Index (overlap-examples-cli-dist 0.3.5 API)

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, String, String, Class<V>, Function<U, V>) - Method in class com.chemaxon.overlap.cli.PipelineRunner
addStatelessTransformation(PipelineStep, String, String, Class, 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: Unguarded comparator for BinaryMetrics.BINARY_COMMONPART_NORMALIZED.
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: Unguarded comparator for BinaryMetrics.BINARY_EUCLIDEAN_NORMALIZED.
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: Deprecated.
Use BinaryVectorDescriptorImpl.BinaryVectorDescriptorImpl(int[], java.lang.Object, int, com.chemaxon.descriptors.common.BinaryVectors.Endianness)
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: Deprecated.
Use BinaryVectorDescriptorImpl.BinaryVectorDescriptorImpl(long[], java.lang.Object, int, com.chemaxon.descriptors.common.BinaryVectors.Endianness) with explicit endianness specification
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: Deprecated.
Use BinaryVectorDescriptorImpl.BinaryVectorDescriptorImpl(byte[], java.lang.Object, int, com.chemaxon.descriptors.common.BinaryVectors.Endianness)
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: Map LinearScaler.byteToFloat(byte) to an array.
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: Equivalent to ProgressObserver.done().
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: Convenience wrapper for Segmenter.composer(java.lang.Appendable, java.io.Closeable).
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: Convert a molecule using MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String).
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: Convert a molecule using MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String).
convertPost(ConversionRequest) - Method in class com.chemaxon.overlap.wui.resources.MolConverter: Convert a molecule using MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String).
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: Deprecated.
Use ProgressObservers.nullProgressObserver() instead.
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: Deprecated.
Use ProgressObservers.noCanceller()
createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers: Deprecated.
Use ProgressObservers.createStrictNullObserver().
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, ComparisonContextFactory<DescriptorComparator, 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: Returns System.currentTimeMillis().
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 - 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 - 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: Map LinearScaler.floatToByte(float) to an array.
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: Map LinearScaler.floatToShort(float) to an array.
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.
use FloatVectorDescriptorImpl.FloatVectorDescriptorImpl(byte[], java.lang.Object, int) with explicit expected vector length instead
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.
Use FloatVectorDescriptorImpl.FloatVectorDescriptorImpl(java.lang.String, Object, int) with explicit expected vector length instead
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: Use a DescriptorComparator as underlying UnguardedDissimilarityCalculator.
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: Iterable wrapper for ScaffoldExtension.iterateFragmentMatches(com.chemaxon.virtuallib.sc.model.sdf.RgFrag).
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: Deprecated.
Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator: Deprecated.
Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator: Deprecated.
Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics)
getBinaryMetricsComparator(BinaryMetrics) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator: Deprecated.
Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics).
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.
Use Guarded.getGuardObject()
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: Deprecated.
Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics).
getFloatMetricsComparator(FloatVectorMetrics) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl: Deprecated.
getFloatVectorComparator(FloatVectorMetrics) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator: Deprecated.
Use FloatVectorMetricFactory.forFloatMetrics(com.chemaxon.descriptors.metrics.FloatVectorMetrics)
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: Delegate FrameworkClusteringResults.getFrameworkAsMolecule(int).
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: Delegate FrameworkClusteringResults.getFrameworkAsSmiles(int).
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: Deprecated.
Use KnnResults.getMinNeighborCount() and KnnResults.getMaxNeighborCount()
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: Missing value for results of KnnResults.getNthNeighborDissimilaritiesOfAll(int).
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: Deprecated.
Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator: Deprecated.
Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator: Deprecated.
Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator: Deprecated.
Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator: Deprecated.
Use BinaryVectorMetricFactory.forTversky(com.chemaxon.descriptors.metrics.TverskyParameters)
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsGenerator: Deprecated.
Use BinaryVectorMetricFactory.forTverskyCoefficients(double, double)
getTverskyComparator(double, double) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator: Deprecated.
Use #forTversky(double, double).
getTverskyComparator(TverskyParameters) - Method in interface com.chemaxon.descriptors.vectors.binary.BvGenerator: Deprecated.
Use BinaryVectorMetricFactory.forBinaryMetrics(com.chemaxon.descriptors.metrics.BinaryMetrics).
getTverskyComparator(double, double) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
getTverskyComparator(TverskyParameters) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
getType() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Value type.
getType() - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Type.
getType() - Method in interface com.chemaxon.calculations.util.cellfield.Column: Represented type.
getType() - Method in class com.chemaxon.calculations.util.cellfield.impl.ColumnImpl
getUnderflowItemCount() - Method in interface com.chemaxon.overlap.result.LinearHistogram: Items smaller than the first bin.
getUnguardedDescriptor(int) - Method in class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl
getUnguardedDescriptor(int) - Method in interface com.chemaxon.overlap.storage.UnguardedPagedStorage: Retrieve a descriptor.
getUnguardedDissimilarityCalculator(int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator: Get a suitable dissimilarity calculator for unguarded packed long[] representations.
getUnguardedDissimilarityCalculator(int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
getUnguardedDissimilarityCalculator() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Gets represented unguarded dissimilarty calculator.
getUnguardedExtractor() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Gets represented unguarded form extractor.
getUnguardedFromBytes() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
getUnguardedsAsFlatList() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds: Get unguarded descriptors in a flat List.
getUnguardedsAsFlatList() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols: Get unguarded descriptors in a flat List.
getUpperBound() - Method in class com.chemaxon.calculations.util.Histo: Upper bound of the histogram.
getUpperBound() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeHistogramComparator
getUpperBound() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeIntersectionComparator
getUpperBound() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeTanimotoComparator
getUpperBound() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeIntersectionComparator
getUpperBound() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeTanimotoComparator
getUpperBound() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
getUpperBound() - Method in interface com.chemaxon.descriptors.common.DescriptorComparator: Get upper bound for the similarity/dissimilarity values if such one can be determined.
getUpperBound() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
getUpperBound() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
getUpperBoundForBinaryVectors(int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator: Possible highest value of similarity/dissimilarity scores.
getUpperBoundForBinaryVectors(int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
getUpperBoundForFloatVectors() - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator: Deprecated.
In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
getUpperLimit() - Method in interface com.chemaxon.overlap.result.LinearHistogram: Largest value assigned to the last bin.
getUrl() - Method in interface com.chemaxon.overlap.wui.res.DescribedResource: URL of the resource.
getUrl() - Method in class com.chemaxon.overlap.wui.res.SimpleDescribedResource
getUrls() - Method in class com.chemaxon.overlap.wui.resources.ProfResResource: Urls of available resources.
getUrls() - Method in class com.chemaxon.overlap.wui.resources.StatResResource: Urls of available resources.
getUsageString(Class<?>) - Static method in class com.chemaxon.overlap.cli.util.CliUtil: Get usage string of a given parameters object
getUsageString(Class<?>, String) - Static method in class com.chemaxon.overlap.cli.util.CliUtil: Get usage string of a given parameters object
getUsageString(Object[]) - Static method in class com.chemaxon.overlap.cli.util.CliUtil: Get usage string of a given parameters object
getValue() - Method in interface com.chemaxon.calculations.io.OrderedElement: Element value.
getVersionInfo() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Get version info object.
getVtInMs() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
getWebapp() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
getWebapp() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
getWorkUnit() - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
getWorkUnit() - Method in interface com.chemaxon.calculations.common.ProgressObservable
getWrittenByteCount() - Method in class com.chemaxon.overlap.cli.util.pipeline.OutputStreamStatCollector: Total bytes written.
getWrittenBytes() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl
getXmlConfig() - Method in class com.chemaxon.descriptors.db.MDTableReader: Gets configuration string.
getXmlConfig() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl
getXmlConfig() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl
getXmlConfig() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters: The XML configuration string.
getXmlConfig() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl
getXmlConfig() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters: The XML configuration string.
getZAttachmentCount() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
git - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Git revision.
gitAbbrev - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Git abbreviated revision.
gitClean() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Repo is clean.
gitClean - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Git clean.
gitRevision() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Git revision.
gitRevisionAbbrev() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Git abbreviated revision.
gout - Variable in class com.chemaxon.virtuallib.sc.cli.ParseSdfParameters
GridInfo - Class in com.chemaxon.overlap.wui.dto: Basic info of grid data.
GridInfo() - Constructor for class com.chemaxon.overlap.wui.dto.GridInfo
GridPane - Class in com.chemaxon.overlap.cli.util.images: Simple rectangular grid.
GridPane() - Constructor for class com.chemaxon.overlap.cli.util.images.GridPane: Construct.
GridRes - Class in com.chemaxon.overlap.wui.res: A generic grid resource.
GridRes(String, long) - Constructor for class com.chemaxon.overlap.wui.res.GridRes: Construct.
grids - Variable in class com.chemaxon.overlap.wui.dto.GridsInfo: List of available descriptors.
GridsInfo - Class in com.chemaxon.overlap.wui.dto: Information of available grids.
GridsInfo() - Constructor for class com.chemaxon.overlap.wui.dto.GridsInfo
GridsResource - Class in com.chemaxon.overlap.wui.resources: Represents generic table resources.
GridsResource() - Constructor for class com.chemaxon.overlap.wui.resources.GridsResource
GSearch - Class in com.chemaxon.descriptors.fingerprints.maccs.cli: This application is a command line interface for Gabor's search engine as it is used for the MACCS fingerprint generation, so the implementation is not general but nomally should work.
GSearch(String) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.cli.GSearch
GsSearch - Class in com.chemaxon.descriptors.fingerprints.maccs: Gabor's Simple Search.
GsSearch(String) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.GsSearch: This constructor is initialized with the query structure represented as SMARTS string.
Guarded - Interface in com.chemaxon.descriptors.common: Represents guarded entities.
Guarded.EnsureThat - Class in com.chemaxon.descriptors.common: Guarded checking utility.
Guarded.New - Class in com.chemaxon.descriptors.common: Create new guard object.
GuardedSerializableReturnValue - Class in com.chemaxon.descriptors.common.reflect: Invocation handler container ensuring guarded return value.
GuardedSerializableReturnValue(InvocationHandler, Object) - Constructor for class com.chemaxon.descriptors.common.reflect.GuardedSerializableReturnValue: Construct.
GuardedSingleArgument - Class in com.chemaxon.descriptors.common.reflect: Invocation handler container ensuring guarded return value.
GuardedSingleArgument(InvocationHandler, Object) - Constructor for class com.chemaxon.descriptors.common.reflect.GuardedSingleArgument: Construct.
guardObject() - Static method in class com.chemaxon.descriptors.common.Guarded.New: New guard object.
Gui - Class in com.chemaxon.overlap.wui: Main class of interactive web based gui.
gzbuffer(int) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
gzip(boolean) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput

H

h - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionRequest
h - Variable in class com.chemaxon.overlap.wui.dto.Histogram: Higher limit.
h - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest: Height of the target images in pixel.
h - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
Halign - Enum in com.chemaxon.overlap.cli.util.images: Horizontal alignment.
handle(Class<ET>, Consumer<ET>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationSpec: Register exception handler.
handle(Class<ET>, Consumer<ET>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationSpec2: Register exception handler.
HasBasicSizeinfo - Interface in com.chemaxon.overlap.wui.res: Basic size info is supplied.
hashCode() - Method in class com.chemaxon.calculations.util.cellfield.impl.RowImpl
hashCode() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
hashCode() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
hashCode() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
hasNext() - Method in class com.chemaxon.overlap.cli.util.pipeline.CharIterator
hasParent(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Check if a cluster has parent cluster id set.
HasSizeinfo - Interface in com.chemaxon.overlap.wui.res: Size info is supplied.
heapMemoryUsage - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Heap memory usage.
heapMemoryUsage - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Heap memory usage.
heapMemoryUsed - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Used heap memory.
heapMemoryUsed - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Used heap memory.
HeatmapBuilder - Class in com.chemaxon.overlap.cli.util.images: Drawing heatmaps for similarity results.
HeatmapBuilder(int, int, HeatmapRenderingParameters) - Constructor for class com.chemaxon.overlap.cli.util.images.HeatmapBuilder: Construct.
heatmapRenderingParameters - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Heatmap rendering parameters.
HeatmapRenderingParameters - Class in com.chemaxon.overlap.cli.util.images: Parameters for heatmap rendering.
HeatmapRenderingParameters() - Constructor for class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
height() - Method in interface com.chemaxon.clustering.common.HierarchicCluster: Distance from the farthest leave.
help - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters: Print help message.
help - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
help - Variable in class com.chemaxon.overlap.cli.JsEvalParameters
help - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters: Print help message.
help - Variable in class com.chemaxon.virtuallib.sc.cli.ConverterParameters
help - Variable in class com.chemaxon.virtuallib.sc.cli.ConvertGroupParameters
help - Variable in class com.chemaxon.virtuallib.sc.cli.ParseSdfParameters
HFlowPane - Class in com.chemaxon.overlap.cli.util.images: Basic horizontal flow plane.
HFlowPane() - Constructor for class com.chemaxon.overlap.cli.util.images.HFlowPane
HierarchicCluster<T> - Interface in com.chemaxon.clustering.common: Represents a group (cluster) of structures, possibly divided into further non overlapping clusters.
HierarchicClustering<T,C extends HierarchicCluster<T>> - Interface in com.chemaxon.clustering.common: A grouping of structures into disjunct hierarchical groups.
HierarchicClustering.Alignment - Enum in com.chemaxon.clustering.common: Level interpretation.
hierarchicIndexOf(T, HierarchicClustering<T, ? extends HierarchicCluster<T>>) - Static method in class com.chemaxon.clustering.util.Util: Consruct a hierarchic index for a given member of a clustering.
hierarchyToString(IDBasedHierarchicClustering, IDBasedAssigner, List<String>, int) - Static method in class com.chemaxon.clustering.util.Util: Render a minimalist dendrogram from a String.
highcount - Variable in class com.chemaxon.overlap.wui.dto.Histogram: Overflow items count.
Histo - Class in com.chemaxon.calculations.util: Simple histogram of values.
Histo(int, int, int, boolean) - Constructor for class com.chemaxon.calculations.util.Histo: Create a histogram containing integers.
Histo(int, int) - Constructor for class com.chemaxon.calculations.util.Histo
Histo(double, double, int, boolean, boolean) - Constructor for class com.chemaxon.calculations.util.Histo: Create a histogram containing real numbers.
Histo(double, double, int) - Constructor for class com.chemaxon.calculations.util.Histo
histogram - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionResult: Dissimilarity distribution histogram.
Histogram - Class in com.chemaxon.overlap.wui.dto: DTO for LinearHistogram.
Histogram(LinearHistogram) - Constructor for class com.chemaxon.overlap.wui.dto.Histogram: Construct.
Histogram() - Constructor for class com.chemaxon.overlap.wui.dto.Histogram: No-arg constructor for deserialization.
horizontal() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Horizontal range.
horizontal() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
horizontalSpec() - Method in interface com.chemaxon.overlap.cli.util.images.AreaSpec: Horizontal range specification.
humanReadableAvgInvocationTime - Variable in class com.chemaxon.calculations.common.TimerStatistics: Average time of a single invocation in human readable format.
humanReadableElapsedTime - Variable in class com.chemaxon.calculations.common.TimerStatistics: Elapsed time in human readable format.
humanReadableFreeMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat: Free memory in human readable form.
humanReadableGctime - Variable in class com.chemaxon.overlap.cli.prof.Memstat: GCtime in human readable form.
humanReadableInvocationCount - Variable in class com.chemaxon.calculations.common.TimerStatistics: Invocation count in human readable format.
humanReadableMaxMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat: Max memory in human readable form.
humanReadableTotalMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat: Total memory in human readable form.
humanReadableUsedMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat: Used memory in human readable form.

I

icon - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
id - Variable in class com.chemaxon.overlap.service.task.Task
id - Variable in class com.chemaxon.overlap.wui.dto.AsyncCallDto: ID of the associated call.
id - Variable in class com.chemaxon.overlap.wui.dto.MoleculeInfo: Molecule ID string or null when absent.
id - Variable in class com.chemaxon.overlap.wui.dto.TaskDto: Unique task ID.
IDBasedAssigner - Interface in com.chemaxon.clustering.common: Assign levels to IDBasedHierarchicClustering.
IDBasedAssignerBuilder - Class in com.chemaxon.clustering.common: An ID based cluster level assigner builder.
IDBasedAssignerBuilder() - Constructor for class com.chemaxon.clustering.common.IDBasedAssignerBuilder
IDBasedClusterBuilder - Class in com.chemaxon.clustering.common: Builder for ID based non-hierarchic clustering.
IDBasedClusterBuilder() - Constructor for class com.chemaxon.clustering.common.IDBasedClusterBuilder: Instantiate an empty builder.
IDBasedClusterBuilderSpec - Interface in com.chemaxon.clustering.common: Allowing fluent API calls to IDBasedHierarchicClusterBuidler.
IDBasedHierarchicCluster - Interface in com.chemaxon.clustering.common: A Hierarchic cluster over integers, preferably IDs; having associated integral ClusterID.
IDBasedHierarchicClusterBuidler - Class in com.chemaxon.clustering.common: Builder for integer ID based hierarchic cluster building.
IDBasedHierarchicClusterBuidler(HierarchicClustering.Alignment) - Constructor for class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: New builder instance.
IDBasedHierarchicClustering - Interface in com.chemaxon.clustering.common: A Hierarchic clustering over integers, preferably IDs.
IDBasedSingleLevelClustering - Interface in com.chemaxon.clustering.common: A SingleLevelClustering of clusters containing Integer IDs.
identifierConfigurationXml(String) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder: Set identifier configuration XML to use for custom typizer.
identifierConfigurationXml(String) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder: Set identifier configuration XML to use for custom typizer.
Identity - Class in com.chemaxon.overlap.splits: Return the whole input String.
Identity() - Constructor for class com.chemaxon.overlap.splits.Identity
identityStandardizer() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers: Identity standardization.
IdGenerator - Interface in com.chemaxon.overlap.util.idgenerator
IdGeneratorFactory - Interface in com.chemaxon.overlap.util.idgenerator
immediateDescendantsCount() - Method in interface com.chemaxon.clustering.common.HierarchicCluster: Sum of child clusters count and leaves count.
impHCount - Variable in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.ScoredExtension
important - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Important flag.
importopts - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest: Import options or null/empty string.
Imports - Class in com.chemaxon.overlap.cli.util: Utilities for importing data for searching.
ImportStorage - Class in com.chemaxon.overlap.cli: Build serialized descriptors storage from custom Strings representation.
ImportStorageParameters - Class in com.chemaxon.overlap.cli: Command line arguments for ImportStorage.
ImportStorageParameters() - Constructor for class com.chemaxon.overlap.cli.ImportStorageParameters
in() - Method in interface com.chemaxon.calculations.util.CmdlineContext: Input stream, usually mapped to System.in.
in() - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
in - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
in - Variable in class com.chemaxon.virtuallib.sc.cli.ConvertGroupParameters
in - Variable in class com.chemaxon.virtuallib.sc.cli.ParseSdfParameters
indentMultiline(String, String) - Static method in class com.chemaxon.overlap.cli.util.Strings: Indent multiline String.
indentTable(String) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder: Indent whole table.
index - Variable in class com.chemaxon.overlap.wui.dto.MoleculeInfo: Molecule index.
IndexedAttachmentGroup - Interface in com.chemaxon.virtuallib.sc.model.sdf: Group of attachments having associated indices.
IndexedAttachmentGroupImpl - Class in com.chemaxon.virtuallib.sc.model.sdf: Implementation.
IndexedAttachmentGroupImpl(Collection<Attachment>) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroupImpl: Construct.
IndexedKnnResultsImpl - Class in com.chemaxon.overlap.result.impl: Arrays of primitives backed implementation of KnnResults for variabl neighbor count.
IndexedKnnResultsImpl(List<int[]>, List<double[]>) - Constructor for class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl: Construct.
indexOf(Row) - Method in interface com.chemaxon.calculations.util.cellfield.CellField: Look up row index.
indexOf(Row) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
IndexProjector - Interface in com.chemaxon.overlap.io: Index projection between a master index and a client index.
IndexProjectorBuilder() - Constructor for class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorBuilder: Construct new builder.
IndexProjectorBuilder(int) - Constructor for class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorBuilder: Construct new builder.
IndexProjectorMcb() - Constructor for class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorMcb: Instantiate without forwarding.
IndexProjectorMcb(MoleculeCallback) - Constructor for class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorMcb: Instantiate with a forwarding callback.
IndexProjectorMcb(int, MoleculeCallback) - Constructor for class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorMcb: Instantiate with a forwarding callback.
IndexProjectors - Class in com.chemaxon.overlap.io: Utilities for index projection.
IndexProjectors.IndexProjectorBuilder - Class in com.chemaxon.overlap.io: Plain index projector builder.
IndexProjectors.IndexProjectorMcb - Class in com.chemaxon.overlap.io: Projector builder over molecule callbacks.
indextoid - Variable in class com.chemaxon.overlap.wui.dto.MoleculeIds: Mapping of index to IDs.
IndexToNameStoringCallback(MoleculeCallback) - Constructor for class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback: Construct.
IndexToNameStoringCallback() - Constructor for class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback: Construct.
IndirectSerializable<T> - Interface in com.chemaxon.overlap.persistence.serialization: Can be serialized in a Deserializer API conform way.
info(Object) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
info(Object, Throwable) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
info - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Human readable String.
init - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryUsageDesc
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.Connect
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.GetSdfProperty
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.Mark
init() - Method in interface com.chemaxon.overlap.cli.util.pipeline.PipelineStep: Initialize the step.
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.ToLines
init() - Method in class com.chemaxon.overlap.cli.util.pipeline.TransformMolecule
init - Variable in class com.chemaxon.overlap.wui.dto.MemoryUsageDescDto
initial(DescriptorGenerator<D>) - Static method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Empty representation with specified DescriptorGenerator.
initial(DescriptorGenerator<D>, DescriptorComparator<D>) - Static method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Empty representation with specified DescriptorGenerator and comparator.
initializeBuilderIfExists(T) - Static method in class com.chemaxon.apidiscovery.Discovery: Create initial Builder if possible.
initializeContext(String, String) - Static method in class com.chemaxon.overlap.ContextJsTools: Initialize a context from optional name and JS hook.
inputCount - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Size of created descriptor storage.
inputformat - Variable in class com.chemaxon.overlap.wui.dto.ConversionResult: Recognized source format.
inputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create InputStream from not nullable location.
inputStreamFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create InputStream from not nullable location.
inputStreamFromLocationWithIae(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.Imports: Delegate CmdlineUtils.inputStreamFromLocation(java.lang.String, boolean) with no checked exceptions.
inputStreamFromLocationWithIae(String) - Static method in class com.chemaxon.overlap.cli.util.Imports: Delegate CmdlineUtils.inputStreamFromLocation(java.lang.String, boolean) with no checked exceptions.
inputStreamFromNullableLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create in input stream from nullable location.
inputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create in input stream from nullable location.
InputStreamStatCollector - Class in com.chemaxon.overlap.cli.util.pipeline: Collect read byte count of an underlying InputStream.
InputStreamStatCollector(InputStream) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
instance() - Static method in class com.chemaxon.overlap.presenter.AsyncCallPresenter
instance() - Static method in class com.chemaxon.overlap.presenter.TaskPresenter
instance() - Static method in class com.chemaxon.overlap.service.async.AsyncCallService
instance() - Static method in class com.chemaxon.overlap.service.CalculateDissimilarityDistributionService
instance() - Static method in class com.chemaxon.overlap.service.FindMostSimilarsService
instance() - Static method in class com.chemaxon.overlap.service.task.TaskService
instance() - Static method in class com.chemaxon.overlap.wui.StartupHandler
InstanceWrapper<T> - Class in com.chemaxon.apidiscovery: Wrapper for Instances.
InstantiateChoice<T> - Interface in com.chemaxon.apidiscovery.linenote: Instantiate choice using parameter value accessors.
intProp(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor
intsToString(int[], String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Convert array of integers to a String.
intTerm(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor
invocation() - Method in interface com.chemaxon.calculations.common.AutoThrottle: Sign an invocation to query next throttled event.
invocationCount - Variable in class com.chemaxon.calculations.common.TimerStatistics: Invocation count.
invoke(ConsolePO) - Method in interface com.chemaxon.calculations.common.ConsolePO.Callback: Callback method.
invoke(long) - Method in class com.chemaxon.calculations.common.Timer: Register one or multiple invocations.
invoke() - Method in class com.chemaxon.calculations.common.Timer: Register one invoceation.
invoke(Object, Method, Object[]) - Method in class com.chemaxon.descriptors.common.reflect.FixedValueInvocationHandler
invoke(Object, Method, Object[]) - Method in class com.chemaxon.descriptors.common.reflect.ForwardingInvocationHandler
invoke(Object, Method, Object[]) - Method in class com.chemaxon.descriptors.common.reflect.GuardedSerializableReturnValue
invoke(Object, Method, Object[]) - Method in class com.chemaxon.descriptors.common.reflect.GuardedSingleArgument
invoke(Object, Method, Object[]) - Method in class com.chemaxon.descriptors.common.reflect.ReturnValueTransformingInvocationHandler
invoke(Object, Method, Object[]) - Method in class com.chemaxon.descriptors.common.reflect.SingleArgumentTransformingInvocationHandler
invoke(Object, Method, Object[]) - Method in class com.chemaxon.descriptors.common.reflect.SingleMethodForwardingInvocationHandler
invoke(PT, CliInvocationEnv) - Method in interface com.chemaxon.overlap.cli.invocation.CliEntry: Entry point of a CLI.
invoke(PT, CliInvocationEnv2<ST>) - Method in interface com.chemaxon.overlap.cli.invocation.CliEntry2: Entry point of a CLI.
invokeLayout(SubPane) - Static method in interface com.chemaxon.overlap.cli.util.images.SubPane: Invoke a layout.
invokeSnapshot() - Method in class com.chemaxon.overlap.cli.prof.Prof: Take a snapshot.
IO() - Constructor for class com.chemaxon.overlap.cli.PipelineRunner.IO
isAttachmentAtom(int) - Method in interface com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroup: Check if given atom index denotes an attachment atom.
isAttachmentAtom(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
isCancelled() - Method in interface com.chemaxon.calculations.common.CancelObserver: Returns whether cancellation of current operation has been requested.
isCancelled() - Method in class com.chemaxon.calculations.common.CancelObserverImpl
isCancelled() - Method in class com.chemaxon.calculations.common.ConsolePO
isCancelled() - Method in class com.chemaxon.calculations.common.ListenableObserver
isCancelled() - Method in class com.chemaxon.calculations.common.NoOverflowAutoDoneProgressObserver
isCancelled() - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
isCancelled() - Method in class com.chemaxon.calculations.common.SplitObserver
isCancelled() - Method in class com.chemaxon.calculations.common.StatPO
isCancelled() - Method in class com.chemaxon.overlap.service.task.ExecutableTask
isClusterRepresentantSet(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Check if cluster representant is present.
isDebugEnabled() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
isDisabled(ServerFeature) - Method in class com.chemaxon.overlap.wui.context.features.FeatureConfig
isDissimilarityZeroIFFEquals() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata: Zero dissimilarity and identity.
isDissimilarityZeroIFFEquals() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
isDone() - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
isDone() - Method in interface com.chemaxon.calculations.common.ProgressObservable
isEmpty() - Method in class com.chemaxon.calculations.util.Histo: Check if the histogram is empty.
isEmpty() - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder: Check if no level info set.
isEmpty() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Check if the tree is empty.
isEnabled(ServerFeature) - Method in class com.chemaxon.overlap.wui.context.features.FeatureConfig
isErrorEnabled() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
isFatalEnabled() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
isFileExists(String) - Method in interface com.chemaxon.calculations.util.CmdlineContext: Check if a file exists.
isFileExists(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Check if a file exists.
isFileExists(String) - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
isFrozen() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean: Check frozen status.
isHelp() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
isHelp() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
isHelp() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
isIdCollected() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResultHandler: Check if IDs were collected.
isIdCollected() - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler: Check if IDs were collected.
isInCurrentBounds(double) - Method in class com.chemaxon.calculations.util.Histo: Check if a bin is associated with the given value.
isInfoEnabled() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
isKeep(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder: Check if an atom is set to be kept.
isMetricSpace() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata: Metric space.
isMetricSpace() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
isMtmqsr() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
isMtsqmr() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
isNobrowse() - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
isNobrowse() - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
isNonNegative() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata: Non negativeness of the dissimilarity values.
isNonNegative() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
isParametrized(Object) - Static method in class com.chemaxon.apidiscovery.Discovery: Check if an object is parametrized.
isPresent(int) - Method in class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
isPresent(int) - Method in class com.chemaxon.overlap.io.CompactStringStorage
isPresent(int) - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
isPresent(int) - Method in interface com.chemaxon.overlap.io.MasterStorage: Check if given entity is present.
isRAtom(Molecule, int) - Static method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment: Check if a given atom is an R atom.
isReadable(Class<?>, Type, Annotation[], MediaType) - Method in class com.chemaxon.overlap.wui.context.MoleculeParsingMessageBodyReader
isRepresentantSet(int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder: Check if cluster representant is set.
isServiceAvailable(Class<S>) - Static method in class com.chemaxon.apidiscovery.util.ServiceUtil: Check if a specific service is defined and implementation can be loaded.
isSsl() - Method in interface com.chemaxon.screen.desktop.JettyStarter.ServerWrapper: Check if SSL connections are accepted.
isStmqsr() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
isStructurePresent(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Check if a given structure ID is present in the clustering.
isStsqsr() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
isSymmetric() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata: Symmetry.
isSymmetric() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
isTerminal() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder: Check if the current state is a terminal extension.
isTraceEnabled() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
isTriangeInequalityHolds() - Method in interface com.chemaxon.descriptors.metrics.MetricMetadata: Triangle inequality.
isTriangeInequalityHolds() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
isTypeNumeric(Class) - Static method in class com.chemaxon.overlap.cli.util.prop.PropertyExtractors: Check if a type is numeric.
isVerbose() - Method in class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
isWarnEnabled() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
isZAtom(Molecule, int) - Static method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment: Check if a given atom has an alias string.
isZero() - Method in class com.chemaxon.overlap.cli.util.images.Px2d
iterateDescriptorPages(int) - Method in class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl
iterateDescriptorPages() - Method in class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl
iterateDescriptorPages(int) - Method in interface com.chemaxon.overlap.storage.UnguardedPagedStorage: Iterate descriptor pages.
iterateDescriptorPages() - Method in interface com.chemaxon.overlap.storage.UnguardedPagedStorage: Iterate descriptor pages.
iterateDescriptors() - Method in class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl
iterateDescriptors() - Method in interface com.chemaxon.overlap.storage.UnguardedPagedStorage: Iterate descriptors.
iterateFragmentMatches(RgFrag) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension: Iterate possible fragment matches if this scaffold extension is compatible with an rg fragment.
iterateLines() - Static method in class com.chemaxon.overlap.cli.util.MultiInputCloseableIterator: Iterate lines of an InputStream.
iterateStructureRecords(String) - Static method in class com.chemaxon.overlap.cli.util.MultiInputCloseableIterator: Create StructureRecordIterator form an InputStream.
iterateUnguardedsInPages(int) - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds: Iterate unguarded descriptors in fixed size lists.
iterator() - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
iterator() - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl

J

JacksonJsonMappingExceptionMapper - Class in com.chemaxon.overlap.wui.resources.exceptions: Map JsonParseException instances to a REST response representing an ErrorReport.
JacksonJsonMappingExceptionMapper() - Constructor for class com.chemaxon.overlap.wui.resources.exceptions.JacksonJsonMappingExceptionMapper
JacksonJsonParseExceptionMapper - Class in com.chemaxon.overlap.wui.resources.exceptions: Map JsonParseException instances to a REST response representing an ErrorReport.
JacksonJsonParseExceptionMapper() - Constructor for class com.chemaxon.overlap.wui.resources.exceptions.JacksonJsonParseExceptionMapper
JacksonUnrecognizedPropertyExceptionMapper - Class in com.chemaxon.overlap.wui.resources.exceptions: Map UnrecognizedProperty instances to a REST response representing an ErrorReport.
JacksonUnrecognizedPropertyExceptionMapper() - Constructor for class com.chemaxon.overlap.wui.resources.exceptions.JacksonUnrecognizedPropertyExceptionMapper
JettyStarter - Class in com.chemaxon.screen.desktop: Utilities for launching embedded Jetty.
JettyStarter.ServerWrapper - Interface in com.chemaxon.screen.desktop: Encapsulates embedded server.
JettyStarter.SslKeystoreSpec - Interface in com.chemaxon.screen.desktop: SSL keystore specification.
join(CharLayout.HA, String, List<String>...) - Static method in class com.chemaxon.calculations.util.CharLayout: Join an arbitrary set of multiliners.
join(List<String>, CharLayout.HA, String, List<String>, CharLayout.HA) - Static method in class com.chemaxon.calculations.util.CharLayout: Join two set of multiliners.
join() - Method in interface com.chemaxon.screen.desktop.JettyStarter.ServerWrapper: Join server.
joinTo(ArrayList<StringBuilder>, List<String>, CharLayout.HA, String) - Static method in class com.chemaxon.calculations.util.CharLayout: Join a new new column to previous column(s) represented as mutable rows.
joinTo(ArrayList<StringBuilder>, String[], CharLayout.HA, String) - Static method in class com.chemaxon.calculations.util.CharLayout: Join a new new column to previous column(s) represented as mutable rows.
joinTo(ArrayList<StringBuilder>, String) - Static method in class com.chemaxon.calculations.util.CharLayout: Join the same line to each row.
js - Variable in class com.chemaxon.overlap.cli.JsEvalParameters
JsEval - Class in com.chemaxon.overlap.cli: Read various serialized storages and dump their contents to the console.
JsEvalParameters - Class in com.chemaxon.overlap.cli: Command line arguments for ImportStorage.
JsEvalParameters() - Constructor for class com.chemaxon.overlap.cli.JsEvalParameters
jsfile - Variable in class com.chemaxon.overlap.cli.JsEvalParameters
JsLineFilter - Class in com.chemaxon.overlap.cli.util: Filter lines using JS execution hook.
JsLineFilter(Iterator<String>, String) - Constructor for class com.chemaxon.overlap.cli.util.JsLineFilter: Construct.

K

k - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Deprecated.
Use KnnInfo.maxneighborcount
keepAtom(int) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder: Designate a fragment atom to keep.
keepAtoms(Iterable<Integer>) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder: Designate multiple fragment atoms to keep.
keepResourceNameFriendlyCharacters(String) - Static method in class com.chemaxon.overlap.wui.context.Contexts: Keep a subset of URL friendly characters.
killAllAndFreeze() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean: Kill first page and freeze worker.
killFirstPage() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean: Kill first page unconditionally.
killFirstPageIfBlocking() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean: Kill first page only if all other pages are ready.
Knn - Class in com.chemaxon.overlap.wui.context: Knn analysis results.
KnnData - Class in com.chemaxon.overlap.wui.dto: Nearest neighbor data.
KnnData() - Constructor for class com.chemaxon.overlap.wui.dto.KnnData
KnnInfo - Class in com.chemaxon.overlap.wui.dto: Info about a knn analysis result.
KnnInfo() - Constructor for class com.chemaxon.overlap.wui.dto.KnnInfo
KnnRes - Class in com.chemaxon.overlap.wui.res: KNN result used as a resource.
KnnRes(String, long, DescRes, DescRes, KnnResults) - Constructor for class com.chemaxon.overlap.wui.res.KnnRes: Construct.
KnnResource - Class in com.chemaxon.overlap.wui.resources: KNN analysis results JAX-RS resource.
KnnResource() - Constructor for class com.chemaxon.overlap.wui.resources.KnnResource
KnnResults - Interface in com.chemaxon.overlap.result: Results of at most K nearest neighbors calculations.
KnnResultsBuilder - Class in com.chemaxon.overlap.result.impl: Build KnnResults instances.
KnnResultsBuilder() - Constructor for class com.chemaxon.overlap.result.impl.KnnResultsBuilder: Construct.
knns - Variable in class com.chemaxon.overlap.wui.dto.KnnsInfo: List of available knn infos.
KnnServlet - Class in com.chemaxon.overlap.servlets
KnnServlet() - Constructor for class com.chemaxon.overlap.servlets.KnnServlet
KnnsInfo - Class in com.chemaxon.overlap.wui.dto: Information of available knn/nn analysis results.
KnnsInfo() - Constructor for class com.chemaxon.overlap.wui.dto.KnnsInfo
KnnTableLabelEntry - Class in com.chemaxon.overlap.wui.dto: Entry for a single query structure.
KnnTableLabelEntry() - Constructor for class com.chemaxon.overlap.wui.dto.KnnTableLabelEntry
KnnTableLabels - Class in com.chemaxon.overlap.wui.dto: Labels for a subset of the neighbors for a subset of queries.
KnnTableLabels() - Constructor for class com.chemaxon.overlap.wui.dto.KnnTableLabels

L

l - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionRequest
l - Variable in class com.chemaxon.overlap.wui.dto.Histogram: Lower limit.
labelColor(String) - Method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer: Label color.
labelFontHeight(int) - Method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer: Label font height.
LanceWilliamsAlgorithm - Class in com.chemaxon.clustering.wards: Agglomerative hierarchical clustering implementation for Lance-Williams algorithm family.
LanceWilliamsMerge - Interface in com.chemaxon.clustering.wards: Instances represent a cluster distance update for agglomerative clusterings.
LanceWilliamsMerges - Class in com.chemaxon.clustering.wards: Singleton instances of various cluster merge operations.
LanceWilliamsMerges() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges
LanceWilliamsMerges.AverageLinkage - Class in com.chemaxon.clustering.wards: Average linkage clustering, also known as UPGMA.
LanceWilliamsMerges.CompleteLinkage - Class in com.chemaxon.clustering.wards: Complete linkage clustering, also known as farthest neighbor clustering.
LanceWilliamsMerges.SingleLinkage - Class in com.chemaxon.clustering.wards: Single linkage clustering also known as nearest neighbor clustering.
LanceWilliamsMerges.Wards - Class in com.chemaxon.clustering.wards: Ward's minimum variance clustering.
landing - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
landingsubres - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
launch() - Method in class com.chemaxon.clustering.framework.BemisMurckoClustering: Launch clustering with no progress monitoring.
launch(SubProgressObserver) - Method in class com.chemaxon.clustering.framework.BemisMurckoClustering: Launch clustering with progress monitoring.
launch(CliEntry<PT>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationSpec: Launch main method.
launch(CliEntry2<PT, ST>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationSpec2: Launch main method.
Launch - Interface in com.chemaxon.overlap.concurrent: Launch processing.
launch() - Method in interface com.chemaxon.overlap.concurrent.Launch: Launch with unknown total work.
launch(long) - Method in interface com.chemaxon.overlap.concurrent.Launch: Launch with known total work.
launch() - Method in class com.chemaxon.overlap.wui.Gui: Load resources, then launch server.
launchAsync() - Method in class com.chemaxon.overlap.wui.Gui: Launch server asynchronously, then load resources.
launchProf(PrintStream, int) - Static method in class com.chemaxon.overlap.cli.prof.Prof: Launch profiling.
layout(Area) - Method in class com.chemaxon.overlap.cli.util.images.BorderedPane
layout(SubPane) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRendering
layout(Area) - Method in class com.chemaxon.overlap.cli.util.images.GridPane
layout(Area) - Method in class com.chemaxon.overlap.cli.util.images.HFlowPane
layout(SubPane) - Method in interface com.chemaxon.overlap.cli.util.images.Rendering: Invoke layout and render.
layout(Area) - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
layout(Area) - Method in interface com.chemaxon.overlap.cli.util.images.SubPane: Layout into an allocated area.
layout(Area) - Method in class com.chemaxon.overlap.cli.util.images.VFlowPane
leafLevel(L) - Method in interface com.chemaxon.clustering.common.LevelAssigner: Level associated to a leaf object.
leafLevelFunction() - Method in interface com.chemaxon.clustering.common.LevelAssigner: Leaf level association.
leaves() - Method in interface com.chemaxon.clustering.common.HierarchicCluster: Access immediate leaves associated to this node.
length() - Method in class com.chemaxon.calculations.util.V3D
length(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder: Set fingerprint length, the bit count of the folded binary fingerprint representation.
length(int) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder: Set fingerprint length, the bit count of the folded binary fingerprint representation.
length(int) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters.Builder: Set fingerprint length, the bit count of the folded binary fingerprint representation.
length(int) - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder: Set fingerprint length.
length(int) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder: Set fingerprint length.
LevelAssigner<L,T extends HierarchicCluster<L>> - Interface in com.chemaxon.clustering.common: Assigns levels for clusters and leaves.
LIB_ID_SDFIELD - Static variable in class com.chemaxon.virtuallib.sc.model.sdf.Scaffold: SD field storing library ID.
linearEuclideanDissimilarityInput(double[]) - Static method in class com.chemaxon.clustering.util.Util: Construct a DissimilarityInput over a set of 1D values.
LinearHistogram - Interface in com.chemaxon.overlap.result: Histogram representation.
LinearHistogramBuilder - Class in com.chemaxon.overlap.result.impl: Simple builder for LinearHistograms.
LinearHistogramBuilder(double, double, int) - Constructor for class com.chemaxon.overlap.result.impl.LinearHistogramBuilder: Construct a new instance.
LinearScaler - Interface in com.chemaxon.descriptors.common.realvector: Scaler.
LinearScalerImpl - Class in com.chemaxon.descriptors.common.realvector: Simple scaler implementation.
LinearScalerImpl(double, double) - Constructor for class com.chemaxon.descriptors.common.realvector.LinearScalerImpl: Construct a scaler.
LinearScalerUtil - Class in com.chemaxon.descriptors.common.realvector: Core scaler functions.
lineIteratorFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create a LineIterator from a not nullable location.
lineIteratorFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create a LineIterator from a not nullable location.
Linenote<T> - Interface in com.chemaxon.apidiscovery.linenote: Linear notation of a parameterization.
LinenoteBuilder<T> - Interface in com.chemaxon.apidiscovery.linenote: Builder for line note representation factory.
LinenoteChoiceDto - Class in com.chemaxon.overlap.wui.dto: Represents descriptive data of a ChoiceDescriptor.
LinenoteChoiceDto(ChoiceDescriptor) - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteChoiceDto: Construct to represent descriptive data of a ChoiceDescriptor.
LinenoteChoiceDto() - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteChoiceDto: No-arg constructor for deserialization.
LinenoteChoiceParameterDto - Class in com.chemaxon.overlap.wui.dto: Represents descriptive data of a ChoiceParameterDescriptor.
LinenoteChoiceParameterDto(ChoiceParameterDescriptor<?>) - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterDto: Construct to represent descriptive data of a ChoiceParameterDescriptor.
LinenoteChoiceParameterDto() - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterDto: No-arg constructor for deserialization.
LinenoteChoiceParameterValueDto - Class in com.chemaxon.overlap.wui.dto: Value-description pair of an enumerated parameter value.
LinenoteChoiceParameterValueDto(String, String) - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterValueDto: Construct.
LinenoteChoiceParameterValueDto() - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterValueDto: No-arg constructor for deserialization.
LinenoteDto - Class in com.chemaxon.overlap.wui.dto: Contains descriptive data from a Linenote instance.
LinenoteDto(Linenote<?>) - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteDto: Construct from a Linenote instance.
LinenoteDto() - Constructor for class com.chemaxon.overlap.wui.dto.LinenoteDto: No-arg constructor for deserialization.
Linenotes - Class in com.chemaxon.apidiscovery.linenote: Utilities for line note representation.
listClasses() - Method in class com.chemaxon.overlap.wui.context.Contexts: List all available resource classes in precedence ordering.
listCreators(Object, Class<T>) - Static method in class com.chemaxon.apidiscovery.Discovery: CreatorWrapper acts as a type-dependent service loader.
listDescriptions(ResourceInfo) - Method in class com.chemaxon.overlap.wui.context.Contexts
ListenableObserver - Class in com.chemaxon.calculations.common: A ProgressObserver decorator that allows to listen for observer events.
ListenableObserver(ProgressObserver) - Constructor for class com.chemaxon.calculations.common.ListenableObserver
listInstances(Class<T>) - Static method in class com.chemaxon.apidiscovery.Discovery: Collect instances of a specific type.
listNames(ResourceInfo) - Method in class com.chemaxon.overlap.wui.context.Contexts
listParameters(Object) - Static method in class com.chemaxon.apidiscovery.Discovery: Retrieve parameters for a mutable parameter object.
listResources(Class<T>) - Method in class com.chemaxon.overlap.wui.context.Contexts: List resources for a resource class.
listResources(ResourceInfo) - Method in class com.chemaxon.overlap.wui.context.Contexts: List resources for a resource info (by its ResourceInfo).
listUrls(ResourceInfo) - Method in class com.chemaxon.overlap.wui.context.Contexts
LoadingStatusDto - Class in com.chemaxon.overlap.wui.dto: Status information about loading tasks.
LoadingStatusDto() - Constructor for class com.chemaxon.overlap.wui.dto.LoadingStatusDto
loadingSuperTask - Variable in class com.chemaxon.overlap.wui.dto.StatisticsDto: Task that represents the whole loading process.
loadService(Class<S>, boolean) - Static method in class com.chemaxon.apidiscovery.util.ServiceUtil: Load and instantiate an implementation for a given service interface.
location(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
location(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
location(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
LOG2_BYTES_IN_INT - Static variable in class com.chemaxon.descriptors.common.BinaryVectors: Log2 of BinaryVectors.BYTES_IN_INT.
LOG2_BYTES_IN_LONG - Static variable in class com.chemaxon.descriptors.common.BinaryVectors: Log2 of BinaryVectors.BYTES_IN_LONG.
logFile(String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Specify logfile.
longProp(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor
longsToBinaryString(long[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Convert array of longs to a binary String.
longsToString(long[], String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Convert array of longs to a String.
longTerm(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor
LookupParamConverterProvider - Class in com.chemaxon.overlap.wui.context: Look up resource name.
LookupParamConverterProvider() - Constructor for class com.chemaxon.overlap.wui.context.LookupParamConverterProvider
lowcount - Variable in class com.chemaxon.overlap.wui.dto.Histogram: Underflow items count.

M

m() - Method in interface com.chemaxon.overlap.cli.util.images.Range: Middle point.
Maccs - Interface in com.chemaxon.descriptors.fingerprints.maccs: Interface to define a compatible descriptor framework for the MACCS fingerprint
Maccs166BinaryString - Class in com.chemaxon.descriptors.alternates: MACCS-166 with binary string representation.
Maccs166BinaryString(String) - Constructor for class com.chemaxon.descriptors.alternates.Maccs166BinaryString: Construct.
MaccsBenchmark - Class in com.chemaxon.descriptors.fingerprints.maccs.cli: This class runs several benchmark computations using the implementation of MDL's MACCS fingerprint.
MaccsBenchmark() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.cli.MaccsBenchmark
MaccsComparator - Interface in com.chemaxon.descriptors.fingerprints.maccs: Interface to define a compatible comparator for the MACCS fingerprint
MaccsGenerator - Interface in com.chemaxon.descriptors.fingerprints.maccs: Interface to define the MACCS fingerprint generator
MaccsParameters - Class in com.chemaxon.descriptors.fingerprints.maccs: Class for MACSS fingerprint parameters.
MaccsParameters(MaccsParameters.Builder) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters: Constructor.
MaccsParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters: Constructor.
MaccsParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.maccs: Build parameters for MACCS fingerprint descriptor generation.
MaccsParameters.ConstructMaccsGenerator - Interface in com.chemaxon.descriptors.fingerprints.maccs: Interface representing Maccs generator constructor.
MadfastImport - Class in com.chemaxon.overlap.cli: Unified structure import/preprocess tool.
MadfastImportParameters - Class in com.chemaxon.overlap.cli: CLI parameters for MadfastImport.
MadfastImportParameters() - Constructor for class com.chemaxon.overlap.cli.MadfastImportParameters
MadfastImportParameters.NoSplitter - Class in com.chemaxon.overlap.cli
MadfastImportStat - Class in com.chemaxon.overlap.cli: Statistics for MadfastImport execution.
MadfastImportStat() - Constructor for class com.chemaxon.overlap.cli.MadfastImportStat
main(String[]) - Static method in class com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator: Main method.
main(String[]) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.BitArrayToBitSet: Main method.
main(String[]) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.DescriptorPreChecker: The names of the sets are given as arguments
main(String[]) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.FpDiff: Main method.
main(String[]) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.GenerMaccs
main(String[]) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.GSearch
main(String[]) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.MaccsBenchmark
main(String[]) - Static method in class com.chemaxon.descriptors.fingerprints.maccs.cli.SmaPieces: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.BuildStorage: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.CalculateOverlap: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.CalculateSelfOverlap: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.CreateAllAbsentMms: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.CreateMms: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.DumpStorage: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.ImportStorage: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.JsEval: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.MadfastImport: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.PagedDescriptorImport: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.PrepareMolecules: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.cli.SearchStorage: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.wui.Gui: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.wui.RealTimeSearchGui: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.wui.SelfOverlapGui: Main method.
main(String[]) - Static method in class com.chemaxon.overlap.wui.SlowlyDeserializingMms: Main method.
main(String[]) - Static method in class com.chemaxon.virtuallib.sc.cli.Converter: Main method.
main(String[]) - Static method in class com.chemaxon.virtuallib.sc.cli.ConvertGroup
main(String[]) - Static method in class com.chemaxon.virtuallib.sc.cli.ParseSdf
makeColumn(String, int, CharLayout.HA, IntFunction<String>) - Static method in class com.chemaxon.calculations.util.CharLayout: Create a column.
managed(MBeanServer, ObjectName) - Method in class com.chemaxon.overlap.concurrent.impl.BppParameters
managed(String) - Method in class com.chemaxon.overlap.concurrent.impl.BppParameters
managedProcessor(String, int, int, SubProgressObserver, ExecutorService) - Static method in class com.chemaxon.overlap.concurrent.Processors: Create a managed processor.
manhattanBytes(byte[]) - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl: Manhattan.
manhattanNorm(float[]) - Static method in class com.chemaxon.descriptors.common.realvector.Util: Manhattan norm of floats.
manhattanShorts(short[]) - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor: Manhattan.
mark(int) - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
Mark - Class in com.chemaxon.overlap.cli.util.pipeline: Mark last node or one of its output.
Mark() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.Mark
markName(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.Connect
markSupported() - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
MasterMoleculeStorage - Interface in com.chemaxon.overlap.io: Master molecule storage is a space efficient storage for Molecules.
masterMoleculeStorageFromFile(InputStream, String, int, StandardizerWrapper, ExecutorService, SubProgressObserver, List<? extends MoleculeCallback>) - Static method in class com.chemaxon.overlap.io.MasterStorages: Create storage from a strcuture file.
MasterMoleculeStorageImpl - Class in com.chemaxon.overlap.io: Master molecule storage is a space efficient storage for Molecules.
MasterMoleculeStorageImpl(CompactStringStorage) - Constructor for class com.chemaxon.overlap.io.MasterMoleculeStorageImpl: Construct over valid sources.
MasterMoleculeStorageImpl(CompactStringStorage, String) - Constructor for class com.chemaxon.overlap.io.MasterMoleculeStorageImpl: Construct over valid sources.
MasterMoleculeStorageSerialization - Class in com.chemaxon.overlap.persistence.storage: Helper class to serialize MasterMoleculeStorage instances.
MasterStorage<T> - Interface in com.chemaxon.overlap.io: Master structure storage represents the molecules from a repository.
MasterStorages - Class in com.chemaxon.overlap.io: Helper method for managing MasterStorages instances.
MasterStorages.MasterStorageBuilder<T> - Interface in com.chemaxon.overlap.io: Builder class for a master storage.
MasterStorages.MoleculeCallbackBuilder - Class in com.chemaxon.overlap.io: Molecule callback based builder.
MasterStringStorage - Interface in com.chemaxon.overlap.io: Convenience interface.
matches(MU.BondList, boolean) - Method in class com.chemaxon.calculations.util.MU.BondList
matches(Molecule) - Method in class com.chemaxon.descriptors.fingerprints.maccs.GsSearch: This method returns true if the query structure(s) match the target given in the
matchesToExtension(ScaffoldExtension) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension: Check if two scaffold extensions are denoting the same extension structure.
max - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryUsageDesc
max - Variable in class com.chemaxon.overlap.wui.dto.MemoryUsageDescDto
MAX_QUEUE_SIZE - Static variable in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap: Max queue size to avoid filling up the completion queue.
MAX_QUEUE_SIZE - Static variable in class com.chemaxon.overlap.io.MasterStorages: Max queue size for import.
MAX_RESULT_QUEUE_SIZE - Static variable in class com.chemaxon.overlap.storage.PagedDescriptorStorage: Max non reported queue elements.
MAX_TRAVERSAL_DEPTH - Static variable in enum com.chemaxon.overlap.wui.dto.SizeInfoMethod: Max traversal depth used when skipping visited reference check.
maxAttachmentIndex() - Method in interface com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroup: Max attachment index value.
maxAttachmentIndex() - Method in class com.chemaxon.virtuallib.sc.model.sdf.IndexedAttachmentGroupImpl
maxBinValue - Variable in class com.chemaxon.overlap.wui.dto.Histogram: Maximal bin value This is a convenience field containing the maximum value from Histogram.bins.
maxCount - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest: Maximal number of most similar targets to find.
maxCount - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
maxDepth(HierarchicClustering<?, ? extends HierarchicCluster<?>>) - Static method in class com.chemaxon.clustering.util.Util: Find max depth.
maxdissim - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Upper bound of dissimilarity values.
maxDissimilarity - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest: Maximal dissimilarity to return; inclusive.
maxDissimilarity - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
maxDouble() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Maximal valid value (inclusive).
maxHeight() - Method in interface com.chemaxon.clustering.common.HierarchicClustering: Maximal height of the clustering.
maximumBytes(byte[]) - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl: Maximum.
maximumNorm(float[]) - Static method in class com.chemaxon.descriptors.common.realvector.Util: Maximum norm of floats.
maximumShorts(short[]) - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor: Maximum.
maxLevel() - Method in interface com.chemaxon.clustering.common.LevelAssigner: Maximal level associated.
maxLong() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Maximal valid value (inclusive).
maxMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat: Max memory.
maxneighborcount - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Maximal neighbor count stored.
maxneighborindex - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Upper bound of neighbor indices.
MDReaderFactory - Interface in com.chemaxon.descriptors.db: Factory class for MDTableReader.
MDTableReader<D extends Descriptor> - Class in com.chemaxon.descriptors.db: Deserialize fingerprint from MDTable (JChem).
MDTableReader() - Constructor for class com.chemaxon.descriptors.db.MDTableReader
memberCount() - Method in interface com.chemaxon.clustering.common.Cluster: Represented member count of this cluster.
members() - Method in interface com.chemaxon.clustering.common.Cluster: Represented members of this cluster.
MemoizedSparseCollection<T> - Interface in com.chemaxon.calculations.io: Represents an ordered sparse collection of memoized items.
MemoizingIterator<E,R> - Class in com.chemaxon.calculations.io: Decorate a CloseableIterator with the availability of retrieval of a transformation of the iterated elements.
MemoryPoolInfoDto - Class in com.chemaxon.overlap.wui.dto: Represents a memory pool.
MemoryPoolInfoDto() - Constructor for class com.chemaxon.overlap.wui.dto.MemoryPoolInfoDto: No-arg constructor required by JAXB.
memoryPoolNames - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.GarbageCollector
memoryPoolNames - Variable in class com.chemaxon.overlap.wui.dto.GarbageCollectorInfoDto
memoryPools - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Representation of the states of the memory pools.
memoryPools - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Representation of the states of the memory pools.
MemoryUsageDesc(MemoryUsage) - Constructor for class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryUsageDesc: Construct and fill fields.
MemoryUsageDescDto - Class in com.chemaxon.overlap.wui.dto: Represents memory usage.
MemoryUsageDescDto() - Constructor for class com.chemaxon.overlap.wui.dto.MemoryUsageDescDto: No-arg constructor required by JAXB.
MemoryUsageDescDto(MemoryUsage) - Constructor for class com.chemaxon.overlap.wui.dto.MemoryUsageDescDto: Construct and fill fields.
Memstat - Class in com.chemaxon.overlap.cli.prof: Memory statistics.
memstatFinal - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Final memory statistics.
memstatFinal - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Final memory statistics.
memstatFinal - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
memstatFinal - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Final memory statistics.
memstatFinal - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
memstatFinal - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Final memory statistics.
memstatInitial - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Initial memory statistics.
memstatInitial - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Initial memory statistics.
memstatInitial - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
memstatInitial - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Initial memory statistics.
memstatInitial - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
memstatInitial - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Initial memory statistics.
message - Variable in class com.chemaxon.overlap.wui.dto.ErrorReport: Associated message.
MetaResource - Class in com.chemaxon.overlap.wui.resources: Description of available resources.
MetaResource() - Constructor for class com.chemaxon.overlap.wui.resources.MetaResource
MetaServlet - Class in com.chemaxon.overlap.servlets: Deprecated.
Use MetaResource instead.
MetaServlet() - Constructor for class com.chemaxon.overlap.servlets.MetaServlet: Deprecated.
method(TransformMolecule.Method) - Method in class com.chemaxon.overlap.cli.util.pipeline.TransformMolecule
method - Variable in class com.chemaxon.overlap.wui.dto.PmapperRequest: Method to use.
metric - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionRequest
metric - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest: Metric to use.
metric - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
MetricFactory<C> - Interface in com.chemaxon.descriptors.metrics: Represents available metrics.
MetricFactory.ToLinenote<C> - Class in com.chemaxon.descriptors.metrics: Utility for creating a default linenote.
metricFactoryClass() - Method in interface com.chemaxon.descriptors.common.comparison.ComparisonContextFactory: Represented metric factory class.
metricFactoryClass() - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
metricFactoryClass() - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
metricFactoryClass() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
metricFactoryClass() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
metricFactoryClass() - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
MetricMetadata - Interface in com.chemaxon.descriptors.metrics: Metric Metadata contains info about a specific metric.
metrics(DRShapeMetrics) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter.Builder
metrics(ShapeMetrics) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter.Builder
midpointOf(Px2d, Px2d) - Static method in class com.chemaxon.overlap.cli.util.images.Px2d: Middle point between two points.
mindissim - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Lower bound of dissimilarity values.
minDouble() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Minimal valid value (inclusive).
minLong() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Minimal valid value (inclusive).
minneighborcount - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Minimal neighbor count stored.
minneighborindex - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Lower bound of neighbor indices.
minSize() - Method in interface com.chemaxon.overlap.cli.util.images.RangeSpec: Minimal size.
minus(V3D) - Method in class com.chemaxon.calculations.util.V3D
minus(Px2d) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
minus(int, int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
minusx(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
minusy(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
missingcount - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropRange: Number of missing values in the MoleculePropRange.values array.
missingvalue - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabels: Value used for missing items.
missingvalue - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropRange: Value returned for missing items.
mjsVersion() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Packaged MarvinJS version.
mjsVersion - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Packaged MarvinJS version.
mms(boolean) - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
mmsImportOpts(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
mol - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest: Molecule to convert.
MolConverter - Class in com.chemaxon.overlap.wui.resources: Expose CXN mol converter functionality for a single molecule.
MolConverter() - Constructor for class com.chemaxon.overlap.wui.resources.MolConverter
molecule - Variable in class com.chemaxon.overlap.wui.dto.PmapperRequest: Source of input molecule.
molecule - Variable in class com.chemaxon.overlap.wui.dto.PmapperResponse: The structure source used.
MoleculeAwareLog - Class in com.chemaxon.calculations.logging.moleculeawarelog: Molecule aware Log implementation.
MoleculeAwareLog(String) - Constructor for class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog: Construct.
MoleculeAwareLogFactory - Class in com.chemaxon.calculations.logging.moleculeawarelog: Molecule aware Log.
MoleculeAwareLogFactory() - Constructor for class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
MoleculeCallback - Interface in com.chemaxon.overlap.io: Callback executed on each molecules.
MoleculeCallbackBuilder() - Constructor for class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder: Construct new empty builder.
MoleculeCallbacks - Class in com.chemaxon.overlap.io: MoleculeCallback related utilities.
MoleculeCallbacks.CountingMoleculeCallback - Interface in com.chemaxon.overlap.io: Error counting callback.
MoleculeCallbacks.IndexToNameStoringCallback - Class in com.chemaxon.overlap.io: A callback storing indexes.
MoleculeContainer - Interface in com.chemaxon.overlap.wui.res: Simple molecule container.
MoleculeContainerImpl - Class in com.chemaxon.overlap.wui.res: Implementation for the molecule container.
MoleculeFrameworks - Class in com.chemaxon.clustering.framework: Molecule transformations used in Bemis-Murcko clustering.
MoleculeFrameworks() - Constructor for class com.chemaxon.clustering.framework.MoleculeFrameworks: Construct.
MoleculeIds - Class in com.chemaxon.overlap.wui.dto: IDs associated to multiple molecules.
MoleculeIds() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculeIds
MoleculeInfo - Class in com.chemaxon.overlap.wui.dto: Information about a molecule.
MoleculeInfo() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculeInfo
MoleculeIo - Class in com.chemaxon.calculations.io: Utility class with Molecule IO related functions.
MoleculeParsingMessageBodyReader - Class in com.chemaxon.overlap.wui.context: Parse structures from POST body.
MoleculeParsingMessageBodyReader() - Constructor for class com.chemaxon.overlap.wui.context.MoleculeParsingMessageBodyReader
MoleculeProp - Class in com.chemaxon.overlap.wui.dto: A single additional property value.
MoleculeProp() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculeProp
MoleculePropInfo - Class in com.chemaxon.overlap.wui.dto: Information about an additional property of a molecule set.
MoleculePropInfo() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculePropInfo
MoleculePropRange - Class in com.chemaxon.overlap.wui.dto: Value of a single property over a range of molecule indices.
MoleculePropRange() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculePropRange
MoleculeProps - Class in com.chemaxon.overlap.wui.dto: Properties associated to multiple molecules.
MoleculeProps() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculeProps
Molecules - Class in com.chemaxon.overlap.wui.context: Molecules.
MoleculeSetInfo - Class in com.chemaxon.overlap.wui.dto: Information about a single molecule set.
MoleculeSetInfo() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculeSetInfo
MoleculeSetsInfo - Class in com.chemaxon.overlap.wui.dto: Information about available molecule sets.
MoleculeSetsInfo() - Constructor for class com.chemaxon.overlap.wui.dto.MoleculeSetsInfo
moleculeseturl - Variable in class com.chemaxon.overlap.wui.dto.DescriptorInfo: Underlying molecule set url.
MoleculesResource - Class in com.chemaxon.overlap.wui.resources: Represents molecule sets.
MoleculesResource() - Constructor for class com.chemaxon.overlap.wui.resources.MoleculesResource
molExporter(String) - Static method in class com.chemaxon.calculations.io.Segmenters: Create exporter.
molExporterToSmilesFunction() - Static method in class com.chemaxon.calculations.io.MoleculeIo: Convert a Molecule to SMILES.
molImporterFromSourceFunction() - Static method in class com.chemaxon.calculations.io.MoleculeIo: Import a String source into a Molecule.
molImporterImport(String) - Static method in class com.chemaxon.calculations.io.MoleculeIo: Import Molecule from source String.
molImporterIterateMolecules(InputStream) - Static method in class com.chemaxon.calculations.io.MoleculeIo: A Closeable Iterator view of a MolImporter.
molImporterMemoizingIterator(CloseableIterator<Molecule>, Consumer<Exception>) - Static method in class com.chemaxon.calculations.io.MoleculeIo: Create a SmilesMemoizingMoleculeIterator over a CloseableIterator of Molecules.
MolInput - Interface in com.chemaxon.clustering.common: Dissimilarity input implementation which can retrieve underlying Molecules.
MolInputBuilder - Class in com.chemaxon.clustering.common: Convenience class to compose input from molecules to a clustering algorithm.
MolInputBuilder() - Constructor for class com.chemaxon.clustering.common.MolInputBuilder: Construct an empty builder.
MolInputBuilder(Collection<? extends Molecule>) - Constructor for class com.chemaxon.clustering.common.MolInputBuilder: Construct a builder with stored structures.
MolInputImpl<D extends Descriptor> - Class in com.chemaxon.clustering.common: Implementation using plain Descriptors API.
MolInputImpl(List<? extends Molecule>, DescriptorGenerator<D>, DescriptorComparator<D>) - Constructor for class com.chemaxon.clustering.common.MolInputImpl: Construct over Molecules.
molname - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest: Molecule name to set.
MolnamePropertyExtractor - Class in com.chemaxon.overlap.cli.util.prop.impl: Extractor for molecule name as String.
MolnamePropertyExtractor(boolean) - Constructor for class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractor
MolnamePropertyExtractorFactory - Class in com.chemaxon.overlap.cli.util.prop.impl: Factory for MolnamePropertyExtractor.
MolnamePropertyExtractorFactory() - Constructor for class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractorFactory
MolProp<T> - Class in com.chemaxon.overlap.cli.util.prop: DTO to store an additional property extracted/calculated from a Molecule.
MolProp(PropertyExtractor<T>, MasterStorage<T>) - Constructor for class com.chemaxon.overlap.cli.util.prop.MolProp: Construct.
molprops - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest: Molecule properties to set.
MolsContext - Class in com.chemaxon.overlap.servlets: Deprecated.
Use unified context
MolsContext() - Constructor for class com.chemaxon.overlap.servlets.MolsContext: Deprecated.
MolsRes - Class in com.chemaxon.overlap.wui.res: Implementation for mols.
MolsRes(String, long, MasterMoleculeStorage, MasterStorage<String>, Map<String, MolProp<?>>) - Constructor for class com.chemaxon.overlap.wui.res.MolsRes: Construct.
MolsServlet - Class in com.chemaxon.overlap.servlets: Deprecated.
MolsServlet() - Constructor for class com.chemaxon.overlap.servlets.MolsServlet: Deprecated.
molToHumanReadable(Molecule) - Static method in class com.chemaxon.overlap.io.Util: Convert molecule to human readable string.
MostSimilarSearchParams(String, Serializable, int, int, int, double, boolean) - Constructor for class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
MostSimilarsRequest - Class in com.chemaxon.overlap.wui.dto: Request DTO of a most similars search.
MostSimilarsRequest() - Constructor for class com.chemaxon.overlap.wui.dto.MostSimilarsRequest
MostSimilarsResult - Class in com.chemaxon.overlap.wui.dto: Result of a most similars search.
MostSimilarsResult() - Constructor for class com.chemaxon.overlap.wui.dto.MostSimilarsResult
MostSimilarsSearchResult() - Constructor for class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarsSearchResult
msb - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
MU - Class in com.chemaxon.calculations.util: Molecule related utilities.
MU.BondList - Class in com.chemaxon.calculations.util: Represents a bond list.
mul(char, int) - Static method in class com.chemaxon.calculations.util.CharLayout
mul(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d: Multiply coordinates.
MultiConversionRequest - Class in com.chemaxon.overlap.wui.dto: Molecule conversion requests for multiple molecules.
MultiConversionRequest() - Constructor for class com.chemaxon.overlap.wui.dto.MultiConversionRequest
MultiConversionResult - Class in com.chemaxon.overlap.wui.dto: Molecule conversion results for multi request.
MultiConversionResult() - Constructor for class com.chemaxon.overlap.wui.dto.MultiConversionResult
MultiInputCloseableIterator<T,CI extends Iterator<T> & Closeable> - Class in com.chemaxon.overlap.cli.util: Iterates entities from multiple InputStream sources.
MultiInputCloseableIterator(Iterable<Supplier<InputStream>>, Function<InputStream, CI>) - Constructor for class com.chemaxon.overlap.cli.util.MultiInputCloseableIterator: Construct.
mulx(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
muly(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d

N

name - Variable in class com.chemaxon.calculations.common.TimerStatistics: Associated name.
name - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
name - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
name - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.GarbageCollector
name - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryPool
name(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.Mark
name - Variable in class com.chemaxon.overlap.cli.util.prop.CliParam: Name of property to extract.
name - Variable in class com.chemaxon.overlap.service.task.Task
name - Variable in class com.chemaxon.overlap.wui.dto.DescriptorInfo: Name of the descriptor data.
name - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalRawFileInfo: Name of the raw file content.
name - Variable in class com.chemaxon.overlap.wui.dto.GarbageCollectorInfoDto
name - Variable in class com.chemaxon.overlap.wui.dto.GridInfo: Name of the descriptor data.
name - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Name of the knn data.
name - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterDto: Parameter name.
name - Variable in class com.chemaxon.overlap.wui.dto.MemoryPoolInfoDto
name - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropInfo: Name of the property.
name - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo: Name of the molecule set.
name - Variable in class com.chemaxon.overlap.wui.dto.PmapperFeature: Name of the feature.
name - Variable in class com.chemaxon.overlap.wui.dto.SizeInfoDetailDto: Name of the component.
name - Variable in class com.chemaxon.overlap.wui.dto.TaskDto: Task name.
name() - Method in class com.chemaxon.screen.Column
name() - Method in class com.chemaxon.screen.DescriptorStorage: Gets the name of storage.
nameOf(Described) - Method in class com.chemaxon.overlap.wui.context.Contexts
nameprefix - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalAddMoleculesRequest: Suggested resource name prefix or null / empty.
names - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
negate() - Method in class com.chemaxon.calculations.util.V3D
neighborCount - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
neighborCount - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Number of targets to return for each query.
New() - Constructor for class com.chemaxon.descriptors.common.Guarded.New
newCalculator(boolean) - Method in enum com.chemaxon.overlap.wui.dto.SizeInfoMethod: Create a new calculator method.
newCellField() - Static method in class com.chemaxon.calculations.util.cellfield.CellFields: Instantiate new empty cell field.
newChildCluster() - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec: Add a child cluster.
newCluster() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Allocates a new cluster and returns a spec to it.
newMoleculeStorage(String) - Static method in class com.chemaxon.screen.Utils: Deserialize Master molecule storage from a location.
newRootAlignedIdDBasedHierarchicClusterBuilder() - Static method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Convenience method.
newRootCluster() - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec: Add a new root cluster.
newRootCluster() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Allocates a new cluster and returns a spec to it.
newRow() - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder: Start building new row.
newSiblingCluster() - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec: Add a child cluster to the same parent.
next() - Method in class com.chemaxon.overlap.cli.util.pipeline.CharIterator
next() - Method in interface com.chemaxon.overlap.util.idgenerator.IdGenerator
next() - Method in class com.chemaxon.overlap.util.idgenerator.SequentialIdGenerator
next() - Method in class com.chemaxon.overlap.util.idgenerator.UUIDGenerator
NnResults - Interface in com.chemaxon.overlap.result: Nearest neighbor (most similars) search result.
NO_CONTENT - Static variable in annotation type com.chemaxon.overlap.wui.application.Status: 204 No Content.
noCanceller() - Static method in class com.chemaxon.calculations.common.ProgressObservers: Returns a cancel observer which wont cancel execution.
nonHeapMemoryUsage - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Non-heap memory usage.
nonHeapMemoryUsage - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Non-heap memory usage.
nonHeapMemoryUsed - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Used non-heap memory.
nonHeapMemoryUsed - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Used non-heap memory.
NoOverflowAutoDoneProgressObserver - Class in com.chemaxon.calculations.common: A Decorator that don't throw exception when NoOverflowAutoDoneProgressObserver.worked(long) calls reach totalWork, but keeps accumulatedWork at totalWork's value in this case.
NoOverflowAutoDoneProgressObserver(ProgressObserver) - Constructor for class com.chemaxon.calculations.common.NoOverflowAutoDoneProgressObserver
norm() - Method in class com.chemaxon.calculations.util.V3D
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpart
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpartNormalized
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongDice
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclidean
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclideanNormalized
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattan
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattanNormalized
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongPetke
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongSimpson
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTanimoto
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTversky
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclid
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclidSqr
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsManhattan
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsMaxDiff
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTanimoto
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTversky
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvEuclid
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvTanimoto
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv.ScaledShortsFvEuclid
normalize(double) - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.SerializingUnguardedDissimilarityCalculator
normalize(double) - Method in interface com.chemaxon.descriptors.common.unguarded.UnguardedDissimilarityCalculator: Normalize dissimilarity value returned by UnguardedDissimilarityCalculator.dissimilarity(java.lang.Object, java.lang.Object).
normalize(double) - Method in class com.chemaxon.overlap.wui.SlowUnguardedComparator
NormalizeUriFilter - Class in com.chemaxon.overlap.wui.application: Filter for normalizing URIs.
NormalizeUriFilter() - Constructor for class com.chemaxon.overlap.wui.application.NormalizeUriFilter
north(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Area
NoSplitter() - Constructor for class com.chemaxon.overlap.cli.CalculateOverlapParameters.NoSplitter
NoSplitter() - Constructor for class com.chemaxon.overlap.cli.MadfastImportParameters.NoSplitter
NoSplitter() - Constructor for class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres.NoSplitter
noThrottle() - Static method in class com.chemaxon.calculations.common.AutoThrottles: No printout requested.
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorMcb
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
notifyMolecule(int, Optional<String>, Molecule, int) - Method in interface com.chemaxon.overlap.io.MoleculeCallback: Introduce new processed molecule.
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
notifyMolecule(int, Optional<String>, Molecule, int) - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorMcb
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
notifyParseError(int, Optional<String>, Throwable) - Method in interface com.chemaxon.overlap.io.MoleculeCallback: Notify a parsing error.
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
notifyParseError(int, Optional<String>, Throwable) - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.IndexProjectors.IndexProjectorMcb
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in interface com.chemaxon.overlap.io.MoleculeCallback: Notify a processing error.
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
notifyProcessingError(int, Optional<String>, Molecule, Throwable) - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
nullCallback() - Static method in class com.chemaxon.overlap.io.MoleculeCallbacks: Null callback.
nullConsumer() - Static method in interface com.chemaxon.overlap.partialresult.PartialResultConsumer
nullInstance() - Static method in interface com.chemaxon.overlap.partialresult.PartialResultHolder
nullProgressObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers: Returns a forgiving observer which wont enforce API contracts.
nullProgressObserver(CancelObserver) - Static method in class com.chemaxon.calculations.common.ProgressObservers: Returns a forgiving cancellable observer which wont enforce API contracts.
numeric - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropInfo: Is the represented type numeric.
numericRepresentation(FvParameters.NumericRepresentation) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder: Set numeric representation of vector coordinates.

O

objectInputStreamFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create ObjectInputStream from a not nullable location.
objectInputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create ObjectInputStream from a not nullable location.
objectInputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Create in object input stream from nullable location.
objectOutputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: ObjectOutputStream from a location.
objectOutputStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: ObjectOutputStream from a nullable location.
objectPendingFinalizationCount - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Approximate number of objects pending finalization.
objectPendingFinalizationCount - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Approximate number of objects pending finalization.
observable - Variable in class com.chemaxon.overlap.service.task.Task
ObservableProgressObserver - Class in com.chemaxon.calculations.common: Implementation that holds observed state, and expose it as a ProgressObservable.
ObservableProgressObserver() - Constructor for class com.chemaxon.calculations.common.ObservableProgressObserver
of(ProgressObserver, ProgressObserver) - Static method in class com.chemaxon.calculations.common.SplitObserver
of(int, T) - Static method in class com.chemaxon.calculations.io.OrderedElements: Create an instance.
of(double, double) - Static method in class com.chemaxon.descriptors.metrics.TverskyParameters: Convenience factory function.
of(Range, Range) - Static method in interface com.chemaxon.overlap.cli.util.images.Area
of(RangeSpec, RangeSpec) - Static method in interface com.chemaxon.overlap.cli.util.images.AreaSpec: Create an instance.
of(int, int) - Static method in class com.chemaxon.overlap.cli.util.images.Px2d: A point.
of(int, int) - Static method in interface com.chemaxon.overlap.cli.util.images.Range
of(Align, int) - Static method in interface com.chemaxon.overlap.cli.util.images.RangeSpec: Create a range specification.
of() - Static method in class com.chemaxon.overlap.service.task.ExecutionMonitoring
of(ProgressObserver) - Static method in class com.chemaxon.overlap.service.task.ExecutionMonitoring: Create without ExecutionMonitoring.partialResultConsumer
of(ProgressObserver, PartialResultConsumer<R>) - Static method in class com.chemaxon.overlap.service.task.ExecutionMonitoring
ofDisableds(Collection<ServerFeature>) - Static method in class com.chemaxon.overlap.wui.context.features.FeatureConfig
ofFormat(String) - Static method in class com.chemaxon.calculations.io.Segmenters: Create a segmenter.
ofIterator(Iterator<T>) - Static method in class com.chemaxon.calculations.io.OrderedElements: Wrap iterated elements.
ofMolecule(Molecule) - Static method in class com.chemaxon.calculations.io.StructureRecords: Wrap a Molecule into a Structure record.
ofMolecules(Iterable<Molecule>) - Static method in class com.chemaxon.clustering.framework.BemisMurckoClustering: Initialize with an Iterable instance.
ofMoleculesIterator(Iterator<Molecule>) - Static method in class com.chemaxon.clustering.framework.BemisMurckoClustering: Initialize with an Iterator instance.
ofMolImporter(MolImporter) - Static method in class com.chemaxon.calculations.io.StructureRecordIterators
ofMolSource(String) - Static method in class com.chemaxon.calculations.util.MU: Read a structure from source
ofOrderedMoleculesIterator(Iterator<OrderedElement<Molecule>>) - Static method in class com.chemaxon.clustering.framework.BemisMurckoClustering: Initialize with an Iterator of OrderedElements of Molecules.
ofParseError(Exception, String) - Static method in class com.chemaxon.calculations.io.StructureRecords: Wrap a failed parse.
ofPixel(int, int) - Static method in interface com.chemaxon.overlap.cli.util.images.Area: Create an area representing a single pixel.
ofPixel(Px2d) - Static method in interface com.chemaxon.overlap.cli.util.images.Area
ofRect(int, int, int, int) - Static method in interface com.chemaxon.overlap.cli.util.images.Area
ofRect(Px2d, Px2d) - Static method in interface com.chemaxon.overlap.cli.util.images.Area
ofSmiles(String) - Static method in class com.chemaxon.calculations.util.MU: Read a structure from SMILES.
ofSource(String, String) - Static method in class com.chemaxon.calculations.io.StructureRecordIterators
ofSource(String, String) - Static method in class com.chemaxon.calculations.io.StructureRecords: Create a record from a single structure source.
ofSourceFunction(String) - Static method in class com.chemaxon.calculations.io.StructureRecords: Transform structure sources into StructureRecord instances.
onDone(ConsolePO.Callback) - Method in class com.chemaxon.calculations.common.ConsolePO: Register a callback to be called when done.
OneKeeperPartialResultHolder<R> - Class in com.chemaxon.overlap.partialresult: A holder that help saving performance by keeps only one result, clear it on take, and only accepts new if previous has been taken.
OneKeeperPartialResultHolder() - Constructor for class com.chemaxon.overlap.partialresult.OneKeeperPartialResultHolder
onServerStarted() - Method in class com.chemaxon.overlap.wui.StartupHandler
openFileInput(String) - Method in interface com.chemaxon.calculations.util.CmdlineContext: Open a file for reading.
openFileInput(String) - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
openFileOutput(String) - Method in interface com.chemaxon.calculations.util.CmdlineContext: Open a file for writing.
openFileOutput(String) - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
openUrlStream(String) - Method in interface com.chemaxon.calculations.util.CmdlineContext: Open a connection to an URL.
openUrlStream(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Open an URL connection.
openUrlStream(String) - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
OptErrorH<S> - Interface in com.chemaxon.overlap.concurrent: Possibility to define error handler.
optionalComposer(Optional<T>) - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
optionalComposer(Optional<T>) - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
optionalComposer(Optional<T>) - Method in interface com.chemaxon.calculations.io.Segmenter: Convenience wrapper for Segmenter.composer(java.lang.Appendable, java.io.Closeable).
OptionalSource<T> - Interface in com.chemaxon.overlap.cli.util: Represents an optional leg of the data flow.
opts(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolImporter
order - Variable in class com.chemaxon.calculations.util.MU.BondList: Bond order.
OrderedElement<T> - Interface in com.chemaxon.calculations.io: An arbitrary element of an ordered collection.
OrderedElements - Class in com.chemaxon.calculations.io: Utilities for OrderedElement.
OrderedInputProcessingException - Exception in com.chemaxon.calculations.io: Processing an item from an ordered list of items failed.
OrderedInputProcessingException(int, Throwable) - Constructor for exception com.chemaxon.calculations.io.OrderedInputProcessingException: Construct.
OrderedInputProcessingException(OrderedElement<?>, Throwable) - Constructor for exception com.chemaxon.calculations.io.OrderedInputProcessingException: Construct.
orTimeout(CancelObserver, long) - Static method in class com.chemaxon.calculations.common.ProgressObservers: Returns a cancel observer which cancels when a passed observer is cancelled or a timeout occured.
out() - Method in interface com.chemaxon.calculations.util.CmdlineContext: Output stream, usually mapped to System.out.
out() - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
out - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
out - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
out - Variable in class com.chemaxon.overlap.cli.JsEvalParameters
output(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.Connect
output(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.Mark
outputStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: OutputStream from a location.
OutputStreamStatCollector - Class in com.chemaxon.overlap.cli.util.pipeline: Collect written byte count to an underlying OutputStream.
OutputStreamStatCollector(OutputStream) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.OutputStreamStatCollector
OverlapAnalysisContext<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.overlap.context: Context for an overlap analysis.
OverlapAnalysisContextFactory - Class in com.chemaxon.overlap: Collections of overlap analysis contexts.
OverlapAnalysisContextWrapper - Class in com.chemaxon.descriptors.alternates: Wrap descriptor generator provided by OverlapAnalysisContextFactory.createtContextByName(java.lang.String).
OverlapAnalysisContextWrapper(String) - Constructor for class com.chemaxon.descriptors.alternates.OverlapAnalysisContextWrapper: Construct.
overlapBuildTimestamp() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Build timestamp.
overlapBuildTimestamp - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Build time stamp, expected format is yyyy-MM-dd HH:mm:ss z.
overlapDevelVersion() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Overlap devel version.
overlapDevelVersion - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Development version info.
OverlapResult(OverlapAnalysisContext<D, T>, String, DescriptorsWithMols<T>, DescriptorsWithMols<T>, KnnResults, String, String, String, String) - Constructor for class com.chemaxon.overlap.cli.CalculateOverlap.OverlapResult: Construct data object.
OverlapVersion - Class in com.chemaxon.overlap.version: Contains information on package version.
OverlapVersion() - Constructor for class com.chemaxon.overlap.version.OverlapVersion
overlapVersion() - Static method in class com.chemaxon.overlap.version.OverlapVersion: Overlap version.
overlapVersion - Variable in class com.chemaxon.overlap.version.OverlapVersionInfo: Overlap-examples package main version.
OverlapVersionInfo - Class in com.chemaxon.overlap.version: Version info.
OverlapVersionInfo() - Constructor for class com.chemaxon.overlap.version.OverlapVersionInfo: Initialize fields from OverlapVersion.

P

p0() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Upper left corner.
p0() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
p1() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Lower right corner (inclusive!).
p1() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
packBytesToInt(byte, byte, byte, byte) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Pack four 8 bit bytes into a 32 bit int.
packBytesToInt(byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Pack four 8 bit bytes into a 32 bit int.
packBytesToInts(byte[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Pack array of bytes into an array of ints.
packBytesToLong(byte, byte, byte, byte, byte, byte, byte, byte) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Pack eight 8 bit bytes into a 64 bit long.
packBytesToLong(byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Pack eight 8 bit bytes into a 64 bit long.
packBytesToLongs(byte[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Pack array of bytes into an array of longs.
packIntIntoBitSet(int, BitSet, int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Pack an int value into a BitSet.
packIntsToLong(int, int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Pack two 32 bit integers into a 64 bit long.
packIntsToLongs(int[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Pack array of ints into an array of longs.
packLongIntoBitSet(long, BitSet, int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Pack a long value into a BitSet.
pad(String, int, CharLayout.HA) - Static method in class com.chemaxon.calculations.util.CharLayout: Align String to the given length.
PagedBuilder<T> - Class in com.chemaxon.overlap.cli.util.pages: Builder for immutable paged storages.
PagedBuilder(int) - Constructor for class com.chemaxon.overlap.cli.util.pages.PagedBuilder: Construct.
PagedDescriptorImport - Class in com.chemaxon.overlap.cli: Example code to excercise paged descriptor storage.
PagedDescriptorImportParameters - Class in com.chemaxon.overlap.cli: Command line parameters for PagedDescriptorImport.
PagedDescriptorImportParameters() - Constructor for class com.chemaxon.overlap.cli.PagedDescriptorImportParameters
PagedDescriptorStorage<D extends Descriptor> - Class in com.chemaxon.overlap.storage: Descriptor storage.
PagedDescriptorStorage(int, DescriptorGenerator<D>) - Constructor for class com.chemaxon.overlap.storage.PagedDescriptorStorage: Construct new empty descriptor storage.
PagedDescriptorStorage(int, DescriptorGenerator<D>, ObjectInputStream, SubProgressObserver) - Constructor for class com.chemaxon.overlap.storage.PagedDescriptorStorage: Construct from a byte [] serialized form.
PagedDescriptorStorage(int, DescriptorGenerator<D>, InputStream, SubProgressObserver) - Constructor for class com.chemaxon.overlap.storage.PagedDescriptorStorage: Construct from a String serialized form.
pagedOverlap() - Method in class com.chemaxon.screen.DescriptorStorage: Gets the unguarded paged overlap.
pagesize(int) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Update pagesize.
paint(Renderer, Area, Molecule, String) - Method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer: Paint.
paint(Renderer, Area, Molecule) - Method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer: Paint.
Paint - Interface in com.chemaxon.overlap.cli.util.images: Callback for painting.
paint(Renderer, Area) - Method in interface com.chemaxon.overlap.cli.util.images.Paint: Paint to the layed out area.
paint(Renderer) - Method in class com.chemaxon.overlap.cli.util.images.SimplePane: Delegate to painting callback.
Parameter - Annotation Type in com.chemaxon.apidiscovery.annotations: Parameter field to be exposed to the user interface.
ParameterBuilder<T> - Interface in com.chemaxon.apidiscovery.interfaces: This interface represents a builder.
ParameterizedContextFactory - Class in com.chemaxon.overlap: Context factory for construction of contexts with parameters.
parameterKeys() - Method in interface com.chemaxon.apidiscovery.linenote.ParseRes: Parameter keys.
parameters() - Method in interface com.chemaxon.apidiscovery.linenote.ParseRes: Represented parameters.
parameters - Variable in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
parameters - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceDto: Parameters for the represented choice.
ParameterSetMode - Enum in com.chemaxon.apidiscovery: Parameter set method.
ParameterWrapper - Class in com.chemaxon.apidiscovery: Wraps a parameter which can be set or get on an object.
ParameterWrapper.ParameterType - Enum in com.chemaxon.apidiscovery: Wrapped parameter types.
Parametrized - Annotation Type in com.chemaxon.apidiscovery.annotations: Indicated that the annotated class has mutable parameters which can be handled by API discovery framework.
parent() - Method in interface com.chemaxon.clustering.common.HierarchicCluster: Get parent for non roots.
parent() - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec: Refers to the parent cluster if present.
parent() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicCluster
parent - Variable in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.EnumeratedExtension
parse(String) - Method in interface com.chemaxon.apidiscovery.linenote.Linenote: Parse a line notation.
parseBinaryStringAsLong(String) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Parse a binary String as a 64 bit long.
parseBinaryStringAsLongs(String, int, BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Parse a binary string of '0' and '1' characters into a packed long array.
parseCustomDescriptors(OverlapAnalysisContext, Iterable<Supplier<InputStream>>, String, String, Supplier<SubProgressObserver>, ExecutorService) - Static method in class com.chemaxon.overlap.cli.util.Imports: Parse custom descriptors.
ParseCustomToDescriptor<D extends Descriptor> - Class in com.chemaxon.overlap.cli.util.importing: Parse Descriptors from Strings optionally with IDs.
ParseCustomToDescriptor(Function<String, String>, Function<String, String>, DescriptorGenerator<D>) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParseCustomToDescriptor: Construct new instance.
ParseCustomToUnguarded<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.overlap.cli.util.importing: Parse Descriptors from Strings optionally with IDs.
ParseCustomToUnguarded(Function<String, String>, Function<String, String>, DescriptorGenerator<D>, UnguardedExtractor<D, T>) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParseCustomToUnguarded: Construct new instance.
parsedChoiceParameterValue(ChoiceParameterDescriptor<T>) - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceParameterValueProvider: Provide parameter value for choice parameter descriptor.
ParsedDescriptorResult<D extends Descriptor> - Class in com.chemaxon.overlap.cli.util.importing: Data object for parsed Descriptor with its its ID.
ParsedDescriptorResultHandler<D extends Descriptor> - Class in com.chemaxon.overlap.cli.util.importing: Results handler for parsed Descriptors.
ParsedDescriptorResultHandler(PagedDescriptorStorage<D>, IndexProjectors.IndexProjectorBuilder, MasterStorages.MasterStorageBuilder<String>, boolean) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParsedDescriptorResultHandler: Create new handler.
parseDescriptorsToUnguardeds(List<String>, SubProgressObserver) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Parse multiple descriptors and transform them into unguarded representations.
parseDescriptorToUnguarded(String) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Parse descriptor and transform it into the unguarded representation.
ParsedUnguardedResult<T extends Serializable> - Class in com.chemaxon.overlap.cli.util.importing: Data object for parsed Descriptor unguarded representation with its its ID.
ParsedUnguardedResult(T, String) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResult: Construct.
ParsedUnguardedResultHandler<T extends Serializable> - Class in com.chemaxon.overlap.cli.util.importing: Results handler for parsed Descriptors.
ParsedUnguardedResultHandler(int, boolean, boolean) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResultHandler: Create new handler.
ParsedUnguardedWithMolResult<T extends Serializable> - Class in com.chemaxon.overlap.cli.util.importing: Data object for parsed Descriptor unguarded representation with its its ID and Molecule source.
ParsedUnguardedWithMolResult(T, String, String, List) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResult: Construct.
ParsedUnguardedWithMolResultHandler<T extends Serializable> - Class in com.chemaxon.overlap.cli.util.importing: Results handler for parsed Descriptors with structur sources.
ParsedUnguardedWithMolResultHandler(int, boolean, boolean, String, List<MasterStorages.MasterStorageBuilder>) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler: Create new handler.
parseInts(String, int, String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Parse an String containing integer values.
parseLongs(String, int, String) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Parse an String containing long values.
parseMolecule() - Method in interface com.chemaxon.overlap.io.StructureRecord: Parse molecule if not parsed successfully already.
parseMoleculeName() - Method in interface com.chemaxon.overlap.io.StructureRecord: Parse molecule name if present.
parseParameters(String[], Class<T>) - Static method in class com.chemaxon.overlap.cli.invocation.CliInvocation: Parse command line parameters.
parseParameters(Class<T>, String[]) - Static method in class com.chemaxon.overlap.cli.util.CliUtil: Parse parameters.
parseParameters(Object[], String[]) - Static method in class com.chemaxon.overlap.cli.util.CliUtil
parseParameterValue(String) - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Parse parameter value from a String.
parseProperties() - Method in interface com.chemaxon.overlap.io.StructureRecord: Parse properties if not parsed already.
ParseRes - Interface in com.chemaxon.apidiscovery.linenote: Parsed linear notation.
ParseSdf - Class in com.chemaxon.virtuallib.sc.cli: Parse SDF representation, build serialized structures.
ParseSdfParameters - Class in com.chemaxon.virtuallib.sc.cli: CLI arguments.
ParseSdfParameters() - Constructor for class com.chemaxon.virtuallib.sc.cli.ParseSdfParameters
parseString(String) - Static method in class com.chemaxon.overlap.cli.util.prop.CliParam: Parse CLI argument string.
parseStringToFloats(String, int) - Static method in class com.chemaxon.descriptors.common.realvector.Util: Parse space/tab sep floats string.
ParseStructureRecordToUnguarded<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.overlap.cli.util.importing: Parse Descriptors from Molecule sources represented as StructureRecords optionally with IDs.
ParseStructureRecordToUnguarded(Function<StructureRecord, String>, StandardizerWrapper, DescriptorGenerator<D>, UnguardedExtractor<D, T>) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParseStructureRecordToUnguarded: Construct new instance.
ParseStructureRecordToUnguardedWithMol<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.overlap.cli.util.importing: Parse Descriptors from Molecule sources represented as StructureRecords optionally with IDs / additional properties.
ParseStructureRecordToUnguardedWithMol(Function<StructureRecord, String>, Function<Molecule, String>, StandardizerWrapper, StandardizerWrapper, DescriptorGenerator<D>, UnguardedExtractor<D, T>, Function<StructureRecord, List>) - Constructor for class com.chemaxon.overlap.cli.util.importing.ParseStructureRecordToUnguardedWithMol: Construct new instance.
parseWithVariableSubstitution(String, String, Function<String, String>) - Method in interface com.chemaxon.apidiscovery.linenote.Linenote: Parse linenote with value parameter substitutions.
partialResult - Variable in class com.chemaxon.overlap.wui.dto.AsyncCallDto: Partial result if possible/requested to return or null.
PartialResultConsumer<R> - Interface in com.chemaxon.overlap.partialresult
partialResultConsumer - Variable in class com.chemaxon.overlap.service.task.ExecutionMonitoring
PartialResultHolder<R> - Interface in com.chemaxon.overlap.partialresult
PartialResultProvider<R> - Interface in com.chemaxon.overlap.partialresult
partition(double) - Method in interface com.chemaxon.clustering.common.LevelAssigner: Create a partition of the associated hierarchic clustering at a specified level.
passDissim0(double) - Method in interface com.chemaxon.overlap.servlets.SelfKnnFilter
passDissim0(double) - Method in class com.chemaxon.overlap.servlets.SelfKnnFilterImpl
passDissim1(double) - Method in interface com.chemaxon.overlap.servlets.SelfKnnFilter
passDissim1(double) - Method in class com.chemaxon.overlap.servlets.SelfKnnFilterImpl
passQuery(int) - Method in interface com.chemaxon.overlap.servlets.SelfKnnFilter
passQuery(int) - Method in class com.chemaxon.overlap.servlets.SelfKnnFilterImpl
passTarget0(int) - Method in interface com.chemaxon.overlap.servlets.SelfKnnFilter
passTarget0(int) - Method in class com.chemaxon.overlap.servlets.SelfKnnFilterImpl
passTarget1(int) - Method in interface com.chemaxon.overlap.servlets.SelfKnnFilter
passTarget1(int) - Method in class com.chemaxon.overlap.servlets.SelfKnnFilterImpl
pc() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Center point.
pc() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
peek() - Method in class com.chemaxon.overlap.cli.util.pipeline.CharIterator
Pf2dWrapper - Class in com.chemaxon.descriptors.alternates: Wrapper for Pf2d fingerprints.
Pf2dWrapper(String) - Constructor for class com.chemaxon.descriptors.alternates.Pf2dWrapper: Construct new instance.
PfComparator - Interface in com.chemaxon.descriptors.fingerprints.pf2d: Comparator for PharmacophoreFP descriptor representation.
PfComparatorImpl - Class in com.chemaxon.descriptors.fingerprints.pf2d: PfComparator implementation.
PfComparatorImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
PfGenerator - Interface in com.chemaxon.descriptors.fingerprints.pf2d: Generates 2D pharmacophore fingerprints.
PfParameters - Class in com.chemaxon.descriptors.fingerprints.pf2d: Pharmacophore FP parameters class.
PfParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters: Constructor using the default settings.
PfParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.pf2d: Builder class for the immutable parameter object.
PfParameters.ConstructPfGenerator - Interface in com.chemaxon.descriptors.fingerprints.pf2d: Interface representing PF generator constructor.
PfReaderFactoryImpl() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl.PfReaderFactoryImpl
PfTableReader - Class in com.chemaxon.descriptors.fingerprints.pf2d: MDTable reader for 2D pharmacophore fingerprints.
PfTableReader() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
PfTableReader.Factory - Interface in com.chemaxon.descriptors.fingerprints.pf2d: Factory class.
PfTableReaderImpl - Class in com.chemaxon.descriptors.fingerprints.pf2d: PfTableReader implementation.
PfTableReaderImpl(String) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl
PfTableReaderImpl.PfReaderFactoryImpl - Class in com.chemaxon.descriptors.fingerprints.pf2d: Factory implementation for PfTableReader.
PharmacophoreFP - Interface in com.chemaxon.descriptors.fingerprints.pf2d: 2D pharmacophore fingerprint representation.
PharmacophoreFPImpl - Class in com.chemaxon.descriptors.fingerprints.pf2d: Pharmacophore fingerprint implementation.
PharmacophoreFPImpl(PharmacophoreFingerprint, Object) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl: Construct.
PipelineContext - Interface in com.chemaxon.overlap.cli.util.pipeline: Composes the pipeline.
PipelineRunner - Class in com.chemaxon.overlap.cli: Responsible for composing the pipeline.
PipelineRunner() - Constructor for class com.chemaxon.overlap.cli.PipelineRunner
PipelineRunner.Connection<T> - Class in com.chemaxon.overlap.cli
PipelineRunner.IO<T> - Class in com.chemaxon.overlap.cli
PipelineRunner.IOType - Enum in com.chemaxon.overlap.cli
PipelineStep - Interface in com.chemaxon.overlap.cli.util.pipeline: Minimal life cycle of a MadFast import pipeline node.
placeCenteredHorizontalTextInto(String, Area) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
placeCenteredHorizontalTextInto(String, Area) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer: Place text into the middle of an area.
placeHorizontalTextInto(String, Halign, Valign, Area, int, int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
placeHorizontalTextInto(String, Halign, Valign, Area, int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer: Render text into an area.
placeVerticalTextInto(String, Halign, Valign, Area, int, int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
placeVerticalTextInto(String, Halign, Valign, Area, int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer: Render rotated text into an area.
pLeftCenter() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pLeftCenter() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
pLowerCenter() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pLowerCenter() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
pLowerLeft() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pLowerLeft() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
pLowerRight() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pLowerRight() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
plus(V3D) - Method in class com.chemaxon.calculations.util.V3D
plus(Px2d) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
plus(int, int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
plusx(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
plusy(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
pmap - Variable in class com.chemaxon.overlap.wui.dto.PmapperResponse: The one-line pharmacophore mapping when structure was specified.
PmapperFeature - Class in com.chemaxon.overlap.wui.dto: Experimental feature description for pharmacophore mapping.
PmapperFeature() - Constructor for class com.chemaxon.overlap.wui.dto.PmapperFeature
PmapperRequest - Class in com.chemaxon.overlap.wui.dto: Experimental request for pharmacophore mapping.
PmapperRequest() - Constructor for class com.chemaxon.overlap.wui.dto.PmapperRequest
PmapperResponse - Class in com.chemaxon.overlap.wui.dto: Experimental pmapper response.
PmapperResponse() - Constructor for class com.chemaxon.overlap.wui.dto.PmapperResponse
pmapperxml - Variable in class com.chemaxon.overlap.wui.dto.PmapperResponse: The XML config used for constructing the underlying PMapper.
position() - Method in interface com.chemaxon.calculations.util.SeekableFileOutput: The actual position in the output.
position(long) - Method in interface com.chemaxon.calculations.util.SeekableFileOutput: Set the position.
postNewRawFile(InputStream, FormDataContentDisposition, String, String, String) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource: Experimental file upload.
PostOrderDfsVisitor<T> - Interface in com.chemaxon.clustering.util: Function passed for DFS post order traversal.
precedence - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
preferredAlignment() - Method in interface com.chemaxon.clustering.common.HierarchicClustering: Preferred alignment of the represented clustering.
prefix(String, List<String>) - Static method in class com.chemaxon.calculations.util.CharLayout: Prefix lines.
prefixMultiline(String, String) - Static method in class com.chemaxon.calculations.util.CharLayout: Prefix multi line String.
PrepareMolecules - Class in com.chemaxon.overlap.cli: Common utilities to prepare molecule sets.
PrepareMoleculesParameters - Class in com.chemaxon.overlap.cli: Command line parameters for PrepareMolecules.
PrepareMoleculesParameters() - Constructor for class com.chemaxon.overlap.cli.PrepareMoleculesParameters
presentcount - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropRange: Number of present values in the MoleculePropRange.values array.
pRightCenter() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pRightCenter() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
print(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
println(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
printStreamFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: PrintStream from a location.
printStreamFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: PrintStream from a nullable location.
printUsage(Class<?>) - Static method in class com.chemaxon.overlap.cli.util.CliUtil: Print usage of a given parameters object.
printUsage(Object[]) - Static method in class com.chemaxon.overlap.cli.util.CliUtil
proc - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
process(int, int, SubProgressObserver, ExecutorService, Iterator<S>, Function<S, T>, ErrorHandler<S>, ResultHandler<S, T>) - Static method in class com.chemaxon.overlap.concurrent.BatchedPagedProcessor: Launch a long running process.
process(Iterator<S>, Function<S, T>, ResultHandler<S, T>) - Method in class com.chemaxon.overlap.concurrent.impl.ProcessorImpl
process(Iterator<S>, Function<S, T>, ResultHandler<S, T>) - Method in interface com.chemaxon.overlap.concurrent.Processor: Specify input, process and target.
processManaged(MBeanServer, ObjectName, int, int, SubProgressObserver, ListeningExecutorService, Iterator<S>, Function<S, T>, ErrorHandler<S>, ResultHandler<S, T>) - Static method in class com.chemaxon.overlap.concurrent.BatchedPagedProcessor: Launch a managed long running process.
Processor - Interface in com.chemaxon.overlap.concurrent: An abstraction of map-reduce.
processor(int, int, SubProgressObserver, ExecutorService) - Static method in class com.chemaxon.overlap.concurrent.Processors: Create an unmanaged processor.
processor(BppParameters) - Static method in class com.chemaxon.overlap.concurrent.Processors: Create a processor with a parameters object.
ProcessorImpl - Class in com.chemaxon.overlap.concurrent.impl: Implementation of Processor map-reduce abstraction.
ProcessorImpl(BppParameters) - Constructor for class com.chemaxon.overlap.concurrent.impl.ProcessorImpl: Construct.
Processors - Class in com.chemaxon.overlap.concurrent: Utility class for Processor based map-reduce reactors.
prof - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
prof - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
prof - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
Prof - Class in com.chemaxon.overlap.cli.prof: Utility methods for in-app profiling.
profres - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
profres - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
profres - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
ProfRes - Class in com.chemaxon.overlap.wui.res: Implementation for profiling result JSONs.
ProfRes(String, long, String, long) - Constructor for class com.chemaxon.overlap.wui.res.ProfRes: Construct.
ProfResResource - Class in com.chemaxon.overlap.wui.resources: Profiling results JAX-RS resource.
ProfResResource() - Constructor for class com.chemaxon.overlap.wui.resources.ProfResResource
ProfSnapshot - Class in com.chemaxon.overlap.cli.prof: VM profiling snapshot.
ProfSnapshot() - Constructor for class com.chemaxon.overlap.cli.prof.ProfSnapshot: Construct snapshot.
ProfSnapshot(boolean) - Constructor for class com.chemaxon.overlap.cli.prof.ProfSnapshot: Construct snapshot.
ProfSnapshot.GarbageCollector - Class in com.chemaxon.overlap.cli.prof: Represents a garbage collector.
ProfSnapshot.MemoryPool - Class in com.chemaxon.overlap.cli.prof: Represents a memory pool.
ProfSnapshot.MemoryUsageDesc - Class in com.chemaxon.overlap.cli.prof: Represents memory usage.
ProfSnapshotDto - Class in com.chemaxon.overlap.wui.dto: VM profiling snapshot.
ProfSnapshotDto() - Constructor for class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Construct snapshot.
profSnapshotFinal - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: More detailed VM state snapshot at the end of execution.
profSnapshotFinal - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: More detailed VM state snapshot at the end of execution.
profSnapshotFinal - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
profSnapshotFinal - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: More detailed VM state snapshot at the end of execution.
profSnapshotFinal - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
profSnapshotFinal - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: More detailed VM state snapshot at the end of execution.
profSnapshotInitial - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: More detailed VM state snapshot at the begining of execution.
profSnapshotInitial - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: More detailed VM state snapshot at the begining of execution.
profSnapshotInitial - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
profSnapshotInitial - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: More detailed VM state snapshot at the begining of execution.
profSnapshotInitial - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
profSnapshotInitial - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: More detailed VM state snapshot at the begining of execution.
ProgressiveDeserializer<T> - Interface in com.chemaxon.overlap.cli.util.pipeline: Reconstruct a serialized object.
ProgressiveSerialization - Interface in com.chemaxon.overlap.cli.util.pipeline: Persist a record oriented storage efficiently.
ProgressiveSerializationImpl - Class in com.chemaxon.overlap.cli.util.pipeline: Implementation of ProgressiveSerialization over FileOutputStream.
ProgressiveSerializationImpl(File, int, boolean) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl
ProgressiveSerializationImpl.DeserializerImpl<T> - Class in com.chemaxon.overlap.cli.util.pipeline: Deserializer.
ProgressiveSerializeToFile - Class in com.chemaxon.overlap.cli.util.pipeline: Write progressively serialized file.
ProgressiveSerializeToFile() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
ProgressiveSerializeToFile(String) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
ProgressObservable - Interface in com.chemaxon.calculations.common
ProgressObserver - Interface in com.chemaxon.calculations.common: Observer for reporting the progress of long running tasks.
progressObserver(String) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationEnv: Create a SubProgressObserver.
progressObserver(String, BiConsumer<ST, TimerStatistics>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationEnv2: Create a SubProgressObserver.
progressObserver - Variable in class com.chemaxon.overlap.service.task.ExecutionMonitoring
ProgressObservers - Class in com.chemaxon.calculations.common: Utility functions for the creation of ProgressObservers.
prop - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
PropertyCollectorCallback - Class in com.chemaxon.overlap.io: Build storage for molecular properties.
PropertyCollectorCallback() - Constructor for class com.chemaxon.overlap.io.PropertyCollectorCallback: Construct builder to represent molecule name.
PropertyCollectorCallback(String) - Constructor for class com.chemaxon.overlap.io.PropertyCollectorCallback: Construct builder to store a given property.
PropertyExtractor<T> - Interface in com.chemaxon.overlap.cli.util.prop: Represents a property extraction/calculation.
PropertyExtractorFactory - Interface in com.chemaxon.overlap.cli.util.prop: Represents a class of property extractions.
PropertyExtractors - Class in com.chemaxon.overlap.cli.util.prop: Utilities for property extraction.
propname(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.GetSdfProperty
propnames - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo: Names of additional properties.
props - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: System properties from System.getProperties().
props - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: System properties from System.getProperties().
props - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat: System properties from System.getProperties().
props - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: System properties from System.getProperties().
props - Variable in class com.chemaxon.overlap.cli.MadfastImportStat: System properties from System.getProperties().
props - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: System properties from System.getProperties().
props - Variable in class com.chemaxon.overlap.wui.dto.MoleculeInfo: Molecule properties (which are present) or null when not requested.
props - Variable in class com.chemaxon.overlap.wui.dto.MoleculeProps: Mapping of index to IDs for each requested properties.
props - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo: Additional properties.
pseudos - Variable in class com.chemaxon.overlap.wui.dto.ConversionRequest: Pseudo atoms to set.
pUpperCenter() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pUpperCenter() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
pUpperLeft() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pUpperLeft() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
pUpperRight() - Method in interface com.chemaxon.overlap.cli.util.images.Area
pUpperRight() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
put(T) - Method in interface com.chemaxon.calculations.io.Sink: Deprecated.

Put new item into this sink.
put(String, MolsRes) - Static method in class com.chemaxon.overlap.servlets.MolsContext: Deprecated.

Put.
put(String, T) - Method in class com.chemaxon.overlap.wui.context.Contexts: Puts resource.
putRawFile(String, InputStream, FormDataContentDisposition, String, String) - Method in class com.chemaxon.overlap.wui.resources.ExperimentalRawFilesResource: Experimental file upload.
putUnique(String, T) - Method in class com.chemaxon.overlap.wui.context.Contexts: Put new resource using an indexed name if exists.
Px2d - Class in com.chemaxon.overlap.cli.util.images: A 2D int coordinate vector.

Q

q - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabels: Entries for queries.
qmolsurl - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: URL of query molecules.
queries - Variable in class com.chemaxon.overlap.wui.dto.KnnData: Query indices.
queriesgroup - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
query - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionRequest
query - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest: Query molecule.
query - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsResult: Query structure/descriptor/id used.
queryCount - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
queryCount - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Number of queries.
querycount - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Number of queries.
queryid - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabelEntry: Textual ID of the query.
queryIdsFontsize - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
queryIdsLength - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
queryindex - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabelEntry: Index of the query in the kNN results.
queryindexproj - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Index projector used for querues.
queryLabelHeight - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
queryLabelText - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
querymolecules - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Description of query molecules.
querymolindex - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabelEntry: Index of the query in the query molecule table.
queryPagesize(int) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Update query pagesize.
querysmi - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsResult: Query as smiles if applicable.

R

RAD_TO_DEG - Static variable in class com.chemaxon.calculations.util.V3D
RADS_TO_DEGS - Static variable in class com.chemaxon.calculations.util.V3D
Range - Interface in com.chemaxon.overlap.cli.util.images: 1D range embedded.
RangeSpec - Interface in com.chemaxon.overlap.cli.util.images: 1D simple range specification.
rAttachments() - Method in class com.chemaxon.virtuallib.sc.model.sdf.Scaffold: R attachments of the scaffold.
rawfiles - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalRawFilesInfo: Available raw files.
REACTANT_ID_SDFIELD - Static variable in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag: SD field storing Reactant ID.
read(byte[]) - Method in class com.chemaxon.descriptors.db.MDTableReader: Generates a descriptor from a byte array.
read(byte[]) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReaderImpl
read(byte[]) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReaderImpl
read(byte[]) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReaderImpl
read() - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
read(byte[]) - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
read(byte[], int, int) - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
reader - Variable in class com.chemaxon.overlap.cli.util.pipeline.ToLines: Underlying reader.
readFrom(Class<MoleculeContainer>, Type, Annotation[], MediaType, MultivaluedMap<String, String>, InputStream) - Method in class com.chemaxon.overlap.wui.context.MoleculeParsingMessageBodyReader
readSerializedStorages(String, String, Supplier<SubProgressObserver>, Supplier<SubProgressObserver>) - Static method in class com.chemaxon.overlap.cli.util.Imports: Read serialized descriptors and optionally IDs from locations.
realAtoms() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
RealTimeSeaarchGuiParmateres - Class in com.chemaxon.overlap.wui: Command line arguments for standalone jetty.
RealTimeSeaarchGuiParmateres() - Constructor for class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
RealTimeSeaarchGuiParmateres.NoSplitter - Class in com.chemaxon.overlap.wui: See https://groups.google.com/forum/#!topic/jcommander/g_bXIyGyHUE
RealTimeSearchGui - Class in com.chemaxon.overlap.wui: Main class of real time screen demo.
RealTimeSearchGuiContext - Class in com.chemaxon.overlap.wui: "Mega" context.
RealTimeSearchGuiContext(MasterMoleculeStorage, List<DescriptorStorage>, ExecutorService, int) - Constructor for class com.chemaxon.overlap.wui.RealTimeSearchGuiContext: Creates new instance.
reduceFragment(RgFrag, IntMatch) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension: Reduce fragment with the given scaffold extension.
reduceGraph() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
Reflect - Class in com.chemaxon.descriptors.common.reflect: Reflection based utilities for the descriptors package.
Reflect.MetricFactory - Annotation Type in com.chemaxon.descriptors.common.reflect: Name of metric factory method to use.
Reflect.Proxied - Interface in com.chemaxon.descriptors.common.reflect: Can provide proxied implementation.
release() - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
remainingDelay() - Method in interface com.chemaxon.calculations.common.AutoThrottle: Remaining delay for intended display.
removeAllExplicitH() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
removeAllExplicitH() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers: Remove all explicit H atoms.
removeAttribute(String) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
removeExtProbe(Supplier<? extends Object>) - Method in class com.chemaxon.overlap.cli.prof.Prof: Remove additional probe.
removeSidechains() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
RemoveSidechainsMolwalk - Class in com.chemaxon.clustering.framework: Remove side chains of the structure.
RemoveSidechainsMolwalk() - Constructor for class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk: Construct.
RemoveSidechainsSc - Class in com.chemaxon.clustering.framework: Remove side chains of the structure.
RemoveSidechainsSc(boolean) - Constructor for class com.chemaxon.clustering.framework.RemoveSidechainsSc: Construct.
removeSmallFragments() - Method in class com.chemaxon.clustering.framework.MoleculeFrameworks
removeSmallFragments() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers: Remove small fragments (disconnected components).
removeStructure(int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder: Remove a structure from its respective cluster.
removeStructure(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Remove a structure from its current parent cluster.
renderDiag - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
Renderer - Interface in com.chemaxon.overlap.cli.util.images: Methods to render onto a target medium.
Rendering<T extends Renderer> - Interface in com.chemaxon.overlap.cli.util.images: Provides factory methods to set up parts of a layout.
replaceAtomWithR(Molecule, int, int) - Static method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment: Replace an atom with an Rn atom and return the appropriate attachment descriptor.
replaceAtomWithR(Molecule, int) - Static method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
representant() - Method in interface com.chemaxon.clustering.common.Cluster: Cluster representant member.
requests - Variable in class com.chemaxon.overlap.wui.dto.MultiConversionRequest: The requests for conversion.
resclasses - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfosDto: Available resource classes.
reset() - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
ResourceClass<T> - Interface in com.chemaxon.overlap.wui.context: Resource class exposed on the web service.
ResourceClassInfoDto - Class in com.chemaxon.overlap.wui.dto: Metadata about a single resource class.
ResourceClassInfoDto() - Constructor for class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
ResourceClassInfoDto(ResourceInfo) - Constructor for class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
ResourceClassInfosDto - Class in com.chemaxon.overlap.wui.dto: Information about resource classes.
ResourceClassInfosDto() - Constructor for class com.chemaxon.overlap.wui.dto.ResourceClassInfosDto
ResourceInfo - Annotation Type in com.chemaxon.overlap.wui.res.annotations: Basic information about a resource class.
result(int, String, ParsedDescriptorResult<D>) - Method in class com.chemaxon.overlap.cli.util.importing.ParsedDescriptorResultHandler
result(int, Object, ParsedUnguardedResult<T>) - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedResultHandler
result(int, Object, ParsedUnguardedWithMolResult<T>) - Method in class com.chemaxon.overlap.cli.util.importing.ParsedUnguardedWithMolResultHandler
result(int, S, T) - Method in interface com.chemaxon.overlap.concurrent.ResultHandler: Report process result.
result - Variable in class com.chemaxon.overlap.wui.dto.AsyncCallDto: Call result object or null if it is not available yet.
result - Variable in class com.chemaxon.overlap.wui.dto.ConversionResult: Converted structure.
ResultHandler<S,T> - Interface in com.chemaxon.overlap.concurrent: Callback to report processing results.
results - Variable in class com.chemaxon.overlap.wui.dto.MultiConversionResult: The requests for conversion.
retrieveId(SingleThreadedDescriptorGeneratorParameters, int, Molecule) - Static method in class com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator: Construct ID.
returnValueSerializableGuardedWith(Object) - Method in class com.chemaxon.descriptors.common.reflect.SingleArgumentTransformingInvocationHandler: Convenience factory.
ReturnValueTransformingInvocationHandler - Class in com.chemaxon.descriptors.common.reflect: Invocation handler transforming return value.
ReturnValueTransformingInvocationHandler(InvocationHandler, Function) - Constructor for class com.chemaxon.descriptors.common.reflect.ReturnValueTransformingInvocationHandler: Construct.
RgDefiniton - Class in com.chemaxon.virtuallib.sc.model.sdf: Group of Rg fragments.
RgDefiniton(Scaffold, IntListSet) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton: Construct.
RgDefiniton.EnumeratedExtension - Class in com.chemaxon.virtuallib.sc.model.sdf
RgDefiniton.ScoredExtension - Class in com.chemaxon.virtuallib.sc.model.sdf
RgFrag - Class in com.chemaxon.virtuallib.sc.model.sdf: An RGroup fragment definition.
RgFrag(Molecule, String, Collection<Attachment>) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.RgFrag: Construct for a molecule and attachment descriptor.
RgFrag(Molecule) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.RgFrag: Construct for a Molecule.
rid - Variable in class com.chemaxon.virtuallib.sc.cli.ConverterParameters
rid - Variable in class com.chemaxon.virtuallib.sc.cli.ParseSdfParameters
RingAtomBs - Class in com.chemaxon.descriptors.fingerprints.maccs: Provides a BitSet which is set for the ring atoms for quick search.
RingAtomBs(Molecule) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.RingAtomBs: Gives the RinAtomBS for the parameter Molecule, mol
RingBondBs - Class in com.chemaxon.descriptors.fingerprints.maccs: Provides a BitSet which is set for the ring bonds for quick search
RingBondBs(Molecule) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.RingBondBs: Constructs a new instance of RingBondBS for Molecule, mol
rings(boolean) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder: Set rings parameter.
ringTorsionsDeg(Molecule, int[]) - Static method in class com.chemaxon.calculations.util.MU: Calculate ring torsions of specified atoms in degrees.
ringTorsionsRad(Molecule, int[]) - Static method in class com.chemaxon.calculations.util.MU: Calculate ring torsions of specified atoms in radians.
root - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
roots() - Method in interface com.chemaxon.clustering.common.HierarchicClustering: Highest level cluster(s).
Row - Interface in com.chemaxon.calculations.util.cellfield: Row represents a row in a cell field.
RowBuilder - Interface in com.chemaxon.calculations.util.cellfield: Builder for a row.
RowImpl - Class in com.chemaxon.calculations.util.cellfield.impl: Simple row implementation.
rowSeparation(int) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder: Number of empty lines between rows.
rowUnderlineChar(char) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder: Specify character for underlining the current row.
run() - Method in class com.chemaxon.overlap.cli.PipelineRunner
runLoadingTasks() - Method in class com.chemaxon.overlap.wui.StartupHandler
runningDurationMs - Variable in class com.chemaxon.overlap.wui.dto.TaskDto: Number of milliseconds since task start.
RXN_ID_SDFIELD - Static variable in class com.chemaxon.virtuallib.sc.model.sdf.Scaffold: SD field storing optional RXN ID.

S

satisfy() - Method in interface com.chemaxon.overlap.cli.util.images.RangeSpec: Construct a minimal Range satisfying this requirement.
Scaffold - Class in com.chemaxon.virtuallib.sc.model.sdf: Scaffold model for SDF based input.
Scaffold(Molecule) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.Scaffold: Construct.
ScaffoldExtension - Class in com.chemaxon.virtuallib.sc.model.sdf: Scaffold extension candidate.
ScaffoldExtension(Molecule, Collection<Attachment>, Collection<Attachment>) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension: Construct.
ScaffoldExtensionBuilder - Class in com.chemaxon.virtuallib.sc.model.sdf: Allows to "build" a scaffold extension by cutting down an r group fragment.
ScaffoldExtensionBuilder(RgFrag) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder: Construct.
ScalarFilter - Class in com.chemaxon.overlap.servlets: Scalar filter.
ScalarFilter(double, double) - Constructor for class com.chemaxon.overlap.servlets.ScalarFilter: Construct.
scale(double) - Method in class com.chemaxon.calculations.util.V3D
ScaledBytesFloatVectorDescriptorImpl - Class in com.chemaxon.descriptors.common.realvector: Float vector descriptor implementation over scaled bytes.
ScaledBytesFloatVectorDescriptorImpl(float[], ScaledFvDescriptorGenerator, int) - Constructor for class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl: Construct.
ScaledBytesFloatVectorDescriptorImpl(byte[], ScaledFvDescriptorGenerator, int) - Constructor for class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl: Construct.
ScaledBytesFvComparisonContextFactory - Class in com.chemaxon.descriptors.common.comparison.impl: Factory for scaled bytes backed float vector descriptors.
ScaledBytesFvComparisonContextFactory(LinearScaler, int, DescriptorSerializer<FloatVectorDescriptor>) - Constructor for class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory: Instantiate.
ScaledBytesFvEuclid - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv: Unguarded euclidean comparator for scaled byte[] backed float vector descriptors.
ScaledBytesFvEuclid(LinearScaler) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvEuclid: Construct.
ScaledBytesFvExtractor - Class in com.chemaxon.descriptors.common.unguarded.impl.extractors: Extract scaled byte [] representation from ScaledBytesFloatVectorDescriptorImpl.
ScaledBytesFvExtractor(int, Object) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledBytesFvExtractor: Construct.
ScaledBytesFvTanimoto - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv: Unguarded tanimoto-like comparator for non-negative float[] vectors.
ScaledBytesFvTanimoto() - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvTanimoto
ScaledFvDescriptor - Interface in com.chemaxon.descriptors.common.realvector: Scaled float vector descriptor supports toData to retrieve compact binary representation.
ScaledFvDescriptorFactory - Interface in com.chemaxon.descriptors.common.realvector: ScaledFvDescriptorFactory encapsulates creation of descriptors from float/byte arrays.
ScaledFvDescriptorGenerator - Interface in com.chemaxon.descriptors.common.realvector: Scaled descriptor generator.
scaledMax(double) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder: Set upper bound for coordinate values used by fixed point backed representation.
scaledMin(double) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder: Set lower bound for coordinate values used by fixed point backed representation.
ScaledShortsFloatVectorDescriptor - Class in com.chemaxon.descriptors.common.realvector: Float vector descriptor implementation over scaled shorts.
ScaledShortsFloatVectorDescriptor(float[], ScaledFvDescriptorGenerator, int) - Constructor for class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor: Construct.
ScaledShortsFloatVectorDescriptor(byte[], ScaledFvDescriptorGenerator, int) - Constructor for class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor: Construct.
ScaledShortsFvCoparisonContextFactory - Class in com.chemaxon.descriptors.common.comparison.impl: Comparison context factory for scaled shorts backed float vector descriptors.
ScaledShortsFvCoparisonContextFactory(LinearScaler, int, DescriptorSerializer<FloatVectorDescriptor>) - Constructor for class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory: Instantiate.
ScaledShortsFvEuclid - Class in com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv: Unguarded euclidean comparator for scaled short[] backed float vector descriptors.
ScaledShortsFvEuclid(LinearScaler, int) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv.ScaledShortsFvEuclid: Construct.
ScaledShortsFvExtractor - Class in com.chemaxon.descriptors.common.unguarded.impl.extractors: Extract scaled short [] representation from ScaledShortsFloatVectorDescriptor.
ScaledShortsFvExtractor(int, Object) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledShortsFvExtractor: Construct.
ScoredExtension(RgDefiniton.EnumeratedExtension, BitSet, int, int, int) - Constructor for class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton.ScoredExtension
scoreExtensions(List<RgDefiniton.EnumeratedExtension>) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton
screen3d() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory: 3D alignment based shape descriptor context with default parameters.
screen3d(Set<String>) - Static method in class com.chemaxon.overlap.ParameterizedContextFactory: Parameterized context for screen3d.
screen3dr() - Static method in class com.chemaxon.overlap.OverlapAnalysisContextFactory: Distance range assisted 3D alignment based shape descriptor context with default parameters.
screen3dr(Set<String>) - Static method in class com.chemaxon.overlap.ParameterizedContextFactory: Parameterized context for screen3d.
SdfPropertyExtractor<T> - Class in com.chemaxon.overlap.cli.util.prop.impl: Extractor for SDF properties.
SdfPropertyExtractorFactory - Class in com.chemaxon.overlap.cli.util.prop.impl: Extractor factory for SdfPropertyExtractor.
SdfPropertyExtractorFactory() - Constructor for class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractorFactory
SdfSegmenter - Class in com.chemaxon.calculations.io.formats
SdfSegmenter() - Constructor for class com.chemaxon.calculations.io.formats.SdfSegmenter
SearchStorage - Class in com.chemaxon.overlap.cli: Search serialized descriptors storage.
SearchStorage.SearchMode - Enum in com.chemaxon.overlap.cli: Search mode.
SearchStorageParameters - Class in com.chemaxon.overlap.cli: Command line arguments for SearchStorage.
SearchStorageParameters() - Constructor for class com.chemaxon.overlap.cli.SearchStorageParameters
SearchStorageStat - Class in com.chemaxon.overlap.cli: Statistics for SearchStorage execution.
SearchStorageStat() - Constructor for class com.chemaxon.overlap.cli.SearchStorageStat
searchtime - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionResult: Search time in ms.
searchtime - Variable in class com.chemaxon.overlap.wui.dto.MoleculeInfo: Elapsed time in milliseconds.
searchtime - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsResult: Search time in ms.
searchtime - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarsSearchResult: Search time in ms.
SecondToken - Class in com.chemaxon.overlap.splits: Return the second token.
SecondToken() - Constructor for class com.chemaxon.overlap.splits.SecondToken
seekableFileOutput(String) - Method in interface com.chemaxon.calculations.util.CmdlineContext: Open a seekable file for writing.
seekableFileOutput(String) - Method in class com.chemaxon.calculations.util.DefaultCmdlineContext
SeekableFileOutput - Interface in com.chemaxon.calculations.util: Represents an OutputStream which can seek.
Segmenter - Interface in com.chemaxon.calculations.io: Represents the composition of text based representation format.
SEGMENTER_FORMATS - Static variable in class com.chemaxon.calculations.io.Segmenters: Available segmenter formats.
Segmenters - Class in com.chemaxon.calculations.io: Utilities.
segments(Iterator<String>) - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
segments(Iterator<String>) - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
segments(Iterator<String>) - Method in interface com.chemaxon.calculations.io.Segmenter: Enumerate multi line segments of the input structure.
segmentsFunction() - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
segmentsFunction() - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
segmentsFunction() - Method in interface com.chemaxon.calculations.io.Segmenter: Function to transform input lines to segments.
selectedsWithMultipleUnselectedLigands() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder: List selected atoms resulting in forbidden configuration.
selectInstance(Class<T>, String) - Static method in class com.chemaxon.apidiscovery.Discovery: Look up an instance by its short name.
selectXmlFragment(Document, String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.XmlUtils
self - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: true when self overlap results are represented.
SelfKnnFilter - Interface in com.chemaxon.overlap.servlets: Server side filter for self knn results.
SelfKnnFilterImpl - Class in com.chemaxon.overlap.servlets: Implementation for filter.
SelfKnnFilterImpl(Predicate<Double>, Predicate<Double>, Predicate<Double>, Predicate<Double>, Predicate<Double>) - Constructor for class com.chemaxon.overlap.servlets.SelfKnnFilterImpl
SelfKnnFilters - Class in com.chemaxon.overlap.servlets: Utilities for filters.
SelfOverlap(OverlapAnalysisContext<D, T>, UnguardedPagedOverlap<T>, IndexProjector, MasterMoleculeStorage, MasterStorage<String>, KnnResults) - Constructor for class com.chemaxon.overlap.cli.CalculateSelfOverlap.SelfOverlap: Construct data object.
SelfOverlapGui - Class in com.chemaxon.overlap.wui: Main class of overlap analysis examination tools.
SelfOverlapGuiContext - Class in com.chemaxon.overlap.wui: "Mega" context for self overlap gui.
SelfOverlapGuiContext(ExecutorService, CalculateSelfOverlap.SelfOverlap, String) - Constructor for class com.chemaxon.overlap.wui.SelfOverlapGuiContext: Construct.
SelfOverlapGuiParmateres - Class in com.chemaxon.overlap.wui: Command line arguments for standalone jetty.
SelfOverlapGuiParmateres() - Constructor for class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
SelfOverlapServlet - Class in com.chemaxon.overlap.servlets
SelfOverlapServlet() - Constructor for class com.chemaxon.overlap.servlets.SelfOverlapServlet
SEPARATOR - Static variable in class com.chemaxon.overlap.cli.util.prop.CliParam
SequentialIdGenerator - Class in com.chemaxon.overlap.util.idgenerator: example: P0000, P0001...
SequentialIdGenerator(String, int) - Constructor for class com.chemaxon.overlap.util.idgenerator.SequentialIdGenerator
SequentialIdGenerator() - Constructor for class com.chemaxon.overlap.util.idgenerator.SequentialIdGenerator
SerializableFunction<F,T> - Interface in com.chemaxon.descriptors.common.reflect: Aggregate Serializable to make anonymous serializable definitions possible.
SerializableInvocationHandler - Interface in com.chemaxon.descriptors.common.reflect: Aggregate Serializable to make anonymous serializable definitions possible.
SerializationUtil - Class in com.chemaxon.overlap.persistence.serialization: Utility for serialization.
serialize() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl: Deprecated.
Use BinaryVectorDescriptorImpl.getFpAsBytes()
serialize() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl: Create serialized byte array representation.
serialize(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.CompactStringStorage: Write into serialized format.
serialize(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl: Write into serialized format.
serialize(T, ObjectOutputStream, SubProgressObserver) - Method in interface com.chemaxon.overlap.persistence.serialization.Serializer: Create custom serialization.
serialize(CompactStringStorage, ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.persistence.storage.CompactStringStorageSerialization
serialize(MasterMoleculeStorageImpl, ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.persistence.storage.MasterMoleculeStorageSerialization
Serializer<T> - Interface in com.chemaxon.overlap.persistence.serialization: Serializer can write an object to an OOS.
serializerIsEqualWith(DescriptorSerializer) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
serializerIsEqualWith(DescriptorSerializer) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
serializerIsEqualWith(DescriptorSerializer) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer
serializerIsEqualWith(DescriptorSerializer) - Method in interface com.chemaxon.descriptors.common.DescriptorSerializer: Check strict equivalence of serializers.
serializerIsEqualWith(DescriptorSerializer) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
serializerIsEqualWith(DescriptorSerializer) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
SerializeTask<D extends Descriptor> - Class in com.chemaxon.overlap.storage: Task to serialize a bunch of descriptors into Strings.
SerializeTask(DescriptorGenerator<D>, List<D>) - Constructor for class com.chemaxon.overlap.storage.SerializeTask: Construct new task.
SerializingComparisonContextFactory<DC extends DescriptorComparator<D>,D extends Descriptor> - Class in com.chemaxon.descriptors.common.comparison.impl: Factory for serializing unguarded contexts.
SerializingComparisonContextFactory(DescriptorSerializer<D>, DC) - Constructor for class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory: Construct.
SerializingUnguardedDissimilarityCalculator - Class in com.chemaxon.descriptors.common.unguarded.impl.calc: Unguarded calculator exposing DescriptorComparator.
SerializingUnguardedDissimilarityCalculator(DescriptorComparator<?>) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.calc.SerializingUnguardedDissimilarityCalculator: Construct.
SerializingUnguardedExtractor<T extends Descriptor> - Class in com.chemaxon.descriptors.common.unguarded.impl.extractors: Extractor using DescriptorSerializer.toByteArray(com.chemaxon.descriptors.common.Descriptor) and DescriptorSerializer.fromByteArray(byte[]) serialization mechanism.
SerializingUnguardedExtractor(DescriptorSerializer<T>) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.extractors.SerializingUnguardedExtractor: Construct.
ServerFeature - Enum in com.chemaxon.overlap.wui.context.features: Feature flags (toggles) for MadFast embedded server.
serverStartTimeMs - Variable in class com.chemaxon.overlap.wui.dto.LoadingStatusDto: Startup time stamp of the server.
serverStartTimeMs - Variable in class com.chemaxon.overlap.wui.dto.StatisticsDto: Startup time stamp of the server.
Service() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl.Service
ServiceUtil - Class in com.chemaxon.apidiscovery.util: Utility class to ease service location.
set(Row, Column<T>, T) - Method in interface com.chemaxon.calculations.util.cellfield.CellField: Set a cell.
set(Row, T) - Method in interface com.chemaxon.calculations.util.cellfield.Column: Set a row.
set(Row, Column<T>, T) - Method in class com.chemaxon.calculations.util.cellfield.impl.CellFieldImpl
set(Row, T) - Method in class com.chemaxon.calculations.util.cellfield.impl.ColumnImpl
set(Column<T>, T) - Method in class com.chemaxon.calculations.util.cellfield.impl.RowImpl
set(Column<T>, T) - Method in interface com.chemaxon.calculations.util.cellfield.Row: Set data in a specific column.
set(Column<T>, T) - Method in interface com.chemaxon.calculations.util.cellfield.RowBuilder: Set column value.
set(int, int, SubPane) - Method in class com.chemaxon.overlap.cli.util.images.GridPane: Set a cell.
set(int, int, int, int, SubPane) - Method in class com.chemaxon.overlap.cli.util.images.GridPane: Set a rowspan/coplspan cell.
set(int, int, double) - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder
setAllowedOrigins(String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Set allowed origins.
setAttribute(String, Object) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLogFactory
setBooleanValue(boolean) - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Set value of a boolean field.
setClusterLevel(int, double) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder: Set the level of a specific cluster.
setClusterPreferredLevel(int, double) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Set cluster level of preferred level assigner.
setClusterRepresentant(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Set cluster representant ID.
setColor(String) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
setColor(String) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer: Set color.
setDeserializer(Class<T>, ProgressiveDeserializer<T>) - Method in interface com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerialization: Specify deserializer to reconstruct the storage.
setDeserializer(Class<T>, ProgressiveDeserializer<T>) - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializationImpl
setDoubleValue(double) - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Set value of a double field.
setExecutorService(ExecutorService) - Method in class com.chemaxon.overlap.wui.context.Contexts: Set executor service to use.
setFeatureConfig(FeatureConfig) - Static method in class com.chemaxon.overlap.wui.context.features.FeatureConfigProvider: Set config.
setFontHeight(int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
setFontHeight(int, double) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
setFontHeight(int) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer: Set a suitable font size for a specific pixel height.
setFontHeight(int, double) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer: Set a suitable font size for a specific pixel height.
setIntValue(int) - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Set int value of a int field.
setLeafLevel(int, double) - Method in class com.chemaxon.clustering.common.IDBasedAssignerBuilder: Set the level of a specific leaf node.
setLeafPreferredLevel(int, double) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Set leaf level of preferred level assigner.
setLevel(double) - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec: Set level.
setLongValue(long) - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Set long value of a long field.
setMasterStorageCounsumer(Consumer<MasterStorage>) - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
setMaxQueueSize(int) - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean: Set new max queue size parameter.
setPageSize(int) - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean: Set new page size.
setProgressiveSerialization(ProgressiveSerialization) - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
setQueryId(int, String) - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder
setRepresentant(int) - Method in interface com.chemaxon.clustering.common.IDBasedClusterBuilderSpec: Set representant.
setRGB(int, int, int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer
setRGB(int, int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Renderer: Set RGB color.
sets - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetsInfo: List of available molecule sets.
setStringValue(String) - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Set String value of a String field.
setTargetId(int, String) - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder
setTp(int) - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres
setTp(int) - Method in class com.chemaxon.overlap.wui.SelfOverlapGuiParmateres
setValue(Object) - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Set value.
setx(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
sety(int) - Method in class com.chemaxon.overlap.cli.util.images.Px2d
Severity - Enum in com.chemaxon.calculations.logging.moleculeawarelog: Log levels.
sgc - Variable in class com.chemaxon.virtuallib.sc.cli.ConvertGroupParameters
Shape - Class in com.chemaxon.descriptors.alignment.shape
Shape(ShapeData, ShapeGenerator) - Constructor for class com.chemaxon.descriptors.alignment.shape.Shape
ShapeComparator<T extends ShapeDescriptor> - Interface in com.chemaxon.descriptors.alignment
ShapeComparatorException - Exception in com.chemaxon.descriptors.alignment
ShapeComparatorException(Throwable) - Constructor for exception com.chemaxon.descriptors.alignment.ShapeComparatorException
ShapeComparatorParameter - Class in com.chemaxon.descriptors.alignment.shape
ShapeComparatorParameter() - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter
ShapeComparatorParameter.Builder - Class in com.chemaxon.descriptors.alignment.shape
ShapeComparisonResult - Interface in com.chemaxon.descriptors.alignment: Flexible alignment based shape descriptor calculation
ShapeDescriptor - Interface in com.chemaxon.descriptors.alignment
shapeFunction(ShapeFunction) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter.Builder
shapeFunction(ShapeFunction) - Method in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter.Builder
ShapeFunction - Enum in com.chemaxon.descriptors.alignment
ShapeGenerator - Class in com.chemaxon.descriptors.alignment.shape
ShapeGenerator(ShapeGeneratorParameter) - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeGenerator
ShapeGeneratorException - Exception in com.chemaxon.descriptors.alignment
ShapeGeneratorException(Throwable) - Constructor for exception com.chemaxon.descriptors.alignment.ShapeGeneratorException
ShapeGeneratorParameter - Class in com.chemaxon.descriptors.alignment.shape
ShapeGeneratorParameter(ShapeGeneratorParameter.Builder) - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter
ShapeGeneratorParameter() - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeGeneratorParameter
ShapeGeneratorParameter.Builder - Class in com.chemaxon.descriptors.alignment.shape
ShapeIntersectionComparator - Class in com.chemaxon.descriptors.alignment.shape
ShapeIntersectionComparator(ShapeGenerator, ShapeComparatorParameter) - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeIntersectionComparator
ShapeMetrics - Enum in com.chemaxon.descriptors.alignment
ShapeTanimotoComparator - Class in com.chemaxon.descriptors.alignment.shape
ShapeTanimotoComparator(ShapeGenerator, ShapeComparatorParameter) - Constructor for class com.chemaxon.descriptors.alignment.shape.ShapeTanimotoComparator
shortDiffSumToDouble(long) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler: Scale the sum of differences of shorts into double.
shortDiffSumToDouble(long) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
shortDomainToDouble(double) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler: Scale short domain representation to the original.
shortDomainToDouble(double) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
shortsFromBytes(byte[], int) - Static method in class com.chemaxon.descriptors.common.realvector.Util: Pack bytes to shorts.
shortSqrDiffSumToDouble(long) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler: Scale the square sum of differences of shorts into double.
shortSqrDiffSumToDouble(long) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
shortsToFloats(short[]) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler: Map LinearScaler.shortToFloat(short) to an array.
shortsToFloats(short[]) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
shortToFloat(short) - Method in interface com.chemaxon.descriptors.common.realvector.LinearScaler: Scale short representation to float.
shortToFloat(short) - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
shrink(int) - Method in interface com.chemaxon.overlap.cli.util.images.Area: Shrink.
shrink(int) - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
shrinkMoleculeArea(int) - Method in class com.chemaxon.overlap.cli.util.images.DrawMoleculeToRenderer: Shrink molecule area.
SimilarityResult - Interface in com.chemaxon.overlap.result: SimilarityResult is a simple wrapper for a single structure in a similarity query based result.
SimilarityResultImpl - Class in com.chemaxon.overlap.result.impl: Similarity result implementation.
SimilarityResultImpl(int, double) - Constructor for class com.chemaxon.overlap.result.impl.SimilarityResultImpl: Construct.
SimilarityResults - Interface in com.chemaxon.overlap.result: Results of similarity calculations.
SimilarityResultsImpl - Class in com.chemaxon.overlap.result.impl: Arrays of primitives backed implementation of SimilarityResults.
SimilarityResultsImpl(int[], int[], double[]) - Constructor for class com.chemaxon.overlap.result.impl.SimilarityResultsImpl: Construct.
SimpleComparisonResult - Class in com.chemaxon.descriptors.common.binary: Simple data object for comparison results.
SimpleComparisonResult(double, double) - Constructor for class com.chemaxon.descriptors.common.binary.SimpleComparisonResult: Create a result object.
SimpleDescribedResource<T extends Described> - Class in com.chemaxon.overlap.wui.res: Simple dto implementation of DescribedResource.
SimpleDescribedResource(T, ResourceInfo, String, String) - Constructor for class com.chemaxon.overlap.wui.res.SimpleDescribedResource
SimpleDfsVisitor - Interface in com.chemaxon.clustering.util: Simple DFS traversal visitor.
SimpleErrorHandling - Enum in com.chemaxon.calculations.io: Error handling preference.
SimpleFrameworkAssociation<T> - Class in com.chemaxon.clustering.framework: Simple implementation of FrameworkIndex with retrieval.
SimpleFrameworkAssociation() - Constructor for class com.chemaxon.clustering.framework.SimpleFrameworkAssociation: Construct.
simplePane(int, int, Paint) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRendering
simplePane(int, int) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRendering
simplePane(int, int, Halign, Valign, Paint) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRendering
simplePane(int, int, Halign, Valign) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRendering
SimplePane - Class in com.chemaxon.overlap.cli.util.images: Simple pane.
SimplePane(Supplier<AreaSpec>, Paint) - Constructor for class com.chemaxon.overlap.cli.util.images.SimplePane: Construct.
SimplePane(int, int, Halign, Valign, Paint) - Constructor for class com.chemaxon.overlap.cli.util.images.SimplePane: Construct.
SimplePane(int, int, Halign, Valign) - Constructor for class com.chemaxon.overlap.cli.util.images.SimplePane: Construct.
SimplePane(int, int) - Constructor for class com.chemaxon.overlap.cli.util.images.SimplePane: Construct.
simplePane(int, int, Paint) - Method in interface com.chemaxon.overlap.cli.util.images.SimplePaneFactory: Delegate to SimplePane.SimplePane(int, int).
simplePane(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.SimplePaneFactory: Delegate to SimplePane.SimplePane(int, int).
simplePane(int, int, Halign, Valign, Paint) - Method in interface com.chemaxon.overlap.cli.util.images.SimplePaneFactory: Delegate to SimplePane.SimplePane(int, int, com.chemaxon.overlap.cli.util.images.Halign, com.chemaxon.overlap.cli.util.images.Valign).
simplePane(int, int, Halign, Valign) - Method in interface com.chemaxon.overlap.cli.util.images.SimplePaneFactory: Delegate to SimplePane.SimplePane(int, int, com.chemaxon.overlap.cli.util.images.Halign, com.chemaxon.overlap.cli.util.images.Valign).
SimplePaneFactory - Interface in com.chemaxon.overlap.cli.util.images: Create areas which can be layed out.
SimplePartialResultHolder<R> - Class in com.chemaxon.overlap.partialresult: Simple implementation that just holds the value.
SimplePartialResultHolder() - Constructor for class com.chemaxon.overlap.partialresult.SimplePartialResultHolder
simpleSingleLinkageClustering(DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.singlelinkage.SingleLinkage: Single linkage clustering implementation.
SingleArgumentTransformingInvocationHandler - Class in com.chemaxon.descriptors.common.reflect: Forward single argument invocation to a function.
SingleArgumentTransformingInvocationHandler(Function) - Constructor for class com.chemaxon.descriptors.common.reflect.SingleArgumentTransformingInvocationHandler: Construct.
SingleLevelClustering<T,C extends Cluster<T>> - Interface in com.chemaxon.clustering.common: A grouping of structures into disjunct groups.
SingleLinkage - Class in com.chemaxon.clustering.singlelinkage: Single linkage similarity clustering algorithm.
SingleLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.SingleLinkage
SingleMethodForwardingInvocationHandler - Class in com.chemaxon.descriptors.common.reflect: Forward methods to an implementation.
SingleMethodForwardingInvocationHandler(Object, Method) - Constructor for class com.chemaxon.descriptors.common.reflect.SingleMethodForwardingInvocationHandler: Construct.
SingleThreadDescriptorGenerator - Class in com.chemaxon.descriptors.alternates.cli: Single threaded descriptor generator to cross-check multi threaded descriptor generator.
SingleThreadDescriptorGenerator.IDLOC - Enum in com.chemaxon.descriptors.alternates.cli: Location of ID relative to the descriptor String.
SingleThreadDescriptorGenerator.IDSEPCHAR - Enum in com.chemaxon.descriptors.alternates.cli
SingleThreadDescriptorGenerator.IDSRC - Enum in com.chemaxon.descriptors.alternates.cli: Source of IDs.
SingleThreadedDescriptorGeneratorParameters - Class in com.chemaxon.descriptors.alternates.cli: Command line parameters from SingleThreadDescriptorGenerator tool.
SingleThreadedDescriptorGeneratorParameters() - Constructor for class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorParameters
SingleThreadedDescriptorGeneratorStat - Class in com.chemaxon.descriptors.alternates.cli: Statistics for SingleThreadDescriptorGenerator.
SingleThreadedDescriptorGeneratorStat() - Constructor for class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat
Sink<T> - Interface in com.chemaxon.calculations.io: Deprecated.
Use Consumer instead.
size() - Method in interface com.chemaxon.calculations.io.MemoizedSparseCollection: Collected items count.
size() - Method in class com.chemaxon.calculations.io.MemoizingIterator
size() - Method in interface com.chemaxon.clustering.common.DissimilarityInput: Item count to be considered.
size() - Method in class com.chemaxon.clustering.common.MolInputBuilder: Added structure count.
size() - Method in class com.chemaxon.clustering.common.MolInputImpl
size() - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity: Total number of descriptors stored.
size() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds: Get represented descriptor count.
size() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols: Get represented descriptor count.
size() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Size.
size() - Method in interface com.chemaxon.overlap.cli.util.images.Range: Size.
size() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
size() - Method in class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
size() - Method in class com.chemaxon.overlap.io.CompactStringStorage
size() - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
size() - Method in interface com.chemaxon.overlap.io.MasterStorage: Number of structures in the storage.
size() - Method in class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl
size() - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage: Stored descriptor count.
size() - Method in interface com.chemaxon.overlap.storage.UnguardedPagedStorage: Total number of descriptors stored.
size - Variable in class com.chemaxon.overlap.wui.dto.DescriptorInfo: Descriptors count.
size - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalRawFileInfo: Content size in bytes.
size - Variable in class com.chemaxon.overlap.wui.dto.GridInfo: Row count.
size - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo: Size of the molecule set.
size - Variable in class com.chemaxon.overlap.wui.dto.SizeInfoDetailDto: Represented approximate size in bytes.
size - Variable in class com.chemaxon.overlap.wui.dto.SizeInfoDto: Represented approximate size in bytes.
size() - Method in class com.chemaxon.overlap.wui.res.MolsRes: Size of storages.
size() - Method in class com.chemaxon.screen.Column
size() - Method in interface com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroup: Size of this attachment group.
size() - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
sizedescription - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
SizeInfoDetailDto - Class in com.chemaxon.overlap.wui.dto: Detail of a size info.
SizeInfoDetailDto() - Constructor for class com.chemaxon.overlap.wui.dto.SizeInfoDetailDto
SizeInfoDto - Class in com.chemaxon.overlap.wui.dto: Hierarchic description of the approximate memory allocation.
SizeInfoDto() - Constructor for class com.chemaxon.overlap.wui.dto.SizeInfoDto: Constrcut.
SizeInfoMethod - Enum in com.chemaxon.overlap.wui.dto: Method to use for size info calculation.
sizes - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
skip(long) - Method in class com.chemaxon.overlap.cli.util.pipeline.InputStreamStatCollector
skipChildTraversal(IDBasedHierarchicCluster, int) - Method in interface com.chemaxon.clustering.util.PostOrderDfsVisitor: Decide if a cluster's children should be traversed.
sleep(long) - Static method in class com.chemaxon.screen.Utils: Sleeps for millis, ignoring interrupts.
SlowlyDeserializingMms - Class in com.chemaxon.overlap.wui: Test tool to write a trivial slowly loading molecule storage.
SlowlyDeserializingMms() - Constructor for class com.chemaxon.overlap.wui.SlowlyDeserializingMms
SlowUnguardedComparator<T> - Class in com.chemaxon.overlap.wui: Diagnostic tool to introduce slow execution speed to similarity search.
SlowUnguardedComparator(UnguardedDissimilarityCalculator<T>, long) - Constructor for class com.chemaxon.overlap.wui.SlowUnguardedComparator
SmaInterpreter - Class in com.chemaxon.descriptors.fingerprints.maccs: Deal with some recursive SMARTS strings which are not correctly imported yet.
SmaInterpreter() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.SmaInterpreter
SmaPieces - Class in com.chemaxon.descriptors.fingerprints.maccs.cli
SmaPieces(String) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.cli.SmaPieces: This constructor is solely for debugging purposes, no testing is needed.
smiles - Variable in class com.chemaxon.overlap.wui.dto.MoleculeInfo: Molecule SMILES source or null when absent.
SmilesMemoizingMoleculeIterator - Class in com.chemaxon.calculations.io: A CloseableIterator of Molecules providing memoization of SMILES representation of returned structures.
SmilesMemoizingMoleculeIterator(CloseableIterator<Molecule>, Function<Molecule, String>, Consumer<Exception>) - Constructor for class com.chemaxon.calculations.io.SmilesMemoizingMoleculeIterator: Construct.
SmilesSegmenter - Class in com.chemaxon.calculations.io.formats
SmilesSegmenter() - Constructor for class com.chemaxon.calculations.io.formats.SmilesSegmenter
socketStopper(int, String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Create a socket based server stopper.
source - Variable in class com.chemaxon.overlap.cli.PipelineRunner.Connection
sourceFromString(String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.XmlUtils
sources - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalAddMoleculesRequest: Molecule sources.
sout - Variable in class com.chemaxon.virtuallib.sc.cli.ParseSdfParameters
south(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Area
sparseCompression(FvParameters.SparseCompression) - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder: Set compression of sparse vectors.
SphereExclusion - Class in com.chemaxon.clustering.sphex: Core functionality related to sphere exclusion clustering.
sphexCentroids(double, int, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion: Identify SphereExclusion clustering based centroids for a given set.
sphexClassify(int[], DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion: Classify input items into clusters determined by nearest centroids.
split(String) - Static method in class com.chemaxon.calculations.util.CharLayout: Split to lines.
split(String) - Method in class com.chemaxon.overlap.cli.CalculateOverlapParameters.NoSplitter
split(String) - Method in class com.chemaxon.overlap.cli.MadfastImportParameters.NoSplitter
split(String) - Method in class com.chemaxon.overlap.wui.RealTimeSeaarchGuiParmateres.NoSplitter
SplitObserver - Class in com.chemaxon.calculations.common: Observer that delegates calls to two given observer.
Splitting - Class in com.chemaxon.overlap.cli.util.importing: Utility class for String splitting in CLI tools.
src - Variable in class com.chemaxon.overlap.wui.dto.ConversionResult: Source structure.
src_it - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
src_s - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
ssl(String, String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Specify keystore for ssl connections.
standardize(Molecule) - Method in class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk
standardize(Molecule) - Method in class com.chemaxon.clustering.framework.RemoveSidechainsSc
standardize(Molecule) - Method in interface com.chemaxon.overlap.io.StandardizerWrapper: Invoke represented transformation.
standardizer(StandardizerWrapper) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Update standardizer.
STANDARDIZER_DEFAULTAROMA_CONFIG_XML - Static variable in class com.chemaxon.overlap.OverlapAnalysisContextFactory: Standardizer configuration XML for default aromatization.
StandardizerWrapper - Interface in com.chemaxon.overlap.io: Wrap Standardizer for the similarity subsystem.
StandardizerWrappers - Class in com.chemaxon.overlap.io: Provide utility methods for StandardizerWrapper.
start() - Method in class com.chemaxon.overlap.service.task.Task: Sets Task.startTimeMs to current time
start - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropRange: Molecule index of the first element in the MoleculePropRange.values array.
start() - Method in class com.chemaxon.screen.desktop.JettyStarter: Configure and start server, register socket listening stopper if specified.
start(String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Configure and start server, register socket listening stopper if specified.
startBlocking(String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Start server in blocking mode.
startBlockingWithBrowse(String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Start server and try to launch browser.
starter(int, String) - Static method in class com.chemaxon.screen.desktop.JettyStarter: Default starter.
startTime - Variable in class com.chemaxon.calculations.common.TimerStatistics: Start time from System.currentTimeMillis().
startTime - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Start time.
startTime - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Start time.
startTime - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
startTime - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Start time.
startTime - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
startTime - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Start time.
startTimeMs - Variable in class com.chemaxon.overlap.wui.dto.TaskDto: Start time or null.
StartupHandler - Class in com.chemaxon.overlap.wui: Handles startup process of server, by maintaining tasks, observers.
StartupHandler() - Constructor for class com.chemaxon.overlap.wui.StartupHandler
startWithBrowse(String) - Method in class com.chemaxon.screen.desktop.JettyStarter: Configure and start server, register socket listening stopper if specified.
stat - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
stat - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
stat - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
statGcFinal - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
statGcFinal - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
statGcFinal - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
statGcInitial - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters
statGcInitial - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
statGcInitial - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
StatisticsDto - Class in com.chemaxon.overlap.wui.dto: Various statistics for the embedded server.
StatisticsDto() - Constructor for class com.chemaxon.overlap.wui.dto.StatisticsDto
StatisticsResource - Class in com.chemaxon.overlap.wui.resources: Simple server statistics.
StatisticsResource() - Constructor for class com.chemaxon.overlap.wui.resources.StatisticsResource
StatPO - Class in com.chemaxon.calculations.common: SubProgressObserver implementation which provides statistics.
StatPO(String) - Constructor for class com.chemaxon.calculations.common.StatPO: Construct.
StatPO(String, CancelObserver) - Constructor for class com.chemaxon.calculations.common.StatPO: Construct.
statProf(Class<ST>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationSpec: Specify execution statistics type.
StatRes - Class in com.chemaxon.overlap.wui.res: Implementation for statistics result JSONs.
StatRes(String, long) - Constructor for class com.chemaxon.overlap.wui.res.StatRes: Construct.
StatResResource - Class in com.chemaxon.overlap.wui.resources: Execution statistics collection resource.
StatResResource() - Constructor for class com.chemaxon.overlap.wui.resources.StatResResource
stats(boolean) - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
stats(boolean) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
stats(boolean) - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
Status - Annotation Type in com.chemaxon.overlap.wui.application: See http://stackoverflow.com/questions/4687271/jax-rs-how-to-return-json-and-http-status-code-together for source
statusClass - Variable in class com.chemaxon.overlap.wui.dto.ErrorReport: HTTP status class.
statusCode - Variable in class com.chemaxon.overlap.wui.dto.ErrorReport: HTTP status code of the response.
StatusFilter - Class in com.chemaxon.overlap.wui.application: See http://stackoverflow.com/questions/4687271/jax-rs-how-to-return-json-and-http-status-code-together for source
StatusFilter() - Constructor for class com.chemaxon.overlap.wui.application.StatusFilter
statusReasonPhrase - Variable in class com.chemaxon.overlap.wui.dto.ErrorReport: HTTP status reason phrase.
step - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
stop() - Method in class com.chemaxon.calculations.common.Timer: Stop.
stop() - Method in interface com.chemaxon.screen.desktop.JettyStarter.ServerWrapper: Stop server.
stopTime - Variable in class com.chemaxon.calculations.common.TimerStatistics: Stop time from System.currentTimeMillis().
stopTime - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Stop time.
stopTime - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Stop time.
stopTime - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
stopTime - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Stop time.
stopTime - Variable in class com.chemaxon.overlap.cli.MadfastImportStat
stopTime - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Stop time.
storageBuilderForType(Class<T>) - Static method in class com.chemaxon.overlap.cli.util.prop.PropertyExtractors: Create a storage builder for an extracted type.
strictEquals(MU.BondList) - Method in class com.chemaxon.calculations.util.MU.BondList
stringFormat(BvParameters.StringFormat) - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder: Set String format.
stringFromLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Read the contents of a location into a String.
stringFromLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Read the contents of a location into a String.
stringFromNullableLocation(String, boolean) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Read the contents of a location when it is not null.
stringFromNullableLocation(String) - Static method in class com.chemaxon.calculations.util.CmdlineUtils: Read the contents of a location when it is not null.
Stringpoint(String) - Constructor for class com.chemaxon.overlap.cli.util.Strings.Stringpoint: Create instance pointing to the begining.
stringProp(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor
Strings - Class in com.chemaxon.overlap.cli.util: String utilities.
Strings.Stringpoint - Class in com.chemaxon.overlap.cli.util: A pointer in a String.
StringScatterPlot() - Constructor for class com.chemaxon.clustering.util.Util.StringScatterPlot: Construct an empty scatter plot.
stringTerm(String, boolean) - Static method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor
StructureRecord - Interface in com.chemaxon.calculations.io: Encapsulate structure input parsing.
StructureRecord - Interface in com.chemaxon.overlap.io: Wraps an imported molecule.
StructureRecordIterator - Class in com.chemaxon.overlap.io: Class encapsulating MRecordReader.
StructureRecordIterator(InputStream, String) - Constructor for class com.chemaxon.overlap.io.StructureRecordIterator: New instance.
StructureRecordIterators - Class in com.chemaxon.calculations.io: Utilities for structure record handling.
StructureRecords - Class in com.chemaxon.calculations.io: Utilities for structure record handling.
submit(Supplier<R>) - Method in class com.chemaxon.overlap.service.async.AsyncCallService: Submit a call.
submit(Function<ProgressObserver, R>) - Method in class com.chemaxon.overlap.service.async.AsyncCallService: Submit a call that uses ProgressObserver (created by this method).
submitWithPartialResults(Function<ExecutionMonitoring<R>, R>) - Method in class com.chemaxon.overlap.service.async.AsyncCallService
SubPane - Interface in com.chemaxon.overlap.cli.util.images: Represents a drawing are which is a subject of layout.
SubProgressObserver - Interface in com.chemaxon.calculations.common: Deprecated.
Use ProgressObserver instead. Will be removed.
subTask(String, long) - Method in class com.chemaxon.calculations.common.ConsolePO
subTask(String, long) - Method in class com.chemaxon.calculations.common.ListenableObserver
subTask(String, long) - Method in class com.chemaxon.calculations.common.NoOverflowAutoDoneProgressObserver
subTask(String, long) - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
subTask(String, long) - Method in interface com.chemaxon.calculations.common.ProgressObserver: Deprecated.
Will be removed.
subTask(String, long) - Method in class com.chemaxon.calculations.common.SplitObserver
subTask(String, long) - Method in class com.chemaxon.calculations.common.StatPO
superTask - Variable in class com.chemaxon.overlap.wui.dto.LoadingStatusDto: Task that represents the whole loading process.
suppliesNull(Runnable) - Static method in class com.chemaxon.screen.Utils: Turns your method to a null supplier.
switchToDeterminate(long) - Method in class com.chemaxon.calculations.common.ConsolePO
switchToDeterminate(long) - Method in class com.chemaxon.calculations.common.ListenableObserver
switchToDeterminate(long) - Method in class com.chemaxon.calculations.common.NoOverflowAutoDoneProgressObserver
switchToDeterminate(long) - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
switchToDeterminate(long) - Method in interface com.chemaxon.calculations.common.ProgressObserver: Notifies that the remaining amount of work units to complete this task is known.
switchToDeterminate(long) - Method in class com.chemaxon.calculations.common.SplitObserver
switchToDeterminate(long) - Method in class com.chemaxon.calculations.common.StatPO
sx() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Horizontal size.
sx - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane: Width of last layed out position.
sx() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
sy() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Vertical size.
sy - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane: Height of last layed out position.
sy() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
symbol - Variable in class com.chemaxon.overlap.wui.dto.PmapperFeature: Symbol of the feature.
systemLoadAverage - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: System load average.
systemLoadAverage - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: System load average.

T

t - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
take() - Method in class com.chemaxon.overlap.partialresult.OneKeeperPartialResultHolder
take() - Method in interface com.chemaxon.overlap.partialresult.PartialResultProvider: Takes partial result if exists.
take() - Method in class com.chemaxon.overlap.partialresult.SimplePartialResultHolder
tanimotoBytes(byte[]) - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl: Tanimoto.
tanimotoShorts(LinearScaler, short[], short[]) - Static method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor: Tanimoto.
target - Variable in class com.chemaxon.overlap.cli.PipelineRunner.Connection
targetCount - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Size of created descriptor storage.
targetCount - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat
targetCount - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Size of created master molecule storage.
targetCount - Variable in class com.chemaxon.overlap.cli.MadfastImportStat: Processed structure count.
targetCount - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Number of targets.
targetcount - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityDistributionResult: Searched target count.
targetcount - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsResult: Searched target count.
targetcount - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarsSearchResult: Searched target count.
targetid - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityTargetInfo: ID string of the target molecule or null.
targetids - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabelEntry: Textual ID of each neighbors.
targetIdsFontsize - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
targetIdsLength - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
targetimageurl - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityTargetInfo: Url of the target molecule as a png image.
targetindex - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityTargetInfo: Index of the target molecule.
targetindexproj - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Index projector used for targets.
targetLabelHeight - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
targetLabelText - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
targetmolecules - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Description of target molecules.
targetmolindices - Variable in class com.chemaxon.overlap.wui.dto.KnnTableLabelEntry: Index of the neighbors in the targets molecule table.
targetmolurl - Variable in class com.chemaxon.overlap.wui.dto.DissimilarityTargetInfo: Url of the target molecule.
targets - Variable in class com.chemaxon.overlap.wui.dto.KnnData: Matching target indices.
targets - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsResult: List of most similar targets.
targets - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarsSearchResult: List of most similar targets.
Task - Class in com.chemaxon.overlap.service.task: Task.endTimeMs automatically set when observable is done.
Task(String, String, ProgressObservable) - Constructor for class com.chemaxon.overlap.service.task.Task
task - Variable in class com.chemaxon.overlap.wui.dto.AsyncCallDto: Status of the underlying task.
TaskDto - Class in com.chemaxon.overlap.wui.dto: Task status.
TaskDto() - Constructor for class com.chemaxon.overlap.wui.dto.TaskDto
TaskNotDeletableException(String) - Constructor for exception com.chemaxon.overlap.service.task.TaskService.TaskNotDeletableException
TaskNotFoundException(String) - Constructor for exception com.chemaxon.overlap.service.task.TaskService.TaskNotFoundException
TaskPresenter - Class in com.chemaxon.overlap.presenter
TaskPresenter() - Constructor for class com.chemaxon.overlap.presenter.TaskPresenter
tasks - Variable in class com.chemaxon.overlap.wui.dto.LoadingStatusDto: Tasks of loading process.
TaskService - Class in com.chemaxon.overlap.service.task
TaskService() - Constructor for class com.chemaxon.overlap.service.task.TaskService
TaskService.TaskNotDeletableException - Exception in com.chemaxon.overlap.service.task
TaskService.TaskNotFoundException - Exception in com.chemaxon.overlap.service.task
text(String, boolean, int, double, int, int, Halign, Valign, Halign, Valign) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRendering
text(String, boolean, int, double, int, int, Halign, Valign, Halign, Valign) - Method in interface com.chemaxon.overlap.cli.util.images.SimplePaneFactory: Add a text which is rendered upon #layout(com.chemaxon.overlap.cli.util.images.SubPane).
TextFileInput - Class in com.chemaxon.overlap.cli.util.pipeline: Read contents from a file.
TextFileInput() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
TextFileInput(String) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
TextFileOutput - Class in com.chemaxon.overlap.cli.util.pipeline: Write contents to a text file.
TextFileOutput() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
TextFileOutput(String) - Constructor for class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
textTableBuilder() - Static method in class com.chemaxon.overlap.cli.util.Strings
TextTableBuilder - Interface in com.chemaxon.overlap.cli.util: Simple text based table formatter.
ThreadLocalizedEcfpParameters - Class in com.chemaxon.descriptors.fingerprints.ecfp: Parameters class for ThreadLocalizedEcfpGenerator.
ThreadLocalizedEcfpParameters(ThreadLocalizedEcfpParameters.Builder) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters: Parametrize from a builder.
ThreadLocalizedEcfpParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters: Construct with default parametrization.
ThreadLocalizedEcfpParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.ecfp: Parameters builder class for ThreadLocalizedEcfpParameters.
ThreadLocalizedEcfpParameters.ConstructThreadLocalizedEcfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.ecfp: Interface representing ECFP generator constructor.
ThreadLocalizedPfParameters - Class in com.chemaxon.descriptors.fingerprints.pf2d: Parameters class for ThreadLocalizedPfGenerator.
ThreadLocalizedPfParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters: Constructor using the default settings.
ThreadLocalizedPfParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.pf2d: Builder class for the immutable parameter object.
ThreadLocalizedPfParameters.ConstructThreadLocalizedPfGenerator - Interface in com.chemaxon.descriptors.fingerprints.pf2d: Interface representing PF generator constructor.
throwingUnsupportedOperationException(Class<T>, String) - Static method in class com.chemaxon.descriptors.common.reflect.Reflect: Proxy throwing UnsupportedOperationException for all invocations.
throwingUnsupportedOperationExceptionGuarded(Class<T>, Object, String) - Static method in class com.chemaxon.descriptors.common.reflect.Reflect: Proxy throwing UnsupportedOperationException for all invocations except guard object check.
time - Variable in class com.chemaxon.overlap.wui.dto.DescriptorInfo: Associated elapsed time in milliseconds.
time - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalRawFileInfo: Associated elapsed time in milliseconds.
time - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: Associated elapsed time in milliseconds.
time - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo: Associated elapsed time in milliseconds.
timeoutCanceller(long) - Static method in class com.chemaxon.calculations.common.ProgressObservers: Returns a cancel observer which cancels after a specified timeout.
Timer - Class in com.chemaxon.calculations.common: Simple timer to measure elapsed times, invocation counts.
Timer(String) - Constructor for class com.chemaxon.calculations.common.Timer: Construct started timer.
TimerStatistics - Class in com.chemaxon.calculations.common: Detailed statistics of a Timer.
TimerStatistics(String, long, long, long) - Constructor for class com.chemaxon.calculations.common.TimerStatistics: Construct.
times - Variable in class com.chemaxon.overlap.wui.dto.ResourceClassInfoDto
timestamp - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: System time snapshot.
timestamp - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: System time snapshot.
timestatBuildStorage - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Statistics for building phase.
timestatBuildStorage - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Statistics for building phase.
timestatBuildStorage - Variable in class com.chemaxon.overlap.cli.MadfastImportStat: Statistics for building phase.
timestatDeserializeStorage - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for deserialization phase.
timestatDissimilarityDistributionCalculation - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for dissimilarity distribution searching phase.
timestatGenerateQueryDescriptors - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for query descriptor generating.
timestatGenerateTargetDescriptors - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for target descriptor generating.
timestatImportQueries - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat: Statistics for query importing.
timestatImportQueryDescriptors - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for query descriptor import.
timestatImportTargetDescriptors - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for target descriptor import.
timestatImportTargets - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat: Statistics for target importing.
timestatOut - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat: Statistics for output.
timestatPrintResults - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for result printout phase.
timestatProcess - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Statistics for building phase.
timestatSearch - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat: Statistics for searching.
timestatSearchStorage - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Statistics for searching phase.
timestatSerializeProperies - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Statistics for serialization of collected properties.
timestatSerializeStorage - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Statistics for serialization phase.
timestatSerializeStorage - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Statistics for serialization of master molecule storage.
timestatSerializeStorage - Variable in class com.chemaxon.overlap.cli.MadfastImportStat: Statistics for serialization phase.
titleHeight - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
titleText - Variable in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
tmolsurl - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: URL of target molecules.
to(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.Connect
toBase64EncMol(Molecule) - Static method in class com.chemaxon.screen.Utils: Convert molecule to Base64 image representation.
toBinaryString() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl: Converts the fingerprint into a binary string containing '0' and '1' characters without further delimiters.
toBinaryString() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor: Convert the fingerprint into a binary string.
toByteArray(D) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
toByteArray() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShape
toByteArray(DRShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
toByteArray() - Method in class com.chemaxon.descriptors.alignment.shape.Shape
toByteArray() - Method in interface com.chemaxon.descriptors.alignment.ShapeDescriptor
toByteArray(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer
toByteArray(B) - Method in interface com.chemaxon.descriptors.common.DescriptorSerializer: Creates the byte array representation of a descriptor object.
toByteArray() - Method in class com.chemaxon.descriptors.common.realvector.ScaledBytesFloatVectorDescriptorImpl
toByteArray() - Method in interface com.chemaxon.descriptors.common.realvector.ScaledFvDescriptor: Create byte array serialized form.
toByteArray() - Method in class com.chemaxon.descriptors.common.realvector.ScaledShortsFloatVectorDescriptor
toByteArray(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
toByteArray(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
toBytes(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage: Deprecated.
Use PagedDescriptorStorage.toBytes(java.io.ObjectOutputStream, com.chemaxon.calculations.common.SubProgressObserver, long) with a sound reset interval.
toBytes(ObjectOutputStream, SubProgressObserver, long) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage: Dump descriptors to a binary file.
toCommaSepString(CellField, Column<?>...) - Static method in class com.chemaxon.calculations.util.cellfield.CellFields: Create comma separated Strings.
toCommaSepStringAll(CellField) - Static method in class com.chemaxon.calculations.util.cellfield.CellFields: Create multiline comma sep string from all column.
toCxBinFormat(String, String, String) - Method in class com.chemaxon.overlap.wui.resources.MolConverter: Convert a molecule using MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String).
toCxBinFormatPost(String, String, String) - Method in class com.chemaxon.overlap.wui.resources.MolConverter: Convert a molecule using MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String).
toCxFormat(String, String, String) - Method in class com.chemaxon.overlap.wui.resources.MolConverter: Convert a molecule using MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String).
toCxFormatPost(String, String, String) - Method in class com.chemaxon.overlap.wui.resources.MolConverter: Convert a molecule using MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String).
toCxSmiles() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag: Return CxSmiles format.
toDecimalString() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl: Deprecated.
Use BinaryVectorDescriptorImpl.toIntDecimalString()
toDecimalString() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorImpl: Converts the fingerprints float array representation into a tab separated string.
toDetailedString(IDBasedSingleLevelClustering) - Static method in class com.chemaxon.clustering.common.IDBasedClusterBuilder: Utility method to create a detailed string representation of a clustering.
toDetailedString() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Create a detailed multiline String representation of the builder state.
toDetailedString(IDBasedHierarchicClustering) - Static method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler: Utility method to create a detailed string representation of a clustering.
toDTO(AsyncCall<?>) - Method in class com.chemaxon.overlap.presenter.AsyncCallPresenter: with partial result
toDTO(AsyncCall<?>, boolean) - Method in class com.chemaxon.overlap.presenter.AsyncCallPresenter
toDTO(T) - Method in class com.chemaxon.overlap.presenter.TaskPresenter
toHistogramString() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFP: Converts the fingerprint into a human readable string.
toHistogramString() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PharmacophoreFPImpl: Converts the fingerprint into a readable string.
toHumanReadableTimeUnit(double) - Static method in class com.chemaxon.calculations.common.Timer: Format to nicely interpretable time unit.
toIecBinaryUnits(long) - Static method in class com.chemaxon.calculations.common.Timer: Format memory units.
toIntDecimalString() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
toIntDecimalString() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor: Converts the fingerprints integer array representation into a tab separated string.
toJsonMixed(IDBasedHierarchicClustering) - Static method in class com.chemaxon.clustering.util.Util: Provide a JSON-like representation for Web GUI widget display.
ToLinenote() - Constructor for class com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory.ToLinenote
ToLinenote() - Constructor for class com.chemaxon.descriptors.metrics.FloatVectorMetricFactory.ToLinenote
ToLinenote() - Constructor for class com.chemaxon.descriptors.metrics.MetricFactory.ToLinenote
ToLines - Class in com.chemaxon.overlap.cli.util.pipeline: Supply individual lines from an input.
ToLines() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.ToLines
toListOfMap(List<Column>) - Static method in class com.chemaxon.screen.Utils: Conversion function.
toLongDecimalString() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
toLongDecimalString() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor: Converts the fingerprints long array representation into a tab separated string.
toMultiline(String, int) - Static method in class com.chemaxon.overlap.cli.util.Strings: Split into multiple lines.
toMultilineString(IDBasedHierarchicClustering, String) - Static method in class com.chemaxon.clustering.util.Util
toMultilineString() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds: Print details to a multiline String.
toMultilineString() - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols: Print details to a multiline String.
toMultilineString() - Method in class com.chemaxon.overlap.persistence.storage.DescriptorContainer: Create detailed multi line human readable String description.
tool - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Name of tool.
tool - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Name of tool.
tool - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat: Name of tool.
tool - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Name of tool.
tool - Variable in class com.chemaxon.overlap.cli.MadfastImportStat: Name of tool.
tool - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Name of tool.
toResponse(JsonMappingException) - Method in class com.chemaxon.overlap.wui.resources.exceptions.JacksonJsonMappingExceptionMapper
toResponse(JsonParseException) - Method in class com.chemaxon.overlap.wui.resources.exceptions.JacksonJsonParseExceptionMapper
toResponse(UnrecognizedPropertyException) - Method in class com.chemaxon.overlap.wui.resources.exceptions.JacksonUnrecognizedPropertyExceptionMapper
toResponse(Exception) - Method in class com.chemaxon.overlap.wui.resources.exceptions.WuiExceptionMapper
ToSdfs - Class in com.chemaxon.overlap.cli.util.pipeline
ToSdfs() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.ToSdfs
toSiPrefixedString(long) - Static method in class com.chemaxon.calculations.common.Timer: Format nicely with SI unit prefixes.
toSmiles(Molecule) - Static method in class com.chemaxon.calculations.util.MU: Convert molecule to SMILES.
toString(T) - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Convert value to String representation.
toString() - Method in class com.chemaxon.calculations.common.ConsolePO
toString(boolean) - Method in class com.chemaxon.calculations.common.Timer
toString() - Method in class com.chemaxon.calculations.common.Timer
toString() - Method in class com.chemaxon.calculations.io.formats.SdfSegmenter
toString() - Method in class com.chemaxon.calculations.io.formats.SmilesSegmenter
toString(List<String>) - Static method in class com.chemaxon.calculations.util.CharLayout: Collapse into a multiline String.
toString(String[]) - Static method in class com.chemaxon.calculations.util.CharLayout: Collapse into a multiline String.
toString(int, boolean) - Method in class com.chemaxon.calculations.util.Histo
toString() - Method in class com.chemaxon.calculations.util.Histo
toString() - Method in class com.chemaxon.calculations.util.MU.BondList
toString() - Method in class com.chemaxon.calculations.util.V3D
toString() - Method in class com.chemaxon.clustering.framework.RemoveSidechainsMolwalk
toString() - Method in class com.chemaxon.clustering.framework.RemoveSidechainsSc
toString(int, int, boolean, boolean) - Method in class com.chemaxon.clustering.util.Util.StringScatterPlot: Create a multiline representation of the given plot.
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.SingleLinkage
toString() - Method in class com.chemaxon.clustering.wards.LanceWilliamsMerges.Wards
toString(D) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
toString() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
toString() - Method in class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
toString() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeComparatorParameter
toString(DRShapeDescriptor) - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
toString() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeGenerator
toString() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeHistogramComparator
toString() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeIntersectionComparator
toString() - Method in class com.chemaxon.descriptors.alignment.drshape.DRShapeTanimotoComparator
toString() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeComparatorParameter
toString() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeIntersectionComparator
toString() - Method in class com.chemaxon.descriptors.alignment.shape.ShapeTanimotoComparator
toString() - Method in class com.chemaxon.descriptors.alternates.CfpBsWrapper
toString() - Method in class com.chemaxon.descriptors.alternates.CfpDsWrapper
toString() - Method in class com.chemaxon.descriptors.alternates.EcfpBsWrapper
toString() - Method in class com.chemaxon.descriptors.alternates.EcfpDsWrapper
toString() - Method in class com.chemaxon.descriptors.alternates.Maccs166BinaryString
toString() - Method in class com.chemaxon.descriptors.alternates.Pf2dWrapper
toString() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
toString() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorImpl
toString(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorSerializer
toString() - Method in class com.chemaxon.descriptors.common.binary.SimpleComparisonResult
toString() - Method in class com.chemaxon.descriptors.common.comparison.impl.BinaryLongComparisonContextFactory
toString() - Method in class com.chemaxon.descriptors.common.comparison.impl.ComparisonContextImpl
toString() - Method in class com.chemaxon.descriptors.common.comparison.impl.FloatsComparisonContextFactory
toString() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledBytesFvComparisonContextFactory
toString() - Method in class com.chemaxon.descriptors.common.comparison.impl.ScaledShortsFvCoparisonContextFactory
toString() - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
toString(B) - Method in interface com.chemaxon.descriptors.common.DescriptorSerializer: Creates the String representation of a descriptor object.
toString() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
toString() - Method in class com.chemaxon.descriptors.common.realvector.LinearScalerImpl
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpart
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongCommonpartNormalized
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongDice
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclidean
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongEuclideanNormalized
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattan
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongManhattanNormalized
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongPetke
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongSimpson
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTanimoto
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.binarylong.BinaryLongTversky
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclid
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsEuclidSqr
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsManhattan
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsMaxDiff
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTanimoto
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.floats.FloatsTversky
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvEuclid
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledbytesfv.ScaledBytesFvTanimoto
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.scaledshortsfv.ScaledShortsFvEuclid
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.calc.SerializingUnguardedDissimilarityCalculator
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.BinaryLongFpExtractor
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.FloatsExtractor
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledBytesFvExtractor
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.ScaledShortsFvExtractor
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.extractors.SerializingUnguardedExtractor
toString() - Method in class com.chemaxon.descriptors.common.unguarded.impl.UnguardedContextImpl
toString() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
toString() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
toString() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.ThreadLocalizedEcfpParameters
toString() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
toString() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters
toString() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
toString(BinaryVectorDescriptor) - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
toString() - Method in class com.chemaxon.descriptors.vectors.binary.BvGeneratorImpl
toString() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters
toString(FloatVectorDescriptor) - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
toString() - Method in class com.chemaxon.descriptors.vectors.floats.FvGeneratorImpl
toString() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters
toString(DescriptorSerializer, Descriptor) - Method in enum com.chemaxon.overlap.cli.DumpStorage.DescOutFormat: Create string representation.
toString() - Method in class com.chemaxon.overlap.cli.util.images.Px2d
toString() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.CloneCxnMolecule
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.Connect
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolExporter
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.CxnFormatsMolImporter
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.GetMoleculeName
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.GetSdfProperty
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.Mark
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.ProgressiveSerializeToFile
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileInput
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.TextFileOutput
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.ToLines
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.ToSdfs
toString() - Method in class com.chemaxon.overlap.cli.util.pipeline.TransformMolecule
toString() - Method in class com.chemaxon.overlap.cli.util.prop.CliParam
toString() - Method in class com.chemaxon.overlap.cli.util.prop.impl.ChemTermPropertyExtractor
toString() - Method in class com.chemaxon.overlap.cli.util.prop.impl.MolnamePropertyExtractor
toString() - Method in class com.chemaxon.overlap.cli.util.prop.impl.SdfPropertyExtractor
toString() - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder
toString(boolean) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Create String representation.
toString() - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext
toString() - Method in class com.chemaxon.overlap.io.CompactStringStorage
toString() - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
toString() - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback
toString() - Method in class com.chemaxon.overlap.io.PropertyCollectorCallback
toString() - Method in class com.chemaxon.overlap.result.impl.FixedKnnResultsImpl
toString() - Method in class com.chemaxon.overlap.result.impl.IndexedKnnResultsImpl
toString() - Method in class com.chemaxon.overlap.result.impl.SimilarityResultImpl
toString() - Method in class com.chemaxon.overlap.result.impl.SimilarityResultsImpl
toString() - Method in class com.chemaxon.overlap.servlets.ScalarFilter
toString() - Method in class com.chemaxon.overlap.servlets.SelfKnnFilterImpl
toString() - Method in class com.chemaxon.overlap.splits.AllButFirstToken
toString() - Method in class com.chemaxon.overlap.splits.FirstToken
toString() - Method in class com.chemaxon.overlap.splits.Identity
toString() - Method in class com.chemaxon.overlap.splits.SecondToken
toString() - Method in class com.chemaxon.overlap.wui.res.MoleculeContainerImpl
toString() - Method in class com.chemaxon.overlap.wui.SlowUnguardedComparator
toString() - Method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment
toString() - Method in interface com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroup
toString(boolean, String) - Method in interface com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroup: Create String representation.
toString(boolean, String) - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
toString() - Method in class com.chemaxon.virtuallib.sc.model.sdf.AttachmentGroupImpl
toString(boolean) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton: Details into human readable String.
toString() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgDefiniton
toString(boolean) - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag: Details into human readable String.
toString() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag
toString(boolean) - Method in class com.chemaxon.virtuallib.sc.model.sdf.Scaffold: Details into human readable String.
toString() - Method in class com.chemaxon.virtuallib.sc.model.sdf.Scaffold
toString(boolean) - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension: Details into human readable String.
toString() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension
toString() - Method in class com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtensionBuilder
toStringRepresentation() - Method in class com.chemaxon.apidiscovery.ParameterWrapper: Create String representation of the represented value.
toStrings(int, boolean) - Method in class com.chemaxon.calculations.util.Histo: Create a String representation.
toStrings() - Method in class com.chemaxon.calculations.util.Histo
ToStrings - Class in com.chemaxon.calculations.util: IO related utilities.
toStrings() - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder: Create multi line representation.
toStrings(List<String>) - Method in interface com.chemaxon.overlap.cli.util.TextTableBuilder: Create multi line representation.
toStrings(PrintStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback: Print index to name associations into escaped strings.
toStrings(PrintStream, SubProgressObserver) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage: Write String representations to a PrintStream.
toStrings(PrintStream, SubProgressObserver, ExecutorService) - Method in class com.chemaxon.overlap.storage.PagedDescriptorStorage: Write String representations to a PrintStream using concurrent conversions.
toTabSepString(CellField, Column<?>...) - Static method in class com.chemaxon.calculations.util.cellfield.CellFields: Create multiline tab sep Strings.
toTabSepStringAll(CellField) - Static method in class com.chemaxon.calculations.util.cellfield.CellFields: Create multiline tab sep string from all column.
totalCollectionCount - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Sum of collection counts.
totalCollectionCount - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Sum of collection counts.
totalCollectionTime - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Sum of collection times.
totalCollectionTime - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Sum of collection times.
totalCompilationTime - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot: Total compilation time.
totalCompilationTime - Variable in class com.chemaxon.overlap.wui.dto.ProfSnapshotDto: Total compilation time.
totalcount - Variable in class com.chemaxon.overlap.wui.dto.Histogram: Total items count.
totaldescriptorcount - Variable in class com.chemaxon.overlap.wui.dto.StatisticsDto: Total number of descriptors exposed.
totalMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat: Total memory.
totalmoleculecount - Variable in class com.chemaxon.overlap.wui.dto.StatisticsDto: Total number of molecules exposed.
totalWork - Variable in class com.chemaxon.overlap.wui.dto.TaskDto: Total work units (optional).
tp - Variable in class com.chemaxon.overlap.cli.CalculateOverlapParameters: Thread pool size.
tp - Variable in class com.chemaxon.overlap.cli.CreateMmsParameters
tp - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters: Thread pool size.
trace(Object) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
trace(Object, Throwable) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
transform(Function<T, U>) - Method in interface com.chemaxon.calculations.io.CloseableIterator: Apply a transformation of the elements of this Iterator.
transform(CloseableIterator<T>, Function<T, U>) - Static method in class com.chemaxon.calculations.io.CloseableIterators: Deprecated.
CloseableIterator.transform(java.util.function.Function) provides default method making this utility not necessary
transform(Function<U, T>) - Method in interface com.chemaxon.calculations.io.CloseableSink: Create a transformation of this sink.
transform(CloseableSink<T>, Function<S, T>) - Static method in class com.chemaxon.calculations.io.CloseableSinks: Create sink accepting transformed representation.
transform(Function<T, R>) - Method in interface com.chemaxon.overlap.partialresult.PartialResultConsumer: Decorates this PartialResultConsumer with a type conversion.
transform(IntListSet) - Method in class com.chemaxon.virtuallib.sc.model.sdf.Attachment: Transform attachment for molecule subset selection.
transformedResult(Function<T, R>) - Method in class com.chemaxon.overlap.service.task.ExecutionMonitoring
TransformMolecule - Class in com.chemaxon.overlap.cli.util.pipeline: Standardize-like Molecule transformation.
TransformMolecule() - Constructor for class com.chemaxon.overlap.cli.util.pipeline.TransformMolecule
transformMolecule(Molecule) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Transform molecule according to the represented context.
TransformMolecule.Method - Enum in com.chemaxon.overlap.cli.util.pipeline
transformMolecules(List<Molecule>, SubProgressObserver) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Transform molecules according to the represented context.
transformPage(Function<D, T>, List<D>) - Static method in class com.chemaxon.overlap.unguarded.Unguardeds: Transform a page of descriptors to unguarded form.
transformReturnValueWith(Function) - Method in class com.chemaxon.descriptors.common.reflect.SingleMethodForwardingInvocationHandler: Apply a transformation on the return value.
transformWith(Function) - Static method in class com.chemaxon.descriptors.common.reflect.SingleArgumentTransformingInvocationHandler: Convenience factory function.
translate(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Area: Translate.
translate(Px2d) - Method in interface com.chemaxon.overlap.cli.util.images.Area: Translate.
translate(int) - Method in interface com.chemaxon.overlap.cli.util.images.Range
translate(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Range
translate(Px2d) - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
translate(int, int) - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
traverse(UnguardedVisitor<T>, SubProgressObserver) - Method in class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl
traverse(UnguardedVisitor<T>, SubProgressObserver) - Method in interface com.chemaxon.overlap.storage.UnguardedPagedStorage: Traverse storage on single thread.
traversePostOrderDFS(PostOrderDfsVisitor<T>, IDBasedHierarchicClustering) - Static method in class com.chemaxon.clustering.util.Util: Invoke recursive DFS post order traversal on a hierarchy.
traverseSimpleDfs(IDBasedHierarchicClustering, SimpleDfsVisitor, SimpleDfsVisitor) - Static method in class com.chemaxon.clustering.util.Util: Simple DFS traversal.
traverseSimplePostOrderDfs(IDBasedHierarchicClustering, SimpleDfsVisitor) - Static method in class com.chemaxon.clustering.util.Util: Simple postorder DFS traversal.
traverseSimplePreOrderDfs(IDBasedHierarchicClustering, SimpleDfsVisitor) - Static method in class com.chemaxon.clustering.util.Util: Simple preorder DFS traversal.
trg - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
TverskyParameters - Class in com.chemaxon.descriptors.metrics: Parameters for Tversky index.
TverskyParameters(TverskyParameters.Builder) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters: Instantiate with builder's actual state.
TverskyParameters() - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters: Instantiate with default values.
TverskyParameters(double, double) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters: Instantiate with weights.
TverskyParameters.Builder - Class in com.chemaxon.descriptors.metrics: Builder for parameter object.
type - Variable in class com.chemaxon.overlap.cli.PipelineRunner.Connection
type - Variable in class com.chemaxon.overlap.cli.PipelineRunner.IO
type - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryPool
type(String) - Method in class com.chemaxon.overlap.cli.util.pipeline.CollectStorage
type - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterDto: Represented parameter type.
type - Variable in class com.chemaxon.overlap.wui.dto.MemoryPoolInfoDto
type - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropInfo: Java data type.

U

U - Class in com.chemaxon.calculations.util: Small utility methods.
unfreeze() - Method in interface com.chemaxon.overlap.concurrent.BppManagerMBean: Unfreeze worker.
unguarded(UnguardedContext<D, N>) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Update represented unguarded layer.
unguarded(UnguardedExtractor<D, N>, UnguardedDissimilarityCalculator<N>) - Method in class com.chemaxon.overlap.context.OverlapAnalysisContext: Update represented unguarded layer.
unguardedComparator() - Method in class com.chemaxon.descriptors.common.unguarded.impl.UnguardedContextImpl
unguardedComparator() - Method in interface com.chemaxon.descriptors.common.unguarded.UnguardedContext: Comparator to compare the unguarded extracted form.
unguardedContext() - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
unguardedContext() - Method in class com.chemaxon.descriptors.common.binary.BinaryVectorDescriptorComparator
unguardedContext() - Method in interface com.chemaxon.descriptors.common.comparison.ComparisonContext: Represented unguarded context.
unguardedContext() - Method in class com.chemaxon.descriptors.common.comparison.impl.ComparisonContextImpl
unguardedContext() - Method in interface com.chemaxon.descriptors.common.DescriptorComparator: Associated unguarded context.
unguardedContext() - Method in class com.chemaxon.descriptors.common.realvector.FloatVectorDescriptorComparator
UnguardedContext<D extends Descriptor,T extends Serializable> - Interface in com.chemaxon.descriptors.common.unguarded: Expose unguarded representations.
unguardedContext() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfComparatorImpl
UnguardedContextImpl<D extends Descriptor,T extends Serializable> - Class in com.chemaxon.descriptors.common.unguarded.impl: Simple implementation of UnguardedContext.
UnguardedContextImpl(UnguardedExtractor<D, T>, UnguardedDissimilarityCalculator<T>) - Constructor for class com.chemaxon.descriptors.common.unguarded.impl.UnguardedContextImpl: Construct.
UnguardedDissimilarityCalculator<T> - Interface in com.chemaxon.descriptors.common.unguarded: Unguarded dissimilarity calculator.
unguardedExtractor() - Method in class com.chemaxon.descriptors.common.unguarded.impl.UnguardedContextImpl
unguardedExtractor() - Method in interface com.chemaxon.descriptors.common.unguarded.UnguardedContext: Extractor to retrieve unguarded form.
UnguardedExtractor<D extends Descriptor,T extends Serializable> - Interface in com.chemaxon.descriptors.common.unguarded: Extract unguarded representation from descriptors.
UnguardedPagedOverlap<T extends Serializable> - Class in com.chemaxon.overlap.bruteforce: Brute force paged similarity search.
UnguardedPagedOverlap(UnguardedDissimilarityCalculator<T>, ImmutableList<ImmutableList<T>>) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap: Construct new immutable reference from prepared storage.
UnguardedPagedOverlap(UnguardedDissimilarityCalculator<T>, ImmutableList<ImmutableList<T>>, int) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap: Deprecated.
Use UnguardedPagedOverlap.UnguardedPagedOverlap(com.chemaxon.descriptors.common.unguarded.UnguardedDissimilarityCalculator, com.google.common.collect.ImmutableList)
UnguardedPagedOverlap(UnguardedDissimilarityCalculator<T>, UnguardedPagedStorage<T>) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap: Construct new immutable reference from prepared storage.
UnguardedPagedOverlap(Function<D, T>, UnguardedDissimilarityCalculator<T>, List<ImmutableList<D>>, List<D>) - Constructor for class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap: Construct new immutable reference from pages of Descriptor instances.
UnguardedPagedStorage<T extends Serializable> - Interface in com.chemaxon.overlap.storage: Page organized storage of unguarded descriptors.
UnguardedPagedStorageImpl<T extends Serializable> - Class in com.chemaxon.overlap.storage.impl: Unguarded paged storage implementation
UnguardedPagedStorageImpl(ImmutableList<ImmutableList<T>>) - Constructor for class com.chemaxon.overlap.storage.impl.UnguardedPagedStorageImpl: Construct new immutable reference from prepared storage.
unguardedQueryDescriptor - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
Unguardeds - Class in com.chemaxon.overlap.unguarded: Utility methods related for unguarded descriptors.
UnguardedVisitor<T> - Interface in com.chemaxon.overlap.unguarded: Simple callback to traverse an unguarded storage.
unitPathAssigner() - Method in interface com.chemaxon.clustering.common.HierarchicClustering: Assigner which consider parent-child edges as unit length.
unitPathAssigner() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicClustering
UnitPathAssigner - Class in com.chemaxon.clustering.common: Assigning unit distance based on path length from leaves/roots.
UnitPathAssigner() - Constructor for class com.chemaxon.clustering.common.UnitPathAssigner
unpackBytesFromInt(int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack four 8 bit bytes from a 32 bit int.
unpackBytesFromInt(int, byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack four 8 bit bytes from a 32 bit int.
unpackBytesFromInts(int[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Unpack array of ints into an array of bytes.
unpackBytesFromLong(long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack eight 8 bit bytes from a 64 bit long.
unpackBytesFromLong(long, byte[], int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack eight 8 bit bytes from a 64 bit long.
unpackBytesFromLongs(long[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Unpack array of longs into an array of bytes.
unpackInt0FromLong(long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack first 32 bit integer from a 64 bit long according to the represented endianness.
unpackInt1FromLong(long) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack second 32 bit integer from a 64 bit long according to the represented endianness.
unpackIntFromBitSet(BitSet, int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack an int value from a BitSet.
unpackIntsFromLongs(long[], BinaryVectors.Endianness) - Static method in class com.chemaxon.descriptors.common.BinaryVectors: Unpack array of longs into an array of ints.
unpackLongFromBitSet(BitSet, int) - Method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Unpack a long value from a BitSet.
updateDefaults() - Method in class com.chemaxon.overlap.cli.util.images.HeatmapRenderingParameters
Updater<D extends Descriptor> - Interface in com.chemaxon.overlap.io: Updater allows the insertion of structures/descriptors to the similarity subsystem.
updateRepresentant(int, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder: Set/update the cluster representant structure.
uptime - Variable in class com.chemaxon.overlap.wui.dto.StatisticsDto: Server uptime in ms.
url - Variable in class com.chemaxon.overlap.wui.dto.DescriptorInfo: URL of the descriptor data.
url - Variable in class com.chemaxon.overlap.wui.dto.ExperimentalRawFileInfo: URL of the raw file content.
url - Variable in class com.chemaxon.overlap.wui.dto.GridInfo: URL of the descriptor data.
url - Variable in class com.chemaxon.overlap.wui.dto.KnnInfo: URL of the knn data.
url - Variable in class com.chemaxon.overlap.wui.dto.MoleculeInfo: URL of the molecule.
url - Variable in class com.chemaxon.overlap.wui.dto.MoleculeSetInfo: URL of the molecule set.
urlOf(T) - Method in class com.chemaxon.overlap.wui.context.Contexts
usage(Supplier<String>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationSpec: Specify usage.
usage(Supplier<String>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationSpec2: Specify usage.
usage - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryPool: Usage of the pool or null when usage not supported.
usage - Variable in class com.chemaxon.overlap.wui.dto.MemoryPoolInfoDto: Usage of the pool or null when usage not supported.
usageUsed - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryPool: Usage of the pool or -1 when usage not supported.
usageUsed - Variable in class com.chemaxon.overlap.wui.dto.MemoryPoolInfoDto: Usage of the pool or -1 when usage not supported.
used - Variable in class com.chemaxon.overlap.cli.prof.ProfSnapshot.MemoryUsageDesc
used - Variable in class com.chemaxon.overlap.wui.dto.MemoryUsageDescDto
usedMemory - Variable in class com.chemaxon.overlap.cli.prof.Memstat: Used memory; difference of totalMemory and freeMemory.
UTF8ENCODING - Static variable in class com.chemaxon.calculations.util.CmdlineUtils: UTF-8 encoding String literal.
Util - Class in com.chemaxon.clustering.util: Clustering related utility methods.
Util - Class in com.chemaxon.descriptors.common.realvector: Utilities related to float vector descriptors.
Util - Class in com.chemaxon.descriptors.db: Utility class for DB import/export implementation.
Util() - Constructor for class com.chemaxon.descriptors.metrics.BinaryVectorComparator.Util
Util - Class in com.chemaxon.overlap.io: IO related utilities.
Util.StringScatterPlot - Class in com.chemaxon.clustering.util: ASCII scatter plot.
Utils - Class in com.chemaxon.descriptors.fingerprints.maccs: Small utilities.
Utils - Class in com.chemaxon.screen: Various utility methods.
UUIDGenerator - Class in com.chemaxon.overlap.util.idgenerator: example: PREFIX-a932185b-4e8f-48ff-8d95-1c924695c065
UUIDGenerator(String) - Constructor for class com.chemaxon.overlap.util.idgenerator.UUIDGenerator

V

v(double, double, double) - Static method in class com.chemaxon.calculations.util.V3D
v(double[]) - Static method in class com.chemaxon.calculations.util.V3D
V3D - Class in com.chemaxon.calculations.util: 3D vector algebra.
valid(String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat: Ensure that guarded context is valid.
validGuardObject(String, Object) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat: Ensure that guard object is valid.
Valign - Enum in com.chemaxon.overlap.cli.util.images: Vertical alignment.
value - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterDto: Parameter default value.
value - Variable in class com.chemaxon.overlap.wui.dto.LinenoteChoiceParameterValueDto: Value (enum constant).
value - Variable in class com.chemaxon.overlap.wui.dto.MoleculeProp: Value of the property.
valueDescriptions() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Description of accepted values.
valueOf(String) - Static method in enum com.chemaxon.apidiscovery.linenote.ChoiceParameterType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.apidiscovery.ParameterSetMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.apidiscovery.ParameterWrapper.ParameterType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.calculations.io.SimpleErrorHandling: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.calculations.logging.moleculeawarelog.Severity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.calculations.util.CharLayout.HA: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.clustering.common.HierarchicClustering.Alignment: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.AtomTyping: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.DRShapeMetrics: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.ShapeFunction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alignment.ShapeMetrics: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator.IDLOC: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator.IDSEPCHAR: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator.IDSRC: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.fingerprints.ecfp.EcfpAtomTypizers: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.metrics.BinaryMetrics: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.metrics.FloatVectorMetrics: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.vectors.binary.BvParameters.StringFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.NumericRepresentation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.SparseCompression: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.cli.DumpStorage.DescOutFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.cli.PipelineRunner.IOType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.cli.SearchStorage.SearchMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.cli.util.images.Align: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.cli.util.images.Halign: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.cli.util.images.Valign: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.cli.util.pipeline.TransformMolecule.Method: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.wui.context.features.ServerFeature: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.chemaxon.overlap.wui.dto.SizeInfoMethod: Returns the enum constant of this type with the specified name.
valueParser() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceParameterDescriptor: Converter for String handling.
values() - Static method in enum com.chemaxon.apidiscovery.linenote.ChoiceParameterType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in interface com.chemaxon.apidiscovery.linenote.ChoiceValueParameterParser: Accepted values.
values() - Static method in enum com.chemaxon.apidiscovery.ParameterSetMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.apidiscovery.ParameterWrapper.ParameterType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.calculations.io.SimpleErrorHandling: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.calculations.logging.moleculeawarelog.Severity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.calculations.util.CharLayout.HA: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.clustering.common.HierarchicClustering.Alignment: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.AtomTyping: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.DRShapeMetrics: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.ShapeFunction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alignment.ShapeMetrics: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator.IDLOC: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator.IDSEPCHAR: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.alternates.cli.SingleThreadDescriptorGenerator.IDSRC: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.common.BinaryVectors.Endianness: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.fingerprints.ecfp.EcfpAtomTypizers: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.metrics.BinaryMetrics: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.metrics.FloatVectorMetrics: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.vectors.binary.BvParameters.StringFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.NumericRepresentation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.descriptors.vectors.floats.FvParameters.SparseCompression: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.cli.DumpStorage.DescOutFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.cli.PipelineRunner.IOType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.cli.SearchStorage.SearchMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.cli.util.images.Align: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.cli.util.images.Halign: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.cli.util.images.Valign: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.cli.util.pipeline.TransformMolecule.Method: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.chemaxon.overlap.wui.context.features.ServerFeature: Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class com.chemaxon.overlap.wui.dto.MoleculePropRange: Value of the property.
values() - Static method in enum com.chemaxon.overlap.wui.dto.SizeInfoMethod: Returns an array containing the constants of this enum type, in the order they are declared.
valueType - Variable in class com.chemaxon.overlap.cli.util.prop.CliParam: Extracted property value type.
varref - Variable in class com.chemaxon.overlap.cli.MadfastImportParameters
vectProd(V3D) - Method in class com.chemaxon.calculations.util.V3D
verbose(String...) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationEnv: Print verbose messages.
verbose(String...) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationEnv2: Print verbose messages.
version - Variable in class com.chemaxon.descriptors.alternates.cli.SingleThreadedDescriptorGeneratorStat: Version info.
version - Variable in class com.chemaxon.overlap.cli.BuildStorageStat: Version info.
version - Variable in class com.chemaxon.overlap.cli.CalculateOverlapStat: Version info.
version - Variable in class com.chemaxon.overlap.cli.CreateMmsStat: Version info.
version - Variable in class com.chemaxon.overlap.cli.MadfastImportStat: Version info.
version - Variable in class com.chemaxon.overlap.cli.SearchStorageStat: Version info.
version - Variable in class com.chemaxon.overlap.wui.dto.StatisticsDto: Version string.
vertical() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Vertical range.
vertical() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
verticalSpec() - Method in interface com.chemaxon.overlap.cli.util.images.AreaSpec: Vertical range specifivation.
VFlowPane - Class in com.chemaxon.overlap.cli.util.images: Basic vertical flow plane.
VFlowPane() - Constructor for class com.chemaxon.overlap.cli.util.images.VFlowPane
visit(IDBasedHierarchicCluster, List<T>, int) - Method in interface com.chemaxon.clustering.util.PostOrderDfsVisitor: Visit a cluster.
visit(List<IDBasedHierarchicCluster>, IDBasedHierarchicCluster) - Method in interface com.chemaxon.clustering.util.SimpleDfsVisitor: Visit cluster.
visitDescriptor(int, T) - Method in interface com.chemaxon.overlap.unguarded.UnguardedVisitor: Visit a single descriptor.
visitDescriptors(int, List<T>) - Method in interface com.chemaxon.overlap.unguarded.UnguardedVisitor: Visit multiple descriptors.

W

w - Variable in class com.chemaxon.overlap.wui.dto.MostSimilarsRequest: Width of the target images in pixel.
w - Variable in class com.chemaxon.overlap.wui.res.search.DescResMostSimilarsSearch.MostSimilarSearchParams
Wards() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.Wards
warn(Object) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
warn(Object, Throwable) - Method in class com.chemaxon.calculations.logging.moleculeawarelog.MoleculeAwareLog
west(int, int) - Method in interface com.chemaxon.overlap.cli.util.images.Area
whenStat(Consumer<ST>) - Method in interface com.chemaxon.overlap.cli.invocation.CliInvocationEnv2: Access execution statistics.
withAdditionalProperties(Map<String, MolProp>) - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols: Represent additional properties.
withAdditionalProperties(Map<String, MolProp>) - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
withComparator(DC) - Method in class com.chemaxon.descriptors.common.comparison.impl.SerializingComparisonContextFactory
withComparator(DescriptorComparator<D>) - Method in class com.chemaxon.overlap.bruteforce.BruteForcePagedSimilarity: Construct another BruteForcePagedSimilarity instance representing a different comparator.
withComparator(UnguardedDissimilarityCalculator<T>) - Method in class com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap: Construct another BruteForcePagedSimilarity instance representing a different comparator.
withComparison(ComparisonContext<?, ?, T>) - Method in class com.chemaxon.overlap.persistence.storage.DescriptorContainer: New instance with a different comparison context.
withErrorHandler(Consumer<Exception>) - Method in class com.chemaxon.clustering.framework.BemisMurckoClustering: Set optional error handler.
withErrorHandler(ErrorHandler<S>) - Method in interface com.chemaxon.overlap.concurrent.OptErrorH: Specify an error handler.
withMetric(String) - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithIds: Use specified metric.
withMetric(String) - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithIdsImpl
withMetric(String) - Method in interface com.chemaxon.overlap.cli.util.DescriptorsWithMols: Use specified metric.
withMetric(String) - Method in class com.chemaxon.overlap.cli.util.DescriptorsWithMolsImpl
worked(long, boolean) - Method in class com.chemaxon.calculations.common.ConsolePO: Report work unit completion.
worked(long) - Method in class com.chemaxon.calculations.common.ConsolePO
worked(long) - Method in class com.chemaxon.calculations.common.ListenableObserver
worked(long) - Method in class com.chemaxon.calculations.common.NoOverflowAutoDoneProgressObserver: Notifies that a given number of work units has been completed.
worked(long) - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
worked(long) - Method in interface com.chemaxon.calculations.common.ProgressObserver: Notifies that a given number of work units has been completed.
worked(long) - Method in class com.chemaxon.calculations.common.SplitObserver
worked(long) - Method in class com.chemaxon.calculations.common.StatPO
worked - Variable in class com.chemaxon.overlap.wui.dto.TaskDto: Number of work units processed.
workUnit(String) - Method in class com.chemaxon.calculations.common.ConsolePO
workUnit(String) - Method in class com.chemaxon.calculations.common.ListenableObserver
workUnit(String) - Method in class com.chemaxon.calculations.common.NoOverflowAutoDoneProgressObserver
workUnit(String) - Method in class com.chemaxon.calculations.common.ObservableProgressObserver
workUnit(String) - Method in interface com.chemaxon.calculations.common.ProgressObserver: Notifies the measure unit of work (such as 'pc', 'file', 'percent', etc).
workUnit(String) - Method in class com.chemaxon.calculations.common.SplitObserver
workUnit(String) - Method in class com.chemaxon.calculations.common.StatPO
workUnit - Variable in class com.chemaxon.overlap.wui.dto.TaskDto: Work unit description (optional).
wrap(Iterator<T>) - Static method in class com.chemaxon.calculations.io.CloseableIterators: Wrap an Iterator into a CloseableIterator.
wrap(Iterator<T>, Closeable) - Static method in class com.chemaxon.calculations.io.CloseableIterators: Compose an Iterator and a Closeable into a CloseableIterator.
wrap(Sink<T>) - Static method in class com.chemaxon.calculations.io.CloseableSinks
wrap(Sink<T>, Closeable) - Static method in class com.chemaxon.calculations.io.CloseableSinks
wrapTransformed(S, Function<? super S, Iterator<T>>) - Static method in class com.chemaxon.calculations.io.CloseableIterators: Make a CloseableIterator from an Iterator resulting from the transformation of a Closeable.
write(OutputStream) - Method in class com.chemaxon.overlap.cli.util.images.HeatmapBuilder: Write image.
write(int) - Method in class com.chemaxon.overlap.cli.util.pipeline.OutputStreamStatCollector
write(byte[]) - Method in class com.chemaxon.overlap.cli.util.pipeline.OutputStreamStatCollector
write(byte[], int, int) - Method in class com.chemaxon.overlap.cli.util.pipeline.OutputStreamStatCollector
write(S, ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.persistence.serialization.AbstractSerialization: Write Deserializer conform representation.
write(T, long, ObjectOutputStream) - Static method in class com.chemaxon.overlap.persistence.serialization.DelegatingDeserializer: Serialize with Deserializer API contracts.
write(PagedDescriptorStorage<?>, long, OverlapAnalysisContext, IndexProjector, ObjectOutputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.persistence.storage.DescriptorContainer: Write byte array based container.
writeCss(CompactStringStorage, ObjectOutputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.persistence.storage.CompactStringStorageSerialization: Write Deserializer conform representation.
writeIndirected(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.AllAbsentMasterMoleculeStorage
writeIndirected(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.CompactStringStorage
writeIndirected(ObjectOutputStream, SubProgressObserver) - Method in class com.chemaxon.overlap.io.MasterMoleculeStorageImpl
writeIndirected(ObjectOutputStream, SubProgressObserver) - Method in interface com.chemaxon.overlap.persistence.serialization.IndirectSerializable: Write Deserializer conform representation.
writeMms(MasterMoleculeStorageImpl, ObjectOutputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.persistence.storage.MasterMoleculeStorageSerialization: Write Deserializer conform representation.
writePlain(T, long, ObjectOutputStream) - Static method in class com.chemaxon.overlap.persistence.serialization.SerializationUtil: Serialize with Deserializer API contracts using standard Java serialization.
writePlain(T, long, ObjectOutputStream, SubProgressObserver) - Static method in class com.chemaxon.overlap.persistence.serialization.SerializationUtil: Serialize with Deserializer API contracts using standard Java serialization.
writePngImage(OutputStream) - Method in class com.chemaxon.overlap.cli.util.images.BufferedImageRenderer: Write image.
wstd - Variable in class com.chemaxon.virtuallib.sc.cli.ParseSdfParameters
WuiBadRequestException - Exception in com.chemaxon.overlap.wui.resources.exceptions: A syntactically valid request could not be understood by the server.
WuiBadRequestException(String) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiBadRequestException
WuiBadRequestException(String, Throwable) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiBadRequestException
WuiException - Exception in com.chemaxon.overlap.wui.resources.exceptions: An exception which is mapped to an ErrorReport to be returned as a REST response in case of an error.
WuiException(String) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiException: Construct with a message.
WuiException(String, Throwable) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiException: Construct with a message and a cause.
WuiExceptionMapper - Class in com.chemaxon.overlap.wui.resources.exceptions: Map WuiException instances to a REST response representing an ErrorReport.
WuiExceptionMapper() - Constructor for class com.chemaxon.overlap.wui.resources.exceptions.WuiExceptionMapper
WuiForbiddenException - Exception in com.chemaxon.overlap.wui.resources.exceptions: The client is forbidden to access a syntactically valid request.
WuiForbiddenException(String) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiForbiddenException
WuiForbiddenException(String, Throwable) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiForbiddenException
WuiInternalServerErrorException - Exception in com.chemaxon.overlap.wui.resources.exceptions: Due to an unexpected condition the request can not be fulfilled.
WuiInternalServerErrorException(String) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiInternalServerErrorException
WuiInternalServerErrorException(String, Throwable) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiInternalServerErrorException
WuiNotFoundException - Exception in com.chemaxon.overlap.wui.resources.exceptions: A resource not found.
WuiNotFoundException(String) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiNotFoundException
WuiNotFoundException(String, Throwable) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiNotFoundException
WuiNotFoundException(Throwable) - Constructor for exception com.chemaxon.overlap.wui.resources.exceptions.WuiNotFoundException: Gets the message from the cause.

X

x - Variable in class com.chemaxon.overlap.cli.util.images.Px2d: X coordinate.
x0() - Method in interface com.chemaxon.overlap.cli.util.images.Area: X coordinate of upper left corner.
x0 - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane: Upper left corner X of last layed out position.
x0() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
x1() - Method in interface com.chemaxon.overlap.cli.util.images.Area: X coordinate of lower right corner (inclusive!).
x1 - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane: Lower right corner X of last layed out position.
x1() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
xmlConfig(String) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder: Sets configuration xml string.
xmlConfig(Optional<String>) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder: Sets configuration xml string.
xmlConfig(String) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder: Sets configuration xml string.
xmlConfig(Optional<String>) - Method in class com.chemaxon.descriptors.fingerprints.pf2d.ThreadLocalizedPfParameters.Builder: Sets configuration xml string.
XmlUtils - Class in com.chemaxon.descriptors.fingerprints.ecfp: Simple XML utilities.
xpathOf(String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.XmlUtils
xsdFromResource(Class<?>, String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.XmlUtils

Y

y - Variable in class com.chemaxon.overlap.cli.util.images.Px2d: Y coordinate.
y0() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Y coordinate of upper left corner.
y0 - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane: Upper left corner Y of last layed out position.
y0() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane
y1() - Method in interface com.chemaxon.overlap.cli.util.images.Area: Y coordinate of lower right corner (inclusive!).
y1 - Variable in class com.chemaxon.overlap.cli.util.images.SimplePane: Lower right corner Y of last layed out position.
y1() - Method in class com.chemaxon.overlap.cli.util.images.SimplePane

Z

zAttachments() - Method in class com.chemaxon.virtuallib.sc.model.sdf.RgFrag: Z attachments.
zero() - Static method in class com.chemaxon.overlap.cli.util.images.Px2d: Zero coordinate.
zero() - Static method in interface com.chemaxon.overlap.cli.util.images.RangeSpec: A zero min sized range spec.

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