.impl.calc
 
com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong - package com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong
 
com.chemaxon.descriptors.common.unguarded.impl.calc.floats - package com.chemaxon.descriptors.common.unguarded.impl.calc.floats
 
com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv - package com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv
 
com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv - package com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv
 
com.chemaxon.descriptors.common.unguarded.impl.extractors - package com.chemaxon.descriptors.common.unguarded.impl.extractors
 
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.maccs - package com.chemaxon.descriptors.fingerprints.maccs
ChemAxon implementation of the MACCS 166 bit fingerprints.
com.chemaxon.descriptors.fingerprints.maccs.cli - package com.chemaxon.descriptors.fingerprints.maccs.cli
 
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.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.
com.chemaxon.overlap - package com.chemaxon.overlap
Overlap analysis related codes.
com.chemaxon.overlap.bruteforce - package com.chemaxon.overlap.bruteforce
Brute force similarity search.
com.chemaxon.overlap.cli - package com.chemaxon.overlap.cli
 
com.chemaxon.overlap.cli.invocation - package com.chemaxon.overlap.cli.invocation
Utilities to handle command line interface invocations.
com.chemaxon.overlap.cli.prof - package com.chemaxon.overlap.cli.prof
 
com.chemaxon.overlap.cli.util - package com.chemaxon.overlap.cli.util
Utilities for command line interfaces.
com.chemaxon.overlap.cli.util.images - package com.chemaxon.overlap.cli.util.images
 
com.chemaxon.overlap.cli.util.importing - package com.chemaxon.overlap.cli.util.importing
 
com.chemaxon.overlap.cli.util.pages - package com.chemaxon.overlap.cli.util.pages
 
com.chemaxon.overlap.cli.util.pipeline - package com.chemaxon.overlap.cli.util.pipeline
Importing pipeline utilities.
com.chemaxon.overlap.cli.util.prop - package com.chemaxon.overlap.cli.util.prop
Property extraction.
com.chemaxon.overlap.cli.util.prop.impl - package com.chemaxon.overlap.cli.util.prop.impl
 
com.chemaxon.overlap.concurrent - package com.chemaxon.overlap.concurrent
Concurrency related utilities.
com.chemaxon.overlap.concurrent.impl - package com.chemaxon.overlap.concurrent.impl
 
com.chemaxon.overlap.context - package com.chemaxon.overlap.context
Overlap analysis context related.
com.chemaxon.overlap.io - package com.chemaxon.overlap.io
 
com.chemaxon.overlap.partialresult - package com.chemaxon.overlap.partialresult
 
com.chemaxon.overlap.persistence.serialization - package com.chemaxon.overlap.persistence.serialization
Utilities for high performance serialization/deserialization.
com.chemaxon.overlap.persistence.storage - package com.chemaxon.overlap.persistence.storage
 
com.chemaxon.overlap.presenter - package com.chemaxon.overlap.presenter
 
com.chemaxon.overlap.result - package com.chemaxon.overlap.result
Overlap analysis related result types.
com.chemaxon.overlap.result.impl - package com.chemaxon.overlap.result.impl
Overlap analysis related result type implementations.
com.chemaxon.overlap.service - package com.chemaxon.overlap.service
 
com.chemaxon.overlap.service.async - package com.chemaxon.overlap.service.async
 
com.chemaxon.overlap.service.task - package com.chemaxon.overlap.service.task
 
com.chemaxon.overlap.servlets - package com.chemaxon.overlap.servlets
This package is deprecated.
com.chemaxon.overlap.splits - package com.chemaxon.overlap.splits
 
com.chemaxon.overlap.storage - package com.chemaxon.overlap.storage
 
com.chemaxon.overlap.storage.impl - package com.chemaxon.overlap.storage.impl
 
com.chemaxon.overlap.unguarded - package com.chemaxon.overlap.unguarded
Unguarded descriptor handling.
com.chemaxon.overlap.util.idgenerator - package com.chemaxon.overlap.util.idgenerator
 
com.chemaxon.overlap.version - package com.chemaxon.overlap.version
 
com.chemaxon.overlap.wui - package com.chemaxon.overlap.wui
 
com.chemaxon.overlap.wui.application - package com.chemaxon.overlap.wui.application
 
com.chemaxon.overlap.wui.context - package com.chemaxon.overlap.wui.context
WebUI context API.
com.chemaxon.overlap.wui.context.features - package com.chemaxon.overlap.wui.context.features
 
com.chemaxon.overlap.wui.dto - package com.chemaxon.overlap.wui.dto
Data transfer objects used by the fast similarity search web application.
com.chemaxon.overlap.wui.res - package com.chemaxon.overlap.wui.res
WebUI classes exposed as resources.
com.chemaxon.overlap.wui.res.annotations - package com.chemaxon.overlap.wui.res.annotations
 
com.chemaxon.overlap.wui.res.search - package com.chemaxon.overlap.wui.res.search
 
com.chemaxon.overlap.wui.resources - package com.chemaxon.overlap.wui.resources
JAX-RS resource classes exposed by the REST interface.
com.chemaxon.overlap.wui.resources.exceptions - package com.chemaxon.overlap.wui.resources.exceptions
 
com.chemaxon.screen - package com.chemaxon.screen
 
com.chemaxon.screen.desktop - package com.chemaxon.screen.desktop
 
com.chemaxon.virtuallib.sc.cli - package com.chemaxon.virtuallib.sc.cli
CLI for scaffold conversion.
com.chemaxon.virtuallib.sc.model.sdf - package com.chemaxon.virtuallib.sc.model.sdf
Model of SDF based virtual library description.
command - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceDto
Choice command.
COMMENT_SDFIELD - Static variable in class com.chemaxon.virtuallib.sc.model.sdf.Scaffold
SD field storing optional Comment.
committed - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryUsageDesc
 
committed - Variable in class com.chemaxon.overlap.wui.dto.MemoryUsageDescDto
 
CompactStringStorage - Class in com.chemaxon.overlap.io
Concatenated UTF-8 byte array backed master String storage.
CompactStringStorage.Builder - Class in com.chemaxon.overlap.io
Builder class.
CompactStringStorageSerialization - Class in com.chemaxon.overlap.persistence.storage
Helper class to serialize CompactStringStorage instances.
comparatorFromString(String) - Static method in class com.chemaxon.overlap.cli.PagedDescriptorImport
Create descriptor comparator from String.
compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
compare(DRShapeDescriptor, DRShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeHistogramComparator
 
compare(DRShapeDescriptor, DRShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeIntersectionComparator
 
compare(DRShapeDescriptor, DRShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeTanimotoComparator
 
compare(ShapeDescriptor, ShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeIntersectionComparator
 
compare(ShapeDescriptor, ShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeTanimotoComparator
 
compare(T, T) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
 
compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
 
compare(BinaryVectorDescriptor, BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
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.
compare(FloatVectorDescriptor, FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
compare(FloatVectorDescriptor, FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
ComparisonContext<DC extends DescriptorComparator<D>,D extends Descriptor,T extends Serializable> - Interface in com.chemaxon.descriptors.common.comparison
Expose descriptor comparison of bare/rich and unguarded representations.
comparisonContext(ComparisonContext<?, D, N>) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Update represented comparison context.
comparisonContextFactory() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
comparisonContextFactory() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
 
ComparisonContextFactory<DC extends DescriptorComparator<D>,D extends Descriptor,T extends Serializable> - Interface in com.chemaxon.descriptors.common.comparison
Creates comparison contexts.
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Get an unguarded context factory.
comparisonContextFactory(ScaledFvDescriptorGenerator) - Method in interface com.chemaxon.descriptors.common.realvector.ScaledFvDescriptorFactory
Create context factory.
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
 
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
 
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator
 
comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
 
comparisonContextFactory() - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
comparisonContextFactory() - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
ComparisonContextImpl<DC extends DescriptorComparator<D>,D extends Descriptor,T extends Serializable> - Class in com.chemaxon.descriptors.common.comparison.impl
Simple implementation of ComparisonContext interface.
ComparisonContextImpl(UnguardedContext<D, T>, DC, DescriptorSerializer<D>) - Constructor for class com.chemaxon.descriptors.common.comparison.impl.ComparisonContextImpl
Construct.
comparisonLinenote() - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
 
comparisonLinenote() - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
 
comparisonLinenote() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
 
comparisonLinenote() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
 
comparisonLinenote() - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
 
comparisonLinenote() - Method in interface com.chemaxon.descriptors.metrics.MetricFactory
Gets the string based parameterization description.
comparisonLinenote() - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
comparisonLinenote() - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
ComparisonResult - Interface in com.chemaxon.descriptors.common
Result of a descriptor comparison.
compatible(Guarded, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat
Ensure the guard object based compatibility of two objects.
compatibleCount - Variable in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.ScoredExtension
 
compatibleWithGuard(Object, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat
Ensure the guard object based compatibility of two objects.
CompleteLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage
 
composer(Appendable, Closeable) - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
 
composer(T) - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
 
composer(Appendable, Closeable) - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
 
composer(T) - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
 
composer(Appendable, Closeable) - Method in interface com.chemaxon.calculations.io.Segmenter
Create composer.
composer(T) - Method in interface com.chemaxon.calculations.io.Segmenter
computeNext() - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
computeNext() - Method in class com.chemaxon.overlap.cli.util.JsLineFilter
 
computeNext() - Method in class com.chemaxon.overlap.cli.util.MultiInputCloseableIterator
 
computeNext() - Method in class com.chemaxon.overlap.io.StructureRecordIterator
 
confCount(Optional<Integer>) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter.Builder
Count of generated random initial conformations during the alignment.
confCount(Optional<Integer>) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter.Builder
Count of generated random initial conformations during the alignment.
Connect - Class in com.chemaxon.overlap.cli.util.pipeline
Connect the last specified node to an arbitrary output.
Connect() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.Connect
 
Connection() - Constructor for class com.chemaxon.overlap.cli.PipelineRunner.Connection
 
ConsolePO - Class in com.chemaxon.calculations.common
Stupid progressObserver to write to console.
ConsolePO(String) - Constructor for class com.chemaxon.calculations.common.ConsolePO
Construct a new instance printing to System.err with a default delay (5s).
ConsolePO(PrintStream, String) - Constructor for class com.chemaxon.calculations.common.ConsolePO
Construct a new instance printing to a specific stream with a default delay (5s).
ConsolePO(String, long) - Constructor for class com.chemaxon.calculations.common.ConsolePO
Construct a new instance printing to System.err.
ConsolePO(PrintStream, String, long) - Constructor for class com.chemaxon.calculations.common.ConsolePO
Construct a new instance printing to a s[ecofoc stream.
ConsolePO.Callback - Interface in com.chemaxon.calculations.common
Callback handle.
construct() - Method in interface com.chemaxon.calculations.util.cellfield.CellFields.ConstructNewCellFieldImpl
Instantiate new empty cell field.
construct() - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl.ConstructWrapper
 
constructBvGenerator(BvParameters) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl.Service
 
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.
constructCfpGenerator(CfpParameters) - Method in class com.chemaxon.descriptors.fingerprints.cfp.ConstructCfpGeneratorImpl
 
ConstructCfpGeneratorImpl - Class in com.chemaxon.descriptors.fingerprints.cfp
Class wrapping constructor for DI.
ConstructCfpGeneratorImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.ConstructCfpGeneratorImpl
 
constructEcfpGenerator(EcfpParameters) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ConstructEcfpGeneratorImpl
 
constructEcfpGenerator(EcfpParameters) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ConstructThreadLocalizedEcfpGeneratorImpl
 
constructEcfpGenerator(EcfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.ConstructEcfpGenerator
Constructor invocation.
constructEcfpGenerator(EcfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.ConstructThreadLocalizedEcfpGenerator
Constructor invocation.
ConstructEcfpGeneratorImpl - Class in com.chemaxon.descriptors.fingerprints.ecfp
Class wrapping constructor for DI.
ConstructEcfpGeneratorImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ConstructEcfpGeneratorImpl
 
constructExtractor(Class<T>, String) - Method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractorFactory
 
constructExtractor(Class<T>, String) - Method in class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractorFactory
 
constructExtractor(Class<T>, String) - Method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractorFactory
 
constructExtractor(Class<T>, String) - Method in interface com.chemaxon.overlap.cli.util.prop.PropertyExtractorFactory
Construct extractor.
constructMaccsGenerator(MaccsParameters) - Method in class com.chemaxon.descriptors.fingerprints.maccs.ConstructMaccsGeneratorImpl
 
constructMaccsGenerator(MaccsParameters) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.ConstructMaccsGenerator
Constructor invocation.
ConstructMaccsGeneratorImpl - Class in com.chemaxon.descriptors.fingerprints.maccs
Class wrapping constructor for DI.
ConstructMaccsGeneratorImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.ConstructMaccsGeneratorImpl
 
constructPfGenerator(PfParameters) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ConstructPfGeneratorImpl
 
constructPfGenerator(PfParameters) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ConstructThreadLocalizedPfGeneratorImpl
 
constructPfGenerator(PfParameters) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.ConstructPfGenerator
Constructor invocation.
constructPfGenerator(PfParameters) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.ConstructThreadLocalizedPfGenerator
Constructor invocation.
ConstructPfGeneratorImpl - Class in com.chemaxon.descriptors.fingerprints.pf2d
Constructor implementation.
ConstructPfGeneratorImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ConstructPfGeneratorImpl
 
constructSingleAtomExtensions(ScaffoldExtension) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
Construct further single atom extensions.
constructSingleAtomExtensions(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
Enumerate all possible single atom scaffold extensions.
ConstructThreadLocalizedEcfpGeneratorImpl - Class in com.chemaxon.descriptors.fingerprints.ecfp
Class wrapping constructor for DI.
ConstructThreadLocalizedEcfpGeneratorImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ConstructThreadLocalizedEcfpGeneratorImpl
 
ConstructThreadLocalizedPfGeneratorImpl - Class in com.chemaxon.descriptors.fingerprints.pf2d
Constructor implementation.
ConstructThreadLocalizedPfGeneratorImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ConstructThreadLocalizedPfGeneratorImpl
 
ConstructWrapper() - Constructor for class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl.ConstructWrapper
 
contains(String, T) - Method in class com.chemaxon.overlap.wui.context.Contexts
 
contenttype - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalRawFileInfo
Content type.
context - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
Context to use.
context - Variable in class com.chemaxon.overlap.wui.dto.DescriptorInfo
Associated OverlapAnalysisContext.
context - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo
Associated context description.
context() - Method in class com.chemaxon.screen.DescriptorStorage
Gets the overlap analysis context.
contextjs - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
Context to use.
ContextJsTools - Class in com.chemaxon.overlap
Utility methods for JS based OAContext creation.
Contexts - Class in com.chemaxon.overlap.wui.context
Unified context.
Contexts() - Constructor for class com.chemaxon.overlap.wui.context.Contexts
 
ContextsProvider - Class in com.chemaxon.overlap.wui.context
Provides a static singleton instance.
ContextsProvider() - Constructor for class com.chemaxon.overlap.wui.context.ContextsProvider
 
converMultiplePost(MultiConversionRequest) - Method in class com.chemaxon.overlap.wui.resources.MolConverter
Invoke multiple independent conversions.
ConversionRequest - Class in com.chemaxon.overlap.wui.dto
Molecule conversion request.
ConversionRequest() - Constructor for class com.chemaxon.overlap.wui.dto.ConversionRequest
 
ConversionResult - Class in com.chemaxon.overlap.wui.dto
Molecule conversion result.
ConversionResult() - Constructor for class com.chemaxon.overlap.wui.dto.ConversionResult
 
convert(String) - Method in class com.chemaxon.overlap.cli.util.prop.CliParam.Converter
 
convert(String, String, String, boolean, boolean) - Method in class com.chemaxon.overlap.wui.resources.MolConverter
Converter() - Constructor for class com.chemaxon.overlap.cli.util.prop.CliParam.Converter
 
Converter - Class in com.chemaxon.virtuallib.sc.cli
Command line entry point for library converter.
ConverterParameters - Class in com.chemaxon.virtuallib.sc.cli
CLI parameters.
ConverterParameters() - Constructor for class com.chemaxon.virtuallib.sc.cli.ConverterParameters
 
ConvertGroup - Class in com.chemaxon.virtuallib.sc.cli
Convert a simple group.
ConvertGroupParameters - Class in com.chemaxon.virtuallib.sc.cli
 
ConvertGroupParameters() - Constructor for class com.chemaxon.virtuallib.sc.cli.ConvertGroupParameters
 
convertPost(PmapperRequest) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalResource
Experimental pharmacophore mapping.
convertPost(String, String, String, boolean, boolean) - Method in class com.chemaxon.overlap.wui.resources.MolConverter
convertPost(ConversionRequest) - Method in class com.chemaxon.overlap.wui.resources.MolConverter
copyNeighborsTo(int, int[], double[]) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
copyNeighborsTo(int, int[], double[]) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
copyNeighborsTo(int, int[], double[]) - Method in interface com.chemaxon.overlap.result.KnnResults
Copy neighbor data to an allocated array.
copyTo(int, int, int[], double[]) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
Low level array copy to target arrays.
count - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
 
count - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropRange
Number of values in the MoleculePropRange.values array.
count - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest
Maximal number of most similar targets to find.
count - Variable in class com.chemaxon.overlap.wui.dto.PmapperFeature
Occurrence count.
countingCallback() - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks
Counting callback.
countMatches(Molecule) - Method in class com.chemaxon.descriptors.fingerprints.maccs.GsSearch
Count the matches for the input molecule,
countMatches(Molecule, int) - Method in class com.chemaxon.descriptors.fingerprints.maccs.GsSearch
Count the matches for the input molecule, with a limited search
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.
create(long, boolean) - Static method in class com.chemaxon.calculations.common.AutoThrottles
Create a timing throttle.
create(String, int) - Method in interface com.chemaxon.overlap.util.idgenerator.IdGeneratorFactory
 
CreateAllAbsentMms - Class in com.chemaxon.overlap.cli
Create master molecules storage containing only absents.
CreateAllAbsentMmsParameters - Class in com.chemaxon.overlap.cli
Command line arguments for CreateMms.
CreateAllAbsentMmsParameters() - Constructor for class com.chemaxon.overlap.cli.CreateAllAbsentMmsParameters
 
createArrayStoreBuilder(Class<T>) - Static method in class com.chemaxon.overlap.io.MasterStorages
Create a generic array storage builder.
createBruteForceOverlap(UnguardedExtractor<D, T>, UnguardedDissimilarityCalculator<T>) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Create a brute force overlap calculator from the current state of the storage.
createCompactStringStoreBuilder() - Static method in class com.chemaxon.overlap.io.MasterStorages
 
createConsolePo(PrintStream, String, Prof) - Static method in class com.chemaxon.overlap.cli.util.CliUtil
Create a progress observer and register if profiler is present.
createContext(String) - Static method in class com.chemaxon.overlap.ParameterizedContextFactory
Creates context based on the input parameter.
CREATED - Static variable in annotation type com.chemaxon.overlap.wui.application.Status
201 Created.
createDoubleStoreBuilder() - Static method in class com.chemaxon.overlap.io.MasterStorages
 
createEmptyGenerator(Class<D>) - Static method in class com.chemaxon.descriptors.db.Util
Create an empty descriptor generator object.
createEmptyStorage() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Create an empty storage.
createForgivingNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
createFromStringsIs() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
Create in input stream.
createIdExtractorWhenSpecified(boolean, String) - Static method in class com.chemaxon.overlap.cli.util.Imports
Create an ID extractor when specified.
createIndexMapPs() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
createIndexToStringStorage(int, String, boolean) - Static method in class com.chemaxon.overlap.io.MasterStorages
Create an master storage returning index as strings.
createInIs() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
Create in input stream.
createIntermediateResult() - Method in interface com.chemaxon.overlap.result.AsyncResult
Create a new intermediate result.
createIntStoreBuilder() - Static method in class com.chemaxon.overlap.io.MasterStorages
 
createLinenote() - Static method in class com.chemaxon.overlap.cli.MadfastImport
 
createLongStoreBuilder() - Static method in class com.chemaxon.overlap.io.MasterStorages
 
createMaccs166Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Maccs-166 implementation.
createMemstat(boolean) - Static method in class com.chemaxon.overlap.cli.prof.Memstat
Create memory statistics.
createMemstatWithGc() - Static method in class com.chemaxon.overlap.cli.prof.Memstat
Create memory statistics.
CreateMms - Class in com.chemaxon.overlap.cli
Create master molecules storage from a structure file.
CreateMmsParameters - Class in com.chemaxon.overlap.cli
Command line arguments for CreateMms.
CreateMmsParameters() - Constructor for class com.chemaxon.overlap.cli.CreateMmsParameters
 
CreateMmsStat - Class in com.chemaxon.overlap.cli
Statistics for CreateMms execution.
CreateMmsStat() - Constructor for class com.chemaxon.overlap.cli.CreateMmsStat
 
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.fingerprints.pf2d.ThreadLocalizedPfParameters
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
createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers
createObjectInputStream(String) - Static method in class com.chemaxon.screen.Utils
Creates new object input stream from file.
createParalelToFilesOS() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
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 class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl.CfpReaderFactoryImpl
 
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader.Factory
 
createReader(String) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl.EcfpReaderFactoryImpl
 
createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader.Factory
 
createReader(String) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl.PfReaderFactoryImpl
 
createSimpleCfp10Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
 
createSimpleCfp4Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Simple CFP-4-1 based context.
createSimpleCfp5Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
 
createSimpleCfp6Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
 
createSimpleCfp7Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
 
createSimpleCfp8Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
 
createSimpleCfp9Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
 
createSimpleEcfp10Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Simple ECFP-10 based context;
createSimpleEcfp4Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Simple ECFP-4 based context;
createSimpleEcfp6Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Simple ECFP-6 based context;
createSimpleEcfp8Context() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Simple ECFP-8 based context;
createSimplePharmaCalcContext() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Simple default PharmaCalc based context;
createSplittingFunction(String) - Static method in class com.chemaxon.overlap.cli.util.importing.Splitting
Create splitting function.
createSplittingFunctionOrNull(String) - Static method in class com.chemaxon.overlap.cli.util.importing.Splitting
Create splitting function or null.
createStrictNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
Returns a SubProgressObserver which ignores observed data.
createStringStoreBuilder(int) - Static method in class com.chemaxon.overlap.io.MasterStorages
Create a String storage builder.
createStringStoreBuilder() - Static method in class com.chemaxon.overlap.io.MasterStorages
Create a String storage builder.
createSweetenedGenerator(Object, Class<G>, Class<C>, Function<Molecule, R>, String, Function, DescriptorSerializer<B>, ComparisonContextFactory<DescriptorComparator<B>, B, T>, DescriptorParameters) - Static method in class com.chemaxon.descriptors.common.reflect.Reflect
Put together a type system sweetened DescriptorGenerator proxy from its components.
createtContextByName(String) - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Get context by name.
createToFilesOS() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
Create PrintStream if toStrings specified.
createWithInitialDelay(Supplier<Long>, long, long) - Static method in class com.chemaxon.calculations.common.AutoThrottles
Create with different initial delay.
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.
ctab(Molecule) - Static method in class com.chemaxon.calculations.util.MU
Extract a ctab.
currentTimeMillisSupplier() - Static method in class com.chemaxon.calculations.common.AutoThrottles
cx() - Method in interface com.chemaxon.overlap.cli.util.images.Area
X coordinate of center.
cx - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane
Center of the last layed out position.
cx() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
 
CxnFormatsMolExporter - Class in com.chemaxon.overlap.cli.util.pipeline
Expose MolExporter.
CxnFormatsMolExporter() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolExporter
 
CxnFormatsMolImporter - Class in com.chemaxon.overlap.cli.util.pipeline
Expose MolImporter.
CxnFormatsMolImporter() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolImporter
 
cxnInternalVersion() - Static method in class com.chemaxon.overlap.version.OverlapVersion
CXN backend internal version.
cxnInternalVersion - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo
CXN backend internal version.
cy() - Method in interface com.chemaxon.overlap.cli.util.images.Area
Y coordinate of center.
cy - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane
Center of the last layed out position.
cy() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
 

D

d - Variable in class com.chemaxon.overlap.cli.JsEvalParameters
 
d - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
 
debug(Object) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
 
debug(Object, Throwable) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
 
deepCopyOf(int[][]) - Static method in class com.chemaxon.calculations.util.U
Create a deep copy of an int[][] array.
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_CONFCOUNT - Static variable in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter
 
DEFAULT_CONSIDER_RINGS - Static variable in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Default ring settings.
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_FLEXIBILITY_MODE - Static variable in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter
 
DEFAULT_IMPORT_PAGESIZE - Static variable in class com.chemaxon.overlap.io.MasterStorages
Page size to use on import.
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_MACCS_LENGTH - Static variable in class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters
The length should be the multiple of 64, so the original 166 will be 192
DEFAULT_METRICS - Static variable in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter
 
DEFAULT_METRICS - Static variable in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter
 
DEFAULT_NODETYPE - Static variable in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter
 
DEFAULT_NUMERIC_REPRESENTATION - Static variable in class com.chemaxon.descriptors.vectors.floats.FvParameters
Default numeric representation.
DEFAULT_PAGESIZE - Static variable in class com.chemaxon.overlap.context.OverlapAnalysisContext
Default pagesize.
DEFAULT_PHARMA_CALC_CONFIG_XML - Static variable in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Default configuration XML for pharma-calc fingerprints.
DEFAULT_PHARMA_FRAG_CONFIG_XML - Static variable in class com.chemaxon.overlap.OverlapAnalysisContextFactory
Default configuration XML for pharma-frag fingerprints.
DEFAULT_QUERY_PAGESIZE - Static variable in class com.chemaxon.overlap.context.OverlapAnalysisContext
Default number for query grouping.
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.
DefaultCmdlineContext - Class in com.chemaxon.calculations.util
Expose standard functionality.
DefaultCmdlineContext() - Constructor for class com.chemaxon.calculations.util.DefaultCmdlineContext
Construct.
defaultComparison() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
defaultComparison() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
 
defaultComparison() - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
 
defaultComparison() - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
 
defaultComparison() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
 
defaultComparison() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
 
defaultComparison() - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
 
defaultComparison() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Default comparator.
defaultComparison() - Method in interface com.chemaxon.descriptors.metrics.MetricFactory
Gets the default comparator object.
defaultComparison() - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
defaultComparison() - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
defaultvalues - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceDto
String form of the represented choice with custom parameters.
DEG_TO_RAD - Static variable in class com.chemaxon.calculations.util.V3D
 
DEGS_TO_RADS - Static variable in class com.chemaxon.calculations.util.V3D
 
delayed_out - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
 
DelegatingDeserializer<T extends Serializable> - Class in com.chemaxon.overlap.persistence.serialization
Delegate deserialization to ObjectInputStream.readUnshared().
delete(String) - Method in class com.chemaxon.overlap.service.task.TaskService
Deletes a completed task (is done).
delete(T) - Method in class com.chemaxon.overlap.wui.context.Contexts
Deletes a resource.
deleteRawFile(ExperimentalRawFile) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
Delete a specific raw file.
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpart
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpartNormalized
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongDice
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclidean
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclideanNormalized
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattan
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattanNormalized
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongPetke
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongSimpson
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTanimoto
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTversky
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclid
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclidSqr
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsManhattan
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsMaxDiff
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTanimoto
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTversky
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvEuclid
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvTanimoto
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv.ScaledShortsFvEuclid
 
denormalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.SerializingUnguardedDissimilarityCalculator
 
denormalize(double) - Method in interface com.chemaxon.descriptors.common.unguarded.UnguardedDissimilarityCalculator
Calculate raw value for a normalized dissimilarity value.
denormalize(double) - Method in class com.chemaxon.overlap.wui.SlowUnguardedComparator
 
depth() - Method in interface com.chemaxon.clustering.common.HierarchicCluster
Distance from the associated root.
desc - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
 
descname - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
 
DescRes - Class in com.chemaxon.overlap.wui.res
Resource for a descriptor over a molecule file.
DescRes(String, long, MolsRes, IndexProjector, UnguardedPagedOverlap, OverlapAnalysisContext) - Constructor for class com.chemaxon.overlap.wui.res.DescRes
Construct.
DescResMostSimilarsSearch - Class in com.chemaxon.overlap.wui.res.search
Command.
DescResMostSimilarsSearch(DescRes, DescResMostSimilarsSearch.MostSimilarSearchParams, ExecutionMonitoring<DescResMostSimilarsSearch.MostSimilarsSearchResult>) - Constructor for class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch
 
DescResMostSimilarsSearch.MostSimilarSearchParams - Class in com.chemaxon.overlap.wui.res.search
 
DescResMostSimilarsSearch.MostSimilarsSearchResult - Class in com.chemaxon.overlap.wui.res.search
 
Described - Interface in com.chemaxon.overlap.wui.res
Item has description.
DescribedResource<T extends Described> - Interface in com.chemaxon.overlap.wui.res
Contains resource description.
Description - Annotation Type in com.chemaxon.apidiscovery.annotations
The annotated element has a description contained in this annotation.
description - Variable in class com.chemaxon.overlap.wui.dto.DescriptorInfo
Description of the descriptor data.
description - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalAddMoleculesRequest
Resource description.
description - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalRawFileInfo
Description of the content.
description - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceDto
Choice description.
description - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterDto
Parameter description.
description - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterValueDto
Human readable description.
description - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo
Description of the molecule set.
description - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
 
descriptiondetails - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
 
descriptions - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
 
Descriptor - Interface in com.chemaxon.descriptors.common
Descriptor represents a molecular descriptor calculated by a specific DescriptorGenerator instance for a specific structure.
Descriptor - Class in com.chemaxon.overlap.wui.context
Molecules.
descriptorComparator() - Method in interface com.chemaxon.descriptors.common.comparison.ComparisonContext
Comparator to compare the bare/rich form of the descriptors.
descriptorComparator() - Method in class com.chemaxon.descriptors.common.comparison.impl.ComparisonContextImpl
 
DescriptorComparator<D extends Descriptor> - Interface in com.chemaxon.descriptors.common
Common functionality for descriptor comparison.
descriptorComparator(DescriptorComparator) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Update descriptor comparator.
descriptorComparatorWithOtherContext(DC, UnguardedContext<D, ?>) - Static method in class com.chemaxon.descriptors.common.reflect.Reflect
Delegate a DescriptorComparator with a new UnguardedContext.
DescriptorContainer<T extends Serializable> - Class in com.chemaxon.overlap.persistence.storage
Stores descriptors with attached context and master index projection.
DescriptorContainer.DescriptorContainerDeserializer - Interface in com.chemaxon.overlap.persistence.storage
Optional callback for the descriptor container deserialization.
DescriptorGenerator<B extends Descriptor> - Interface in com.chemaxon.descriptors.common
DescriptorGenerator implements molecule to descriptor calculation functionality.
DescriptorInfo - Class in com.chemaxon.overlap.wui.dto
Basic info of descriptor data.
DescriptorInfo() - Constructor for class com.chemaxon.overlap.wui.dto.DescriptorInfo
 
DescriptorParameters - Interface in com.chemaxon.descriptors.common
Descriptor calculator parameters base interface.
DescriptorPreChecker - Class in com.chemaxon.descriptors.fingerprints.maccs.cli
This class provides standardized molecules for MACCS fingerprint generation.
DescriptorPreChecker() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.cli.DescriptorPreChecker
 
descriptors - Variable in class com.chemaxon.overlap.wui.dto.DescriptorsInfo
List of available descriptors.
descriptorSerializer() - Method in interface com.chemaxon.descriptors.common.comparison.ComparisonContext
Serializer to transform descriptors to/from String representation.
descriptorSerializer() - Method in interface com.chemaxon.descriptors.common.comparison.ComparisonContextFactory
Associated descriptor serializer.
descriptorSerializer() - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
 
descriptorSerializer() - Method in class com.chemaxon.descriptors.common.comparison.impl.ComparisonContextImpl
 
descriptorSerializer() - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
 
descriptorSerializer() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
 
descriptorSerializer() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
 
descriptorSerializer() - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
 
DescriptorSerializer<B extends Descriptor> - Interface in com.chemaxon.descriptors.common
DescriptorSerializer represents descriptor IO.
DescriptorsInfo - Class in com.chemaxon.overlap.wui.dto
Information of available descriptors.
DescriptorsInfo() - Constructor for class com.chemaxon.overlap.wui.dto.DescriptorsInfo
 
DescriptorsResource - Class in com.chemaxon.overlap.wui.resources
Molecular desciptors JAX-RS resource.
DescriptorsResource() - Constructor for class com.chemaxon.overlap.wui.resources.DescriptorsResource
 
DescriptorStorage<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.screen
Representing a descriptor.
DescriptorStorage(String, OverlapAnalysisContext<D, T>, UnguardedPagedOverlap) - Constructor for class com.chemaxon.screen.DescriptorStorage
Construct a new descriptor storage.
DescriptorStorage(String, OverlapAnalysisContext<D, T>, String) - Constructor for class com.chemaxon.screen.DescriptorStorage
Constructs a new descriptor storage.
DescriptorsWithIds<T extends Serializable> - Interface in com.chemaxon.overlap.cli.util
Represents unguarded descriptors with IDs.
DescriptorsWithIdsImpl<T extends Serializable> - Class in com.chemaxon.overlap.cli.util
Simple container implementation.
DescriptorsWithIdsImpl(DescriptorContainer) - Constructor for class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
Construct without separate IDs.
DescriptorsWithIdsImpl(MasterStringStorage, DescriptorContainer<T>) - Constructor for class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
Construct.
DescriptorsWithIdsImpl(OverlapAnalysisContext<?, T>, ParsedUnguardedResultHandler<T>) - Constructor for class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
Construct.
DescriptorsWithMols<T extends Serializable> - Interface in com.chemaxon.overlap.cli.util
Represents unguarded descriptors with associated molecules, IDs and optional properties.
DescriptorsWithMolsImpl<T extends Serializable> - Class in com.chemaxon.overlap.cli.util
Simple container implementation.
DescriptorsWithMolsImpl(MasterMoleculeStorage, MasterStringStorage, DescriptorContainer<T>, Map<String, MolProp<?>>) - Constructor for class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
Construct.
DescriptorsWithMolsImpl(OverlapAnalysisContext<?, T>, ParsedUnguardedWithMolResultHandler<T>) - Constructor for class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
Construct.
DescriptorWrapper - Interface in com.chemaxon.descriptors.alternates
Descriptor wrapper.
deserialize(Map<String, Object>, ObjectInputStream, SubProgressObserver) - Method in interface com.chemaxon.overlap.cli.util.pipeline.ProgressiveDeserializer
Reconstruct object.
deserialize(ObjectInputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl.DeserializerImpl
 
deserialize(ObjectInputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.io.CompactStringStorage
Deserialize from an object input stream.
deserialize(ObjectInputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
Deserialize from an object input stream.
deserialize(ObjectInputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.persistence.serialization.DelegatingDeserializer
 
deserialize(ObjectInputStream, SubProgressObserver) - Method in interface com.chemaxon.overlap.persistence.serialization.Deserializer
Deserialize.
deserialize(ObjectInputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.persistence.storage.CompactStringStorageSerialization
 
deserialize(ObjectInputStream, SubProgressObserver, Sink<OverlapAnalysisContext>, Sink<IndexProjector>, Sink<Descriptor>) - Method in interface com.chemaxon.overlap.persistence.storage.DescriptorContainer.DescriptorContainerDeserializer
Deserialize container.
deserialize(ObjectInputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.persistence.storage.MasterMoleculeStorageSerialization
 
deserialize(ObjectInputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.wui.SlowlyDeserializingMms
 
Deserializer<T> - Interface in com.chemaxon.overlap.persistence.serialization
Reads an object from an ObjectInputStream.
DeserializerImpl(Class<T>, ProgressiveDeserializer<T>) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl.DeserializerImpl
 
deserializeUnguarded(int, DescriptorGenerator<D>, UnguardedExtractor<D, T>, UnguardedDissimilarityCalculator<T>, ObjectInputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Deserialize an UnguardedPagedSimilarity from a binary serialized form.
deserializeUnguarded(int, DescriptorGenerator<D>, UnguardedExtractor<D, T>, UnguardedDissimilarityCalculator<T>, ObjectInputStream, Sink<Descriptor>, SubProgressObserver) - Static method in class com.chemaxon.overlap.storage.PagedDescriptorStorage
Deserialize an UnguardedPagedSimilarity from a binary serialized form.
deserializeUnguardedPagedOverlap(ObjectInputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Deserialize an UnguardedPagedSimilarity from binary serialized from.
deserializeUnguardedPagedOverlap(ObjectInputStream, Sink<Descriptor>, SubProgressObserver) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Deserialize an UnguardedPagedSimilarity from binary serialized from.
detachToRootCluster(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Remove a cluster from its current parent cluster.
detailedVersionInfo() - Static method in class com.chemaxon.overlap.version.OverlapVersion
Detailed version info as String.
details - Variable in class com.chemaxon.overlap.wui.dto.SizeInfoDto
Optional details.
df - Variable in class com.chemaxon.overlap.cli.JsEvalParameters
 
df - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
 
diameter(int) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
Sets diameter.
diameter(int) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder
Sets diameter.
dihedralDeg(double[], double[], double[], double[]) - Static method in class com.chemaxon.calculations.util.V3D
Calculate dihedral angle in degrees.
dihedralRad(double[], double[], double[], double[]) - Static method in class com.chemaxon.calculations.util.V3D
Calculate dihedral angle in radians.
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.
dissimilarities - Variable in class com.chemaxon.overlap.wui.dto.KnnData
Dissimilarities, This field contains a list of double arrays with dissimilarities for each query.
dissimilarities - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabelEntry
Dissimilarity of each neighbors.
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.MolInputImpl
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpart
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpartNormalized
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongDice
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclidean
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclideanNormalized
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattan
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattanNormalized
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongPetke
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongSimpson
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTanimoto
 
dissimilarity(long[], long[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTversky
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclid
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclidSqr
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsManhattan
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsMaxDiff
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTanimoto
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTversky
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvEuclid
 
dissimilarity(float[], float[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvTanimoto
 
dissimilarity(Serializable, Serializable) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv.ScaledShortsFvEuclid
 
dissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.SerializingUnguardedDissimilarityCalculator
 
dissimilarity(T, T) - Method in interface com.chemaxon.descriptors.common.unguarded.UnguardedDissimilarityCalculator
Compare dissimilarity of two objects.
dissimilarity - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityTargetInfo
Dissimilarity of the target.
dissimilarity(T, T) - Method in class com.chemaxon.overlap.wui.SlowUnguardedComparator
 
DissimilarityDistributionCalculation - Class in com.chemaxon.overlap.bruteforce
Distribution of the dissimilarities calculator for a single query.
DissimilarityDistributionRequest - Class in com.chemaxon.overlap.wui.dto
Request DTO of a dissimilarity distribution search.
DissimilarityDistributionRequest() - Constructor for class com.chemaxon.overlap.wui.dto.DissimilarityDistributionRequest
 
DissimilarityDistributionRequest(String, String, double, double, int) - Constructor for class com.chemaxon.overlap.wui.dto.DissimilarityDistributionRequest
 
DissimilarityDistributionResult - Class in com.chemaxon.overlap.wui.dto
Dissimilarity distribution conversion result.
DissimilarityDistributionResult() - Constructor for class com.chemaxon.overlap.wui.dto.DissimilarityDistributionResult
 
DissimilarityInput - Interface in com.chemaxon.clustering.common
DissimilarityInput represents an input set for similarity based clustering algorithm.
DissimilarityTargetInfo - Class in com.chemaxon.overlap.wui.dto
Similarity of a target.
DissimilarityTargetInfo() - Constructor for class com.chemaxon.overlap.wui.dto.DissimilarityTargetInfo
 
documentFromString(String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.XmlUtils
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class com.chemaxon.overlap.servlets.KnnServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class com.chemaxon.overlap.servlets.MetaServlet
Deprecated.
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class com.chemaxon.overlap.servlets.MolsServlet
Deprecated.
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class com.chemaxon.overlap.servlets.SelfOverlapServlet
 
done() - Method in class com.chemaxon.calculations.common.ConsolePO
 
done() - Method in class com.chemaxon.calculations.common.ListenableObserver
 
done() - Method in class com.chemaxon.calculations.common.NoOverflowAutoDoneProgressObserver
 
done() - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
 
done() - Method in interface com.chemaxon.calculations.common.ProgressObserver
Notifies that the represented task is done and no further work will be done.
done() - Method in class com.chemaxon.calculations.common.SplitObserver
 
done() - Method in class com.chemaxon.calculations.common.StatPO
 
done() - Method in interface com.chemaxon.calculations.util.cellfield.RowBuilder
Build row.
done - Variable in class com.chemaxon.overlap.wui.dto.TaskDto
Set when task execution is finished.
dot(V3D) - Method in class com.chemaxon.calculations.util.V3D
 
dot() - Method in class com.chemaxon.calculations.util.V3D
 
doubleProp(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor
 
doubleTerm(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor
 
drawBorder(Area, int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
 
drawBorder(Area, int) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer
Draw border in/around an Area.
drawEllipse(Area) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
 
drawEllipse(Area) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer
Draw an ellipse or circle.
drawLine(int, int, int, int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
 
drawLine(Px2d, Px2d) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
 
drawLine(int, int, int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer
Draw a line.
drawLine(Px2d, Px2d) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer
Draw a line.
drawMolecule(Molecule, Area) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
 
drawMolecule(Molecule, Area) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer
Render a Molecule into an area.
DrawMoleculeToRenderer - Class in com.chemaxon.overlap.cli.util.images
Utility to draw a Molecule to a Renderer.
DrawMoleculeToRenderer() - Constructor for class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer
Construct with default settings.
drawMoleculeToRenderer() - Static method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer
 
DRShape - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShape(ShapeData, DRShapeGenerator) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShape
 
DRShapeComparatorParameter - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeComparatorParameter() - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter
 
DRShapeComparatorParameter.Builder - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeDescriptor - Interface in com.chemaxon.descriptors.alignment
Descriptor (serialized data) for the Distance range assisted shape alignment comparison.
DRShapeGenerator - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeGenerator(DRShapeGeneratorParameter) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
DRShapeGeneratorParameter - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeGeneratorParameter(DRShapeGeneratorParameter.Builder) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter
 
DRShapeGeneratorParameter() - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter
 
DRShapeGeneratorParameter.Builder - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeHistogramComparator - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeHistogramComparator(DRShapeGenerator, DRShapeComparatorParameter) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeHistogramComparator
 
DRShapeIntersectionComparator - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeIntersectionComparator(DRShapeGenerator, DRShapeComparatorParameter) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeIntersectionComparator
 
DRShapeMetrics - Enum in com.chemaxon.descriptors.alignment
Metrics for distance range assisted shape comparison.
DRShapeTanimotoComparator - Class in com.chemaxon.descriptors.alignment.drshape
 
DRShapeTanimotoComparator(DRShapeGenerator, DRShapeComparatorParameter) - Constructor for class com.chemaxon.descriptors.alignment.drshape.DRShapeTanimotoComparator
 
dumpDesc(PrintStream, DescriptorContainer, int, String, boolean, List<UnguardedVisitor>) - Static method in class com.chemaxon.overlap.cli.DumpStorage
 
DumpStorage - Class in com.chemaxon.overlap.cli
Read various serialized storages and dump their contents to the console.
DumpStorage.DescOutFormat - Enum in com.chemaxon.overlap.cli
Descriptor output format.
DumpStorageParameters - Class in com.chemaxon.overlap.cli
Command line arguments for ImportStorage.
DumpStorageParameters() - Constructor for class com.chemaxon.overlap.cli.DumpStorageParameters
 

E

east(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Area
 
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.
EcfpBsWrapper - Class in com.chemaxon.descriptors.alternates
Wrapper for ECFP - folded binary vector as binary string.
EcfpBsWrapper(String) - Constructor for class com.chemaxon.descriptors.alternates.EcfpBsWrapper
Construct new instance.
EcfpComparator - Interface in com.chemaxon.descriptors.fingerprints.ecfp
Comparator for Ecfp descriptor representation.
EcfpDsWrapper - Class in com.chemaxon.descriptors.alternates
Wrapper for ECFP - folded binary vector as default decimal string.
EcfpDsWrapper(String) - Constructor for class com.chemaxon.descriptors.alternates.EcfpDsWrapper
Construct new instance.
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.ConstructEcfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.ecfp
Interface representing ECFP generator constructor.
EcfpReaderFactoryImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl.EcfpReaderFactoryImpl
 
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.
EcfpTableReaderImpl - Class in com.chemaxon.descriptors.fingerprints.ecfp
EcfpTableReader implementation.
EcfpTableReaderImpl(String) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl
 
EcfpTableReaderImpl.EcfpReaderFactoryImpl - Class in com.chemaxon.descriptors.fingerprints.ecfp
Factory implementation for EcfpTableReader.
EHandler - Class in com.chemaxon.overlap.cli.invocation
Utility for exception handling.
EHandler() - Constructor for class com.chemaxon.overlap.cli.invocation.EHandler
 
elapsedTime - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat
Elapsed time.
elapsedTime - Variable in class com.chemaxon.overlap.cli.BuildStorageStat
Elapsed time.
elapsedTime - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
 
elapsedTime - Variable in class com.chemaxon.overlap.cli.CreateMmsStat
Elapsed time.
elapsedTime - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
 
elapsedTime - Variable in class com.chemaxon.overlap.cli.SearchStorageStat
Elapsed time.
elapsedTimeInMs - Variable in class com.chemaxon.calculations.common.TimerStatistics
Elapsed time in ms.
embedInto(Area) - Method in interface com.chemaxon.overlap.cli.util.images.AreaSpec
Embed into a parent area.
embedInto(Range) - Method in interface com.chemaxon.overlap.cli.util.images.RangeSpec
Embed into a Range.
emptyCompatibleBuilder() - Method in class com.chemaxon.overlap.result.impl.LinearHistogramBuilder
Create an empty compatible builder.
endianness(BinaryVectors.Endianness) - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
Set endianness of packing operations.
ensureSerializable(Object) - Static method in class com.chemaxon.descriptors.common.reflect.Reflect
Ensure that serializable.
ensureSerializable(String, Object) - Static method in class com.chemaxon.descriptors.common.reflect.Reflect
Ensure that serializable.
EnsureThat() - Constructor for class com.chemaxon.descriptors.common.Guarded.EnsureThat
 
ensureValidRepresentation(Molecule, String) - Method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
Ensure that structure mapping is consistent.
EnumeratedExtension(ScaffoldExtension, String) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.EnumeratedExtension
 
enumeration - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterDto
Possible values for enumerated parameters (enums).
env - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat
Environment from System.getenv().
env - Variable in class com.chemaxon.overlap.cli.BuildStorageStat
Environment from System.getenv().
env - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
Environment from System.getenv().
env - Variable in class com.chemaxon.overlap.cli.CreateMmsStat
Environment from System.getenv().
env - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
Environment from System.getenv().
env - Variable in class com.chemaxon.overlap.cli.SearchStorageStat
Environment from System.getenv().
EPS - Static variable in class com.chemaxon.calculations.util.V3D
 
equals(Object) - Method in class com.chemaxon.calculations.util.cellfield.impl.RowImpl
 
equals(Object) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
equals(Object) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
 
equals(Object) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
err() - Method in interface com.chemaxon.calculations.util.CmdlineContext
Error stream, usually mapped to System.err.
err() - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
 
error(Object) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
 
error(Object, Throwable) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
 
error(int, String, Throwable) - Method in class com.chemaxon.overlap.cli.util.importing.ParsedDescriptorResultHandler
 
error(int, Object, Throwable) - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResultHandler
 
error(int, Object, Throwable) - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler
 
error(int, S, Throwable) - Method in interface com.chemaxon.overlap.concurrent.ErrorHandler
Process error report.
error - Variable in class com.chemaxon.overlap.wui.dto.AsyncCallDto
Error object if the call thrown an exception or null .
errorCount - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat
Error count.
ErrorHandler<S> - Interface in com.chemaxon.overlap.concurrent
Callback to accept process errors.
ErrorHandlers - Class in com.chemaxon.overlap.concurrent
Utilities related to ErrorHandler.
errorLoggingCallback(Log) - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks
Error logging callback.
errorPropagatingHandler() - Static method in class com.chemaxon.overlap.concurrent.ErrorHandlers
Error propagating handler.
ErrorReport - Class in com.chemaxon.overlap.wui.dto
Response in case of an error.
ErrorReport() - Constructor for class com.chemaxon.overlap.wui.dto.ErrorReport
 
ErrorReport(Throwable, Response.Status, String) - Constructor for class com.chemaxon.overlap.wui.dto.ErrorReport
 
ErrorReport(WuiException) - Constructor for class com.chemaxon.overlap.wui.dto.ErrorReport
 
ErrorReport(Throwable, int) - Constructor for class com.chemaxon.overlap.wui.dto.ErrorReport
 
errorVerbosingCallback() - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks
Error verbosing callback.
euclideanNorm(float[]) - Static method in class com.chemaxon.descriptors.common.realvector.Util
Euclidean norm of floats.
euclidSqrBytes(LinearScaler, byte[], byte[]) - Static method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
Square of euclidean.
euclidSqrShorts(short[]) - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
Square of euclidean.
evalJs(OverlapAnalysisContext, String) - Static method in class com.chemaxon.overlap.ContextJsTools
Evaluate JavaScript segment for creation of OverlapAnalysisContextFactory.
exceptionMessage - Variable in class com.chemaxon.overlap.wui.dto.ErrorReport
Message of associated exception or null.
exceptionStackTrace - Variable in class com.chemaxon.overlap.wui.dto.ErrorReport
Full stack trace of associated exception or null.
ExecutableTask<R> - Class in com.chemaxon.overlap.service.task
A Task that has an executable method.
ExecutableTask(String, String, T, Consumer<ExecutionMonitoring<R>>) - Constructor for class com.chemaxon.overlap.service.task.ExecutableTask
 
ExecutableTask(String, String, T, Function<ExecutionMonitoring<R>, R>) - Constructor for class com.chemaxon.overlap.service.task.ExecutableTask
 
ExecutableTask(String, String, T, PartialResultHolder<R>, Function<ExecutionMonitoring<R>, R>) - Constructor for class com.chemaxon.overlap.service.task.ExecutableTask
 
ExecutableTask(String, String, ProgressObservable, ProgressObserver, PartialResultHolder<R>, Function<ExecutionMonitoring<R>, R>) - Constructor for class com.chemaxon.overlap.service.task.ExecutableTask
 
ExecutableTask(String, String, ProgressObservable, ProgressObserver, PartialResultProvider<R>, PartialResultConsumer<R>, Function<ExecutionMonitoring<R>, R>) - Constructor for class com.chemaxon.overlap.service.task.ExecutableTask
 
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.CfpBsWrapper
 
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.CfpDsWrapper
 
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.Clean2dWrapper
 
execute(Molecule) - Method in interface com.chemaxon.descriptors.alternates.DescriptorWrapper
Execute descriptor generation and output transformation.
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.EcfpBsWrapper
 
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.EcfpDsWrapper
 
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.Maccs166BinaryString
 
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.OverlapAnalysisContextWrapper
 
execute(Molecule) - Method in class com.chemaxon.descriptors.alternates.Pf2dWrapper
 
execute() - Method in class com.chemaxon.overlap.service.task.ExecutableTask
Starts task, executes method, then "done"-s observer.
execute() - Method in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch
 
ExecutionMonitoring<R> - Class in com.chemaxon.overlap.service.task
Holder for objects may needed to monitor an execution.
executorService() - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationEnv
Acquire an ExecutorService to use.
executorService() - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationEnv2
Acquire an ExecutorService to use.
exit(int) - Method in interface com.chemaxon.calculations.util.CmdlineContext
Terminate execution with given status code.
exit(int) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Terminate execution with given status code.
exit(int) - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
 
ExitWithNonZeroStatus() - Constructor for exception com.chemaxon.calculations.util.CmdlineContext.ExitWithNonZeroStatus
 
ExitWithZeroStatus() - Constructor for exception com.chemaxon.calculations.util.CmdlineContext.ExitWithZeroStatus
 
expect(Class<T>, ObjectInputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.persistence.serialization.SerializationUtil
Deserialize an expected type.
ExperimentalAddMoleculesRequest - Class in com.chemaxon.overlap.wui.dto
DTO for add molecules request.
ExperimentalAddMoleculesRequest() - Constructor for class com.chemaxon.overlap.wui.dto.ExperimentalAddMoleculesRequest
 
ExperimentalAsyncCallsResource - Class in com.chemaxon.overlap.wui.resources
Async calls REST API endpoint.
ExperimentalAsyncCallsResource() - Constructor for class com.chemaxon.overlap.wui.resources.ExperimentalAsyncCallsResource
 
ExperimentalRawFile - Class in com.chemaxon.overlap.wui.res
Experimental Implementation for arbitrary binary data.
ExperimentalRawFile(String, long, String, byte[]) - Constructor for class com.chemaxon.overlap.wui.res.ExperimentalRawFile
Construct.
ExperimentalRawFileInfo - Class in com.chemaxon.overlap.wui.dto
Info about a raw file content.
ExperimentalRawFileInfo() - Constructor for class com.chemaxon.overlap.wui.dto.ExperimentalRawFileInfo
 
ExperimentalRawFilesContentResource - Class in com.chemaxon.overlap.wui.resources
Experimental REST API endpoint for accessing rawfiles.
ExperimentalRawFilesContentResource() - Constructor for class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesContentResource
 
ExperimentalRawFilesInfo - Class in com.chemaxon.overlap.wui.dto
Info about all available raw file content.
ExperimentalRawFilesInfo() - Constructor for class com.chemaxon.overlap.wui.dto.ExperimentalRawFilesInfo
 
ExperimentalRawFilesResource - Class in com.chemaxon.overlap.wui.resources
Experimental REST API endpoint for rawfile handling.
ExperimentalRawFilesResource() - Constructor for class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
 
ExperimentalResource - Class in com.chemaxon.overlap.wui.resources
Experimental REST API endpoint with various functionalities.
ExperimentalResource() - Constructor for class com.chemaxon.overlap.wui.resources.ExperimentalResource
 
extend(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.RangeSpec
 
extension - Variable in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.EnumeratedExtension
 
extract(StructureRecord) - Method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor
 
extract(StructureRecord) - Method in class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractor
 
extract(StructureRecord) - Method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor
 
extract(StructureRecord) - Method in interface com.chemaxon.overlap.cli.util.prop.PropertyExtractor
Extract/calculate represented property from a structure.
extractor - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropInfo
Property extractor.
extractorFromCliParam(CliParam) - Static method in class com.chemaxon.overlap.cli.util.prop.PropertyExtractors
Create an extractor from the CliParam spec.
extractorIsEqualWith(UnguardedExtractor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.BinaryLongFpExtractor
 
extractorIsEqualWith(UnguardedExtractor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.FloatsExtractor
 
extractorIsEqualWith(UnguardedExtractor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledBytesFvExtractor
 
extractorIsEqualWith(UnguardedExtractor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledShortsFvExtractor
 
extractorIsEqualWith(UnguardedExtractor) - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.SerializingUnguardedExtractor
 
extractorIsEqualWith(UnguardedExtractor) - Method in interface com.chemaxon.descriptors.common.unguarded.UnguardedExtractor
Check strict equivalence of extractors.
extractorsFromCliParams(List<CliParam>) - Static method in class com.chemaxon.overlap.cli.util.prop.PropertyExtractors
Create extractors from multiple CliParam specs.

F

f - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest
Format string to pass to MolExporter#exportToFormat(chemaxon.struc.Molecule, java.lang.String).
fatal(Object) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
 
fatal(Object, Throwable) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
 
FeatureConfig - Class in com.chemaxon.overlap.wui.context.features
Configuration of the available server features.
FeatureConfigProvider - Class in com.chemaxon.overlap.wui.context.features
Provides a static singleton config.
FeatureConfigProvider() - Constructor for class com.chemaxon.overlap.wui.context.features.FeatureConfigProvider
 
features - Variable in class com.chemaxon.overlap.wui.dto.PmapperResponse
Pharmacophore features.
fillArea(Area, int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
 
fillArea(Area, int) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer
Fill an area.
fillEllipse(Area) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
 
fillEllipse(Area) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer
Draw an ellipse or circle.
fillPartialContent(byte[], long, long) - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
Return part of the content.
filter(ContainerRequestContext) - Method in class com.chemaxon.overlap.wui.application.NormalizeUriFilter
 
filter(ContainerRequestContext, ContainerResponseContext) - Method in class com.chemaxon.overlap.wui.application.StatusFilter
 
filterFromJson(Map<String, ?>) - Static method in class com.chemaxon.overlap.servlets.SelfKnnFilters
 
filterFromJson(String) - Static method in class com.chemaxon.overlap.servlets.SelfKnnFilters
Parse JSON string and construct filter.
findId(String) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Find ID.
findId(MolsRes, String, boolean) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Find index of an ID.
findMostSimilar(List<D>, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Brute force find most similar structure for a set of structures.
findMostSimilar(UnguardedPagedStorage<T>, int, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Brute force find most similar structure for a set of structures.
findMostSimilar(List<T>, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Brute force find most similar structure for a set of structures.
findMostSimilarMolecules(Molecule, int) - Method in class com.chemaxon.overlap.wui.RealTimeSearchGuiContext
Search most similar molecules.
findMostSimilarOnSingleThread(List<D>, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Single threaded reference for multi query most similar lookup.
findMostSimilarOnSingleThread(D, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Find most similar for a given query structure.
findMostSimilarOnSingleThread(List<T>, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Single threaded reference for multi query most similar lookup.
findMostSimilarOnSingleThread(T, SubProgressObserver) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Find most similar for a given query structure.
findMostSimilars(T, int, ProgressObserver, PartialResultConsumer<List<SimilarityResult>>, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Find most similar structures for a single query.
findMostSimilars(int, UnguardedPagedStorage<T>, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Brute force find k-most similar structures for a set of queries.
findMostSimilars(DescRes, MostSimilarsRequest) - Method in class com.chemaxon.overlap.service.FindMostSimilarsService
Without observer
findMostSimilars(DescRes, MostSimilarsRequest, ExecutionMonitoring<MostSimilarsResult>) - Method in class com.chemaxon.overlap.service.FindMostSimilarsService
 
findMostSimilarsByDescriptor(DescRes, String, String, int, int, int, double, boolean) - Method in class com.chemaxon.overlap.service.FindMostSimilarsService
 
findMostSimilarsByDescriptor(DescRes, String, String, int, int, int, double, boolean) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Invoke a most similars search of a query descriptor.
findMostSimilarsByDescriptorPost(DescRes, String, String, int, int, int, double, boolean) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Invoke a most similars search of a query descriptor.
findMostSimilarsById(DescRes, String, String, int, int, int, double, boolean) - Method in class com.chemaxon.overlap.service.FindMostSimilarsService
 
findMostSimilarsById(DescRes, String, String, int, int, int, double, boolean) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Invoke a most similars search of a molecule identified by its ID.
findMostSimilarsForMultipleQueries(List<T>, int, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Find most multiple similar structures for multiple queries.
findMostSimilarsGet(DescRes, String, String, int, int, int, int, double, boolean) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Invoke a most similars search of a query molecule.
findMostSimilarsOnSingleThread(D, SubProgressObserver, int) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity
Find most similars for a given query structure.
findMostSimilarsOnSingleThread(T, SubProgressObserver, int) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Find most similars for a given query structure.
findMostSimilarsPostBody(DescRes, MostSimilarsRequest) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Invoke a most similars search of a query molecule.
findMostSimilarsPostBodyAsync(DescRes, MostSimilarsRequest, Long) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Launch asynchronous similarity search.
findMostSimilarsPostForm(DescRes, String, String, int, int, int, int, double, boolean) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Invoke a most similars search of a query molecule.
FindMostSimilarsService - Class in com.chemaxon.overlap.service
 
FindMostSimilarsService() - Constructor for class com.chemaxon.overlap.service.FindMostSimilarsService
 
FirstToken - Class in com.chemaxon.overlap.splits
Return the first token.
FirstToken() - Constructor for class com.chemaxon.overlap.splits.FirstToken
 
FixedKnnResultsImpl - Class in com.chemaxon.overlap.result.impl
Arrays of primitives backed implementation of KnnResults.
FixedKnnResultsImpl(int, int, int[], double[]) - Constructor for class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
Construct.
fixedSPHEX(double, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
Sphere exclusion clustering with defined sphere radius.
FixedValueInvocationHandler - Class in com.chemaxon.descriptors.common.reflect
Always return a fixed value for every method calls.
FixedValueInvocationHandler(Object) - Constructor for class com.chemaxon.descriptors.common.reflect.FixedValueInvocationHandler
Construct.
flexibilityMode(AlignmentProperties.FlexibilityMode) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter.Builder
 
flexibilityMode(AlignmentProperties.FlexibilityMode) - Method in interface com.chemaxon.descriptors.alignment.FlexibilityModeParameterBuilder
 
flexibilityMode(AlignmentProperties.FlexibilityMode) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter.Builder
 
FlexibilityModeParameterBuilder - Interface in com.chemaxon.descriptors.alignment
 
FloatsComparisonContextFactory - Class in com.chemaxon.descriptors.common.comparison.impl
Factory for comparison contexts of float [] vector descriptors.
FloatsComparisonContextFactory(int, DescriptorSerializer<FloatVectorDescriptor>, FloatVectorMetrics) - Constructor for class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
Instantiate.
FloatsComparisonContextFactory(int, DescriptorSerializer<FloatVectorDescriptor>) - Constructor for class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
Instantiate.
FloatsEuclid - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.floats
Unguarded square of euclidean comparator for float[] vectors.
FloatsEuclid() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclid
 
FloatsEuclidSqr - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.floats
Unguarded square of euclidean comparator for float[] vectors.
FloatsEuclidSqr() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclidSqr
 
FloatsExtractor - Class in com.chemaxon.descriptors.common.unguarded.impl.extractors
Extract float [] vector descriptor from a FloatVectorDescriptor.
FloatsExtractor(int, Object) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.extractors.FloatsExtractor
Construct.
floatsFromBytes(byte[], int) - Static method in class com.chemaxon.descriptors.common.realvector.Util
Deserialize byte arrays to floats.
FloatsManhattan - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.floats
Unguarded manhattan dissimilarity for float[] vectors.
FloatsManhattan() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsManhattan
 
FloatsMaxDiff - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.floats
Unguarded maximum diff dissimilarity for float[] vectors.
FloatsMaxDiff() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsMaxDiff
 
FloatsTanimoto - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.floats
Unguarded tanimoto-like comparator for non-negative float[] vectors.
FloatsTanimoto() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTanimoto
 
floatsToBytes(float[]) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
floatsToBytes(float[]) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
floatsToDecimalString(float[]) - Static method in class com.chemaxon.descriptors.common.realvector.Util
Create tab sep string from floats.
floatsToShorts(float[]) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
floatsToShorts(float[]) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
FloatsTversky - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.floats
Unguarded tversky-like comparator for non-negative float[] vectors.
FloatsTversky(double, double) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTversky
Construct.
floatToByte(float) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
Scale float into the byte representation.
floatToByte(float) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
floatToShort(float) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler
Scale float into the short representation.
floatToShort(float) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
 
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.
FloatVectorComparisonContextFactory - Interface in com.chemaxon.descriptors.common.comparison
Comparison context factory for float vector descriptors.
FloatVectorDescriptor - Interface in com.chemaxon.descriptors.common
FloatVectorDescriptor is a Descriptor which holds a float vector fingerprint.
FloatVectorDescriptorComparator - Class in com.chemaxon.descriptors.common.realvector
Descriptor comparator for float vectors.
FloatVectorDescriptorComparator(DescriptorSerializer<FloatVectorDescriptor>, FloatVectorComparator, int, UnguardedContext<FloatVectorDescriptor, ?>) - Constructor for class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
Construct.
FloatVectorDescriptorImpl - Class in com.chemaxon.descriptors.common.realvector
Float vector descriptor implementation.
FloatVectorDescriptorImpl(float[], Object) - Constructor for class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
Deprecated.
Use FloatVectorDescriptorImpl.FloatVectorDescriptorImpl(float[], Object, int) with explicit expected vector length parameter
FloatVectorDescriptorImpl(float[], Object, int) - Constructor for class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
Construct new instance.
FloatVectorDescriptorImpl(byte[], Object) - Constructor for class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
Deprecated.
FloatVectorDescriptorImpl(byte[], Object, int) - Constructor for class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
Construct from serialized form.
FloatVectorDescriptorImpl(String, Object) - Constructor for class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
Deprecated.
FloatVectorDescriptorImpl(String, Object, int) - Constructor for class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
Construct from decimal String representation.
FloatVectorMetricFactory<C> - Interface in com.chemaxon.descriptors.metrics
Represents available metrics for float vector based descriptors.
FloatVectorMetricFactory.ToLinenote<C> - Class in com.chemaxon.descriptors.metrics
Utility for creating a default linenote.
FloatVectorMetrics - Enum in com.chemaxon.descriptors.metrics
Simple metrics for float vectors.
flush() - Method in class com.chemaxon.overlap.cli.util.pipeline.OutputStreamStatCollector
 
forBinaryMetrics(BinaryMetrics) - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
 
forBinaryMetrics(BinaryMetrics) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory
Creates a new instance according to the given metric.
forBinaryMetrics(BinaryMetrics) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
forceSmilesWithId(int) - Method in class com.chemaxon.overlap.wui.res.MolsRes
 
forComparator(DC) - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
forFloatMetrics(FloatVectorMetrics) - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
 
forFloatMetrics(FloatVectorMetrics) - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
 
forFloatMetrics(FloatVectorMetrics) - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
 
forFloatMetrics(FloatVectorMetrics) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorMetricFactory
Creates a new Comparator instance according to the given metric.
forFloatMetrics(FloatVectorMetrics) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
forFragmentZ(Molecule, int) - Static method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
Create attachment description for a fragment Z atom.
forGenerator(DescriptorGenerator<D>) - Static method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
Construct for a generator with default comparator.
format(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolExporter
 
forScaffoldR(Molecule, int) - Static method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
Create attachment description for scaffold's R atom.
forTversky(TverskyParameters) - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
 
forTversky(TverskyParameters) - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
 
forTversky(TverskyParameters) - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
 
forTversky(TverskyParameters) - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
 
forTversky(TverskyParameters) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory
Creates a new Comparator instance according to the given Tversky metric parameters.
forTversky(TverskyParameters) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorMetricFactory
Creates a new Comparator instance according to the given Tversky metric parameters.
forTversky(TverskyParameters) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
forTversky(TverskyParameters) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
forTverskyCoefficients(double, double) - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
 
forTverskyCoefficients(double, double) - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
 
forTverskyCoefficients(double, double) - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
 
forTverskyCoefficients(double, double) - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
 
forTverskyCoefficients(double, double) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory
Creates a new Comparator instance according to the given Tversky metric parameters.
forTverskyCoefficients(double, double) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorMetricFactory
Creates a new Comparator instance according to the given Tversky metric parameters.
forTverskyCoefficients(double, double) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
forTverskyCoefficients(double, double) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
ForwardingInvocationHandler - Class in com.chemaxon.descriptors.common.reflect
Forward invocations to an implementation.
ForwardingInvocationHandler(Object) - Constructor for class com.chemaxon.descriptors.common.reflect.ForwardingInvocationHandler
Construct.
FpDiff - Class in com.chemaxon.descriptors.fingerprints.maccs.cli
Simple diff tool for binary fingerprints.
FpDiffParameters - Class in com.chemaxon.descriptors.fingerprints.maccs.cli
CLI parameters for FpDiff.
FpDiffParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.cli.FpDiffParameters
 
fragmentCompatibility - Variable in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.ScoredExtension
 
fragmentMatches(RgFrag) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
FrameworkClustering - Class in com.chemaxon.clustering.framework
Create cluster hierarchy from framework associations.
FrameworkClustering() - Constructor for class com.chemaxon.clustering.framework.FrameworkClustering
 
frameworkClustering(Iterator<OrderedElement<S>>, Function<S, Iterator<F>>, FrameworkIndex<F>, Consumer<Exception>, SubProgressObserver) - Static method in class com.chemaxon.clustering.framework.FrameworkClustering
Build hierarchy.
FrameworkClusteringResults - Interface in com.chemaxon.clustering.framework
Results of a framework based clustering.
FrameworkClusteringResultsMolImpl - Class in com.chemaxon.clustering.framework
Implementation of FrameworkClusteringResults.
FrameworkClusteringResultsMolImpl(IDBasedHierarchicClustering, List<Molecule>) - Constructor for class com.chemaxon.clustering.framework.FrameworkClusteringResultsMolImpl
Construct.
FrameworkClusteringResultsSmiImpl - Class in com.chemaxon.clustering.framework
Implementation of FrameworkClusteringResults.
FrameworkClusteringResultsSmiImpl(IDBasedHierarchicClustering, List<String>) - Constructor for class com.chemaxon.clustering.framework.FrameworkClusteringResultsSmiImpl
Construct.
FrameworkIndex<F> - Interface in com.chemaxon.clustering.framework
Index association for frameworks.
frameworkIndex(int, F) - Method in interface com.chemaxon.clustering.framework.FrameworkIndex
Retrieve or create a unique ID for a framework.
frameworkIndex(int, T) - Method in class com.chemaxon.clustering.framework.SimpleFrameworkAssociation
 
freeMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat
Free memory.
freeze() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Freeze worker.
from(ProgressObserver) - Static method in interface com.chemaxon.calculations.common.SubProgressObserver
Deprecated.
Creates a delegator to the given ProgressObserver.
fromBitSet(BitSet) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator
Create a descriptor from a BitSet representation.
fromBitSet(BitSet) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
fromByteArray(byte[]) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
fromByteArray(byte[]) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
 
fromByteArray(byte[]) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer
 
fromByteArray(byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorSerializer
Builds a descriptor from its byte array representation.
fromByteArray(byte[]) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
fromByteArray(byte[]) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
fromBytes(byte[], ScaledFvDescriptorGenerator) - Method in interface com.chemaxon.descriptors.common.realvector.ScaledFvDescriptorFactory
Create from serialized form.
fromCliArgsOptional(String, List<String>, String) - Static method in class com.chemaxon.overlap.cli.util.Imports
Create InputStream for inline and location specifications.
fromCliArgsPresent(String, String, List<String>, String) - Static method in class com.chemaxon.overlap.cli.util.Imports
Create InputStream for inline and location specifications.
fromFloats(float[], ScaledFvDescriptorGenerator) - Method in interface com.chemaxon.descriptors.common.realvector.ScaledFvDescriptorFactory
Create from floating point representation.
fromFloats(float[]) - Method in interface com.chemaxon.descriptors.vectors.floats.FvGenerator
Create a descriptor from a custom representation.
fromFloats(float[]) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
fromJsonMapEntry(Object) - Static method in class com.chemaxon.overlap.servlets.ScalarFilter
From json map entry.
fromSmiles(String) - Static method in class com.chemaxon.overlap.wui.res.MoleculeContainerImpl
 
fromSource(String) - Static method in class com.chemaxon.overlap.wui.res.MoleculeContainerImpl
 
fromStandardizer(Standardizer) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Extract actions from a Standardizer instance.
fromStandardizerCfgLocation(String) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap a Standardizer with config file location.
fromStandardizerConfigXml(String) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
Wrap a Standardizer with config XML location.
fromString(String) - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser
Parse value from String.
fromString(String) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
fromString(String) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
fromString(String) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer
 
fromString(String) - Method in interface com.chemaxon.descriptors.common.DescriptorSerializer
Builds a descriptor from its string representation.
fromString(String) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
fromString(String) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
FvGenerator - Interface in com.chemaxon.descriptors.vectors.floats
Generator for generic binary vector descriptors.
FvGeneratorImpl - Class in com.chemaxon.descriptors.vectors.floats
Implementation for float vectors.
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.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

gain - Variable in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.ScoredExtension
 
GarbageCollectorInfoDto - Class in com.chemaxon.overlap.wui.dto
Represents a garbage collector.
GarbageCollectorInfoDto() - Constructor for class com.chemaxon.overlap.wui.dto.GarbageCollectorInfoDto
No-arg constructor required by JAXB.
garbageCollectors - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot
Representation of garbage collector states.
garbageCollectors - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto
Representation of garbage collector states.
gc - Variable in class com.chemaxon.virtuallib.sc.cli.ConvertGroupParameters
 
gctime - Variable in class com.chemaxon.overlap.cli.prof.Memstat
Time spent in calling gc() in ms.
generalize(boolean, boolean) - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
 
generate(Molecule) - Method in class com.chemaxon.descriptors.fingerprints.maccs.GenerateMaccsFp
Provides the BitSet representation of the 166 bit long MACCS fingerprint
generateDescriptor(Molecule) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
generateDescriptor(Molecule) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
 
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.maccs.MaccsGenerator
 
generateDescriptor(Molecule) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
 
generateDescriptor(Molecule) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
generateDescriptor(Molecule) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
generateDescriptors(OverlapAnalysisContext, Iterable<Supplier<InputStream>>, boolean, String, Supplier<SubProgressObserver>, ExecutorService) - Static method in class com.chemaxon.overlap.cli.util.Imports
Generate descriptors.
generateDescriptorsWithMols(OverlapAnalysisContext, Iterable<Supplier<InputStream>>, boolean, String, Map<String, PropertyExtractor>, SubProgressObserver, ExecutorService) - Static method in class com.chemaxon.overlap.cli.util.Imports
Generate descriptors, store molecules.
GenerateErrorResponse - Class in com.chemaxon.overlap.wui.resources
Diagnostic resource to generate error response.
GenerateErrorResponse() - Constructor for class com.chemaxon.overlap.wui.resources.GenerateErrorResponse
 
GenerateMaccsFp - Class in com.chemaxon.descriptors.fingerprints.maccs
ChemAxon MACCS-166 fingerprint calculation.
GenerateMaccsFp() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.GenerateMaccsFp
Construct.
generatePlaceholderPng(int, int) - Static method in class com.chemaxon.overlap.wui.res.MolsRes
Generate a placeholder image.
generatorFromString(boolean, String, Optional<String>, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Static method in class com.chemaxon.overlap.cli.PagedDescriptorImport
Construct a DescriptorGenerator instance from a String representation.
generatorToString(DescriptorGenerator<?>) - Static method in class com.chemaxon.overlap.cli.PagedDescriptorImport
Deprecated.
GenerMaccs - Class in com.chemaxon.descriptors.fingerprints.maccs.cli
Simple example code to demostrate the calculation of MACCS 166 bit Fingerprint.
GenerMaccs() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.cli.GenerMaccs
 
gerRawFileSegment(ExperimentalRawFile, long, long) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
Get a segment of the raw file.
get() - Method in class com.chemaxon.apidiscovery.InstanceWrapper
Get the actual wrapped instance.
get(Row, Column<T>) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Get a cell.
get(Row) - Method in interface com.chemaxon.calculations.util.cellfield.Column
Retrieve stored data.
get(Row, Column<T>) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
get(Row) - Method in class com.chemaxon.calculations.util.cellfield.impl.ColumnImpl
 
get(Column<T>) - Method in class com.chemaxon.calculations.util.cellfield.impl.RowImpl
 
get(Column<T>) - Method in interface com.chemaxon.calculations.util.cellfield.Row
Get data in a specific column.
get() - Method in enum com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator.IDSEPCHAR
 
get() - Method in class com.chemaxon.descriptors.fingerprints.maccs.RingAtomBs
Gives back the resulting BitSet, creates it if necessary.
get() - Method in class com.chemaxon.descriptors.fingerprints.maccs.RingBondBs
Gives back the results, calculates it if necessary.
get(int) - Method in class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
 
get(int) - Method in class com.chemaxon.overlap.io.CompactStringStorage
 
get(int) - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
 
get(int) - Method in interface com.chemaxon.overlap.io.MasterStorage
Get given structure identified with an index.
get(String) - Method in class com.chemaxon.overlap.service.async.AsyncCallService
Type unsafety.
get(String) - Method in class com.chemaxon.overlap.service.task.TaskService
 
get(String) - Static method in class com.chemaxon.overlap.servlets.MolsContext
Deprecated.
Get.
get(String, Class<T>) - Method in class com.chemaxon.overlap.wui.context.Contexts
 
get() - Static method in class com.chemaxon.overlap.wui.context.ContextsProvider
 
get() - Static method in class com.chemaxon.overlap.wui.context.features.FeatureConfigProvider
Get config.
get(String, boolean) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalAsyncCallsResource
Status of an asynchronous call.
get(int, String) - Method in class com.chemaxon.overlap.wui.resources.GenerateErrorResponse
Generate an error report.
get() - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Description of available KNN results.
get() - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Create JSON list of available molecule sets.
getAbsentCount() - Method in class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
 
getAbsentCount() - Method in class com.chemaxon.overlap.io.CompactStringStorage
 
getAbsentCount() - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
 
getAbsentCount() - Method in interface com.chemaxon.overlap.io.MasterStorage
Number of absent structures.
getAccumulatedWork() - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
 
getAccumulatedWork() - Method in interface com.chemaxon.calculations.common.ProgressObservable
 
getAdditionalProperties() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler
Additional built properties.
getAlignedQuery() - Method in interface com.chemaxon.descriptors.alignment.ShapeComparisonResult
 
getAlignedTarget() - Method in interface com.chemaxon.descriptors.alignment.ShapeComparisonResult
 
getAll() - Method in class com.chemaxon.overlap.service.task.TaskService
 
getAllDescribedResources(ResourceInfo) - Method in class com.chemaxon.overlap.wui.context.Contexts
Get all resource instances as DescribedResource, sorted by name.
getAllLeaves(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Return the IDs of all immediate and transitive leaves.
getAllNeighborAtoms(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
Get all neighbor atom indices.
getAllNeighborCount() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getAllNeighborCount() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getAllNeighborCount() - Method in interface com.chemaxon.overlap.result.KnnResults
All stored neighbor count.
getAllPropNames() - Method in class com.chemaxon.overlap.wui.res.MolsRes
Return all property names.
getAnnotation(Class<T>, Object) - Static method in class com.chemaxon.apidiscovery.Discovery
Retrieve an annotation on an object.
getAnnotationForClass(Class<T>, Class<?>) - Static method in class com.chemaxon.apidiscovery.Discovery
Retrieve annotation for a class.
getAnnotationIfPresent(Class<T>, Object) - Static method in class com.chemaxon.apidiscovery.Discovery
Retrieve an annotation on an object if present.
getAPIFieldName() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
API field name.
getAsyncStatSnapshotSupplier() - Method in class com.chemaxon.calculations.common.ConsolePO
Create an asynchronous statistics snapshot supplier.
getAtomCount() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
All atom count.
getAtomTyping() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
 
getAtomTypizer() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Atom typizer to use.
getAttachedAtomIndex() - Method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
Attached atom index.
getAttachmentAtomIndex() - Method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
Attachment atom index.
getAttachmentIndex() - Method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
Attachemnt index.
getAttribute(String) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
 
getAttributeNames() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
 
getBareDescriptor(D) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
getBareDescriptor(DRShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
getBareDescriptor(B) - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Get bare-only form of a descriptor.
getBareDescriptor(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
getBareDescriptor(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
getBaseWhenProxied() - Static method in class com.chemaxon.descriptors.common.reflect.Reflect
Get base object for a proxied.
getBin(int) - Method in class com.chemaxon.calculations.util.Histo
Get the value from a bin.
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator
getBinaryMetricsComparator(BinaryMetrics) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
getBinCount() - Method in class com.chemaxon.calculations.util.Histo
Get bin count.
getBinCount() - Method in interface com.chemaxon.overlap.result.LinearHistogram
Bin count.
getBinIndex(double) - Method in class com.chemaxon.calculations.util.Histo
Look up associated bin.
getBinLowerBound(int) - Method in class com.chemaxon.calculations.util.Histo
Lower bound of a bin.
getBinUpperBound(int) - Method in class com.chemaxon.calculations.util.Histo
Upper bound of a bin.
getBinValues() - Method in interface com.chemaxon.overlap.result.LinearHistogram
Get bin values.
getBinWidth() - Method in interface com.chemaxon.overlap.result.LinearHistogram
Bin width.
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).
getBondOrder() - Method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
Represented bond order.
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.
getBytes() - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
Get scaled bytes representation.
getCellCount() - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder
Total cell count.
getChildClusters(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Return the IDs of child cluster IDs.
getChoiceLabels() - Method in interface com.chemaxon.apidiscovery.linenote.Linenote
Get all available choice labels.
getClientIndex(int) - Method in interface com.chemaxon.overlap.io.IndexProjector
Associated client index if present.
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.
getClusterIndexOf(int) - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
Cluster ID of a leaf.
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.
getCols() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
 
getColumnName() - Method in interface com.chemaxon.calculations.util.cellfield.Column
Name of the represented column.
getColumnName() - Method in class com.chemaxon.calculations.util.cellfield.impl.ColumnImpl
 
getColumnNames() - Method in class com.chemaxon.overlap.wui.res.GridRes
Column names.
getColumns() - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Get all columns.
getColumns() - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
getCommand() - Method in interface com.chemaxon.apidiscovery.linenote.ParseRes
Represented command.
getComp() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getConnectivity() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
 
getContent() - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
Return content.
getContentType() - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
Stored content type.
getContext() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getContext() - Method in class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap
 
getContext() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getContext() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds
Get represented OverlapAnalysisContext.
getContext() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
 
getContext() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols
Get represented OverlapAnalysisContext.
getContext() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
 
getContext() - Method in class com.chemaxon.overlap.persistence.storage.DescriptorContainer
Get represented context.
getContext() - Static method in class com.chemaxon.overlap.wui.RealTimeSearchGui
Get mega context.
getContext() - Method in class com.chemaxon.overlap.wui.res.DescRes
Get overlap analysis context.
getContext() - Static method in class com.chemaxon.overlap.wui.SelfOverlapGui
Get mega context.
getConverter(Class<T>, Type, Annotation[]) - Method in class com.chemaxon.overlap.wui.context.LookupParamConverterProvider
 
getCount() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getCurrentValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Current value.
getCurrentValueOn(Object) - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Current value on a different object.
getCxBinFormat(MolsRes, int, boolean, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get molecule in an arbitrary binary format.
getCxFormat(MolsRes, int, boolean, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get molecule in an arbitrary text based format.
getCxnFormatName() - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
 
getCxnFormatName() - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
 
getCxnFormatName() - Method in interface com.chemaxon.calculations.io.Segmenter
Format name used by MolImporter and MolExporter.
getCxSmiles() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
Get canonical CXSMILES of the candidate.
getDefaultComparator() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
Deprecated.
getDefaultComparator() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
Deprecated.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Deprecated.
This method is kept for compatibility reason. Use ComparisonContext#descriptorComparator() on the instance returned by MetricFactory.defaultComparison() from DescriptorGenerator.comparisonContextFactory()
getDefaultComparator() - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
Deprecated.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
Deprecated.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator
Deprecated.
getDefaultComparator() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
Deprecated.
getDefaultComparator() - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
getDefaultComparator() - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
getDefaultValue() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceParameterDescriptor
Default represented value.
getDefaultValueAsString() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceParameterDescriptor
Default represented value as String.
getDelimited(String, int, String, boolean) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.SmaInterpreter
Get the next bracketed substring which starts with begDelim bracket-like character and ends with the corresponding terminating bracket-like character, found automatically here.
getDesc() - Method in class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap
 
getDesc() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedDescriptorResult
Get descriptor
getDesc() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResult
Get descriptor.
getDesc() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResult
Get descriptor.
getDesc() - Method in class com.chemaxon.overlap.wui.res.DescRes
Get descriptor storage with default metric.
getDescName() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getDescP() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getDescpBitsPerPattern() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getDescpBondCount() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getDescpDiameter() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getDescpXmlConfigFile() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
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.linenote.ChoiceDescriptor
Description of the current choice.
getDescription() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceParameterDescriptor
Parameter description.
getDescription() - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
 
getDescription() - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
 
getDescription() - Method in interface com.chemaxon.calculations.io.Segmenter
Short human readable description.
getDescription() - Method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractorFactory
 
getDescription() - Method in class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractorFactory
 
getDescription() - Method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractorFactory
 
getDescription() - Method in interface com.chemaxon.overlap.cli.util.prop.PropertyExtractorFactory
Detailed description of the extraction.
getDescription() - Method in class com.chemaxon.overlap.wui.res.DescRes
 
getDescription() - Method in interface com.chemaxon.overlap.wui.res.Described
Human readable description of the instance.
getDescription() - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
 
getDescription() - Method in class com.chemaxon.overlap.wui.res.GridRes
 
getDescription() - Method in class com.chemaxon.overlap.wui.res.KnnRes
 
getDescription() - Method in class com.chemaxon.overlap.wui.res.MolsRes
 
getDescription() - Method in class com.chemaxon.overlap.wui.res.ProfRes
 
getDescription() - Method in class com.chemaxon.overlap.wui.res.StatRes
 
getDescriptionAnnotation(Object) - Static method in class com.chemaxon.apidiscovery.Discovery
Retrieve the description annotation on an object.
getDescriptorAsString(int, boolean) - Method in class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl
 
getDescriptorAsString(int, boolean) - Method in interface com.chemaxon.overlap.storage.UnguardedPagedStorage
Retrieve descriptor as String.
getDescriptorComparator() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Gets represented descriptor comparator.
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShape
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGeneratorParameter
 
getDescriptorGenerator() - Method in interface com.chemaxon.descriptors.alignment.DRShapeDescriptor
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.alignment.shape.Shape
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter
 
getDescriptorGenerator() - Method in interface com.chemaxon.descriptors.alignment.ShapeDescriptor
Deprecated.
getDescriptorGenerator() - Method in interface com.chemaxon.descriptors.common.DescriptorParameters
Return the represented descriptor generator.
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.db.MDTableReader
Associated descriptor generator.
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters
Gives the descriptor generator based on this parameters
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
 
getDescriptorGenerator() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Gets represented descriptor generator.
getDescriptorInfo(String, String) - Method in class com.chemaxon.overlap.wui.res.DescRes
Get info about the represented set.
getDescriptors() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds
Represented descriptors.
getDescriptors() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
 
getDescriptors() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols
Represented descriptors.
getDescriptors() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
 
getDescriptors() - Method in class com.chemaxon.overlap.persistence.storage.DescriptorContainer
Get stored descriptors.
getDescWithMetric(String) - Method in class com.chemaxon.overlap.wui.res.DescRes
Get descriptor storage with specified metric.
getDeserializedType() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl.DeserializerImpl
 
getDeserializedType() - Method in class com.chemaxon.overlap.persistence.serialization.AbstractSerialization
 
getDeserializedType() - Method in class com.chemaxon.overlap.persistence.serialization.DelegatingDeserializer
 
getDeserializedType() - Method in interface com.chemaxon.overlap.persistence.serialization.Deserializer
Type to be deserialized.
getDeserializedType() - Method in class com.chemaxon.overlap.wui.SlowlyDeserializingMms
 
getDetailedDescription() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Detailed description.
getDetailedDescription() - Method in enum com.chemaxon.overlap.wui.context.features.ServerFeature
Human readable detailed description of the represented toggle.
getDiameter() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
The maximum diameter of the circular neighborhoods.
getDissimc() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getDissimilarities(int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getDissimilarities(int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getDissimilarities(int) - Method in interface com.chemaxon.overlap.result.KnnResults
Dissimilarity.
getDissimilarity() - Method in class com.chemaxon.descriptors.common.binary.SimpleComparisonResult
 
getDissimilarity() - Method in interface com.chemaxon.descriptors.common.ComparisonResult
Dissimilarity score of the comparison.
getDissimilarity(int, int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getDissimilarity(int, int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getDissimilarity(int) - Method in class com.chemaxon.overlap.result.impl.SimilarityResultsImpl
 
getDissimilarity(int, int) - Method in interface com.chemaxon.overlap.result.KnnResults
Dissimilarity of a single neighbor.
getDissimilarity(int) - Method in interface com.chemaxon.overlap.result.SimilarityResults
Dissimilarity.
getDissimilarityComparator() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Get represented dissimilarity comparison.
getDissimiliarity() - Method in class com.chemaxon.overlap.result.impl.SimilarityResultImpl
 
getDissimiliarity() - Method in interface com.chemaxon.overlap.result.SimilarityResult
Get the represented dissimilarity value.
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.
getElapsedTime() - Method in class com.chemaxon.calculations.common.Timer
Elapsed time.
getEndianness() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
Endianness of packing operations.
getEndTimeMs() - Method in class com.chemaxon.overlap.service.task.Task
 
getEnumParameterClass() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Return enum class for enum field.
getEnumValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of an enum field.
getErr() - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Get stderr to use.
getEuclideanNorm() - Method in interface com.chemaxon.descriptors.common.FloatVectorDescriptor
Euclidean norm of the represented vector.
getEuclideanNorm() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
 
getEuclideanNorm() - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
 
getEuclideanNorm() - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
 
getEx() - Method in class com.chemaxon.overlap.concurrent.impl.BppParameters
 
getExecutorService() - Method in class com.chemaxon.overlap.wui.context.Contexts
Get executor service to use.
getExtractedType() - Method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor
 
getExtractedType() - Method in class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractor
 
getExtractedType() - Method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor
 
getExtractedType() - Method in interface com.chemaxon.overlap.cli.util.prop.PropertyExtractor
Extracted type.
getExtractor() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getExtractor() - Method in class com.chemaxon.overlap.cli.util.prop.MolProp
Get property extractor.
getFirstPageSources() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Inputs represented by the first enqueued page in String format.
getFlexibilityMode() - Method in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
getFloatMetricsComparator(FloatVectorMetrics) - Method in interface com.chemaxon.descriptors.vectors.floats.FvGenerator
getFloatMetricsComparator(FloatVectorMetrics) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
Deprecated.
getFloatVectorComparator(FloatVectorMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
getFormat() - Method in class com.chemaxon.overlap.io.StructureRecordIterator
Get format.
getFP() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
 
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.
getFP() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
 
getFP() - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
 
getFP() - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
 
getFpAsBitset() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
 
getFpAsBitset() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
Get BitSet representation of this fingerprint.
getFpAsBytes() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
 
getFpAsBytes() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
Convert to byte array.
getFpAsLongs() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
 
getFpAsLongs() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
Get long array representation of this fingerprint.
getFragments() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton
Get fragments list.
getFrameworkAsMolecule(int) - Method in interface com.chemaxon.clustering.framework.FrameworkClusteringResults
Get framework as Molecule.
getFrameworkAsMolecule(int) - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsMolImpl
 
getFrameworkAsMolecule(int) - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsSmiImpl
 
getFrameworkAsMoleculeFunction() - Method in interface com.chemaxon.clustering.framework.FrameworkClusteringResults
getFrameworkAsMoleculeFunction() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsMolImpl
 
getFrameworkAsMoleculeFunction() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsSmiImpl
 
getFrameworkAsSmiles(int) - Method in interface com.chemaxon.clustering.framework.FrameworkClusteringResults
Get framework as SMILES.
getFrameworkAsSmiles(int) - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsMolImpl
 
getFrameworkAsSmiles(int) - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsSmiImpl
 
getFrameworkAsSmilesFunction() - Method in interface com.chemaxon.clustering.framework.FrameworkClusteringResults
getFrameworkAsSmilesFunction() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsMolImpl
 
getFrameworkAsSmilesFunction() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsSmiImpl
 
getFrameworkForIndex(int) - Method in class com.chemaxon.clustering.framework.SimpleFrameworkAssociation
Get a stored framework.
getFrameworks() - Method in class com.chemaxon.clustering.framework.SimpleFrameworkAssociation
Get all frameworks.
getFrameworksCount() - Method in interface com.chemaxon.clustering.framework.FrameworkClusteringResults
Total represented frameworks.
getFrameworksCount() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsMolImpl
 
getFrameworksCount() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsSmiImpl
 
getFrameworkToIndexMapping(int) - Method in class com.chemaxon.clustering.framework.SimpleFrameworkAssociation
Index mapping for a level.
getFromBytes() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getFromStrings() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getGridInfo(String, String) - Method in class com.chemaxon.overlap.wui.res.GridRes
Get info about the represented grid.
getGridsSummary() - Method in class com.chemaxon.overlap.wui.resources.GridsResource
 
getGuardObject() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
getGuardObject() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
getGuardObject() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShape
 
getGuardObject() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
getGuardObject() - Method in class com.chemaxon.descriptors.alignment.shape.Shape
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.comparison.impl.ComparisonContextImpl
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
 
getGuardObject() - Method in interface com.chemaxon.descriptors.common.Guarded
Gets the guard object associated to the generated descriptors/utilities.
getGuardObject() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.BinaryLongFpExtractor
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.FloatsExtractor
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledBytesFvExtractor
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledShortsFvExtractor
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.SerializingUnguardedExtractor
 
getGuardObject() - Method in class com.chemaxon.descriptors.common.unguarded.impl.UnguardedContextImpl
 
getGuardObject() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
getGuardObject() - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
getGuardObject() - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
getGuardObject() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
 
getHelp() - Static method in class com.chemaxon.overlap.cli.CalculateOverlapParameters
Construct help message.
getHelp() - Static method in class com.chemaxon.overlap.cli.CreateMmsParameters
 
getHelp() - Static method in class com.chemaxon.overlap.cli.MadfastImportParameters
Construct help message.
getHelpMessage() - Static method in class com.chemaxon.overlap.ContextJsTools
Get context initialization help message.
getHierarchy() - Method in interface com.chemaxon.clustering.framework.FrameworkClusteringResults
Get clustering hierarchy.
getHierarchy() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsMolImpl
 
getHierarchy() - Method in class com.chemaxon.clustering.framework.FrameworkClusteringResultsSmiImpl
 
getHistoBody(int) - Method in class com.chemaxon.calculations.util.Histo
Compose histogram body
getIconUrl() - Method in class com.chemaxon.overlap.wui.context.Descriptor
 
getIconUrl() - Method in class com.chemaxon.overlap.wui.context.Knn
 
getIconUrl() - Method in class com.chemaxon.overlap.wui.context.Molecules
 
getIconUrl() - Method in interface com.chemaxon.overlap.wui.context.ResourceClass
Icon image url.
getId() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedDescriptorResult
Get ID.
getId() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResult
Get ID.
getId() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResult
Get ID.
getId() - Method in class com.chemaxon.overlap.service.async.AsyncCall
 
getId(int) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Get ID.
getId(MolsRes, int) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get ID of a single molecule.
getId(int) - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
 
getIdentifierConfigurationXml() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
Identifier configuration for {@link
getIdp() - Method in class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap
 
getIds() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds
Represented IDs.
getIds() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
 
getIds() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols
Represented IDs.
getIds() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
 
getIds() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResultHandler
Get collected IDs.
getIds() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler
Get collected IDs.
getIds() - Method in class com.chemaxon.overlap.service.async.AsyncCallService
 
getIds() - Method in class com.chemaxon.overlap.service.task.TaskService
NOTE: Probably will be removed in this way as linear explosion of new added tasks.
getIds() - Method in class com.chemaxon.overlap.wui.resources.ExperimentalAsyncCallsResource
List of asynchronous call IDs.
getIds(MolsRes, List<Integer>, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Fetch IDs for multiple molecules.
getImageSize() - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder
Underlying image size in pixels.
getImmediateLeaves(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Return the IDs of immediate leaves.
getImportOpts() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getIn() - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Get stdin to use.
getIn() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getIn() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
 
getIndex() - Method in interface com.chemaxon.calculations.io.OrderedElement
Element index.
getIndexMap() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getIndexProjector() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds
Get represented index projector.
getIndexProjector() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
 
getIndexProjector() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols
Get represented index projector.
getIndexProjector() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
 
getIndexProjector() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResultHandler
Get ID projection for pages.
getIndexProjector() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler
Get ID projection for pages.
getIndexProjector() - Method in class com.chemaxon.overlap.persistence.storage.DescriptorContainer
Get represented index projector.
getIndexProjector() - Method in class com.chemaxon.overlap.wui.res.DescRes
Get master index projector.
getIndexToName() - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
Get a clone of index to name association.
getIndices() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton
Get covered RG indices.
getInfoJson() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
Compose info JSON object.
getInitialPagesize() - Method in class com.chemaxon.overlap.concurrent.impl.BppParameters
 
getInputCount() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Number of individual inputs read from the input source.
getInputIndex() - Method in exception com.chemaxon.calculations.io.OrderedInputProcessingException
Represented element index.
getInstance(Class) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
 
getInstance(String) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
 
getInstance() - Static method in class com.chemaxon.overlap.wui.context.Descriptor
 
getInstance() - Static method in class com.chemaxon.overlap.wui.context.Knn
 
getInstance() - Static method in class com.chemaxon.overlap.wui.context.Molecules
 
getIntValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of an int field.
getInvocationCount() - Method in class com.chemaxon.calculations.common.Timer
Get total invocation count.
getItemCount() - Method in interface com.chemaxon.overlap.result.LinearHistogram
Represented item count.
getIterator() - Method in class com.chemaxon.overlap.cli.util.pipeline.ToLines
 
getJson() - Method in class com.chemaxon.overlap.wui.res.ProfRes
Return JSON content.
getJson() - Method in class com.chemaxon.overlap.wui.res.StatRes
Return JSON content.
getK() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getK() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getK() - Method in interface com.chemaxon.overlap.result.KnnResults
getKeystorePassword() - Method in interface com.chemaxon.screen.desktop.JettyStarter.SslKeystoreSpec
Keystore password.
getKeystorePath() - Method in interface com.chemaxon.screen.desktop.JettyStarter.SslKeystoreSpec
Keystore path.
getKnn() - Method in class com.chemaxon.overlap.wui.res.KnnRes
Represented kNN.
getKnn() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
 
getKnnData(String, String) - Method in class com.chemaxon.overlap.wui.res.KnnRes
 
getKnnData(String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Knn data.
getKnnInfo(String, String) - Method in class com.chemaxon.overlap.wui.res.KnnRes
 
getKnnInfo(String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Description of a knn result.
getKnnJson() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
Get knn results.
getKnnResults() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getLabel() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceDescriptor
Label of the current choice.
getLandingPageUrl() - Method in class com.chemaxon.overlap.wui.context.Descriptor
 
getLandingPageUrl() - Method in class com.chemaxon.overlap.wui.context.Knn
 
getLandingPageUrl() - Method in class com.chemaxon.overlap.wui.context.Molecules
 
getLandingPageUrl() - Method in interface com.chemaxon.overlap.wui.context.ResourceClass
Landing page for primary handling.
getLastStep(Class<T>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
getLastStep(Class<T>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineContext
Get last step from the pipeline.
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.fingerprints.maccs.GenerateMaccsFp
Length of the represented descriptor.
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.
getLex() - Method in class com.chemaxon.overlap.concurrent.impl.BppParameters
 
getListeningPort() - Method in interface com.chemaxon.screen.desktop.JettyStarter.ServerWrapper
Get listening port.
getLoadingStatus() - Method in class com.chemaxon.overlap.wui.resources.StatisticsResource
Loading status of the server.
getLoadingSuperTask() - Method in class com.chemaxon.overlap.wui.StartupHandler
 
getLoadingTasks() - Method in class com.chemaxon.overlap.wui.StartupHandler
 
getLog() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
 
getLog() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
 
getLongValue() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Value of an long field.
getLowerBound() - Method in class com.chemaxon.calculations.util.Histo
Lower bound of the histogram.
getLowerBound() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
 
getLowerBound() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
getLowerBound() - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Get lower bound for the similarity/dissimilarity values if such one can be determined.
getLowerBound() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
getLowerBound() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
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.
getLowLimit() - Method in interface com.chemaxon.overlap.result.LinearHistogram
Lowest value assigned to the first bin.
getManhattanNorm() - Method in interface com.chemaxon.descriptors.common.FloatVectorDescriptor
Manhattan norm of the represented vector.
getManhattanNorm() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
 
getManhattanNorm() - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
 
getManhattanNorm() - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
 
getMasterIndex(int) - Method in interface com.chemaxon.overlap.io.IndexProjector
Master index for a client index.
getMaxClusterID() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
Maximal ClusterID present in this clustering.
getMaxDissimilarity() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMaxDissimilarity() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMaxDissimilarity() - Method in interface com.chemaxon.overlap.result.NnResults
Upper bound of dissimilarity values.
getMaxDouble() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Largest possible floating point value for floating point fields.
getMaximumNorm() - Method in interface com.chemaxon.descriptors.common.FloatVectorDescriptor
Maximum norm of the represented vector.
getMaximumNorm() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl
 
getMaximumNorm() - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
 
getMaximumNorm() - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
 
getMaxLeafID() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
Maximal leaf ID referenced in this clustering.
getMaxLong() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Largest possible fixed point value for fixed point fields.
getMaxMasterIndex() - Method in interface com.chemaxon.overlap.io.IndexProjector
Largest master index.
getMaxNeighborCount() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMaxNeighborCount() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMaxNeighborCount() - Method in interface com.chemaxon.overlap.result.KnnResults
Maximal neighbor count represented.
getMaxNeighborIndex() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMaxNeighborIndex() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMaxNeighborIndex() - Method in interface com.chemaxon.overlap.result.NnResults
Upper bound of neighbor index values.
getMaxQid() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
 
getMaxQueueSize() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Current results queue size limit.
getMaxQueueSize() - Method in class com.chemaxon.overlap.concurrent.impl.BppParameters
 
getMaxTid() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
 
getMemoized(int) - Method in interface com.chemaxon.calculations.io.MemoizedSparseCollection
Get a non-missing memoiozed.
getMemoized(int) - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
getMemoizedFunction() - Method in interface com.chemaxon.calculations.io.MemoizedSparseCollection
Function to access captured non-missing memoizeds.
getMemoizedFunction() - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
getMemoizedIfPresent(int) - Method in interface com.chemaxon.calculations.io.MemoizedSparseCollection
Get item when present.
getMemoizedIfPresent(int) - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
getMemoizedOrDefault(int, T) - Method in interface com.chemaxon.calculations.io.MemoizedSparseCollection
Get item when present or a default value when missing.
getMemoizedOrDefault(int, R) - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
getMemoizedOrDefaultFunction(T) - Method in interface com.chemaxon.calculations.io.MemoizedSparseCollection
Function to access present items with a default value for missing items.
getMemoizedOrDefaultFunction(R) - Method in class com.chemaxon.calculations.io.MemoizingIterator
 
getMetricMetadata() - Method in interface com.chemaxon.clustering.common.DissimilarityInput
Metadata about the underlying metric.
getMetricMetadata() - Method in class com.chemaxon.clustering.common.MolInputImpl
 
getMetricMetadata() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeHistogramComparator
 
getMetricMetadata() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeIntersectionComparator
 
getMetricMetadata() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeTanimotoComparator
 
getMetricMetadata() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeIntersectionComparator
 
getMetricMetadata() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeTanimotoComparator
 
getMetricMetadata() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
 
getMetricMetadata() - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
Metadata about this metric.
getMetricMetadata() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
 
getMetricMetadata() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
 
getMetrics() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter
 
getMetrics() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter
 
getMetrics() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getMetricsHelp() - Static method in class com.chemaxon.overlap.cli.util.CliUtil
Compose detailed help string on available metrics.
getMetricSpec() - Method in class com.chemaxon.overlap.wui.res.DescRes
Available metrics specification.
getMids() - Method in class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap
 
getMinDissimilarity() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMinDissimilarity() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMinDissimilarity() - Method in interface com.chemaxon.overlap.result.NnResults
Lower bound of dissimilarity values.
getMinDouble() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Smallest possible floating point value for floating point fields.
getMinLong() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Smallest possible fixed point value for fixed point fields.
getMinNeighborCount() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMinNeighborCount() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMinNeighborCount() - Method in interface com.chemaxon.overlap.result.KnnResults
Minimal neighbor count represented.
getMinNeighborIndex() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMinNeighborIndex() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMinNeighborIndex() - Method in interface com.chemaxon.overlap.result.NnResults
Lower bound of neighbor index values.
getMms() - Method in class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap
 
getMms() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler
Get built MMS.
getMms() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
 
getMol(int) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Get molecule.
getMol(int) - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
 
getMolecule() - Method in interface com.chemaxon.calculations.io.StructureRecord
Get represented structure.
getMolecule(int) - Method in interface com.chemaxon.clustering.common.MolInput
Retrieve a structure.
getMolecule(int) - Method in class com.chemaxon.clustering.common.MolInputImpl
Retrieve a structure.
getMolecule() - Method in interface com.chemaxon.overlap.wui.res.MoleculeContainer
Get represented structure.
getMolecule() - Method in class com.chemaxon.overlap.wui.res.MoleculeContainerImpl
 
getMolecule() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
 
getMoleculeCount() - Method in class com.chemaxon.overlap.wui.RealTimeSearchGuiContext
Size of molecule database.
GetMoleculeName - Class in com.chemaxon.overlap.cli.util.pipeline
Get name of the input molecule.
GetMoleculeName() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.GetMoleculeName
 
getMolecules() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols
Represented molecules.
getMolecules() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
 
getMolecules(int, int) - Method in class com.chemaxon.overlap.wui.RealTimeSearchGuiContext
 
getMolInfo(String, int, boolean) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Fill single molecule info.
getMolInfo(String, int, boolean, boolean) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Fill single molecule info.
getMolInfo(MolsRes, int, boolean, boolean) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Create description of a single molecule.
getMols() - Method in class com.chemaxon.overlap.wui.res.DescRes
Associated molecules storage.
getMolsRef() - Method in class com.chemaxon.overlap.wui.res.DescRes
URL of associated molecules storage.
getMostSimilarDissimilarity(int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMostSimilarDissimilarity(int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMostSimilarDissimilarity(int) - Method in interface com.chemaxon.overlap.result.NnResults
Dissimilarity of the most similar neighbor.
getMostSimilarNeighbor(int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getMostSimilarNeighbor(int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getMostSimilarNeighbor(int) - Method in interface com.chemaxon.overlap.result.NnResults
Index of most similar neighbor.
getMsc() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
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 interface com.chemaxon.apidiscovery.linenote.ChoiceParameterDescriptor
Parameter name.
getName() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Name.
getName() - Method in class com.chemaxon.calculations.common.Timer
Name of the timer.
getName() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getName(Molecule) - Method in class com.chemaxon.overlap.cli.util.pipeline.GetMoleculeName
 
getName() - Method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractorFactory
 
getName() - Method in class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractorFactory
 
getName() - Method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractorFactory
 
getName() - Method in interface com.chemaxon.overlap.cli.util.prop.PropertyExtractorFactory
Unique name of extraction.
getName() - Method in interface com.chemaxon.overlap.wui.res.DescribedResource
Resource name.
getName() - Method in class com.chemaxon.overlap.wui.res.SimpleDescribedResource
 
getNames() - Static method in class com.chemaxon.overlap.servlets.MolsContext
Deprecated.
 
getNeighbor(int, int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getNeighbor(int, int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getNeighbor(int, int) - Method in interface com.chemaxon.overlap.result.KnnResults
Index of a single neighbor.
getNeighborCounts(KnnRes) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Stored neighbor count for each record.
getNeighborCountsOfAll() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getNeighborCountsOfAll() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getNeighborCountsOfAll() - Method in interface com.chemaxon.overlap.result.KnnResults
Neighbor count of all queries.
getNeighborDissimilarities(KnnRes, int, String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Dissimilarities of the k-th most similar neighbors.
getNeighborDissimilaritiesMissingValue() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getNeighborDissimilaritiesMissingValue() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getNeighborDissimilaritiesMissingValue() - Method in interface com.chemaxon.overlap.result.KnnResults
getNeighborIndices(KnnRes, int, String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Indices of the k-th most similar neighbors.
getNeighborPngOrPlaceholder(KnnRes, int, int, int, int, String, String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Get molecule image for a specific neighbor in PNG format or a placeholder image for absent molecules.
getNeighborProps(KnnRes, int, String, String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Additional stored property of the k-th most similar neighbors for all queries.
getNeighbors(int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getNeighbors(int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getNeighbors(int) - Method in interface com.chemaxon.overlap.result.KnnResults
ID of the nearest neighbors of query.
getNodeType() - Method in enum com.chemaxon.descriptors.alignment.ShapeFunction
 
getNonFinishedCount() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Non finished items in the queue.
getNthNeighborDissimilaritiesOfAll(int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getNthNeighborDissimilaritiesOfAll(int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getNthNeighborDissimilaritiesOfAll(int) - Method in interface com.chemaxon.overlap.result.KnnResults
Get n-th neighbor dissimilarities for all queries.
getNthNeighborIdsOfAll(int) - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getNthNeighborIdsOfAll(int) - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getNthNeighborIdsOfAll(int) - Method in interface com.chemaxon.overlap.result.KnnResults
Get n-th neighbor indices for all queries.
getNumericRepresentation() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Numeric representation.
getObjectOutputStream() - Method in interface com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerialization
Get output to write remainder data.
getObjectOutputStream() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl
 
getOkCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Count of OKs.
getOrPut(String, Class<T>, Supplier<T>) - Method in class com.chemaxon.overlap.wui.context.Contexts
Get a resource object or create new if not exists.
getOut() - Static method in class com.chemaxon.calculations.util.CmdlineUtils
Get stdout to use.
getOutputCount() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Number of reported results.
getOutputStream() - Method in interface com.chemaxon.calculations.util.SeekableFileOutput
The represented stream.
getOverflowItemCount() - Method in interface com.chemaxon.overlap.result.LinearHistogram
Items larger than the last bin.
getPages() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResultHandler
Get collected pages.
getPages() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler
Get collected pages.
getPagesize() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getPageSize() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Current page size.
getPagesize() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Gets represented page size.
getParameterClass() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser
Class of underlying parameter.
getParameterClass() - Method in class com.chemaxon.apidiscovery.ParameterWrapper
Parameter field class.
getParameterNames() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceDescriptor
Parameter names.
getParameters() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceDescriptor
Parameters of the current choice.
getParameters() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
 
getParameters() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
getParameters() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
Gets the parameter object.
getParameters() - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
 
getParameters() - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
 
getParameters() - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator
 
getParameters() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
 
getParameters() - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
 
getParameters() - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
 
getParametrizationHelp() - Method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractorFactory
 
getParametrizationHelp() - Method in class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractorFactory
 
getParametrizationHelp() - Method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractorFactory
 
getParametrizationHelp() - Method in interface com.chemaxon.overlap.cli.util.prop.PropertyExtractorFactory
Help on parameterization.
getParams() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
Delegated parameters.
getParentClusterID(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
Looks up a clusters parent cluster ID.
getParentClusterIndexOf(int) - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
Cluster ID of a cluster's parent.
getParseErrorCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Parse error count.
getPartialContent(long, long) - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
Return part of the content.
getPartialResultProvider() - Method in class com.chemaxon.overlap.service.task.ExecutableTask
 
getPieces(String) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.SmaInterpreter
This method finds automatically the pieces in the recursive SMARTS string and gives them back as an array, so they will be imported as a molecule and not as a query string.
getPng(int, Sink<Molecule>, int, int) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Get PNG of molecule if present.
getPng(int, int, int) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Get PNG of molecule if present.
getPng(MolsRes, int, int, int, String, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get molecule image in PNG format.
getPngOrPlaceholder(MolsRes, int, int, int, String, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get molecule image in PNG format or a placeholder image for absent molecules.
getPort() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
 
getPort() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
 
getPreferredAssigner() - Method in interface com.chemaxon.clustering.common.HierarchicClustering
Preferred assigner.
getPreferredAssigner() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
 
getProcessingErrorCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Processing error count.
getProfilingSnapshot() - Method in class com.chemaxon.overlap.wui.resources.StatisticsResource
Create a profiling snapshot.
getProp(String) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Get an additional property container.
getProperties() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols
Additional stored property containers.
getProperties() - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
 
getProperty(String) - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols
Get additional property container.
getProperty(Molecule) - Method in class com.chemaxon.overlap.cli.util.pipeline.GetSdfProperty
 
getPropertyOnIndexRange(MolsRes, String, int, int, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Fetch property values for a range of Molecule indices.
getPropertyOnIndexRangePOST(MolsRes, String, int, int, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Fetch property values for a range of Molecule indices - POST endpoint.
getProps(MolsRes, List<Integer>, List<String>, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Fetch multiple property values
getPropsOrNull() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResult
Get additional properties.
getPropType() - Method in class com.chemaxon.overlap.cli.util.prop.MolProp
Get represented type.
getProxiedImplementation() - Method in interface com.chemaxon.descriptors.common.reflect.Reflect.Proxied
Return underlying proxied implementation.
getQf() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getQm() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getQueries() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getQuery(int) - Method in class com.chemaxon.overlap.result.impl.SimilarityResultsImpl
 
getQuery(int) - Method in interface com.chemaxon.overlap.result.SimilarityResults
ID of stored query.
getQueryCount() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
 
getQueryCount() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
 
getQueryCount() - Method in interface com.chemaxon.overlap.result.NnResults
Number of queries stored.
getQueryIndices(KnnRes, String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Indices of the queries.
getQueryMasterIndex(int) - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
 
getQueryMasterIndexProjector() - Method in class com.chemaxon.overlap.wui.res.KnnRes
Get index projector for queries.
getQueryMols() - Method in class com.chemaxon.overlap.wui.res.KnnRes
Get query molecules.
getQueryName() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getQueryPagesize() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
 
getQueryPngOrPlaceholder(KnnRes, int, int, int, String, String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Get molecule image for a query in PNG format or a placeholder image for absent molecules.
getQueueSize() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean
Current size of the results queue.
getRAttachmentCount() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
 
getRawFileInfo(ExperimentalRawFile) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
Get raw file info DTO.
getRawFilesInfo() - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
List experimental raw files.
getRawFileSizeinfo(ExperimentalRawFile, SizeInfoMethod) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
Experimental endpoint to estimate allocated size.
getRawFileWithContentDisposition(ExperimentalRawFile) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
Get the raw file content with content-disposition.
getRawFileWithNoContentDisposition(ExperimentalRawFile) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesContentResource
Get the raw file content with no content-disposition.
getRawFileWithNoContentDisposition(ExperimentalRawFile) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource
Get the raw file content with no content-disposition.
getRcpriv() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
 
getRcpub() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
 
getReactantId() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
 
getReadByteCount() - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
Total bytes read.
getReader() - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
Get represented Reader.
getReadIndex() - Method in interface com.chemaxon.overlap.io.StructureRecord
Represented structure/record index.
getRealAtomCount() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
Chemical atom count.
getRealAtomCount() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
Real chemical atoms represented by this extension.
getRealNeighborAtoms(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
Get all real atom neighbor indices.
getResource() - Method in interface com.chemaxon.overlap.wui.res.DescribedResource
Actual resource.
getResource() - Method in class com.chemaxon.overlap.wui.res.SimpleDescribedResource
 
getResourceDescriptions() - Method in class com.chemaxon.overlap.wui.resources.MetaResource
All available resources.
getResourceInfo() - Method in interface com.chemaxon.overlap.wui.res.DescribedResource
Resource info annotation.
getResourceInfo() - Method in class com.chemaxon.overlap.wui.res.SimpleDescribedResource
 
getResult() - Method in interface com.chemaxon.overlap.result.AsyncResult
Get the representation of the long running task.
getResult(ProfRes) - Method in class com.chemaxon.overlap.wui.resources.ProfResResource
Get a profiling result.
getResult(StatRes) - Method in class com.chemaxon.overlap.wui.resources.StatResResource
Get a statistics result.
getResultOrNull() - Method in class com.chemaxon.overlap.service.async.AsyncCall
Gets the result if the call has been completed or null if not.
getRings() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
Return rings settings.
getRootUrl() - Method in class com.chemaxon.overlap.wui.context.Descriptor
 
getRootUrl() - Method in class com.chemaxon.overlap.wui.context.Knn
 
getRootUrl() - Method in class com.chemaxon.overlap.wui.context.Molecules
 
getRootUrl() - Method in interface com.chemaxon.overlap.wui.context.ResourceClass
Root URL of the handler servlet.
getRow(int) - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Get a row.
getRow(int) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
getRowCount() - Method in interface com.chemaxon.calculations.util.cellfield.CellField
Rows.
getRowCount() - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
 
getRowNumber() - Method in class com.chemaxon.calculations.util.cellfield.impl.RowImpl
Get row number.
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.
getSdf(MolsRes, int) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get molecule in SDF format.
GetSdfProperty - Class in com.chemaxon.overlap.cli.util.pipeline
Retrieve an SDF property String.
GetSdfProperty() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.GetSdfProperty
 
getSelecteds() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder
Get current state of selection.
getSelfKnn() - Method in class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap
 
getSerializer() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
 
getServerStartTime() - Method in class com.chemaxon.overlap.wui.StartupHandler
Time stamp of server startup.
getServerUpDuration() - Method in class com.chemaxon.overlap.wui.StartupHandler
 
getSetInfo(String, String) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Fill molecule set info.
getSetInfo(String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Create description of a molecule set.
getShapeComparator(DRShapeComparatorParameter) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
 
getShapeComparator(ShapeComparatorParameter) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
 
getShapeData() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShape
 
getShapeData() - Method in class com.chemaxon.descriptors.alignment.shape.Shape
 
getShapeData() - Method in interface com.chemaxon.descriptors.alignment.ShapeDescriptor
 
getShapeFunction() - Method in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
getShortDescription() - Method in enum com.chemaxon.overlap.wui.context.features.ServerFeature
Short, human readable description of the feature toggle.
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.
getShorts() - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
Get scaled shorts representation.
getSimilarity() - Method in class com.chemaxon.descriptors.common.binary.SimpleComparisonResult
 
getSimilarity() - Method in interface com.chemaxon.descriptors.common.ComparisonResult
Similarity score of the comparison.
getSimilars() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
 
getSimilarsCount() - Method in class com.chemaxon.overlap.wui.RealTimeSearchGuiContext
 
getSingleProperty(MolsRes, int, String) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get a single property value.
getSize() - Method in class com.chemaxon.overlap.wui.res.DescRes
 
getSize() - Method in interface com.chemaxon.overlap.wui.res.Described
Size of the represented resource.
getSize() - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
 
getSize() - Method in class com.chemaxon.overlap.wui.res.GridRes
 
getSize() - Method in class com.chemaxon.overlap.wui.res.KnnRes
 
getSize() - Method in class com.chemaxon.overlap.wui.res.MolsRes
 
getSize() - Method in class com.chemaxon.overlap.wui.res.ProfRes
 
getSize() - Method in class com.chemaxon.overlap.wui.res.StatRes
 
getSizeInfo(Function<Object, Long>, Function<Object, Long>) - Method in class com.chemaxon.overlap.wui.res.DescRes
 
getSizeInfo(Function<Object, Long>) - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
 
getSizeInfo(Function<Object, Long>) - Method in interface com.chemaxon.overlap.wui.res.HasBasicSizeinfo
Invoke size calculation.
getSizeInfo(Function<Object, Long>, Function<Object, Long>) - Method in interface com.chemaxon.overlap.wui.res.HasSizeinfo
Invoke size calculation.
getSizeInfo(Function<Object, Long>) - Method in class com.chemaxon.overlap.wui.res.KnnRes
 
getSizeInfo(Function<Object, Long>, Function<Object, Long>) - Method in class com.chemaxon.overlap.wui.res.MolsRes
 
getSizeInfo(Function<Object, Long>) - Method in class com.chemaxon.overlap.wui.res.ProfRes
 
getSizeInfo(Function<Object, Long>) - Method in class com.chemaxon.overlap.wui.res.StatRes
 
getSizeinfo(DescRes, SizeInfoMethod, boolean) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Experimental endpoint to estimate allocated size.
getSizeinfo(KnnRes, SizeInfoMethod) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Experimental endpoint to estimate allocated size.
getSizeinfo(MolsRes, SizeInfoMethod, boolean) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Experimental endpoint to estimate allocated size.
getSizeinfo(ProfRes, SizeInfoMethod) - Method in class com.chemaxon.overlap.wui.resources.ProfResResource
Experimental endpoint to estimate allocated size.
getSizeinfo(StatRes, SizeInfoMethod) - Method in class com.chemaxon.overlap.wui.resources.StatResResource
Experimental endpoint to estimate allocated size.
getSkip() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getSmallestBinsBlock(int) - Method in class com.chemaxon.calculations.util.Histo
Compose the list of smallest bins block.
getSmiles() - Method in interface com.chemaxon.overlap.wui.res.MoleculeContainer
Represented structure as Smiles.
getSmiles() - Method in class com.chemaxon.overlap.wui.res.MoleculeContainerImpl
 
getSmiles(int) - Method in class com.chemaxon.overlap.wui.res.MolsRes
Get SMILES source.
getSmiles(MolsRes, int) - Method in class com.chemaxon.overlap.wui.resources.MoleculesResource
Get molecule in Smiles format.
getSmiles() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
Get canonical SMILES of the candidate without cxsmiles extension (pseudo atom labels).
getSource() - Method in interface com.chemaxon.calculations.io.StructureRecord
Get represented source.
getSource() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResult
Get source.
getSource(int) - Method in class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
 
getSource(int) - Method in interface com.chemaxon.overlap.io.MasterMoleculeStorage
Return given structure source as stored.
getSource(int) - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
 
getSource() - Method in interface com.chemaxon.overlap.wui.res.MoleculeContainer
Source used to create this container.
getSource() - Method in class com.chemaxon.overlap.wui.res.MoleculeContainerImpl
 
getSparseCompression() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
Sparse compression.
getSplittersHelpMessage() - Static method in class com.chemaxon.overlap.cli.util.importing.Splitting
Help message.
getStandardizer() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getStandardizer() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
Gets represented standardizer wrapper.
getStandardizerWrapper() - Method in class com.chemaxon.descriptors.db.MDTableReader
Get represented standardizer wrapper.
getStandardizerWrapper() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl
 
getStandardizerWrapper() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl
 
getStandardizerWrapper() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl
 
getStartTime() - Method in class com.chemaxon.calculations.common.Timer
Start time.
getStartTimeMs() - Method in class com.chemaxon.overlap.service.task.Task
 
getStatBlock() - Method in class com.chemaxon.calculations.util.Histo
Compose statistics block.
getStatistics() - Method in class com.chemaxon.calculations.common.ConsolePO
Get timer statistic of this observer.
getStatistics() - Method in class com.chemaxon.calculations.common.StatPO
Get statistics from underlying Timer.getStatistics().
getStatistics() - Method in class com.chemaxon.calculations.common.Timer
Statistics of a stopped timer.
getStatistics() - Method in class com.chemaxon.overlap.wui.resources.StatisticsResource
Get basic server statistics.
getStatus() - Method in exception com.chemaxon.overlap.wui.resources.exceptions.WuiBadRequestException
 
getStatus() - Method in exception com.chemaxon.overlap.wui.resources.exceptions.WuiException
Associated status.
getStatus() - Method in exception com.chemaxon.overlap.wui.resources.exceptions.WuiForbiddenException
 
getStatus() - Method in exception com.chemaxon.overlap.wui.resources.exceptions.WuiInternalServerErrorException
 
getStatus() - Method in exception com.chemaxon.overlap.wui.resources.exceptions.WuiNotFoundException
 
getSteps() - Method in class com.chemaxon.overlap.cli.PipelineRunner
 
getStorage() - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap
Get represented unguarded storage.
getStorage() - Method in class com.chemaxon.overlap.cli.util.prop.MolProp
Get property storage.
getStoredType() - Method in class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
 
getStoredType() - Method in class com.chemaxon.overlap.io.CompactStringStorage
 
getStoredType() - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
 
getStoredType() - Method in interface com.chemaxon.overlap.io.MasterStorage
Represented type.
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.
getStructureSource() - Method in interface com.chemaxon.overlap.io.StructureRecord
Structure source if applicable.
getSuitableErrorHandler() - Method in enum com.chemaxon.calculations.io.SimpleErrorHandling
Get a default error handler.
getSummaryOnAllDescriptors() - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Description of available molecular descriptor data.
getSummaryOnDescriptor(String) - Method in class com.chemaxon.overlap.wui.resources.DescriptorsResource
Get info of descriptor data.
getSummaryOnGrid(String) - Method in class com.chemaxon.overlap.wui.resources.GridsResource
Get summary info of a grid.
getSx() - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
Horizontal size.
getSy() - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
Vertical size.
getTableLabels(KnnRes, List<Integer>, List<Integer>, String) - Method in class com.chemaxon.overlap.wui.resources.KnnResource
Get labels to be displayed in a k-NN view table.
getTarget(int) - Method in class com.chemaxon.overlap.result.impl.SimilarityResultsImpl
 
getTarget(int) - Method in interface com.chemaxon.overlap.result.SimilarityResults
ID of the stored target.
getTargetIndex() - Method in class com.chemaxon.overlap.result.impl.SimilarityResultImpl
 
getTargetIndex() - Method in interface com.chemaxon.overlap.result.SimilarityResult
Get the internal index of the represented target structure.
getTargetMasterIndex(int) - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiContext
 
getTargetMasterIndexProjector() - Method in class com.chemaxon.overlap.wui.res.KnnRes
Get index projector for targets.
getTargetMols() - Method in class com.chemaxon.overlap.wui.res.KnnRes
Get target molecules.
getTargetName() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getTargetProp(String) - Method in class com.chemaxon.overlap.wui.res.KnnRes
Get target property.
getTargets() - Method in class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult
 
getTask() - Method in class com.chemaxon.overlap.service.async.AsyncCall
 
getTime() - Method in class com.chemaxon.overlap.wui.res.DescRes
 
getTime() - Method in interface com.chemaxon.overlap.wui.res.Described
Init/load/prepare time of the represented resource.
getTime() - Method in class com.chemaxon.overlap.wui.res.ExperimentalRawFile
 
getTime() - Method in class com.chemaxon.overlap.wui.res.GridRes
 
getTime() - Method in class com.chemaxon.overlap.wui.res.KnnRes
 
getTime() - Method in class com.chemaxon.overlap.wui.res.MolsRes
 
getTime() - Method in class com.chemaxon.overlap.wui.res.ProfRes
 
getTime() - Method in class com.chemaxon.overlap.wui.res.StatRes
 
getToBytes() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getToStrings() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getToStringsP() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getTotalNotifyCount() - Method in interface com.chemaxon.overlap.io.MoleculeCallbacks.CountingMoleculeCallback
Count of all notify calls.
getTotalRealAtomCount() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton
Sum of chemical atom counts from all definitions.
getTotalSizeinfo(SizeInfoMethod, boolean) - Method in class com.chemaxon.overlap.wui.resources.StatisticsResource
Experimental endpoint to estimate allocated size of all of the resources.
getTotalWork() - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
 
getTotalWork() - Method in interface com.chemaxon.calculations.common.ProgressObservable
 
getTp() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
 
getTp() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
 
getTp() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
 
getTripletCount() - Method in class com.chemaxon.overlap.result.impl.SimilarityResultsImpl
 
getTripletCount() - Method in interface com.chemaxon.overlap.result.SimilarityResults
Number of stored query-target-dissimilarity triplets.
getTryCount() - Method in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
 
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator
Deprecated.
Use #forTversky(double, double).