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yoink-core 0.0.3 API

Packages 
Package Description
org.wallerlab.yoink
this package contains Main class.
org.wallerlab.yoink.adaptive.config
this package contains the configure classes.
org.wallerlab.yoink.adaptive.smooth
this package contains smoothers to calculate smoothing factors for buffer molecules.
org.wallerlab.yoink.adaptive.smooth.smoothfunction
This packages contains the various smoothing functions
org.wallerlab.yoink.api.model.bootstrap
this packages are domain model interfaces for subproject bootstrap.
org.wallerlab.yoink.api.model.cube
this packages are domain model interfaces for subproject cube.
org.wallerlab.yoink.api.model.density
this packages are domain model interfaces for subproject density.
org.wallerlab.yoink.api.model.molecular
This package is the interfaces for domain models in molecular system
org.wallerlab.yoink.api.model.regionizer
this packages are domain model interfaces for subproject regionizer.
org.wallerlab.yoink.api.service
this package is for service/function interfaces for calculation and factory methods.
org.wallerlab.yoink.api.service.adaptive
this package is for service/function interfaces for subproject adaptive
org.wallerlab.yoink.api.service.adaptiveProcessor
this package is for service/function interfaces for subproject adaptiveProcessor
org.wallerlab.yoink.api.service.bootstrap
this package is for service/function interfaces for subproject bootstrap
org.wallerlab.yoink.api.service.cube
this package is for service/function interfaces for subproject cube
org.wallerlab.yoink.api.service.math
this package is for service/function interfaces for subproject math
org.wallerlab.yoink.api.service.molecular
this package is for service/function interfaces for subproject math
org.wallerlab.yoink.api.service.regionizer
this package is for service/function interfaces for subproject regionizer
org.wallerlab.yoink.clustering  
org.wallerlab.yoink.clustering.louvain  
org.wallerlab.yoink.clustering.utils  
org.wallerlab.yoink.config
this package is to configure project yoink
org.wallerlab.yoink.cube.domain
this package is the domain models for project cube
org.wallerlab.yoink.cube.service
this package is for service classed in project cube
org.wallerlab.yoink.density.config
this package is to configure density project
org.wallerlab.yoink.density.domain
this package contains domain models for project density
org.wallerlab.yoink.density.service.density
this package is to calculate density and density ratio.
org.wallerlab.yoink.density.service.densityProperties
this package is to calculate properties based on density
org.wallerlab.yoink.domain
this package is for domain models
org.wallerlab.yoink.math.config
this package is the configuration of project math.
org.wallerlab.yoink.math.constants
this package is for constants.
org.wallerlab.yoink.math.linear
this package is for linear library adaptor.
org.wallerlab.yoink.math.map
this package contains some methods for Map
org.wallerlab.yoink.math.set
this package are some methods for Set.
org.wallerlab.yoink.molecular.config
this package is for molecular project configuration
org.wallerlab.yoink.molecular.data
this package contains readers and writers for molecular project
org.wallerlab.yoink.molecular.domain
this package is domain models for project molecular.
org.wallerlab.yoink.molecular.service.calculator
this package is calculate distance and center of mass.
org.wallerlab.yoink.molecular.service.translator
this package is to translate JAXBElement Cml to domain models
org.wallerlab.yoink.processor.config
this package is the configuration of project processor.
org.wallerlab.yoink.processor.service  
org.wallerlab.yoink.processor.service.chem
This package is to interact with external software to obtain energies and gradients for QM, MM and/or QM/MM.
org.wallerlab.yoink.regionizer.config
this package is for configuration of regionizer project
org.wallerlab.yoink.regionizer.domain
this package is for domain models in regionizer project
org.wallerlab.yoink.regionizer.partitioner
this package is for all partitioners in density based partitioning
org.wallerlab.yoink.regionizer.service
this package is for all regionizers in density/distance/number based partitioning
org.wallerlab.yoink.service
this package contains service classes to execute batch adaptive partitioning processors
org.wallerlab.yoink.service.clustering  
org.wallerlab.yoink.service.jobbuilder  
org.wallerlab.yoink.service.processor  
org.wallerlab.yoink.service.request
this package is to get all job requests
org.wallerlab.yoink.service.response
this package is for job response
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