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A

AbstractAdaptiveQMMMProcessor<I,O> - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute adaptive QM/MM partitioning.
AbstractAdaptiveQMMMProcessor() - Constructor for class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
AbstractClusteringProcessor<I,O> - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute clustering based on DORI analysis.
AbstractClusteringProcessor() - Constructor for class org.wallerlab.yoink.service.processor.AbstractClusteringProcessor
 
AbstractJaxbReader - Class in org.wallerlab.yoink.molecular.data
this class is to use JAXB to read input.
AbstractJaxbReader() - Constructor for class org.wallerlab.yoink.molecular.data.AbstractJaxbReader
 
AbstractJaxbWriter - Class in org.wallerlab.yoink.molecular.data
this class is to use jaxb to write an object out.
AbstractJaxbWriter() - Constructor for class org.wallerlab.yoink.molecular.data.AbstractJaxbWriter
 
AbstractJobBuilder<I,O> - Class in org.wallerlab.yoink.service.jobbuilder
this class is to read in all inputs (like molecular system and parameters) needed for adaptive QM/MM partitioning.
AbstractJobBuilder() - Constructor for class org.wallerlab.yoink.service.jobbuilder.AbstractJobBuilder
 
AdaptiveConfig - Class in org.wallerlab.yoink.adaptive.config
this class is for adaptive project configuration
AdaptiveConfig() - Constructor for class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
AdaptiveProcessor - Interface in org.wallerlab.yoink.api.service.adaptiveProcessor
this interface is to process energy and force during adaptive qm/mm.
AdaptiveQMMMJob - Class in org.wallerlab.yoink.domain
the domain model for job in adaptive qm/mm partitioning
AdaptiveQMMMJob() - Constructor for class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
AdaptiveQMMMProcessor - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute adaptive QM/MM partitioning.
AdaptiveQMMMProcessor() - Constructor for class org.wallerlab.yoink.service.processor.AdaptiveQMMMProcessor
 
adaptiveQMMMRegionizers - Variable in class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
AdaptiveQMMMSmoothnerRouter - Class in org.wallerlab.yoink.adaptive.smooth
this class is to choose different smoothner to smooth the buffer region
AdaptiveQMMMSmoothnerRouter() - Constructor for class org.wallerlab.yoink.adaptive.smooth.AdaptiveQMMMSmoothnerRouter
 
adaptiveQMMMSmoothnerRouter - Variable in class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
AdaptiveRegionizer - Class in org.wallerlab.yoink.regionizer.service
this class is to find adaptive QM region or adaptive QM core region.
AdaptiveRegionizer(DensityPoint.DensityType, Partitioner) - Constructor for class org.wallerlab.yoink.regionizer.service.AdaptiveRegionizer
 
adaptiveRegionName - Variable in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
add(Matrix) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
add one matrix to this matrix
add(Vector) - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the sum of this vector with another vector
add(Matrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
add(Vector) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
addAll(Map<Molecule, Integer>) - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
add a map into the region
addAll(Map<Molecule, Integer>) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
add a Map(Molecule, Integer) to this molecularMap
addMolecule(Molecule, Integer) - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
add one molecule into molecularMap
addMolecule(Molecule, Integer) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
add one element(Molecule,Integer) in this molecularMap
addProperty(String, V) - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
add one element in properties
addProperty(String, V) - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
addToEntry(int, int, double) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
add a value to one element in this matrix
addToEntry(int, int, double) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
ANGSTROM_TO_BOHR - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
array2DRowRealMatrix(double[][]) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
initialize this matrix with two-dimensional double array
array2DRowRealMatrix(double[][]) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
assign(T, K, V) - Method in interface org.wallerlab.yoink.api.service.cube.Assigner
the method is to assign t to a group/category/object , etc.
assign(Coord, Map<Region.Name, Region>, Region.Name) - Method in class org.wallerlab.yoink.regionizer.partitioner.GridPointAssigner
for a grid point, get its two neighbours from Voronoi partitioning, if it satisfies the criteria(two neighbours are different, not both in QM core region or in non-QM core adaptive search region.), it will be used for following calculation of density interaction analysis(like DORI and SEDD).
Assigner<T,K,V> - Interface in org.wallerlab.yoink.api.service.cube
this interface is to assign one object t to a group/category/object, etc., and it needs to use another two arguments.
Atom - Interface in org.wallerlab.yoink.api.model.molecular
this interface is for domain model atom
AtomDensityCalculator - Class in org.wallerlab.yoink.density.service.density
this class is to calculate density from one atom
AtomDensityCalculator() - Constructor for class org.wallerlab.yoink.density.service.density.AtomDensityCalculator
 
AtomicDensityPropertiesCalculator - Class in org.wallerlab.yoink.density.service.densityProperties
This class is to calculate the Properties of a density point from an atom.
AtomicDensityPropertiesCalculator() - Constructor for class org.wallerlab.yoink.density.service.densityProperties.AtomicDensityPropertiesCalculator
 
AtomicDensityRatioCalculator - Class in org.wallerlab.yoink.density.service.density
this class is to get the density ratio between two atoms on a grid point.
AtomicDensityRatioCalculator() - Constructor for class org.wallerlab.yoink.density.service.density.AtomicDensityRatioCalculator
 
atomMass() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
atomNumber() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
attributeName - Variable in class org.wallerlab.yoink.clustering.louvain.LouvainAlgoImpl
 

B

BatchConfig - Class in org.wallerlab.yoink.config
This class is configuration for spring batch
BatchConfig() - Constructor for class org.wallerlab.yoink.config.BatchConfig
 
batchStep(StepBuilderFactory, ItemReader<Cml>, ItemProcessor<JAXBElement, Job>, ItemWriter<Job>) - Method in class org.wallerlab.yoink.config.BatchConfig
build executing steps
BOHR_TO_ANGTROM - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
BrooksSmoothFunction - Class in org.wallerlab.yoink.adaptive.smooth.smoothfunction
this class is smooth function used in Hot-spot.
BrooksSmoothFunction() - Constructor for class org.wallerlab.yoink.adaptive.smooth.smoothfunction.BrooksSmoothFunction
 
BufferAdaptiveProcessor - Class in org.wallerlab.yoink.processor.service
This class is to get adaptive forces in buffered force method.
BufferAdaptiveProcessor() - Constructor for class org.wallerlab.yoink.processor.service.BufferAdaptiveProcessor
 
BufferRegionizer - Class in org.wallerlab.yoink.regionizer.service
this class is to locate buffer region based on the densiyt of qm core
BufferRegionizer() - Constructor for class org.wallerlab.yoink.regionizer.service.BufferRegionizer
 
build(I) - Method in interface org.wallerlab.yoink.api.service.bootstrap.JobBuilder
this method take the builderInput to build a job
build(double[], T) - Method in interface org.wallerlab.yoink.api.service.cube.CubeBuilder
 
build(double[], Set<Molecule>) - Method in class org.wallerlab.yoink.cube.service.CubeBuilderImpl
build a cube based on a Set of molecules
build(I) - Method in class org.wallerlab.yoink.service.jobbuilder.AbstractJobBuilder
read in cml file, and convert it to molecular system and parameters for building a new adaptive qmmm job.
build(String) - Method in class org.wallerlab.yoink.service.jobbuilder.JobFileBuilderImpl
read in cml file, and convert it to molecular system and parameters for building a new adaptive qmmm job.
build(JAXBElement) - Method in class org.wallerlab.yoink.service.jobbuilder.JobJaxbBuilderImpl
read in cml file, and convert it to molecular system and parameters for building a new adaptive qmmm job.
build(String) - Method in class org.wallerlab.yoink.service.jobbuilder.JobStringBuilderImpl
read in cml file, and convert it to molecular system and parameters for building a new adaptive qmmm job.
buildAndExecute(String) - Method in class org.wallerlab.yoink.service.processor.FileAdaptiveQMMMProcessor
 
buildAndExecute(String) - Method in class org.wallerlab.yoink.service.processor.FileClusteringProcessor
 
buildAndExecute(String) - Method in class org.wallerlab.yoink.service.processor.FileInteractionSetProcessor
 
buildAndExecute(String) - Method in class org.wallerlab.yoink.service.processor.StringAdaptiveQMMMProcessor
 
BuloSmoothFunction - Class in org.wallerlab.yoink.adaptive.smooth.smoothfunction
this class is for smooth function used in DAS.
BuloSmoothFunction() - Constructor for class org.wallerlab.yoink.adaptive.smooth.smoothfunction.BuloSmoothFunction
 

C

c1() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
c2() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
c3() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
calculate(K, V) - Method in interface org.wallerlab.yoink.api.service.Calculator
this method is to do calculation with k and v, and return one value in type T
calculate(K) - Method in interface org.wallerlab.yoink.api.service.Computer
this method just takes one parameter k, and returns one value in type T after calculation.
calculate(int[], Cube) - Method in class org.wallerlab.yoink.cube.service.CoordInCubeCalculator
calculate the coordinate of a grid point in cube based on current x/y/z steps, x/y/z stepsize and the grid origin of cube
calculate(Coord, Set<Molecule>) - Method in class org.wallerlab.yoink.cube.service.VoronoiCalculator
find two closest atoms and molecules for a grid point
calculate(Coord, Atom) - Method in class org.wallerlab.yoink.density.service.density.AtomDensityCalculator
calculate the density of a point from an atom
calculate(Coord, Atom[]) - Method in class org.wallerlab.yoink.density.service.density.AtomicDensityRatioCalculator
the density ratio of two atoms on a grid point.
calculate(Coord, Set<Molecule>) - Method in class org.wallerlab.yoink.density.service.density.DensityCalculator
calculate the density of a point from molecules.
calculate(Coord, Molecule[]) - Method in class org.wallerlab.yoink.density.service.density.MolecularDensityRatioCalculator
the density ratio of two molecules on a grid point.
calculate(DensityPoint, Atom) - Method in class org.wallerlab.yoink.density.service.densityProperties.AtomicDensityPropertiesCalculator
calculate a density point's properties from an atom
calculate(Set<Atom>, Coord) - Method in class org.wallerlab.yoink.density.service.densityProperties.DensityPropertiesCalculator
calculate a density point's properties from atoms
calculate(DensityPoint) - Method in class org.wallerlab.yoink.density.service.densityProperties.ReducedDensityGradientComputer
calculate RDG of a density point
calculate(DensityPoint) - Method in class org.wallerlab.yoink.density.service.densityProperties.SilvaDensityComputer
calculate Silva density analysis value for a density point
calculate(Set<Molecule>) - Method in class org.wallerlab.yoink.molecular.service.calculator.CenterOfMassComputer
calculate the center of mass of molecules.
calculate(Coord, Molecule) - Method in class org.wallerlab.yoink.molecular.service.calculator.ClosestDistanceToMoleculeCalculator
calculate the distance minimum between a coordinate and a molecule.
calculate(Coord, Atom) - Method in class org.wallerlab.yoink.molecular.service.calculator.DistanceCalculator
calculate the distance between a coordinate and an atom.
calculate(Coord, Set<Molecule>) - Method in class org.wallerlab.yoink.molecular.service.calculator.SortedDistancesCalculator
This method is to calculate the distances between molecules and a point, make a map(sortedDistances) for molecule(as key) and corresponding distance(as value), and sort the map by distance.
calculate(Atom, Atom) - Method in class org.wallerlab.yoink.molecular.service.calculator.TwoAtomsDistanceCalculator
calculate the distance between two atoms
calculate(Coord, Coord) - Method in class org.wallerlab.yoink.molecular.service.calculator.TwoCoordsDistanceCalculator
calculate the distance between two coordinates
calculateQMAdaptiveAndBufferRegionRegion(Region, Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.ParameterRegionizer
 
calculateQMRegion(Map<Region.Name, Region>, Region) - Method in class org.wallerlab.yoink.regionizer.service.ParameterRegionizer
 
calculateSilvaValue(DensityPoint, double) - Method in class org.wallerlab.yoink.density.service.densityProperties.SilvaDensityComputer
 
calculateStreamParallelstream(Set<Molecule>, double, double, Coord) - Method in class org.wallerlab.yoink.regionizer.service.DistanceRegionizer
 
Calculator<T,K,V> - Interface in org.wallerlab.yoink.api.service
this interface is for calculation taking two parameters and returning one value
centerOfMassComputer - Variable in class org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl
 
CenterOfMassComputer - Class in org.wallerlab.yoink.molecular.service.calculator
This class is to get the center of mass for a set of molecules.
CenterOfMassComputer() - Constructor for class org.wallerlab.yoink.molecular.service.calculator.CenterOfMassComputer
 
changeMolecularId() - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
set molecular name as same as region name
changeMolecularId(Region.Name) - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
change molecular name as the given name
changeMolecularId() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
change the id of molecules with the name of region
changeMolecularId(Region.Name) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
change the id of molecules with the given name
checkCriteria(Map<Region.Name, Region>, Region, GridPoint, Set<Molecule>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.partitioner.DensityOverlapRegionsIndicatorPartitioner
for a grid point which satisfies the criteria: density is larger than densityThreshold and dori value is the range[doriThreshold, 1] ,the non-QM molecule of the grid point will be in QM region.
checkCriteria(Map<Region.Name, Region>, Region, GridPoint, Set<Molecule>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
checkCriteria(Map<Region.Name, Region>, Region, GridPoint, Set<Molecule>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.partitioner.SingleExponentialDecayDetectorPartitioner
This method is to get QM core region and QM core adaptive region .
checkCriteria(Map<Region.Name, Region>, List<List<Integer>>, GridPoint, Set<Molecule>, List<Integer>, Map<JobParameter, Object>, List<Double>, Set<Set<Integer>>) - Method in class org.wallerlab.yoink.service.clustering.InteractionSet
 
checkCriteriaFunc(Region, Region, Coord, Set<Molecule>, double, double) - Method in class org.wallerlab.yoink.regionizer.service.DistanceRegionizer
 
checkEveryNonQMCoreMolecule(Region, Map<JobParameter, Object>, Region, Coord, Set<Molecule>) - Method in class org.wallerlab.yoink.regionizer.service.DistanceRegionizer
In this method, if the distance between one atom in a non-QM core molecule and the center of mass of QM core is smaller than the distanceThreshold, then this molecule is treated by QM method.
checkEveryNonQMCoreMolecule(Region, Map<JobParameter, Object>, Region, Coord, Set<Molecule>) - Method in class org.wallerlab.yoink.regionizer.service.NumberRegionizer
moleculeSequence is ordered by the ascending distance between molecule and the center of mass of QM core, and take first qmNumber of molecules from the moleculeSequence as adaptive QM molecules.
checkEveryNonQMCoreMolecule(Region, Map<JobParameter, Object>, Region, Coord, Set<Molecule>) - Method in class org.wallerlab.yoink.regionizer.service.ParameterRegionizer
 
checkEveryNonQMCoreMolecule(Region, Map<JobParameter, Object>, Region, Coord, Set<Molecule>) - Method in class org.wallerlab.yoink.regionizer.service.SizeConsistentRegionizer
moleculeSequence is ordered by the ascending distance between molecule and the center of mass of QM core, and take first 2/3 qmNumber of molecules from the moleculeSequence as adaptive QM molecules.
clearDb() - Method in class org.wallerlab.yoink.clustering.DatabaseService
Attention: clearDb() will delete everything under DB_PATH!
clock - Variable in class org.wallerlab.yoink.clustering.utils.Timer
 
ClosestDistanceToMoleculeCalculator - Class in org.wallerlab.yoink.molecular.service.calculator
This class is to calculate the closest distance between one point in space and a molecule
ClosestDistanceToMoleculeCalculator() - Constructor for class org.wallerlab.yoink.molecular.service.calculator.ClosestDistanceToMoleculeCalculator
 
cluster(Job) - Method in interface org.wallerlab.yoink.api.service.bootstrap.Clustering
 
cluster(int) - Method in class org.wallerlab.yoink.clustering.LouvainClusteringFacade
 
cluster(Job) - Method in class org.wallerlab.yoink.service.DoriClustering
 
Clustering - Interface in org.wallerlab.yoink.api.service.bootstrap
 
clusteringStep(StepBuilderFactory, ItemReader<Cml>, ItemProcessor<JAXBElement, Job>, ItemWriter<Job>) - Method in class org.wallerlab.yoink.config.BatchConfig
 
CmlFileResponseWriter - Class in org.wallerlab.yoink.service.response
This class is almost identical to CmlFilesResponse, except it is not processing a list of a list of jobs.
CmlFileResponseWriter() - Constructor for class org.wallerlab.yoink.service.response.CmlFileResponseWriter
 
CmlFilesRequest - Class in org.wallerlab.yoink.service.request
this class is for job request, to get all xml files in a folder
CmlFilesRequest() - Constructor for class org.wallerlab.yoink.service.request.CmlFilesRequest
 
CmlFilesResponse - Class in org.wallerlab.yoink.service.response
This class is for job response, to write adaptive qmmm result into a cml file.
CmlFilesResponse() - Constructor for class org.wallerlab.yoink.service.response.CmlFilesResponse
 
COLUMN_NUMBER_IN_EACH_ROW - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
CommonsMatrix - Class in org.wallerlab.yoink.math.linear
Matrix Adaptor pattern.
CommonsMatrix() - Constructor for class org.wallerlab.yoink.math.linear.CommonsMatrix
 
CommonsMatrix(int, int) - Constructor for class org.wallerlab.yoink.math.linear.CommonsMatrix
 
CommonsVector3D - Class in org.wallerlab.yoink.math.linear
Vector Adaptor pattern.
CommonsVector3D(double, double, double) - Constructor for class org.wallerlab.yoink.math.linear.CommonsVector3D
 
CommonsVector3D() - Constructor for class org.wallerlab.yoink.math.linear.CommonsVector3D
 
CommonsVector3D(double[]) - Constructor for class org.wallerlab.yoink.math.linear.CommonsVector3D
 
communities() - Method in class org.wallerlab.yoink.clustering.louvain.LouvainAlgoImpl
 
Computer<T,K> - Interface in org.wallerlab.yoink.api.service
this interface is for calculation only with one argument and one return value.
ConfigurationAdaptiveProcessor - Class in org.wallerlab.yoink.processor.service
this class is to get adaptive energy and forces.
ConfigurationAdaptiveProcessor() - Constructor for class org.wallerlab.yoink.processor.service.ConfigurationAdaptiveProcessor
 
Constants - Class in org.wallerlab.yoink.math.constants
 
Constants() - Constructor for class org.wallerlab.yoink.math.constants.Constants
 
containsAll(Set<Molecule>) - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
check if the regions contains all molecules
containsAll(Set<Molecule>) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
check if all molecules are in the region
Converter - Interface in org.wallerlab.yoink.api.service.molecular
this interface contains enum UnitConverterType
Converter.UnitConverterType - Enum in org.wallerlab.yoink.api.service.molecular
unit convert coefficient for angstrom to bohr and bohr to angstrom
Coord - Interface in org.wallerlab.yoink.api.model.molecular
this interface for domain model Coord
CoordInCubeCalculator - Class in org.wallerlab.yoink.cube.service
this class is to get the coordinate of a grid point in cube
CoordInCubeCalculator() - Constructor for class org.wallerlab.yoink.cube.service.CoordInCubeCalculator
 
create() - Method in interface org.wallerlab.yoink.api.service.Factory
use default constructor to generate a new object of T
create(K) - Method in interface org.wallerlab.yoink.api.service.Factory
make a new object of type T with an initial value
create() - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPointFactory
 
create(Coord) - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPointFactory
 
create(double, double, double) - Method in class org.wallerlab.yoink.math.linear.SimpleVector3DFactory
create a 3D vector from its coordinates
create(double[]) - Method in class org.wallerlab.yoink.math.linear.SimpleVector3DFactory
use an double array with 3 elements to create a 3D vector
create() - Method in class org.wallerlab.yoink.molecular.domain.SimpleCoordFactory
make a new Coord.
create(double[]) - Method in class org.wallerlab.yoink.molecular.domain.SimpleCoordFactory
use an array with 3 elements to make a new Coord
create() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegionFactory
 
create(Region.Name) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegionFactory
 
Cube - Interface in org.wallerlab.yoink.api.model.cube
this interface is for domain model cube
CubeBuilder<T> - Interface in org.wallerlab.yoink.api.service.cube
 
CubeBuilderImpl - Class in org.wallerlab.yoink.cube.service
This class is to calculate the grid origin and the number of steps along XYZ axis to construct a cube.
CubeBuilderImpl() - Constructor for class org.wallerlab.yoink.cube.service.CubeBuilderImpl
 
CubePartitioner - Class in org.wallerlab.yoink.regionizer.partitioner
This class is to get those grid points that belong to the intersection region of QM core region and non-QM core region.
CubePartitioner() - Constructor for class org.wallerlab.yoink.regionizer.partitioner.CubePartitioner
 
cVector() - Method in interface org.wallerlab.yoink.api.model.density.ElementVector
get value of the cVector.
cz1() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
cz2() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
cz3() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
czz1() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
czz2() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
czz3() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 

D

DASWeightFactors - Class in org.wallerlab.yoink.adaptive.smooth
this class is to get weight factor in DAS.
DASWeightFactors() - Constructor for class org.wallerlab.yoink.adaptive.smooth.DASWeightFactors
 
DatabaseService - Class in org.wallerlab.yoink.clustering
 
DENSITY_DEFAULT - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
DensityBasedRegionizer - Class in org.wallerlab.yoink.regionizer.service
this class is to find adaptive QM core region, adaptive QM region and buffer region busing density based adaptive qm/mm partitioning.
DensityBasedRegionizer() - Constructor for class org.wallerlab.yoink.regionizer.service.DensityBasedRegionizer
 
DensityCalculator - Class in org.wallerlab.yoink.density.service.density
this class is to calculate the density of molecules on a point
DensityCalculator() - Constructor for class org.wallerlab.yoink.density.service.density.DensityCalculator
 
DensityConfig - Class in org.wallerlab.yoink.density.config
this class is to configure density project
DensityConfig() - Constructor for class org.wallerlab.yoink.density.config.DensityConfig
 
DensityOverlapRegionsIndicatorComputer - Class in org.wallerlab.yoink.density.service.densityProperties
This class is to get the density overlap regions indicator(DORI) value of a grid point.
DensityOverlapRegionsIndicatorComputer() - Constructor for class org.wallerlab.yoink.density.service.densityProperties.DensityOverlapRegionsIndicatorComputer
 
DensityOverlapRegionsIndicatorPartitioner - Class in org.wallerlab.yoink.regionizer.partitioner
This class is to analyze Density Overlap Regions Indicator(DORI) for those grid points in the intersection between QM core region and non-QM core region based on Voronoi partitioning.
DensityOverlapRegionsIndicatorPartitioner() - Constructor for class org.wallerlab.yoink.regionizer.partitioner.DensityOverlapRegionsIndicatorPartitioner
 
DensityPartitioner - Class in org.wallerlab.yoink.regionizer.partitioner
This class is to use the density of qm core to define the region (adaptive search region) to look for the potential QM core or QM adaptive molecules.
DensityPartitioner() - Constructor for class org.wallerlab.yoink.regionizer.partitioner.DensityPartitioner
 
DensityPoint - Interface in org.wallerlab.yoink.api.model.density
this interface is for a point involved in density properties calculation
DensityPoint.DensityType - Enum in org.wallerlab.yoink.api.model.density
 
DensityPropertiesCalculator - Class in org.wallerlab.yoink.density.service.densityProperties
This class is to calculate the Properties of a Density point from atoms.
DensityPropertiesCalculator() - Constructor for class org.wallerlab.yoink.density.service.densityProperties.DensityPropertiesCalculator
 
densityPropertiesCalculator - Variable in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
densityPropertiesCalculator - Variable in class org.wallerlab.yoink.service.clustering.InteractionSet
 
DensitySmoothner - Class in org.wallerlab.yoink.adaptive.smooth
this class is to electronic density based smoothing.
DensitySmoothner(SmoothFunction) - Constructor for class org.wallerlab.yoink.adaptive.smooth.DensitySmoothner
the constructor of DensitySmoothner with specified smooth function.
densitySmoothnerBF() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
densitySmoothnerDAS() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
densitySmoothnerPAP() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
densitySmoothnerSPOT() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
densitySmoothnerXS() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
diff(Map<? extends K, ? extends V>, Map<? extends K, ? extends V>) - Static method in class org.wallerlab.yoink.math.map.MapDifference
this method is to get the difference between map1 and map2.
diff(Set<? extends T>, Set<? extends T>) - Static method in class org.wallerlab.yoink.math.set.SetDifference
This method is to calculate the difference of two Sets.
distance(Matrix) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the distance between this matrix and another matrix m.it works when matrix is a vector
distance(Vector) - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the distance between this vector and another vector
distance(Matrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
distance(Vector) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
DISTANCE_DEFAULT - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
DistanceCalculator - Class in org.wallerlab.yoink.molecular.service.calculator
This class is to calculate the distance between one point in space and an atom.
DistanceCalculator() - Constructor for class org.wallerlab.yoink.molecular.service.calculator.DistanceCalculator
 
DistanceRegionizer - Class in org.wallerlab.yoink.regionizer.service
This class is for setting up distance based adaptive QM/MM partitioning to get the QM region and buffer region
DistanceRegionizer() - Constructor for class org.wallerlab.yoink.regionizer.service.DistanceRegionizer
 
DistanceSmoothner - Class in org.wallerlab.yoink.adaptive.smooth
this class is to do distance based smoothing.
DistanceSmoothner(SmoothFunction) - Constructor for class org.wallerlab.yoink.adaptive.smooth.DistanceSmoothner
the constructor of DistanceSmoothner with specified smooth function.
distanceSmoothnerBF() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
distanceSmoothnerDAS() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
distanceSmoothnerPAP() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
distanceSmoothnerSPOT() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
distanceSmoothnerXS() - Method in class org.wallerlab.yoink.adaptive.config.AdaptiveConfig
 
DORI_DEFAULT - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
DoriClustering - Class in org.wallerlab.yoink.service
This class is to build a graph based on DORI interaction(yes or no) and do louvain clustering.
DoriClustering() - Constructor for class org.wallerlab.yoink.service.DoriClustering
 
dotProduct() - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the dot product of this matrix.
dotProduct(Matrix) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the dot product of this matrix and another matrix m.
dotProduct() - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the dot product of this vector with itself
dotProduct() - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
dotProduct(Matrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
dotProduct() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 

E

ebeMultiply(Matrix) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
multiply this matrix with another matrix m element by element
ebeMultiply(Vector) - Method in interface org.wallerlab.yoink.api.service.math.Vector
multiply this vector with another vector element by element
ebeMultiply(Matrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
Element-by-element multiplication of two 3D vectors.
ebeMultiply(Vector) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
Element - Enum in org.wallerlab.yoink.api.model.molecular
Enum Element(c1, c2, c3, z1, z2, z3,atomMass,atomNumber).
elementType - Variable in class org.wallerlab.yoink.molecular.domain.SimpleAtom
 
ElementVector - Interface in org.wallerlab.yoink.api.model.density
this interface is to get the element density parameters in the form of vector
equals(Matrix) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
check if this matrix equals another matrix m.
equals(Vector) - Method in interface org.wallerlab.yoink.api.service.math.Vector
check if this vector equals another vector m.
equals(Matrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
equals(Vector) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
evaluate(double, double, double) - Method in class org.wallerlab.yoink.adaptive.smooth.smoothfunction.BrooksSmoothFunction
this smooth function is used in hot-spot method.
evaluate(double, double, double) - Method in class org.wallerlab.yoink.adaptive.smooth.smoothfunction.BuloSmoothFunction
this smooth function is used in difference-based adaptive solvation(DAS) method.
evaluate(double, double, double) - Method in class org.wallerlab.yoink.adaptive.smooth.smoothfunction.MorokumaSmoothFunction
this smooth function is used in ONIOM-XS method.
evaluate(double, double, double) - Method in class org.wallerlab.yoink.adaptive.smooth.smoothfunction.PermutedSmoothFunction
this smooth function is used in PAP and SAP methods.
evaluate(double, double, double) - Method in class org.wallerlab.yoink.adaptive.smooth.smoothfunction.SCMPSmoothFunction
this smooth function is used in SCMP method.
evaluate(double, double, double) - Method in interface org.wallerlab.yoink.api.service.adaptive.SmoothFunction
 
executeClustering(Job) - Method in class org.wallerlab.yoink.service.processor.AbstractClusteringProcessor
 
executeQMMMPartitioning(Job) - Method in class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
exp() - Method in interface org.wallerlab.yoink.api.service.math.Vector
do Math.exp() calculation for every element in the vector
exp() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 

F

Factory<T,K> - Interface in org.wallerlab.yoink.api.service
this interface is to create a new instances of a class.
FileAdaptiveQMMMProcessor - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute adaptive QM/MM partitioning.
FileAdaptiveQMMMProcessor() - Constructor for class org.wallerlab.yoink.service.processor.FileAdaptiveQMMMProcessor
 
FileClusteringProcessor - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute clustering.
FileClusteringProcessor() - Constructor for class org.wallerlab.yoink.service.processor.FileClusteringProcessor
 
FileInteractionSetProcessor - Class in org.wallerlab.yoink.service.processor
This class is to set up and get all interaction pairs.
FileInteractionSetProcessor() - Constructor for class org.wallerlab.yoink.service.processor.FileInteractionSetProcessor
 
FilesReader<T,K> - Interface in org.wallerlab.yoink.api.service.molecular
 
FilesWriter<T> - Interface in org.wallerlab.yoink.api.service.molecular
this interface is to write one object into a file
findAdaptiveRegion(Map<Region.Name, Region>) - Method in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
findRegion(Map<Region.Name, Region>, Map<JobParameter, Object>, List<GridPoint>) - Method in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
FIRESAdaptiveProcessor - Class in org.wallerlab.yoink.processor.service
this class is to get FIRES adaptive energy and forces.
FIRESAdaptiveProcessor() - Constructor for class org.wallerlab.yoink.processor.service.FIRESAdaptiveProcessor
 
FIRESmoothner - Class in org.wallerlab.yoink.adaptive.smooth
 
FIRESmoothner() - Constructor for class org.wallerlab.yoink.adaptive.smooth.FIRESmoothner
 
first - Variable in class org.wallerlab.yoink.clustering.InteractionTriple
 
FORCE_CONSTANT - Static variable in class org.wallerlab.yoink.math.constants.Constants
 

G

gatherResult(int) - Method in class org.wallerlab.yoink.clustering.louvain.LouvainAlgoImpl
 
getA() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getA() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getAtoms() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the atoms in the cube
getAtoms() - Method in interface org.wallerlab.yoink.api.model.molecular.MolecularSystem
get all the atoms in the molecular system
getAtoms() - Method in interface org.wallerlab.yoink.api.model.molecular.Molecule
get all atoms in the molecule
getAtoms() - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
Convenient method for getting atoms from a region
getAtoms() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
get all atoms in the cube
getAtoms() - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecularSystem
get all atoms in the molecular system.
getAtoms() - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecule
get atoms in molecule
getAtoms() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
get all atoms in the region
getAtomsInTwoClosestMolecules() - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
get atoms of two closest molecules of a grid point
getAtomsInTwoClosestMolecules() - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
getB() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getB() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getBeans(AnnotationConfigApplicationContext) - Method in class org.wallerlab.yoink.Yoink
 
getCenterOfMass() - Method in interface org.wallerlab.yoink.api.model.molecular.Molecule
get the center of mass of this molecule.
getCenterOfMass() - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
get the center of mass of this region
getCenterOfMass() - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecule
 
getCenterOfMass() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
get the center of mass of the region
getClusters() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the clustering result
getClusters() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getCoefficients_of_first_derivative() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getCoefficients_of_first_derivative() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getCoefficients_of_second_derivative() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getCoefficients_of_second_derivative() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getCoordinate() - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
get the value of coordinate
getCoordinate() - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
get the coordinate of this atom
getCoordinate() - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
getCoordinate() - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
get the coordinate of the atom
getCoordinates() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the coordinates of grid points in the cube
getCoordinates() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getCoords() - Method in interface org.wallerlab.yoink.api.model.molecular.Coord
get the value of coordinate
getCoords() - Method in class org.wallerlab.yoink.molecular.domain.SimpleCoord
get the value of coordinates
getCore_cutdens() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getCore_cutdens() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getCurrentCoord() - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
get the coordinate of the point
getCurrentCoord() - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
get the coordinate
getData() - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the value of this matrix in the form a two-dimensional double array
getData() - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
getDensity() - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
get the electronic density of this point
getDensity() - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
get density
getDensityType() - Method in class org.wallerlab.yoink.regionizer.service.AdaptiveRegionizer
 
getDensityTypes() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the value of density types of the cube
getDensityTypes() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getDoriInteractionSet(Job) - Method in class org.wallerlab.yoink.service.clustering.InteractionSet
 
getElementType() - Method in interface org.wallerlab.yoink.api.model.density.ElementVector
get the value of element.
getElementType() - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
get the element of this atom
getElementType() - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
get the element type of the atom
getEnergy() - Method in interface org.wallerlab.yoink.api.service.adaptiveProcessor.AdaptiveProcessor
This method calls an external program to get an energy
getEnergy() - Method in class org.wallerlab.yoink.processor.service.chem.MMProcessor
 
getEnergy() - Method in class org.wallerlab.yoink.processor.service.chem.QMMMProcessor
 
getEnergy() - Method in class org.wallerlab.yoink.processor.service.chem.QMProcessor
 
getEntry(int, int) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the value of one element in this matrix
getEntry(int) - Method in interface org.wallerlab.yoink.api.service.math.Vector
get one element in this vector
getEntry(int, int) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
getEntry(int) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
getFirst_derivative_of_grid_values() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getFirst_derivative_of_grid_values() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getForces() - Method in interface org.wallerlab.yoink.api.service.adaptiveProcessor.AdaptiveProcessor
This method calls an external program to get the forces
getForces() - Method in class org.wallerlab.yoink.processor.service.chem.MMProcessor
 
getForces() - Method in class org.wallerlab.yoink.processor.service.chem.QMMMProcessor
 
getForces() - Method in class org.wallerlab.yoink.processor.service.chem.QMProcessor
 
getGradient() - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
get the density gradient value at this point
getGradient() - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
get gradient
getGradientVector() - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
get the density gradient vector at this point
getGradientVector() - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
get gradient vector.
getGrid_positions() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getGrid_positions() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getGrid_values() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getGrid_values() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getGridOrigin() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the value of origin coordinate of the cube
getGridOrigin() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getHessian() - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
get the hessian matrix at this point
getHessian() - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
get hessian
getIndex() - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
get the index of this atom in molecular system
getIndex() - Method in interface org.wallerlab.yoink.api.model.molecular.Molecule
get the index of molecule in the molecular system
getIndex() - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
get the atomic index in molecular system
getIndex() - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecule
get molecular index in molecular system
getIndexInCube() - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
get the index of a grid point in cube
getIndexInCube() - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
getInput() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the value of input in the job
getInput() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getInteractionList() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the interaction pairs
getInteractionList() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getInteractionWeight() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the weight(strength) of the interaction
getInteractionWeight() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getInternalMatrix() - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the value of internal matrix of this matrix
getInternalMatrix() - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
getInternalVector() - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the value of internal vector of this vector in the vector type in the library
getInternalVector() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
getJmsItemReader() - Method in class org.wallerlab.yoink.service.request.JmsRequestReader
 
getJmsItemWriter() - Method in class org.wallerlab.yoink.service.response.JmsJobItemWriter
 
getMolecularMap() - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
get the value of molecularMap
getMolecularMap() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
get the molecularMap in the region
getMolecularSystem() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the value of molecular system in the job
getMolecularSystem() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getMolecules() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the molecules in the cube
getMolecules() - Method in interface org.wallerlab.yoink.api.model.molecular.MolecularSystem
get all molecules in the molecular system
getMolecules() - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
get all molecules in the region
getMolecules() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getMolecules() - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecularSystem
get all molecules in molecular system.
getMolecules() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
get molecules in the region
getName() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the name of the cube
getName() - Method in interface org.wallerlab.yoink.api.model.molecular.Molecule
get the name of molecule.
getName() - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
get the name of the region
getName() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getName() - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecule
get the molecular name
getName() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
get the name of the region
getNgrid() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getNgrid() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getNode_offsets() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getNode_offsets() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getNorm() - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the norm of this matrix.
getNorm() - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the norm of this vector
getNorm() - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
getNorm() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
getNumberOfXYZSteps() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the number of steps along xyz axes
getNumberOfXYZSteps() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getOriginalMinAndMax(List<Double>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.adaptive.smooth.DensitySmoothner
 
getOriginalMinAndMax(List<Double>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.adaptive.smooth.DistanceSmoothner
 
getOriginalMinAndMax(List<Double>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl
 
getOutput() - Method in class org.wallerlab.yoink.molecular.data.JaxbStringWriter
 
getParameters() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the parameters during the job
getParameters() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getPosition_max() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getPosition_max() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getPrefactor_of_first_derivative() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getPrefactor_of_first_derivative() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getPrefactor_of_second_derivative() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getPrefactor_of_second_derivative() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getProperSmoothParameters(Set<Molecule>, List<Double>, Molecule) - Method in class org.wallerlab.yoink.adaptive.smooth.DensitySmoothner
 
getProperSmoothParameters(Set<Molecule>, List<Double>, Molecule) - Method in class org.wallerlab.yoink.adaptive.smooth.DistanceSmoothner
 
getProperSmoothParameters(Set<Molecule>, List<Double>, Molecule) - Method in class org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl
 
getProperties() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the value of properties in the job.
getProperties() - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
get the value of properties
getProperties() - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
getProperties() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getProperty(String) - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
get one element's value in properties by key K
getProperty(String) - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
getRadialGrid() - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
get the radial grid
getRadialGrid() - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
set the radial grid
getRegionNames() - Method in class org.wallerlab.yoink.regionizer.service.RegionizerService
get the region names
getRegions() - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
get the value of regions in the job
getRegions() - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
getResult(int) - Method in class org.wallerlab.yoink.clustering.LouvainClusteringFacade
Return the set of communities at a certain hierarchy/aggregation level.
getRow(int) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
get the value of one row in this matrix in the form of one-dimensional double array.
getRow(int) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
getSecond_derivative_of_grid_values() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getSecond_derivative_of_grid_values() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getSilvaValue(DensityPoint, double) - Method in class org.wallerlab.yoink.density.service.densityProperties.DensityOverlapRegionsIndicatorComputer
calculate dori value of a grid point
getSilvaValue(DensityPoint, double) - Method in class org.wallerlab.yoink.density.service.densityProperties.SilvaDensityComputer
 
getSilvaValue(DensityPoint, double) - Method in class org.wallerlab.yoink.density.service.densityProperties.SingleExponentialDecayDetectorComputer
calculate SEDD of a denstiy point
getSize() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the number of grid points in the cube
getSize() - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
get the number of molecules in the region
getSize() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getSize() - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
get the number of molecules in the region
getSquare_position_max() - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
getSquare_position_max() - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
getTwoClosestAtoms() - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
get two closest atoms in properties
getTwoClosestAtoms() - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
getTwoClosestMolecules() - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
get two closest molecules in properties
getTwoClosestMolecules() - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
getValues() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the values of grid points in the cube
getValues() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getX() - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the value of x coordinate of this vector
getX() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
getX3() - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
get the x coordinate of this atom
getX3() - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
get the x coordinate of the atom
getXyzStepSize() - Method in interface org.wallerlab.yoink.api.model.cube.Cube
get the step size along xyz axes
getXyzStepSize() - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
getY() - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the value of y coordinate of this vector
getY() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
getY3() - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
get the y coordinate of this atom
getY3() - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
get the y coordinate of the atom
getZ() - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the value of z coordinate of this vector
getZ() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
getZ3() - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
get the z coordinate of this atom
getZ3() - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
get the z coordinate of the atom
graphDb() - Method in class org.wallerlab.yoink.clustering.DatabaseService
 
GridPoint<String,V> - Interface in org.wallerlab.yoink.api.model.cube
this interface is for a grid point in the cube Cube
GridPointAssigner - Class in org.wallerlab.yoink.regionizer.partitioner
This class is to determine if a grid point is in the intersection region between QM core and non-QM core in adaptiveSearch region.
GridPointAssigner() - Constructor for class org.wallerlab.yoink.regionizer.partitioner.GridPointAssigner
 

H

HOTSPOTAdaptiveProcessor - Class in org.wallerlab.yoink.processor.service
this class is go get the adaptive energy and forces in hot-spot method.
HOTSPOTAdaptiveProcessor() - Constructor for class org.wallerlab.yoink.processor.service.HOTSPOTAdaptiveProcessor
 

I

importBatchJob(JobBuilderFactory) - Method in class org.wallerlab.yoink.config.BatchConfig
build a batch job using a batch based approach.
importClusteringJob(JobBuilderFactory) - Method in class org.wallerlab.yoink.config.BatchConfig
 
importJmsJob(JobBuilderFactory) - Method in class org.wallerlab.yoink.config.BatchConfig
build a batch job using a JMS based approach.
importServiceJob(JobBuilderFactory) - Method in class org.wallerlab.yoink.config.BatchConfig
build whole job using a service based job
index - Variable in class org.wallerlab.yoink.molecular.domain.SimpleAtom
 
init() - Method in class org.wallerlab.yoink.clustering.louvain.LouvainAlgoImpl
initialize the graph by assigning a community label = nodeId to all nodes.
init(Object) - Method in class org.wallerlab.yoink.molecular.data.AbstractJaxbReader
 
initialize(Map<Region.Name, Region>) - Method in class org.wallerlab.yoink.regionizer.partitioner.DensityOverlapRegionsIndicatorPartitioner
 
initialize(Map<Region.Name, Region>) - Method in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
initialize(Map<Region.Name, Region>) - Method in class org.wallerlab.yoink.regionizer.partitioner.SingleExponentialDecayDetectorPartitioner
 
input - Variable in class org.wallerlab.yoink.molecular.data.JaxbFileReader
 
input - Variable in class org.wallerlab.yoink.molecular.data.JaxbStringReader
 
instance - Static variable in class org.wallerlab.yoink.clustering.utils.Timer
 
InteractionPartitioner - Class in org.wallerlab.yoink.regionizer.partitioner
This class is to do density interaction analysis (dori/sedd ) for those grid points in the intersection between QM core region and non-QM core region based on Voronoi partition.
InteractionPartitioner() - Constructor for class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
InteractionSet - Class in org.wallerlab.yoink.service.clustering
This class is to get all pairs having interaction(yes or no) base on DORI analysis.
InteractionSet() - Constructor for class org.wallerlab.yoink.service.clustering.InteractionSet
 
InteractionTriple<T> - Class in org.wallerlab.yoink.clustering
 
InteractionTriple(T, T, double) - Constructor for class org.wallerlab.yoink.clustering.InteractionTriple
 
inverseZVector() - Method in interface org.wallerlab.yoink.api.model.density.ElementVector
get the value of inverse of zVector.

J

jaxbContext - Variable in class org.wallerlab.yoink.molecular.data.AbstractJaxbReader
 
jaxbContext - Variable in class org.wallerlab.yoink.molecular.data.AbstractJaxbWriter
 
JaxbFileReader - Class in org.wallerlab.yoink.molecular.data
this class is to use JAXB to read a file.
JaxbFileReader() - Constructor for class org.wallerlab.yoink.molecular.data.JaxbFileReader
 
JaxbFileWriter - Class in org.wallerlab.yoink.molecular.data
this class is to use jaxb to write an object into CML file.
JaxbFileWriter() - Constructor for class org.wallerlab.yoink.molecular.data.JaxbFileWriter
 
jaxbMarshaller - Variable in class org.wallerlab.yoink.molecular.data.AbstractJaxbWriter
 
jaxbObject - Variable in class org.wallerlab.yoink.molecular.data.AbstractJaxbWriter
 
JaxbStringReader - Class in org.wallerlab.yoink.molecular.data
this class is to use JAXB to read a xml string.
JaxbStringReader() - Constructor for class org.wallerlab.yoink.molecular.data.JaxbStringReader
 
JaxbStringWriter - Class in org.wallerlab.yoink.molecular.data
this class is to use jaxb to write an object into a string.
JaxbStringWriter() - Constructor for class org.wallerlab.yoink.molecular.data.JaxbStringWriter
 
jaxbUnmarshaller - Variable in class org.wallerlab.yoink.molecular.data.AbstractJaxbReader
 
JmsJobItemWriter - Class in org.wallerlab.yoink.service.response
This class converts a job to a string using JAXB, and then delegates to a standard JmsItemWriter from Spring batch.
JmsJobItemWriter() - Constructor for class org.wallerlab.yoink.service.response.JmsJobItemWriter
 
JmsRequestReader - Class in org.wallerlab.yoink.service.request
this class is for job request, to get all xml files off JMS
JmsRequestReader() - Constructor for class org.wallerlab.yoink.service.request.JmsRequestReader
 
jmsStep(StepBuilderFactory) - Method in class org.wallerlab.yoink.config.BatchConfig
build executing steps
Job<T> - Interface in org.wallerlab.yoink.api.model.bootstrap
this interface is for the Job domain model
JobBuilder<I,O> - Interface in org.wallerlab.yoink.api.service.bootstrap
this interface is to build a job - Job
JobFileBuilderImpl - Class in org.wallerlab.yoink.service.jobbuilder
this class is to read in all inputs (like molecular system and parameters) needed for adaptive QM/MM partitioning.
JobFileBuilderImpl() - Constructor for class org.wallerlab.yoink.service.jobbuilder.JobFileBuilderImpl
 
JobJaxbBuilderImpl - Class in org.wallerlab.yoink.service.jobbuilder
this class is to read in all inputs (like molecular system and parameters) needed for adaptive QM/MM partitioning.
JobJaxbBuilderImpl() - Constructor for class org.wallerlab.yoink.service.jobbuilder.JobJaxbBuilderImpl
 
JobParameter - Enum in org.wallerlab.yoink.api.model.bootstrap
JobParameter is used to describe the type of parameter in parameters of job Job.
JobStringBuilderImpl - Class in org.wallerlab.yoink.service.jobbuilder
this class is to read in all inputs (like molecular system and parameters) needed for adaptive QM/MM partitioning.
JobStringBuilderImpl() - Constructor for class org.wallerlab.yoink.service.jobbuilder.JobStringBuilderImpl
 

L

log - Static variable in class org.wallerlab.yoink.density.service.density.DensityCalculator
 
log - Static variable in class org.wallerlab.yoink.service.processor.AdaptiveQMMMProcessor
 
log - Static variable in class org.wallerlab.yoink.service.processor.FileAdaptiveQMMMProcessor
 
log - Static variable in class org.wallerlab.yoink.service.processor.FileClusteringProcessor
 
log - Static variable in class org.wallerlab.yoink.service.processor.FileInteractionSetProcessor
 
log - Static variable in class org.wallerlab.yoink.service.processor.SerialAdaptiveQMMMProcessor
 
log - Static variable in class org.wallerlab.yoink.service.processor.SerialClusteringProcessor
 
log - Static variable in class org.wallerlab.yoink.service.processor.StringAdaptiveQMMMProcessor
 
log - Static variable in class org.wallerlab.yoink.service.request.CmlFilesRequest
 
log - Static variable in class org.wallerlab.yoink.service.response.CmlFileResponseWriter
 
log - Static variable in class org.wallerlab.yoink.service.response.CmlFilesResponse
 
log - Static variable in class org.wallerlab.yoink.service.response.JmsJobItemWriter
 
loopOverAllBufferMolecules(Job) - Method in class org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl
 
loopOverGridPoints(Map<Region.Name, Region>, Region, List<GridPoint>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
loopOverHessian(DensityPoint, double) - Method in class org.wallerlab.yoink.density.service.densityProperties.SilvaDensityComputer
 
loopOverMoleculesInNonQmRegion(Region, Map<Region.Name, Region>, Map<JobParameter, Object>, Region) - Method in class org.wallerlab.yoink.regionizer.service.ParameterRegionizer
 
louvain(int) - Method in class org.wallerlab.yoink.clustering.louvain.LouvainAlgoImpl
 
LouvainAlgoImpl - Class in org.wallerlab.yoink.clustering.louvain
notation follows "Fast unfolding of communities in large networks" by Blondel et al.
LouvainAlgoImpl(GraphDatabaseService, RelationshipType) - Constructor for class org.wallerlab.yoink.clustering.louvain.LouvainAlgoImpl
 
louvainClustering(List<InteractionTriple<Integer>>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.service.DoriClustering
 
LouvainClusteringFacade<T> - Class in org.wallerlab.yoink.clustering
Convenience class to start, populate, cluster and return the results.
LouvainClusteringFacade(String) - Constructor for class org.wallerlab.yoink.clustering.LouvainClusteringFacade
 

M

main(String[]) - Static method in class org.wallerlab.yoink.Yoink
use Spring boot to start Yoink application
MapDifference - Class in org.wallerlab.yoink.math.map
this class is to get the difference of two maps
MapDifference() - Constructor for class org.wallerlab.yoink.math.map.MapDifference
 
MapSorter - Class in org.wallerlab.yoink.math.map
This calss is to sort a map
MapSorter() - Constructor for class org.wallerlab.yoink.math.map.MapSorter
 
marshal() - Method in class org.wallerlab.yoink.molecular.data.AbstractJaxbWriter
 
marshal() - Method in class org.wallerlab.yoink.molecular.data.JaxbFileWriter
 
marshal() - Method in class org.wallerlab.yoink.molecular.data.JaxbStringWriter
 
marshall() - Method in class org.wallerlab.yoink.molecular.data.AbstractJaxbWriter
use JAXB writer to write out an instance to a file.
MathConfig - Class in org.wallerlab.yoink.math.config
This class is to make configuration for project Math
MathConfig() - Constructor for class org.wallerlab.yoink.math.config.MathConfig
 
Matrix<T> - Interface in org.wallerlab.yoink.api.service.math
It is an interface for external Matrix libraries.
matrix() - Method in class org.wallerlab.yoink.math.linear.SimpleMatrixFactory
 
Matrix.Type - Enum in org.wallerlab.yoink.api.service.math
matrix type is named after the library it is in.
matrix3x3() - Method in class org.wallerlab.yoink.math.linear.SimpleMatrixFactory
 
MMProcessor - Class in org.wallerlab.yoink.processor.service.chem
this class is to call MM calculation
MMProcessor() - Constructor for class org.wallerlab.yoink.processor.service.chem.MMProcessor
 
MolecularConfig - Class in org.wallerlab.yoink.molecular.config
this class is to configure molecular project
MolecularConfig() - Constructor for class org.wallerlab.yoink.molecular.config.MolecularConfig
 
MolecularDensityRatioCalculator - Class in org.wallerlab.yoink.density.service.density
this class is to get the density ratio of two molecules on a grid point.
MolecularDensityRatioCalculator() - Constructor for class org.wallerlab.yoink.density.service.density.MolecularDensityRatioCalculator
 
MolecularSystem - Interface in org.wallerlab.yoink.api.model.molecular
this interface is for domain model MolecularSystem
MolecularSystemTranslator - Class in org.wallerlab.yoink.molecular.service.translator
This class is to translate JAXB Cml to MolecularSystem model.
MolecularSystemTranslator() - Constructor for class org.wallerlab.yoink.molecular.service.translator.MolecularSystemTranslator
 
molecularSystemTranslator - Variable in class org.wallerlab.yoink.service.jobbuilder.AbstractJobBuilder
 
Molecule - Interface in org.wallerlab.yoink.api.model.molecular
this interface is for domain model Molecule
MorokumaSmoothFunction - Class in org.wallerlab.yoink.adaptive.smooth.smoothfunction
this class is for smooth function used in ONIOM-XS.
MorokumaSmoothFunction() - Constructor for class org.wallerlab.yoink.adaptive.smooth.smoothfunction.MorokumaSmoothFunction
 

N

name - Variable in class org.wallerlab.yoink.molecular.domain.SimpleMolecule
 
newTimer() - Static method in class org.wallerlab.yoink.clustering.utils.Timer
 
NumberRegionizer - Class in org.wallerlab.yoink.regionizer.service
this class is the calculation of number based qm/mm partitioning.
NumberRegionizer() - Constructor for class org.wallerlab.yoink.regionizer.service.NumberRegionizer
 

O

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

P

PAPAdaptiveProcessor - Class in org.wallerlab.yoink.processor.service
This class is to get PAP adaptive energy and force
PAPAdaptiveProcessor() - Constructor for class org.wallerlab.yoink.processor.service.PAPAdaptiveProcessor
 
ParameterRegionizer - Class in org.wallerlab.yoink.regionizer.service
this class is for parameter based adaptive qm/mm partitioning (distance and number).
ParameterRegionizer() - Constructor for class org.wallerlab.yoink.regionizer.service.ParameterRegionizer
 
ParameterTranslator - Class in org.wallerlab.yoink.molecular.service.translator
this class is to get a Map(JobParameter - JobParameter, Object) by parsing ParameterList in JAXBElement Cml.
ParameterTranslator() - Constructor for class org.wallerlab.yoink.molecular.service.translator.ParameterTranslator
 
parameterTranslator - Variable in class org.wallerlab.yoink.service.jobbuilder.AbstractJobBuilder
 
partition(Map<Region.Name, Region>, Map<JobParameter, Object>, V) - Method in interface org.wallerlab.yoink.api.service.regionizer.Partitioner
 
partition(Map<Region.Name, Region>, Map<JobParameter, Object>, DensityPoint.DensityType) - Method in class org.wallerlab.yoink.regionizer.partitioner.CubePartitioner
loop over all grid points in the cube, find the grid points whose two closest neighbours are from different regions(QM core region and non-QM core region ).
partition(Map<Region.Name, Region>, Map<JobParameter, Object>, DensityPoint.DensityType) - Method in class org.wallerlab.yoink.regionizer.partitioner.DensityPartitioner
based on the density of QM core , define adaptive search region , the non-QM core molecules in adaptive search region, and buffer region.
partition(Map<Region.Name, Region>, Map<JobParameter, Object>, List<GridPoint>) - Method in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
Partitioner<K,V> - Interface in org.wallerlab.yoink.api.service.regionizer
this interface contains method partition() and enum Partitioner.Type.
Partitioner.Type - Enum in org.wallerlab.yoink.api.service.regionizer
 
PermutedSmoothFunction - Class in org.wallerlab.yoink.adaptive.smooth.smoothfunction
this class is for smooth function used in PAP and SAP.
PermutedSmoothFunction() - Constructor for class org.wallerlab.yoink.adaptive.smooth.smoothfunction.PermutedSmoothFunction
 
PI - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
populate(Set<Set<T>>) - Method in class org.wallerlab.yoink.clustering.LouvainClusteringFacade
Creates the graph from the provided interacting pairs.
populate(List<InteractionTriple<T>>) - Method in class org.wallerlab.yoink.clustering.LouvainClusteringFacade
 
process(Job<JAXBElement>) - Method in class org.wallerlab.yoink.service.jobbuilder.AbstractJobBuilder
 
process(List<File>) - Method in class org.wallerlab.yoink.service.processor.AdaptiveQMMMProcessor
read in a list of requests and execute them.
process(String) - Method in class org.wallerlab.yoink.service.processor.FileAdaptiveQMMMProcessor
read in a list of requests and execute them.
process(String) - Method in class org.wallerlab.yoink.service.processor.FileClusteringProcessor
read in a list of requests and execute them.
process(String) - Method in class org.wallerlab.yoink.service.processor.FileInteractionSetProcessor
read in a list of requests and execute them.
process(JAXBElement) - Method in class org.wallerlab.yoink.service.processor.SerialAdaptiveQMMMProcessor
read in a list of requests and execute them.
process(JAXBElement) - Method in class org.wallerlab.yoink.service.processor.SerialClusteringProcessor
read in a list of requests and execute them.
process(String) - Method in class org.wallerlab.yoink.service.processor.StringAdaptiveQMMMProcessor
read in a list of inputsand execute them.
ProcessorConfig - Class in org.wallerlab.yoink.processor.config
This class is to make configuration for project Processor
ProcessorConfig() - Constructor for class org.wallerlab.yoink.processor.config.ProcessorConfig
 
propertySourcesPlaceholderConfigurer() - Static method in class org.wallerlab.yoink.config.BatchConfig
 
propertyWrapper - Variable in class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
PropertyWrapper - Class in org.wallerlab.yoink.service
this class is to wrap adaptive qmmm result to JAXB element PropertyList
PropertyWrapper() - Constructor for class org.wallerlab.yoink.service.PropertyWrapper
 

Q

QMMMProcessor - Class in org.wallerlab.yoink.processor.service.chem
this class is to call QM/MM calculation
QMMMProcessor() - Constructor for class org.wallerlab.yoink.processor.service.chem.QMMMProcessor
 
QMProcessor - Class in org.wallerlab.yoink.processor.service.chem
this class is to call QM calculation
QMProcessor() - Constructor for class org.wallerlab.yoink.processor.service.chem.QMProcessor
 

R

RadialGrid - Interface in org.wallerlab.yoink.api.model.molecular
 
RadialGridReader - Class in org.wallerlab.yoink.molecular.data
 
RadialGridReader() - Constructor for class org.wallerlab.yoink.molecular.data.RadialGridReader
 
radialGridReader - Variable in class org.wallerlab.yoink.regionizer.partitioner.DensityPartitioner
 
radialGridReader - Variable in class org.wallerlab.yoink.service.clustering.InteractionSet
 
RDG_COEFFICIENT - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
RDG_DEFAULT - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
read(K, T) - Method in interface org.wallerlab.yoink.api.service.molecular.FilesReader
 
read(String, Object) - Method in class org.wallerlab.yoink.molecular.data.AbstractJaxbReader
 
read(String, Object) - Method in class org.wallerlab.yoink.molecular.data.JaxbFileReader
jaxb reader to read in an instance from a file.
read(String, Object) - Method in class org.wallerlab.yoink.molecular.data.JaxbStringReader
jaxb reader to read in an instance from a file.
read(String, RadialGrid) - Method in class org.wallerlab.yoink.molecular.data.RadialGridReader
 
read() - Method in class org.wallerlab.yoink.service.request.CmlFilesRequest
get all xml files in the input directory
read() - Method in class org.wallerlab.yoink.service.request.JmsRequestReader
 
readInMolecularSystem(Job<JAXBElement>) - Method in class org.wallerlab.yoink.service.jobbuilder.AbstractJobBuilder
 
readInParameters(Job<JAXBElement>) - Method in class org.wallerlab.yoink.service.jobbuilder.AbstractJobBuilder
 
readWFC(Map<JobParameter, Object>, Region) - Method in class org.wallerlab.yoink.regionizer.partitioner.DensityPartitioner
 
ReducedDensityGradientComputer - Class in org.wallerlab.yoink.density.service.densityProperties
This class is to get the reduced density gradient(RDG) value of a point.
ReducedDensityGradientComputer() - Constructor for class org.wallerlab.yoink.density.service.densityProperties.ReducedDensityGradientComputer
 
Region - Interface in org.wallerlab.yoink.api.model.regionizer
this interface is for domain model region which contains a certain type of molecules
Region.Name - Enum in org.wallerlab.yoink.api.model.regionizer
the names of regions used during adaptive QM/MM partitioning
regionize(Map<Region.Name, Region>, K) - Method in interface org.wallerlab.yoink.api.service.regionizer.Regionizer
 
regionize(Map<Region.Name, Region>, K) - Method in interface org.wallerlab.yoink.api.service.regionizer.RegionizerComponent
 
regionize(Map<Region.Name, Region>, K) - Method in interface org.wallerlab.yoink.api.service.regionizer.RegionizerMath
 
regionize(Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.AdaptiveRegionizer
set up adaptive QM region partitioning first, density partitioner finds those molecules for cube building second, cube partitioner finds those grid points for the following density interaction analysis third, partitioner is to do interaction analysis to find the adaptive QM or adaptive QM core
regionize(Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.BufferRegionizer
set up buffer region partitioning
regionize(Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.DensityBasedRegionizer
execute density based adaptive regionizer by looping over all regionizer components in it
regionize(Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.DistanceRegionizer
 
regionize(Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.NumberRegionizer
 
regionize(Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.ParameterRegionizer
 
regionize(Map<Region.Name, Region>, MolecularSystem) - Method in class org.wallerlab.yoink.regionizer.service.RegionizerService
choose the corresponding region for every element in regionNames
regionize(Map<Region.Name, Region>, Region.Name) - Method in class org.wallerlab.yoink.regionizer.service.SingleRegionizerService
get the region content for a given region name
regionize(Map<Region.Name, Region>, Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.regionizer.service.SizeConsistentRegionizer
 
regionize(Job) - Method in class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
Regionizer<T,K> - Interface in org.wallerlab.yoink.api.service.regionizer
this interface is for region operations
RegionizerComponent<T,K> - Interface in org.wallerlab.yoink.api.service.regionizer
this interface is for region operations
RegionizerConfig - Class in org.wallerlab.yoink.regionizer.config
This class is the configuration for regionizer project.
RegionizerConfig() - Constructor for class org.wallerlab.yoink.regionizer.config.RegionizerConfig
 
RegionizerMath<T,K> - Interface in org.wallerlab.yoink.api.service.regionizer
this interface is for region operations
RegionizerService - Class in org.wallerlab.yoink.regionizer.service
this class is to get molecules for those regions in the List regionNames.
RegionizerService() - Constructor for class org.wallerlab.yoink.regionizer.service.RegionizerService
 
regionizerServiceEnding - Variable in class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
regionizerServiceStarting - Variable in class org.wallerlab.yoink.service.processor.AbstractAdaptiveQMMMProcessor
 
regionizerServiceStarting - Variable in class org.wallerlab.yoink.service.processor.AbstractClusteringProcessor
 
regionizerServiceStarting - Variable in class org.wallerlab.yoink.service.processor.FileClusteringProcessor
 
regionizerServiceStarting - Variable in class org.wallerlab.yoink.service.processor.FileInteractionSetProcessor
 
regionizerServiceStarting - Variable in class org.wallerlab.yoink.service.processor.SerialClusteringProcessor
 
regionName - Variable in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
run(Job<JAXBElement>) - Method in interface org.wallerlab.yoink.api.service.adaptiveProcessor.AdaptiveProcessor
this method is to process energy and force during adaptive qm/mm.
run(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.chem.MMProcessor
 
run(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.chem.QMMMProcessor
 
run(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.chem.QMProcessor
 

S

SAPWeightFactors - Class in org.wallerlab.yoink.adaptive.smooth
this class is to get weight factor in SAP.
SAPWeightFactors() - Constructor for class org.wallerlab.yoink.adaptive.smooth.SAPWeightFactors
 
scalarMultiply(double) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
scalar this matrix with a double value
scalarMultiply(double) - Method in interface org.wallerlab.yoink.api.service.math.Vector
multiply this vector with a scalar value
scalarMultiply(double) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
scalarMultiply(double) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
SCMPSmoothFunction - Class in org.wallerlab.yoink.adaptive.smooth.smoothfunction
this class is for one smooth function used in SCMP for QM lambda.
SCMPSmoothFunction() - Constructor for class org.wallerlab.yoink.adaptive.smooth.smoothfunction.SCMPSmoothFunction
 
SCMPWeightFactors - Class in org.wallerlab.yoink.adaptive.smooth
this class is to get weight factor in SCMP.
SCMPWeightFactors() - Constructor for class org.wallerlab.yoink.adaptive.smooth.SCMPWeightFactors
 
second - Variable in class org.wallerlab.yoink.clustering.InteractionTriple
 
SEDD_DEFAULT - Static variable in class org.wallerlab.yoink.math.constants.Constants
 
SerialAdaptiveQMMMProcessor - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute adaptive QM/MM partitioning.
SerialAdaptiveQMMMProcessor() - Constructor for class org.wallerlab.yoink.service.processor.SerialAdaptiveQMMMProcessor
 
SerialClusteringProcessor - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute clustering.
SerialClusteringProcessor() - Constructor for class org.wallerlab.yoink.service.processor.SerialClusteringProcessor
 
serviceStep(StepBuilderFactory, ItemReader<List<File>>, ItemProcessor<List<File>, List<Job>>, ItemWriter<List<Job>>) - Method in class org.wallerlab.yoink.config.BatchConfig
build executing steps
setA(double) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setA(double) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setApplicationContext(ApplicationContext) - Method in class org.wallerlab.yoink.config.BatchConfig
 
setApplicationContext(ApplicationContext) - Method in class org.wallerlab.yoink.density.config.DensityConfig
 
setApplicationContext(ApplicationContext) - Method in class org.wallerlab.yoink.molecular.config.MolecularConfig
 
setB(double) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setB(double) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setCenterOfMass(Coord) - Method in interface org.wallerlab.yoink.api.model.molecular.Molecule
set the center of mass of this molecule.
setCenterOfMass(Coord) - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecule
 
setCenterOfMassComputer(Computer<Coord, Set<Molecule>>) - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
set the value of CenterOfMassComputer
setCenterOfMassComputer(Computer<Coord, Set<Molecule>>) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
set the value of this.centerOfMassComputer
setClusters(List<Set<Integer>>) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the clustering result
setClusters(List<Set<Integer>>) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
setCoordinate(Coord) - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
set the coordinate of a grid point
setCoordinate(Coord) - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
setCoordinates(List<Coord>) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set the coordinates of grid points in the cube
setCoordinates(List<Coord>) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
setCoords(Vector) - Method in interface org.wallerlab.yoink.api.model.molecular.Coord
set the value of coordinate
setCoords(Vector) - Method in class org.wallerlab.yoink.molecular.domain.SimpleCoord
set the value of the coordinates
setDensity(double) - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
set the value of density at this point
setDensity(double) - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
set density
setDensityTypes(List<DensityPoint.DensityType>) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set the value of density types of the cube
setDensityTypes(List<DensityPoint.DensityType>) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
SetDifference - Class in org.wallerlab.yoink.math.set
this class is to calculate the difference of two sets
SetDifference() - Constructor for class org.wallerlab.yoink.math.set.SetDifference
 
setElementType(Element) - Method in interface org.wallerlab.yoink.api.model.density.ElementVector
set the value of element.
setEntry(int, int, double) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
set the value of one element in this matrix
setEntry(int, int, double) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
setFirst_derivative_of_grid_values(double[]) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setFirst_derivative_of_grid_values(double[]) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setGradient(double) - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
set the density gradient value at this point
setGradient(double) - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
set gradient
setGradientVector(Vector) - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
set the value of density gradient vector at this point
setGradientVector(Vector) - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
set gradient vector.
setGrid_positions(double[]) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setGrid_positions(double[]) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setGrid_values(double[]) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setGrid_values(double[]) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setGridOrigin(Coord) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set the value of origin coordinate of the cube
setGridOrigin(Coord) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
setHessian(Matrix) - Method in interface org.wallerlab.yoink.api.model.density.DensityPoint
set the hessian matrix at this point
setHessian(Matrix) - Method in class org.wallerlab.yoink.density.domain.SimpleDensityPoint
set hessian
setIndexInCube(int) - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
set the index of a grid point in cube
setIndexInCube(int) - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
setInput(T) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the value of input in the job
setInput(JAXBElement) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
SetInteractionList(List<List<Integer>>) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the interaction pairs
SetInteractionList(List<List<Integer>>) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
SetInteractionWeight(List<Double>) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the weight(strength) of the interaction
SetInteractionWeight(List<Double>) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
setInternalMatrix(T) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
set the value of internal matrix of this matrix
setInternalMatrix(RealMatrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
setInternalVector(T) - Method in interface org.wallerlab.yoink.api.service.math.Vector
set the value of internal vector
setInternalVector(Vector3D) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
setJmsItemReader(ItemReader<String>) - Method in class org.wallerlab.yoink.service.request.JmsRequestReader
 
setJmsItemWriter(ItemWriter<String>) - Method in class org.wallerlab.yoink.service.response.JmsJobItemWriter
 
setMatrixType(Matrix.Type) - Method in class org.wallerlab.yoink.math.linear.SimpleMatrixFactory
 
setMolecularMap(Map<Molecule, Integer>) - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
set the value of moleculeMap
setMolecularMap(Map<Molecule, Integer>) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
set the molecularMap in the region
setMolecularSystem(MolecularSystem) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the value of molecular system
setMolecularSystem(MolecularSystem) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
setMolecules(Set<Molecule>) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set the value of molecules in the cube
setMolecules(Set<Molecule>) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
setMyVectorType(Vector.Vector3DType) - Method in class org.wallerlab.yoink.math.linear.SimpleVector3DFactory
set the value of myVectorType
setName(String) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set the name of the cube
setName(Region.Name) - Method in interface org.wallerlab.yoink.api.model.molecular.Molecule
set the name of molecule.
setName(Region.Name) - Method in interface org.wallerlab.yoink.api.model.regionizer.Region
set the name of the region
setName(String) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
setName(Region.Name) - Method in class org.wallerlab.yoink.molecular.domain.SimpleMolecule
set the molecular name
setName(Region.Name) - Method in class org.wallerlab.yoink.regionizer.domain.SimpleRegion
set the name of the region
setNgrid(int) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setNgrid(int) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setNumberOfXYZSteps(int[]) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set the number of steps along xyz axes
setNumberOfXYZSteps(int[]) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
setOutput(StringWriter) - Method in class org.wallerlab.yoink.molecular.data.JaxbStringWriter
 
setParameters(Map<JobParameter, Object>) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the value of parameters
setParameters(Map<JobParameter, Object>) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
setPosition_max(double) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setPosition_max(double) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setProperties(Map<String, Object>) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the value of properties in the job.
setProperties(Map<String, V>) - Method in interface org.wallerlab.yoink.api.model.cube.GridPoint
set the value of properties
setProperties(Map<String, V>) - Method in class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
setProperties(Map<String, Object>) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
setRadialGrid(RadialGrid) - Method in interface org.wallerlab.yoink.api.model.molecular.Atom
set the radial grid
setRadialGrid(RadialGrid) - Method in class org.wallerlab.yoink.molecular.domain.SimpleAtom
get the radial grid
setRegionNames(List<Region.Name>) - Method in class org.wallerlab.yoink.regionizer.service.RegionizerService
set the region names
setRegions(Map<Region.Name, Region>) - Method in interface org.wallerlab.yoink.api.model.bootstrap.Job
set the value of regions in the job
setRegions(Map<Region.Name, Region>) - Method in class org.wallerlab.yoink.domain.AdaptiveQMMMJob
 
setSecond_derivative_of_grid_values(double[]) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setSecond_derivative_of_grid_values(double[]) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setSize(int) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set the number of grid points in the cube
setSize(int) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
setSquare_position_max(double) - Method in interface org.wallerlab.yoink.api.model.molecular.RadialGrid
 
setSquare_position_max(double) - Method in class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
setValues(List<Double>) - Method in interface org.wallerlab.yoink.api.model.cube.Cube
set teh values of grid points in the cube
setValues(List<Double>) - Method in class org.wallerlab.yoink.cube.domain.SimpleCube
 
shutdown() - Method in class org.wallerlab.yoink.clustering.DatabaseService
 
shutdown() - Method in class org.wallerlab.yoink.clustering.LouvainClusteringFacade
 
SilvaDensityComputer - Class in org.wallerlab.yoink.density.service.densityProperties
This class is to do Silva density analysis calculation for a point.
SilvaDensityComputer() - Constructor for class org.wallerlab.yoink.density.service.densityProperties.SilvaDensityComputer
 
SimpleAtom - Class in org.wallerlab.yoink.molecular.domain
the domain model of atom
SimpleAtom(int, Element, Coord) - Constructor for class org.wallerlab.yoink.molecular.domain.SimpleAtom
 
SimpleCoord - Class in org.wallerlab.yoink.molecular.domain
this domain model of coordinate stores the information of coordinate in the format of 3D vector.
SimpleCoord(Vector) - Constructor for class org.wallerlab.yoink.molecular.domain.SimpleCoord
construct a new simple coord with its coordinate vector
SimpleCoord() - Constructor for class org.wallerlab.yoink.molecular.domain.SimpleCoord
 
SimpleCoordFactory - Class in org.wallerlab.yoink.molecular.domain
factory to generate new SimpleCoord instance
SimpleCoordFactory() - Constructor for class org.wallerlab.yoink.molecular.domain.SimpleCoordFactory
 
SimpleCube - Class in org.wallerlab.yoink.cube.domain
Cube domain Model stores all information about cube.
SimpleCube(double[]) - Constructor for class org.wallerlab.yoink.cube.domain.SimpleCube
use xyz step sizes construct a cube and convert the unit of step size from angstrom to bohr
SimpleCube(int) - Constructor for class org.wallerlab.yoink.cube.domain.SimpleCube
Construct when size is known, or use setter to set number of size
SimpleCube() - Constructor for class org.wallerlab.yoink.cube.domain.SimpleCube
default cube constructor
SimpleDensityPoint - Class in org.wallerlab.yoink.density.domain
This class is to store all density based properties on a point, those properties will be used during DORI/SEDD/RDG calculation.
SimpleDensityPoint() - Constructor for class org.wallerlab.yoink.density.domain.SimpleDensityPoint
 
SimpleDensityPoint(Coord) - Constructor for class org.wallerlab.yoink.density.domain.SimpleDensityPoint
 
SimpleDensityPointFactory - Class in org.wallerlab.yoink.density.domain
 
SimpleDensityPointFactory() - Constructor for class org.wallerlab.yoink.density.domain.SimpleDensityPointFactory
 
SimpleGridPoint<String,V> - Class in org.wallerlab.yoink.cube.domain
This domain model is to store information and properties of a grid point
SimpleGridPoint() - Constructor for class org.wallerlab.yoink.cube.domain.SimpleGridPoint
 
SimpleMatrixFactory - Class in org.wallerlab.yoink.math.linear
 
SimpleMatrixFactory() - Constructor for class org.wallerlab.yoink.math.linear.SimpleMatrixFactory
 
SimpleMolecularSystem - Class in org.wallerlab.yoink.molecular.domain
the domain model for molecular system.
SimpleMolecularSystem(List<Molecule>) - Constructor for class org.wallerlab.yoink.molecular.domain.SimpleMolecularSystem
 
SimpleMolecule - Class in org.wallerlab.yoink.molecular.domain
the domain model for molecule.
SimpleMolecule(int, List<Atom>) - Constructor for class org.wallerlab.yoink.molecular.domain.SimpleMolecule
 
SimpleRadialGrid - Class in org.wallerlab.yoink.molecular.domain
 
SimpleRadialGrid() - Constructor for class org.wallerlab.yoink.molecular.domain.SimpleRadialGrid
 
SimpleRegion - Class in org.wallerlab.yoink.regionizer.domain
This domain model Region contains a certain type molecules.
SimpleRegion() - Constructor for class org.wallerlab.yoink.regionizer.domain.SimpleRegion
default Region constructor
SimpleRegion(Region.Name) - Constructor for class org.wallerlab.yoink.regionizer.domain.SimpleRegion
construct a new Region with the region name
SimpleRegionFactory - Class in org.wallerlab.yoink.regionizer.domain
factory to generate new SimpleRegion instance
SimpleRegionFactory() - Constructor for class org.wallerlab.yoink.regionizer.domain.SimpleRegionFactory
 
simpleRegionFactory - Variable in class org.wallerlab.yoink.regionizer.service.ParameterRegionizer
 
SimpleVector3DFactory - Class in org.wallerlab.yoink.math.linear
this class is Vector 3D factory
SimpleVector3DFactory() - Constructor for class org.wallerlab.yoink.math.linear.SimpleVector3DFactory
 
SimpleVector3DFactory(Vector.Vector3DType) - Constructor for class org.wallerlab.yoink.math.linear.SimpleVector3DFactory
 
SingleExponentialDecayDetectorComputer - Class in org.wallerlab.yoink.density.service.densityProperties
This class is to get the single exponential decay detector(SEDD) value of a grid point.
SingleExponentialDecayDetectorComputer() - Constructor for class org.wallerlab.yoink.density.service.densityProperties.SingleExponentialDecayDetectorComputer
 
SingleExponentialDecayDetectorPartitioner - Class in org.wallerlab.yoink.regionizer.partitioner
This class is to analyze SEDD for those grid points in the intersection between QM core region and non-QM core region based on Voronoi partitioning.
SingleExponentialDecayDetectorPartitioner() - Constructor for class org.wallerlab.yoink.regionizer.partitioner.SingleExponentialDecayDetectorPartitioner
 
singleRegionizerService - Variable in class org.wallerlab.yoink.regionizer.partitioner.InteractionPartitioner
 
SingleRegionizerService - Class in org.wallerlab.yoink.regionizer.service
this class is to get molecules in one region
SingleRegionizerService() - Constructor for class org.wallerlab.yoink.regionizer.service.SingleRegionizerService
 
SizeConsistentRegionizer - Class in org.wallerlab.yoink.regionizer.service
this class is the calculation of size consistent qm/mm partitioning.
SizeConsistentRegionizer() - Constructor for class org.wallerlab.yoink.regionizer.service.SizeConsistentRegionizer
 
smooth(Job) - Method in class org.wallerlab.yoink.adaptive.smooth.AdaptiveQMMMSmoothnerRouter
 
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.adaptive.smooth.DASWeightFactors
use smooth factors to calculate the weight factors.
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.adaptive.smooth.FIRESmoothner
 
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.adaptive.smooth.SAPWeightFactors
use smooth factors to calculate the weight factors.
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.adaptive.smooth.SCMPWeightFactors
use smooth factors to calculate the weight factors.
smooth(Job) - Method in class org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl
calculate smooth factors for molecules in buffer region
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.adaptive.smooth.XSWeightFactors
use smooth factors to calculate the weight factors.
smooth(Job<JAXBElement>) - Method in interface org.wallerlab.yoink.api.service.adaptive.Smoothner
calculate smoothing factors for buffer region
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.BufferAdaptiveProcessor
 
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.ConfigurationAdaptiveProcessor
 
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.FIRESAdaptiveProcessor
 
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.HOTSPOTAdaptiveProcessor
 
smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.PAPAdaptiveProcessor
 
SmoothFunction - Interface in org.wallerlab.yoink.api.service.adaptive
this interface is for the smooth function
Smoothner - Interface in org.wallerlab.yoink.api.service.adaptive
this interface contains method smooth and enum smoothner type
Smoothner.Type - Enum in org.wallerlab.yoink.api.service.adaptive
 
SmoothnerImpl - Class in org.wallerlab.yoink.adaptive.smooth
this class is for smoothing the buffer region.
SmoothnerImpl(SmoothFunction) - Constructor for class org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl
SmoothnerImpl constructor with specified smooth function.
sortByValue(Map<K, V>) - Static method in class org.wallerlab.yoink.math.map.MapSorter
This method is to sort a map by its value in ascending way.
SortedDistancesCalculator - Class in org.wallerlab.yoink.molecular.service.calculator
This class is to get the sortedDistances which is a Map(molecule as key and distance as value) sorted by distance in ascending way.
SortedDistancesCalculator() - Constructor for class org.wallerlab.yoink.molecular.service.calculator.SortedDistancesCalculator
 
split(int[]) - Static method in class org.wallerlab.yoink.math.set.Subsets
 
split(int[], int) - Static method in class org.wallerlab.yoink.math.set.Subsets
this method is to get all subsets with the same size of an integer array.
splitDoubleArray(double[]) - Static method in class org.wallerlab.yoink.math.set.Subsets
 
start() - Method in class org.wallerlab.yoink.clustering.utils.Timer
 
startDb() - Method in class org.wallerlab.yoink.clustering.DatabaseService
 
stop() - Method in class org.wallerlab.yoink.clustering.utils.Timer
 
StringAdaptiveQMMMProcessor - Class in org.wallerlab.yoink.service.processor
This class is to set up and execute adaptive QM/MM partitioning.
StringAdaptiveQMMMProcessor() - Constructor for class org.wallerlab.yoink.service.processor.StringAdaptiveQMMMProcessor
 
Subsets - Class in org.wallerlab.yoink.math.set
this class is to get all subsets of an integer array,return an list of integer lists
Subsets() - Constructor for class org.wallerlab.yoink.math.set.Subsets
 
subtract(Matrix) - Method in interface org.wallerlab.yoink.api.service.math.Matrix
subtract one matrix from this matrix
subtract(Vector) - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the result of this vector subtracts another vector
subtract(Matrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
subtract(Vector) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 

T

te - Variable in class org.wallerlab.yoink.clustering.utils.Timer
 
Timer - Class in org.wallerlab.yoink.clustering.utils
 
Timer() - Constructor for class org.wallerlab.yoink.clustering.utils.Timer
 
timer() - Static method in class org.wallerlab.yoink.clustering.utils.Timer
 
toArray() - Method in interface org.wallerlab.yoink.api.service.math.Vector
get the value of this vector in the form of a double array
toArray() - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
 
totalTime() - Method in class org.wallerlab.yoink.clustering.utils.Timer
 
translate(K) - Method in interface org.wallerlab.yoink.api.service.molecular.Translator
 
translate(JAXBElement<Cml>) - Method in class org.wallerlab.yoink.molecular.service.translator.MolecularSystemTranslator
translate JAXBElement Cml to MolecularSystem
translate(JAXBElement<Cml>) - Method in class org.wallerlab.yoink.molecular.service.translator.ParameterTranslator
get parameters a Map(JobParameter - JobParameter, Object) from JAXBElement ParameterList ParameterList in JAXBElement Cml Cml.
Translator<T,K> - Interface in org.wallerlab.yoink.api.service.molecular
this interface is for method translate K to T
transpose() - Method in interface org.wallerlab.yoink.api.service.math.Matrix
transpose this matrix
transpose() - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
 
ts - Variable in class org.wallerlab.yoink.clustering.utils.Timer
 
TwoAtomsDistanceCalculator - Class in org.wallerlab.yoink.molecular.service.calculator
this class is to get the distance between two atoms
TwoAtomsDistanceCalculator() - Constructor for class org.wallerlab.yoink.molecular.service.calculator.TwoAtomsDistanceCalculator
 
TwoCoordsDistanceCalculator - Class in org.wallerlab.yoink.molecular.service.calculator
This class is to calculate the distance between two points
TwoCoordsDistanceCalculator() - Constructor for class org.wallerlab.yoink.molecular.service.calculator.TwoCoordsDistanceCalculator
 

U

unmarshal(Object) - Method in class org.wallerlab.yoink.molecular.data.AbstractJaxbReader
 
unmarshal(Object) - Method in class org.wallerlab.yoink.molecular.data.JaxbFileReader
 
unmarshal(Object) - Method in class org.wallerlab.yoink.molecular.data.JaxbStringReader
 

V

value() - Method in enum org.wallerlab.yoink.api.service.molecular.Converter.UnitConverterType
 
valueOf(String) - Static method in enum org.wallerlab.yoink.api.model.bootstrap.JobParameter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.model.density.DensityPoint.DensityType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.model.molecular.Element
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.model.regionizer.Region.Name
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.service.adaptive.Smoothner.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.service.math.Matrix.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.service.math.Vector.Vector3DType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.service.molecular.Converter.UnitConverterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.wallerlab.yoink.api.service.regionizer.Partitioner.Type
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.wallerlab.yoink.api.model.bootstrap.JobParameter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.model.density.DensityPoint.DensityType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.model.molecular.Element
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.model.regionizer.Region.Name
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.service.adaptive.Smoothner.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.service.math.Matrix.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.service.math.Vector.Vector3DType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.service.molecular.Converter.UnitConverterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.wallerlab.yoink.api.service.regionizer.Partitioner.Type
Returns an array containing the constants of this enum type, in the order they are declared.
Vector<T> - Interface in org.wallerlab.yoink.api.service.math
It is an interface for external Vector libraries and enum of 3D Vector types.
Vector.Vector3DType - Enum in org.wallerlab.yoink.api.service.math
3D Vector type is named after the library it is in.
vector3D() - Method in class org.wallerlab.yoink.math.linear.SimpleMatrixFactory
 
VoronoiCalculator - Class in org.wallerlab.yoink.cube.service
This class assigns a grid point to two molecules and two atoms it is closest to based on Voronoi partitioning and returns two molecules and two atoms in a map.
VoronoiCalculator() - Constructor for class org.wallerlab.yoink.cube.service.VoronoiCalculator
 

W

weight - Variable in class org.wallerlab.yoink.clustering.InteractionTriple
 
wrap(T) - Method in interface org.wallerlab.yoink.api.service.bootstrap.Wrapper
 
wrap(Job<JAXBElement>) - Method in class org.wallerlab.yoink.service.PropertyWrapper
wrap molecular name( Region.Name, like QM or QM_ADAPTIVE) and buffer region smoothing in JAXBElemnt Cml
Wrapper<T> - Interface in org.wallerlab.yoink.api.service.bootstrap
this interface is for wrapping certain data
write(String, T) - Method in interface org.wallerlab.yoink.api.service.molecular.FilesWriter
 
write(String, Object) - Method in class org.wallerlab.yoink.molecular.data.JaxbFileWriter
use JAXB writer to write out an instance to a file.
write(String, Object) - Method in class org.wallerlab.yoink.molecular.data.JaxbStringWriter
use JAXB writer to write out an instance to string.
write(List<? extends Job<JAXBElement>>) - Method in class org.wallerlab.yoink.service.response.CmlFileResponseWriter
write adaptive qmmm result into a cml file.
write(List<? extends List<Job<JAXBElement>>>) - Method in class org.wallerlab.yoink.service.response.CmlFilesResponse
write adaptive qmmm result into a cml file.
write(List<? extends Job>) - Method in class org.wallerlab.yoink.service.response.JmsJobItemWriter
write adaptive QM/MM result into a String, and then send to a JMS queue.

X

XSWeightFactors - Class in org.wallerlab.yoink.adaptive.smooth
this class is to get weight factor in XS.
XSWeightFactors() - Constructor for class org.wallerlab.yoink.adaptive.smooth.XSWeightFactors
 

Y

Yoink - Class in org.wallerlab.yoink
This class is the main class of Yoink
Yoink() - Constructor for class org.wallerlab.yoink.Yoink
 

Z

z1() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
z2() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
z3() - Method in enum org.wallerlab.yoink.api.model.molecular.Element
 
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