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getAllLabelClasses(String)
- Method in class io.reader.
RandomAccessMDLReader
returns all possible labels for this data set
getAtomLabel(IAtom)
- Method in class tools.moltyping.
ExtendedAtomAndBondTyper
Acessor function that returns atom type depending on AtomLabelType chosen.
getAtomLabelType()
- Method in class fingerprinters.
EncodingFingerprint
getAtomLabelType()
- Method in class tools.moltyping.
ExtendedAtomAndBondTyper
getAtomLabeltypeForIndex(int)
- Static method in class tools.moltyping.enumerations.
EnumerationsAtomTypes
getAtomsHash()
- Method in class fingerprinters.topological.
DepthFirstSearch.DepthFirstSearchFeature
getAtomSymbol(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
getAtomType(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
returns the CDK atom type
getAtomTypeName(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
getAttribute()
- Method in class tools.tree.trie.gml.
GMLNode
getBond()
- Method in class fingerprinters.topological.features.
DanglingBond
getBondSymbol(IBond)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
returns the bond symbol for a given bond
getBondSymbolNoAromatic(IBond)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
returns the bond symbol for a given bond
getbuffpos()
- Method in class io.reader.
BufferedRandomAccessFile
getCallNumber()
- Method in class tools.progressbar.
AbstractProgressBar
getChildren()
- Method in class tools.tree.trie.
TrieNode
getColor()
- Method in class tools.tree.trie.gml.
GMLNode
getComment()
- Method in class tools.tree.trie.gml.
GMLGraph
getCompleteStringPattern()
- Method in class tools.tree.trie.pattern.
PatternContainer
getConnectedAtom()
- Method in class fingerprinters.topological.features.
DanglingBond
getConnectedAtomPosition()
- Method in class fingerprinters.topological.features.
DanglingBond
getContent()
- Method in class io.
JarInput
getCoreAtom()
- Method in class fingerprinters.topological.features.
ECFPFeature
getCount()
- Method in class tools.tree.trie.pattern.
PatternContainer
getCount()
- Method in class tools.tree.trie.
TrieNode
getDanglingBond(int)
- Method in class fingerprinters.topological.features.
ECFPFeature
getDaylightInvariant(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
getDaylightInvariantRing(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
Daylight Invariant + Ring as Atom Label: Symbol.
getDescription()
- Method in class tools.moltyping.pharmacophore.
PotentialPharmacophorePoint
getDirected()
- Method in class tools.tree.trie.gml.
GMLGraph
getDistance(DistanceFactory.DistanceType)
- Static method in class distance.
DistanceFactory
getDistance()
- Method in class tools.moltyping.pharmacophore.
PotentialPharmacophorePointPair
getDistanceCutoff()
- Method in class fingerprinters.geometrical.
Encoding3D
getDistanceMeasure()
- Method in class io.writer.
ExporterLIBSVMMatrix
getDsimilarity()
- Method in class tools.tree.trie.
TrieResultContainer
getElementNeighborRingType(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
returns the element plus neighbor count type plus ring information
getElementNeighborType(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
returns the element plus neighbor count type
getErrorCode()
- Method in exception fingerprinters.
FingerPrinterException
getEstimateTime()
- Method in class tools.progressbar.
AbstractProgressBar
getExporter(ExporterFactory.ExporterType)
- Static method in class io.writer.
ExporterFactory
getExporterType(int)
- Static method in class io.writer.
ExporterFactory
getFeatureString()
- Method in class fingerprinters.topological.
DepthFirstSearch.DepthFirstSearchFeature
getFilePointer()
- Method in class io.reader.
BufferedRandomAccessFile
getFingerprint(IAtomContainer)
- Method in class fingerprinters.
EncodingFingerprint
getFingerprint(IAtomContainer)
- Method in class fingerprinters.geometrical.
Encoding3DAtomPair
getFingerprint(IAtomContainer)
- Method in class fingerprinters.geometrical.
Encoding3DAtomTriple
getFingerprint(IAtomContainer)
- Method in class fingerprinters.geometrical.
Encoding3DCATS
getFingerprint(IAtomContainer)
- Method in class fingerprinters.geometrical.
Encoding3DMolprint
getFingerprint(IAtomContainer)
- Method in class fingerprinters.geometrical.
Encoding3DPharmacophore2Point
getFingerprint(IAtomContainer)
- Method in class fingerprinters.geometrical.
Encoding3DPharmacophore3Point
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
DepthFirstSearch
Generates a fingerprint of the default size for the given AtomContainer.
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DAllPaths
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DAllShortestPath
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DAtomPair
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DAtomTriple
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DCATS
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DExtendedConnectivity
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DLocalAtomEnvironment
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DMolprint
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DPharmacophore2Point
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DPharmacophore3Point
getFingerprint(IAtomContainer)
- Method in class fingerprinters.topological.
Encoding2DSHEDKey
getFingerprint2Point(IAtomContainer, int[][], int, ExtendedAtomAndBondTyper)
- Method in class fingerprinters.
CombinatorialPatternHelper
generates all possible patters between two atoms
getFingerprint2PointPPP(IAtomContainer, int[][], int)
- Method in class fingerprinters.
CombinatorialPatternHelper
returns all possible 2 point PPP patterns with max distanceCutOff.
getFingerprint3Point(IAtomContainer, int[][], int, ExtendedAtomAndBondTyper)
- Method in class fingerprinters.
CombinatorialPatternHelper
generates all possible patterns between three atoms
getFingerprint3PointPPP(IAtomContainer, int[][], int)
- Method in class fingerprinters.
CombinatorialPatternHelper
returns all possible 3 point PPP patterns with max distanceCutOff.
getFingerprinter(FingerPrinterFactory.FingerprintType)
- Static method in class fingerprinters.
FingerPrinterFactory
getFingerPrintType(int)
- Static method in class distance.
DistanceFactory
getFingerPrintType(int)
- Static method in class fingerprinters.
FingerPrinterFactory
getFirstAtom()
- Method in class fingerprinters.topological.
DepthFirstSearch.DepthFirstSearchFeature
getFirstPPP()
- Method in class tools.moltyping.pharmacophore.
PotentialPharmacophorePointPair
getFormalneighbourCount(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
getGMLEdgeString()
- Method in class tools.tree.trie.gml.
GMLEdge
returns an edge in GML string encoding
getGMLNodeString()
- Method in class tools.tree.trie.gml.
GMLNode
returns a gml node string representation for this node
getGMLString()
- Method in class tools.tree.trie.
Trie
returns a GML representation of this trie
getGMLStringPPP()
- Method in class tools.tree.trie.
Trie
returns a GML representation of this trie
getHashedFingerPrint(int)
- Method in class fingerprinters.features.
FeatureMap
returns a hashed binary fingerprint of size hashSpace
getHashFingerprint(IAtomContainer, int, int)
- Method in class fingerprinters.topological.
DepthFirstSearch
returns a hashed fingerprint
getHashSpace()
- Method in class io.writer.
ExporterFullFingerprintCSV
getHashSpace()
- Method in class io.writer.
ExporterHashLinear
getHydrogenCount(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
getId()
- Method in class tools.tree.trie.gml.
GMLGraph
getId()
- Method in class tools.tree.trie.gml.
GMLNode
getIdentifier()
- Method in class distance.
DistanceMinMax
getIdentifier()
- Method in class distance.
DistanceTanimoto
getIdentifier()
- Method in interface distance.
IDistanceMeasure
getIndex4PPPP(PotentialPharmacophorePointPair, int)
- Method in class tools.moltyping.
PharmacophorePointAssigner
returns the bit position in the CATS autocorrelation vector
getIterationNumber()
- Method in class fingerprinters.topological.features.
ECFPFeature
getKeySet()
- Method in class fingerprinters.features.
FeatureMap
getKSubsets(int, int)
- Static method in class tools.algorithms.
KSubsetsRecursive
getLabel()
- Method in class fingerprinters.features.
FeatureMap
getLabel(int, String)
- Method in class io.reader.
RandomAccessMDLReader
returns the mdl sd tag for the ith molecule
getLabel()
- Method in class tools.tree.trie.gml.
GMLEdge
getLabel()
- Method in class tools.tree.trie.gml.
GMLGraph
getLabel()
- Method in class tools.tree.trie.gml.
GMLNode
getLabel()
- Method in class tools.tree.trie.pattern.
PatternString
getLabel()
- Method in class tools.tree.trie.
TrieNode
getLastAtom()
- Method in class fingerprinters.topological.
DepthFirstSearch.DepthFirstSearchFeature
getLastChildNode()
- Method in class tools.tree.trie.
TrieNode
getLastId()
- Method in class tools.tree.trie.
Trie.IdManager
getMaxAB()
- Method in class tools.tree.trie.
TrieResultContainer
getMDLMolString(int)
- Method in class io.reader.
RandomAccessMDLReader
returns the ith molecule in the random access file as plain mol file (e.g. to display it with Marvin)
getMinAB()
- Method in class tools.tree.trie.
TrieResultContainer
getMol(int)
- Method in class io.reader.
RandomAccessMDLReader
returns the ith molecule in the random access file
getMolName(IAtomContainer)
- Static method in class io.writer.
ExporterHelper
returns the name of the chemical compound
getNameOfFingerPrinter()
- Method in class fingerprinters.
EncodingFingerprint
getNameOfFingerPrinter()
- Method in class fingerprinters.geometrical.
Encoding3DAtomPair
getNameOfFingerPrinter()
- Method in class fingerprinters.geometrical.
Encoding3DAtomTriple
getNameOfFingerPrinter()
- Method in class fingerprinters.geometrical.
Encoding3DCATS
getNameOfFingerPrinter()
- Method in class fingerprinters.geometrical.
Encoding3DMolprint
getNameOfFingerPrinter()
- Method in class fingerprinters.geometrical.
Encoding3DPharmacophore2Point
getNameOfFingerPrinter()
- Method in class fingerprinters.geometrical.
Encoding3DPharmacophore3Point
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
DepthFirstSearch
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DAllPaths
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DAllShortestPath
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DAtomPair
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DAtomTriple
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DCATS
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DExtendedConnectivity
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DLocalAtomEnvironment
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DMolprint
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DPharmacophore2Point
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DPharmacophore3Point
getNameOfFingerPrinter()
- Method in class fingerprinters.topological.
Encoding2DSHEDKey
getNonDeepCloneOfSubstructure()
- Method in class fingerprinters.topological.features.
ECFPFeature
getNumberFromString(int, String)
- Static method in class tools.progressbar.
Utils
getNumberFromString(String, String)
- Static method in class tools.progressbar.
Utils
Funzt nur f�r positive, nat�rliche Zahlen!
getNumberOfFeatures()
- Method in class tools.tree.trie.
Trie
returns the number of leaves
getNumericValue()
- Method in class tools.tree.trie.pattern.
PatternContainer
getNumLabel()
- Method in class tools.tree.trie.pattern.
HashedPattern
getNumLabel()
- Method in interface tools.tree.trie.pattern.
InterfacePattern
getNumLabel()
- Method in class tools.tree.trie.pattern.
Pattern
getNumLabel()
- Method in class tools.tree.trie.pattern.
PatternString
getNumlabel()
- Method in class tools.tree.trie.
TrieNode
getPattern()
- Method in class tools.tree.trie.pattern.
PatternString
getPattern4String(String, int)
- Static method in class tools.tree.trie.pattern.
PatternGenerator
creates a simple pattern by decomposing a string to its characters
getPatterns()
- Method in class tools.tree.trie.pattern.
PatternContainer
getPatternsBondSeparated(String)
- Static method in class tools.tree.trie.pattern.
PatternGenerator
creates a simple pattern by decomposing a string to its characters, this function weights the position in the string
getPatternsBondSeparatedWeighted(String)
- Static method in class tools.tree.trie.pattern.
PatternGenerator
creates a simple pattern by decomposing a string to its characters, this function weights the position in the string
getPatternsBondSeparatedWeightedByProbability(String)
- Static method in class tools.tree.trie.pattern.
PatternGenerator
creates a simple pattern by decomposing a string to its characters, this function weights the symbols by their probability
getPharmacophorePoints(IAtomContainer)
- Method in class tools.moltyping.
PharmacophorePointAssigner
returns a vector of potential pharmacophore points for a molecule
getPharmacophoreType()
- Method in class tools.moltyping.pharmacophore.
PotentialPharmacophorePoint
getRingAtomType(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
returns a cdk atom type flagged with r and aromaticity information
getRoot()
- Method in class tools.tree.trie.
Trie
returns the root of this trie
getSearchDepth()
- Method in class fingerprinters.topological.
Encoding2D
getSecondPPP()
- Method in class tools.moltyping.pharmacophore.
PotentialPharmacophorePointPair
getSimilarity(FeatureMap, FeatureMap)
- Method in class distance.
DistanceMinMax
getSimilarity(FeatureMap, FeatureMap)
- Method in class distance.
DistanceTanimoto
getSimilarity(FeatureMap, FeatureMap)
- Method in interface distance.
IDistanceMeasure
getSimilarity()
- Method in class tools.tree.trie.
TrieResultContainer
getSize()
- Method in class fingerprinters.features.
FeatureMap
getSize()
- Method in class io.reader.
RandomAccessMDLReader
returns the number of structures contained in the MDL SD file
getSMARTSPattern()
- Method in class tools.moltyping.pharmacophore.
PotentialPharmacophorePoint
getSomevalue1()
- Method in class tools.tree.trie.
TrieResultContainer
getSomevalue2()
- Method in class tools.tree.trie.
TrieResultContainer
getSomevalue3()
- Method in class tools.tree.trie.
TrieResultContainer
getSomevalue4()
- Method in class tools.tree.trie.
TrieResultContainer
getSource()
- Method in class tools.tree.trie.gml.
GMLEdge
getStretchingFactor()
- Method in class fingerprinters.geometrical.
Encoding3D
getTarget()
- Method in class tools.tree.trie.gml.
GMLEdge
getTimeString(long)
- Static method in class tools.progressbar.
Utils
Given the miliseconds elapsed, returns a formatted time string up to a max deph of 3. e.g. "16h 4m 4s" or "2d 16h 4m" or "4s 126dms"
getTotalFeatureCount()
- Method in class tools.tree.trie.
Trie
returns the total number of features, taking the counts of the features into account
getTotalNodeCount()
- Method in class tools.tree.trie.
Trie
returns the number of all nodes in the trie
getTyper()
- Method in class fingerprinters.
EncodingFingerprint
getValency(IAtom)
- Static method in class tools.moltyping.
ExtendedAtomAndBondTyper
getValue(IFeature)
- Method in class fingerprinters.features.
FeatureMap
getValue()
- Method in interface fingerprinters.features.
IFeature
getValue()
- Method in class fingerprinters.features.
NumericStringFeature
getValue()
- Method in class fingerprinters.topological.features.
ECFPFeature
getWeight()
- Method in class tools.tree.trie.pattern.
HashedPattern
getWeight()
- Method in interface tools.tree.trie.pattern.
InterfacePattern
getWeight()
- Method in class tools.tree.trie.pattern.
Pattern
getWeight()
- Method in class tools.tree.trie.pattern.
PatternString
getWeight()
- Method in class tools.tree.trie.
Trie
returns the total weight of all features of this trie, returns null if no weights are set
getWeight()
- Method in class tools.tree.trie.
TrieNode
getWeightedPattern4String(String, int)
- Static method in class tools.tree.trie.pattern.
PatternGenerator
creates a simple pattern by decomposing a string to its characters, this function weights the position in the string
GMLEdge
- Class in
tools.tree.trie.gml
GMLEdge()
- Constructor for class tools.tree.trie.gml.
GMLEdge
GMLGraph
- Class in
tools.tree.trie.gml
GMLGraph()
- Constructor for class tools.tree.trie.gml.
GMLGraph
GMLNode
- Class in
tools.tree.trie.gml
GMLNode(int)
- Constructor for class tools.tree.trie.gml.
GMLNode
GREEN
- Static variable in class tools.tree.trie.gml.
ConstantsYEditColor
GREY
- Static variable in class tools.tree.trie.gml.
ConstantsYEditColor
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
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