- 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
-
- 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
-
- 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
-
- 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
-
- 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
- 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
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use smooth factors to calculate the weight factors.
- smooth(Job) - Method in class org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl
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calculate smooth factors for molecules in buffer region
- smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.adaptive.smooth.XSWeightFactors
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use smooth factors to calculate the weight factors.
- smooth(Job<JAXBElement>) - Method in interface org.wallerlab.yoink.api.service.adaptive.Smoothner
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calculate smoothing factors for buffer region
- smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.BufferAdaptiveProcessor
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- smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.ConfigurationAdaptiveProcessor
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- smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.FIRESAdaptiveProcessor
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- smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.HOTSPOTAdaptiveProcessor
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- smooth(Job<JAXBElement>) - Method in class org.wallerlab.yoink.processor.service.PAPAdaptiveProcessor
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- 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
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- 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
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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
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- 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
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- 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
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get the result of this vector subtracts another vector
- subtract(Matrix) - Method in class org.wallerlab.yoink.math.linear.CommonsMatrix
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- subtract(Vector) - Method in class org.wallerlab.yoink.math.linear.CommonsVector3D
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- value() - Method in enum org.wallerlab.yoink.api.service.molecular.Converter.UnitConverterType
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- 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
-