A B C D E F G H I J K L M N P R S T U V W Y

G

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
 

A B C D E F G H I J K L M N P R S T U V W Y