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Package Hierarchies:
org.wallerlab.yoink
,
org.wallerlab.yoink.adaptive.config
,
org.wallerlab.yoink.adaptive.smooth
,
org.wallerlab.yoink.adaptive.smooth.smoothfunction
,
org.wallerlab.yoink.api.model.bootstrap
,
org.wallerlab.yoink.api.model.cube
,
org.wallerlab.yoink.api.model.density
,
org.wallerlab.yoink.api.model.molecular
,
org.wallerlab.yoink.api.model.regionizer
,
org.wallerlab.yoink.api.service
,
org.wallerlab.yoink.api.service.adaptive
,
org.wallerlab.yoink.api.service.adaptiveProcessor
,
org.wallerlab.yoink.api.service.bootstrap
,
org.wallerlab.yoink.api.service.cube
,
org.wallerlab.yoink.api.service.math
,
org.wallerlab.yoink.api.service.molecular
,
org.wallerlab.yoink.api.service.regionizer
,
org.wallerlab.yoink.clustering
,
org.wallerlab.yoink.clustering.louvain
,
org.wallerlab.yoink.clustering.utils
,
org.wallerlab.yoink.config
,
org.wallerlab.yoink.cube.domain
,
org.wallerlab.yoink.cube.service
,
org.wallerlab.yoink.density.config
,
org.wallerlab.yoink.density.domain
,
org.wallerlab.yoink.density.service.density
,
org.wallerlab.yoink.density.service.densityProperties
,
org.wallerlab.yoink.domain
,
org.wallerlab.yoink.math.config
,
org.wallerlab.yoink.math.constants
,
org.wallerlab.yoink.math.linear
,
org.wallerlab.yoink.math.map
,
org.wallerlab.yoink.math.set
,
org.wallerlab.yoink.molecular.config
,
org.wallerlab.yoink.molecular.data
,
org.wallerlab.yoink.molecular.domain
,
org.wallerlab.yoink.molecular.service.calculator
,
org.wallerlab.yoink.molecular.service.translator
,
org.wallerlab.yoink.processor.config
,
org.wallerlab.yoink.processor.service
,
org.wallerlab.yoink.processor.service.chem
,
org.wallerlab.yoink.regionizer.config
,
org.wallerlab.yoink.regionizer.domain
,
org.wallerlab.yoink.regionizer.partitioner
,
org.wallerlab.yoink.regionizer.service
,
org.wallerlab.yoink.service
,
org.wallerlab.yoink.service.clustering
,
org.wallerlab.yoink.service.jobbuilder
,
org.wallerlab.yoink.service.processor
,
org.wallerlab.yoink.service.request
,
org.wallerlab.yoink.service.response
Class Hierarchy
java.lang.Object
org.wallerlab.yoink.service.processor.
AbstractAdaptiveQMMMProcessor
<I,O> (implements org.springframework.batch.item.ItemProcessor<I,O>)
org.wallerlab.yoink.service.processor.
AdaptiveQMMMProcessor
org.wallerlab.yoink.service.processor.
FileAdaptiveQMMMProcessor
org.wallerlab.yoink.service.processor.
SerialAdaptiveQMMMProcessor
org.wallerlab.yoink.service.processor.
StringAdaptiveQMMMProcessor
org.wallerlab.yoink.service.processor.
AbstractClusteringProcessor
<I,O> (implements org.springframework.batch.item.ItemProcessor<I,O>)
org.wallerlab.yoink.service.processor.
FileClusteringProcessor
org.wallerlab.yoink.service.processor.
SerialClusteringProcessor
org.wallerlab.yoink.molecular.data.
AbstractJaxbReader
(implements org.wallerlab.yoink.api.service.molecular.
FilesReader
<T,K>)
org.wallerlab.yoink.molecular.data.
JaxbFileReader
org.wallerlab.yoink.molecular.data.
JaxbStringReader
org.wallerlab.yoink.molecular.data.
AbstractJaxbWriter
(implements org.wallerlab.yoink.api.service.molecular.
FilesWriter
<T>)
org.wallerlab.yoink.molecular.data.
JaxbFileWriter
org.wallerlab.yoink.molecular.data.
JaxbStringWriter
org.wallerlab.yoink.service.jobbuilder.
AbstractJobBuilder
<I,O> (implements org.wallerlab.yoink.api.service.bootstrap.
JobBuilder
<I,O>)
org.wallerlab.yoink.service.jobbuilder.
JobFileBuilderImpl
org.wallerlab.yoink.service.jobbuilder.
JobJaxbBuilderImpl
org.wallerlab.yoink.service.jobbuilder.
JobStringBuilderImpl
org.wallerlab.yoink.adaptive.config.
AdaptiveConfig
org.wallerlab.yoink.domain.
AdaptiveQMMMJob
(implements org.wallerlab.yoink.api.model.bootstrap.
Job
<T>)
org.wallerlab.yoink.adaptive.smooth.
AdaptiveQMMMSmoothnerRouter
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.regionizer.service.
AdaptiveRegionizer
(implements org.wallerlab.yoink.api.service.regionizer.
RegionizerComponent
<T,K>)
org.wallerlab.yoink.density.service.density.
AtomDensityCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.density.service.densityProperties.
AtomicDensityPropertiesCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.density.service.density.
AtomicDensityRatioCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.config.
BatchConfig
org.wallerlab.yoink.adaptive.smooth.smoothfunction.
BrooksSmoothFunction
(implements org.wallerlab.yoink.api.service.adaptive.
SmoothFunction
)
org.wallerlab.yoink.processor.service.
BufferAdaptiveProcessor
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.regionizer.service.
BufferRegionizer
(implements org.wallerlab.yoink.api.service.regionizer.
RegionizerComponent
<T,K>)
org.wallerlab.yoink.adaptive.smooth.smoothfunction.
BuloSmoothFunction
(implements org.wallerlab.yoink.api.service.adaptive.
SmoothFunction
)
org.wallerlab.yoink.molecular.service.calculator.
CenterOfMassComputer
(implements org.wallerlab.yoink.api.service.
Computer
<T,K>)
org.wallerlab.yoink.molecular.service.calculator.
ClosestDistanceToMoleculeCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.service.response.
CmlFileResponseWriter
(implements org.springframework.batch.item.ItemWriter<T>)
org.wallerlab.yoink.service.request.
CmlFilesRequest
(implements org.springframework.batch.item.ItemReader<T>)
org.wallerlab.yoink.service.response.
CmlFilesResponse
(implements org.springframework.batch.item.ItemWriter<T>)
org.wallerlab.yoink.math.linear.
CommonsMatrix
(implements org.wallerlab.yoink.api.service.math.
Matrix
<T>)
org.wallerlab.yoink.math.linear.
CommonsVector3D
(implements org.wallerlab.yoink.api.service.math.
Vector
<T>)
org.wallerlab.yoink.processor.service.
ConfigurationAdaptiveProcessor
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.math.constants.
Constants
org.wallerlab.yoink.cube.service.
CoordInCubeCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.cube.service.
CubeBuilderImpl
(implements org.wallerlab.yoink.api.service.cube.
CubeBuilder
<T>)
org.wallerlab.yoink.regionizer.partitioner.
CubePartitioner
(implements org.wallerlab.yoink.api.service.regionizer.
Partitioner
<K,V>)
org.wallerlab.yoink.adaptive.smooth.
DASWeightFactors
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.clustering.
DatabaseService
org.wallerlab.yoink.regionizer.service.
DensityBasedRegionizer
(implements org.wallerlab.yoink.api.service.regionizer.
Regionizer
<T,K>)
org.wallerlab.yoink.density.service.density.
DensityCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.density.config.
DensityConfig
(implements org.springframework.context.ApplicationContextAware)
org.wallerlab.yoink.regionizer.partitioner.
DensityPartitioner
(implements org.wallerlab.yoink.api.service.regionizer.
Partitioner
<K,V>)
org.wallerlab.yoink.density.service.densityProperties.
DensityPropertiesCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.molecular.service.calculator.
DistanceCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.service.
DoriClustering
(implements org.wallerlab.yoink.api.service.bootstrap.
Clustering
)
org.wallerlab.yoink.service.processor.
FileInteractionSetProcessor
(implements org.springframework.batch.item.ItemProcessor<I,O>)
org.wallerlab.yoink.processor.service.
FIRESAdaptiveProcessor
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.adaptive.smooth.
FIRESmoothner
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.regionizer.partitioner.
GridPointAssigner
(implements org.wallerlab.yoink.api.service.cube.
Assigner
<T,K,V>)
org.wallerlab.yoink.processor.service.
HOTSPOTAdaptiveProcessor
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.regionizer.partitioner.
InteractionPartitioner
(implements org.wallerlab.yoink.api.service.regionizer.
Partitioner
<K,V>)
org.wallerlab.yoink.regionizer.partitioner.
DensityOverlapRegionsIndicatorPartitioner
org.wallerlab.yoink.regionizer.partitioner.
SingleExponentialDecayDetectorPartitioner
org.wallerlab.yoink.service.clustering.
InteractionSet
org.wallerlab.yoink.clustering.
InteractionTriple
<T>
org.wallerlab.yoink.service.response.
JmsJobItemWriter
(implements org.springframework.batch.item.ItemWriter<T>)
org.wallerlab.yoink.service.request.
JmsRequestReader
(implements org.springframework.batch.item.ItemReader<T>)
org.wallerlab.yoink.clustering.louvain.
LouvainAlgoImpl
org.wallerlab.yoink.clustering.
LouvainClusteringFacade
<T>
org.wallerlab.yoink.math.map.
MapDifference
org.wallerlab.yoink.math.map.
MapSorter
org.wallerlab.yoink.math.config.
MathConfig
org.wallerlab.yoink.processor.service.chem.
MMProcessor
(implements org.wallerlab.yoink.api.service.adaptiveProcessor.
AdaptiveProcessor
)
org.wallerlab.yoink.molecular.config.
MolecularConfig
(implements org.springframework.context.ApplicationContextAware)
org.wallerlab.yoink.density.service.density.
MolecularDensityRatioCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.molecular.service.translator.
MolecularSystemTranslator
(implements org.wallerlab.yoink.api.service.molecular.
Translator
<T,K>)
org.wallerlab.yoink.adaptive.smooth.smoothfunction.
MorokumaSmoothFunction
(implements org.wallerlab.yoink.api.service.adaptive.
SmoothFunction
)
org.wallerlab.yoink.processor.service.
PAPAdaptiveProcessor
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.regionizer.service.
ParameterRegionizer
(implements org.wallerlab.yoink.api.service.regionizer.
Regionizer
<T,K>)
org.wallerlab.yoink.regionizer.service.
DistanceRegionizer
org.wallerlab.yoink.regionizer.service.
NumberRegionizer
org.wallerlab.yoink.regionizer.service.
SizeConsistentRegionizer
org.wallerlab.yoink.molecular.service.translator.
ParameterTranslator
(implements org.wallerlab.yoink.api.service.molecular.
Translator
<T,K>)
org.wallerlab.yoink.adaptive.smooth.smoothfunction.
PermutedSmoothFunction
(implements org.wallerlab.yoink.api.service.adaptive.
SmoothFunction
)
org.wallerlab.yoink.processor.config.
ProcessorConfig
org.wallerlab.yoink.service.
PropertyWrapper
(implements org.wallerlab.yoink.api.service.bootstrap.
Wrapper
<T>)
org.wallerlab.yoink.processor.service.chem.
QMMMProcessor
(implements org.wallerlab.yoink.api.service.adaptiveProcessor.
AdaptiveProcessor
)
org.wallerlab.yoink.processor.service.chem.
QMProcessor
(implements org.wallerlab.yoink.api.service.adaptiveProcessor.
AdaptiveProcessor
)
org.wallerlab.yoink.molecular.data.
RadialGridReader
(implements org.wallerlab.yoink.api.service.molecular.
FilesReader
<T,K>)
org.wallerlab.yoink.density.service.densityProperties.
ReducedDensityGradientComputer
(implements org.wallerlab.yoink.api.service.
Computer
<T,K>)
org.wallerlab.yoink.regionizer.config.
RegionizerConfig
org.wallerlab.yoink.regionizer.service.
RegionizerService
(implements org.wallerlab.yoink.api.service.regionizer.
RegionizerMath
<T,K>)
org.wallerlab.yoink.adaptive.smooth.
SAPWeightFactors
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.adaptive.smooth.smoothfunction.
SCMPSmoothFunction
(implements org.wallerlab.yoink.api.service.adaptive.
SmoothFunction
)
org.wallerlab.yoink.adaptive.smooth.
SCMPWeightFactors
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.math.set.
SetDifference
org.wallerlab.yoink.density.service.densityProperties.
SilvaDensityComputer
(implements org.wallerlab.yoink.api.service.
Computer
<T,K>)
org.wallerlab.yoink.density.service.densityProperties.
DensityOverlapRegionsIndicatorComputer
org.wallerlab.yoink.density.service.densityProperties.
SingleExponentialDecayDetectorComputer
org.wallerlab.yoink.molecular.domain.
SimpleAtom
(implements org.wallerlab.yoink.api.model.molecular.
Atom
)
org.wallerlab.yoink.molecular.domain.
SimpleCoord
(implements org.wallerlab.yoink.api.model.molecular.
Coord
)
org.wallerlab.yoink.molecular.domain.
SimpleCoordFactory
(implements org.wallerlab.yoink.api.service.
Factory
<T,K>)
org.wallerlab.yoink.cube.domain.
SimpleCube
(implements org.wallerlab.yoink.api.model.cube.
Cube
)
org.wallerlab.yoink.density.domain.
SimpleDensityPoint
(implements org.wallerlab.yoink.api.model.density.
DensityPoint
)
org.wallerlab.yoink.density.domain.
SimpleDensityPointFactory
(implements org.wallerlab.yoink.api.service.
Factory
<T,K>)
org.wallerlab.yoink.cube.domain.
SimpleGridPoint
<String,V> (implements org.wallerlab.yoink.api.model.cube.
GridPoint
<String,V>)
org.wallerlab.yoink.math.linear.
SimpleMatrixFactory
org.wallerlab.yoink.molecular.domain.
SimpleMolecularSystem
(implements org.wallerlab.yoink.api.model.molecular.
MolecularSystem
)
org.wallerlab.yoink.molecular.domain.
SimpleMolecule
(implements org.wallerlab.yoink.api.model.molecular.
Molecule
)
org.wallerlab.yoink.molecular.domain.
SimpleRadialGrid
(implements org.wallerlab.yoink.api.model.molecular.
RadialGrid
)
org.wallerlab.yoink.regionizer.domain.
SimpleRegion
(implements org.wallerlab.yoink.api.model.regionizer.
Region
)
org.wallerlab.yoink.regionizer.domain.
SimpleRegionFactory
(implements org.wallerlab.yoink.api.service.
Factory
<T,K>)
org.wallerlab.yoink.math.linear.
SimpleVector3DFactory
org.wallerlab.yoink.regionizer.service.
SingleRegionizerService
(implements org.wallerlab.yoink.api.service.regionizer.
RegionizerMath
<T,K>)
org.wallerlab.yoink.adaptive.smooth.
SmoothnerImpl
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.adaptive.smooth.
DensitySmoothner
org.wallerlab.yoink.adaptive.smooth.
DistanceSmoothner
org.wallerlab.yoink.molecular.service.calculator.
SortedDistancesCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.math.set.
Subsets
org.wallerlab.yoink.clustering.utils.
Timer
org.wallerlab.yoink.molecular.service.calculator.
TwoAtomsDistanceCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.molecular.service.calculator.
TwoCoordsDistanceCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.cube.service.
VoronoiCalculator
(implements org.wallerlab.yoink.api.service.
Calculator
<T,K,V>)
org.wallerlab.yoink.adaptive.smooth.
XSWeightFactors
(implements org.wallerlab.yoink.api.service.adaptive.
Smoothner
)
org.wallerlab.yoink.
Yoink
Interface Hierarchy
org.wallerlab.yoink.api.service.adaptiveProcessor.
AdaptiveProcessor
org.wallerlab.yoink.api.service.cube.
Assigner
<T,K,V>
org.wallerlab.yoink.api.model.molecular.
Atom
org.wallerlab.yoink.api.service.
Calculator
<T,K,V>
org.wallerlab.yoink.api.service.bootstrap.
Clustering
org.wallerlab.yoink.api.service.
Computer
<T,K>
org.wallerlab.yoink.api.service.molecular.
Converter
org.wallerlab.yoink.api.model.molecular.
Coord
org.wallerlab.yoink.api.model.cube.
Cube
org.wallerlab.yoink.api.service.cube.
CubeBuilder
<T>
org.wallerlab.yoink.api.model.density.
DensityPoint
org.wallerlab.yoink.api.model.density.
ElementVector
org.wallerlab.yoink.api.service.
Factory
<T,K>
org.wallerlab.yoink.api.service.molecular.
FilesReader
<T,K>
org.wallerlab.yoink.api.service.molecular.
FilesWriter
<T>
org.wallerlab.yoink.api.model.cube.
GridPoint
<String,V>
org.wallerlab.yoink.api.model.bootstrap.
Job
<T>
org.wallerlab.yoink.api.service.bootstrap.
JobBuilder
<I,O>
org.wallerlab.yoink.api.service.math.
Matrix
<T>
org.wallerlab.yoink.api.model.molecular.
MolecularSystem
org.wallerlab.yoink.api.model.molecular.
Molecule
org.wallerlab.yoink.api.service.regionizer.
Partitioner
<K,V>
org.wallerlab.yoink.api.model.molecular.
RadialGrid
org.wallerlab.yoink.api.model.regionizer.
Region
org.wallerlab.yoink.api.service.regionizer.
Regionizer
<T,K>
org.wallerlab.yoink.api.service.regionizer.
RegionizerComponent
<T,K>
org.wallerlab.yoink.api.service.regionizer.
RegionizerMath
<T,K>
org.wallerlab.yoink.api.service.adaptive.
SmoothFunction
org.wallerlab.yoink.api.service.adaptive.
Smoothner
org.wallerlab.yoink.api.service.molecular.
Translator
<T,K>
org.wallerlab.yoink.api.service.math.
Vector
<T>
org.wallerlab.yoink.api.service.bootstrap.
Wrapper
<T>
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.wallerlab.yoink.api.model.bootstrap.
JobParameter
org.wallerlab.yoink.api.model.density.
DensityPoint.DensityType
org.wallerlab.yoink.api.model.molecular.
Element
org.wallerlab.yoink.api.model.regionizer.
Region.Name
org.wallerlab.yoink.api.service.adaptive.
Smoothner.Type
org.wallerlab.yoink.api.service.math.
Matrix.Type
org.wallerlab.yoink.api.service.math.
Vector.Vector3DType
org.wallerlab.yoink.api.service.molecular.
Converter.UnitConverterType
org.wallerlab.yoink.api.service.regionizer.
Partitioner.Type
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