Serialized Form (magpie API)

Package magpie.attributes.expanders
- Class magpie.attributes.expanders.BaseAttributeExpander extends java.lang.Object implements Serializable
- Class magpie.attributes.expanders.CrossExpander extends BaseAttributeExpander implements Serializable
- Class magpie.attributes.expanders.FunctionExpander extends BaseAttributeExpander implements Serializable
  - Serialized Fields
    - Functions
```
java.util.List<E> Functions
```
      List of functions
- Class magpie.attributes.expanders.PowerExpander extends BaseAttributeExpander implements Serializable
  - Serialized Fields
    - Exponent
```
java.util.List<E> Exponent
```
      List of exponents to use when creating new attributes
Package magpie.attributes.generators
- Class magpie.attributes.generators.BaseAttributeGenerator extends java.lang.Object implements Serializable
- Class magpie.attributes.generators.LookupTableAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - LookupTable
```
java.util.List<E> LookupTable
```
      Lookup table for attributes. Key is a string describing an entry, value is a list of attributes to be added.
    - NewNames
```
java.util.List<E> NewNames
```
      New attribute names
- Class magpie.attributes.generators.ModelPredictionAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - ModelName
```
java.lang.String ModelName
```
      Name of model. Used to create unique names for attributes
    - Model
```
BaseModel Model
```
      Model to evaluate
    - ModelData
```
Dataset ModelData
```
      Dataset used to compute attributes for ModelPredictionAttributeGenerator.Model.
- Class magpie.attributes.generators.PropertyAsAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - Properties
```
java.util.Set<E> Properties
```
      List of properties to use as attributes.
Package magpie.attributes.generators.composition
- Class magpie.attributes.generators.composition.APEAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - PackingThreshold
```
double PackingThreshold
```
      Threshold at which to define a cluster as efficiently packed. Packing efficiency is defined by |APE - 1|. Default value for this parameter is 0.01;
    - NNearestToEval
```
java.util.NavigableSet<E> NNearestToEval
```
      Number of nearest clusters to assess.
      Dev Note: NavigableSet ensures that the iterators always goes in the same order. So, you can use this set to iterate w/o needing to first transfer to a list.
    - RadiusProperty
```
java.lang.String RadiusProperty
```
      Name of elemental property to use as atomic radius. By default, uses the radii from doi: 10.1179/095066010X12646898728200.
- Class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - ChargeGuesser
```
OxidationStateGuesser ChargeGuesser
```
      Tool used to compute electronegativity
    - IonizationEnergies
```
double[][] IonizationEnergies
```
      Ionization energies of each element
- Class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - ElementalProperties
```
java.util.List<E> ElementalProperties
```
      Elemental properties used to generate attributes
- Class magpie.attributes.generators.composition.ElementFractionAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.composition.ElementPairPropertyAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - ElementalProperties
```
java.util.List<E> ElementalProperties
```
      Elemental properties used to generate attributes
- Class magpie.attributes.generators.composition.GCLPAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - Calculator
```
GCLPCalculator Calculator
```
      Tool used to compute ground states
    - CountPhases
```
boolean CountPhases
```
      Whether to include the number of phases at equilibrium
- Class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - MaxFormulaUnit
```
int MaxFormulaUnit
```
      Maximum number of atoms per formula unit
- Class magpie.attributes.generators.composition.IonicityAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.composition.MeredigAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.composition.StoichiometricAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - PNorms
```
java.util.Set<E> PNorms
```
      List of p norms to compute
- Class magpie.attributes.generators.composition.ValenceShellAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.composition.YangOmegaAttributeGenerator extends BaseAttributeGenerator implements Serializable
Package magpie.attributes.generators.crystal
- Class magpie.attributes.generators.crystal.APRDFAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - CutoffDistance
```
double CutoffDistance
```
      Cutoff distance for RDF
    - NumPoints
```
int NumPoints
```
      Number of points to evaluate
    - SmoothParameter
```
double SmoothParameter
```
      Smoothing parameter for AP-RDF
    - ElementalProperties
```
java.util.Set<E> ElementalProperties
```
      List of elemental properties to use for weighting
- Class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - Shells
```
java.util.Set<E> Shells
```
      Shells to compute the WC attribute for
    - Weighted
```
boolean Weighted
```
      Whether to compute weighted WC ordering parameters.
- Class magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - NEigenvalues
```
int NEigenvalues
```
      Maximum number of atoms to consider. Defines number of attributes
- Class magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - ElementalProperties
```
java.util.List<E> ElementalProperties
```
      Elemental properties used to generate attributes
    - Shells
```
java.util.Set<E> Shells
```
      Shells to consider.
    - AttrName
```
java.lang.String AttrName
```
      Property name
    - AttrDescription
```
java.lang.String AttrDescription
```
      Property description (used in description output)
- Class magpie.attributes.generators.crystal.LocalPropertyVarianceAttributeGenerator extends LocalPropertyDifferenceAttributeGenerator implements Serializable
- Class magpie.attributes.generators.crystal.PackingEfficiencyAttributeGenerator extends BaseAttributeGenerator implements Serializable
- Class magpie.attributes.generators.crystal.PRDFAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - CutoffDistance
```
double CutoffDistance
```
      Cutoff distance for PRDF
    - NPoints
```
int NPoints
```
      Number of distance points to evaluate
    - ElementList
```
java.util.SortedSet<E> ElementList
```
      List of ElementList to use in PRDF
- Class magpie.attributes.generators.crystal.StructuralHeterogeneityAttributeGenerator extends BaseAttributeGenerator implements Serializable
Package magpie.attributes.generators.element
- Class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - ElementalProperties
```
java.util.List<E> ElementalProperties
```
      List of element properties to use as attributes
Package magpie.attributes.generators.prototype
- Class magpie.attributes.generators.prototype.PairSiteAttributeGenerator extends SingleSiteAttributeGenerator implements Serializable
  - Serialized Fields
    - SiteInfo
```
PrototypeSiteInformation SiteInfo
```
      Information of this particular prototype
- Class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator extends BaseAttributeGenerator implements Serializable
  - Serialized Fields
    - ElementalProperties
```
java.util.List<E> ElementalProperties
```
      List of properties used to compute attributes
    - SingleSites
```
java.util.List<E> SingleSites
```
      List of groups with a single site
    - MultipleSites
```
java.util.List<E> MultipleSites
```
      List of groups with a multiple site
Package magpie.attributes.selectors
- Class magpie.attributes.selectors.BaseAttributeSelector extends java.lang.Object implements Serializable
  - Serialized Fields
    - trained
```
boolean trained
```
      Whether this BaseAttributeSelector has been trained
    - Attribute_ID
```
java.util.List<E> Attribute_ID
```
      List of attributes that were selected
    - Attribute_Names
```
java.util.List<E> Attribute_Names
```
      Names of attributes that were selected
- Class magpie.attributes.selectors.BestIndividualSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - NToSelect
```
int NToSelect
```
      Number of attributes to select
    - Evaluator
```
BaseAttributeEvaluator Evaluator
```
      Evaluator used to assess individual attributes
- Class magpie.attributes.selectors.ExhaustiveAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - Model
```
BaseModel Model
```
      Model used for cross-validation
    - MinSubsetSize
```
int MinSubsetSize
```
      Minimum attribute subset size
    - MaxSubsetSize
```
int MaxSubsetSize
```
      Maximum attribute subset size
    - KFolds
```
int KFolds
```
      If test method is K-Fold: Number of folds used in cross-validation test
    - TestMethod
```
ExhaustiveAttributeSelector.EvaluationMethod TestMethod
```
      Method used to evaluate models
    - RandomTestFraction
```
double RandomTestFraction
```
      If method is random split, fraction of entries withheld for test set
    - RandomTestCount
```
int RandomTestCount
```
      If method is random split, number of times to repeat test
    - SetIterator
```
java.util.Iterator<E> SetIterator
```
      Iterator over subsets of attributes to be tested
- Class magpie.attributes.selectors.LassoAttributeSelector extends PythonBasedAttributeSelector implements Serializable
  - Serialized Fields
    - NLASSO
```
int NLASSO
```
      Number of attributes to pick via LASSO. Default = 20
    - NDownselect
```
int NDownselect
```
      Number of entries to downselect to based on correlations. A negative number indicates that this step should be skipped. Default: Skip
    - MaxCount
```
int MaxCount
```
      Maximum number of attributes to select. Default = 5
    - CVFraction
```
double CVFraction
```
      Fraction of entries to withhold of cv test set. A negative number indicates that CV will not be used. Default: No CV
    - CVIterations
```
int CVIterations
```
      Number of times to repeat CV test. Default: 100
    - SelectSizeAutomatically
```
boolean SelectSizeAutomatically
```
      Whether to pick dataset size via cross-validation.
- Class magpie.attributes.selectors.MeredigAttributeSelector extends UserSpecifiedAttributeSelector implements Serializable
- Class magpie.attributes.selectors.PythonBasedAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - Debug
```
boolean Debug
```
      Debug mode. Pipe output from subprocess to stdout
- Class magpie.attributes.selectors.RandomForestAttributeSelector extends PythonBasedAttributeSelector implements Serializable
  - Serialized Fields
    - NumAttributes
```
int NumAttributes
```
      Number of attributes to select.
    - NumSteps
```
int NumSteps
```
      Number of selection steps
    - NumTrees
```
int NumTrees
```
      Number of trees to use in RandomForest
- Class magpie.attributes.selectors.RegexAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - Regex
```
java.util.regex.Pattern Regex
```
      Regular expression to be matched
    - IncludeMatching
```
boolean IncludeMatching
```
      Whether to include attributes that match
- Class magpie.attributes.selectors.RemoveCorrelatedAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - Measure
```
RemoveCorrelatedAttributeSelector.CorrelationMeasure Measure
```
      Correlation measure used for this class
    - Threshold
```
double Threshold
```
      Threshold at which attributes are marked as correlated.
    - UseClass
```
boolean UseClass
```
      Whether to pick the attribute most strongly correlated with the class variable
- Class magpie.attributes.selectors.RemoveDuplicateAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - Tolerance
```
double Tolerance
```
      Maximum absolute difference at which to declare two floats equal
- Class magpie.attributes.selectors.RemoveNaNAttributeSelector extends BaseAttributeSelector implements Serializable
- Class magpie.attributes.selectors.StagedAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - Selectors
```
java.util.List<E> Selectors
```
      List of attribute selectors to use for selection. [0] is the first selector to be run.
- Class magpie.attributes.selectors.UserSpecifiedAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - SelectedAttributes
```
java.util.List<E> SelectedAttributes
```
      Names of attributes to be used
- Class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector extends UserSpecifiedAttributeSelector implements Serializable
- Class magpie.attributes.selectors.WekaAttributeSelector extends BaseAttributeSelector implements Serializable
  - Serialized Fields
    - Searcher
```
weka.attributeSelection.ASSearch Searcher
```
      Weka class used to populate a list of attributes
    - Evaluator
```
weka.attributeSelection.ASEvaluation Evaluator
```
      Weka class that is used to rank subsets of attributes
Package magpie.cluster
- Class magpie.cluster.BaseClusterer extends java.lang.Object implements Serializable
  - Serialized Fields
    - trained
```
boolean trained
```
      Whether this clusterer has been trained
    - AttributeSelector
```
BaseAttributeSelector AttributeSelector
```
      BaseAttributeSelector used to screen attributes during training
    - Statistics
```
ClustererStatistics Statistics
```
      Stores statistics about this clusterer
- Class magpie.cluster.WekaClusterer extends BaseClusterer implements Serializable
  - Serialized Fields
    - Clusterer
```
weka.clusterers.AbstractClusterer Clusterer
```
      Clusterer used internally
Package magpie.csp.diagramdata
- Class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics extends PhaseDiagramStatistics implements Serializable
  - Serialized Fields
    - CompoundLookup
```
java.util.List<E> CompoundLookup
```
      Lookup tables for elements compound with 1, 2, 3, ... components. Each element of this list contains a sorted map that links each known compound's composition (rounded to exactly match a composition from the PhaseDiagramStatistics.CommonCompositions list to the index of the prototype structure of that compound. Uses a sorted map so that one can lookup all compounds in a particular system quickly.
    - CommonCompositionCopy
```
java.util.List<E> CommonCompositionCopy
```
      Copy of PhaseDiagramStatistics.CommonCompositions used to enable faster lookup from OnTheFlyPhaseDiagramStatistics.getCompositionIndex(double[]).
    - CompositionComparatorCopy
```
java.util.Comparator<T> CompositionComparatorCopy
```
      Comparator for OnTheFlyPhaseDiagramStatistics.CommonCompositionCopy. Must be keep up-to-date with PhaseDiagramStatistics.CompositionComparator.
    - ElemChoices
```
java.util.List<E> ElemChoices
```
      Stores the possible choices of elements when running OnTheFlyPhaseDiagramStatistics.getCompoundVector(int[]). Cached to avoid re-generating it
- Class magpie.csp.diagramdata.PhaseDiagramStatistics extends java.lang.Object implements Serializable
  - Serialized Fields
    - MinDistance
```
double MinDistance
```
      Minimum Manhattan distance between compositions to be considered equal
    - NComponents
```
int NComponents
```
      Order of phase diagram
    - ElementProbability
```
double ElementProbability
```
      Probability that each element appears in a phase diagram
    - CommonCompositions
```
java.util.List<E> CommonCompositions
```
      List of common compositions and the names of prototypes found at that composition. Compositions with identical stoichiometry (i.e. AB and BA) share the same list. Key of the pair is an array where [0] is the number of elements, and the other entries are the stoichiometries (ex:, A3B -> [0.75,0.25]) Value is the names prototypes observed at that stoichiometries
    - StructureProbability
```
double[][] StructureProbability
```
      For each composition, probability of each structure existing in a phase diagram. [][0] is the no-structure condition.
    - CompositionComparator
```
java.util.Comparator<T> CompositionComparator
```
      Used to sort PhaseDiagramStatistics.CommonCompositions. Only sorts by the composition, never the list of prototype names.
    - NCompounds
```
int NCompounds
```
      Number compounds stored by this object
Package magpie.data
- Class magpie.data.BaseEntry extends java.lang.Object implements Serializable
  - Serialized Fields
    - AttributeList
```
double[] AttributeList
```
      Values of attributes
    - Class
```
double Class
```
      Measured value of class variable
    - ClassProbabilites
```
double[] ClassProbabilites
```
      Probably of entry existing in each possible class (for classification)
    - PredictedClass
```
double PredictedClass
```
      Class variable predicted by a model
    - measured
```
boolean measured
```
      Whether this entry has a measured class variable
    - predicted
```
boolean predicted
```
      Whether this entry has a predicted class variable
- Class magpie.data.Dataset extends java.lang.Object implements Serializable
  - Serialized Fields
    - AttributeName
```
java.util.ArrayList<E> AttributeName
```
      Names of attributes that describe each entry
    - Entries
```
java.util.ArrayList<E> Entries
```
      Internal array that stores entries
    - Expanders
```
java.util.List<E> Expanders
```
      Tools to generate new attributes based on existing ones
    - Generators
```
java.util.List<E> Generators
```
      Tools to generate special-purpose attributes
    - ClassName
```
java.lang.String[] ClassName
```
      Names of the class(s) of each entry
- Class magpie.data.MultiPropertyDataset extends Dataset implements Serializable
  - Serialized Fields
    - PClassNames
```
java.util.List<E> PClassNames
```
      For properties with multiple classes, store the acceptable class names
    - PNames
```
java.util.List<E> PNames
```
      Names of the properties known about each entry
    - TargetProperty
```
int TargetProperty
```
      Which property is currently used as the class variable
- Class magpie.data.MultiPropertyEntry extends BaseEntry implements Serializable
  - Serialized Fields
    - MeasuredProperty
```
double[] MeasuredProperty
```
      List of values of each measured property at this composition. Value is equal to Double.NaN if no measured property has been set.
    - PredictedProperty
```
double[][] PredictedProperty
```
      List of predictions of each property at this composition. Stores them in a 2-D array so that this same storage device can also hold class probabilities. Value is equal to null if this property has not been predicted.
    - TargetProperty
```
int TargetProperty
```
      Index of property being used as class variable. Equal to -1 if no property is being used.
Package magpie.data.materials
- Class magpie.data.materials.CompositionDataset extends MultiPropertyDataset implements Serializable
  - Serialized Fields
    - ElementNames
```
java.lang.String[] ElementNames
```
      List of element names
    - SortingOrder
```
int[] SortingOrder
```
      Order in which elements are sorted (used when printing)
    - DataDirectory
```
java.lang.String DataDirectory
```
      Location of lookup date files
    - ElementalProperties
```
java.util.List<E> ElementalProperties
```
      List of properties used when generating attributes
    - ElementPairProperties
```
java.util.List<E> ElementPairProperties
```
      List of properties of pairs of elements used when generating attributes
    - PropertyData
```
java.util.SortedMap<K,V> PropertyData
```
      Map of elemental property names to values
    - PairPropertyData
```
java.util.SortedMap<K,V> PairPropertyData
```
      Map of properties of pairs of elements
    - OxidationStates
```
double[][] OxidationStates
```
      Oxidation states of every element
- Class magpie.data.materials.CompositionEntry extends MultiPropertyEntry implements Serializable
  - Serialized Fields
    - HTMLFormat
```
boolean HTMLFormat
```
      Whether to print composition in HTML Format
    - ElementNames
```
java.lang.String[] ElementNames
```
      Names of each element
    - SortingOrder
```
int[] SortingOrder
```
      Rank of each element (used in display order)
    - Element
```
int[] Element
```
      Elements present in composition
    - Fraction
```
double[] Fraction
```
      Fraction of each element
    - NumberInCell
```
double NumberInCell
```
      Number of atoms in cell (used to convert when printing)
- Class magpie.data.materials.CrystalStructureDataset extends CompositionDataset implements Serializable
- Class magpie.data.materials.CrystalStructureEntry extends CompositionEntry implements Serializable
  - Serialized Fields
    - Structure
```
vassal.data.Cell Structure
```
      Crystal structure
    - Name
```
java.lang.String Name
```
      Name of entry
    - Radii
```
double[] Radii
```
      Link to atomic radii array
    - Voronoi
```
vassal.analysis.VoronoiCellBasedAnalysis Voronoi
```
      Voronoi tessellation of this structure
- Class magpie.data.materials.ElementDataset extends MultiPropertyDataset implements Serializable
  - Serialized Fields
    - LookupDirectory
```
java.lang.String LookupDirectory
```
      Directory containing elemental property lookup tables
    - ElementalProperties
```
java.util.List<E> ElementalProperties
```
      List of elemental properties used when computing attributes
    - PropertyData
```
java.util.Map<K,V> PropertyData
```
      Lookup table of elemental properties
- Class magpie.data.materials.ElementEntry extends MultiPropertyEntry implements Serializable
  - Serialized Fields
    - ElementName
```
java.lang.String ElementName
```
      Element name
    - ElementID
```
int ElementID
```
      Element ID. (Z-1)
- Class magpie.data.materials.PrototypeDataset extends CompositionDataset implements Serializable
  - Serialized Fields
    - SiteInfo
```
PrototypeSiteInformation SiteInfo
```
      Stores information about each site
- Class magpie.data.materials.PrototypeEntry extends CompositionEntry implements Serializable
  - Serialized Fields
    - SiteInfo
```
PrototypeSiteInformation SiteInfo
```
      Link to site information from corresponding dataset
    - SiteComp
```
CompositionEntry[] SiteComp
```
      Composition of each site
Package magpie.data.materials.util
- Class magpie.data.materials.util.GCLPCalculator extends java.lang.Object implements Serializable
  - Serialized Fields
    - Phases
```
java.util.Map<K,V> Phases
```
      Phases to consider for equilibria and their energy. Only contains the lowest-energy phase at each entry
- Class magpie.data.materials.util.PrototypeSiteInformation extends java.lang.Object implements Serializable
  - Serialized Fields
    - NAtoms
```
double[] NAtoms
```
      Number of atoms on each site
    - IsIncluded
```
boolean[] IsIncluded
```
      Which sites are included in attribute calculations
    - SiteGroup
```
java.util.List<E> SiteGroup
```
      Groups of sites. Each entry in this list contains the index # of all sites in a group of equivalent sites.
    - equivalentArrangements
```
java.util.List<E> equivalentArrangements
```
      List of all orders of sites that are equivalent
Package magpie.data.utilities.filters
- Class magpie.data.utilities.filters.AllMetalsFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - isMetal
```
boolean[] isMetal
```
      List indicating which elements are metals
- Class magpie.data.utilities.filters.AttributeFilter extends ComparisonOperatorFilter implements Serializable
  - Serialized Fields
    - TargetAttribute
```
java.lang.String TargetAttribute
```
      Name of feature to base filter on
- Class magpie.data.utilities.filters.BaseDatasetFilter extends java.lang.Object implements Serializable
  - Serialized Fields
    - Exclude
```
boolean Exclude
```
      Whether to exclude entries that pass a filter
- Class magpie.data.utilities.filters.BestInAlloySystemFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Ranker
```
BaseEntryRanker Ranker
```
      Ranker used to score entries
    - NPerDiagram
```
int NPerDiagram
```
      Number of top entries to select
- Class magpie.data.utilities.filters.ClassFilter extends ComparisonOperatorFilter implements Serializable
  - Serialized Fields
    - UseMeasured
```
boolean UseMeasured
```
      Whether to use measured class variable
- Class magpie.data.utilities.filters.ClassProbabilityFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - ClassName
```
java.lang.String ClassName
```
      Name of class used for filtering
    - Threshold
```
double Threshold
```
      Probability threshold
- Class magpie.data.utilities.filters.ClassRangeFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - useMeasured
```
boolean useMeasured
```
      Whether to use predicted or measured classes
    - insideRange
```
boolean insideRange
```
      Keep entries inside range?
    - lowerBound
```
double lowerBound
```
      Lower bound of range
    - upperBound
```
double upperBound
```
      Upper bound of range
- Class magpie.data.utilities.filters.ComparisonOperatorFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Threshold
```
double Threshold
```
      Threshold value
    - Equal
```
boolean Equal
```
      Should entries with Feature==Threshold be kept?
    - GreaterThan
```
boolean GreaterThan
```
      Should entries with Feature < Threshold be kept?
    - LessThan
```
boolean LessThan
```
      Should entries with Feature > Threshold be kept?
- Class magpie.data.utilities.filters.CompositionDistanceFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - TargetComposition
```
CompositionEntry TargetComposition
```
      Target composition
    - Threshold
```
double Threshold
```
      Threshold distance
- Class magpie.data.utilities.filters.CompositionSetDistanceFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Compositions
```
java.util.Set<E> Compositions
```
      Set of compositions to consider
    - UseManhattan
```
boolean UseManhattan
```
      Whether to use Manhattan distance (or Euclidean)
    - Threshold
```
double Threshold
```
      Set distance threshold
- Class magpie.data.utilities.filters.ContainsElementFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - ElementList
```
java.lang.String[] ElementList
```
      Elements that compounds are not allowed to contain
    - ExcludedIndex
```
int[] ExcludedIndex
```
      List of IDs of those elements
- Class magpie.data.utilities.filters.EntryRankerFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - NumberToFilter
```
int NumberToFilter
```
      Number of entries to filter
    - Ranker
```
BaseEntryRanker Ranker
```
      Entry ranking method
- Class magpie.data.utilities.filters.IQROutlierFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Threshold
```
double Threshold
```
      Maximum number of IQRs away a non-outlier can be
    - Median
```
double Median
```
      Median from training set
    - ICQ
```
double ICQ
```
      IQR from training set
- Class magpie.data.utilities.filters.MultiFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Filters
```
java.util.List<E> Filters
```
      List of filters currently in use
- Class magpie.data.utilities.filters.PhaseDiagramExclusionFilter extends ContainsElementFilter implements Serializable
- Class magpie.data.utilities.filters.PredictionOutlierFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - RobustUtility
```
RobustRegressionUtility RobustUtility
```
      Class used to calculate outliers
    - K
```
int K
```
      Number of fitting parameters in a model
- Class magpie.data.utilities.filters.PropertyFilter extends AttributeFilter implements Serializable
  - Serialized Fields
    - UseMeasured
```
boolean UseMeasured
```
      Whether to use measured or predicted property values
- Class magpie.data.utilities.filters.PropertyRangeFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Target
```
java.lang.String Target
```
      Name of target property
    - useMeasured
```
boolean useMeasured
```
      Whether to use predicted or measured classes
    - insideRange
```
boolean insideRange
```
      Keep entries inside range?
    - lowerBound
```
double lowerBound
```
      Lower bound of range
    - upperBound
```
double upperBound
```
      Upper bound of range
- Class magpie.data.utilities.filters.RegressionErrorFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Threshold
```
double Threshold
```
      Error threshold
- Class magpie.data.utilities.filters.StabilityFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - GCLPCalculator
```
GCLPCalculator GCLPCalculator
```
      Tool used to perform GCLP
    - UsePredicted
```
boolean UsePredicted
```
      Whether to use predicted class
    - Threshold
```
double Threshold
```
      Stability threshold
- Class magpie.data.utilities.filters.ZScoreOutlierFilter extends BaseDatasetFilter implements Serializable
  - Serialized Fields
    - Tolerance
```
double Tolerance
```
      Number of standard deviation away from mean used when defining outliers
    - ScreenAttributes
```
boolean ScreenAttributes
```
      Whether to screen based on attributes
    - ScreenClass
```
boolean ScreenClass
```
      Whether to screen based on class variable
    - AttributeMean
```
double[] AttributeMean
```
      Means of attributes
    - AttributeStdDev
```
double[] AttributeStdDev
```
      Standard deviation of attributes
    - ClassMean
```
double ClassMean
```
      Mean of class variable
    - ClassStdDev
```
double ClassStdDev
```
      Standard deviation of class variable
    - Trained
```
boolean Trained
```
      Whether this class has been trained
    - AttributeNames
```
java.lang.String[] AttributeNames
```
      Names of attributes. Used to check if attributes used to train filter are the same as those during labeling.
Package magpie.data.utilities.modifiers
- Class magpie.data.utilities.modifiers.AddPropertyModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - ToAdd
```
java.util.List<E> ToAdd
```
      List of properties to be added
- Class magpie.data.utilities.modifiers.BaseDatasetModifier extends java.lang.Object implements Serializable
- Class magpie.data.utilities.modifiers.ClassEliminationModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - classToEliminate
```
java.lang.String classToEliminate
```
      Name of class to be eliminated
    - newClassName
```
java.lang.String newClassName
```
      Optional: Name of new name for those classes
- Class magpie.data.utilities.modifiers.ClassIntervalModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - Edges
```
double[] Edges
```
      Interval Edges
- Class magpie.data.utilities.modifiers.CompositionSetDistanceModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - Compositions
```
java.util.Set<E> Compositions
```
      Set of compositions to compute distance from
    - UseManhattan
```
boolean UseManhattan
```
      Whether to use Manhattan distance (vs Euclidean)
- Class magpie.data.utilities.modifiers.DiscreteToContinuousModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - ClassName
```
java.lang.String ClassName
```
      Name of class for which to compute probability.
- Class magpie.data.utilities.modifiers.ErrorSignalModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - Model
```
BaseModel Model
```
      Model used to make class predictions
    - ComputeAbsolute
```
boolean ComputeAbsolute
```
      Whether to calculate absolute error
- Class magpie.data.utilities.modifiers.HHICalculationModifier extends BaseDatasetModifier implements Serializable
- Class magpie.data.utilities.modifiers.NaNToMeanModifier extends BaseDatasetModifier implements Serializable
- Class magpie.data.utilities.modifiers.NonZeroClassModifier extends BaseDatasetModifier implements Serializable
- Class magpie.data.utilities.modifiers.PartitionToClassModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - splitter
```
BaseDatasetSplitter splitter
```
      Splitter used to partition data
- Class magpie.data.utilities.modifiers.SetClassNamesModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - ClassNames
```
java.lang.String[] ClassNames
```
      New class names
- Class magpie.data.utilities.modifiers.SetPropertyValueModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - PropertyName
```
java.lang.String PropertyName
```
      Name of property to be set
    - PropertyValue
```
java.lang.String PropertyValue
```
      Value to set for property. Can be numeric or name of a class, will be stored as a string either way
- Class magpie.data.utilities.modifiers.StabilityCalculationModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - GCLPCalculator
```
GCLPCalculator GCLPCalculator
```
      Tool used to perform GCLP
    - EnergyName
```
java.lang.String EnergyName
```
      Name of property containing energy
    - StabilityName
```
java.lang.String StabilityName
```
      Name of new property containing stability
- Class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier extends BaseDatasetModifier implements Serializable
  - Serialized Fields
    - perCell
```
int perCell
```
      Number of atoms per cell in the unit cell
Package magpie.data.utilities.modifiers.duplicates
- Class magpie.data.utilities.modifiers.duplicates.AveragingDuplicateResolver extends BaseDuplicateResolver implements Serializable
- Class magpie.data.utilities.modifiers.duplicates.BaseDuplicateResolver extends BaseDatasetModifier implements Serializable
- Class magpie.data.utilities.modifiers.duplicates.RankingDuplicateResolver extends BaseDuplicateResolver implements Serializable
  - Serialized Fields
    - Ranker
```
BaseEntryRanker Ranker
```
      Ranker used to choose entries
Package magpie.data.utilities.normalizers
- Class magpie.data.utilities.normalizers.BaseDatasetNormalizer extends java.lang.Object implements Serializable
  - Serialized Fields
    - Trained
```
boolean Trained
```
      Whether this normalizer has been trained
    - NormalizeAttributes
```
boolean NormalizeAttributes
```
      Whether to normalize attributes
    - NormalizeClass
```
boolean NormalizeClass
```
      Whether to class variable
    - AttributeNames
```
java.lang.String[] AttributeNames
```
      Names of attributes (to make sure the dataset is not different)
- Class magpie.data.utilities.normalizers.IndependentVariableNormalizer extends BaseDatasetNormalizer implements Serializable
- Class magpie.data.utilities.normalizers.InverseNormalizer extends BaseDatasetNormalizer implements Serializable
  - Serialized Fields
    - Scale
```
double Scale
```
      Scale of data
- Class magpie.data.utilities.normalizers.MultiNormalizer extends BaseDatasetNormalizer implements Serializable
  - Serialized Fields
    - Normalizers
```
java.util.List<E> Normalizers
```
      List of normalizers to use
- Class magpie.data.utilities.normalizers.RegularSolutionNormalizer extends BaseDatasetNormalizer implements Serializable
- Class magpie.data.utilities.normalizers.RescalingNormalizer extends IndependentVariableNormalizer implements Serializable
  - Serialized Fields
    - AttributeMinimum
```
double[] AttributeMinimum
```
      Minimum value of each attribute
    - AttributeRange
```
double[] AttributeRange
```
      Range of each attribute
    - ClassMinimum
```
double ClassMinimum
```
      Minimum value of class variable
    - ClassRange
```
double ClassRange
```
      Range of class variable
- Class magpie.data.utilities.normalizers.SoftmaxNormalizer extends ZScoreNormalizer implements Serializable
  - Serialized Fields
    - R
```
double R
```
      Scaling factor
- Class magpie.data.utilities.normalizers.ZScoreNormalizer extends IndependentVariableNormalizer implements Serializable
  - Serialized Fields
    - AttributeMean
```
double[] AttributeMean
```
      Minimum value of each attribute
    - AttributeStdDev
```
double[] AttributeStdDev
```
      Range of each attribute
    - ClassMean
```
double ClassMean
```
      Minimum value of class variable
    - ClassStdDev
```
double ClassStdDev
```
      Range of class variable
Package magpie.data.utilities.splitters
- Class magpie.data.utilities.splitters.AllMetalsSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - isMetal
```
boolean[] isMetal
```
      List indicating which elements are metals
- Class magpie.data.utilities.splitters.AttributeIntervalSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - AttributeName
```
java.lang.String AttributeName
```
      Name of attribute used for split
    - AttributeID
```
int AttributeID
```
      ID of attribute used for split
    - BinEdges
```
double[] BinEdges
```
      Values to use as bin edges
- Class magpie.data.utilities.splitters.BaseDatasetSplitter extends java.lang.Object implements Serializable
- Class magpie.data.utilities.splitters.ClustererSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - Clusterer
```
BaseClusterer Clusterer
```
      Clusterer used to perform splitting
    - trainedPreviously
```
boolean trainedPreviously
```
      If it was provided as a trained clusterer
- Class magpie.data.utilities.splitters.FilterSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - Filter
```
BaseDatasetFilter Filter
```
      Filter used for splitting the data
- Class magpie.data.utilities.splitters.MeasuredClassSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - ClassNames
```
java.lang.String[] ClassNames
```
      Names of classes
- Class magpie.data.utilities.splitters.MixedMetalsSplitter extends AllMetalsSplitter implements Serializable
- Class magpie.data.utilities.splitters.MultipleElementGroupsSplitter extends SingleElementGroupSplitter implements Serializable
  - Serialized Fields
    - ElementGroups
```
java.util.List<E> ElementGroups
```
      List of element groups
- Class magpie.data.utilities.splitters.NonZeroClassificationSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - Clfr
```
BaseModel Clfr
```
      Model to use for splitting
    - ProbabilityThreshold
```
double ProbabilityThreshold
```
      Probability of being of class #0 below which entry gets placed in entry #1
- Class magpie.data.utilities.splitters.ObjectiveFunctionSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - SplitAbove
```
boolean SplitAbove
```
      Whether class 0 should be entries above the threshold
    - Threshold
```
double Threshold
```
      Threshold on which to split data
    - objFun
```
BaseEntryRanker objFun
```
      Objective function used to split entries
- Class magpie.data.utilities.splitters.PredictedClassIntervalSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - Clfr
```
BaseModel Clfr
```
      Classifier used to predict range
    - Edges
```
double[] Edges
```
      Edges on which to split data
- Class magpie.data.utilities.splitters.SingleElementGroupSplitter extends BaseDatasetSplitter implements Serializable
  - Serialized Fields
    - Elements
```
java.util.List<E> Elements
```
      List of elements that define a subclass
Package magpie.models
- Class magpie.models.BaseModel extends java.lang.Object implements Serializable
  - Serialized Fields
    - TrainingStats
```
BaseStatistics TrainingStats
```
      Statistics about performance on training set
    - ValidationStats
```
BaseStatistics ValidationStats
```
      Statistics generated during model validation
    - trained
```
boolean trained
```
      Records whether model has been trained
    - validated
```
boolean validated
```
      Records whether model has been validated
    - AttributeSelector
```
BaseAttributeSelector AttributeSelector
```
      BaseAttributeSelector used to screen attributes during training
    - Normalizer
```
BaseDatasetNormalizer Normalizer
```
      Used to normalize attributes before training / running model
    - Filter
```
BaseDatasetFilter Filter
```
      Filter used to clean data before training model
    - ValidationMethod
```
java.lang.String ValidationMethod
```
      Stores description how this model validated.
    - TrainTime
```
java.util.Date TrainTime
```
      Date model was trained
    - AttributeNames
```
java.lang.String[] AttributeNames
```
      Names of attributes used to train model
- Class magpie.models.SplitModel extends BaseModel implements Serializable
  - Serialized Fields
    - Model
```
java.util.ArrayList<E> Model
```
      List of of models used by this model
    - Partitioner
```
BaseDatasetSplitter Partitioner
```
      Class used to partition data into similar groups
    - GenericModel
```
BaseModel GenericModel
```
      Model used to if a model template for a certain split is not defined
Package magpie.models.classification
- Class magpie.models.classification.BaseClassifier extends BaseModel implements Serializable
  - Serialized Fields
    - NClasses
```
int NClasses
```
      Number of classes to distinguish between
    - ClassNames
```
java.lang.String[] ClassNames
```
      Names of classes this model can distinguish between
- Class magpie.models.classification.CumulantExpansionClassifier extends BaseClassifier implements Serializable
  - Serialized Fields
    - ClassProbability
```
double[] ClassProbability
```
      Probability that the desired compound is stable
    - Cumulants
```
double[][][] Cumulants
```
      Cumulants functions between an entry being each class and each condition
    - NComponents
```
int NComponents
```
      Number of constituents in prototype
    - NBins
```
int[] NBins
```
      Desired number of composition bins.
    - PhaseDiagramStats
```
PhaseDiagramStatistics PhaseDiagramStats
```
      Data about what compositions have compounds in all phase diagrams
- Class magpie.models.classification.ScikitLearnClassifier extends BaseClassifier implements Serializable
  - Serialized Fields
    - ScikitModel
```
java.util.List<E> ScikitModel
```
      Scikit-learn model. This is just the the pickle file as a char array that has been split into chunks
    - BufferSize
```
int BufferSize
```
      Buffer size when reading in files / from sockets.
    - CompressionLevel
```
int CompressionLevel
```
      Compression level on ScikitLearn model
    - Debug
```
boolean Debug
```
      Whether to print output from python stdout to screen
- Class magpie.models.classification.SplitClassifier extends SplitModel implements Serializable
  - Serialized Fields
    - TrainingStatsPtr
```
ClassificationStatistics TrainingStatsPtr
```
      Pointer to ClassificationStatistics interface of TrainingStats
    - ValidationStatsPtr
```
ClassificationStatistics ValidationStatsPtr
```
      Pointer to ClassificationStatistics interface of ValidationStates
    - NClasses
```
int NClasses
```
      Number of classes model can distinguish between
    - ClassNames
```
java.lang.String[] ClassNames
```
      Names of classes this model can distinguish between
- Class magpie.models.classification.WekaClassifier extends BaseClassifier implements Serializable
  - Serialized Fields
    - Model
```
weka.classifiers.AbstractClassifier Model
```
      Link to Weka-based model
    - model_defined
```
boolean model_defined
```
      Whether model type has been defined
    - Model_Type
```
java.lang.String Model_Type
```
      Name of model type currently in use
    - Model_Options
```
java.lang.String[] Model_Options
```
      Options supplied when instantiating Model
Package magpie.models.regression
- Class magpie.models.regression.AbstractNonlinearRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - MaxIter
```
int MaxIter
```
      Maximum of number of iterations the optimizer can perform
    - VariableNames
```
java.util.List<E> VariableNames
```
      Stores the names of attributes used a dependant variables
    - FittingNames
```
java.util.List<E> FittingNames
```
      Names of fitting coefficients
    - VariableIndices
```
int[] VariableIndices
```
      Stores the indices of attributes used as dependant variables
    - InitialGuess
```
java.util.List<E> InitialGuess
```
      Initial guesses supplied to optimization algorithm
    - FittedCoefficients
```
double[] FittedCoefficients
```
      Final result from parameter fitting
    - initialized
```
boolean initialized
```
      Whether program has been initialized (i.e. variables defined)
- Class magpie.models.regression.AbstractParsedNonlinearRegression extends AbstractNonlinearRegression implements Serializable
  - Serialized Fields
    - UserFormula
```
java.lang.String UserFormula
```
      Stores the user-provided formula
- Class magpie.models.regression.BaseRegression extends BaseModel implements Serializable
  - Serialized Fields
    - Q
```
double Q
```
      Robust regression parameter. Default: Don't do it
- Class magpie.models.regression.ClassificationRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Clfr
```
BaseModel Clfr
```
      Classification algorithm that this class wraps around
    - ObjFunction
```
BaseEntryRanker ObjFunction
```
      Entry ranker used to order entries
    - Threshold
```
double Threshold
```
      Threshold on which to split data into classes
    - MinObjFun
```
double MinObjFun
```
      Minimum value of objective function of all entries in training set
    - ObjFunRange
```
double ObjFunRange
```
      Range between minimum and maximum value of objective function of entries in the training set.
- Class magpie.models.regression.CompositeRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Model
```
java.util.List<E> Model
```
      Collections of models used by this class
    - GenericModel
```
BaseRegression GenericModel
```
      Generic composite regression model (use wisely)
- Class magpie.models.regression.GuessMeanRegression extends SingleGuessRegression implements Serializable
- Class magpie.models.regression.LASSORegression extends BaseRegression implements Serializable
  - Serialized Fields
    - MaxNumberTerms
```
int MaxNumberTerms
```
      Maximum number of features allowed in model (-1 is unlimited)
    - Terms
```
java.util.List<E> Terms
```
      Terms used in the model
    - TermNames
```
java.util.List<E> TermNames
```
      Names of terms used in the model
    - Coefficients
```
java.util.List<E> Coefficients
```
      Coefficients for linear model
    - Intercept
```
double Intercept
```
      Intercept of the linear model
- Class magpie.models.regression.LinearCorrectedRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Submodel
```
BaseModel Submodel
```
      Model to be corrected
    - A
```
double A
```
      Intercept of linear correction
    - B
```
double B
```
      Slope of correction term
- Class magpie.models.regression.MetallurgicalHeuristicRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - HullHolder
```
magpie.models.regression.BinaryConvexHullHolder HullHolder
```
      Holds binary convex hulls
    - FitCorrection
```
boolean FitCorrection
```
      Whether to fit correction factors
    - FitSlope
```
double FitSlope
```
      Correction slope term
    - FitIntercept
```
double FitIntercept
```
      Correction intercept term
- Class magpie.models.regression.MixingRuleRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - PropertyName
```
java.lang.String PropertyName
```
      Property used for weighting
    - LookupTable
```
double[] LookupTable
```
      Lookup table for property of interest
    - UseInverse
```
boolean UseInverse
```
      Whether to compute harmonic mean.
    - CorrectionFactors
```
double[] CorrectionFactors
```
      Coefficients used for correction factor. 0 = Intercept. 1 = Slope.
    - UseCorrection
```
boolean UseCorrection
```
      Whether to apply correction factors
    - FittedElements
```
java.util.List<E> FittedElements
```
      Elements to fit using least squares
    - FittedElementIndices
```
java.util.List<E> FittedElementIndices
```
      Indices of fitted elements
- Class magpie.models.regression.MultiObjectiveRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Models
```
java.util.Map<K,V> Models
```
      Map of property name to model used to predict it.
    - ObjFunction
```
MultiObjectiveEntryRanker ObjFunction
```
      Objective function used to calculate class variable.
    - GenericModel
```
BaseModel GenericModel
```
      Generic model (in case one has not already been defined)
- Class magpie.models.regression.MultiPropertyRegression extends MultiObjectiveRegression implements Serializable
- Class magpie.models.regression.NonlinearRegressionExpr extends AbstractParsedNonlinearRegression implements Serializable
  - Serialized Fields
    - Evaluator
```
expr.Expr Evaluator
```
      Handles the evaluation of the user-defined formula
    - Variables
```
java.util.List<E> Variables
```
      List of Variables used by the Expr library. This list is ordered with the attribute variables first, and then the fitting coefficients.
- Class magpie.models.regression.PolynomialRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Order
```
int Order
```
      Desired Order of polynomial
    - numAttributes
```
int numAttributes
```
      Number of attributes used in model
    - coefficients
```
double[] coefficients
```
      Coefficients of each term in the polynomial
    - attributeNames
```
java.lang.String[] attributeNames
```
      Names of attributes
    - PrintAccuracy
```
int PrintAccuracy
```
      Number of significant figures to print
- Class magpie.models.regression.RandomGuessRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - LowerBound
```
double LowerBound
```
      Lower bound of guess
    - UpperBound
```
double UpperBound
```
      Upper bound of guess
- Class magpie.models.regression.ScikitLearnRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - ScikitModel
```
java.util.List<E> ScikitModel
```
      Scikit-learn model. This is just the the pickle file as a char array that has been split into chunks
    - BufferSize
```
int BufferSize
```
      Buffer size when reading in files / from sockets.
    - CompressionLevel
```
int CompressionLevel
```
      Compression level on ScikitLearn model
    - Debug
```
boolean Debug
```
      Whether to print output from python stdout to screen
- Class magpie.models.regression.SingleGuessRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Guess
```
double Guess
```
      Guess for all classes
    - Jitter
```
double Jitter
```
      Amount of jitter added to the answer
- Class magpie.models.regression.SplitRegression extends SplitModel implements Serializable
  - Serialized Fields
    - Q
```
double Q
```
      Robust regression parameter. Default: Don't do it
- Class magpie.models.regression.StagedRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Model
```
java.util.List<E> Model
```
      Collections of regression models
    - GenericModel
```
BaseRegression GenericModel
```
      Generic composite regression model
    - PropogateAbsolute
```
boolean PropogateAbsolute
```
      Whether absolute or relative error is passed
- Class magpie.models.regression.WekaRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Model
```
weka.classifiers.AbstractClassifier Model
```
      Link to Weka-based model
    - model_defined
```
boolean model_defined
```
      Whether model type has been defined
    - Model_Type
```
java.lang.String Model_Type
```
      Name of model type currently in use
    - Model_Options
```
java.lang.String[] Model_Options
```
      Options supplied when instantiating Model
Package magpie.models.regression.crystal
- Class magpie.models.regression.crystal.CoulombEwaldMatrixRegression extends StructureKRRBasedRegression implements Serializable
  - Serialized Fields
    - Sigma
```
double Sigma
```
      Normalization term in kernel function
- Class magpie.models.regression.crystal.CoulombSineMatrixRegression extends StructureKRRBasedRegression implements Serializable
  - Serialized Fields
    - Sigma
```
double Sigma
```
      Normalization term in kernel function
- Class magpie.models.regression.crystal.PRDFRegression extends StructureKRRBasedRegression implements Serializable
  - Serialized Fields
    - Sigma
```
double Sigma
```
      Normalization term in kernel function
    - NBins
```
int NBins
```
      Number of bins in PRDF
    - Cutoff
```
double Cutoff
```
      Cutoff distance of PRDF
- Class magpie.models.regression.crystal.StructureKRRBasedRegression extends BaseRegression implements Serializable
  - Serialized Fields
    - Lambda
```
double Lambda
```
      Regularization parameter (lambda)
    - Alpha
```
double[] Alpha
```
      Coefficients of model
    - TrainingStructures
```
java.util.List<E> TrainingStructures
```
      Representation of structures in the training set.
    - TrainingStructureNames
```
java.util.List<E> TrainingStructureNames
```
      Names of each object in the training set.
Package magpie.models.regression.nonlinear
- Class magpie.models.regression.nonlinear.SimpleLinearModelExample extends AbstractNonlinearRegression implements Serializable
Package magpie.statistics.performance
- Class magpie.statistics.performance.BaseStatistics extends java.lang.Object implements Serializable
  - Serialized Fields
    - NumberTested
```
int NumberTested
```
      Number of entries evaluated
    - ROC
```
double[][] ROC
```
      Receiver operating characteristic curve
    - ROC_AUC
```
double ROC_AUC
```
      Area under receiver operating characteristic curve normalized such that 1.0 is a perfect classifier and 0.0 is a perfectly-random classifier.
    - Measured
```
double[] Measured
```
      Measured value of class variable
    - Predicted
```
double[] Predicted
```
      Predicted value of class variable
- Class magpie.statistics.performance.ClassificationStatistics extends BaseStatistics implements Serializable
  - Serialized Fields
    - NumberCorrect
```
int NumberCorrect
```
      Number of entries assigned to the correct class
    - FractionCorrect
```
double FractionCorrect
```
      Fraction of entries assigned to correct class
    - Kappa
```
double Kappa
```
      Fraction correct modified such that 0 is random guessing and 1 is perfect classification
    - ContingencyTable
```
int[][] ContingencyTable
```
      Description of how often instances are assigned to each class. Same as ClassificationStatistics.ContingencyTable for binary cases. Entry [i][j] is the number of entries classified as class j that were measured to be class i.
    - ConfusionMatrix
```
int[][] ConfusionMatrix
```
      Contingency table. For binary cases, this is equivalent to ClassificationStatistics.ConfusionMatrix. For cases with >2 classes, this is the confusion matrix for a simplified classification problem of "not class 0" vs "class 0."
    - TP
```
int TP
```
      Number of True Positives. For >2 classes, the this the true positive rate of correctly identifying the first class
    - FP
```
int FP
```
      Number of False Positives
    - FN
```
int FN
```
      Number of False Negatives
    - TN
```
int TN
```
      Number of True Negatives
    - Sensitivity
```
double Sensitivity
```
      Sensitivity (aka True Positive Rate
    - FPR
```
double FPR
```
      False Positive Rate
    - Accuracy
```
double Accuracy
```
      Accuracy
    - Specificity
```
double Specificity
```
      Specificity (True Negative Rate)
    - PPV
```
double PPV
```
      Positive Predictive Value
    - NPV
```
double NPV
```
      Negative Predictive Value
    - FDR
```
double FDR
```
      False Detection Rate
    - MCC
```
double MCC
```
      Matthews Correlation Coefficient
    - F1
```
double F1
```
      F1 Score
    - LogLoss
```
double LogLoss
```
      Log-loss
    - ClassNames
```
java.lang.String[] ClassNames
```
      Names of classes (used when printing)
    - MeasuredLargestClassFraction
```
double MeasuredLargestClassFraction
```
      Fraction of entries in the most-prevalent class
    - BaselineLogLoss
```
double BaselineLogLoss
```
      Log-loss of zero-r classifier. This is the log-loss of a model that predicts the fractions of each class in the training set as the class probabilities for each prediction.
- Class magpie.statistics.performance.ClustererStatistics extends java.lang.Object implements Serializable
  - Serialized Fields
    - trained
```
boolean trained
```
      Whether any clusterer has been evaluated
    - NEntries
```
int NEntries
```
      How many entries were considered
    - AttributesUsed
```
java.util.List<E> AttributesUsed
```
      List of attribute used during clustering
    - NClusters
```
int NClusters
```
      Number of clusters formed
    - ClusterSize
```
int[] ClusterSize
```
      Number of entries in each cluster
    - ClusterMean
```
double[][] ClusterMean
```
      Mean of each attribute for each cluster
    - AttributePower
```
double[] AttributePower
```
      Power of each attribute
    - AttributeRanks
```
int[] AttributeRanks
```
      Ranks for each attribute based on deviation between clusters. The first entry in this array is the index of the most powerful attribute. Note that this gets sorted in ascending order.
- Class magpie.statistics.performance.RegressionStatistics extends BaseStatistics implements Serializable
  - Serialized Fields
    - MAE
```
double MAE
```
      Mean absolute error
    - MRE
```
double MRE
```
      Mean relative error
    - RMSE
```
double RMSE
```
      Root mean squared error
    - R
```
double R
```
      Pearson's correlation coefficient
    - Rho
```
double Rho
```
      Spearman's correlation coefficient
    - Tau
```
double Tau
```
      Kendall's rank correlation coefficient
    - MeasuredStdDev
```
double MeasuredStdDev
```
      Standard deviation of measured values
    - MeasuredMAD
```
double MeasuredMAD
```
      Mean absolute deviation of measured values
    - MeasuredRange
```
double MeasuredRange
```
      Range of measured values
    - MeasuredMedian
```
double MeasuredMedian
```
      Median of mesaured values
- Class magpie.statistics.performance.TargetRegressionStatistics extends RegressionStatistics implements Serializable
  - Serialized Fields
    - Target
```
double Target
```
      Target value of class variable
    - Tolerance
```
double Tolerance
```
      Tolerance for successful prediction
    - MaxWindowSize
```
double MaxWindowSize
```
      Maximum tolerance during window size analysis
    - MaxCandidates
```
int MaxCandidates
```
      Maximum number of candidates for ranking analysis
    - NSteps
```
int NSteps
```
      How many steps to use in window/ranking analysis
    - rankAnalysis
```
double[][] rankAnalysis
```
      Results from candidate analysis. First column is number of top candidates selected, second is average distance from target, third is number within tolerance
    - windowAnalysis
```
double[][] windowAnalysis
```
      Results from window analysis. First column is window size, second is the number of entries inside window, third is fraction within tolerance
Package magpie.utility
- Class magpie.utility.ParsedFunction extends java.lang.Object implements Serializable
  - Serialized Fields
    - Variables
```
java.util.List<E> Variables
```
      Variables of this function
    - VariableNames
```
java.util.List<E> VariableNames
```
      Names of variables known to user. Created to allow variable names to contain characters that are not parseable
    - Input
```
java.lang.String Input
```
      String that was originally supplied to parser
    - Function
```
expr.Expr Function
```
      Function that was parsed
Package magpie.utility.tools
- Class magpie.utility.tools.OxidationStateGuesser extends java.lang.Object implements Serializable
  - Serialized Fields
    - OxidationStates
```
int[][] OxidationStates
```
      Allowed oxidation states for each element
    - Electronegativity
```
double[] Electronegativity
```
      Electronegativity for each element

Serialized Form

Package magpie.attributes.expanders

Class magpie.attributes.expanders.BaseAttributeExpander extends java.lang.Object implements Serializable

Class magpie.attributes.expanders.CrossExpander extends BaseAttributeExpander implements Serializable

Class magpie.attributes.expanders.FunctionExpander extends BaseAttributeExpander implements Serializable

Serialized Fields

Functions

Class magpie.attributes.expanders.PowerExpander extends BaseAttributeExpander implements Serializable

Serialized Fields

Exponent

Package magpie.attributes.generators

Class magpie.attributes.generators.BaseAttributeGenerator extends java.lang.Object implements Serializable

Class magpie.attributes.generators.LookupTableAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

LookupTable

NewNames

Class magpie.attributes.generators.ModelPredictionAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

ModelName

Model

ModelData

Class magpie.attributes.generators.PropertyAsAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

Properties

Package magpie.attributes.generators.composition

Class magpie.attributes.generators.composition.APEAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

PackingThreshold

NNearestToEval

RadiusProperty

Class magpie.attributes.generators.composition.ChargeDependentAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

ChargeGuesser

IonizationEnergies

Class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

ElementalProperties

Class magpie.attributes.generators.composition.ElementFractionAttributeGenerator extends BaseAttributeGenerator implements Serializable

Class magpie.attributes.generators.composition.ElementPairPropertyAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

ElementalProperties

Class magpie.attributes.generators.composition.GCLPAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

Calculator

CountPhases

Class magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

MaxFormulaUnit

Class magpie.attributes.generators.composition.IonicityAttributeGenerator extends BaseAttributeGenerator implements Serializable

Class magpie.attributes.generators.composition.MeredigAttributeGenerator extends BaseAttributeGenerator implements Serializable

Class magpie.attributes.generators.composition.StoichiometricAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

PNorms

Class magpie.attributes.generators.composition.ValenceShellAttributeGenerator extends BaseAttributeGenerator implements Serializable

Class magpie.attributes.generators.composition.YangOmegaAttributeGenerator extends BaseAttributeGenerator implements Serializable

Package magpie.attributes.generators.crystal

Class magpie.attributes.generators.crystal.APRDFAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

CutoffDistance

NumPoints

SmoothParameter

ElementalProperties

Class magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

Shells

Weighted

Class magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator extends BaseAttributeGenerator implements Serializable

Class magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

NEigenvalues

Class magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator extends BaseAttributeGenerator implements Serializable

Class magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator extends BaseAttributeGenerator implements Serializable

Class magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator extends BaseAttributeGenerator implements Serializable

Serialized Fields

ElementalProperties

Shells

AttrName

AttrDescription

Class magpie.attributes.generators.crystal.LocalPropertyVarianceAttributeGenerator extends LocalPropertyDifferenceAttributeGenerator implements Serializable

Class magpie.attributes.generators.crystal.PackingEfficiencyAttributeGenerator extends BaseAttributeGenerator implements Serializable