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JOELib
Computational Chemistry Package

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AE_ANDHI - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_ANDLO - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_LEAF - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_NOT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_OR - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AE_RECUR - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
ALL_DESCRIPTORS - Static variable in class joelib.desc.data.MolDescCounter: Description of the Field
AL_ANTICLOCKWISE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_AROM - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CHIRAL - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CLOCKWISE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CONNECT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_CONST - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_DEGREE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Degree of an atom (including explicit H), in SMARTS: D.
AL_ELECTRONEGATIVE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_ELEM - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_GROUP - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_HCOUNT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_HEAVY_CONNECT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Degree of an atom regarding only heavy atoms, in SMARTS: Q.
AL_HYB - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_IMPLICIT - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_MASS - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_NEGATIVE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_POSITIVE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_RINGS - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_SIZE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
AL_VALENCE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
ANDFilter - class joelib.process.filter.ANDFilter.: Molecule process filter AND condition.
ANDFilter() - Constructor for class joelib.process.filter.ANDFilter: Constructor for the DescriptorFilter object
ANDFilter(Filter, Filter) - Constructor for class joelib.process.filter.ANDFilter: Constructor for the DescriptorFilter object
ANGLE - Static variable in class joelib.io.types.cml.CMLCoreModule
ANY - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Any bond type
APWekaHelper - class joelib.algo.datamining.weka.APWekaHelper.: Atom pair descriptor helper for Weka data mining algorithms.
APWekaHelper() - Constructor for class joelib.algo.datamining.weka.APWekaHelper
APropDoubleArrResult - class joelib.desc.result.APropDoubleArrResult.: Atom representation.
APropDoubleArrResult() - Constructor for class joelib.desc.result.APropDoubleArrResult: Constructor for the BFSResult object
APropDoubleResult - class joelib.desc.result.APropDoubleResult.: Double value descriptor which was calculated by using an atom property (AtomProperties).
APropDoubleResult() - Constructor for class joelib.desc.result.APropDoubleResult: Constructor for the IntResult object
APropIntResult - class joelib.desc.result.APropIntResult.: Atom representation.
APropIntResult() - Constructor for class joelib.desc.result.APropIntResult: Constructor for the IntResult object
APropertyBFS - class joelib.algo.APropertyBFS.: Breadh First Search.
APropertyBFS() - Constructor for class joelib.algo.APropertyBFS: Constructor for the KierShape1 object
APropertyDistanceMatrix - class joelib.desc.types.APropertyDistanceMatrix.: Calculates the Distance Matrix (shortest paths from each atom to each atom) of a molecule
APropertyDistanceMatrix() - Constructor for class joelib.desc.types.APropertyDistanceMatrix: Constructor for the DistanceMatrix object
AROMATIC - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Aromatic bond type
ARRAY - Static variable in class joelib.io.types.cml.CMLCoreModule
ASYM_BOND_PROPERTY_INDEX - Static variable in class joelib.io.types.ClearTextFormat: Data element for storing the access information for the asymmetric bond properties.
ATOM - Static variable in class joelib.io.types.cml.CMLCoreModule
ATOMARRAY - Static variable in class joelib.io.types.cml.CMLCoreModule
ATOMEXPRPOOL - Static variable in class joelib.smarts.ParseSmart: Description of the Field
ATOMPOOL - Static variable in class joelib.smarts.Pattern: Description of the Field
ATOM_NUMBERS - Static variable in class joelib.desc.AtomsCounter
ATOM_PICKED - Static variable in class joelib.gui.molviewer.java3d.util.MolViewerEvent: Description of the Field
ATOM_PROPERTIES - Static variable in class joelib.desc.types.atompair.TopologicalAtomPair
ATOM_PROPERTIES - Static variable in class joelib.process.types.AtomPropertyMatrix: Description of the Field
ATOM_PROPERTY - Static variable in class joelib.desc.result.AtomDynamicResult
ATOM_PROPERTY - Static variable in class joelib.desc.types.Autocorrelation
ATOM_PROPERTY - Static variable in class joelib.desc.types.BCUT
ATOM_PROPERTY - Static variable in class joelib.desc.types.BurdenEigenvalues
ATOM_PROPERTY - Static variable in class joelib.desc.types.BurdenModifiedEigenvalues
ATOM_PROPERTY - Static variable in class joelib.desc.types.GlobalTopologicalChargeIndex
ATOM_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
ATOM_PROPERTY1 - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY1 - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY1_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY1_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY2 - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY2 - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY2_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY2_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY3 - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY3 - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY3_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY3_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY4 - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY4 - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY4_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY4_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY5 - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY5 - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY5_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY5_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY6 - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY6 - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY6_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
ATOM_PROPERTY6_WEIGHT - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
ATOM_PROPERTY_MATRIX - Static variable in class joelib.process.types.AtomPropertyMatrix
ATOM_PROPERTY_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
ATOM_PROPERTY_WEIGHT - Static variable in class joelib.desc.types.BCUT
ATOM_PROPERTY_WEIGHT - Static variable in class joelib.desc.types.BurdenEigenvalues
ATOM_PROPERTY_WEIGHT - Static variable in class joelib.desc.types.BurdenModifiedEigenvalues
AbstractDatabase - class joelib.util.database.AbstractDatabase.: Helper class to access and store molecules.
AbstractDatabase() - Constructor for class joelib.util.database.AbstractDatabase
AcidicGroups - class joelib.desc.types.AcidicGroups.: Number of acidic groups.
AcidicGroups() - Constructor for class joelib.desc.types.AcidicGroups
Acme - package Acme
Acme.JPM.Encoders - package Acme.JPM.Encoders
AliphaticOHGroups - class joelib.desc.types.AliphaticOHGroups.: Number of aliphatic hydroxy groups.
AliphaticOHGroups() - Constructor for class joelib.desc.types.AliphaticOHGroups
Amber - class joelib.io.types.Amber.: Reader for AmberPrep file format.
Amber() - Constructor for class joelib.io.types.Amber
Angle - class joelib.gui.molviewer.java3d.math.geometry.Angle.: A class that provides mathematical definition of geometric angle
Angle() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: default constructor: value is 0.0;
Angle(double, boolean) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: full constructor
Angle(double) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: constructor
Angle(Angle) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Angle: copy constructor
AromaticBonds - class joelib.desc.types.AromaticBonds.: Number of aromatic bonds.
AromaticBonds() - Constructor for class joelib.desc.types.AromaticBonds: Constructor for the KierShape1 object
AromaticOHGroups - class joelib.desc.types.AromaticOHGroups.: Number of aromatic hydroxy groups.
AromaticOHGroups() - Constructor for class joelib.desc.types.AromaticOHGroups
ArrayBinning - class wsi.ra.tool.ArrayBinning.: A class to store simple binning statistics
ArrayBinning(int, ArrayStatistic) - Constructor for class wsi.ra.tool.ArrayBinning: Constructor for the ArrayBinning object
ArrayCML - class joelib.io.types.cml.elements.ArrayCML.: Scalar CML element.
ArrayCML(Vector) - Constructor for class joelib.io.types.cml.elements.ArrayCML: Constructor for the StringString object
ArrayHelper - class joelib.util.ArrayHelper.: Array helper methods for writing and loading arrays.
ArraySizeComparator - class joelib.sort.ArraySizeComparator.: Comparator for array size (int or double).
ArraySizeComparator() - Constructor for class joelib.sort.ArraySizeComparator: Initializes the ArraySizeComparator-Comparator.
ArrayStatistic - class wsi.ra.tool.ArrayStatistic.: A class to store simple statistics
ArrayStatistic() - Constructor for class wsi.ra.tool.ArrayStatistic
ArrayStatistic(int, double, double, double, double, double, double) - Constructor for class wsi.ra.tool.ArrayStatistic
Arrow - class joelib.gui.render.Arrow.: Holding single arrow informations.
Arrow() - Constructor for class joelib.gui.render.Arrow
Arrows - class joelib.gui.render.Arrows.: Holding multiple arrow informations.
Arrows(JOEMol, String) - Constructor for class joelib.gui.render.Arrows
AtomArrayInt - class joelib.util.types.AtomArrayInt.: Atom array and integer value.
AtomArrayInt() - Constructor for class joelib.util.types.AtomArrayInt
AtomAtomProperties - interface joelib.molecule.types.AtomAtomProperties.: Interface to access atom-atom properties.
AtomDouble - class joelib.algo.morgan.AtomDouble.: Helper class for resolving renumbering ties.
AtomDouble() - Constructor for class joelib.algo.morgan.AtomDouble: Constructor for the IntInt object
AtomDouble(int, double) - Constructor for class joelib.algo.morgan.AtomDouble: Constructor for the IntInt object
AtomDoubleComparator - class joelib.algo.morgan.AtomDoubleComparator.: Comparator for resolving renumbering ties..
AtomDoubleComparator() - Constructor for class joelib.algo.morgan.AtomDoubleComparator: Initializes the RingSizeComparator-Comparator.
AtomDoubleParent - class joelib.algo.morgan.AtomDoubleParent.: Helper class for resolving renumbering ties.
AtomDoubleParent() - Constructor for class joelib.algo.morgan.AtomDoubleParent: Constructor for the IntInt object
AtomDoubleParent(int, double, int, boolean) - Constructor for class joelib.algo.morgan.AtomDoubleParent: Constructor for the IntInt object
AtomDoubleResult - class joelib.desc.result.AtomDoubleResult.: Double results of atom properties.
AtomDoubleResult() - Constructor for class joelib.desc.result.AtomDoubleResult: Constructor for the DoubleResult object
AtomDynamicResult - class joelib.desc.result.AtomDynamicResult.: Dynamic results of atom properties.
AtomDynamicResult() - Constructor for class joelib.desc.result.AtomDynamicResult: Constructor for the DoubleResult object
AtomExpr - class joelib.smarts.atomexpr.AtomExpr.: Atom expression in SMARTS substructure search.
AtomExpr() - Constructor for class joelib.smarts.atomexpr.AtomExpr: Constructor for the AtomExpr object
AtomExpr(int) - Constructor for class joelib.smarts.atomexpr.AtomExpr: Constructor for the AtomExpr object
AtomHCount - class joelib.util.types.AtomHCount.: Atom and number of hydrogen atoms.
AtomHCount(JOEAtom, int) - Constructor for class joelib.util.types.AtomHCount: Constructor for the AtomHCount object
AtomInAcceptor - class joelib.desc.types.AtomInAcceptor.: Is this atom an acceptor (acceptor field) for a carbonyl oxygen probe.
AtomInAcceptor() - Constructor for class joelib.desc.types.AtomInAcceptor: Constructor for the KierShape1 object
AtomInAromaticSystem - class joelib.desc.types.AtomInAromaticSystem.: Is this atom part of an aromatic system.
AtomInAromaticSystem() - Constructor for class joelib.desc.types.AtomInAromaticSystem: Constructor for the KierShape1 object
AtomInConjEnvironment - class joelib.desc.types.AtomInConjEnvironment.: Is this atom part of a conjugated system.
AtomInConjEnvironment() - Constructor for class joelib.desc.types.AtomInConjEnvironment: Constructor for the KierShape1 object
AtomInDonAcc - class joelib.desc.types.AtomInDonAcc.: Is this atom an acceptor or donor (acceptor/donor field) for a carbonyl oxygen or amino hydrogen probe.
AtomInDonAcc() - Constructor for class joelib.desc.types.AtomInDonAcc: Constructor for the KierShape1 object
AtomInDonor - class joelib.desc.types.AtomInDonor.: Is this atom an donor (donor field) for a amino hydrogen probe.
AtomInDonor() - Constructor for class joelib.desc.types.AtomInDonor: Constructor for the KierShape1 object
AtomInRing - class joelib.desc.types.AtomInRing.: Is this atom a ring atom.
AtomInRing() - Constructor for class joelib.desc.types.AtomInRing: Constructor for the KierShape1 object
AtomInTerminalCarbon - class joelib.desc.types.AtomInTerminalCarbon.: Is this atom a terminal carbon atom.
AtomInTerminalCarbon() - Constructor for class joelib.desc.types.AtomInTerminalCarbon: Constructor for the KierShape1 object
AtomIntInt - class joelib.util.types.AtomIntInt.: Atom and IntInt.
AtomIntInt(JOEAtom, IntInt) - Constructor for class joelib.util.types.AtomIntInt: Constructor for the AtomIntInt object
AtomIntResult - class joelib.desc.result.AtomIntResult.: Integer results of atom properties.
AtomIntResult() - Constructor for class joelib.desc.result.AtomIntResult: Constructor for the DoubleResult object
AtomIsNegative - class joelib.desc.types.AtomIsNegative.: Is this atom negatively charged atom.
AtomIsNegative() - Constructor for class joelib.desc.types.AtomIsNegative: Constructor for the KierShape1 object
AtomIsPositive - class joelib.desc.types.AtomIsPositive.: Is this atom positively charged atom.
AtomIsPositive() - Constructor for class joelib.desc.types.AtomIsPositive: Constructor for the KierShape1 object
AtomIterator - class joelib.util.iterator.AtomIterator.: Gets an iterator over all atoms in a molecule.
AtomIterator(Vector) - Constructor for class joelib.util.iterator.AtomIterator: Constructor for the AtomIterator object
AtomMass - class joelib.desc.types.AtomMass.: Atom mass.
AtomMass() - Constructor for class joelib.desc.types.AtomMass: Constructor for the KierShape1 object
AtomNode - class joelib.gui.molviewer.java3d.graphics3D.AtomNode.: Description of the Class
AtomPair - class joelib.desc.types.atompair.AtomPair.: Single atom pair (depends on atom properties used).
AtomPair(AtomProperties[], JOEAtom, JOEAtom, double) - Constructor for class joelib.desc.types.atompair.AtomPair
AtomPairAtomType - class joelib.desc.types.atompair.AtomPairAtomType.: Atom type for pair descriptor (depends on atom properties used).
AtomPairAtomType(int, double[]) - Constructor for class joelib.desc.types.atompair.AtomPairAtomType
AtomPairResult - class joelib.desc.types.atompair.AtomPairResult.: Atom pair descriptor (depends on atom properties used).
AtomPairResult() - Constructor for class joelib.desc.types.atompair.AtomPairResult: Constructor for the IntResult object
AtomPairTypeComparator - class joelib.desc.types.atompair.AtomPairTypeComparator.: Comparator for atom pairs.
AtomPairTypeComparator() - Constructor for class joelib.desc.types.atompair.AtomPairTypeComparator: Initializes the AtomPairComparator-Comparator.
AtomPairTypeHolder - class joelib.desc.types.atompair.AtomPairTypeHolder.: Atom type singleton class to cache the types (depends on atom properties used).
AtomProperties - interface joelib.molecule.types.AtomProperties.: Interface to access atom properties.
AtomPropertyColoring - class joelib.molecule.types.AtomPropertyColoring.: Some methods to faciliate the work with descriptors.
AtomPropertyColoring() - Constructor for class joelib.molecule.types.AtomPropertyColoring: Constructor for the DescriptorHelper object
AtomPropertyDescriptors - class joelib.desc.util.AtomPropertyDescriptors.: Example for loading molecules and get atom properties.
AtomPropertyDescriptors() - Constructor for class joelib.desc.util.AtomPropertyDescriptors
AtomPropertyMatrix - class joelib.process.types.AtomPropertyMatrix.: Calling processor classes if the filter rule fits.
AtomPropertyMatrix() - Constructor for class joelib.process.types.AtomPropertyMatrix: Constructor for the DescSelectionWriter object
AtomSpec - class joelib.smarts.AtomSpec.: Atom specification of a SMARTS bond expression.
AtomSpec() - Constructor for class joelib.smarts.AtomSpec: Constructor for the AtomSpec object
AtomStringResult - class joelib.desc.result.AtomStringResult.: Integer results of atom properties.
AtomStringResult() - Constructor for class joelib.desc.result.AtomStringResult: Constructor for the DoubleResult object
AtomType - class joelib.desc.types.AtomType.: Atom type (JOELib internal).
AtomType() - Constructor for class joelib.desc.types.AtomType: Constructor for the AtomType object
AtomTypePair - class joelib.desc.types.atompair.AtomTypePair.: Atom type pair (depends on atom properties used).
AtomTypePair(AtomPair) - Constructor for class joelib.desc.types.atompair.AtomTypePair
AtomValence - class joelib.desc.types.AtomValence.: Atom valence.
AtomValence() - Constructor for class joelib.desc.types.AtomValence: Constructor for the KierShape1 object
AtomVanDerWaalsVolume - class joelib.desc.types.AtomVanDerWaalsVolume.: Atom Van der Waals volume.
AtomVanDerWaalsVolume() - Constructor for class joelib.desc.types.AtomVanDerWaalsVolume: Constructor for the KierShape1 object
AtomZPos - class joelib.util.types.AtomZPos.: Atom and double z value.
AtomZPos(JOEAtom, double) - Constructor for class joelib.util.types.AtomZPos: Constructor for the AtomZPos object
AtomZPosComparator - class joelib.molecule.AtomZPosComparator.: Comparator for the z position of molecules.
AtomZPosComparator() - Constructor for class joelib.molecule.AtomZPosComparator: Initializes the z position Comparator.
AtomsCounter - class joelib.desc.AtomsCounter.: Abstract descriptor class for counting the number of atoms.
AtomsCounter() - Constructor for class joelib.desc.AtomsCounter: Initializes descriptor class for counting the number of atoms.
Autocorrelation - class joelib.desc.types.Autocorrelation.: Moreau-Broto autocorrelation.
Autocorrelation() - Constructor for class joelib.desc.types.Autocorrelation
a - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
a - Variable in class joelib.util.types.AtomIntInt: Description of the Field
a1 - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: From and to atoms, respectively
a2 - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: From and to atoms, respectively
aalloc - Variable in class joelib.smarts.Pattern: Description of the Field
abortOnErrors - Variable in class joelib.io.types.cml.CMLErrorHandler
accept(File) - Method in class joelib.gui.util.MolFileFilter: Return true if this file should be shown in the directory pane, false if it shouldn't.
accept(JOEMol) - Method in class joelib.process.filter.ANDFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.DescriptorFilter: Description of the Method
accept(JOEMol) - Method in interface joelib.process.filter.Filter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.HasAllDataFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.HasDataFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.NOTFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.NativeValueFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.ORFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.RuleOf5Filter: Returns only true if less than two of the four rules fullfills the rules.
accept(JOEMol) - Method in class joelib.process.filter.SMARTSFilter: Description of the Method
accept(JOEMol) - Method in class joelib.process.filter.SelectionFilter: Description of the Method
accept(File, String) - Method in class wsi.ra.io.RegExpFilenameFilter
acceptObjects() - Method in interface joelib.io.types.cml.CDOInterface: The next procedure must be implemented by each CDO and return a CDOAcceptedObjects class with the names of the objects that can be handled.
acceptObjects() - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
accepted - Variable in class joelib.math.symmetry.SymStatistic
acceptedProperties() - Method in class joelib.algo.APropertyBFS
acceptedProperties() - Method in class joelib.algo.BFS
acceptedProperties() - Method in class joelib.algo.DFS
acceptedProperties() - Method in class joelib.desc.AtomsCounter: Return the accepted properties.
acceptedProperties() - Method in class joelib.desc.SMARTSCounter
acceptedProperties() - Method in class joelib.desc.SimpleBooleanDesc
acceptedProperties() - Method in class joelib.desc.SimpleDoubleAtomProperty
acceptedProperties() - Method in class joelib.desc.SimpleDoubleDesc
acceptedProperties() - Method in class joelib.desc.SimpleDynamicAtomProperty
acceptedProperties() - Method in class joelib.desc.SimpleIntDesc
acceptedProperties() - Method in class joelib.desc.SimpleStringAtomProperty
acceptedProperties() - Method in class joelib.desc.types.APropertyDistanceMatrix
acceptedProperties() - Method in class joelib.desc.types.Autocorrelation
acceptedProperties() - Method in class joelib.desc.types.BCUT
acceptedProperties() - Method in class joelib.desc.types.BurdenEigenvalues
acceptedProperties() - Method in class joelib.desc.types.BurdenModifiedEigenvalues
acceptedProperties() - Method in class joelib.desc.types.ConjElectroTopolState
acceptedProperties() - Method in class joelib.desc.types.DistanceDistanceMatrix
acceptedProperties() - Method in class joelib.desc.types.DistanceMatrix
acceptedProperties() - Method in class joelib.desc.types.ElectrogeometricalState
acceptedProperties() - Method in class joelib.desc.types.ElectrotopologicalState
acceptedProperties() - Method in class joelib.desc.types.GeomDistanceMatrix
acceptedProperties() - Method in class joelib.desc.types.GlobalTopologicalChargeIndex
acceptedProperties() - Method in class joelib.desc.types.HeavyBonds
acceptedProperties() - Method in class joelib.desc.types.HeteroCycles
acceptedProperties() - Method in class joelib.desc.types.RadialDistributionFunction
acceptedProperties() - Method in class joelib.desc.types.SSKey3DS
acceptedProperties() - Method in class joelib.desc.types.WeightedBurdenEigenvalues
acceptedProperties() - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
acceptedProperties() - Method in class joelib.desc.types.atompair.TopologicalAtomPair
acceptedProperties() - Method in class joelib.ext.SimpleExternalProcess
acceptedProperties() - Method in class joelib.process.ProcessPipe
acceptedProperties() - Method in class joelib.process.SimpleProcess
acceptedProperties() - Method in class joelib.process.types.AtomPropertyMatrix: Description of the Method
acceptedProperties() - Method in class joelib.process.types.CreateFileName: Description of the Method
acceptedProperties() - Method in class joelib.process.types.MoleculeFileCreation
acceptedProperties() - Method in class joelib.process.types.MoleculeFileDeletion
acceptedProperties() - Method in interface joelib.util.PropertyAcceptor
acount - Variable in class joelib.smarts.Pattern: Description of the Field
actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerUsage: Close the dialog on a button event
actual() - Method in class joelib.util.iterator.NbrAtomIterator: Description of the Method
actual() - Method in class joelib.util.iterator.VectorIterator: Returns the actual Object .
actualBond() - Method in class joelib.util.iterator.NbrAtomIterator: Description of the Method
actualIndex() - Method in class joelib.util.iterator.VectorIterator: Returns the index number ot the sctual Object .
actualName() - Method in class joelib.util.iterator.NativeValueIterator
add(MolInstance) - Method in class joelib.algo.datamining.weka.MolInstances: Adds one instance to the end of the set.
add(IntInt) - Method in class joelib.data.JOERgroupData: Add new atom-Rgroup entry.
add(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: rotat the vector by a factor add a vector to this vector
add(JOEMol) - Method in class joelib.gui.render.RenderingAtoms
add(String) - Method in class joelib.io.types.cml.CDOAcceptedObjects: Adds the name of an accepted object.
add(JOECoordTrans) - Method in class joelib.math.JOECoordTrans: Combine two transformations.
add(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
add(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
add(XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
add(JOERing) - Method in class joelib.ring.JOERingData: Description of the Method
add(double) - Method in class wsi.ra.tool.ArrayBinning: Adds a value to the observed values
add(double, double) - Method in class wsi.ra.tool.ArrayBinning: Adds a value that has been seen n times to the observed values
add(double) - Method in class wsi.ra.tool.ArrayStatistic: Adds a value to the observed values
add(double, int) - Method in class wsi.ra.tool.ArrayStatistic: Adds a value that has been seen n times to the observed values
add(Object) - Method in class wsi.ra.tool.SortedVector: Appends the specified element to the end of this Vector.
add(int, Object) - Method in class wsi.ra.tool.SortedVector: Inserts the specified element at the specified position in this Vector.
addAll(Collection) - Method in class wsi.ra.tool.SortedVector: Appends all of the elements in the specified Collection to the end of this Vector, in the order that they are returned by the specified Collection's Iterator.
addAll(int, Collection) - Method in class wsi.ra.tool.SortedVector: Inserts all of the elements in in the specified Collection into this Vector at the specified position.
addAtom(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Add an atom to this molecule
addAtom(JOEAtom) - Method in class joelib.molecule.JOEMol: Adds (cloned) atom to the JOEMol.
addAtom(JOEAtom) - Method in class joelib.molecule.JOEResidue
addAtom(int, float, double, double, double) - Method in class joelib.util.ghemical.GhemicalInterface
addAtomNode(AtomNode) - Method in class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode: Adds a feature to the AtomNode attribute of the MoleculeNode object
addBond(ViewerBond) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Add a bond to this molecule
addBond(JOEBond) - Method in class joelib.molecule.JOEAtom: Adds a bond to this atom.
addBond(int, int, int) - Method in class joelib.molecule.JOEMol: Adds a bond to the JOEMol.
addBond(int, int, int, int) - Method in class joelib.molecule.JOEMol: Adds a bond to the JOEMol.
addBond(int, int, int, int, int) - Method in class joelib.molecule.JOEMol: Adds a bond to the JOEMol.
addBond(JOEBond) - Method in class joelib.molecule.JOEMol: Adds (cloned) bond to the JOEMol.
addBond(int, int, int) - Method in class joelib.util.ghemical.GhemicalInterface: Add ghemical bond.
addBondNode(BondNode) - Method in class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode: Adds a feature to the BondNode attribute of the MoleculeNode object
addCMLProperty(StringString) - Method in class joelib.desc.result.BitArrayResult
addCMLProperty(StringString) - Method in class joelib.desc.result.BitResult
addCMLProperty(StringString) - Method in class joelib.desc.result.BooleanResult
addCMLProperty(StringString) - Method in class joelib.desc.result.DoubleArrayResult
addCMLProperty(StringString) - Method in class joelib.desc.result.DoubleMatrixResult
addCMLProperty(StringString) - Method in class joelib.desc.result.DoubleResult
addCMLProperty(StringString) - Method in class joelib.desc.result.DynamicArrayResult
addCMLProperty(StringString) - Method in class joelib.desc.result.FloatMatrixResult
addCMLProperty(StringString) - Method in class joelib.desc.result.IntArrayResult: Constructor for the IntArrayResult object
addCMLProperty(StringString) - Method in class joelib.desc.result.IntBitArrayResult
addCMLProperty(StringString) - Method in class joelib.desc.result.IntMatrixResult
addCMLProperty(StringString) - Method in class joelib.desc.result.IntResult
addCMLProperty(StringString) - Method in class joelib.desc.result.StringArrayResult
addCMLProperty(StringString) - Method in class joelib.desc.result.StringResult
addCMLProperty(StringString) - Method in interface joelib.io.types.cml.ResultCMLProperties
addCSEntry(JCAMPDataBlock) - Method in class joelib.jcamp.JCAMPData
addChangeListener(Renderer2DChangeListener) - Method in class joelib.gui.render.Renderer2DModel: Adds a change listener to the list of listeners
addConformer(double[]) - Method in class joelib.molecule.JOEMol: Adds conformer coordinates to this molecule.
addDXEntry(JCAMPDataBlock) - Method in class joelib.jcamp.JCAMPData
addData(JOEGenericData, boolean) - Method in class joelib.molecule.GenericDataHolder: Adds a feature to the Data attribute of the GenericDataHolder object
addData(JOEGenericData) - Method in class joelib.molecule.JOEMol: Adds a JOEGenericData object to this molecule but don't overwrite existing data elements with the same name, if they exists already.
addData(JOEGenericData, boolean) - Method in class joelib.molecule.JOEMol: Adds a JOEGenericData object to this molecule.
addElement(Object) - Method in class wsi.ra.tool.SortedVector: Adds the specified component to the end of this vector, increasing its size by one.
addExtension(String) - Method in class joelib.gui.util.MolFileFilter: Adds a filetype "dot" extension to filter against.
addHardCodedKernel(HardCodedKernel) - Method in class joelib.data.JOEKernel
addHydrogens() - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(boolean) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(boolean, boolean) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(boolean, boolean, boolean) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to this molecule.
addHydrogens(JOEAtom) - Method in class joelib.molecule.JOEMol: Adds hydrogens atoms to the given atom.
addLassoPoint(Point) - Method in class joelib.gui.render.Renderer2DModel: Adds a point to the list of lasso points
addLinkEntry(JCAMPDataBlock) - Method in class joelib.jcamp.JCAMPData
addMol(JOEMol) - Method in class joelib.molecule.JOEMolVector: Add molecule to this molecule vector.
addMolViewerEventListener(MolViewerEventListener) - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.Viewer: Adds a feature to the Molecule attribute of the Viewer object
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Adds a feature to the Molecule attribute of the ViewerFrame object
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D: Adds a feature to the Molecule attribute of the Panel3D object
addMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Adds a feature to the Molecule attribute of the MolecularScene object
addOSNameToLibraryPath(boolean) - Static method in class joelib.util.ghemical.GhemicalInterface: Determines if the OS name (like 'windows' or 'linux') will be appended automatically to the library path.
addObject(String, Object) - Method in class joelib.gui.molviewer.java3d.util.CentralLookup: Adds a feature to the Object attribute of the CentralLookup object
addPolarHydrogens() - Method in class joelib.molecule.JOEMol: Add polar hydrogens to molecule.
addProcess(JOEProcess) - Method in class joelib.process.ProcessPipe
addProcess(JOEProcess, Hashtable) - Method in class joelib.process.ProcessPipe
addProcess(JOEProcess, Filter) - Method in class joelib.process.ProcessPipe
addProcess(JOEProcess, Filter, Hashtable) - Method in class joelib.process.ProcessPipe
addResidue(JOEResidue) - Method in class joelib.molecule.JOEMol: Adds residue information to this molecule.
addReturn(AtomPairAtomType) - Method in class joelib.desc.types.atompair.AtomPairTypeHolder
addRingFromClosure(JOEMol, JOEBond, int) - Method in class joelib.ring.JOERingSearch: Adds a feature to the RingFromClosure attribute of the JOERingSearch object
addRule(String, String) - Method in class joelib.smarts.Patty: Adds a new PATTY rule.
addRule(JOESmartsPattern, String) - Method in class joelib.smarts.Patty: Adds a new PATTY rule.
addRules(Vector) - Method in class joelib.smarts.Patty: Adds a new rules to the pattern typer.
addSkipExtension(String) - Method in class wsi.ra.io.RegExpFilenameFilter
addSoftCodedKernel(SoftCodedKernel) - Method in class joelib.data.JOEKernel
addStringRule(String) - Method in class joelib.smarts.Patty: Adds a new rule to the pattern typer.
adding(JOECoordTrans) - Method in class joelib.math.JOECoordTrans: Changes this transform to the orginal transform followed by an additional transform.
adding(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
adding(double[]) - Method in class joelib.math.XYZVector: Description of the Method
align(JOEAtom, JOEAtom, XYZVector, XYZVector) - Method in class joelib.molecule.JOEMol: Aligns atom a1 on p1 and atom a2 along p1->p2 vector.
alignRight - Variable in class joelib.gui.render.Arrow
alignRight - Variable in class joelib.gui.render.OrthoLine
allocAtomExpr(int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
allocBondExpr(int) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
allocPattern() - Static method in class joelib.smarts.Pattern: Description of the Method
analyseDataset(String, GroupContributions) - Static method in class joelib.test.GroupContributionTest
and(BitSet14) - Method in class joelib.util.BitSet14: Performs a logical AND of this target bit set with the argument bit set.
and(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
and(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec: Description of the Method
andAtomExpr(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
andAtomExprLeaf(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
andCount(BitSet14) - Method in class joelib.util.JOEBitVec: Returns the number of bits which are set in this BitSet14 AND the BitSet14 b.
andNot(BitSet14) - Method in class joelib.util.BitSet14: Clears all of the bits in this BitSet14 whose corresponding bit is set in the specified BitSet14.
andSet(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
angle(Point3D, Point3D, Point3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: calculate angle among three points in 3D space note: calling Point3D.distSquare() is more efficient than Point3D.distance().
angle(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector
angleWith(Point3D, Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: calculate angle among three points in 3D space note: calling distSquare() is more efficient than distance().
append(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtoms: Append an atom to the end of vector
append(ViewerBond) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Append a bond to the end of vector
append(String) - Method in class joelib.gui.util.JLog4JPanel: Appends a string to the textarea and scrolls it down.
apply(JOEMol) - Method in class joelib.data.JOEChemTransformation: Description of the Method
apply(String[]) - Method in class jtt.docbook.DocBookArticles
apply(String[]) - Method in class jtt.docbook.DocBookEquations
apply(String[]) - Method in class jtt.docbook.DocBookMolecules
arg - Variable in class joelib.smarts.atomexpr.MonAtomExpr: Description of the Field
arg - Variable in class joelib.smarts.bondexpr.MonBondExpr: Description of the Field
aromflag - Variable in class joelib.molecule.Element: Description of the Field
arrayStat - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
arrows - Variable in class joelib.gui.render.Arrows
assignAromaticFlags(JOEMol) - Method in class joelib.data.JOEAromaticTyper: Assign the aromaticity flag to atoms and bonds.
assignBonds(JOEMol, JOEBitVec) - Method in class joelib.data.JOEResidueData
assignCisTrans(JOESmiNode) - Method in class joelib.smiles.JOEMol2Smi: Traverse the tree searching for acyclic olefins and assign stereochemistry if it has at least one heavy atom attachment on each end.
assignHyb(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
assignImplicitValence(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
assignPartialCharges(JOEMol) - Method in class joelib.molecule.charge.JOEGastChrg: Description of the Method
assignSeedPartialCharge(JOEMol) - Method in class joelib.data.JOEPhModel: Description of the Method
assignTypes(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
assignTypes(JOEMol) - Method in class joelib.smarts.Patty: Assigns identifier's to the first matching atom in the SMARTS pattern.
assignTypes(JOEMol, int[]) - Method in class joelib.smarts.Patty: Assigns identifier's to the first matching atom in the SMARTS pattern.
assignTypes2All(JOEMol) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern.
assignTypes2All(JOEMol, int[]) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern.
assignTypes2Groups(JOEMol) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern and returns all matching lists.
assignTypes2Groups(JOEMol, int[], Vector) - Method in class joelib.smarts.Patty: Assigns identifier's to all matching atoms in the SMARTS pattern and returns all matching lists.
atom - Variable in class joelib.gui.render.RenderAtom
atom - Variable in class joelib.smarts.Pattern: Description of the Field
atom - Variable in class joelib.util.types.AtomHCount: Description of the Field
atom - Variable in class joelib.util.types.AtomZPos: Description of the Field
atom - Variable in class joelib.util.types.StackType: Description of the Field
atomContributions - Variable in class joelib.algo.contribution.GroupContributions
atomElements - Variable in class joelib.io.types.cml.CMLCoreModule
atomExprConflict(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomExprImplied(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomExprImplies(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomIdx - Variable in class joelib.algo.morgan.AtomDouble: Atom index of the atom.
atomIdx - Variable in class joelib.algo.morgan.AtomDoubleParent: Atom index of the atom.
atomIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over all atoms in this molecule.
atomIterator() - Method in class joelib.molecule.JOEResidue: Gets an iterator over all atoms in this residue.
atomLeafConflict(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomLeafImplies(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
atomPairs - Variable in class joelib.desc.types.atompair.AtomPairResult
atomPicked(MolViewerEvent) - Method in class joelib.gui.molviewer.java3d.util.MolViewerEventAdapter
atomPicked(MolViewerEvent) - Method in interface joelib.gui.molviewer.java3d.util.MolViewerEventListener
atomProperties - Variable in class joelib.desc.types.atompair.AtomPairAtomType
atomProperty - Variable in class joelib.desc.result.APropDoubleArrResult: Description of the Field
atomProperty - Variable in class joelib.desc.result.APropDoubleResult: Description of the Field
atomProperty - Variable in class joelib.desc.result.APropIntResult: Description of the Field
atomPropertyName - Variable in class joelib.gui.molviewer.java3d.graphics3D.RenderTable
atomPropertyNames - Variable in class joelib.desc.types.atompair.AtomPairResult
atomSmarts - Variable in class joelib.algo.contribution.GroupContributions
atomicNumber - Variable in class joelib.desc.types.atompair.AtomPairAtomType
atoms - Variable in class joelib.util.types.AtomArrayInt: Description of the Field
attributeSparse(int) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Returns the attribute associated with the internal index.
automaticFormalCharge() - Method in class joelib.molecule.JOEMol: Gets the flag if the automatic calculation of the formal charge of the atoms is allowed.
automaticPartialCharge() - Method in class joelib.molecule.JOEMol: Gets the flag if the automatic calculation of the partial charge of the atoms is allowed.
availableDescriptors() - Method in class joelib.desc.data.MolDescCounter: Description of the Method
availableMolIdentifiers() - Method in class joelib.desc.data.MolDescCounter: Description of the Method
availableMolNames() - Method in class joelib.desc.data.MolDescCounter: Description of the Method

B

BALL_AND_STICK - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
BALL_AND_STICK - Static variable in class joelib.io.types.Matlab: Description of the Field
BALL_AND_STICK - Static variable in class joelib.io.types.POVRay: Description of the Field
BALL_AND_STICK_S - Static variable in class joelib.io.types.POVRay
BALL_RADIUS - Static variable in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: The Radius of the balls int ball and stick mode *
BCUT - class joelib.desc.types.BCUT.: BCUT matrix descriptor (depends on atom properties used).
BCUT() - Constructor for class joelib.desc.types.BCUT: Constructor for the BCUT object
BE_ANDHI - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_ANDLO - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_LEAF - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_NOT - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BE_OR - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BFS - class joelib.algo.BFS.: Breadh First Search.
BFS() - Constructor for class joelib.algo.BFS: Constructor for the KierShape1 object
BFSResult - class joelib.algo.BFSResult.: Result of a BFS.
BFSResult() - Constructor for class joelib.algo.BFSResult: Constructor for the BFSResult object
BF_NONRINGDOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGDOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGTRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_NONRINGUP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGAROM - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGDOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGDOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGTRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BF_RINGUP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BL_CONST - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BL_TYPE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BMP - class joelib.io.types.BMP.: Writer for a Windows Bitmap (BMP) image.
BMP() - Constructor for class joelib.io.types.BMP
BMPFile - class wsi.ra.image.BMPFile.: A BMP file encoder.
BMPFile() - Constructor for class wsi.ra.image.BMPFile
BOND - Static variable in class joelib.io.types.cml.CMLCoreModule
BONDARRAY - Static variable in class joelib.io.types.cml.CMLCoreModule
BONDEXPRPOOL - Static variable in class joelib.smarts.ParseSmart: Description of the Field
BONDPOOL - Static variable in class joelib.smarts.Pattern: Description of the Field
BOND_PICKED - Static variable in class joelib.gui.molviewer.java3d.util.MolViewerEvent: Description of the Field
BOND_PROPERTY - Static variable in class joelib.desc.result.BondDynamicResult
BOND_STEREO - Static variable in class joelib.io.types.cml.CMLCoreModule
BOOLEAN - Static variable in class joelib.desc.result.DynamicArrayResult: Description of the Field
BOSum() - Method in class joelib.molecule.JOEAtom: Sum of the bond orders of the bonds to the atom.
BS_ALL - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_AROM - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DEFAULT - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_DOWNUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_RING - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_SINGLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_TRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_UP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BS_UPUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_AROM - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_DOUBLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_DOWN - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_DOWNUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_RING - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_SINGLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_TRIPLE - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_UP - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BT_UPUNSPEC - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
BUFF_SIZE - Static variable in class joelib.util.JOEHelper: Description of the Field
BUFMAX - Static variable in class joelib.smarts.ParseSmart: Description of the Field
BasicAPDistanceMetric - class joelib.desc.types.atompair.BasicAPDistanceMetric.: Distance metric based on the atom pair descriptor (depends on atom properties used).
BasicAPDistanceMetric() - Constructor for class joelib.desc.types.atompair.BasicAPDistanceMetric
BasicFactoryInfo - class joelib.util.types.BasicFactoryInfo.: Create informations for a class which can be get by a factory class using Java reflection.
BasicFactoryInfo(String, String, String) - Constructor for class joelib.util.types.BasicFactoryInfo: Create informations for a class which can be get by a factory class.
BasicGroups - class joelib.desc.types.BasicGroups.: Number of basic groups.
BasicGroups() - Constructor for class joelib.desc.types.BasicGroups
BasicTieResolver - class joelib.algo.morgan.types.BasicTieResolver.: Interface for resolving renumbering ties.
BasicTieResolver() - Constructor for class joelib.algo.morgan.types.BasicTieResolver
BatchScriptReplacer - class wsi.ra.io.BatchScriptReplacer.: Contains static methods for reading data from temporary files.
BinAtomExpr - class joelib.smarts.atomexpr.BinAtomExpr.: Binary atom expression for SMARTS substructure search.
BinAtomExpr() - Constructor for class joelib.smarts.atomexpr.BinAtomExpr: Constructor for the BinAtomExpr object
BinAtomExpr(int) - Constructor for class joelib.smarts.atomexpr.BinAtomExpr: Constructor for the BinAtomExpr object
BinBondExpr - class joelib.smarts.bondexpr.BinBondExpr.: Binary bond expression for SMARTS.
BinBondExpr() - Constructor for class joelib.smarts.bondexpr.BinBondExpr: Constructor for the BinBondExpr object
BinBondExpr(int) - Constructor for class joelib.smarts.bondexpr.BinBondExpr: Constructor for the BinBondExpr object
BinaryValue - interface joelib.desc.BinaryValue.: Interface to have a fast method to getting binary (bit string) descriptor values.
BitArrayResult - class joelib.desc.result.BitArrayResult.: Atom representation.
BitArrayResult() - Constructor for class joelib.desc.result.BitArrayResult: Constructor for the IntResult object
BitResult - class joelib.desc.result.BitResult.: Atom representation.
BitResult() - Constructor for class joelib.desc.result.BitResult: Constructor for the IntResult object
BitSet14 - class joelib.util.BitSet14.: This class implements a vector of bits that grows as needed.
BitSet14() - Constructor for class joelib.util.BitSet14: Creates a new bit set.
BitSet14(int) - Constructor for class joelib.util.BitSet14: Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range 0 through nbits-1.
BondComparator - class joelib.molecule.BondComparator.: Comparator for bonds.
BondComparator() - Constructor for class joelib.molecule.BondComparator: Initializes the bond comparator.
BondDoubleResult - class joelib.desc.result.BondDoubleResult.: Double results of bond properties.
BondDoubleResult() - Constructor for class joelib.desc.result.BondDoubleResult: Constructor for the DoubleResult object
BondDynamicResult - class joelib.desc.result.BondDynamicResult.: Dynamic results of bond properties.
BondDynamicResult() - Constructor for class joelib.desc.result.BondDynamicResult: Constructor for the DoubleResult object
BondExpr - class joelib.smarts.bondexpr.BondExpr.: Bond expression for SMARTS.
BondExpr() - Constructor for class joelib.smarts.bondexpr.BondExpr: Constructor for the BondExpr object
BondExpr(int) - Constructor for class joelib.smarts.bondexpr.BondExpr: Constructor for the BondExpr object
BondInt - class joelib.util.types.BondInt.: Bond and integer value.
BondInt(JOEBond, int) - Constructor for class joelib.util.types.BondInt: Constructor for the BondInt object
BondIntResult - class joelib.desc.result.BondIntResult.: Integer results of atom properties.
BondIntResult() - Constructor for class joelib.desc.result.BondIntResult: Constructor for the DoubleResult object
BondIterator - class joelib.util.iterator.BondIterator.: Gets an iterator over all bonds in a molecule.
BondIterator(Vector) - Constructor for class joelib.util.iterator.BondIterator: Constructor for the BondIterator object
BondNode - class joelib.gui.molviewer.java3d.graphics3D.BondNode.: Description of the Class
BondProperties - interface joelib.molecule.types.BondProperties.: Interface to access bond properties.
BondSpec - class joelib.smarts.BondSpec.: Bond specification of a SMARTS bond expression.
BondSpec() - Constructor for class joelib.smarts.BondSpec
BooleanResult - class joelib.desc.result.BooleanResult.: Integer result.
BooleanResult() - Constructor for class joelib.desc.result.BooleanResult: Constructor for the IntResult object
BurdenEigenvalues - class joelib.desc.types.BurdenEigenvalues.: Burden matrix descriptor (depends on single atom property used).
BurdenEigenvalues() - Constructor for class joelib.desc.types.BurdenEigenvalues: Constructor for the BCUT object
BurdenModifiedEigenvalues - class joelib.desc.types.BurdenModifiedEigenvalues.: Burden modified matrix descriptor (depends on single atom property used).
BurdenModifiedEigenvalues() - Constructor for class joelib.desc.types.BurdenModifiedEigenvalues: Constructor for the BCUT object
b - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
balloc - Variable in class joelib.smarts.Pattern: Description of the Field
bcount - Variable in class joelib.smarts.Pattern: Description of the Field
beginModify() - Method in class joelib.molecule.JOEMol: Begins modification of atoms and increase modification counter.
binning - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
binomialStandardError(double, int) - Static method in class wsi.ra.tool.Statistics: Computes standard error for observed values of a binomial random variable.
bitIsOn(int) - Method in class joelib.util.JOEBitVec: Description of the Method
bitIsSet(int) - Method in class joelib.util.JOEBitVec: Description of the Method
bond - Variable in class joelib.smarts.Pattern: Description of the Field
bond - Variable in class joelib.util.types.BondInt: Description of the Field
bond - Variable in class joelib.util.types.StackType: Description of the Field
bondIterator() - Method in class joelib.molecule.JOEAtom: Returns a BondIterator for all bonds in this atom.
bondIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over all bonds.
bondPicked(MolViewerEvent) - Method in class joelib.gui.molviewer.java3d.util.MolViewerEventAdapter
bondPicked(MolViewerEvent) - Method in interface joelib.gui.molviewer.java3d.util.MolViewerEventListener
bondflags - Variable in class joelib.smiles.ClosureBond: Flags of the bond.
booleanArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper
booleanArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper: Loads boolean array from String .
booleanArrayFromString(String) - Method in class joelib.util.ArrayHelper: Loads boolean array from String .
booleanArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper: Loads boolean array from String .
booleanArrayFromString(String) - Static method in class joelib.util.LineArrayHelper: Description of the Method
booleanArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper: Description of the Method
booleanArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper: Description of the Method
booleanArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper: Gets boolean arrays from a Reader.
booleanArrayFromString(StringTokenizer, int) - Static method in class joelib.util.LineArrayHelper: Gets boolean arrays from a Reader.
booleanArrayFromTrueFalseString(String) - Method in class joelib.util.ArrayHelper
booleanArrayFromTrueFalseString(String, String) - Static method in class joelib.util.ArrayHelper: Loads boolean array from String .
booleans - Variable in class joelib.smarts.RSCacheEntry: Description of the Field
buffer - Variable in class joelib.smarts.ParseSmart: Description of the Field
buildAtomBin(int, AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildAtomLeaf(int, int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildAtomNot(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildAtomRecurs(Pattern) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
buildBondBin(int, BondExpr, BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
buildBondLeaf(int, int) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
buildBondNot(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
buildOERTreeVector(JOEAtom, JOERTree, JOERTree[], JOEBitVec) - Static method in class joelib.util.JHM
buildTree(JOESmiNode) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
byteMatrixFromString(String) - Method in class joelib.util.MatrixHelper: Description of the Method
byteMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper: Description of the Method

C

CDKConvention - class joelib.io.types.cml.CDKConvention.: This is an implementation for the CDK convention.
CDKConvention(CDOInterface) - Constructor for class joelib.io.types.cml.CDKConvention
CDKConvention(ModuleInterface) - Constructor for class joelib.io.types.cml.CDKConvention
CDKTools - class joelib.util.cdk.CDKTools.: Helper class to faciliate access to tools of the Chemical Development Kit (CDK).
CDKTools() - Constructor for class joelib.util.cdk.CDKTools: Constructor for the CDKTools.
CDOAcceptedObjects - class joelib.io.types.cml.CDOAcceptedObjects.: List of names (String classes) of objects accepted by CDO.
CDOAcceptedObjects() - Constructor for class joelib.io.types.cml.CDOAcceptedObjects: Constructor.
CDOInterface - interface joelib.io.types.cml.CDOInterface.: Chemical Markup Language (CML) interface definition.
CHEMICAL_STRUCTURE - Static variable in class joelib.jcamp.JCAMPParser: data representation: definition for the parameter of a chemical structure
CISTRANS_ISOMERISM_UNDEFINED - Static variable in class joelib.util.IsomerismDetection
CIS_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
CMLCoreModule - class joelib.io.types.cml.CMLCoreModule.: Core CML 1.x and 2.0 elements are parsed by this class.
CMLCoreModule(CDOInterface) - Constructor for class joelib.io.types.cml.CMLCoreModule
CMLCoreModule(ModuleInterface) - Constructor for class joelib.io.types.cml.CMLCoreModule
CMLErrorHandler - class joelib.io.types.cml.CMLErrorHandler.: CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document.
CMLErrorHandler() - Constructor for class joelib.io.types.cml.CMLErrorHandler: Constructor a SAX2 ErrorHandler that uses the cdk.tools.LoggingTool class to output errors and warnings to.
CMLHandler - class joelib.io.types.cml.CMLHandler.: SAX2 implementation for CML XML fragment reading.
CMLHandler(CDOInterface) - Constructor for class joelib.io.types.cml.CMLHandler: Constructor for the CMLHandler.
CMLIDCreator - class joelib.io.types.cml.CMLIDCreator.: Class that provides methods to give unique IDs to ChemObjects.
CMLIDCreator() - Constructor for class joelib.io.types.cml.CMLIDCreator
CMLMoleculeWriter - interface joelib.io.types.cml.CMLMoleculeWriter.: Interface for a CML molecule writer.
CMLMoleculeWriterBase - class joelib.io.types.cml.CMLMoleculeWriterBase.: Basic CML molecule writer.
CMLMoleculeWriterBase(PrintStream, CMLWriterProperties) - Constructor for class joelib.io.types.cml.CMLMoleculeWriterBase
CMLPropertyWriter - class joelib.io.types.cml.CMLPropertyWriter.: Helper class for a CML molecule property (descriptor) writer.
CMLPropertyWriter() - Constructor for class joelib.io.types.cml.CMLPropertyWriter
CMLReactionModule - class joelib.io.types.cml.CMLReactionModule.: Chemical Markup Language (CML) reaction module.
CMLReactionModule(CDOInterface) - Constructor for class joelib.io.types.cml.CMLReactionModule
CMLReactionModule(ModuleInterface) - Constructor for class joelib.io.types.cml.CMLReactionModule
CMLResolver - class joelib.io.types.cml.CMLResolver.: This class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation.
CMLResolver() - Constructor for class joelib.io.types.cml.CMLResolver
CMLResolver(String) - Constructor for class joelib.io.types.cml.CMLResolver
CMLSequentialSAXReader - class joelib.io.types.cml.CMLSequentialSAXReader.: Sequential reader for Chemical Markup Language (CML) files.
CMLSequentialSAXReader() - Constructor for class joelib.io.types.cml.CMLSequentialSAXReader
CMLStack - class joelib.io.types.cml.CMLStack.: Low weigth alternative to Sun's Stack class.
CMLStack() - Constructor for class joelib.io.types.cml.CMLStack
CMLSymmetryWriter - class joelib.io.types.cml.CMLSymmetryWriter.: Helper class for a CML molecule symmetry writer.
CMLSymmetryWriter() - Constructor for class joelib.io.types.cml.CMLSymmetryWriter
CMLWriterProperties - interface joelib.io.types.cml.CMLWriterProperties.: Interface for a CML molecule writer.
CML_HARD_KERNEL - Static variable in class joelib.data.JOEKernel
CML_KERNEL_REFERENCE - Static variable in class joelib.data.JOEKernel
CML_KERNEL_REFERENCE_PREFIX - Static variable in class joelib.data.JOEKernel
CML_SOFT_KERNEL - Static variable in class joelib.data.JOEKernel
CML_VERSION_1 - Static variable in class joelib.io.types.ChemicalMarkupLanguage
CML_VERSION_2 - Static variable in class joelib.io.types.ChemicalMarkupLanguage
COLUMNS - Static variable in class joelib.io.types.cml.elements.MatrixCML
CONTACT_E_MAIL - Static variable in class joelib.util.JOEHelper: Description of the Field
CONTINUE - Static variable in class joelib.test.Convert
CONTINUE - Static variable in class joelib.test.ConvertSkip
CONTINUE - Static variable in class joelib.test.DescriptorCalculation
CONTINUE - Static variable in class joelib.test.DescriptorStatistic
COORDINATE2 - Static variable in class joelib.io.types.cml.CMLCoreModule
COORDINATE3 - Static variable in class joelib.io.types.cml.CMLCoreModule
COORDINATES_2D_X - Static variable in class joelib.io.types.cml.CMLPropertyWriter
COORDINATES_2D_Y - Static variable in class joelib.io.types.cml.CMLPropertyWriter
COORDINATES_3D_X - Static variable in class joelib.io.types.cml.CMLPropertyWriter
COORDINATES_3D_Y - Static variable in class joelib.io.types.cml.CMLPropertyWriter
COORDINATES_3D_Z - Static variable in class joelib.io.types.cml.CMLPropertyWriter
CPK - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
CRYSTAL - Static variable in class joelib.io.types.cml.CMLCoreModule
CS_TYPE - Static variable in class joelib.jcamp.JCAMPDataBlock
CentralDisplayAdapter - class joelib.gui.molviewer.java3d.util.CentralDisplayAdapter.: Description of the Class
CentralDisplayAdapter(JPanel3D) - Constructor for class joelib.gui.molviewer.java3d.util.CentralDisplayAdapter: Constructor for the CentralDisplayAdapter object
CentralLookup - class joelib.gui.molviewer.java3d.util.CentralLookup.: Description of the Class
ChemicalMarkupLanguage - class joelib.io.types.ChemicalMarkupLanguage.: Reader/Writer for Chemical Markup Language (CML) files.
ChemicalMarkupLanguage() - Constructor for class joelib.io.types.ChemicalMarkupLanguage
ClearTextFormat - class joelib.io.types.ClearTextFormat.: Reader/Writer for ClearTeXt (CTX) files.
ClearTextFormat() - Constructor for class joelib.io.types.ClearTextFormat
ClosureBond - class joelib.smiles.ClosureBond.: Closure bond of an SMILES expression.
ClosureBond(int, int, int, int, int) - Constructor for class joelib.smiles.ClosureBond: Initialize the ClosureBond
Combine - class joelib.test.Combine.: Example for converting molecules.
Combine() - Constructor for class joelib.test.Combine: Constructor for the ConvertSkip object
Comparison - class joelib.test.Comparison.: Example for converting molecules.
Comparison() - Constructor for class joelib.test.Comparison
ComparisonHelper - class joelib.util.ComparisonHelper.: Example for converting molecules.
ComparisonHelper(IOType, String) - Constructor for class joelib.util.ComparisonHelper
ComparisonHelper(IOType, String, int) - Constructor for class joelib.util.ComparisonHelper: Constructor for the ComparisonHelper object
ComparisonHelper(JOEMol) - Constructor for class joelib.util.ComparisonHelper: Constructor for the ComparisonHelper object
ComparisonHelper() - Constructor for class joelib.util.ComparisonHelper
Compress() - Method in class com.obrador.JpegEncoder
ConformerIterator - class joelib.util.iterator.ConformerIterator.: Gets an iterator over all conformers in a molecule.
ConformerIterator(Vector) - Constructor for class joelib.util.iterator.ConformerIterator
ConjElectroTopolState - class joelib.desc.types.ConjElectroTopolState.: Conjugated electrotopological state descriptor.
ConjElectroTopolState() - Constructor for class joelib.desc.types.ConjElectroTopolState: Constructor for the KierShape1 object
ConjugatedRing - class joelib.gui.render.ConjugatedRing.: Holding special conjugated ring informations for a single ring.
ConjugatedRing() - Constructor for class joelib.gui.render.ConjugatedRing
ConjugatedRings - class joelib.gui.render.ConjugatedRings.: Holding special conjugated ring informations for multiple rings.
ConjugatedRings(JOEMol, String) - Constructor for class joelib.gui.render.ConjugatedRings
ConjugatedTopologicalDistance - class joelib.desc.types.ConjugatedTopologicalDistance.: Conjugated topological distance.
ConjugatedTopologicalDistance() - Constructor for class joelib.desc.types.ConjugatedTopologicalDistance: Constructor for the KierShape1 object
ContiguousFragments - class joelib.molecule.fragmentation.ContiguousFragments.: Fragmentation implementation for contiguous fragments in a molecule.
ContiguousFragments() - Constructor for class joelib.molecule.fragmentation.ContiguousFragments
ConventionInterface - interface joelib.io.types.cml.ConventionInterface.: This interface describes the procedures classes must implement to be plugable into the CMLHandler.
Convert - class joelib.test.Convert.: Example for converting molecules and calculating descriptors.
Convert() - Constructor for class joelib.test.Convert
ConvertPanel - class joelib.gui.test.ConvertPanel.: DOCUMENT ME!
ConvertPanel() - Constructor for class joelib.gui.test.ConvertPanel
ConvertSkip - class joelib.test.ConvertSkip.: Example for converting/skipping molecules.
ConvertSkip() - Constructor for class joelib.test.ConvertSkip: Constructor for the ConvertSkip object
CreateFileName - class joelib.process.types.CreateFileName.: Calling processor classes if the filter rule fits.
CreateFileName() - Constructor for class joelib.process.types.CreateFileName: Constructor for the DescSelectionWriter object
CrystalGeometryTools - class joelib.math.CrystalGeometryTools.: A set of static methods for working with crystal coordinates.
CrystalGeometryTools() - Constructor for class joelib.math.CrystalGeometryTools
Cylinder - class joelib.gui.molviewer.java3d.graphics3D.Cylinder.: Description of the Class
Cylinder(float, float, int, Appearance) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.Cylinder: Constructor for the Cylinder object
c - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
cRings - Variable in class joelib.gui.render.ConjugatedRings
calcAxesAngle(double[], double[]) - Static method in class joelib.math.CrystalGeometryTools: Calculates the angle between two axes.
calcAxisLength(double[]) - Static method in class joelib.math.CrystalGeometryTools: Calculates the length of a cell axis.
calcInvertedAxes(double[], double[], double[]) - Static method in class joelib.math.CrystalGeometryTools: Inverts three cell axes.
calcPerpUnitVec(float, float, float, float, float[], float[]) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Calculates 2D vector perpendicular to bond
calcTorsionAngle(XYZVector, XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
calcVarianceNorm(DescStatistic) - Method in class joelib.algo.datamining.weka.MolInstancesCache
calcVarianceNorm(DescStatistic) - Method in interface joelib.desc.data.MoleculeCache
calcVarianceNorm(DescStatistic) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Calculate descriptor normalization using the given descriptor statistic.
calculate(JOEMol) - Method in class joelib.algo.APropertyBFS: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.algo.APropertyBFS: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.algo.APropertyBFS: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.algo.APropertyBFS: Description of the Method
calculate(JOEMol) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.algo.BFS: Description of the Method
calculate(JOEMol) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.algo.DFS: Description of the Method
calculate(JOEMol) - Method in class joelib.algo.morgan.Morgan: Calculate the morgan numbers of a molecule.
calculate(JOEMol) - Method in class joelib.desc.AtomsCounter: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.AtomsCounter: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.AtomsCounter: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.AtomsCounter: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in interface joelib.desc.Descriptor: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in interface joelib.desc.Descriptor: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in interface joelib.desc.Descriptor: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in interface joelib.desc.Descriptor: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.SMARTSCounter: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.SMARTSCounter: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.SMARTSCounter: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SMARTSCounter: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.SimpleBooleanDesc: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleBooleanDesc: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleBooleanDesc: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleBooleanDesc: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.SimpleDoubleAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleDoubleAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleDoubleAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleDoubleAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.SimpleDoubleDesc: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleDoubleDesc: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleDoubleDesc: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleDoubleDesc: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.SimpleDynamicAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleDynamicAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleDynamicAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleDynamicAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.SimpleIntDesc: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleIntDesc: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleIntDesc: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleIntDesc: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.SimpleStringAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, Map) - Method in class joelib.desc.SimpleStringAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult) - Method in class joelib.desc.SimpleStringAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.SimpleStringAtomProperty: Calculate descriptor for this molecule.
calculate(JOEMol) - Method in class joelib.desc.types.APropertyDistanceMatrix: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.APropertyDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.APropertyDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.APropertyDistanceMatrix: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.BCUT: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.BCUT: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.BCUT: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.BCUT: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.BurdenEigenvalues: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.BurdenEigenvalues: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.BurdenEigenvalues: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.BurdenEigenvalues: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.ConjElectroTopolState: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.ConjElectroTopolState: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.ConjElectroTopolState: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.ConjElectroTopolState: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.DistanceDistanceMatrix: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.DistanceDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.DistanceDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.DistanceDistanceMatrix: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.ElectrogeometricalState: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.ElectrogeometricalState: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.ElectrogeometricalState: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.ElectrogeometricalState: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.ElectrotopologicalState: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.ElectrotopologicalState: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.ElectrotopologicalState: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.ElectrotopologicalState: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.RadialDistributionFunction: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.RadialDistributionFunction: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.RadialDistributionFunction: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.RadialDistributionFunction: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Description of the Method
calculate(JOEMol, Map) - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Description of the Method
calculate(JOEMol, DescResult) - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Description of the Method
calculate(JOEMol, DescResult, Map) - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Description of the Method
calculate(JOEMol) - Method in class joelib.desc.util.AtomPropertyDescriptors: A unit test for JUnit
calculate(JOEMol, boolean) - Method in class joelib.desc.util.SMARTSDescriptors: A unit test for JUnit
calculateAtomPair(AtomProperties[], JOEAtom, JOEAtom, double) - Method in class joelib.desc.types.atompair.AtomPair
calculateDerived() - Method in class wsi.ra.tool.ArrayBinning: Tells the object to calculate any statistics that don't have their values automatically updated during add.
calculateDerived() - Method in class wsi.ra.tool.ArrayStatistic: Tells the object to calculate any statistics that don't have their values automatically updated during add.
calculateNumericDescriptors() - Method in class joelib.test.DescriptorCalculation: A unit test for JUnit
calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class joelib.gui.render.RenderHelper: Determines the normalized vector orthogonal on the vector p1->p2.
calculateSSKeys(JOEMol) - Method in class joelib.desc.util.SMARTSDescriptors: Pharmacophore fingerprint.
callTransformation(Symmetry, SymmetryElement, SymAtom, SymAtom) - Method in class joelib.math.symmetry.TransformationAtom
canReadExtension(String) - Method in class joelib.io.IOTypeHolder: Returns true if this file with the appropriate input type can be readed.
canWriteExtension(String) - Method in class joelib.io.IOTypeHolder: Returns true if this file with the appropriate output type can be written.
canonicaliseBond(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
capExternalBonds(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
cardinality() - Method in class joelib.util.BitSet14: Returns the number of bits set to true in this BitSet14.
cartesianToFractional(double[], double[], double[], double[]) - Static method in class joelib.math.CrystalGeometryTools: Converts real coordinate (x,y,z) to a fractional coordinates (xf, yf, zf).
cartesianToNotional(double[], double[], double[]) - Static method in class joelib.math.CrystalGeometryTools: Calculates notional coordinates for unit cell axes from cartesian axes coordinates.
center(RenderingAtoms, Dimension) - Static method in class joelib.gui.render.RenderHelper: Centers the molecule in the given area
center() - Method in class joelib.molecule.JOEMol: Centers molecule.
center(int) - Method in class joelib.molecule.JOEMol: Centers conformer.
centralDisplayChange(MolViewerEvent) - Method in class joelib.gui.molviewer.java3d.util.CentralDisplayAdapter: Description of the Method
centralDisplayChange(MolViewerEvent) - Method in class joelib.gui.molviewer.java3d.util.MolViewerEventAdapter: Description of the Method
centralDisplayChange(MolViewerEvent) - Method in interface joelib.gui.molviewer.java3d.util.MolViewerEventListener: Description of the Method
cformat - package cformat: Provides classes allowing printf and scanf functionality for Java.
characterData(char[], int, int) - Method in class joelib.io.types.cml.CDKConvention
characterData(CMLStack, char[], int, int) - Method in class joelib.io.types.cml.CMLCoreModule
characterData(char[], int, int) - Method in class joelib.io.types.cml.CMLReactionModule
characterData(CMLStack, char[], int, int) - Method in interface joelib.io.types.cml.ModuleInterface
characterData(String) - Method in class joelib.io.types.cml.elements.ArrayCML
characterData(String) - Method in interface joelib.io.types.cml.elements.ElementCML
characterData(String) - Method in class joelib.io.types.cml.elements.MatrixCML
characterData(String) - Method in class joelib.io.types.cml.elements.ScalarCML
characters(char[], int, int) - Method in class joelib.io.types.cml.CMLHandler: Implementation of the characters() procedure overwriting the DefaultHandler interface.
characters(char[], int, int) - Method in class joelib.io.types.cml.XMLHandler
charge - Variable in class joelib.gui.render.ConjugatedRing
checkAromaticity(JOEAtom, int) - Method in class joelib.data.JOEAromaticTyper: Check aromaticity starting from the root atom.
checkGetInputType(String) - Static method in class joelib.io.SimpleReader: Gets the input type by the input file.
checkGetOutputType(String) - Static method in class joelib.io.SimpleWriter: Gets the output type by the output file.
checkProperties(PropertyAcceptor, Map) - Static method in class joelib.util.JOEPropertyHelper: Description of the Method
chi - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
chiSquaredProbability(double, double) - Static method in class wsi.ra.tool.Statistics: Returns chi-squared probability for given value and degrees of freedom.
chiral - Variable in class joelib.smarts.AtomSpec: Chiral flag.
clear() - Method in class Acme.IntHashtable
clear() - Method in class joelib.algo.APropertyBFS: Description of the Method
clear() - Method in class joelib.algo.BFS: Description of the Method
clear() - Method in class joelib.algo.DFS: Description of the Method
clear() - Method in class joelib.desc.AtomsCounter: Clear descriptor calculation method for a new molecule.
clear() - Method in interface joelib.desc.Descriptor: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.SMARTSCounter: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.SimpleBooleanDesc: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.SimpleDoubleAtomProperty: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.SimpleDoubleDesc: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.SimpleDynamicAtomProperty: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.SimpleIntDesc: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.SimpleStringAtomProperty: Clear descriptor calculation method for a new molecule.
clear() - Method in class joelib.desc.data.MolDescCounter: Description of the Method
clear() - Method in class joelib.desc.types.APropertyDistanceMatrix: Description of the Method
clear() - Method in class joelib.desc.types.Autocorrelation: Description of the Method
clear() - Method in class joelib.desc.types.BCUT: Description of the Method
clear() - Method in class joelib.desc.types.BurdenEigenvalues: Description of the Method
clear() - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Description of the Method
clear() - Method in class joelib.desc.types.ConjElectroTopolState: Description of the Method
clear() - Method in class joelib.desc.types.DistanceDistanceMatrix: Description of the Method
clear() - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
clear() - Method in class joelib.desc.types.ElectrogeometricalState: Description of the Method
clear() - Method in class joelib.desc.types.ElectrotopologicalState: Description of the Method
clear() - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
clear() - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Description of the Method
clear() - Method in class joelib.desc.types.HeavyBonds: Description of the Method
clear() - Method in class joelib.desc.types.HeteroCycles: Description of the Method
clear() - Method in class joelib.desc.types.RadialDistributionFunction: Description of the Method
clear() - Method in class joelib.desc.types.SSKey3DS: Description of the Method
clear() - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Description of the Method
clear() - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Description of the Method
clear() - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Description of the Method
clear() - Method in class joelib.ext.SimpleExternalProcess
clear() - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
clear() - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D: Sets the fast attribute of the JPanel3D object Sets the nice attribute of the JPanel3D object Description of the Method
clear() - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Description of the Method
clear() - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable
clear() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule
clear() - Method in class joelib.io.types.cml.elements.ArrayCML
clear() - Method in interface joelib.io.types.cml.elements.ElementCML
clear() - Method in class joelib.io.types.cml.elements.MatrixCML
clear() - Method in class joelib.io.types.cml.elements.ScalarCML
clear() - Method in class joelib.math.JOECoordTrans: Clears the object as if it were just constructed.
clear() - Method in class joelib.math.symmetry.SymStatistic
clear() - Method in class joelib.molecule.GenericDataHolder: Description of the Method
clear() - Method in class joelib.molecule.JOEAtom: Deletes all contained informations in this atom.
clear() - Method in class joelib.molecule.JOEBond
clear() - Method in class joelib.molecule.JOEMol: Clears molecule.
clear() - Method in class joelib.molecule.JOEResidue
clear() - Method in interface joelib.process.JOEProcess
clear() - Method in class joelib.process.ProcessPipe
clear() - Method in class joelib.process.SimpleProcess
clear() - Method in class joelib.process.types.AtomPropertyMatrix: Description of the Method
clear() - Method in class joelib.process.types.CreateFileName: Description of the Method
clear() - Method in class joelib.process.types.DescBinning: Description of the Method
clear() - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
clear() - Method in class joelib.process.types.DescStatistic: Description of the Method
clear() - Method in class joelib.process.types.DescVarianceNorm: Description of the Method
clear() - Method in class joelib.process.types.DistanceCalculation: Description of the Method
clear() - Method in class joelib.process.types.MoleculeFileCreation
clear() - Method in class joelib.process.types.MoleculeFileDeletion
clear(int) - Method in class joelib.util.BitSet14: Sets the bit specified by the index to false.
clear(int, int) - Method in class joelib.util.BitSet14: Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to false.
clear() - Method in class joelib.util.BitSet14: Sets all of the bits in this BitSet14 to false.
clearCoordPtr() - Method in class joelib.molecule.JOEAtom: Clear coordinate array.
clearHighlightedAtoms() - Method in class joelib.gui.render.Renderer2DModel
clearHighlightedBonds() - Method in class joelib.gui.render.Renderer2DModel
clearLookAheadChar() - Method in class cformat.ScanfReader: Clears the look-ahead character.
clone() - Method in class Acme.IntHashtable
clone(BFSResult) - Method in class joelib.algo.BFSResult
clone() - Method in class joelib.algo.BFSResult
clone(DFSResult) - Method in class joelib.algo.DFSResult
clone() - Method in class joelib.algo.DFSResult
clone(MoleculeCache) - Method in class joelib.algo.datamining.weka.MolInstancesCache
clone() - Method in interface joelib.desc.DescResult
clone(MoleculeCache) - Method in interface joelib.desc.data.MoleculeCache
clone(MoleculeCache) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
clone(APropDoubleArrResult) - Method in class joelib.desc.result.APropDoubleArrResult
clone() - Method in class joelib.desc.result.APropDoubleArrResult
clone(APropDoubleResult) - Method in class joelib.desc.result.APropDoubleResult
clone() - Method in class joelib.desc.result.APropDoubleResult
clone(APropIntResult) - Method in class joelib.desc.result.APropIntResult
clone() - Method in class joelib.desc.result.APropIntResult
clone(AtomDoubleResult) - Method in class joelib.desc.result.AtomDoubleResult
clone() - Method in class joelib.desc.result.AtomDoubleResult
clone(AtomDynamicResult, int) - Method in class joelib.desc.result.AtomDynamicResult
clone() - Method in class joelib.desc.result.AtomDynamicResult
clone(AtomIntResult) - Method in class joelib.desc.result.AtomIntResult
clone() - Method in class joelib.desc.result.AtomIntResult
clone(AtomStringResult) - Method in class joelib.desc.result.AtomStringResult
clone() - Method in class joelib.desc.result.AtomStringResult
clone(BitArrayResult) - Method in class joelib.desc.result.BitArrayResult
clone() - Method in class joelib.desc.result.BitArrayResult
clone(BitResult) - Method in class joelib.desc.result.BitResult
clone() - Method in class joelib.desc.result.BitResult
clone(BondDoubleResult) - Method in class joelib.desc.result.BondDoubleResult
clone() - Method in class joelib.desc.result.BondDoubleResult
clone(BondDynamicResult, int) - Method in class joelib.desc.result.BondDynamicResult
clone() - Method in class joelib.desc.result.BondDynamicResult
clone(BondIntResult) - Method in class joelib.desc.result.BondIntResult
clone() - Method in class joelib.desc.result.BondIntResult
clone(BooleanResult) - Method in class joelib.desc.result.BooleanResult
clone() - Method in class joelib.desc.result.BooleanResult
clone(DoubleArrayResult) - Method in class joelib.desc.result.DoubleArrayResult
clone() - Method in class joelib.desc.result.DoubleArrayResult
clone(DoubleMatrixResult) - Method in class joelib.desc.result.DoubleMatrixResult
clone() - Method in class joelib.desc.result.DoubleMatrixResult
clone(DoubleResult) - Method in class joelib.desc.result.DoubleResult
clone() - Method in class joelib.desc.result.DoubleResult
clone(DynamicArrayResult, int) - Method in class joelib.desc.result.DynamicArrayResult
clone() - Method in class joelib.desc.result.DynamicArrayResult
clone(FloatMatrixResult) - Method in class joelib.desc.result.FloatMatrixResult
clone() - Method in class joelib.desc.result.FloatMatrixResult
clone(IntArrayResult) - Method in class joelib.desc.result.IntArrayResult
clone() - Method in class joelib.desc.result.IntArrayResult
clone(IntBitArrayResult) - Method in class joelib.desc.result.IntBitArrayResult
clone() - Method in class joelib.desc.result.IntBitArrayResult
clone(IntMatrixResult) - Method in class joelib.desc.result.IntMatrixResult
clone() - Method in class joelib.desc.result.IntMatrixResult
clone(IntResult) - Method in class joelib.desc.result.IntResult
clone() - Method in class joelib.desc.result.IntResult
clone(StringArrayResult) - Method in class joelib.desc.result.StringArrayResult
clone() - Method in class joelib.desc.result.StringArrayResult
clone(StringResult) - Method in class joelib.desc.result.StringResult
clone() - Method in class joelib.desc.result.StringResult
clone(AtomPairResult) - Method in class joelib.desc.types.atompair.AtomPairResult
clone() - Method in class joelib.desc.types.atompair.AtomPairResult
clone() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns a clone (Object) of matrix
clone() - Method in class joelib.math.XYZVector: Description of the Method
clone(JOEAtom, JOEAtom) - Static method in class joelib.molecule.JOEAtom: Clone the JOEAtom src to the JOEAtom to.
clone() - Method in class joelib.molecule.JOEAtom: Clone this JOEAtom object.
clone(JOEBond, JOEBond) - Static method in class joelib.molecule.JOEBond: Clone the JOEBond src to the JOEBond to.
clone() - Method in class joelib.molecule.JOEBond
clone() - Method in class joelib.molecule.JOEMol: Clones molecule without additional data (e.g.
clone(boolean) - Method in class joelib.molecule.JOEMol: Clones this molecule.
clone(boolean, String[]) - Method in class joelib.molecule.JOEMol: Clones this molecule.
clone() - Method in class joelib.molecule.JOEResidue
clone(JOEResidue) - Method in class joelib.molecule.JOEResidue
clone(JOEResidue, JOEResidue) - Static method in class joelib.molecule.JOEResidue
clone() - Method in class joelib.process.types.DescStatistic
clone() - Method in class joelib.sort.XYDoubleArray: Description of the Method
clone() - Method in class joelib.sort.XYIntArray: Description of the Method
clone() - Method in class joelib.util.BitSet14: Cloning this BitSet14 produces a new BitSet14 that is equal to it.
clone() - Method in class joelib.util.iterator.AtomIterator
clone() - Method in class joelib.util.iterator.VectorIterator: Description of the Method
clone() - Method in class wsi.ra.tool.SortedVector: Returns a clone of this vector.
close() - Method in class cformat.ScanfReader: Closes the stream.
close() - Method in class joelib.io.SimpleReader: Close the simple reader.
close() - Method in class joelib.io.SimpleReaderWriterPipe: Closes the reader/writer.
close() - Method in class joelib.io.SimpleWriter: Close the simple reader.
closeReader() - Method in interface joelib.io.MoleculeFileType: Description of the Method
closeReader() - Method in class joelib.io.SimpleImageWriter: Description of the Method
closeReader() - Method in class joelib.io.types.Amber: Description of the Method
closeReader() - Method in class joelib.io.types.ChemicalMarkupLanguage
closeReader() - Method in class joelib.io.types.ClearTextFormat
closeReader() - Method in class joelib.io.types.Flat: Description of the Method
closeReader() - Method in class joelib.io.types.Gaussian: Description of the Method
closeReader() - Method in class joelib.io.types.HIN: Description of the Method
closeReader() - Method in class joelib.io.types.JCAMP: Description of the Method
closeReader() - Method in class joelib.io.types.MDLSD: Description of the Method
closeReader() - Method in class joelib.io.types.Matlab: Description of the Method
closeReader() - Method in class joelib.io.types.MolconnZ: Description of the Method
closeReader() - Method in class joelib.io.types.Mopac: Description of the Method
closeReader() - Method in class joelib.io.types.PDB: Description of the Method
closeReader() - Method in class joelib.io.types.PDF: Description of the Method
closeReader() - Method in class joelib.io.types.POVRay: Description of the Method
closeReader() - Method in class joelib.io.types.Smiles: Description of the Method
closeReader() - Method in class joelib.io.types.SybylMol2
closeReader() - Method in class joelib.io.types.Tinker
closeReader() - Method in class joelib.io.types.Undefined
closeReader() - Method in class joelib.io.types.XYZ
closeReader() - Method in class joelib.io.types.ZIP
closeWriter() - Method in interface joelib.io.MoleculeFileType: Description of the Method
closeWriter() - Method in class joelib.io.SimpleImageWriter: Description of the Method
closeWriter() - Method in class joelib.io.types.Amber: Description of the Method
closeWriter() - Method in class joelib.io.types.ChemicalMarkupLanguage
closeWriter() - Method in class joelib.io.types.ClearTextFormat
closeWriter() - Method in class joelib.io.types.Flat: Description of the Method
closeWriter() - Method in class joelib.io.types.Gaussian: Description of the Method
closeWriter() - Method in class joelib.io.types.HIN: Description of the Method
closeWriter() - Method in class joelib.io.types.JCAMP: Description of the Method
closeWriter() - Method in class joelib.io.types.MDLSD: Description of the Method
closeWriter() - Method in class joelib.io.types.Matlab: Description of the Method
closeWriter() - Method in class joelib.io.types.MolconnZ: Description of the Method
closeWriter() - Method in class joelib.io.types.Mopac: Description of the Method
closeWriter() - Method in class joelib.io.types.PDB: Description of the Method
closeWriter() - Method in class joelib.io.types.PDF: Description of the Method
closeWriter() - Method in class joelib.io.types.POVRay: Description of the Method
closeWriter() - Method in class joelib.io.types.Smiles: Description of the Method
closeWriter() - Method in class joelib.io.types.SybylMol2
closeWriter() - Method in class joelib.io.types.Tinker
closeWriter() - Method in class joelib.io.types.Undefined
closeWriter() - Method in class joelib.io.types.XYZ
closeWriter() - Method in class joelib.io.types.ZIP
closindex - Variable in class joelib.smarts.ParseState: Description of the Field
closord - Variable in class joelib.smarts.ParseState: Description of the Field
closure - Variable in class joelib.smarts.ParseState: Description of the Field
closureNumber - Variable in class joelib.smiles.ClosureBond: Number of the closure bond.
com.obrador - package com.obrador
commonLDRs - Static variable in class joelib.jcamp.JCAMPParser: An array of the commonly used LDR's (Label Data Records).
compare(Object, Object) - Method in class joelib.algo.morgan.AtomDoubleComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.desc.types.atompair.AtomPairTypeComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.math.symmetry.SymAxesComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.molecule.AtomZPosComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.molecule.BondComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.ring.RingSizeComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.sort.ArraySizeComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.sort.RotorComparator: Compares two objects.
compare(Object, Object) - Method in class joelib.sort.VectorSizeComparator: Compares two objects.
compare(JOEMol) - Method in class joelib.util.ComparisonHelper: Description of the Method
compare(JOEMol, String, double[]) - Method in class joelib.util.ComparisonHelper: Description of the Method.
compare(JOEMol, JOEMol) - Method in class joelib.util.ComparisonHelper
compareBonds(JOEBond, JOEBond) - Method in class joelib.util.JHM: Description of the Method
complexInit(boolean) - Method in class joelib.util.ghemical.TestInterface
compress(Image, OutputStream) - Method in class Acme.JPM.Encoders.GrayJPEG
configOK() - Static method in class joelib.gui.molviewer.java3d.util.Java3DHelper
conformerIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over all conformers.
conformerNum() - Method in class joelib.molecule.JOEMol: Returns the number of conformers.
connectTheDots() - Method in class joelib.molecule.JOEMol: Use inter-atomic distances to identify bonds.
constrainRecursion(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
contains(Object) - Method in class Acme.IntHashtable
contains(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the Renderer which draws this molecule Return true iff the atom in the parameter is one of the atoms in this molecule
contains(ViewerBond) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return true iff the bond in the parameter is one of the bonds in this molecule
contains(String) - Method in class joelib.io.types.cml.CDOAcceptedObjects: Determine if an object name is contained in this list.
contains(String) - Method in class joelib.util.MoleculeDataCacheHolder
containsKey(int) - Method in class Acme.IntHashtable
containsNaN - Variable in class wsi.ra.tool.ArrayBinning
contiguousFragments(Vector) - Method in class joelib.molecule.JOEMol: Each Vector contains the atom numbers of a contiguous fragment.
convert() - Method in class joelib.test.Convert: A unit test for JUnit
convert() - Method in class joelib.test.ConvertSkip: Convert and skip test.
convertPlain2XML(String) - Static method in class joelib.io.types.cml.XMLSpecialCharacter: Converts plain strings to XML formatted string entries.
coord - Variable in class joelib.math.symmetry.SymCoordinates
copy() - Method in class joelib.algo.datamining.weka.MolInstance: Produces a shallow copy of this instance.
copy() - Method in class joelib.algo.datamining.weka.MolSparseInstance: Produces a shallow copy of this instance.
copyAtomExpr(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
copyBondExpr(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
copyConformer(double[], int) - Method in class joelib.molecule.JOEMol: Copies given conformer to this molecule.
copyConformer(float[], int) - Method in class joelib.molecule.JOEMol: Copies given conformer to this molecule.
copyInto(Object[]) - Method in class wsi.ra.tool.SortedVector: Copies the components of this vector into the specified array.
copyPattern(Pattern) - Static method in class joelib.smarts.Pattern: Description of the Method
correctAromaticAmineCharge(JOEMol) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
correctAromaticNitrogens(JOEMol) - Method in class joelib.data.JOEAtomTyper: Description of the Method
correctBadResonanceForm(JOEMol) - Static method in class joelib.util.JHM: Description of the Method
correctForPH(JOEMol) - Method in class joelib.data.JOEPhModel: Corrects the molecule for PH.
correctForPH() - Method in class joelib.molecule.JOEMol: Corrects pH value of the molecule.
correctedBondRad(int) - Method in class joelib.data.JOEElementTable: Description of the Method
correctedBondRad(int, int) - Method in class joelib.data.JOEElementTable: Description of the Method
correctedVdwRad(int) - Method in class joelib.data.JOEElementTable: Description of the Method
correctedVdwRad(int, int) - Method in class joelib.data.JOEElementTable: Description of the Method
correlation(double[], double[], int) - Static method in class wsi.ra.tool.StatisticUtils: Returns the correlation coefficient of two double vectors.
count(IOType, String) - Method in class joelib.desc.data.MolDescCounter: Description of the Method
count - Variable in class joelib.util.types.Template: Description of the Field
count - Variable in class wsi.ra.tool.ArrayStatistic: The number of values seen
countBits() - Method in class joelib.util.JOEBitVec: Description of the Method
countBondsOfOrder(int) - Method in class joelib.molecule.JOEAtom: Count the bonds of the bond order order .
countDescriptors(JOEMol) - Method in class joelib.desc.data.MolDescCounter: Description of the Method
countFreeOxygens() - Method in class joelib.molecule.JOEAtom: Count the number of free oxygens.
covariance(double[], double[]) - Static method in class wsi.ra.tool.StatisticUtils: Calculates the covariance between the two double arrays a and b.
createArticle(String) - Method in class jtt.docbook.DocBookArticles
createAtom() - Method in class joelib.molecule.JOEMol: Creates only a new atom.
createAtom(Pattern, AtomExpr, int) - Static method in class joelib.smarts.Pattern: Description of the Method
createAtom(Pattern, AtomExpr, int, int) - Static method in class joelib.smarts.Pattern: Description of the Method
createAtomAndBondIDs(JOEMol, String, Hashtable, Hashtable) - Static method in class joelib.io.types.cml.CMLIDCreator: Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 scheme often used in CML.
createAtomAndBondIDs(JOEMol, String, Hashtable, Hashtable, int, int) - Static method in class joelib.io.types.cml.CMLIDCreator: Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 scheme often used in CML.
createBatchFile(Reader, Writer, Hashtable) - Method in class wsi.ra.io.BatchScriptReplacer: Description of the Method
createBond() - Method in class joelib.molecule.JOEMol: Creates only a new bond.
createBond(Pattern, BondExpr, int, int) - Static method in class joelib.smarts.Pattern: Description of the Method
createGIFimage(String, String, String) - Method in class jtt.docbook.DocBookMolecules
createGeometryOptimizer() - Method in class joelib.util.ghemical.GhemicalInterface
createGeometryOptimizer(int, float) - Method in class joelib.util.ghemical.GhemicalInterface
createGhemicalModel(JOEMol, boolean) - Method in class joelib.util.ghemical.GhemicalInterface
createGhemicalModel() - Method in class joelib.util.ghemical.GhemicalInterface
createHyperLinkListener() - Method in class joelib.gui.test.InfoPanel
createImage(String, String, String, String) - Method in class jtt.docbook.DocBookEquations
createLastDirectory(File) - Method in class wsi.ra.io.FileUtilities: Description of the Method
createMolInstances(JOEMolVector, String[], int[]) - Static method in class joelib.algo.datamining.weka.InstancesHelper
createMolInstances(JOEMolVector, String[], int[]) - Static method in class joelib.algo.datamining.weka.MolInstances
createMoleculeID(JOEMol) - Static method in class joelib.io.types.cml.CMLIDCreator
createMoleculeID(JOEMol, boolean) - Static method in class joelib.io.types.cml.CMLIDCreator
createNewFileName(String) - Method in class wsi.ra.io.FileUtilities
createNewFileName(String, int) - Method in class wsi.ra.io.FileUtilities
createNewMolecule(JOEMol, IntInt[], JOEMol[]) - Method in class joelib.molecule.generation.MolGenerationHelper: Create molecule by adding R-groups to the given base molecule.
createOrthoXYZVector(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
createSmiString(JOEMol, StringBuffer) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
createTable(String) - Method in class joelib.util.database.AbstractDatabase
createTable(String) - Method in interface joelib.util.database.DatabaseInterface
createTable() - Method in class joelib.util.database.SimpleJOELibDatabase
createTable(String) - Method in class joelib.util.database.SimpleJOELibDatabase
createWire(ViewerBond) - Static method in class joelib.gui.molviewer.java3d.graphics3D.BondNode: Description of the Method
cross(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: cross product with another vector
cross(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
cross(XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
cross(XYZVector) - Method in class joelib.math.XYZVector
current() - Method in class joelib.io.types.cml.CMLStack: Returns the last added entry.

D

DASH - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Wedge down bond type
DATA_TYPE - Static variable in class joelib.io.types.cml.elements.ArrayCML
DATA_TYPE - Static variable in class joelib.io.types.cml.elements.MatrixCML
DATA_TYPE - Static variable in class joelib.io.types.cml.elements.ScalarCML
DATA_TYPE_PEAKS - Static variable in class joelib.jcamp.JCAMPParser: Description of the Field
DATA_TYPE_SPECTRUM - Static variable in class joelib.jcamp.JCAMPParser: Description of the Field
DEFAULT - Static variable in class joelib.desc.types.AcidicGroups
DEFAULT - Static variable in class joelib.desc.types.AliphaticOHGroups
DEFAULT - Static variable in class joelib.desc.types.AromaticOHGroups
DEFAULT - Static variable in class joelib.desc.types.BasicGroups
DEFAULT - Static variable in class joelib.desc.types.HBA1
DEFAULT - Static variable in class joelib.desc.types.HBA2
DEFAULT - Static variable in class joelib.desc.types.HBD1
DEFAULT - Static variable in class joelib.desc.types.HBD2
DEFAULT - Static variable in class joelib.desc.types.HydrophobicGroups
DEFAULT - Static variable in class joelib.desc.types.NO2Groups
DEFAULT - Static variable in class joelib.desc.types.OSOGroups
DEFAULT - Static variable in class joelib.desc.types.SO2Groups
DEFAULT - Static variable in class joelib.desc.types.SOGroups
DEFAULT_ATOM_PROPERTIES - Static variable in class joelib.desc.types.atompair.TopologicalAtomPair
DEFAULT_DELIMITER - Static variable in class joelib.io.types.ChemicalMarkupLanguage
DEFAULT_DESC_NAMES - Static variable in class joelib.desc.util.AtomPropertyDescriptors
DEFAULT_DISTANCE_INFLUENCE - Static variable in class joelib.desc.types.ConjElectroTopolState
DEFAULT_DISTANCE_INFLUENCE - Static variable in class joelib.desc.types.ElectrotopologicalState
DEFAULT_OUTPUT_TYPE - Static variable in class joelib.io.types.Matlab: Description of the Field
DEFAULT_OUTPUT_TYPE - Static variable in class joelib.io.types.POVRay: Description of the Field
DEFAULT_SEPARATOR - Static variable in class joelib.util.ArrayHelper: Description of the Field
DEFAULT_SEPARATOR - Static variable in class joelib.util.MatrixHelper: Description of the Field
DEG_TO_RAD - Static variable in class joelib.math.Matrix3x3: Description of the Field
DEG_TO_RAD - Static variable in class joelib.math.XYZVector: Description of the Field
DEG_TO_RAD - Static variable in class joelib.util.JHM: Description of the Field
DELIMITER - Static variable in class joelib.io.types.cml.elements.ArrayCML
DELIMITER - Static variable in class joelib.io.types.cml.elements.MatrixCML
DESCRIPTORS - Static variable in class joelib.process.types.DescSelectionWriter: Description of the Field
DESC_KEY - Static variable in class joelib.algo.APropertyBFS
DESC_KEY - Static variable in class joelib.algo.BFS
DESC_KEY - Static variable in class joelib.algo.DFS
DESC_KEY - Static variable in class joelib.desc.types.APropertyDistanceMatrix
DESC_KEY - Static variable in class joelib.desc.types.AcidicGroups
DESC_KEY - Static variable in class joelib.desc.types.AliphaticOHGroups
DESC_KEY - Static variable in class joelib.desc.types.AromaticBonds
DESC_KEY - Static variable in class joelib.desc.types.AromaticOHGroups
DESC_KEY - Static variable in class joelib.desc.types.AtomInAcceptor
DESC_KEY - Static variable in class joelib.desc.types.AtomInAromaticSystem
DESC_KEY - Static variable in class joelib.desc.types.AtomInConjEnvironment
DESC_KEY - Static variable in class joelib.desc.types.AtomInDonAcc
DESC_KEY - Static variable in class joelib.desc.types.AtomInDonor
DESC_KEY - Static variable in class joelib.desc.types.AtomInRing
DESC_KEY - Static variable in class joelib.desc.types.AtomInTerminalCarbon
DESC_KEY - Static variable in class joelib.desc.types.AtomIsNegative
DESC_KEY - Static variable in class joelib.desc.types.AtomIsPositive
DESC_KEY - Static variable in class joelib.desc.types.AtomMass
DESC_KEY - Static variable in class joelib.desc.types.AtomType
DESC_KEY - Static variable in class joelib.desc.types.AtomValence
DESC_KEY - Static variable in class joelib.desc.types.AtomVanDerWaalsVolume
DESC_KEY - Static variable in class joelib.desc.types.Autocorrelation
DESC_KEY - Static variable in class joelib.desc.types.BCUT
DESC_KEY - Static variable in class joelib.desc.types.BasicGroups
DESC_KEY - Static variable in class joelib.desc.types.BurdenEigenvalues
DESC_KEY - Static variable in class joelib.desc.types.BurdenModifiedEigenvalues
DESC_KEY - Static variable in class joelib.desc.types.ConjElectroTopolState
DESC_KEY - Static variable in class joelib.desc.types.ConjugatedTopologicalDistance
DESC_KEY - Static variable in class joelib.desc.types.DistanceDistanceMatrix
DESC_KEY - Static variable in class joelib.desc.types.DistanceMatrix
DESC_KEY - Static variable in class joelib.desc.types.ElectrogeometricalState
DESC_KEY - Static variable in class joelib.desc.types.ElectronAffinity
DESC_KEY - Static variable in class joelib.desc.types.ElectronegativityPauling
DESC_KEY - Static variable in class joelib.desc.types.ElectrotopologicalState
DESC_KEY - Static variable in class joelib.desc.types.FractionRotatableBonds
DESC_KEY - Static variable in class joelib.desc.types.GeomDistanceMatrix
DESC_KEY - Static variable in class joelib.desc.types.GeometricalDiameter
DESC_KEY - Static variable in class joelib.desc.types.GeometricalRadius
DESC_KEY - Static variable in class joelib.desc.types.GeometricalShapeCoefficient
DESC_KEY - Static variable in class joelib.desc.types.GlobalTopologicalChargeIndex
DESC_KEY - Static variable in class joelib.desc.types.GraphPotentials
DESC_KEY - Static variable in class joelib.desc.types.GraphShapeCoefficient
DESC_KEY - Static variable in class joelib.desc.types.HBA1
DESC_KEY - Static variable in class joelib.desc.types.HBA2
DESC_KEY - Static variable in class joelib.desc.types.HBD1
DESC_KEY - Static variable in class joelib.desc.types.HBD2
DESC_KEY - Static variable in class joelib.desc.types.HeavyBonds
DESC_KEY - Static variable in class joelib.desc.types.HeteroCycles
DESC_KEY - Static variable in class joelib.desc.types.HydrophobicGroups
DESC_KEY - Static variable in class joelib.desc.types.IntrinsicState
DESC_KEY - Static variable in class joelib.desc.types.KierShape1
DESC_KEY - Static variable in class joelib.desc.types.KierShape2
DESC_KEY - Static variable in class joelib.desc.types.KierShape3
DESC_KEY - Static variable in class joelib.desc.types.LogP
DESC_KEY - Static variable in class joelib.desc.types.MolarRefractivity
DESC_KEY - Static variable in class joelib.desc.types.MolecularWeight
DESC_KEY - Static variable in class joelib.desc.types.NO2Groups
DESC_KEY - Static variable in class joelib.desc.types.NumberOfAtoms
DESC_KEY - Static variable in class joelib.desc.types.NumberOfB
DESC_KEY - Static variable in class joelib.desc.types.NumberOfBonds
DESC_KEY - Static variable in class joelib.desc.types.NumberOfBr
DESC_KEY - Static variable in class joelib.desc.types.NumberOfC
DESC_KEY - Static variable in class joelib.desc.types.NumberOfCl
DESC_KEY - Static variable in class joelib.desc.types.NumberOfF
DESC_KEY - Static variable in class joelib.desc.types.NumberOfHal
DESC_KEY - Static variable in class joelib.desc.types.NumberOfI
DESC_KEY - Static variable in class joelib.desc.types.NumberOfN
DESC_KEY - Static variable in class joelib.desc.types.NumberOfO
DESC_KEY - Static variable in class joelib.desc.types.NumberOfP
DESC_KEY - Static variable in class joelib.desc.types.NumberOfS
DESC_KEY - Static variable in class joelib.desc.types.OSOGroups
DESC_KEY - Static variable in class joelib.desc.types.PolarSurfaceArea
DESC_KEY - Static variable in class joelib.desc.types.RadialDistributionFunction
DESC_KEY - Static variable in class joelib.desc.types.RotatableBonds
DESC_KEY - Static variable in class joelib.desc.types.SO2Groups
DESC_KEY - Static variable in class joelib.desc.types.SOGroups
DESC_KEY - Static variable in class joelib.desc.types.SSKey3DS
DESC_KEY - Static variable in class joelib.desc.types.TopologicalDiameter
DESC_KEY - Static variable in class joelib.desc.types.TopologicalRadius
DESC_KEY - Static variable in class joelib.desc.types.WeightedBurdenEigenvalues
DESC_KEY - Static variable in class joelib.desc.types.WeightedBurdenModifiedEigenvalues
DESC_KEY - Static variable in class joelib.desc.types.ZagrebIndex1
DESC_KEY - Static variable in class joelib.desc.types.ZagrebIndex2
DESC_KEY - Static variable in class joelib.desc.types.atompair.TopologicalAtomPair
DESC_KEY - Static variable in class joelib.molecule.charge.GasteigerMarsili
DFS - class joelib.algo.DFS.: Depth First Search.
DFS() - Constructor for class joelib.algo.DFS: Constructor for the KierShape1 object
DFSResult - class joelib.algo.DFSResult.: Result of a DFS.
DFSResult() - Constructor for class joelib.algo.DFSResult: Constructor for the DFSResult object
DICT_REF - Static variable in class joelib.io.types.cml.elements.MatrixCML
DICT_REF - Static variable in class joelib.io.types.cml.elements.ScalarCML
DIMENSION - Static variable in class joelib.math.symmetry.SymCoordinates
DIMENSION_2D - Static variable in class joelib.io.types.MDLSD: Description of the Field
DIMENSION_3D - Static variable in class joelib.io.types.MDLSD
DISTANCE_INFLUENCE - Static variable in class joelib.desc.types.ConjElectroTopolState
DISTANCE_INFLUENCE - Static variable in class joelib.desc.types.ElectrogeometricalState
DISTANCE_INFLUENCE - Static variable in class joelib.desc.types.ElectrotopologicalState
DOUBLE - Static variable in class joelib.desc.result.DynamicArrayResult: Description of the Field
DOUBLE - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Double bond type
DOWN_BOND_FLAG - Static variable in class joelib.smiles.JOESmilesParser
DX_TYPE - Static variable in class joelib.jcamp.JCAMPDataBlock
DatabaseConnection - class wsi.ra.database.DatabaseConnection.: Simple JDBC database connection.
DatabaseInterface - interface joelib.util.database.DatabaseInterface.: Database interface definition.
DecimalFormatHelper - class wsi.ra.text.DecimalFormatHelper.: Some methods to faciliate the work with descriptors.
DecimalFormatter - interface wsi.ra.text.DecimalFormatter.: Interface for defining a decimal formatter.
Deque - class wsi.ra.tool.Deque.: Deque implementation.
Deque(DequeNode) - Constructor for class wsi.ra.tool.Deque
Deque() - Constructor for class wsi.ra.tool.Deque
DequeIterator - class wsi.ra.tool.DequeIterator.: Iterator class for the list.
DequeIterator(Deque) - Constructor for class wsi.ra.tool.DequeIterator
DequeNode - class wsi.ra.tool.DequeNode.: Deque node representation.
DequeNode(DequeNode, Object, DequeNode) - Constructor for class wsi.ra.tool.DequeNode
DequeNode(DequeNode, Object) - Constructor for class wsi.ra.tool.DequeNode
DequeNode(Object) - Constructor for class wsi.ra.tool.DequeNode
DescBinning - class joelib.process.types.DescBinning.: Calling processor classes if the filter rule fits.
DescBinning() - Constructor for class joelib.process.types.DescBinning: Constructor for the DescSelectionWriter object
DescDescription - class joelib.desc.DescDescription.: Access class to the descriptor descripton files.
DescDescription(String) - Constructor for class joelib.desc.DescDescription: Initialize the access class to the descriptor descripton files.
DescResult - interface joelib.desc.DescResult.: Interface definition for descriptor results.
DescSelectionWriter - class joelib.process.types.DescSelectionWriter.: Calling processor classes if the filter rule fits.
DescSelectionWriter() - Constructor for class joelib.process.types.DescSelectionWriter: Constructor for the DescSelectionWriter object
DescStatistic - class joelib.process.types.DescStatistic.: Calling processor classes if the filter rule fits.
DescStatistic() - Constructor for class joelib.process.types.DescStatistic: Constructor for the DescSelectionWriter object
DescVarianceNorm - class joelib.process.types.DescVarianceNorm.: Scales the values in one descriptor so that they have similar magnitudes.
DescVarianceNorm() - Constructor for class joelib.process.types.DescVarianceNorm: Constructor for the DescSelectionWriter object
Description - class joelib.desc.Description.: Description for a descriptor.
Descriptor - interface joelib.desc.Descriptor.: Interface for defining descriptors, which can be calculated by using JOELib.
DescriptorCalculation - class joelib.test.DescriptorCalculation.: Example for loading molecules and get atom properties.
DescriptorCalculation() - Constructor for class joelib.test.DescriptorCalculation
DescriptorException - exception joelib.desc.DescriptorException.: Descriptor exception.
DescriptorException() - Constructor for class joelib.desc.DescriptorException: Constructor for the DescriptorException object.
DescriptorException(String) - Constructor for class joelib.desc.DescriptorException: Constructor for the DescriptorException object.
DescriptorFactory - class joelib.desc.DescriptorFactory.: Factory class to get descriptor calculation classes.
DescriptorFilter - class joelib.process.filter.DescriptorFilter.: Interface definition for calling external programs from JOELib.
DescriptorFilter() - Constructor for class joelib.process.filter.DescriptorFilter: Constructor for the DescriptorFilter object
DescriptorFilter(String, boolean) - Constructor for class joelib.process.filter.DescriptorFilter: Constructor for the DescriptorFilter object
DescriptorFilter(Vector) - Constructor for class joelib.process.filter.DescriptorFilter: Constructor for the DescriptorFilter object
DescriptorHelper - class joelib.desc.DescriptorHelper.: Some methods to faciliate the work with descriptors.
DescriptorInfo - class joelib.desc.DescriptorInfo.: Informations for a descriptor.
DescriptorInfo(String, String, String, int, String, String, String) - Constructor for class joelib.desc.DescriptorInfo: Deprecated. the required dimension is strongly connected to the descriptor type, so it would be better to use the internal resolving used in DescriptorInfo.DescriptorInfo(String, String, String, String, String, String)
DescriptorInfo(String, String, String, String, String, String) - Constructor for class joelib.desc.DescriptorInfo: Initializes a descriptor information.
DescriptorInfo(String, int, String, String, String, String) - Constructor for class joelib.desc.DescriptorInfo: Initializes a descriptor information.
DescriptorSelection - class joelib.test.DescriptorSelection.: Example for converting molecules.
DescriptorSelection() - Constructor for class joelib.test.DescriptorSelection
DescriptorStatistic - class joelib.test.DescriptorStatistic.: Example for converting molecules.
DescriptorStatistic() - Constructor for class joelib.test.DescriptorStatistic
DistanceCalculation - class joelib.process.types.DistanceCalculation.: Calling processor classes if the filter rule fits.
DistanceCalculation() - Constructor for class joelib.process.types.DistanceCalculation: Constructor for the DescSelectionWriter object
DistanceDistanceMatrix - class joelib.desc.types.DistanceDistanceMatrix.: Calculates the Distance Matrix (shortest paths from each atom to each atom) of a molecule
DistanceDistanceMatrix() - Constructor for class joelib.desc.types.DistanceDistanceMatrix: Constructor for the DistanceMatrix object
DistanceMatrix - class joelib.desc.types.DistanceMatrix.: Calculates the Distance Matrix (shortest paths from each atom to each atom) of a molecule
DistanceMatrix() - Constructor for class joelib.desc.types.DistanceMatrix: Constructor for the DistanceMatrix object
DistanceMetric - interface joelib.math.similarity.DistanceMetric.: Interface for getting different similarity metric implementation for miscelangelous descriptor result classes (e.g.
DistanceMetricHelper - class joelib.math.similarity.DistanceMetricHelper.: Helper class to load distance metric representation classes using reflection.
DistanceMetricHelper() - Constructor for class joelib.math.similarity.DistanceMetricHelper
DistanceMetricValue - interface joelib.desc.DistanceMetricValue.: Interface to have a fast method to getting similarity metric values.
DocBookArticles - class jtt.docbook.DocBookArticles.: Interface for defining a decimal formatter.
DocBookArticles() - Constructor for class jtt.docbook.DocBookArticles
DocBookEquations - class jtt.docbook.DocBookEquations.: Interface for defining a decimal formatter.
DocBookEquations() - Constructor for class jtt.docbook.DocBookEquations
DocBookMolecules - class jtt.docbook.DocBookMolecules.: Interface for defining a decimal formatter.
DocBookMolecules() - Constructor for class jtt.docbook.DocBookMolecules
DoubleArrayResult - class joelib.desc.result.DoubleArrayResult.: Double array results of variable size.
DoubleArrayResult() - Constructor for class joelib.desc.result.DoubleArrayResult: Constructor for the IntArrayResult object
DoubleInt - class joelib.util.types.DoubleInt.: Double and integer value.
DoubleInt() - Constructor for class joelib.util.types.DoubleInt: Constructor for the IntInt object
DoubleInt(double, int) - Constructor for class joelib.util.types.DoubleInt: Constructor for the IntInt object
DoubleMatrixResult - class joelib.desc.result.DoubleMatrixResult.: Double matrix results of variable size.
DoubleMatrixResult() - Constructor for class joelib.desc.result.DoubleMatrixResult: Constructor for the IntMatrixResult object
DoubleResult - class joelib.desc.result.DoubleResult.: Double results.
DoubleResult() - Constructor for class joelib.desc.result.DoubleResult: Constructor for the DoubleResult object
DoubleType - class joelib.util.types.DoubleType.: Two integers to represent a (BINARY) double value.
DoubleType() - Constructor for class joelib.util.types.DoubleType
DragBehavior - class joelib.gui.molviewer.java3d.graphics3D.DragBehavior.: Description of the Class
DynamicArrayResult - class joelib.desc.result.DynamicArrayResult.: Dynamic array results of variable size.
DynamicArrayResult() - Constructor for class joelib.desc.result.DynamicArrayResult: Constructor for the IntArrayResult object
d - Variable in class joelib.util.types.DoubleInt: Description of the Field
data - Variable in class joelib.jcamp.LabelData
dataSize() - Method in class joelib.molecule.JOEMol: Returns the number of data elements in this molecule.
deScale(double) - Method in class wsi.ra.tool.ArrayStatistic
decrementImplicitValence() - Method in class joelib.molecule.JOEAtom: Decrement the implicit valence.
decrementMod() - Method in class joelib.molecule.JOEMol: Decrease modification counter.
defaultPointGroups - Static variable in class joelib.math.symmetry.PointGroups
defaultTableName - Variable in class joelib.util.database.SimpleJOELibDatabase
degreeValue() - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Return angle value in degree unit
dehighlight() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Dehighlighted all highlighted atoms.
deleteAtom(JOEAtom) - Method in class joelib.molecule.JOEMol: Delete atom from molecule.
deleteBond(JOEBond) - Method in class joelib.molecule.JOEAtom: Delete a bond from this atom.
deleteBond(JOEBond) - Method in class joelib.molecule.JOEMol: Delete the given JOEBond from this molecule.
deleteConformer(int) - Method in class joelib.molecule.JOEMol: Delete conformer from molecule.
deleteData(String) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteData(JOEDataType) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteData(JOEGenericData) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteData(Vector) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
deleteData(String) - Method in class joelib.molecule.JOEMol: Description of the Method
deleteData(JOEDataType) - Method in class joelib.molecule.JOEMol: Deletes all data elements os the given JOEDataType .
deleteData(JOEGenericData) - Method in class joelib.molecule.JOEMol: Delete all data elements which are equal to the given JOEGenericData element.
deleteData(Vector) - Method in class joelib.molecule.JOEMol: Description of the Method
deleteFileName(String) - Method in class wsi.ra.io.FileUtilities
deleteHydrogen(JOEAtom) - Method in class joelib.molecule.JOEMol: Deletes hydrogen atom.
deleteHydrogens() - Method in class joelib.molecule.JOEMol: Delete all hydrogen atoms from molecule.
deleteHydrogens(JOEAtom) - Method in class joelib.molecule.JOEMol: Delete all hydrogen atoms from given atom.
deleteNonPolarHydrogens() - Method in class joelib.molecule.JOEMol: Delete all non polar hydrogens from molecule.
deleteResidue() - Method in class joelib.molecule.JOEAtom
deleteResidue(JOEResidue) - Method in class joelib.molecule.JOEMol: Description of the Method
denom - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field
descFromMol(JOEMol, String, boolean) - Static method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descFromMol(JOEMol, String, DescResult, boolean) - Static method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descFromMol(JOEMol, String) - Method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descFromMol(JOEMol, String, DescResult) - Method in class joelib.desc.DescriptorHelper: Getting descriptor values from a molecule and try to calculate a descriptor value if it is not already available.
descInfo - Variable in class joelib.desc.AtomsCounter
descInfo - Variable in class joelib.desc.SMARTSCounter
descInfo - Variable in class joelib.desc.SimpleBooleanDesc
descInfo - Variable in class joelib.desc.SimpleDoubleAtomProperty
descInfo - Variable in class joelib.desc.SimpleDoubleDesc
descInfo - Variable in class joelib.desc.SimpleDynamicAtomProperty
descInfo - Variable in class joelib.desc.SimpleIntDesc
descInfo - Variable in class joelib.desc.SimpleStringAtomProperty
descriptors() - Method in class joelib.desc.DescriptorHelper: Returns a Enumeration of all available descriptor names that could be calculated by using JOELib.
descriptors2ignore() - Method in class joelib.process.types.DescVarianceNorm
deselect() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Deselects all selected atoms
destroyAtom(JOEAtom) - Method in class joelib.molecule.JOEMol: Destroys atom.
destroyBond(JOEBond) - Method in class joelib.molecule.JOEMol: Destroys all bond.
determinant() - Method in class joelib.math.Matrix3x3: Description of the Method
determineFRJ(JOEMol) - Static method in class joelib.util.JHM: Description of the Method
differentialShannon(int[], int[], int, int, int) - Static method in class wsi.ra.tool.StatisticUtils: Computes differential shannon entropy
dimension - Static variable in class joelib.io.types.MDLSD
direction - Variable in class joelib.math.symmetry.SymmetryElement
discovered - Variable in class joelib.algo.DFSResult: Description of the Field
display() - Method in class joelib.gui.render.MoleculeViewer2D: Contructs a JFrame into which this JPanel is put and displays the frame with the molecule.
display(JOEMol) - Static method in class joelib.gui.render.MoleculeViewer2D
display(JOEMol, JOESmartsPattern, String, String, String, String) - Static method in class joelib.gui.render.MoleculeViewer2D
display(JOEMol, String, JOESmartsPattern, String, String, String, String) - Static method in class joelib.gui.render.MoleculeViewer2D
displayAndAromElem(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displayAtomExpr(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displayAtomLeaf(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displayBondExpr(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
displayBondLeaf(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
displayOrAromElem(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displaySMARTSAtom(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
displaySMARTSBond(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
displaySMARTSPart(Pattern, ParseState, int, OutputStream) - Static method in class joelib.smarts.ParseSmart: Description of the Method
displaySimpleAtomExpr(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
distSq(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
distSquareTo(Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: calculate the squre of distance from this point to the other
distance(Point3D, Point3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: calculate distance between two points in 3D space
distance - Variable in class joelib.math.symmetry.SymmetryElement
distanceCalculator(int[], double) - Static method in class joelib.gui.render.RenderHelper: Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
distanceTo(Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Line: Return the distance from a given point to the line
distanceTo(Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: calculate distance from this point to the other
div(int) - Method in class joelib.math.XYZVector: Description of the Method
div(XYZVector, int) - Static method in class joelib.math.XYZVector: Description of the Method
div(XYZVector, XYZVector, double) - Static method in class joelib.math.XYZVector: Description of the Method
divideAndRound(int, int) - Static method in class joelib.gui.molviewer.java3d.math.util.MathUtils: Perform a division of the input integers, and round to the next integer if the divisor is not a even multiple of the dividend.
diving(double) - Method in class joelib.math.Matrix3x3: Description of the Method
diving(double) - Method in class joelib.math.XYZVector: Description of the Method
doGeometryOptimization(JOEMol, int, double, double, boolean) - Method in class joelib.util.ghemical.GhemicalInterface
doGeometryOptimization(boolean) - Method in class joelib.util.ghemical.GhemicalInterface
doGeometryOptimization(int, double, double, boolean) - Method in class joelib.util.ghemical.GhemicalInterface
doRandomSearch(int, int) - Method in class joelib.util.ghemical.GhemicalInterface
doRandomSearch(boolean) - Method in class joelib.util.ghemical.TestInterface
doSystematicSearch(int, int) - Method in class joelib.util.ghemical.GhemicalInterface
doSystematicSearch(boolean) - Method in class joelib.util.ghemical.TestInterface
doctypeDecl(String, String, String) - Method in class joelib.io.types.cml.CMLHandler
doctypeDecl(String, String, String) - Method in class joelib.io.types.cml.XMLHandler
dot(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: dot product with another vector
dot(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
doubleArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper: Loads integer array from String .
doubleArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper: Loads integer array from String .
doubleArrayFromString(String) - Method in class joelib.util.ArrayHelper: Loads double array from String .
doubleArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper: Loads double array from String .
doubleArrayFromString(String) - Static method in class joelib.util.LineArrayHelper: Description of the Method
doubleArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper: Description of the Method
doubleArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper: Description of the Method
doubleArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper: Gets double arrays from a Reader.
doubleArrayFromString(StringTokenizer, int) - Static method in class joelib.util.LineArrayHelper: Gets double arrays from a Reader.
doubleMatrixFromRectangleString(String) - Method in class joelib.util.MatrixHelper: Description of the Method
doubleMatrixFromRectangleString(String, String) - Static method in class joelib.util.MatrixHelper: Description of the Method
doubleMatrixFromSimpleString(String, int, int) - Method in class joelib.util.MatrixHelper
doubleMatrixFromSimpleString(String, int, int, String) - Static method in class joelib.util.MatrixHelper: Description of the Method
doubleMatrixFromString(String) - Static method in class joelib.util.LineMatrixHelper: Description of the Method
doubleMatrixFromString(String) - Method in class joelib.util.MatrixHelper: Description of the Method
doubleMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper: Description of the Method
drawNumbers() - Method in class joelib.gui.render.Renderer2DModel: Returns if the drawing of atom numbers is switched on for this model
dst - Variable in class joelib.smarts.BondSpec: Index of the SMARTS atom expression which is the destination of this bond expression.
dumpAtomExpr(AtomExpr, OutputStream) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
dumpBondExpr(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
dumpBondLeaf(BondExpr, OutputStream) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method

E

ELECTRON - Static variable in class joelib.io.types.cml.CMLCoreModule
ELEMMAX - Static variable in class joelib.smarts.ParseSmart: Description of the Field
EQ(String, String) - Static method in class joelib.util.JOEHelper: Description of the Method
EQUAL - Static variable in class joelib.process.filter.NativeValueFilter
EQUAL - Static variable in class joelib.process.filter.SMARTSFilter
EQn(String, String, int) - Static method in class joelib.util.JOEHelper: Description of the Method
ERROR_BASIS - Static variable in class joelib.io.types.cml.elements.ArrayCML
ERROR_BASIS - Static variable in class joelib.io.types.cml.elements.ScalarCML
ERROR_VALUE - Static variable in class joelib.io.types.cml.elements.ScalarCML
ERROR_VALUES - Static variable in class joelib.io.types.cml.elements.ArrayCML
EZ_ISOMERISM_UNDEFINED - Static variable in class joelib.util.IsomerismDetection
E_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
ElectrogeometricalState - class joelib.desc.types.ElectrogeometricalState.: Electrogeometrical state descriptor (EGSTATE).
ElectrogeometricalState() - Constructor for class joelib.desc.types.ElectrogeometricalState: Constructor for the KierShape1 object
ElectronAffinity - class joelib.desc.types.ElectronAffinity.: Electron affinity.
ElectronAffinity() - Constructor for class joelib.desc.types.ElectronAffinity: Constructor for the KierShape1 object
ElectronegativityPauling - class joelib.desc.types.ElectronegativityPauling.: Electronegativity after Pauling.
ElectronegativityPauling() - Constructor for class joelib.desc.types.ElectronegativityPauling: Constructor for the KierShape1 object
ElectrotopologicalState - class joelib.desc.types.ElectrotopologicalState.: Electrotolpogical state descriptor (ESTATE).
ElectrotopologicalState() - Constructor for class joelib.desc.types.ElectrotopologicalState: Constructor for the KierShape1 object
Element - class joelib.molecule.Element.: Element.
Element() - Constructor for class joelib.molecule.Element
ElementCML - interface joelib.io.types.cml.elements.ElementCML.: Interface for defining CML elements.
EuklidianComparison - class joelib.test.EuklidianComparison.: Example for converting molecules.
EuklidianComparison() - Constructor for class joelib.test.EuklidianComparison
Executable - class jtt.util.Executable.: Calls corina to create 3D structures.
Executable() - Constructor for class jtt.util.Executable: Constructor for the Corina object
External - interface joelib.ext.External.: Interface definition for calling external programs from JOELib.
ExternalException - exception joelib.ext.ExternalException.: External molecule process exception.
ExternalException() - Constructor for class joelib.ext.ExternalException: Constructor for the DescriptorException object
ExternalException(String) - Constructor for class joelib.ext.ExternalException: Constructor for the DescriptorException object
ExternalFactory - class joelib.ext.ExternalFactory.: Factory class to get external molecule process classes.
ExternalHelper - class joelib.ext.ExternalHelper.: Some helper methods for calling external programs.
ExternalInfo - class joelib.ext.ExternalInfo.: Informations for an external process.
ExternalInfo(String, String, String, String, String, String, Vector) - Constructor for class joelib.ext.ExternalInfo: Constructor for the DescriptorInfo object
earlyRemovedCandidates - Variable in class joelib.math.symmetry.SymStatistic
ele - Variable in class joelib.math.Matrix3x3: Description of the Field
elem - Variable in class joelib.util.types.Template: Description of the Field
elementAt(int) - Method in class wsi.ra.tool.SortedVector: Returns the component at the specified index.
elements() - Method in class Acme.IntHashtable
elements() - Method in class joelib.io.types.cml.CDOAcceptedObjects: Returns the names in this list as a Enumeration class.
elements - Variable in class joelib.io.types.cml.CMLCoreModule
elements() - Method in class wsi.ra.tool.SortedVector: Returns an enumeration of the components of this vector.
empty() - Method in class joelib.molecule.JOEMol: Returns true if this molecule contains no atoms.
empty() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
empty() - Method in class joelib.util.JOEBitVec: Description of the Method
encode() - Method in class Acme.JPM.Encoders.ImageEncoder
endBit() - Method in class joelib.util.JOEBitVec: Description of the Method
endDocument() - Method in class joelib.io.types.cml.CDKConvention
endDocument() - Method in interface joelib.io.types.cml.CDOInterface: Called just after XML parsing has ended.
endDocument() - Method in class joelib.io.types.cml.CMLCoreModule
endDocument() - Method in class joelib.io.types.cml.CMLHandler: Calling this procedure signals the end of the XML document.
endDocument() - Method in class joelib.io.types.cml.CMLReactionModule
endDocument() - Method in interface joelib.io.types.cml.ModuleInterface
endDocument() - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
endDocument() - Method in class joelib.io.types.cml.XMLHandler
endElement(String, String, String) - Method in class joelib.io.types.cml.CDKConvention
endElement(CMLStack, String, String, String) - Method in class joelib.io.types.cml.CMLCoreModule
endElement(String, String, String) - Method in class joelib.io.types.cml.CMLHandler
endElement(String, String, String) - Method in class joelib.io.types.cml.CMLReactionModule
endElement(CMLStack, String, String, String) - Method in interface joelib.io.types.cml.ModuleInterface
endElement(String) - Method in class joelib.io.types.cml.XMLHandler
endElement(String) - Method in class joelib.io.types.cml.elements.ArrayCML
endElement(String) - Method in interface joelib.io.types.cml.elements.ElementCML
endElement(String) - Method in class joelib.io.types.cml.elements.MatrixCML
endElement(String) - Method in class joelib.io.types.cml.elements.ScalarCML
endModify() - Method in class joelib.molecule.JOEMol: Ends modification of atoms and decrease modification counter.
endModify(boolean) - Method in class joelib.molecule.JOEMol: Ends modification of atoms and decrease modification counter.
endObject(String) - Method in interface joelib.io.types.cml.CDOInterface: End the process of adding a new object to the CDO of a certain type.
endObject(String) - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
entropy - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
eol - Static variable in class joelib.util.JHM
eq(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is equal to b.
equalAtomExpr(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
equals(Object) - Method in class joelib.algo.morgan.AtomDouble
equals(Object) - Method in class joelib.algo.morgan.AtomDoubleComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.algo.morgan.AtomDoubleParent
equals(Object) - Method in class joelib.data.JOEDataType: Description of the Method
equals(JOEGenericData) - Method in class joelib.data.JOEGenericData
equals(Description) - Method in class joelib.desc.Description: Description of the Method
equals(Object) - Method in class joelib.desc.types.atompair.AtomPair
equals(AtomPair) - Method in class joelib.desc.types.atompair.AtomPair
equals(Object) - Method in class joelib.desc.types.atompair.AtomPairAtomType
equals(AtomPairAtomType) - Method in class joelib.desc.types.atompair.AtomPairAtomType
equals(Object) - Method in class joelib.desc.types.atompair.AtomPairTypeComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.desc.types.atompair.AtomTypePair
equals(ViewerMolecule) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Compares this molecule with another
equals(IOType) - Method in class joelib.io.IOType: Description of the Method
equals(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
equals(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
equals(Object) - Method in class joelib.math.symmetry.SymAxesComparator: Indicates whether some other object is "equal to" this Comparator.
equals(TransformationAtom) - Method in class joelib.math.symmetry.TransformationAtom
equals(Object) - Method in class joelib.molecule.AtomZPosComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.molecule.BondComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.molecule.JOEAtom: Checks if two atoms are equal.
equals(JOEAtom, boolean) - Method in class joelib.molecule.JOEAtom: Checks if two atoms are equal.
equals(Object) - Method in class joelib.molecule.JOEBond: Checks if two bonds are equal.
equals(JOEBond, boolean) - Method in class joelib.molecule.JOEBond: Checks if two bonds are equal.
equals(Object) - Method in class joelib.molecule.JOEMol: Checks if two molecules are equal, ignoring descriptor values.
equals(JOEMol) - Method in class joelib.molecule.JOEMol: Checks if two molecules are equal, ignoring descriptor values.
equals(Object) - Method in class joelib.process.ProcessPipeEntry: Two entries are equal, if they contain the same JOEProcess object.
equals(Object) - Method in class joelib.ring.RingSizeComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.smarts.Patty
equals(Object) - Method in class joelib.sort.ArraySizeComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.sort.RotorComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.sort.VectorSizeComparator: Indicates whether some other object is "equal to" this Comparator.
equals(Object) - Method in class joelib.util.BitSet14: Compares this object against the specified object.
equals(Object) - Method in class joelib.util.JOEProperty
equals(Object) - Method in class joelib.util.types.AtomZPos: Compare this object with another object.
equals(Object) - Method in class joelib.util.types.DoubleInt
equals(Object) - Method in class joelib.util.types.Int
equals(Object) - Method in class joelib.util.types.IntInt
equals(Object) - Method in class joelib.util.types.IntIntInt
error(SAXParseException) - Method in class joelib.io.types.cml.CMLErrorHandler: Outputs a SAXParseException error to the logger.
evalAtomExpr(AtomExpr, JOEAtom) - Method in class joelib.smarts.ParseSmart: Description of the Method
evalBondExpr(BondExpr, JOEBond) - Static method in class joelib.smarts.ParseSmart: Description of the Method
excludeSmallRing(JOEMol) - Method in class joelib.data.JOEAromaticTyper: Remove 3 membered rings from consideration.
execute(String, String, String) - Method in class jtt.docbook.Jade
execute(String, String, String[]) - Static method in class jtt.util.Executable
execute(String[], boolean) - Static method in class jtt.util.Executable: Description of the Method
existInstance() - Static method in class wsi.ra.tool.PropertyHolder: Exists an instance for this PropertyHolder.
existsBinningFileFor(String) - Static method in class joelib.process.types.DescBinning: Description of the Method
existsBond(int, int) - Method in class joelib.molecule.JOEMol: Returns true if this bond exists.
existsMatrixFileFor(String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
existsMatrixFileFor(String) - Method in interface joelib.desc.data.MoleculeCache
existsMatrixFileFor(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
existsStatisticFileFor(String) - Static method in class joelib.process.types.DescStatistic: Description of the Method
existsTable(String) - Method in class joelib.util.database.AbstractDatabase
existsTable(String) - Method in interface joelib.util.database.DatabaseInterface
existsTable() - Method in class joelib.util.database.SimpleJOELibDatabase
existsTable(String) - Method in class joelib.util.database.SimpleJOELibDatabase
existsTable(String) - Method in class wsi.ra.database.DatabaseConnection: Checks if a table of the given name is available through the given database connection (looks only for standard, not system tables).
expandKekule(JOEMol, Vector, AtomIterator, int[], boolean) - Static method in class joelib.util.JHM
explicitHydrogenCount() - Method in class joelib.molecule.JOEAtom: Returns the number of explicit hydrogens.
expr - Variable in class joelib.smarts.AtomSpec: Representation of the SMARTS atom expression.
expr - Variable in class joelib.smarts.BondSpec: Representation of the SMARTS bond expression.
externals() - Method in class joelib.ext.ExternalFactory: Description of the Method

F

FEATURE - Static variable in class joelib.io.types.cml.CMLCoreModule
FLOAT - Static variable in class joelib.io.types.cml.CMLCoreModule
FLOATARRAY - Static variable in class joelib.io.types.cml.CMLCoreModule
FLOATMATRIX - Static variable in class joelib.io.types.cml.CMLCoreModule
FOO - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
FProbability(double, int, int) - Static method in class wsi.ra.tool.Statistics: Computes probability of F-ratio.
FREE_ELECTRONS_NOT_DEF - Static variable in class joelib.molecule.JOEAtom
FileUtilities - class wsi.ra.io.FileUtilities.: Usefull functions for file handling.
FileUtilities() - Constructor for class wsi.ra.io.FileUtilities
Filter - interface joelib.process.filter.Filter.: Interface definition for filter options for a molecule process.
FilterException - exception joelib.process.filter.FilterException.: Molecule process filter exception.
FilterException() - Constructor for class joelib.process.filter.FilterException: Constructor for the DescriptorException object
FilterException(String) - Constructor for class joelib.process.filter.FilterException: Constructor for the DescriptorException object
FilterFactory - class joelib.process.filter.FilterFactory.: Factory class to get molecule process filter classes.
FilterInfo - class joelib.process.filter.FilterInfo.: Molecule process filter informations.
FilterInfo(String, String, String) - Constructor for class joelib.process.filter.FilterInfo: Constructor for the DescriptorInfo object
Flat - class joelib.io.types.Flat.: Flat file format support.
Flat() - Constructor for class joelib.io.types.Flat: Constructor for the Smiles object
FloatMatrixResult - class joelib.desc.result.FloatMatrixResult.: Double matrix results of variable size.
FloatMatrixResult() - Constructor for class joelib.desc.result.FloatMatrixResult: Constructor for the IntMatrixResult object
FractionRotatableBonds - class joelib.desc.types.FractionRotatableBonds.: Fraction of rotatable bonds.
FractionRotatableBonds() - Constructor for class joelib.desc.types.FractionRotatableBonds: Constructor for the KierShape2 object
Fragmentation - interface joelib.molecule.fragmentation.Fragmentation.: Interface for defining a fragmentation algorithm.
FromToAtoms - class joelib.gui.render.FromToAtoms.: Abstract base class for two point informations generated from the atom positions.
FromToAtoms() - Constructor for class joelib.gui.render.FromToAtoms
fastSingleMatch(JOEMol, Pattern, Vector) - Method in class joelib.smarts.ParseSmart
fatalError(SAXParseException) - Method in class joelib.io.types.cml.CMLErrorHandler: Outputs as fatal SAXParseException error to the logger.
filenameToType(String) - Method in class joelib.io.IOTypeHolder: Gets an appropriate molecule input/output type for the given filename.
fillOrth(double, double, double, double, double, double) - Method in class joelib.math.Matrix3x3: Description of the Method
filters() - Method in class joelib.process.filter.FilterFactory: Description of the Method
finalize() - Method in class joelib.data.JOEChemTransformation: Description of the Method
finalize() - Method in class joelib.data.JOEElementTable: Description of the Method
finalize() - Method in class joelib.data.JOEExternalBond: Description of the Method
finalize() - Method in class joelib.data.JOEGenericData: Description of the Method
finalize() - Method in class joelib.data.JOEGroupContribution: Description of the Method
finalize() - Method in class joelib.data.JOEIsotopeTable: Description of the Method
finalize() - Method in class joelib.data.JOEResidueData: Description of the Method
finalize() - Method in class joelib.data.JOETypeTable: Description of the Method
finalize() - Method in class joelib.io.JOEFileFormat: Description of the Method
finalize() - Method in class joelib.math.JOECoordTrans: Description of the Method
finalize() - Method in class joelib.math.JOESqrtTbl: Description of the Method
finalize() - Method in class joelib.math.XYZVector: Description of the Method
finalize() - Method in class joelib.molecule.GenericDataHolder: Description of the Method
finalize() - Method in class joelib.molecule.JOEAtom: Destructor for the JOEAtom object.
finalize() - Method in class joelib.molecule.JOEBond: Description of the Method
finalize() - Method in class joelib.molecule.JOEMol: Destructor for this molecule.
finalize() - Method in class joelib.molecule.JOEMolVector: Functions for dealing with groups of molecules.
finalize() - Method in class joelib.molecule.JOERTree: Desctructor
finalize() - Method in class joelib.molecule.JOEResidue
finalize() - Method in class joelib.molecule.charge.GasteigerState: Description of the Method
finalize() - Method in class joelib.molecule.charge.JOEGastChrg: Description of the Method
finalize() - Method in class joelib.smarts.JOESSMatch: Description of the Method
finalize() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
finalize() - Method in class joelib.smarts.Patty
finalize() - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
finalize() - Method in class joelib.smiles.JOESmiNode: Description of the Method
findAromaticBonds(JOEMol, JOEAtom, int) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
findAromaticBonds(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
findAtom(float, float, float, float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Returns closest atom to point within FINDRADIUS, null if nothing is found,
findBB() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Determines bounding box of a molecule (sets xmax,xmin,ymax,ymin,zmax,zmin)
findCenterAndNormal(XYZVector, XYZVector, XYZVector) - Method in class joelib.ring.JOERing: Description of the Method
findChildren(Vector, int, int) - Method in class joelib.molecule.JOEMol: Locates all atoms for which there exists a path to second without going through first children does not include second .
findChildren(Vector, JOEAtom, JOEAtom) - Method in class joelib.molecule.JOEMol: locates all atoms for which there exists a path to 'second' without going through 'first' children does not include 'second'
findChiralCenters() - Method in class joelib.molecule.JOEMol: Description of the Method
findClosureBonds(JOEMol) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
findLargestFragment(JOEBitVec) - Method in class joelib.molecule.JOEMol: each vector contains the atom numbers of a contig fragment the vectors are sorted by size from largest to smallest
findRingAtomsAndBonds() - Method in class joelib.molecule.JOEMol: Description of the Method
findRings(JOEMol, Vector, JOEBitVec, JOEBitVec, int, int) - Static method in class joelib.ring.JOERingSearch
findRings(JOEMol, Vector, JOEBitVec, JOEBitVec, int, int) - Static method in class joelib.util.JHM
findSSSR() - Method in class joelib.molecule.JOEMol: Finds the Smallest Set of Smallest Rings (SSSR).
findSymmetryElements() - Method in class joelib.math.symmetry.Symmetry
findSymmetryElements(boolean) - Method in class joelib.math.symmetry.Symmetry
finished - Variable in class joelib.algo.DFSResult: Description of the Field
fireChange() - Method in class joelib.gui.render.Renderer2DModel: Notifies registered listeners of certain changes that have occurred in this model.
firstBit() - Method in class joelib.util.JOEBitVec: Returns the index of the first bit that is set to true.
firstElement() - Method in class wsi.ra.tool.SortedVector: Returns the first component (the item at index 0) of this vector.
firstLineLoaded - Variable in class joelib.io.types.Flat
fitsAnyRule(JOEMol) - Method in class joelib.smarts.Patty: Returns true if one ore more rules can be assigned.
flag - Variable in class joelib.util.types.Template: Description of the Field
flip(int) - Method in class joelib.util.BitSet14: Sets the bit at the specified index to to the complement of its current value.
flip(int, int) - Method in class joelib.util.BitSet14: Sets each bit from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the complement of its current value.
fold(int) - Method in class joelib.util.JOEBitVec: Description of the Method
forceWriteFormalCharge() - Method in class joelib.io.types.ChemicalMarkupLanguage
forceWriteFormalCharge() - Method in interface joelib.io.types.cml.CMLWriterProperties
format(double) - Method in class wsi.ra.text.DecimalFormatHelper: Formats a double value using the initialized DecimalFormat object.
format(double) - Method in interface wsi.ra.text.DecimalFormatter: A unit test for JUnit
formatDescription(IOType) - Method in class joelib.algo.BFSResult: Description of the Method
formatDescription(IOType) - Method in class joelib.algo.DFSResult: Description of the Method
formatDescription(IOType) - Method in interface joelib.desc.DescResult
formatDescription(IOType) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.APropIntResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.BitResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.BooleanResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DoubleArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DoubleMatrixResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DoubleResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.FloatMatrixResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.IntArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.IntMatrixResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.IntResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.StringArrayResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.result.StringResult: Description of the Method
formatDescription(IOType) - Method in class joelib.desc.types.atompair.AtomPairResult: Description of the Method
frAtom - Variable in class joelib.gui.render.RenderAtom: Fragment render atom.
frMol - Variable in class joelib.gui.render.RenderAtom: Fragment render molecule.
fraLabel - Variable in class joelib.gui.render.RenderAtom
fractionalToCartesian(double[], double[], double[], double[]) - Static method in class joelib.math.CrystalGeometryTools: Method that transforms fractional coordinates into cartesian coordinates.
freeAtomExpr(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
freeBondExpr(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
freePattern(Pattern) - Static method in class joelib.smarts.Pattern: Description of the Method
from - Variable in class joelib.gui.render.FromToAtoms
fromBoolArray(boolean[]) - Method in class joelib.util.JOEBitVec
fromFile(String) - Method in class joelib.process.types.DescBinning: Description of the Method
fromFile(String) - Method in class joelib.process.types.DescStatistic: Description of the Method
fromFileFor(String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
fromFileFor(String) - Method in interface joelib.desc.data.MoleculeCache
fromFileFor(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
fromFileFor(String) - Method in class joelib.process.types.DescBinning
fromFileFor(String) - Method in class joelib.process.types.DescStatistic
fromIntArray(int[]) - Method in class joelib.util.JOEBitVec: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.algo.BFSResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.algo.DFSResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in interface joelib.desc.DescResult
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.APropIntResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.BitResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.BooleanResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DoubleArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DoubleMatrixResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DoubleResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.FloatMatrixResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntMatrixResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.IntResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.StringArrayResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.result.StringResult: Description of the Method
fromPairData(IOType, JOEPairData) - Method in class joelib.desc.types.atompair.AtomPairResult: Description of the Method
fromResource(String, String, Hashtable) - Method in class wsi.ra.io.BatchScriptReplacer: Description of the Method
fromString(IOType, String) - Method in class joelib.algo.BFSResult: Description of the Method
fromString(IOType, String) - Method in class joelib.algo.DFSResult: Description of the Method
fromString(IOType, String) - Method in interface joelib.desc.DescResult
fromString(IOType, String) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.APropIntResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.BitResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.BooleanResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DoubleArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DoubleMatrixResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DoubleResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.FloatMatrixResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.IntArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.IntMatrixResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.IntResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.StringArrayResult: Description of the Method
fromString(IOType, String) - Method in class joelib.desc.result.StringResult: Description of the Method
fromString(LineNumberReader, int) - Static method in class joelib.desc.types.atompair.AtomPair
fromString(LineNumberReader, int) - Static method in class joelib.desc.types.atompair.AtomPairAtomType
fromString(IOType, String) - Method in class joelib.desc.types.atompair.AtomPairResult: Description of the Method
fromString(String) - Method in class joelib.process.filter.NativeValueFilter
fromString(String) - Method in class joelib.process.filter.SMARTSFilter
fromString(String, boolean) - Method in class joelib.process.filter.SMARTSFilter
fromString(String) - Method in class joelib.util.JOEBitVec: Reads this bit vector from a String.
fromVectorWithIntArray(Vector) - Method in class joelib.util.JOEBitVec

G

GCPredictor - class joelib.algo.contribution.GCPredictor.: Value prediction based on a group contribution model.
GCPredictor() - Constructor for class joelib.algo.contribution.GCPredictor
GIF - class joelib.io.types.GIF.: Writer for a CompuServe Graphics Interchange (GIF) image.
GIF() - Constructor for class joelib.io.types.GIF
GRADIENT_STEP_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
GREATER - Static variable in class joelib.process.filter.NativeValueFilter
GREATER - Static variable in class joelib.process.filter.SMARTSFilter
GREATER_EQUAL - Static variable in class joelib.process.filter.NativeValueFilter
GREATER_EQUAL - Static variable in class joelib.process.filter.SMARTSFilter
GasteigerMarsili - class joelib.molecule.charge.GasteigerMarsili.: Partial charge calculation.
GasteigerMarsili() - Constructor for class joelib.molecule.charge.GasteigerMarsili: Constructor for the partial charge calculation.
GasteigerState - class joelib.molecule.charge.GasteigerState.: Stores actual Gasteiger charge state.
GasteigerState() - Constructor for class joelib.molecule.charge.GasteigerState: Constructor for the GasteigerState object
Gaussian - class joelib.io.types.Gaussian.: Atom representation.
Gaussian() - Constructor for class joelib.io.types.Gaussian
GenericDataHolder - class joelib.molecule.GenericDataHolder.: Holder class of generic data objects for one molecule.
GenericDataHolder(JOEMol, int, int) - Constructor for class joelib.molecule.GenericDataHolder: Constructor for the GenericDataHolder object
GenericDataIterator - class joelib.util.iterator.GenericDataIterator.: Iterator over generic data elements.
GenericDataIterator(Vector, Hashtable) - Constructor for class joelib.util.iterator.GenericDataIterator: Constructor for the GenericDataIterator object
GeoVector3D - class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D.: A geometric vector class that provides vector computations: length, normalize, dot and cross.
GeoVector3D() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Default constructor, all component are 0.0
GeoVector3D(double, double, double) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Full constructor
GeoVector3D(Point3D, Point3D) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: constructor
GeoVector3D(GeoVector3D) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: copy constructor
GeomDistanceMatrix - class joelib.desc.types.GeomDistanceMatrix.: Geometrical distance matrix.
GeomDistanceMatrix() - Constructor for class joelib.desc.types.GeomDistanceMatrix: Constructor for the DistanceMatrix object
GeometricalDiameter - class joelib.desc.types.GeometricalDiameter.: Calculates the geometrical diameter.
GeometricalDiameter() - Constructor for class joelib.desc.types.GeometricalDiameter
GeometricalRadius - class joelib.desc.types.GeometricalRadius.: Calculates the geometrical radius.
GeometricalRadius() - Constructor for class joelib.desc.types.GeometricalRadius
GeometricalShapeCoefficient - class joelib.desc.types.GeometricalShapeCoefficient.: Calculates the geometrical shape coefficient.
GeometricalShapeCoefficient() - Constructor for class joelib.desc.types.GeometricalShapeCoefficient
Geometry - class joelib.gui.molviewer.java3d.math.geometry.Geometry.: A public class that provides mathematical calculation on some geometry entities.
Geometry() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Geometry
GhemicalException - exception joelib.util.ghemical.GhemicalException.: JOELib property exception.
GhemicalException() - Constructor for class joelib.util.ghemical.GhemicalException: Constructor for the DescriptorException object
GhemicalException(String) - Constructor for class joelib.util.ghemical.GhemicalException: Constructor for the DescriptorException object
GhemicalInterface - class joelib.util.ghemical.GhemicalInterface.: This interface class to Ghemical defines some native methods for accessing parts of the Ghemical functionality.
GhemicalTest - class joelib.test.GhemicalTest.: Example for converting molecules.
GhemicalTest() - Constructor for class joelib.test.GhemicalTest
GifEncoder - class Acme.JPM.Encoders.GifEncoder.: Write out an image as a GIF.
GifEncoder(Image, OutputStream) - Constructor for class Acme.JPM.Encoders.GifEncoder
GifEncoder(Image, OutputStream, boolean) - Constructor for class Acme.JPM.Encoders.GifEncoder
GifEncoder(ImageProducer, OutputStream) - Constructor for class Acme.JPM.Encoders.GifEncoder
GifEncoder(ImageProducer, OutputStream, boolean) - Constructor for class Acme.JPM.Encoders.GifEncoder
GlobalTopologicalChargeIndex - class joelib.desc.types.GlobalTopologicalChargeIndex.: Calculates the Topological Charge Index.
GlobalTopologicalChargeIndex() - Constructor for class joelib.desc.types.GlobalTopologicalChargeIndex: Constructor for the GlobalTopologicalChargeIndex object
GraphPotentials - class joelib.desc.types.GraphPotentials.: External rotational symmetry or graph potentials.
GraphPotentials() - Constructor for class joelib.desc.types.GraphPotentials
GraphShapeCoefficient - class joelib.desc.types.GraphShapeCoefficient.: Calculates the graph shape coefficient.
GraphShapeCoefficient() - Constructor for class joelib.desc.types.GraphShapeCoefficient
GrayJPEG - class Acme.JPM.Encoders.GrayJPEG.: DOCUMENT ME!
GrayJPEG() - Constructor for class Acme.JPM.Encoders.GrayJPEG
GroupContributionTest - class joelib.test.GroupContributionTest.: Test for contribution lists for different models (e.g.
GroupContributionTest() - Constructor for class joelib.test.GroupContributionTest
GroupContributions - class joelib.algo.contribution.GroupContributions.: Group contribution informations.
GroupContributions(String) - Constructor for class joelib.algo.contribution.GroupContributions: Constructor for the StringString object
gSVResize(int) - Method in class joelib.molecule.charge.JOEGastChrg: Description of the Method
generate2D(JOEMol) - Static method in class joelib.util.cdk.CDKTools
generateAromElem(int, int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
generateArticleFile(String, String, String) - Method in class jtt.docbook.DocBookArticles
generateDefaultBond() - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
generateDescInfo(String, Class, String, String, String) - Static method in class joelib.desc.DescriptorHelper: Faciliates the generation of a descriptor information.
generateElement(int) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
generateLatexFile(String, String, String) - Method in class jtt.docbook.DocBookEquations
generateSMARTSString(Pattern, OutputStream) - Static method in class joelib.smarts.ParseSmart: Description of the Method
generatedOutput - Variable in class joelib.test.Combine: Description of the Field
generatedOutput - Variable in class joelib.test.Comparison: Description of the Field
generatedOutput - Variable in class joelib.test.Convert: Description of the Field
generatedOutput - Variable in class joelib.test.ConvertSkip: Description of the Field
generatedOutput - Variable in class joelib.test.EuklidianComparison: Description of the Field
generatedOutput - Variable in class joelib.test.GhemicalTest: Description of the Field
genericDataIterator() - Method in class joelib.molecule.GenericDataHolder: Gets the data attribute of the JOEMol object
genericDataIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over the generic data elements of this molecule.
geomOptimizer(boolean) - Method in class joelib.util.ghemical.TestInterface
get(int) - Method in class Acme.IntHashtable
get(Object) - Method in class Acme.IntHashtable
get(int, int) - Method in class joelib.math.Matrix3x3: Description of the Method
get(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
get(double[]) - Method in class joelib.math.XYZVector: Description of the Method
get(double[], int) - Method in class joelib.math.XYZVector: Description of the Method
get(int) - Method in class joelib.util.BitSet14: Returns the value of the bit with the specified index.
get(int, int) - Method in class joelib.util.BitSet14: Returns a new BitSet14 composed of bits from this BitSet14 from fromIndex(inclusive) to toIndex(exclusive).
get(String) - Method in class joelib.util.MoleculeDataCacheHolder
get(int) - Method in class wsi.ra.tool.SortedVector: Returns the element at the specified position in this Vector.
get2DCenter(Vector) - Static method in class joelib.gui.render.RenderHelper: Calculates the center of the given atoms and returns it as a Point2d
get2DCentreOfMass(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get2DDimension(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Returns the java.awt.Dimension of a molecule
get3DCentreOfMass(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
getAPType(AtomProperties[], JOEAtom) - Method in class joelib.desc.types.atompair.AtomPairTypeHolder
getAddingPolicy() - Method in class joelib.desc.DescriptorHelper
getAdditionalInformation(String) - Method in class joelib.jcamp.JCAMPParser: Gets the label infoType.
getAllCharacterData() - Method in class joelib.io.types.cml.elements.ScalarCML
getAllFittingRules(JOEMol) - Method in class joelib.smarts.Patty: Returns Vector of all assigned rules.
getAllTypes() - Static method in class joelib.data.JOEDataType
getAllredRochowEN(int) - Method in class joelib.data.JOEElementTable: Gets the atom electronegativity after Allred and Rochow.
getAllredRochowEN() - Method in class joelib.molecule.JOEElement: Gets the atom electronegativity after Allred and Rochow.
getAngle(double, double) - Static method in class joelib.gui.render.RenderHelper
getAppender() - Method in class joelib.gui.util.JLog4JPanel: Method declaration
getArguments() - Method in class joelib.ext.ExternalInfo: Gets the arguments attribute of the ExternalInfo object
getArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the array attribute of the DynamicArrayResult object
getArray(double[]) - Method in class joelib.math.Matrix3x3: Gets the array attribute of the Matrix3x3 object
getArrayStatistic() - Method in class wsi.ra.tool.ArrayBinning: Gets the descriptorStatistic attribute of the DescStatistic object
getArrowColor() - Method in class joelib.gui.render.Renderer2DModel
getArrowOffset() - Method in class joelib.gui.render.Renderer2DModel
getArrowSize() - Method in class joelib.gui.render.Renderer2DModel
getArrows() - Method in class joelib.gui.render.Renderer2DModel
getAtom() - Method in class joelib.data.JOEExternalBond: Gets the atom attribute of the JOEExternalBond object
getAtom(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtoms: Returns atom at specified index
getAtom(JOEAtom) - Method in class joelib.gui.render.RenderingAtoms
getAtom(int) - Method in class joelib.molecule.JOEMol: Gets an atom of the JOEMol object Atom index must be between 1 to numAtoms() .
getAtom() - Method in class joelib.smiles.JOESmiNode: Gets the atom attribute of the JOESmiNode object
getAtomBackColor(JOEAtom) - Method in class joelib.gui.render.Renderer2DModel
getAtomColor(JOEAtom) - Method in class joelib.molecule.types.AtomPropertyColoring
getAtomContainer() - Method in class joelib.gui.render.MoleculeViewer2D: Returns the AtomContainer which is being displayed
getAtomForeColor(JOEAtom) - Method in class joelib.gui.render.Renderer2DModel
getAtomFromId(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return an atom in this molecule whose id matches the input id
getAtomID(JOEAtom) - Method in class joelib.molecule.JOEResidue
getAtomIdToIndex() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return atomIdToIndex
getAtomIdx() - Method in class joelib.molecule.JOERTree: Gets the atom index of this atom tree node.
getAtomPropDescs() - Method in class joelib.desc.DescriptorHelper: Gets the names of all available AtomProperties descriptors.
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.SimpleDynamicAtomProperty: Gets the dynamic atom property values.
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomInAcceptor
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomInAromaticSystem
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomInConjEnvironment
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomInDonAcc
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomInDonor
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomInRing
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomInTerminalCarbon
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomIsNegative
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomIsPositive
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomMass
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomValence
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.AtomVanDerWaalsVolume
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.ConjugatedTopologicalDistance
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.ElectronAffinity
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.ElectronegativityPauling
getAtomPropertiesArray(JOEMol) - Method in class joelib.desc.types.IntrinsicState
getAtomPropertyColoring() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule
getAtomRadius() - Method in class joelib.gui.render.Renderer2DModel: XXX No idea what this is about
getAtomType1() - Method in class joelib.desc.types.atompair.AtomPair
getAtomType2() - Method in class joelib.desc.types.atompair.AtomPair
getAtomicMass() - Method in class joelib.molecule.JOEAtom
getAtomicNum(String) - Method in class joelib.data.JOEElementTable: Gets the atomicNum attribute of the JOEElementTable object
getAtomicNum() - Method in class joelib.molecule.JOEAtom: Gets the atomic number of the JOEAtom object.
getAtomicNum() - Method in class joelib.molecule.JOEElement: Gets the atomicNum attribute of the JOEElement object
getAtomicNum(int) - Method in class joelib.smarts.JOESmartsPattern: Gets the atomicNum attribute of the JOESmartsPattern object
getAtoms() - Method in class joelib.ring.JOERing: Returns all atom indexes of atoms which are contained in this ring.
getAttribute() - Method in class joelib.data.JOEGenericData: Gets the attribute attribute of the JOEGenericData object
getAttribute() - Method in class joelib.process.filter.NativeValueFilter
getAttributeNames(Hashtable) - Static method in class joelib.algo.datamining.weka.APWekaHelper
getAttributeValues(Hashtable) - Static method in class joelib.algo.datamining.weka.APWekaHelper
getAxes() - Method in class joelib.math.symmetry.Symmetry: Gets the normal axis of the molecule.
getBO() - Method in class joelib.molecule.JOEBond: Gets the bond order for this bond.
getBORad(int) - Method in class joelib.data.JOEElementTable: Gets the bORad attribute of the JOEElementTable object
getBack() - Method in class wsi.ra.tool.Deque: Returns the back DequeNode of this stack.
getBackColor() - Method in class joelib.gui.render.Renderer2DModel: Returns the background color
getBadOptimization() - Method in class joelib.math.symmetry.Symmetry
getBeginAtom() - Method in class joelib.molecule.JOEBond: Gets the beginAtom attribute of the JOEBond object
getBeginAtomIdx() - Method in class joelib.molecule.JOEBond: Gets the beginAtomIdx attribute of the JOEBond object
getBestAlignmentForLabel(RenderingAtoms, JOEAtom) - Static method in class joelib.gui.render.RenderHelper: Determines the best alignment for the label of an atom in 2D space.
getBgn() - Method in class joelib.data.JOEVirtualBond: Gets the bgn attribute of the JOEVirtualBond object
getBinaryValue() - Method in interface joelib.desc.BinaryValue
getBinaryValue() - Method in class joelib.desc.result.BitArrayResult: Gets the double attribute of the DoubleResult object
getBinaryValue() - Method in class joelib.desc.result.BitResult
getBinaryValue() - Method in class joelib.desc.result.IntBitArrayResult: Gets the double attribute of the DoubleResult object
getBinning(int, boolean) - Method in class joelib.algo.datamining.weka.MolInstancesCache: Generates a hashtable containg one ArrayBinning Object for each Attribute
getBinning(int) - Method in class joelib.algo.datamining.weka.MolInstancesCache
getBinning(int) - Method in interface joelib.desc.data.MoleculeCache
getBinning(int, boolean) - Method in interface joelib.desc.data.MoleculeCache
getBinning(int) - Method in class joelib.desc.data.MoleculesDescriptorMatrix
getBinning(int, boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
getBlockData() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the data of this JCAMP block.
getBlockID() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the ID of this JCAMP block.
getBlockType() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the type of this JCAMP block.
getBoRad() - Method in class joelib.molecule.JOEElement: Gets the boRad attribute of the JOEElement object
getBond() - Method in class joelib.data.JOEExternalBond: Gets the bond attribute of the JOEExternalBond object
getBond(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Returns bond at specified index
getBond(JOEAtom) - Method in class joelib.molecule.JOEAtom: Gets the bond attribute of the JOEAtom object
getBond(int) - Method in class joelib.molecule.JOEMol: Gets a bond of the JOEMol object.
getBond(int, int) - Method in class joelib.molecule.JOEMol: Gets the bond attribute of the JOEMol object Atom index must be between 1 to numAtoms() .
getBond(JOEAtom, JOEAtom) - Method in class joelib.molecule.JOEMol: Gets the bond attribute of the JOEMol object
getBond(IntIntInt, int) - Method in class joelib.smarts.JOESmartsPattern: Gets the bond attribute of the JOESmartsPattern object
getBondColor(JOEBond) - Method in class joelib.gui.render.Renderer2DModel
getBondCoordinates(JOEBond) - Static method in class joelib.gui.render.RenderHelper: Writes the coordinates of the atoms participating the given bond into an array.
getBondDistance() - Method in class joelib.gui.render.Renderer2DModel: Returns the distance between two lines in a double or triple bond
getBondExprIndex(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Gets the bondExprIndex attribute of the ParseSmart class
getBondFromId(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return a bond in this molecule whose id matches the input id
getBondLeafIndex(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Gets the bondLeafIndex attribute of the ParseSmart class
getBondLength() - Method in class joelib.gui.render.Renderer2DModel: Returns the length of a bond line.
getBondOrder() - Method in class joelib.molecule.JOEBond: Gets the bond order for this bond.
getBondPropDescs() - Method in class joelib.desc.DescriptorHelper: Gets the names of all available BondProperties descriptors.
getBondWidth() - Method in class joelib.gui.render.Renderer2DModel: Returns the thickness of a bond line.
getBonds() - Method in class joelib.molecule.JOEAtom: Returns a Vector for all bonds in this atom.
getBonds() - Method in class joelib.ring.JOERing
getBoolean() - Method in class joelib.desc.result.BooleanResult: Gets the double attribute of the DoubleResult object
getBooleanArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the booleanArray attribute of the DynamicArrayResult object
getBooleanValue(JOEMol) - Method in class joelib.desc.SimpleBooleanDesc: Gets the boolean descriptor value.
getBurdenEigenvalues(JOEMol, String, double) - Static method in class joelib.desc.types.BurdenEigenvalues
getBurdenEigenvalues(JOEMol, String[], double[]) - Static method in class joelib.desc.types.WeightedBurdenEigenvalues
getBytesFromResourceLocation(String) - Method in class wsi.ra.tool.ResourceLoader: Gets the byte data from a file at the given resource location.
getCIdx() - Method in class joelib.molecule.JOEAtom: Gets the cIdx attribute of the JOEAtom object
getCMLProperties() - Method in class joelib.desc.result.BitArrayResult
getCMLProperties() - Method in class joelib.desc.result.BitResult
getCMLProperties() - Method in class joelib.desc.result.BooleanResult
getCMLProperties() - Method in class joelib.desc.result.DoubleArrayResult
getCMLProperties() - Method in class joelib.desc.result.DoubleMatrixResult
getCMLProperties() - Method in class joelib.desc.result.DoubleResult
getCMLProperties() - Method in class joelib.desc.result.DynamicArrayResult
getCMLProperties() - Method in class joelib.desc.result.FloatMatrixResult
getCMLProperties() - Method in class joelib.desc.result.IntArrayResult
getCMLProperties() - Method in class joelib.desc.result.IntBitArrayResult
getCMLProperties() - Method in class joelib.desc.result.IntMatrixResult
getCMLProperties() - Method in class joelib.desc.result.IntResult
getCMLProperties() - Method in class joelib.desc.result.StringArrayResult
getCMLProperties() - Method in class joelib.desc.result.StringResult
getCMLProperties() - Method in interface joelib.io.types.cml.ResultCMLProperties
getCMLversion() - Method in class joelib.io.types.ChemicalMarkupLanguage
getCMLversion() - Method in interface joelib.io.types.cml.CMLWriterProperties
getCRings() - Method in class joelib.gui.render.Renderer2DModel
getChain() - Method in class joelib.molecule.JOEResidue
getChainNum() - Method in class joelib.molecule.JOEResidue
getCharNumber() - Method in class cformat.ScanfReader: Gets the current character number (equal to the number of characters that have been consumed by the stream).
getCharge() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the atomic charge
getCharge(int) - Method in class joelib.smarts.JOESmartsPattern: Gets the charge attribute of the JOESmartsPattern object
getCheck() - Method in class joelib.math.symmetry.PointGroup
getChiralFlag(AtomExpr) - Static method in class joelib.smarts.ParseSmart: Gets the chiralFlag attribute of the ParseSmart class
getChiralStereo(JOESmiNode, StringBuffer) - Method in class joelib.smiles.JOEMol2Smi: Gets the chiralStereo attribute of the JOEMol2Smi object
getCisTransFrom2D3D(JOEBond) - Static method in class joelib.util.IsomerismDetection: Checks bonds for cis/trans isomerism using 2D/3D informations.
getCisTransFrom2D3D(JOEBond, boolean) - Static method in class joelib.util.IsomerismDetection: Checks bonds for cis/trans isomerism using 2D/3D informations.
getClosestAtom(int, int, RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Returns the atom of the given molecule that is closest to the given coordinates.
getClosureAtoms(JOEAtom, Vector) - Method in class joelib.smiles.JOEMol2Smi
getClosureDigits(JOEAtom) - Method in class joelib.smiles.JOEMol2Smi
getColor(int) - Method in class joelib.data.JOEElementTable: Gets the color attribute of the JOEElementTable object
getColor() - Method in class joelib.molecule.JOEElement: Gets the color attribute of the JOEElement object
getComment() - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Return comment
getComment() - Method in class joelib.process.types.DescSelectionWriter: Gets the comment attribute of the DescSelectionWriter object
getConformer(int) - Method in class joelib.molecule.JOEMol: Gets the conformer attribute of the JOEMol object
getConformers() - Method in class joelib.molecule.JOEMol: Returns a Vector of all conformer coordinates (double[] values).
getConjRingColor() - Method in class joelib.gui.render.Renderer2DModel
getConnection() - Method in class wsi.ra.database.DatabaseConnection
getCoordinate() - Method in class joelib.molecule.JOEAtom: Gets the coordinate attribute of the JOEAtom object
getCoordinateIdx() - Method in class joelib.molecule.JOEAtom: Gets the coordinateIdx attribute of the JOEAtom object.
getCoordinates() - Method in class joelib.molecule.JOEMol: Gets the coordinate array of this molecule.
getCorrelationCoefficient(double[], double[]) - Static method in class wsi.ra.tool.StatisticUtils: Returns the correlation coefficient r^2.
getCovalentRad(int) - Method in class joelib.data.JOEElementTable: Gets the covalentRad attribute of the JOEElementTable object
getCovalentRad() - Method in class joelib.molecule.JOEElement: Gets the covalentRad attribute of the JOEElement object
getCurrentValence(JOEAtom) - Static method in class joelib.util.JHM: Gets the currentValence attribute of the JHM class
getDFFVector(JOEMol, Vector, JOEBitVec) - Static method in class joelib.util.JHM
getDSE(ArrayBinning, ArrayBinning) - Static method in class wsi.ra.tool.ArrayBinning: Gets the differential shannon entropy.
getDXEntry(int) - Method in class joelib.jcamp.JCAMPData
getData() - Method in class joelib.data.JOECommentData: Gets the data attribute of the JOECommentData object
getData() - Method in class joelib.data.JOERgroupData: Gets the Rgroup informations.
getData() - Method in class joelib.jcamp.LabelData
getData(JOEDataType) - Method in class joelib.molecule.GenericDataHolder: Gets the data attribute of the GenericDataHolder object
getData(String, boolean) - Method in class joelib.molecule.GenericDataHolder: Gets the data attribute of the GenericDataHolder object
getData(JOEDataType) - Method in class joelib.molecule.JOEMol: Returns the first data entry of the given data type.
getData(String) - Method in class joelib.molecule.JOEMol: Returns the data entry with the given name, if multiple data entries exists only the first one is taken.
getData(String, boolean) - Method in class joelib.molecule.JOEMol: Returns the data entry with the given name, if multiple data entries exists only the first one is taken.
getData() - Method in class joelib.ring.JOERingData
getDataDescription() - Method in class joelib.desc.result.DynamicArrayResult: Gets the dataDescription attribute of the DynamicArrayResult object
getDataInLine(String) - Static method in class joelib.jcamp.JCAMPDataBlock: Gets the 'Label Data Record'-data of the actual line.
getDataType() - Method in class joelib.data.JOEGenericData: Gets the dataType attribute of the JOEGenericData object
getDataType() - Method in class joelib.io.types.cml.elements.ScalarCML
getDataType() - Method in class joelib.jcamp.JCAMPParser: Gets the data type of this data set.
getDataUnit() - Method in class joelib.desc.result.DynamicArrayResult: Gets the dataUnit attribute of the DynamicArrayResult object
getDefaultAtoms() - Method in class joelib.desc.AtomsCounter: Gets the default atoms to calculate.
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfB: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfBr: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfC: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfCl: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfF: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfHal: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfI: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfN: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfO: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfP: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAtoms() - Method in class joelib.desc.types.NumberOfS: Gets the defaultAtoms attribute of the NumberOfC object
getDefaultAttr() - Method in class joelib.data.JOEDataType: Gets the defaultAttr attribute of the JOEDataType object
getDefaultDelimiter() - Static method in class joelib.io.types.ChemicalMarkupLanguage
getDefaultHeight() - Method in class joelib.gui.render.Mol2Image
getDefaultProperty() - Method in class joelib.util.JOEProperty
getDefaultSMARTS() - Method in class joelib.desc.SMARTSCounter: Gets the default number of SMARTS pattern in the molecule.
getDefaultSMARTS() - Method in class joelib.desc.types.AcidicGroups
getDefaultSMARTS() - Method in class joelib.desc.types.AliphaticOHGroups
getDefaultSMARTS() - Method in class joelib.desc.types.AromaticOHGroups
getDefaultSMARTS() - Method in class joelib.desc.types.BasicGroups
getDefaultSMARTS() - Method in class joelib.desc.types.HBA1
getDefaultSMARTS() - Method in class joelib.desc.types.HBA2
getDefaultSMARTS() - Method in class joelib.desc.types.HBD1
getDefaultSMARTS() - Method in class joelib.desc.types.HBD2
getDefaultSMARTS() - Method in class joelib.desc.types.HydrophobicGroups
getDefaultSMARTS() - Method in class joelib.desc.types.NO2Groups
getDefaultSMARTS() - Method in class joelib.desc.types.OSOGroups
getDefaultSMARTS() - Method in class joelib.desc.types.SO2Groups
getDefaultSMARTS() - Method in class joelib.desc.types.SOGroups
getDefaultWidth() - Method in class joelib.gui.render.Mol2Image
getDelimiter() - Method in class joelib.process.types.DescSelectionWriter: Gets the delimiter attribute of the DescSelectionWriter object
getDepth() - Method in class joelib.jcamp.JCAMPDataBlock: Gets the depth of this JCAMP block.
getDequeIterator() - Method in class wsi.ra.tool.Deque: Returns an DequeIterator for this stack, which starts with the front DequeNode.
getDescBinning(IOType, String) - Static method in class joelib.process.types.DescBinning: Gets the descBinning attribute of the DescBinning class
getDescBinning(JOEMolVector) - Static method in class joelib.process.types.DescBinning: Gets the descBinning attribute of the DescBinning class
getDescBinning(IOType, String, int) - Static method in class joelib.process.types.DescBinning
getDescContainsNaN() - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescContainsNaN() - Method in interface joelib.desc.data.MoleculeCache
getDescContainsNaN() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets the descContainsNaN attribute of the MoleculesDescriptorMatrix object
getDescFromMolByIdentifier(String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescFromMolByIdentifier(String) - Method in interface joelib.desc.data.MoleculeCache
getDescFromMolByIdentifier(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all descriptors from molecule by identifier.
getDescFromMolByIndex(int) - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescFromMolByIndex(int) - Method in interface joelib.desc.data.MoleculeCache
getDescFromMolByIndex(int) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all descriptors from molecule by molecule index.
getDescFromMolByName(String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescFromMolByName(String) - Method in interface joelib.desc.data.MoleculeCache
getDescFromMolByName(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all descriptors from a molecule.
getDescInfo() - Method in class joelib.algo.APropertyBFS: Description of the Method
getDescInfo() - Method in class joelib.algo.BFS: Description of the Method
getDescInfo() - Method in class joelib.algo.DFS: Description of the Method
getDescInfo() - Method in class joelib.desc.AtomsCounter: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in interface joelib.desc.Descriptor: Gets the descriptor informations for this descriptor.
getDescInfo(String) - Method in class joelib.desc.DescriptorHelper: Returns a descriptor information for the given descriptor name.
getDescInfo() - Method in class joelib.desc.SMARTSCounter: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in class joelib.desc.SimpleBooleanDesc: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in class joelib.desc.SimpleDoubleAtomProperty: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in class joelib.desc.SimpleDoubleDesc: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in class joelib.desc.SimpleDynamicAtomProperty: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in class joelib.desc.SimpleIntDesc: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in class joelib.desc.SimpleStringAtomProperty: Gets the descriptor informations for this descriptor.
getDescInfo() - Method in class joelib.desc.types.APropertyDistanceMatrix: Description of the Method
getDescInfo() - Method in class joelib.desc.types.Autocorrelation: Description of the Method
getDescInfo() - Method in class joelib.desc.types.BCUT: Description of the Method
getDescInfo() - Method in class joelib.desc.types.BurdenEigenvalues: Description of the Method
getDescInfo() - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Description of the Method
getDescInfo() - Method in class joelib.desc.types.ConjElectroTopolState: Description of the Method
getDescInfo() - Method in class joelib.desc.types.DistanceDistanceMatrix: Description of the Method
getDescInfo() - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
getDescInfo() - Method in class joelib.desc.types.ElectrogeometricalState: Description of the Method
getDescInfo() - Method in class joelib.desc.types.ElectrotopologicalState: Description of the Method
getDescInfo() - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
getDescInfo() - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Description of the Method
getDescInfo() - Method in class joelib.desc.types.HeavyBonds: Description of the Method
getDescInfo() - Method in class joelib.desc.types.HeteroCycles: Description of the Method
getDescInfo() - Method in class joelib.desc.types.RadialDistributionFunction: Description of the Method
getDescInfo() - Method in class joelib.desc.types.SSKey3DS: Description of the Method
getDescInfo() - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Description of the Method
getDescInfo() - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Description of the Method
getDescInfo() - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Description of the Method
getDescNames() - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescNames() - Method in interface joelib.desc.data.MoleculeCache
getDescNames() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all descriptor names.
getDescResult(String) - Method in class joelib.desc.ResultFactory: Gets the descResult attribute of the ResultFactory class
getDescStatistic() - Method in class joelib.process.types.DescBinning: Gets the descStatistic attribute of the DescBinning object
getDescStatistic(JOEMolVector) - Static method in class joelib.process.types.DescStatistic
getDescStatistic(IOType, String) - Static method in class joelib.process.types.DescStatistic: Gets the descStatistic attribute of the DescStatistic class
getDescValues(String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescValues(String[], int[], int[]) - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescValues(String[]) - Method in class joelib.algo.datamining.weka.MolInstancesCache
getDescValues(String) - Method in interface joelib.desc.data.MoleculeCache
getDescValues(String[]) - Method in interface joelib.desc.data.MoleculeCache
getDescValues(String[], int[], int[]) - Method in interface joelib.desc.data.MoleculeCache
getDescValues(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all values for a specific descriptor.
getDescValues(String[]) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all values for a set of descriptor.
getDescValues(String[], int[], int[]) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all values for a set of descriptor.
getDescription() - Method in class joelib.algo.APropertyBFS: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.algo.BFS: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.algo.DFS: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.AtomsCounter: Gets the descriptor description.
getDescription() - Method in interface joelib.desc.Descriptor: Gets the descriptor description.
getDescription() - Method in class joelib.desc.SMARTSCounter: Gets the descriptor description.
getDescription() - Method in class joelib.desc.SimpleBooleanDesc: Gets the descriptor description.
getDescription() - Method in class joelib.desc.SimpleDoubleAtomProperty: Gets the descriptor description.
getDescription() - Method in class joelib.desc.SimpleDoubleDesc: Gets the descriptor description.
getDescription() - Method in class joelib.desc.SimpleDynamicAtomProperty: Gets the descriptor description.
getDescription() - Method in class joelib.desc.SimpleIntDesc: Gets the descriptor description.
getDescription() - Method in class joelib.desc.SimpleStringAtomProperty: Gets the descriptor description.
getDescription() - Method in class joelib.desc.types.APropertyDistanceMatrix: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.Autocorrelation: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.BCUT: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.BurdenEigenvalues: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.ConjElectroTopolState: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.DistanceDistanceMatrix: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.DistanceMatrix: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.ElectrogeometricalState: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.ElectrotopologicalState: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.GeomDistanceMatrix: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.HeavyBonds: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.HeteroCycles: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.RadialDistributionFunction: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.SSKey3DS: Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Sets the descriptionFile attribute of the Descriptor object Gets the description attribute of the Descriptor object
getDescription() - Method in class joelib.gui.util.MolFileFilter: Returns the human readable description of this filter.
getDescriptionFile() - Method in class joelib.desc.DescDescription: Gets base file to the descriptor description files.
getDescriptionFile() - Method in interface joelib.ext.External
getDescriptionFile() - Method in class joelib.ext.SimpleExternalProcess: Gets the descriptionFile attribute of the Corina object
getDescriptionFile() - Method in class joelib.util.types.BasicFactoryInfo: Gets base directory for the descriptorion for the class.
getDescriptor(String) - Static method in class joelib.desc.DescriptorFactory: Gets a descriptor calculation class instance.
getDescriptor(String, Map) - Static method in class joelib.desc.DescriptorFactory: Gets a descriptor calculation class instance.
getDescriptorBinning(String) - Method in class joelib.process.types.DescBinning: Gets the descriptorBinning attribute of the DescBinning object
getDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic: Gets the descriptorStatistic attribute of the DescStatistic object
getDescriptors() - Method in class joelib.process.types.DescBinning: Gets the descriptors attribute of the DescBinning object
getDescriptors() - Method in class joelib.process.types.DescStatistic: Gets the descriptors attribute of the DescStatistic object
getDictRef() - Method in class joelib.io.types.cml.elements.ScalarCML
getDimensionFromType(String) - Static method in class joelib.desc.DescriptorInfo: Gets required descriptor dimension.
getDistance(Object) - Method in interface joelib.desc.DistanceMetricValue
getDistance() - Method in class joelib.desc.types.atompair.AtomPair
getDistance(Object) - Method in class joelib.desc.types.atompair.AtomPairResult
getDistance(Object, Object) - Method in class joelib.desc.types.atompair.BasicAPDistanceMetric
getDistance(Object, Object) - Method in interface joelib.math.similarity.DistanceMetric
getDistanceMetric(String) - Static method in class joelib.math.similarity.DistanceMetricHelper
getDistanceValues() - Method in class joelib.process.types.DistanceCalculation
getDistinct(Vector) - Static method in class joelib.algo.datamining.weka.APWekaHelper
getDouble() - Method in class joelib.desc.result.APropDoubleResult: Gets the double attribute of the DoubleResult object
getDouble() - Method in class joelib.desc.result.DoubleResult: Gets the double attribute of the DoubleResult object
getDouble(Properties, String, double) - Static method in class wsi.ra.tool.PropertyHolder: Gets the double attribute of the PropertyHolder class
getDouble(Properties, String, double, double, double) - Static method in class wsi.ra.tool.PropertyHolder: Gets the double attribute of the PropertyHolder class
getDouble(Object, String, double) - Method in class wsi.ra.tool.PropertyHolder: Method getDouble.
getDouble(Object, String, double, double, double) - Method in class wsi.ra.tool.PropertyHolder: Method getDouble.
getDouble(Properties, Object, String, double) - Static method in class wsi.ra.tool.PropertyHolder: Method getDouble.
getDouble(Properties, Object, String, double, double, double) - Static method in class wsi.ra.tool.PropertyHolder: Method getDouble.
getDoubleArray() - Method in class joelib.desc.result.DoubleArrayResult: Gets the double attribute of the IntArrayResult object
getDoubleArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the doubleArray attribute of the DynamicArrayResult object
getDoubleAtomProperties(JOEMol) - Method in class joelib.desc.SimpleDoubleAtomProperty: Gets the double atom property values.
getDoubleAtomProperties(JOEMol) - Method in class joelib.desc.types.GraphPotentials
getDoubleAtomProperties(JOEMol) - Method in class joelib.molecule.charge.GasteigerMarsili
getDoubleNV() - Method in interface joelib.desc.NativeValue
getDoubleNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the doubleNV attribute of the APropDoubleResult object
getDoubleNV() - Method in class joelib.desc.result.APropIntResult: Gets the doubleNV attribute of the APropIntResult object
getDoubleNV() - Method in class joelib.desc.result.BooleanResult: Gets the doubleNV attribute of the IntResult object
getDoubleNV() - Method in class joelib.desc.result.DoubleResult: Gets the doubleNV attribute of the DoubleResult object
getDoubleNV() - Method in class joelib.desc.result.IntResult: Gets the doubleNV attribute of the IntResult object
getDoubleValue(JOEMol) - Method in class joelib.desc.SimpleDoubleDesc: Gets the double descriptor value.
getDoubleValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getDoubleValue(int) - Method in class joelib.desc.result.AtomDoubleResult
getDoubleValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the doubleValue attribute of the AtomDynamicResult object
getDoubleValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the doubleValue attribute of the AtomIntResult object
getDoubleValue(int) - Method in class joelib.desc.result.AtomStringResult: Gets the doubleValue attribute of the AtomIntResult object
getDoubleValue(int) - Method in class joelib.desc.result.BondDoubleResult
getDoubleValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the doubleValue attribute of the AtomDynamicResult object
getDoubleValue(int) - Method in class joelib.desc.result.BondIntResult
getDoubleValue(JOEMol) - Method in class joelib.desc.types.FractionRotatableBonds: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GeometricalDiameter: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GeometricalRadius: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GeometricalShapeCoefficient: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.GraphShapeCoefficient: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.KierShape1: Gets the doubleValue attribute of the KierShape1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.KierShape2: Gets the doubleValue attribute of the KierShape2 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.KierShape3: Gets the doubleValue attribute of the KierShape3 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.LogP: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.MolarRefractivity: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.MolecularWeight: Gets the doubleValue attribute of the KierShape1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.PolarSurfaceArea: Gets the defaultAtoms attribute of the NumberOfC object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.ZagrebIndex1: Gets the doubleValue attribute of the ZagrebIndex1 object
getDoubleValue(JOEMol) - Method in class joelib.desc.types.ZagrebIndex2
getDoubleValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getDoubleValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the doubleValue attribute of the AtomProperties object
getDoubleValue(int) - Method in interface joelib.molecule.types.BondProperties
getENAllredRochow() - Method in class joelib.molecule.JOEAtom: Gets the atom electronegativity after Allred and Rochow.
getENPauling() - Method in class joelib.molecule.JOEAtom: Gets the atom electronegativity after Pauling.
getENSanderson() - Method in class joelib.molecule.JOEAtom: Gets the atom electronegativity after Pauling.
getElectronAffinity(int) - Method in class joelib.data.JOEElementTable: Gets the electronAffinity attribute of the JOEElement object
getElectronAffinity() - Method in class joelib.molecule.JOEAtom: Gets the electronAffinity attribute of the JOEElement object
getElectronAffinity() - Method in class joelib.molecule.JOEElement: Gets the electronAffinity attribute of the JOEElement object
getEnd() - Method in class joelib.data.JOEVirtualBond: Gets the end attribute of the JOEVirtualBond object
getEndAtom() - Method in class joelib.molecule.JOEBond: Gets the endAtom attribute of the JOEBond object
getEndAtomIdx() - Method in class joelib.molecule.JOEBond: Gets the endAtomIdx attribute of the JOEBond object
getEnergy() - Method in class joelib.molecule.JOEMol: Gets the energy attribute of the JOEMol object
getEnergy() - Method in class joelib.util.ghemical.GhemicalInterface
getEquibLength() - Method in class joelib.molecule.JOEBond: Gets the equibLength attribute of the JOEBond object
getErrorBasis() - Method in class joelib.io.types.cml.elements.ScalarCML
getErrorValue() - Method in class joelib.io.types.cml.elements.ScalarCML
getEulerTranslation(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b rotation and \b translation (applied in that order) corresponding to this objects transformation.
getExactMass(int) - Method in class joelib.data.JOEIsotopeTable: Return the exact masss of the isotope.
getExactMass(int, int) - Method in class joelib.data.JOEIsotopeTable: Return the exact masss of the isotope.
getExactMass() - Method in class joelib.molecule.JOEAtom
getExactMass() - Method in class joelib.molecule.JOEMol: Gets mass given by isotopes (or most abundant isotope as necessary).
getExecutable() - Method in class joelib.ext.ExternalInfo: Gets the executable for the actual operating system.
getExecutable(String) - Method in class joelib.ext.ExternalInfo: Gets the executable attribute of the ExternalInfo object
getExprOrder(BondExpr) - Static method in class joelib.smarts.ParseSmart: Gets the exprOrder attribute of the ParseSmart class
getExtension(File) - Method in class joelib.gui.util.MolFileFilter: Return the extension portion of the file's name .
getExteriorElectrons(int) - Method in class joelib.data.JOEElementTable: Gets the exteriorElectrons attribute of the JOEElementTable object
getExteriorElectrons() - Method in class joelib.molecule.JOEElement: Gets the exteriorElectrons attribute of the JOEElement object
getExternal(String) - Method in class joelib.ext.ExternalFactory: Gets the external attribute of the ExternalFactory class
getExternalInfo() - Method in interface joelib.ext.External
getExternalInfo(String) - Method in class joelib.ext.ExternalFactory: Gets the externalInfo attribute of the ExternalFactory object
getExternalInfo() - Method in class joelib.ext.SimpleExternalProcess: Gets the externalInfo attribute of the Corina object
getExternalSubset(String, String) - Method in class joelib.io.types.cml.CMLResolver: Not implemented: always returns null.
getFileList() - Method in class jtt.docbook.DocBookArticles
getFileList() - Method in class jtt.docbook.DocBookEquations
getFileList() - Method in class jtt.docbook.DocBookMolecules
getFileTypes() - Method in class joelib.io.IOTypeHolder: Gets an enumeration with all available file types.
getFilter(String) - Method in class joelib.process.filter.FilterFactory: Gets the external attribute of the ExternalFactory class
getFilterInfo() - Method in class joelib.process.filter.ANDFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.DescriptorFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in interface joelib.process.filter.Filter
getFilterInfo(String) - Method in class joelib.process.filter.FilterFactory: Gets the externalInfo attribute of the ExternalFactory object
getFilterInfo() - Method in class joelib.process.filter.HasAllDataFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.HasDataFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.NOTFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.NativeValueFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.ORFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.RuleOf5Filter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.SMARTSFilter: Gets the processInfo attribute of the DescriptorFilter object
getFilterInfo() - Method in class joelib.process.filter.SelectionFilter: Gets the processInfo attribute of the DescriptorFilter object
getFirstAtom() - Method in class joelib.molecule.JOEMol: Gets the firstAtom attribute of the JOEMol object
getFlags() - Method in class joelib.molecule.JOEBond: Gets the flags attribute of the JOEBond object
getFlags() - Method in class joelib.molecule.JOEMol: Gets the flags attribute of the JOEMol object
getForeColor() - Method in class joelib.gui.render.Renderer2DModel: returns the foreground color for the drawing
getFormalCharge() - Method in class joelib.molecule.JOEAtom: Gets the formal charge of the JOEAtom .
getFragmentation(JOEMol) - Method in class joelib.molecule.fragmentation.ContiguousFragments: Fragments a molecule and single atoms occuring in the molecule are allowed.
getFragmentation(JOEMol, boolean, Vector) - Method in class joelib.molecule.fragmentation.ContiguousFragments: Returns all contiguous fragments of this molecule as single JOEMol objects.
getFragmentation(JOEMol) - Method in interface joelib.molecule.fragmentation.Fragmentation: Fragments a molecule and single atoms occuring in the molecule are allowed.
getFragmentation(JOEMol, boolean) - Method in interface joelib.molecule.fragmentation.Fragmentation
getFragmentation(JOEMol, boolean, Vector) - Method in interface joelib.molecule.fragmentation.Fragmentation
getFragmentation(JOEMol) - Method in class joelib.molecule.fragmentation.SMARTSFragmentation: Fragments a molecule and single atoms occuring in the molecule are allowed.
getFragmentation(JOEMol, boolean, Vector) - Method in class joelib.molecule.fragmentation.SMARTSFragmentation: Fragments the molecule using SMARTS rules.
getFrame() - Method in class joelib.gui.render.MoleculeViewer2D: Gets the Frame attribute of the MoleculeViewer2D object
getFreeElectrons() - Method in class joelib.molecule.JOEAtom: Get the number of free electrons.
getFront() - Method in class wsi.ra.tool.Deque: Returns the front DequeNode of this stack.
getGOAtomPosX(int) - Method in class joelib.util.ghemical.GhemicalInterface
getGOAtomPosY(int) - Method in class joelib.util.ghemical.GhemicalInterface
getGOAtomPosZ(int) - Method in class joelib.util.ghemical.GhemicalInterface
getGTDVector(int[]) - Method in class joelib.molecule.JOEMol: Gets the gTDVector attribute of the JOEMol object
getGradientStep() - Method in class joelib.math.symmetry.Symmetry: Finite step used in numeric gradient evaluation.
getGroup() - Method in class joelib.molecule.JOEElement: Gets the group attribute of the JOEElement object
getGroupContributions(String) - Method in class joelib.data.JOEGroupContribution: Description of the Method
getGroupName() - Method in class joelib.math.symmetry.PointGroup
getHTMLDescription() - Method in class joelib.desc.DescDescription: Gets the HTML description for the descriptor.
getHTMLInfo(double, double) - Method in interface joelib.util.ToolTipInfo: Gets the tool tip text.
getHashcode(JOEMol) - Static method in class joelib.util.database.AbstractDatabase: Sloppy Hashcode which uses only topological informations without E/Z isomerism and S/R chirality.
getHeteroValence() - Method in class joelib.molecule.JOEAtom: Returns the number of heteroatoms connected to an atom.
getHighlightAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the highlighted atoms vector
getHighlightColor() - Method in class joelib.gui.render.Renderer2DModel: Returns the color used for highlighting things in this model
getHighlightRadius() - Method in class joelib.gui.render.Renderer2DModel: Returns the radius around an atoms, for which the atom is marked highlighted if a pointer device is placed within this radius
getHighlightedAtoms() - Method in class joelib.gui.render.Renderer2DModel: Returns the atom currently highlighted
getHighlightedBond() - Method in class joelib.gui.render.Renderer2DModel: Returns the Bond currently highlighted
getHvyValence() - Method in class joelib.molecule.JOEAtom: Returns the number of non-hydrogens connected to an atom.
getHyb() - Method in class joelib.molecule.JOEAtom: Gets the hybridisation of the JOEAtom .
getIOType() - Method in class joelib.gui.util.MolFileFilter
getIOType(String) - Method in class joelib.io.IOTypeHolder: Gets the IOType from a given input/output name.
getId() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Compares this atom with another Returns String representation of Atom Returns id of the atom
getId() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Returns id of the bond
getId() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Draw the molecule recommend to avoid, but to use renderer approach Returns id of this molecule
getIdx() - Method in class joelib.data.JOEExternalBond: Gets the idx attribute of the JOEExternalBond object
getIdx() - Method in class joelib.molecule.JOEAtom: Gets the index number of the JOEAtom object.
getIdx() - Method in class joelib.molecule.JOEBond: Gets the idx attribute of the JOEBond object
getIdx() - Method in class joelib.molecule.JOEResidue
getImplicitValence() - Method in class joelib.molecule.JOEAtom: Gets the implicit valence attribute of the JOEAtom .
getImproperAxes() - Method in class joelib.math.symmetry.Symmetry: Gets the improper axis of the molecule.
getInputType() - Method in class joelib.molecule.JOEMol: Gets the inputType attribute of the JOEMol object
getInt() - Method in class joelib.desc.result.APropIntResult: Gets the double attribute of the DoubleResult object
getInt() - Method in class joelib.desc.result.IntResult: Gets the double attribute of the DoubleResult object
getInt(Properties, String, int, int, int) - Static method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder class
getInt(String) - Method in class wsi.ra.tool.PropertyHolder
getInt(String, int) - Method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder object
getInt(String, int, int, int) - Method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder object
getInt(Properties, String, int) - Static method in class wsi.ra.tool.PropertyHolder: Gets the int attribute of the PropertyHolder class
getInt(Object, String, int) - Method in class wsi.ra.tool.PropertyHolder: Method getInt.
getInt(Object, String, int, int, int) - Method in class wsi.ra.tool.PropertyHolder: Method getInt.
getInt(Properties, Object, String, int) - Static method in class wsi.ra.tool.PropertyHolder: Method getInt.
getInt(Properties, Object, String, int, int, int) - Static method in class wsi.ra.tool.PropertyHolder: Method getInt.
getIntArray() - Method in class joelib.desc.result.DynamicArrayResult: Gets the intArray attribute of the DynamicArrayResult object
getIntArray() - Method in class joelib.desc.result.IntArrayResult: Gets the double attribute of the IntArrayResult object
getIntNV() - Method in interface joelib.desc.NativeValue
getIntNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the intNV attribute of the APropDoubleResult object
getIntNV() - Method in class joelib.desc.result.APropIntResult: Gets the intNV attribute of the APropIntResult object
getIntNV() - Method in class joelib.desc.result.BooleanResult: Gets the intNV attribute of the IntResult object
getIntNV() - Method in class joelib.desc.result.DoubleResult: Gets the intNV attribute of the DoubleResult object
getIntNV() - Method in class joelib.desc.result.IntResult: Gets the intNV attribute of the IntResult object
getIntValue(JOEMol) - Method in class joelib.desc.SimpleIntDesc: Gets the integer descriptor value.
getIntValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getIntValue(int) - Method in class joelib.desc.result.AtomDoubleResult: Constructor for the DoubleResult object
getIntValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the intValue attribute of the AtomDynamicResult object.
getIntValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the intValue attribute of the AtomIntResult object
getIntValue(int) - Method in class joelib.desc.result.AtomStringResult: Gets the intValue attribute of the AtomIntResult object
getIntValue(int) - Method in class joelib.desc.result.BondDoubleResult: Constructor for the DoubleResult object
getIntValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the intValue attribute of the AtomDynamicResult object.
getIntValue(int) - Method in class joelib.desc.result.BondIntResult
getIntValue(JOEMol) - Method in class joelib.desc.types.AromaticBonds: Gets the doubleValue attribute of the KierShape1 object
getIntValue(JOEMol) - Method in class joelib.desc.types.NumberOfAtoms: Gets the doubleValue attribute of the KierShape1 object
getIntValue(JOEMol) - Method in class joelib.desc.types.NumberOfBonds: Gets the doubleValue attribute of the KierShape1 object
getIntValue(JOEMol) - Method in class joelib.desc.types.RotatableBonds: Gets the doubleValue attribute of the KierShape1 object
getIntValue(JOEMol) - Method in class joelib.desc.types.TopologicalDiameter: Gets the defaultAtoms attribute of the NumberOfC object
getIntValue(JOEMol) - Method in class joelib.desc.types.TopologicalRadius: Gets the defaultAtoms attribute of the NumberOfC object
getIntValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getIntValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the intValue attribute of the AtomProperties object
getIntValue(int) - Method in interface joelib.molecule.types.BondProperties
getInversionCenter() - Method in class joelib.math.symmetry.Symmetry: Gets the inversion centre of the molecule.
getIsotope() - Method in class joelib.molecule.JOEAtom: Isotpe value for this atom.
getJCAMPData() - Method in class joelib.io.types.JCAMP
getJCampDataType() - Method in class joelib.jcamp.JCAMPParser: Gets the JCAMP data type of this data set.
getJOEAtom() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom
getJOEBond() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBond
getJOEMol() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule
getKekuleStructure() - Method in class joelib.gui.render.Renderer2DModel
getKernelHash() - Method in class joelib.data.JOEKernel
getKernelID() - Method in class joelib.data.JOEKernel
getKernelInformations() - Method in class joelib.data.JOEKernel
getKernelTitles() - Method in class joelib.data.JOEKernel
getLabel() - Method in class joelib.jcamp.LabelData
getLabelInLine(String) - Static method in class joelib.jcamp.JCAMPDataBlock: Gets the 'Label Data Record'-label of the actual line.
getLassoPoints() - Method in class joelib.gui.render.Renderer2DModel: Returns a set of points constituating a selected region
getLength() - Method in class joelib.jcamp.JCAMPParser: Gets the length of the X and Y array.
getLength() - Method in class joelib.molecule.JOEBond: Gets the length of the JOEBond object.
getLineCounter() - Method in class joelib.data.SoftCodedKernelBase: Gets the lineCounter attribute of the JOEGlobalDataBase object
getLineNumber() - Method in class cformat.ScanfReader: Gets the current line number.
getLoadFileChooser() - Method in class joelib.gui.util.MolFileChooser
getLookAheadChar() - Method in class cformat.ScanfReader: Returns the look-ahead character.
getLookup() - Static method in class joelib.gui.molviewer.java3d.util.CentralLookup: Gets the lookup attribute of the CentralLookup class
getMapList() - Method in class joelib.smarts.JOESmartsPattern: Get list of matching atoms.
getMass(int) - Method in class joelib.data.JOEElementTable: Gets the mass attribute of the JOEElementTable object
getMass() - Method in class joelib.molecule.JOEElement: Gets the mass attribute of the JOEElement object
getMaterial(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: get the material for atom a*
getMatrix() - Method in class joelib.algo.datamining.weka.MolInstancesCache
getMatrix() - Method in interface joelib.desc.data.MoleculeCache
getMatrix() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all stored descriptor values for all molecules.
getMatrix3D() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return 3D transformation matrix
getMax() - Method in class joelib.io.types.cml.elements.ScalarCML
getMaxAxisOrder() - Method in class joelib.math.symmetry.Symmetry: Maximum order of rotation axis to look for.
getMaxBitSize() - Method in class joelib.desc.result.BitResult: Gets the double attribute of the DoubleResult object
getMaxBonds(int) - Method in class joelib.data.JOEElementTable: Gets the maxBonds attribute of the JOEElementTable object
getMaxBonds() - Method in class joelib.molecule.JOEElement: Gets the maxBonds attribute of the JOEElement object
getMaxOptCycles() - Method in class joelib.math.symmetry.Symmetry: Maximum allowed number of cycles in symmetry element optimization.
getMaxOptStep() - Method in class joelib.math.symmetry.Symmetry: Maximum allowed number of cycles in symmetry element optimization.
getMin() - Method in class joelib.io.types.cml.elements.ScalarCML
getMinMax(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.
getMinOptStep() - Method in class joelib.math.symmetry.Symmetry: Termination criterion in symmetry element optimization.
getMod() - Method in class joelib.molecule.JOEMol: Gets the mod attribute of the JOEMol object
getMol(int) - Method in class joelib.molecule.JOEMolVector: Get a specific molecule from a OEMolVector.
getMolIdentifier() - Method in class joelib.desc.data.MolDescCounter: Gets the molIdentifier attribute of the MolDescCounter object
getMolNames() - Method in class joelib.algo.datamining.weka.MolInstancesCache
getMolNames() - Method in interface joelib.desc.data.MoleculeCache
getMolNames() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets all molecule names.
getMolReader(InputStream, IOType) - Static method in class joelib.io.JOEFileFormat: Gets the molReader attribute of the JOEFileFormat class.
getMolWriter(OutputStream, IOType) - Static method in class joelib.io.JOEFileFormat: Description of the Method
MoleculeFileType saver = JOEFileFormat.getMolWrite(OutputStream os, IOType type) if (saver.writeable()) { boolean success = saver.write(os, mol, title); return success; } else { logger.warn(type.getRepresentation() + " is not writeable."); return false; }
getMolWt() - Method in class joelib.molecule.JOEMol: Gets standard molar mass given by IUPAC atomic masses.
getMolecule() - Method in class joelib.algo.datamining.weka.MolInstance: Returns molecule.
getMoleculeFileType(IOType) - Static method in class joelib.io.JOEFileFormat: Gets the moleculeFileType attribute of the JOEFileFormat class
getMoleculeForColoring() - Method in class joelib.molecule.types.AtomPropertyColoring
getMoleculeHASH(JOEMol) - Method in class joelib.util.database.AbstractDatabase: Sloppy Hashcode which uses only topological informations without E/Z isomerism and S/R chirality
getMolecules() - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene
getMyAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Returns atom vector of this molecule
getMyBonds() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return bond vector of this molecule
getName(Description) - Static method in class joelib.desc.Description: Gets the name attribute of the Description class
getName(int) - Static method in class joelib.desc.Description: Gets the name attribute of the Description class
getName() - Method in class joelib.desc.Description: Gets the name attribute of the Description object
getName() - Method in class joelib.desc.DescriptorInfo: Gets descriptor name.
getName() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the elemental name
getName() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Returns name of molecule
getName() - Method in class joelib.io.IOType: Gets the name attribute of the IOType class
getName() - Method in class joelib.molecule.JOEResidue
getName() - Method in class joelib.util.types.BasicFactoryInfo: Gets name to access the class.
getNamespace() - Method in class joelib.io.types.ChemicalMarkupLanguage
getNamespace() - Method in interface joelib.io.types.cml.CMLWriterProperties
getNativeDescs() - Method in class joelib.desc.DescriptorHelper: Gets the names of all available NativeValue descriptors.
getNbrAtom(JOEAtom) - Method in class joelib.molecule.JOEBond: Gets the nbrAtom attribute of the JOEBond object
getNbrAtomIdx(JOEAtom) - Method in class joelib.molecule.JOEBond: Gets the nbrAtomIdx attribute of the JOEBond object
getNewArray(String, int) - Static method in class joelib.desc.result.DynamicArrayResult: Gets the newArray attribute of the DynamicArrayResult class
getNewBondVector(XYZVector, double) - Method in class joelib.molecule.JOEAtom: Gets the newBondVector attribute of the JOEAtom object
getNextAtom() - Method in class joelib.molecule.JOEAtom: Gets the nextAtom attribute of the JOEAtom object
getNextAtom(int) - Method in class joelib.smiles.JOESmiNode: Gets the nextAtom attribute of the JOESmiNode object
getNextBond(int) - Method in class joelib.smiles.JOESmiNode: Gets the nextBond attribute of the JOESmiNode object
getNextNode(int) - Method in class joelib.smiles.JOESmiNode: Gets the nextNode attribute of the JOESmiNode object
getNominalIndex(int[]) - Static method in class joelib.algo.datamining.weka.APWekaHelper
getNormalizationFactor(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Calculates the normalization factor in order to get an average bond length of 1.5.
getNum() - Method in class joelib.molecule.JOEResidue
getNumAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return ring vector of this molecule Return number of atoms in this molecule
getNumBonds() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return number of bonds in this molecule
getNumberColor() - Method in class joelib.gui.render.Renderer2DModel
getNumberOfDescriptors() - Method in class joelib.process.types.DescStatistic
getNumericTypes(Hashtable) - Static method in class joelib.algo.datamining.weka.APWekaHelper
getOLines() - Method in class joelib.gui.render.Renderer2DModel
getObject(String) - Method in class joelib.gui.molviewer.java3d.util.CentralLookup: Gets the object attribute of the CentralLookup object
getOperationSystemName() - Static method in class joelib.ext.ExternalHelper: Returns the name of the operation system.
getOperationSystemName() - Static method in class joelib.util.ghemical.GhemicalInterface
getOptChangeHits() - Method in class joelib.math.symmetry.Symmetry: Number of minchange cycles before optimization stops
getOptChangeThreshold() - Method in class joelib.math.symmetry.Symmetry: Minimum allowed change in target methodName.
getOrder() - Method in class joelib.data.JOEVirtualBond: Gets the order attribute of the JOEVirtualBond object
getOrthoLineColor() - Method in class joelib.gui.render.Renderer2DModel
getOrthoLineOffset() - Method in class joelib.gui.render.Renderer2DModel
getOutputOrder() - Method in class joelib.smiles.JOEMol2Smi
getOutputType() - Method in class joelib.io.types.Matlab: Gets the outputType attribute of the POVRay object
getOutputType() - Method in class joelib.io.types.POVRay: Gets the outputType attribute of the POVRay object
getOutputType() - Method in class joelib.molecule.JOEMol: Gets the outputType attribute of the JOEMol object
getParam() - Method in class joelib.gui.molviewer.java3d.util.MolViewerEvent: Gets the param attribute of the MolViewerEvent object
getParameter() - Method in class joelib.jcamp.JCAMPParser: Get all LDR's (data label records) that are stored.
getParameter(String[]) - Method in class joelib.jcamp.JCAMPParser
getParameter(String) - Method in class joelib.jcamp.JCAMPParser
getParent() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom
getParent() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBond
getParent() - Method in class joelib.molecule.JOEAtom: Gets the parent attribute of the JOEAtom object
getParent() - Method in class joelib.molecule.JOEBond: Gets the parent attribute of the JOEBond object
getParent() - Method in class joelib.ring.JOERing: Returns the parent molecule for this ring.
getParent() - Method in class joelib.smiles.JOESmiNode: Gets the parent attribute of the JOESmiNode object
getPartialCharge() - Method in class joelib.molecule.JOEAtom: Gets the partialCharge attribute of the JOEAtom object
getPartialChargeVendor() - Method in class joelib.molecule.JOEMol
getPassedTime() - Method in class wsi.ra.tool.StopWatch: Returns the passed time since last 'reset stop watch' call in millis.
getPaulingEN(int) - Method in class joelib.data.JOEElementTable: Gets the atom electronegativity after Pauling.
getPaulingEN() - Method in class joelib.molecule.JOEElement: Gets the atom electronegativity after Pauling.
getPeriod(int) - Method in class joelib.data.JOEElementTable: Gets the period of the JOEElement object.
getPeriod() - Method in class joelib.molecule.JOEElement: Gets the period attribute of the JOEElement object
getPlanes() - Method in class joelib.math.symmetry.Symmetry: Gets the symmetry planes of the molecule.
getPointerVectorEnd() - Method in class joelib.gui.render.Renderer2DModel: Returns the end of the pointer vector
getPointerVectorStart() - Method in class joelib.gui.render.Renderer2DModel: Returns the start of a pointer vector
getPrefix() - Method in class cformat.PrintfFormat: Gets the prefix string associated with the format.
getProcess(String) - Method in class joelib.process.ProcessFactory: Gets the external attribute of the ExternalFactory class
getProcessInfo() - Method in class joelib.ext.SimpleExternalProcess: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in interface joelib.process.JOEProcess
getProcessInfo(String) - Method in class joelib.process.ProcessFactory: Gets the externalInfo attribute of the ExternalFactory object
getProcessInfo() - Method in class joelib.process.ProcessPipe: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.SimpleProcess: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.types.AtomPropertyMatrix: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.types.CreateFileName: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.types.MoleculeFileCreation: Gets the processInfo attribute of the ProcessPipe object
getProcessInfo() - Method in class joelib.process.types.MoleculeFileDeletion: Gets the processInfo attribute of the ProcessPipe object
getPropFile() - Method in class wsi.ra.tool.PropertyHolder: Gets the propFile attribute of the PropertyHolder object
getProperties() - Method in class wsi.ra.tool.PropertyHolder: Gets the properties attribute of the PropertyHolder object
getProperty(String, Map) - Static method in class joelib.util.JOEPropertyHelper: Gets single process property.
getProperty(PropertyAcceptor, String, Map) - Static method in class joelib.util.JOEPropertyHelper: Gets single process property or default value if not defined or null.
getProperty(Object, String) - Method in class wsi.ra.tool.PropertyHolder: Gets the property attribute of the RegressionHelper object
getProperty(Properties, Object, String) - Static method in class wsi.ra.tool.PropertyHolder
getPropertyType() - Method in class joelib.desc.result.DynamicArrayResult: Gets the propertyType attribute of the DynamicArrayResult object
getQuality() - Method in class com.obrador.JpegEncoder
getQuoteCharacter() - Method in class wsi.ra.io.BatchScriptReplacer: Gets the quoteCharacter attribute of the BatchScriptReplacer object
getRGBFloats(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: get the R,G,B values (between 0.0f and 1.0f) of the color for atom a *
getRadius(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: get the radius for atom a *
getReleaseDate() - Method in interface joelib.data.HardCodedKernel: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOEAromaticTyper: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOEAtomTyper: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOEElementTable: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOEGroupContribution: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOEIsotopeTable: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOEPhModel: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOEResidueData: Release date for this expert system (hard coded).
getReleaseDate() - Method in class joelib.data.JOETypeTable: Release date for this expert system (hard coded).
getReleaseDateExternal() - Method in interface joelib.data.SoftCodedKernel: Release date of external (soft coded) data for this expert system.
getReleaseDateExternal() - Method in class joelib.data.SoftCodedKernelBase: Release date of external (soft coded) data for this expert system.
getReleaseVersion() - Method in interface joelib.data.HardCodedKernel: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOEAromaticTyper: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOEAtomTyper: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOEElementTable: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOEGroupContribution: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOEIsotopeTable: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOEPhModel: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOEResidueData: Release version for this expert system (hard coded).
getReleaseVersion() - Method in class joelib.data.JOETypeTable: Release version for this expert system (hard coded).
getReleaseVersionExternal() - Method in interface joelib.data.SoftCodedKernel: Release version of external (soft coded) data for this expert system.
getReleaseVersionExternal() - Method in class joelib.data.SoftCodedKernelBase: Release version of external (soft coded) data for this expert system.
getRenderAtom(JOEAtom) - Method in class joelib.gui.render.RenderingAtoms: Gets analogue rendering atom for the original atom of the original molecule.
getRenderAtom(int) - Method in class joelib.gui.render.RenderingAtoms
getRenderAtomAtom(int) - Method in class joelib.gui.render.RenderingAtoms: Gets rendering atom.
getRenderAtomCount() - Method in class joelib.gui.render.RenderingAtoms
getRenderAtomLabel(int) - Method in class joelib.gui.render.RenderingAtoms
getRenderAtomNumber(JOEAtom) - Method in class joelib.gui.render.RenderingAtoms
getRenderAtoms() - Method in class joelib.gui.render.RenderingAtoms
getRenderBonds() - Method in class joelib.gui.render.RenderingAtoms
getRenderFragments() - Method in class joelib.gui.render.RenderingAtoms
getRenderRings() - Method in class joelib.gui.render.RenderingAtoms
getRenderer2DModel() - Method in class joelib.gui.render.MoleculeViewer2D: Gets the Renderer2DModel which determins the way a molecule is displayed
getRenderer2DModel() - Method in class joelib.gui.render.Renderer2D
getRepresentation() - Method in class joelib.io.IOType: Gets the representation attribute of the IOType class
getRepresentation() - Method in class joelib.util.types.BasicFactoryInfo: Representation for class with package path and class name.
getResidue() - Method in class joelib.molecule.JOEAtom
getResidue(int) - Method in class joelib.molecule.JOEMol: Gets the residue attribute of the JOEMol object
getResolvingValue(AtomDoubleParent, JOEMol) - Method in interface joelib.algo.morgan.SingleTieResolver
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverBO
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverDistance
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverENGrad
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverElectrons
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverElement
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverGraphPot
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverImpVal
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverImpValGrad
getResolvingValue(AtomDoubleParent, JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverPartCh
getResourceExternal() - Method in interface joelib.data.SoftCodedKernel: Resource for this soft coded expert system.
getResourceExternal() - Method in class joelib.data.SoftCodedKernelBase: Resource for this soft coded expert system.
getResult() - Method in class joelib.desc.DescriptorInfo: Gets the descriptor result class representation name.
getRingIterator() - Method in class joelib.molecule.JOEMol: Gets iterator for the Smallest Set of Smallest Rings (SSSR).
getRingIterator() - Method in class joelib.ring.JOERingSearch: Gets the ringIterator attribute of the JOERingSearch object
getRmatrixTranslation(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b rotation and \b translation (applied in that order) coresponding to this objects transformation.
getRmatrixTranslation(Matrix3x3, XYZVector) - Method in class joelib.math.JOECoordTrans: Returns a \b rotation and \b translation (applied in that order) coresponding to this objects transformation.
getSMARTS() - Method in class joelib.smarts.JOESmartsPattern: Gets the sMARTS attribute of the JOESmartsPattern object
getSMILESHashcode(JOEMol) - Static method in class joelib.util.database.AbstractDatabase: Strict SMILES hashcode which uses the (hopefully) unique SMILES pattern.
getSSSR() - Method in class joelib.molecule.JOEMol: Gets the Smallest Set of Smallest Rings (SSSR).
getSandersonEN(int) - Method in class joelib.data.JOEElementTable
getSandersonEN() - Method in class joelib.molecule.JOEElement: Gets the atom electronegativity after Pauling.
getSaveFileChooser() - Method in class joelib.gui.util.MolFileChooser
getScalarStorage() - Method in class joelib.io.types.cml.elements.ScalarCML
getScaleFactor(RenderingAtoms, double) - Static method in class joelib.gui.render.RenderHelper: Determines the scale factor for displaying a structure loaded from disk in a frame.
getScaleFactor() - Method in class joelib.gui.render.Renderer2DModel: A scale factor for the drawing.
getSelectAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the selected atoms vector
getSelectRect() - Method in class joelib.gui.render.Renderer2DModel: Returns selected rectangular
getSelectedPart() - Method in class joelib.gui.render.Renderer2DModel: Get selected atoms
getSeparator() - Method in class joelib.util.ArrayHelper: Gets the separator attribute of the ArrayHelper object
getSeparator() - Method in class joelib.util.MatrixHelper: Gets the separator attribute of the MatrixHelper object
getSerialNum(JOEAtom) - Method in class joelib.molecule.JOEResidue
getSetAtomPositions(boolean) - Method in class joelib.util.ghemical.TestInterface
getShape() - Method in class joelib.gui.molviewer.java3d.graphics3D.Cylinder: Gets the shape attribute of the Cylinder object
getShape() - Method in class joelib.gui.molviewer.java3d.graphics3D.IcoSphere: Gets the shape attribute of the IcoSphere object
getShape() - Method in class joelib.gui.molviewer.java3d.graphics3D.SharedBondGroup
getSharedAtomGroup(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: Gets the sharedAtomGroup attribute of the RenderTable object
getSharedBondGroup(ViewerBond, ViewerAtom, float) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: Gets the sharedBondGroup attribute of the RenderTable object
getShowEndCarbons() - Method in class joelib.gui.render.Renderer2DModel
getSize() - Method in class joelib.molecule.JOEMolVector: Gets the size attribute of the JOEMolVector object
getSmilesElement(JOESmiNode, StringBuffer) - Method in class joelib.smiles.JOEMol2Smi: Gets the smilesElement attribute of the JOEMol2Smi object
getStatement() - Method in class wsi.ra.database.DatabaseConnection
getStatistic() - Method in class joelib.algo.datamining.weka.MolInstancesCache
getStatistic() - Method in interface joelib.desc.data.MoleculeCache
getStatistic() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Gets used descriptor statistic for this data set.
getStepLength() - Method in class joelib.util.ghemical.GhemicalInterface
getStereo() - Method in class joelib.data.JOEVirtualBond: Gets the stereo attribute of the JOEVirtualBond object
getStoreDescriptors() - Method in class joelib.desc.data.MolDescCounter: Gets the storeDescriptors attribute of the MolDescCounter object
getStoreLineInfo() - Method in class joelib.io.types.Flat: Gets the storeLineInfo attribute of the Smiles object
getStoreLineInfo() - Method in class joelib.io.types.Smiles: Gets the storeLineInfo attribute of the Smiles object
getStringArray() - Method in class joelib.desc.result.StringArrayResult: Gets the double attribute of the IntArrayResult object
getStringAtomProperties(JOEMol, ResultCMLProperties) - Method in class joelib.desc.SimpleStringAtomProperty: Gets the double atom property values.
getStringAtomProperties(JOEMol, ResultCMLProperties) - Method in class joelib.desc.types.AtomType
getStringFromType(int) - Method in class joelib.smarts.Patty: Gets the identifier name from the given identifier index.
getStringNV() - Method in interface joelib.desc.NativeValue
getStringNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the stringNV attribute of the APropDoubleResult object
getStringNV() - Method in class joelib.desc.result.APropIntResult: Gets the stringNV attribute of the APropIntResult object
getStringNV() - Method in class joelib.desc.result.BooleanResult: Gets the stringNV attribute of the IntResult object
getStringNV() - Method in class joelib.desc.result.DoubleResult: Gets the stringNV attribute of the DoubleResult object
getStringNV() - Method in class joelib.desc.result.IntResult: Gets the stringNV attribute of the IntResult object
getStringValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getStringValue(int) - Method in class joelib.desc.result.AtomDoubleResult
getStringValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the stringValue attribute of the AtomDynamicResult object
getStringValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the stringValue attribute of the AtomIntResult object
getStringValue(int) - Method in class joelib.desc.result.AtomStringResult: Gets the stringValue attribute of the AtomIntResult object
getStringValue(int) - Method in class joelib.desc.result.BondDoubleResult
getStringValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the stringValue attribute of the AtomDynamicResult object
getStringValue(int) - Method in class joelib.desc.result.BondIntResult
getStringValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getStringValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the stringValue attribute of the AtomProperties object
getStringValue(int) - Method in interface joelib.molecule.types.BondProperties
getStyle() - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: What is the current rendering style ? *
getSuffix() - Method in class cformat.PrintfFormat: Gets the suffix string associated with the format.
getSymbol(int) - Method in class joelib.data.JOEElementTable: Gets the symbol attribute of the JOEElementTable object
getSymbol() - Method in class joelib.molecule.JOEElement: Gets the symbol attribute of the JOEElement object
getSymmetryCode() - Method in class joelib.math.symmetry.PointGroup
getSymmetryCode() - Method in class joelib.math.symmetry.Symmetry
getTable() - Static method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: the accessor method for rthe instance of the RenderTable *
getTableProperties() - Method in class joelib.util.database.SimpleJOELibDatabase
getTargetMols() - Method in class joelib.process.types.DistanceCalculation
getTargetMols() - Method in class joelib.util.ComparisonHelper
getTempFileBase() - Static method in class joelib.util.JHM
getTextDescription() - Method in class joelib.desc.DescDescription: Gets the text description for the descriptor.
getTieResolverHashcode() - Method in interface joelib.algo.morgan.TieResolver
getTieResolverHashcode() - Method in class joelib.algo.morgan.types.BasicTieResolver
getTieResolvers() - Method in interface joelib.algo.morgan.TieResolver
getTieResolvers() - Method in class joelib.algo.morgan.types.BasicTieResolver
getTitle() - Method in class joelib.io.types.cml.elements.ScalarCML
getTitle() - Method in class joelib.molecule.JOEMol: Gets the title attribute of the JOEMol object.
getToleranceFinal() - Method in class joelib.math.symmetry.Symmetry: Final criterion for atom equivalence.
getTolerancePrimary() - Method in class joelib.math.symmetry.Symmetry: Initial loose criterion for atom equivalence.
getToleranceSame() - Method in class joelib.math.symmetry.Symmetry: Atoms are colliding if distance falls below this value.
getTorsion(int, int, int, int) - Method in class joelib.molecule.JOEMol: Gets the torsion attribute of the JOEMol object
getTorsion(JOEAtom, JOEAtom, JOEAtom, JOEAtom) - Method in class joelib.molecule.JOEMol: Gets the torsion attribute of the JOEMol object
getTranslationEuler(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b translation and \b rotation (applied in that order) coresponding to this objects transformation.
getTranslationRmatrix(double[], double[]) - Method in class joelib.math.JOECoordTrans: Returns a \b translation and \b rotation (applied in that order) coresponding to this objects transformation.
getTranslationRmatrix(XYZVector, Matrix3x3) - Method in class joelib.math.JOECoordTrans: Returns a \b translation and \b rotation (applied in that order) coresponding to this objects transformation.
getTx() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the transformed x coordinate of the atom
getTy() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the transformed y coordinate of the atom
getType(int) - Static method in class joelib.desc.Description: Gets the type attribute of the Description class
getType(String) - Static method in class joelib.desc.Description: Gets the type attribute of the Description class
getType() - Method in class joelib.desc.DescriptorInfo: Gets descriptor type, e.g.
getType() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns SYBYL force field atom type
getType() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Returns bond type
getType() - Method in class joelib.gui.molviewer.java3d.util.MolViewerEvent: Gets the type attribute of the MolViewerEvent object
getType() - Method in class joelib.molecule.JOEAtom: Gets the type of the JOEAtom.
getType() - Method in interface joelib.util.ToolTipInfo: Gets the information type for this tool tip, e.g "infrared data"
getTypeDimension() - Method in class joelib.desc.DescriptorInfo: Gets descriptor type dimensions.
getTypeFromDimension(int) - Static method in class joelib.desc.DescriptorInfo: Gets descriptor type, e.g.
getTypeNumber() - Method in class joelib.io.IOType: Gets the type attribute of the IOType class
getTz() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the transformed z coordinate of the atom
getUMapList() - Method in class joelib.smarts.JOESmartsPattern: Get unique list of matching atoms.
getURLFromProperty(String) - Method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder object
getURLFromProperty(String, boolean) - Method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder object
getURLFromProperty(Properties, String) - Static method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder class
getURLFromProperty(Properties, String, boolean) - Static method in class wsi.ra.tool.PropertyHolder: Gets the uRLFromProperty attribute of the PropertyHolder class
getUnits() - Method in class joelib.io.types.cml.elements.ScalarCML
getUnusedIndex() - Method in class joelib.smiles.JOEMol2Smi: Gets the unusedIndex attribute of the JOEMol2Smi object
getUseUnixStyle() - Method in class joelib.io.types.Tinker
getValence() - Method in class joelib.molecule.JOEAtom: Gets the valence of the JOEAtom object.
getValue() - Method in class joelib.data.JOEPairData: Gets the value attribute of the JOEPairData object
getValue(Description) - Static method in class joelib.desc.Description: Gets the value attribute of the Description class
getValue() - Method in class joelib.desc.Description: Gets the value attribute of the Description object
getValue(int) - Method in class joelib.desc.result.APropDoubleArrResult
getValue(int) - Method in class joelib.desc.result.AtomDoubleResult
getValue(int) - Method in class joelib.desc.result.AtomDynamicResult: Gets the value attribute of the AtomDynamicResult object
getValue(int) - Method in class joelib.desc.result.AtomIntResult: Gets the value attribute of the AtomIntResult object
getValue(int) - Method in class joelib.desc.result.AtomStringResult: Gets the value attribute of the AtomIntResult object
getValue(int) - Method in class joelib.desc.result.BondDoubleResult
getValue(int) - Method in class joelib.desc.result.BondDynamicResult: Gets the value attribute of the AtomDynamicResult object
getValue(int) - Method in class joelib.desc.result.BondIntResult
getValue(int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
getValue(int) - Method in interface joelib.molecule.types.AtomProperties: Gets the value attribute of the AtomProperties object
getValue(int) - Method in interface joelib.molecule.types.BondProperties
getValueFromName(String) - Static method in class joelib.desc.Description: Gets the valueFromName attribute of the Description class
getVdwRad(int) - Method in class joelib.data.JOEElementTable: Gets the vdwRad attribute of the JOEElementTable object
getVdwRad() - Method in class joelib.molecule.JOEElement: Gets the vdwRad attribute of the JOEElement object
getVector() - Method in class joelib.molecule.JOEAtom: Gets the vector attribute of the JOEAtom object
getVector() - Method in class joelib.molecule.JOEMolVector
getVectorBinding(int) - Method in class joelib.smarts.JOESmartsPattern: Gets the vector binding of this smarts pattern for SMARTS atom with idx.
getVectorBinding() - Method in class joelib.smarts.ParseSmart: Gets the vectorBinding attribute of the ParseSmart class
getVendor() - Method in interface joelib.data.HardCodedKernel: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOEAromaticTyper: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOEAtomTyper: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOEElementTable: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOEGroupContribution: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOEIsotopeTable: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOEPhModel: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOEResidueData: Vendor for this expert system (hard coded).
getVendor() - Method in class joelib.data.JOETypeTable: Vendor for this expert system (hard coded).
getVendorExternal() - Method in interface joelib.data.SoftCodedKernel: Vendor of external (soft coded) data for this expert system.
getVendorExternal() - Method in class joelib.data.SoftCodedKernelBase: Vendor of external (soft coded) data for this expert system.
getX() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Return component x
getX() - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Return X coordinate
getX() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the x coordinate of the atom
getX() - Method in class joelib.molecule.JOEAtom: Gets the x coordinate of the JOEAtom .
getXData() - Method in class joelib.jcamp.JCAMPParser: Gets the X array.
getXLabel() - Method in class joelib.jcamp.JCAMPParser: Gets the label for the X axis.
getXMLDeclaration() - Method in class joelib.io.types.ChemicalMarkupLanguage
getXMLDeclaration() - Method in interface joelib.io.types.cml.CMLWriterProperties
getXMLDescription() - Method in class joelib.desc.DescDescription: Gets the XML description for the descriptor.
getXScale() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns X scale
getXmax() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the maxmum x coordinate
getXmin() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the minimum x coordinate of this molelcule
getY() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Return component y
getY() - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Return Y coordinate
getY() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the y coordinate of the atom
getY() - Method in class joelib.molecule.JOEAtom: Gets the y coordinate of the JOEAtom .
getYData() - Method in class joelib.jcamp.JCAMPParser: Gets the Y array.
getYLabel() - Method in class joelib.jcamp.JCAMPParser: Gets the label for the Y axis.
getYScale() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns Y scale
getYmax() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the maxmum y coordinate
getYmin() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the minimum y coordinate
getZ() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Return component z
getZ() - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Return Z coordinate
getZ() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns the z coordinate of the atom
getZ() - Method in class joelib.molecule.JOEAtom: Gets the z coordinate of the JOEAtom .
getZScale() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Returns Z scale
getZmax() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the maxmum z coordinate
getZmin() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Return the minimum z coordinate
getZoomFactor() - Method in class joelib.gui.render.Renderer2DModel: A zoom factor for the drawing.
gr(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is greater than b.
grOrEq(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is greater or equal to b.
graphPotentials(JOEMol) - Static method in class joelib.desc.types.GraphPotentials: Calculate the Graph Potentials of a molecule based on V.E.
grow - Variable in class joelib.smarts.BondSpec: Growing evaluation flag.

H

HBA1 - class joelib.desc.types.HBA1.: Number of Hydrogen Bond Acceptors (HBA).
HBA1() - Constructor for class joelib.desc.types.HBA1
HBA2 - class joelib.desc.types.HBA2.: Number of Hydrogen Bond Acceptors (HBA).
HBA2() - Constructor for class joelib.desc.types.HBA2
HBD1 - class joelib.desc.types.HBD1.: Number of Hydrogen Bond Donors (HBD).
HBD1() - Constructor for class joelib.desc.types.HBD1
HBD2 - class joelib.desc.types.HBD2.: Number of Hydrogen Bond Donors (HBD).
HBD2() - Constructor for class joelib.desc.types.HBD2
HIN - class joelib.io.types.HIN.: Atom representation.
HIN() - Constructor for class joelib.io.types.HIN
HTML - Static variable in class joelib.desc.Description: Description of the Field
HardCodedKernel - interface joelib.data.HardCodedKernel.: Interface for defining a hard coded kernel part.
HasAllDataFilter - class joelib.process.filter.HasAllDataFilter.: Molecule process filter for available descriptor entries.
HasAllDataFilter() - Constructor for class joelib.process.filter.HasAllDataFilter: Constructor for the DescriptorFilter object
HasAllDataFilter(String) - Constructor for class joelib.process.filter.HasAllDataFilter: Constructor for the DescriptorFilter object
HasAllDataFilter(Vector) - Constructor for class joelib.process.filter.HasAllDataFilter
HasDataFilter - class joelib.process.filter.HasDataFilter.: Molecule process filter for available descriptor entries.
HasDataFilter() - Constructor for class joelib.process.filter.HasDataFilter: Constructor for the DescriptorFilter object
HasDataFilter(String) - Constructor for class joelib.process.filter.HasDataFilter: Constructor for the DescriptorFilter object
HeavyBonds - class joelib.desc.types.HeavyBonds.: Number of heavy bonds.
HeavyBonds() - Constructor for class joelib.desc.types.HeavyBonds: Constructor for the KierShape1 object
HeteroCycles - class joelib.desc.types.HeteroCycles.: Number of hetero cycles.
HeteroCycles() - Constructor for class joelib.desc.types.HeteroCycles: Constructor for the KierShape1 object
HtoMethyl() - Method in class joelib.molecule.JOEAtom: Modifies a hydrogen atom to methyl group with three explicit hydrogens.
HydrophobicGroups - class joelib.desc.types.HydrophobicGroups.: Number of hydrophobic groups.
HydrophobicGroups() - Constructor for class joelib.desc.types.HydrophobicGroups
hCount - Variable in class joelib.util.types.AtomHCount: Description of the Field
handleMolecule(JOEMol) - Method in interface joelib.io.MoleculeCallback
handleMolecule(JOEMol) - Method in class joelib.test.Convert
has2D() - Method in class joelib.molecule.JOEMol: Description of the Method
has2DCoordinates(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Determines if this AtomContainer contains 2D coordinates.
has2DCoordinates(JOEAtom) - Static method in class joelib.gui.render.RenderHelper: Determines if this Atom contains 2D coordinates.
has2DCoordinates(JOEBond) - Static method in class joelib.gui.render.RenderHelper
has3D() - Method in class joelib.molecule.JOEMol: Description of the Method
has3DCoordinates(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Determines if this model contains 3D coordinates
hasAlphaBetaUnsat() - Method in class joelib.molecule.JOEAtom: Returns true if this atom is part of an alpha beta unsaturated fragment.
hasAlphaBetaUnsat(boolean) - Method in class joelib.molecule.JOEAtom: Returns true if this atom is part of an alpha beta unsaturated fragment.
hasAromaticBond() - Method in class joelib.molecule.JOEAtom: Returns true if atom has an aromatic bond.
hasAromaticCorrected() - Method in class joelib.molecule.JOEMol: Description of the Method
hasAromaticPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasAtomTypesPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasBondOfOrder(int) - Method in class joelib.molecule.JOEAtom: Returns true if atom has bond of given order.
hasChainsPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasChiralityPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasChiralitySpecified() - Method in class joelib.molecule.JOEAtom: Returns true if the chirality was specified for this atom.
hasClosureBondsPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasData(String) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
hasData(JOEDataType) - Method in class joelib.molecule.GenericDataHolder: Description of the Method
hasData(String) - Method in class joelib.molecule.JOEMol: Description of the Method
hasData(JOEDataType) - Method in class joelib.molecule.JOEMol: Returns true if one ore more entries of the given JOEDataType exists.
hasDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic: Description of the Method
hasDoubleBond() - Method in class joelib.molecule.JOEAtom: Returns true if atom has a double bond.
hasHTMLDescription() - Method in class joelib.desc.DescDescription: Returns true if a HTML description file for the descriptor exists.
hasHybridizationPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasHydrogensAdded() - Method in class joelib.molecule.JOEMol: Description of the Method
hasImplicitValencePerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasInterface(Object, String) - Static method in class joelib.util.JOEHelper: Checks if an class implements an interface.
hasKekulePerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasNext() - Method in class joelib.util.iterator.GenericDataIterator: Description of the Method
hasNext() - Method in class joelib.util.iterator.NativeValueIterator: Description of the Method
hasNext() - Method in class joelib.util.iterator.VectorIterator: Description of the Method
hasNext() - Method in class wsi.ra.tool.DequeIterator
hasNextFileEntry(JOEMol) - Method in class joelib.io.types.ZIP
hasNonZeroCoords() - Method in class joelib.molecule.JOEMol: Description of the Method
hasPartialChargesPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasRenderAtomLabel(int) - Method in class joelib.gui.render.RenderingAtoms
hasResidue() - Method in class joelib.molecule.JOEAtom
hasRingAtomsAndBondsPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasSSSRPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
hasSelectedAtoms() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Returns true if molecule has selected atoms
hasSingleBond() - Method in class joelib.molecule.JOEAtom: Returns true if atom has a single bond.
hasTextDescription() - Method in class joelib.desc.DescDescription: Returns true if a text description file for the descriptor exists.
hasXMLDescription() - Method in class joelib.desc.DescDescription: Returns true if a XML description file for the descriptor exists.
hashCode() - Method in class joelib.desc.types.atompair.AtomPair
hashCode() - Method in class joelib.desc.types.atompair.AtomPairAtomType
hashCode() - Method in class joelib.desc.types.atompair.AtomTypePair
hashCode() - Method in class joelib.molecule.JOEAtom: Calculates the hashcode for an atom.
hashCode() - Method in class joelib.molecule.JOEBond: Calculates the hashcode for a bond.
hashCode() - Method in class joelib.molecule.JOEMol: Calculates the hashcode of a molecule using the methods AbstractDatabase.getHashcode and AbstractDatabase.getSMILESHashcode.
hashCode() - Method in class joelib.util.BitSet14: Returns a hash code value for this bit set.
head - Variable in class wsi.ra.tool.Deque
hi - Variable in class joelib.util.types.DoubleType: Description of the Field
highlight(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Designates an atom as highlighted.
highlight(ViewerAtoms) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Designates an atom list as highlighted.
hydrogenContributions - Variable in class joelib.algo.contribution.GroupContributions
hydrogenSmarts - Variable in class joelib.algo.contribution.GroupContributions

I

IFALSE - Static variable in class joelib.smarts.ParseSmart: Description of the Field
INCREMENTAL_SPHERES - Static variable in class joelib.process.types.AtomPropertyMatrix
INT - Static variable in class joelib.desc.result.DynamicArrayResult: Description of the Field
INTEGER - Static variable in class joelib.io.types.cml.CMLCoreModule
INTEGERARRAY - Static variable in class joelib.io.types.cml.CMLCoreModule
INVISIBLE - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
IOHelper - class joelib.io.IOHelper.: Some methods to faciliate the work with descriptors.
IOType - class joelib.io.IOType.: Input/output type for molecules.
IOTypeHolder - class joelib.io.IOTypeHolder.: Holder for input/output types for molecules.
ITRUE - Static variable in class joelib.smarts.ParseSmart: Description of the Field
IcoSphere - class joelib.gui.molviewer.java3d.graphics3D.IcoSphere.: Description of the Class
IcoSphere(float, int, Appearance) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.IcoSphere: Constructor for the IcoSphere object
ImageEncoder - class Acme.JPM.Encoders.ImageEncoder.: Abstract class for writing out an image.
ImageEncoder(Image, OutputStream) - Constructor for class Acme.JPM.Encoders.ImageEncoder
ImageEncoder(ImageProducer, OutputStream) - Constructor for class Acme.JPM.Encoders.ImageEncoder
IndexedCylinder - class joelib.gui.molviewer.java3d.graphics3D.IndexedCylinder.: Description of the Class
IndexedCylinder(float, float, int, Appearance) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.IndexedCylinder: Constructor for the IndexedCylinder object
InfoPanel - class joelib.gui.test.InfoPanel.: DOCUMENT ME!
InfoPanel() - Constructor for class joelib.gui.test.InfoPanel
InsertSort - class joelib.sort.InsertSort.: Insert Sort.
InsertSort() - Constructor for class joelib.sort.InsertSort
InsertSort() - Method in class joelib.sort.InsertSort: Description of the Method
InstancesHelper - class joelib.algo.datamining.weka.InstancesHelper.: Helper class to create Weka data instances.
InstancesHelper() - Constructor for class joelib.algo.datamining.weka.InstancesHelper
Int - class joelib.util.types.Int.: Two integer values.
Int() - Constructor for class joelib.util.types.Int: Constructor for the IntInt object
Int(int) - Constructor for class joelib.util.types.Int: Constructor for the IntInt object
IntArrayResult - class joelib.desc.result.IntArrayResult.: Integer array results of variable size.
IntArrayResult() - Constructor for class joelib.desc.result.IntArrayResult: Constructor for the IntArrayResult object
IntBitArrayResult - class joelib.desc.result.IntBitArrayResult.: Atom representation.
IntBitArrayResult() - Constructor for class joelib.desc.result.IntBitArrayResult: Constructor for the IntResult object
IntHashtable - class Acme.IntHashtable.: A Hashtable that uses ints as the keys.
IntHashtable(int, float) - Constructor for class Acme.IntHashtable
IntHashtable(int) - Constructor for class Acme.IntHashtable
IntHashtable() - Constructor for class Acme.IntHashtable
IntInt - class joelib.util.types.IntInt.: Two integer values.
IntInt() - Constructor for class joelib.util.types.IntInt: Constructor for the IntInt object
IntInt(int, int) - Constructor for class joelib.util.types.IntInt: Constructor for the IntInt object
IntIntInt - class joelib.util.types.IntIntInt.: IntInt and one more integer value.
IntIntInt() - Constructor for class joelib.util.types.IntIntInt: Constructor for the IntIntInt object
IntIntInt(IntInt, int) - Constructor for class joelib.util.types.IntIntInt: Constructor for the IntIntInt object
IntMatrixResult - class joelib.desc.result.IntMatrixResult.: Integer matrix results of variable size.
IntMatrixResult() - Constructor for class joelib.desc.result.IntMatrixResult: Constructor for the IntMatrixResult object
IntResult - class joelib.desc.result.IntResult.: Integer result.
IntResult() - Constructor for class joelib.desc.result.IntResult: Constructor for the IntResult object
IntrinsicState - class joelib.desc.types.IntrinsicState.: Atom valences.
IntrinsicState() - Constructor for class joelib.desc.types.IntrinsicState: Constructor for the KierShape1 object
IsomerismDetection - class joelib.util.IsomerismDetection.: Helper class to detect E/Z isomerism.
IsomerismDetection() - Constructor for class joelib.util.IsomerismDetection
IteratorException - exception joelib.util.iterator.IteratorException.: Vector iterator exception.
IteratorException() - Constructor for class joelib.util.iterator.IteratorException: Constructor for the IteratorException object
IteratorException(String) - Constructor for class joelib.util.iterator.IteratorException: Constructor for the IteratorException object
i - Variable in class joelib.smarts.types.SMARTSPatternInt: Description of the Field
i - Variable in class joelib.util.types.AtomArrayInt: Description of the Field
i - Variable in class joelib.util.types.BondInt: Description of the Field
i - Variable in class joelib.util.types.DoubleInt: Description of the Field
i - Variable in class joelib.util.types.Int: Description of the Field
i - Variable in class joelib.util.types.IntIntInt: Description of the Field
i - Variable in class joelib.util.types.StringInt: Description of the Field
i1 - Variable in class joelib.util.types.IntInt: Description of the Field
i2 - Variable in class joelib.util.types.IntInt: Description of the Field
identifyPointGroup() - Method in class joelib.math.symmetry.Symmetry
identifyPointGroup(boolean) - Method in class joelib.math.symmetry.Symmetry
ii - Variable in class joelib.smarts.types.SMARTSPatternIntInt: Description of the Field
ii - Variable in class joelib.util.types.AtomIntInt: Description of the Field
ii - Variable in class joelib.util.types.IntIntInt: Description of the Field
imageComplete(int) - Method in class Acme.JPM.Encoders.ImageEncoder
implicitHydrogenCount() - Method in class joelib.molecule.JOEAtom: Returns the number of implicit hydrogens.
in(InputStream) - Method in class joelib.util.JOEBitVec: Description of the Method
incompleteBeta(double, double, double) - Static method in class wsi.ra.tool.Statistics: Returns the Incomplete Beta Function evaluated from zero to xx.
incrementImplicitValence() - Method in class joelib.molecule.JOEAtom: Increment the implicit valence.
incrementMod() - Method in class joelib.molecule.JOEMol: Increase modification counter.
index(int) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Returns the index of the attribute stored at the given position.
indexOf(Object, int) - Method in class wsi.ra.tool.SortedVector: Searches for the first occurence of the given argument, beginning the search at index, and testing for equality using the equals method.
info(int[]) - Static method in class wsi.ra.tool.StatisticUtils: Computes entropy for an array of integers.
inherit(ModuleInterface) - Method in class joelib.io.types.cml.CMLCoreModule
inherit(ModuleInterface) - Method in interface joelib.io.types.cml.ModuleInterface
init(String) - Method in class joelib.algo.BFSResult: Constructor for the BFSResult object
init(String) - Method in class joelib.algo.DFSResult: Constructor for the DFSResult object
init(JOEMol) - Method in interface joelib.algo.morgan.SingleTieResolver
init(JOEMol) - Method in interface joelib.algo.morgan.TieResolver
init(JOEMol) - Method in class joelib.algo.morgan.types.BasicTieResolver
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverBO
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverDistance
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverENGrad
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverElectrons
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverElement
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverGraphPot
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverImpVal
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverImpValGrad
init(JOEMol) - Method in class joelib.algo.morgan.types.SingleTieResolverPartCh
init(String, String) - Method in class joelib.data.JOEChemTransformation: Description of the Method
init() - Method in class joelib.data.JOEGroupContribution: Description of the Method
init() - Method in class joelib.data.SoftCodedKernelBase: Description of the Method
init(String) - Method in interface joelib.desc.DescResult
init(String) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
init(String) - Method in class joelib.desc.result.APropDoubleResult: Constructor for the DoubleResult object
init(String) - Method in class joelib.desc.result.APropIntResult: Constructor for the DoubleResult object
init(String) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
init(String) - Method in class joelib.desc.result.BitResult: Constructor for the DoubleResult object
init(String) - Method in class joelib.desc.result.BooleanResult
init(String) - Method in class joelib.desc.result.DoubleArrayResult: Constructor for the IntArrayResult object
init(String) - Method in class joelib.desc.result.DoubleMatrixResult: Constructor for the IntMatrixResult object
init(String) - Method in class joelib.desc.result.DoubleResult: Constructor for the DoubleResult object
init(String) - Method in class joelib.desc.result.DynamicArrayResult
init(String) - Method in class joelib.desc.result.FloatMatrixResult: Constructor for the IntMatrixResult object
init(String) - Method in class joelib.desc.result.IntArrayResult
init(String) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
init(String) - Method in class joelib.desc.result.IntMatrixResult: Constructor for the IntMatrixResult object
init(String) - Method in class joelib.desc.result.IntResult
init(String) - Method in class joelib.desc.result.StringArrayResult
init(String) - Method in class joelib.desc.result.StringResult
init(String) - Method in class joelib.desc.types.atompair.AtomPairResult
init() - Method in class joelib.gui.util.MolFileChooser
init(double, double) - Method in class joelib.math.JOESqrtTbl: Description of the Method
init(Filter, Filter) - Method in class joelib.process.filter.ANDFilter: Description of the Method
init(String, boolean) - Method in class joelib.process.filter.DescriptorFilter: Description of the Method
init(Vector) - Method in class joelib.process.filter.DescriptorFilter: Description of the Method
init(Vector) - Method in class joelib.process.filter.HasAllDataFilter: Description of the Method
init(String) - Method in class joelib.process.filter.HasDataFilter: Description of the Method
init(Filter) - Method in class joelib.process.filter.NOTFilter: Description of the Method
init(String, int, double) - Method in class joelib.process.filter.NativeValueFilter: Description of the Method
init(Filter, Filter) - Method in class joelib.process.filter.ORFilter: Description of the Method
init(String, int, int, boolean) - Method in class joelib.process.filter.SMARTSFilter: Description of the Method
init(DescStatistic) - Method in class joelib.process.types.DescBinning: Description of the Method
init(DescStatistic, int) - Method in class joelib.process.types.DescBinning: Description of the Method
init(IOType, String) - Method in class joelib.process.types.DescBinning: Description of the Method
init(IOType, String, int) - Method in class joelib.process.types.DescBinning: Description of the Method
init(OutputStream, IOType) - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
init(String, IOType) - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
init(String, IOType, Vector, int) - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
init(OutputStream, IOType, Vector, int) - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
init(DescStatistic) - Method in class joelib.process.types.DescVarianceNorm: Description of the Method
init(IOType, String) - Method in class joelib.process.types.DescVarianceNorm: Description of the Method
init(ComparisonHelper) - Method in class joelib.process.types.DistanceCalculation: Description of the Method
init(IOType, String, String) - Method in class joelib.process.types.DistanceCalculation: Description of the Method
init(IOType, String, String[]) - Method in class joelib.process.types.DistanceCalculation
init(JOEMol, String) - Method in class joelib.process.types.DistanceCalculation
init(JOEMol, String[]) - Method in class joelib.process.types.DistanceCalculation
init(char[]) - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
init(String) - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
init() - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
initParser() - Method in class joelib.io.types.Flat: Description of the Method
initParser() - Method in class joelib.io.types.Smiles: Description of the Method
initReader(InputStream) - Method in interface joelib.io.MoleculeFileType: Description of the Method
initReader(InputStream) - Method in class joelib.io.SimpleImageWriter
initReader(InputStream) - Method in class joelib.io.types.Amber
initReader(InputStream) - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.ClearTextFormat: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.Flat: Description of the Method
initReader(InputStream, boolean) - Method in class joelib.io.types.Flat
initReader(InputStream) - Method in class joelib.io.types.Gaussian
initReader(InputStream) - Method in class joelib.io.types.HIN
initReader(InputStream) - Method in class joelib.io.types.JCAMP: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.MDLSD: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.Matlab: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.MolconnZ: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.Mopac
initReader(InputStream) - Method in class joelib.io.types.PDB: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.PDF
initReader(InputStream) - Method in class joelib.io.types.POVRay: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.Smiles: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.SybylMol2: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.Tinker: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.Undefined: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.XYZ: Description of the Method
initReader(InputStream) - Method in class joelib.io.types.ZIP: Description of the Method
initReader(InputStream, MoleculeCallback) - Method in class joelib.io.types.cml.CMLSequentialSAXReader
initSMARTSParser() - Static method in class joelib.smarts.ParseSmart: Description of the Method
initWriter(OutputStream) - Method in interface joelib.io.MoleculeFileType: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.SimpleImageWriter: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Amber: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.ClearTextFormat: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Flat: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Gaussian: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.HIN: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.JCAMP: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.MDLSD: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Matlab: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.MolconnZ: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Mopac: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.PDB: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.PDF: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.POVRay: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Smiles: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.SybylMol2: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Tinker: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.Undefined: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.XYZ: Description of the Method
initWriter(OutputStream) - Method in class joelib.io.types.ZIP: Description of the Method
initialize(Map) - Method in class joelib.algo.APropertyBFS: Description of the Method
initialize(Map) - Method in class joelib.algo.BFS: Description of the Method
initialize(Map) - Method in class joelib.algo.DFS: Description of the Method
initialize(Map) - Method in class joelib.desc.AtomsCounter: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in interface joelib.desc.Descriptor: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.SMARTSCounter: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.SimpleBooleanDesc: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.SimpleDoubleAtomProperty: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.SimpleDoubleDesc: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.SimpleDynamicAtomProperty: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.SimpleIntDesc: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.SimpleStringAtomProperty: Initialize descriptor calculation method for all following molecules.
initialize(Map) - Method in class joelib.desc.types.APropertyDistanceMatrix: Description of the Method
initialize(Map) - Method in class joelib.desc.types.Autocorrelation: Description of the Method
initialize(Map) - Method in class joelib.desc.types.BCUT: Description of the Method
initialize(Map) - Method in class joelib.desc.types.BurdenEigenvalues: Description of the Method
initialize(Map) - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Description of the Method
initialize(Map) - Method in class joelib.desc.types.ConjElectroTopolState: Description of the Method
initialize(Map) - Method in class joelib.desc.types.DistanceDistanceMatrix: Description of the Method
initialize(Map) - Method in class joelib.desc.types.DistanceMatrix: Description of the Method
initialize(Map) - Method in class joelib.desc.types.ElectrogeometricalState: Description of the Method
initialize(Map) - Method in class joelib.desc.types.ElectrotopologicalState: Description of the Method
initialize(Map) - Method in class joelib.desc.types.GeomDistanceMatrix: Description of the Method
initialize(Map) - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Description of the Method
initialize(Map) - Method in class joelib.desc.types.HeavyBonds: Description of the Method
initialize(Map) - Method in class joelib.desc.types.HeteroCycles: Description of the Method
initialize(Map) - Method in class joelib.desc.types.RadialDistributionFunction: Description of the Method
initialize(Map) - Method in class joelib.desc.types.SSKey3DS: Description of the Method
initialize(Map) - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Description of the Method
initialize(Map) - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Description of the Method
initialize(Map) - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Description of the Method
initialize() - Method in class joelib.gui.molviewer.java3d.graphics3D.DragBehavior: Description of the Method
initializeParser() - Method in class joelib.io.types.MolconnZ
inputDescription() - Method in interface joelib.io.MoleculeFileType: Description of the Method
inputDescription() - Method in class joelib.io.SimpleImageWriter
inputDescription() - Method in class joelib.io.types.Amber
inputDescription() - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
inputDescription() - Method in class joelib.io.types.ClearTextFormat: Description of the Method
inputDescription() - Method in class joelib.io.types.Flat: Description of the Method
inputDescription() - Method in class joelib.io.types.Gaussian
inputDescription() - Method in class joelib.io.types.HIN
inputDescription() - Method in class joelib.io.types.JCAMP: Description of the Method
inputDescription() - Method in class joelib.io.types.MDLSD
inputDescription() - Method in class joelib.io.types.Matlab: Description of the Method
inputDescription() - Method in class joelib.io.types.MolconnZ: Description of the Method
inputDescription() - Method in class joelib.io.types.Mopac
inputDescription() - Method in class joelib.io.types.PDB: Description of the Method
inputDescription() - Method in class joelib.io.types.PDF: Description of the Method
inputDescription() - Method in class joelib.io.types.POVRay: Description of the Method
inputDescription() - Method in class joelib.io.types.Smiles: Description of the Method
inputDescription() - Method in class joelib.io.types.SybylMol2: Description of the Method
inputDescription() - Method in class joelib.io.types.Tinker: Description of the Method
inputDescription() - Method in class joelib.io.types.Undefined: Description of the Method
inputDescription() - Method in class joelib.io.types.XYZ: Description of the Method
inputDescription() - Method in class joelib.io.types.ZIP: Description of the Method
inputFileExtensions() - Method in interface joelib.io.MoleculeFileType: Description of the Method
inputFileExtensions() - Method in class joelib.io.SimpleImageWriter
inputFileExtensions() - Method in class joelib.io.types.Amber
inputFileExtensions() - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.ClearTextFormat: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.Flat: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.Gaussian
inputFileExtensions() - Method in class joelib.io.types.HIN
inputFileExtensions() - Method in class joelib.io.types.JCAMP: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.MDLSD: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.Matlab: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.MolconnZ: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.Mopac
inputFileExtensions() - Method in class joelib.io.types.PDB: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.PDF: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.POVRay: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.Smiles: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.SybylMol2: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.Tinker: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.Undefined: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.XYZ: Description of the Method
inputFileExtensions() - Method in class joelib.io.types.ZIP: Description of the Method
insert(Object) - Method in class joelib.util.iterator.VectorIterator: Description of the Method
insertAfter(DequeNode, Object) - Method in class wsi.ra.tool.Deque
insertAtom(JOEAtom) - Method in class joelib.molecule.JOEMol: Description of the Method
insertBefore(DequeNode, Object) - Method in class wsi.ra.tool.Deque
insertBond(VectorIterator, JOEBond) - Method in class joelib.molecule.JOEAtom: Insert a bond to this atom.
insertElementAt(Object, int) - Method in class wsi.ra.tool.SortedVector: Inserts the specified object as a component in this vector at the specified index.
insertMolecule(String, JOEMol, int) - Method in class joelib.util.database.AbstractDatabase
insertMolecule(String, JOEMol, int) - Method in interface joelib.util.database.DatabaseInterface
insertMolecule(String, JOEMol, int) - Method in class joelib.util.database.SimpleJOELibDatabase
insertMolecule(String, JOEMol, int, boolean, boolean) - Method in class joelib.util.database.SimpleJOELibDatabase
instance() - Static method in class joelib.data.JOEAromaticTyper: Gets an instance of this aromatic typer factory class.
instance() - Static method in class joelib.data.JOEAtomTyper: Description of the Method
instance() - Static method in class joelib.data.JOEElementTable: Description of the Method
instance() - Static method in class joelib.data.JOEGroupContribution: Description of the Method
instance() - Static method in class joelib.data.JOEIsotopeTable: Description of the Method
instance() - Static method in class joelib.data.JOEKernel
instance() - Static method in class joelib.data.JOEPhModel: Description of the Method
instance() - Static method in class joelib.data.JOEResidueData: Description of the Method
instance() - Static method in class joelib.data.JOETypeTable: Description of the Method
instance() - Static method in class joelib.desc.DescriptorFactory: Gets the instance for the descriptor factory helper class.
instance() - Static method in class joelib.desc.DescriptorHelper: Gets the instance of the descriptor helper factory.
instance() - Static method in class joelib.desc.ResultFactory: Description of the Method
instance() - Static method in class joelib.desc.types.atompair.AtomPairTypeHolder: Description of the Method
instance() - Static method in class joelib.ext.ExternalFactory: Description of the Method
instance() - Static method in class joelib.gui.molviewer.java3d.Viewer: Description of the Method
instance() - Static method in class joelib.gui.render.Mol2Image: Description of the Method
instance() - Static method in class joelib.gui.util.MolFileChooser: Description of the Method
instance() - Static method in class joelib.io.IOHelper: Gets the instance of the input/output helper factory.
instance() - Static method in class joelib.io.IOTypeHolder: Gets the instance of the input/output holder factory.
instance() - Static method in class joelib.process.ProcessFactory: Description of the Method
instance() - Static method in class joelib.process.filter.FilterFactory: Description of the Method
instance() - Static method in class joelib.util.ArrayHelper: Description of the Method
instance() - Static method in class joelib.util.JHM: Description of the Method
instance() - Static method in class joelib.util.LineArrayHelper: Description of the Method
instance() - Static method in class joelib.util.LineMatrixHelper: Description of the Method
instance() - Static method in class joelib.util.MatrixHelper: Description of the Method
instance() - Static method in class joelib.util.MoleculeDataCacheHolder
instance() - Static method in class joelib.util.ghemical.GhemicalInterface: Tries to create an instance of our interface class.
instance() - Static method in class wsi.ra.database.DatabaseConnection: Returns a valid instance of this class.
instance() - Static method in class wsi.ra.io.BatchScriptReplacer: Description of the Method
instance() - Static method in class wsi.ra.io.FileUtilities
instance() - Static method in class wsi.ra.text.DecimalFormatHelper
instance() - Static method in class wsi.ra.tool.PropertyHolder: Description of the Method
instance(String) - Static method in class wsi.ra.tool.PropertyHolder: Description of the Method
instance() - Static method in class wsi.ra.tool.ResourceLoader: Description of the Method
intArrayFromSimpleString(String) - Method in class joelib.util.ArrayHelper: Loads integer array from String .
intArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper: Loads integer array from String .
intArrayFromString(String) - Method in class joelib.util.ArrayHelper: Loads integer array from String .
intArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper: Loads integer array from String .
intArrayFromString(String) - Static method in class joelib.util.LineArrayHelper: Description of the Method
intArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper: Description of the Method
intArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper: Description of the Method
intArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper: Gets int arrays from a Reader.
intArrayFromString(StringTokenizer, int) - Static method in class joelib.util.LineArrayHelper: Gets int arrays from a Reader.
intMatrixFromSimpleString(String, int, int) - Method in class joelib.util.MatrixHelper
intMatrixFromSimpleString(String, int, int, String) - Static method in class joelib.util.MatrixHelper: Description of the Method
intMatrixFromString(String) - Static method in class joelib.util.LineMatrixHelper: Description of the Method
intMatrixFromString(String) - Method in class joelib.util.MatrixHelper: Description of the Method
intMatrixFromString(String, String) - Static method in class joelib.util.MatrixHelper: Description of the Method
internalToCartesian(Vector, JOEMol) - Static method in class joelib.util.JHM
intersects(BitSet14) - Method in class joelib.util.BitSet14: Returns true if the specified BitSet14 has any bits set to true that are also set to true in this BitSet14.
invert() - Method in class joelib.math.JOECoordTrans: Inverts this objects transformation.
invert() - Method in class joelib.math.Matrix3x3: Description of the Method
invertRelation() - Method in class joelib.process.filter.NativeValueFilter
invertRelation() - Method in class joelib.process.filter.SMARTSFilter
isAmide() - Method in class joelib.molecule.JOEBond: Gets the amide attribute of the JOEBond object
isAmideNitrogen() - Method in class joelib.molecule.JOEAtom: Returns true if nitrogen is part of an amide.
isAntiClockwise() - Method in class joelib.molecule.JOEAtom: Gets the antiClockwise attribute of the JOEAtom object
isAromatic() - Method in class joelib.molecule.JOEAtom: Returns true if this is a aromatic atom.
isAromatic() - Method in class joelib.molecule.JOEBond: Gets the aromatic state of this bond.
isAromatic() - Method in class joelib.ring.JOERing: Returns true if this ring is a aromatic ring.
isAromaticNOxide() - Method in class joelib.molecule.JOEAtom: Returns true if this is an aromatic N-Oxide atom.
isAtomHighlighted(JOEAtom) - Method in class joelib.gui.render.Renderer2DModel
isAtomPropDesc(String) - Method in class joelib.desc.DescriptorHelper: Checks if this is a AtomProperties descriptor.
isAvailable() - Method in class wsi.ra.database.DatabaseConnection
isAxial() - Method in class joelib.molecule.JOEAtom: Returns true if this is a axial atom.
isBondHighlighted(JOEBond) - Method in class joelib.gui.render.Renderer2DModel
isBondPropDesc(String) - Method in class joelib.desc.DescriptorHelper: Checks if this is a BondProperties descriptor.
isBooleanAtomLeaf(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Gets the booleanAtomLeaf attribute of the ParseSmart class
isBooleanValue(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix
isCarbon() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Return true if the atom is a carbon atom
isCarbon() - Method in class joelib.molecule.JOEAtom: Returns true if this is a carbon atom.
isCarbonyl() - Method in class joelib.molecule.JOEBond: Gets the carbonyl attribute of the JOEBond object
isCarboxylOxygen() - Method in class joelib.molecule.JOEAtom: Returns true if carbon is part of an carboxyl group.
isChiral() - Method in class joelib.molecule.JOEAtom: Returns true if this is a chiral atom.
isChiral() - Method in class joelib.molecule.JOEMol: Gets the chiral attribute of the JOEMol object
isCisTransBond(JOEBond) - Static method in class joelib.util.IsomerismDetection: Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
E/trans -- bondDOWN/doubleBond/bondDOWN
Z/cis -- bondUP/doubleBond/bondDOWN
Z/cis -- bondDOWN/doubleBond/bondUP

This method does not check multiple definitions.
isCisTransBond(JOEBond, boolean) - Static method in class joelib.util.IsomerismDetection: Checks bonds for cis/trans isomerism using the SMILES flags up/down bond connected to a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
E/trans -- bondDOWN/doubleBond/bondDOWN
Z/cis -- bondUP/doubleBond/bondDOWN
Z/cis -- bondDOWN/doubleBond/bondUP

This method does not check multiple definitions.
isClockwise() - Method in class joelib.molecule.JOEAtom: Gets the clockwise attribute of the JOEAtom object
isClosure() - Method in class joelib.molecule.JOEBond: Gets the closure attribute of the JOEBond object
isConnected(JOEAtom) - Method in class joelib.molecule.JOEAtom: Returns true if this atom is connected to the atom at .
isConnectionAvailable() - Method in class wsi.ra.database.DatabaseConnection
isCorrectedForPH() - Method in class joelib.molecule.JOEMol: Gets the correctedForPH attribute of the JOEMol object
isDouble() - Method in class joelib.molecule.JOEBond: Gets the double attribute of the JOEBond object
isDoubleNV() - Method in interface joelib.desc.NativeValue
isDoubleNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the doubleNV attribute of the APropDoubleResult object
isDoubleNV() - Method in class joelib.desc.result.APropIntResult: Gets the doubleNV attribute of the APropIntResult object
isDoubleNV() - Method in class joelib.desc.result.BooleanResult: Gets the doubleNV attribute of the IntResult object
isDoubleNV() - Method in class joelib.desc.result.DoubleResult: Gets the doubleNV attribute of the DoubleResult object
isDoubleNV() - Method in class joelib.desc.result.IntResult: Gets the doubleNV attribute of the IntResult object
isDown() - Method in class joelib.molecule.JOEBond: Gets the down attribute of the JOEBond object
isDrawCarbonAtoms() - Method in class joelib.gui.render.Renderer2DModel
isElectronegative() - Method in class joelib.molecule.JOEAtom: Returns true if electronegative atom of type N, O, F, Cl, Br.
isElementOfGroup(int) - Method in class joelib.molecule.JOEAtom
isEmpty() - Method in class Acme.IntHashtable
isEmpty() - Method in class joelib.util.BitSet14: Returns true if this BitSet14 contains no bits that are set to true.
isEmpty() - Method in class wsi.ra.tool.Deque
isEster() - Method in class joelib.molecule.JOEBond: Gets the ester attribute of the JOEBond object
isExtensionListInDescription() - Method in class joelib.gui.util.MolFileFilter: Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
isFast() - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Gets the fast attribute of the MolecularScene object
isHalogen() - Method in class joelib.molecule.JOEAtom: Returns true if this is a halogen atom.
isHash() - Method in class joelib.molecule.JOEBond: Gets the hash attribute of the JOEBond object
isHetAtom(JOEAtom) - Method in class joelib.molecule.JOEResidue
isHetero() - Method in class joelib.ring.JOERing: Returns true if this ring is a heterocycle.
isHeteroatom() - Method in class joelib.molecule.JOEAtom: Returns true if this is a hetero atom.
isHighlighted() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns true if the atom is highlighted by user
isHydrogen() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Return true if the atom is a hydrogen atom
isHydrogen() - Method in class joelib.molecule.JOEAtom: Returns true if this is a hydrogen atom.
isInRing() - Method in class joelib.molecule.JOEAtom: Returns true if this is a ring atom.
isInRing() - Method in class joelib.molecule.JOEBond: Gets the inRing attribute of the JOEBond object
isInRing(int) - Method in class joelib.ring.JOERing: Returns true if the atom with index i is contained in this ring.
isInRingSize(int) - Method in class joelib.molecule.JOEAtom: Returns true if this is a atom in a ring of given size.
isIntNV() - Method in interface joelib.desc.NativeValue
isIntNV() - Method in class joelib.desc.result.APropDoubleResult: Gets the intNV attribute of the APropDoubleResult object
isIntNV() - Method in class joelib.desc.result.APropIntResult: Gets the intNV attribute of the APropIntResult object
isIntNV() - Method in class joelib.desc.result.BooleanResult: Gets the intNV attribute of the IntResult object
isIntNV() - Method in class joelib.desc.result.DoubleResult: Gets the intNV attribute of the DoubleResult object
isIntNV() - Method in class joelib.desc.result.IntResult: Gets the intNV attribute of the IntResult object
isInvalidAtom(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Gets the invalidAtom attribute of the ParseSmart class
isKDouble() - Method in class joelib.molecule.JOEBond: Returns true if this is a double bond in the Kekule structure of this molecule.
isKSingle() - Method in class joelib.molecule.JOEBond: Returns true if this is a single bond in the Kekule structure of this molecule.
isKTriple() - Method in class joelib.molecule.JOEBond: Returns true if this is a triple bond in the Kekule structure of this molecule.
isMember(JOEAtom) - Method in class joelib.ring.JOERing: Returns true if the atom is contained in this ring.
isMember(JOEBond) - Method in class joelib.ring.JOERing: Returns true if the bond is contained in this ring.
isMissing(int) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Tests if a specific value is "missing".
isNative(String) - Method in class joelib.process.types.DescStatistic: Gets the descriptorStatistic attribute of the DescStatistic object
isNativeDesc(String) - Method in class joelib.desc.DescriptorHelper: Checks if this is a NativeValue descriptor.
isNegatingAtomLeaf(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Gets the negatingAtomLeaf attribute of the ParseSmart class
isNitroOxygen() - Method in class joelib.molecule.JOEAtom: Returns true if nitrogen is part of a nitro group.
isNitrogen() - Method in class joelib.molecule.JOEAtom: Returns true if this is a nitrogen atom.
isNonPolarHydrogen() - Method in class joelib.molecule.JOEAtom: Returns true if this is a non polar hydrogen atom.
isOneFour(JOEAtom) - Method in class joelib.molecule.JOEAtom: Returns true if this atom (first) is with atom (fourth) connected to another two atoms (second, third).
isOneThree(JOEAtom) - Method in class joelib.molecule.JOEAtom: Returns true if this atom (first) is with atom (third) connected to another atom (second).
isOptional() - Method in class joelib.util.JOEProperty
isOxygen() - Method in class joelib.molecule.JOEAtom: Returns true if this is a oxygen atom.
isPhosphateOxygen() - Method in class joelib.molecule.JOEAtom: Returns true if phospor is part of an phosphat.
isPhosphorus() - Method in class joelib.molecule.JOEAtom: Returns true if this is a phospor atom.
isPolarHydrogen() - Method in class joelib.molecule.JOEAtom: Returns true if this is a polar hydrogen atom.
isPrimaryAmide() - Method in class joelib.molecule.JOEBond: Gets the primaryAmide attribute of the JOEBond object
isReadable(String) - Method in class joelib.io.IOTypeHolder: Returns true if this input type is readable.
isRotor() - Method in class joelib.molecule.JOEBond: Returns true if this is a ratatable single bond.
isSecondaryAmide() - Method in class joelib.molecule.JOEBond: Gets the secondaryAmide attribute of the JOEBond object
isSelected() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Returns true if the atom is selected by user
isSingle() - Method in class joelib.molecule.JOEBond: Gets the single attribute of the JOEBond object
isSulfateOxygen() - Method in class joelib.molecule.JOEAtom: Returns true if sulfur is part of a sulfat.
isSulfur() - Method in class joelib.molecule.JOEAtom: Returns true if this is a sulfur atom.
isThisOSsupported() - Method in interface joelib.ext.External: Description of the Method
isThisOSsupported() - Method in class joelib.ext.SimpleExternalProcess: Gets the thisOSsupported attribute of the Corina object
isThisOSsupported() - Method in class joelib.ext.Title2Data: Gets the thisOSsupported attribute of the Corina object
isTriple() - Method in class joelib.molecule.JOEBond
isUnsatType(String) - Static method in class joelib.util.JOEHelper: Gets the unsatType attribute of the JOEHelper class
isUp() - Method in class joelib.molecule.JOEBond: Gets the up attribute of the JOEBond object
isValid() - Method in class joelib.smarts.JOESmartsPattern: Gets the valid attribute of the JOESmartsPattern object
isWedge() - Method in class joelib.molecule.JOEBond: Gets the wedge attribute of the JOEBond object
isWriteable(String) - Method in class joelib.io.IOTypeHolder: Returns true if this output type is writeable.
ischiral - Variable in class joelib.smarts.Pattern: Description of the Field

J

JCAMP - class joelib.io.types.JCAMP.: A class to interpret JCAMP-DX data (JCAMP-CS is not implemented yet).
JCAMP() - Constructor for class joelib.io.types.JCAMP: Constructor for the Undefined object
JCAMPData - class joelib.jcamp.JCAMPData.: Stores single JCAMP data.
JCAMPData() - Constructor for class joelib.jcamp.JCAMPData
JCAMPDataBlock - class joelib.jcamp.JCAMPDataBlock.: Defines a JCAMP data block and type of the block.
JCAMPDataBlock() - Constructor for class joelib.jcamp.JCAMPDataBlock
JCAMPException - exception joelib.jcamp.JCAMPException.: Exception for JCAMP parser.
JCAMPException() - Constructor for class joelib.jcamp.JCAMPException
JCAMPException(String) - Constructor for class joelib.jcamp.JCAMPException: Constructor for the JCAMPException object
JCAMPParser - class joelib.jcamp.JCAMPParser.: A class to interpret JCAMP-DX data (JCAMP-CS is not implemented yet).
JCAMPParser(String) - Constructor for class joelib.jcamp.JCAMPParser: Initializes this JCampInterpreter and gets the JCAMP data in the String s.
JEditorPaneAndPagePrinter - class joelib.gui.util.JEditorPaneAndPagePrinter.: An JEditorPane which can print his Text.
JEditorPaneAndPagePrinter() - Constructor for class joelib.gui.util.JEditorPaneAndPagePrinter
JEditorPaneAndPagePrinter(URL) - Constructor for class joelib.gui.util.JEditorPaneAndPagePrinter
JHM - class joelib.util.JHM.: JOELib hepler methods.
JLog4JPanel - class joelib.gui.util.JLog4JPanel.: JPanel for log4j output and general logging.
JLog4JPanel() - Constructor for class joelib.gui.util.JLog4JPanel: Contructor for a standard logframe
JOE - class joelib.JOE.: Class for converting molecules and calculating descriptors.
JOE() - Constructor for class joelib.JOE
JOEAromaticTyper - class joelib.data.JOEAromaticTyper.: Aromatic typer.
JOEAtom - class joelib.molecule.JOEAtom.: Atom representation.
JOEAtom() - Constructor for class joelib.molecule.JOEAtom: Constructor for the JOEAtom object.
JOEAtomTyper - class joelib.data.JOEAtomTyper.: Atom typer based on structural expert rules.
JOEBitVec - class joelib.util.JOEBitVec.: BitSet14 extensions.
JOEBitVec() - Constructor for class joelib.util.JOEBitVec: Vector of int[1]
JOEBitVec(int) - Constructor for class joelib.util.JOEBitVec: Constructor for the JOEBitVec object
JOEBitVec(JOEBitVec) - Constructor for class joelib.util.JOEBitVec: Constructor for the JOEBitVec object
JOEBond - class joelib.molecule.JOEBond.: Bond representation.
JOEBond() - Constructor for class joelib.molecule.JOEBond: Constructor for the JOEBond object
JOEChemTransformation - class joelib.data.JOEChemTransformation.: Transformation of chemical groups.
JOEChemTransformation() - Constructor for class joelib.data.JOEChemTransformation: Constructor for the JOEChemTransformation object
JOECommentData - class joelib.data.JOECommentData.: Comment data.
JOECommentData() - Constructor for class joelib.data.JOECommentData: Constructor for the JOECommentData object
JOECommentData(JOECommentData) - Constructor for class joelib.data.JOECommentData: Constructor for the JOECommentData object
JOECoordTrans - class joelib.math.JOECoordTrans.: An object for storing, manipulating and applying coordinate transformations.
JOECoordTrans() - Constructor for class joelib.math.JOECoordTrans: Constructor for the JOECoordTrans object
JOEDataType - class joelib.data.JOEDataType.: Data type.
JOEElement - class joelib.molecule.JOEElement.: Element entry in periodic table.
JOEElement() - Constructor for class joelib.molecule.JOEElement: Constructor for the JOEElement object
JOEElement(int, String, double, double, double, int, Color, double, String, byte, byte, double, double, double, double) - Constructor for class joelib.molecule.JOEElement: Constructor for the JOEElement object
JOEElementTable - class joelib.data.JOEElementTable.: Element table.
JOEExternalBond - class joelib.data.JOEExternalBond.: External bond.
JOEExternalBond() - Constructor for class joelib.data.JOEExternalBond: Constructor for the JOEExternalBond object
JOEExternalBond(JOEAtom, JOEBond, int) - Constructor for class joelib.data.JOEExternalBond: Constructor for the JOEExternalBond object
JOEExternalBond(JOEExternalBond) - Constructor for class joelib.data.JOEExternalBond: Constructor for the JOEExternalBond object
JOEExternalBondData - class joelib.data.JOEExternalBondData.: External bond data.
JOEExternalBondData() - Constructor for class joelib.data.JOEExternalBondData: Constructor for the JOEExternalBondData object
JOEFileFormat - class joelib.io.JOEFileFormat.: Factory class to get loader/writer classes.
JOEFileFormat() - Constructor for class joelib.io.JOEFileFormat: Constructor for the JOEFileFormat object
JOEGastChrg - class joelib.molecule.charge.JOEGastChrg.: Partial charge calculation.
JOEGastChrg() - Constructor for class joelib.molecule.charge.JOEGastChrg: Constructor for the JOEGastChrg object
JOEGenericData - class joelib.data.JOEGenericData.: Base class for generic data elements.
JOEGenericData() - Constructor for class joelib.data.JOEGenericData: Constructor for the JOEGenericData object
JOEGenericData(JOEGenericData) - Constructor for class joelib.data.JOEGenericData: Constructor for the JOEGenericData object
JOEGlobalDataBase - class joelib.data.JOEGlobalDataBase.: Base class for handling JOELib data.
JOEGlobalDataBase() - Constructor for class joelib.data.JOEGlobalDataBase: Constructor for the JOEGlobalDataBase object
JOEGlobalDataBase(Properties) - Constructor for class joelib.data.JOEGlobalDataBase: Constructor for the JOEGlobalDataBase object
JOEGroupContribution - class joelib.data.JOEGroupContribution.: Holds group contribution lists for different models (e.g.
JOEHelper - class joelib.util.JOEHelper.: JOELib helper methods.
JOEHelper() - Constructor for class joelib.util.JOEHelper
JOEInternalCoord - class joelib.util.types.JOEInternalCoord.: Internal coordinates for three atoms.
JOEInternalCoord() - Constructor for class joelib.util.types.JOEInternalCoord
JOEInternalCoord(JOEAtom, JOEAtom, JOEAtom) - Constructor for class joelib.util.types.JOEInternalCoord
JOEIsotopeTable - class joelib.data.JOEIsotopeTable.: Isotope element table.
JOEKernel - class joelib.data.JOEKernel.: Chemistry kernel informations.
JOEKernel() - Constructor for class joelib.data.JOEKernel
JOELibTestGUI - class joelib.gui.test.JOELibTestGUI.
JOEMol - class joelib.molecule.JOEMol.: Molecule representation.
JOEMol() - Constructor for class joelib.molecule.JOEMol: Constructor for the JOEMol.
JOEMol(IOType, IOType) - Constructor for class joelib.molecule.JOEMol: Constructor for the JOEMol.
JOEMol(JOEMol, boolean, String[]) - Constructor for class joelib.molecule.JOEMol: Constructor for the JOEMol.
JOEMol(JOEMol, boolean) - Constructor for class joelib.molecule.JOEMol: Constructor for the JOEMol.
JOEMol(JOEMol) - Constructor for class joelib.molecule.JOEMol: Clones the molecule without data elements.
JOEMol2Smi - class joelib.smiles.JOEMol2Smi.: Molecule to SMILES methods.
JOEMol2Smi() - Constructor for class joelib.smiles.JOEMol2Smi: Constructor for the JOEMol2Smi object
JOEMolVector - class joelib.molecule.JOEMolVector.: Molecule vector to load single and multiple molecule files.
JOEMolVector() - Constructor for class joelib.molecule.JOEMolVector: Creates an empty molecule vector.
JOEMolVector(InputStream) - Constructor for class joelib.molecule.JOEMolVector: Constructor for the JOEMolVector object
JOEMolVector(InputStream, int) - Constructor for class joelib.molecule.JOEMolVector: Constructor for the JOEMolVector object
JOEMolVector(InputStream, IOType, IOType) - Constructor for class joelib.molecule.JOEMolVector: Constructor for the JOEMolVector object
JOEMolVector(InputStream, IOType, IOType, int) - Constructor for class joelib.molecule.JOEMolVector: Constructor for the JOEMolVector object
JOEPairData - class joelib.data.JOEPairData.: Use to store attribute/value relationships.
JOEPairData() - Constructor for class joelib.data.JOEPairData: Constructor for the JOEPairData object
JOEPairData(String, Object) - Constructor for class joelib.data.JOEPairData: Constructor for the JOEPairData object
JOEPhModel - class joelib.data.JOEPhModel.: Model for the protonation/deprotonation of molecules.
JOEProcess - interface joelib.process.JOEProcess.: Interface definition for calling molecule processes.
JOEProcessException - exception joelib.process.JOEProcessException.: Molecule process exception.
JOEProcessException() - Constructor for class joelib.process.JOEProcessException: Constructor for the DescriptorException object
JOEProcessException(String) - Constructor for class joelib.process.JOEProcessException: Constructor for the DescriptorException object
JOEProperty - class joelib.util.JOEProperty.: JOELib property representation.
JOEProperty(String, String, String, boolean) - Constructor for class joelib.util.JOEProperty: Constructor for a JOELib property without default value.
JOEProperty(String, String, String, boolean, Object) - Constructor for class joelib.util.JOEProperty: Constructor for a JOELib property.
JOEPropertyException - exception joelib.util.JOEPropertyException.: JOELib property exception.
JOEPropertyException() - Constructor for class joelib.util.JOEPropertyException: Constructor for the DescriptorException object
JOEPropertyException(String) - Constructor for class joelib.util.JOEPropertyException: Constructor for the DescriptorException object
JOEPropertyHelper - class joelib.util.JOEPropertyHelper.: Some helper methods for calling classes which accept properties (PropertyAcceptor).
JOERTree - class joelib.molecule.JOERTree.: Atom tree.
JOERTree(JOEAtom, JOERTree) - Constructor for class joelib.molecule.JOERTree: Constructor for the atom tree.
JOERandom - class joelib.util.JOERandom.: Random generator.
JOERandom() - Constructor for class joelib.util.JOERandom: Constructor for the JOERandom object
JOERandom(int) - Constructor for class joelib.util.JOERandom: Constructor for the JOERandom object
JOEResidue - class joelib.molecule.JOEResidue.: Residue informations.
JOEResidue() - Constructor for class joelib.molecule.JOEResidue
JOEResidueData - class joelib.data.JOEResidueData.: Type table.
JOERgroupData - class joelib.data.JOERgroupData.: Stores Rgroup data.
JOERgroupData() - Constructor for class joelib.data.JOERgroupData: Constructor for the JOERgroup object
JOERing - class joelib.ring.JOERing.: Ring representation.
JOERing() - Constructor for class joelib.ring.JOERing: Constructor for the JOERing object
JOERing(Vector, int) - Constructor for class joelib.ring.JOERing
JOERingData - class joelib.ring.JOERingData.: Stores ring data.
JOERingData() - Constructor for class joelib.ring.JOERingData: Constructor for the JOERingData object
JOERingSearch - class joelib.ring.JOERingSearch.: Finds the Smallest Set of Smallest Rings (SSSR).
JOERingSearch() - Constructor for class joelib.ring.JOERingSearch: Constructor for the JOERingSearch object
JOESSMatch - class joelib.smarts.JOESSMatch.: The JOESSMatch class performs exhaustive matching using recursion Explicit stack handling is used to find just a single match in match()
JOESSMatch(ParseSmart, JOEMol, Pattern) - Constructor for class joelib.smarts.JOESSMatch: Constructor for the JOESSMatch object
JOESmartsPattern - class joelib.smarts.JOESmartsPattern.: Class to parse SMART pattern and store the search expressions.
JOESmartsPattern() - Constructor for class joelib.smarts.JOESmartsPattern: Constructor for the JOESmartsPattern object
JOESmiNode - class joelib.smiles.JOESmiNode.: SMILES node holding atom and bond informations.
JOESmiNode(JOEAtom) - Constructor for class joelib.smiles.JOESmiNode: Constructor for the JOESmiNode object
JOESmilesParser - class joelib.smiles.JOESmilesParser.: Parser for Simplified Molecular Input Line Entry System (SMILES) strings.
JOESmilesParser() - Constructor for class joelib.smiles.JOESmilesParser
JOESqrtTbl - class joelib.math.JOESqrtTbl.: Sqrt table.
JOESqrtTbl() - Constructor for class joelib.math.JOESqrtTbl: Constructor for the JOESqrtTbl object
JOESqrtTbl(double, double) - Constructor for class joelib.math.JOESqrtTbl: Constructor for the JOESqrtTbl object
JOETypeTable - class joelib.data.JOETypeTable.: Type table to map internal atom types to atom types of other file formats.
JOEVirtualBond - class joelib.data.JOEVirtualBond.: Virtual bond.
JOEVirtualBond() - Constructor for class joelib.data.JOEVirtualBond: Constructor for the JOEVirtualBond object
JOEVirtualBond(int, int, int) - Constructor for class joelib.data.JOEVirtualBond: Constructor for the JOEVirtualBond object
JOEVirtualBond(int, int, int, int) - Constructor for class joelib.data.JOEVirtualBond: Constructor for the JOEVirtualBond object
JOE_3RING_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is in a ring of size 3.
JOE_4RING_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is in a ring of size 4.
JOE_ACCEPTOR_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is a acceptor.
JOE_ACSTEREO_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is a anti-clockwise stereo atom.
JOE_AROMATIC_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is aromatic.
JOE_AROMATIC_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is aromatic bond
JOE_AROMATIC_BOND_ORDER - Static variable in class joelib.molecule.JOEBond: Bond order: aromatic bond
JOE_AROMATIC_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: aromaticity calculated.
JOE_AROM_CORRECTED_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: aromaticity corrected molecule.
JOE_ATOMTYPES_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: atom types perceived.
JOE_CHAINS_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: chain molecule.
JOE_CHIRALITY_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: atom chirality flags perceived.
JOE_CHIRAL_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is a chiral atom (stereo center).
JOE_CLOSURE_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is closure bond
JOE_CLOSURE_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: closure bonds perceived.
JOE_COMMENT_DATA - Static variable in class joelib.data.JOEDataType: Comment data.
JOE_COMPRESS_DATA - Static variable in class joelib.data.JOEDataType: Description of the Field
JOE_CSTEREO_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is a clockwise stereo atom.
JOE_CURRENT_CONFORMER - Static variable in class joelib.molecule.JOEMol: Molecule flag: current conformer.
JOE_DONOR_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is a donor.
JOE_ENERGY_DATA - Static variable in class joelib.data.JOEDataType: Description of the Field
JOE_EXTERNAL_BOND_DATA - Static variable in class joelib.data.JOEDataType: Description of the Field
JOE_HASH_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is hash bond
JOE_HYBRID_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: atom hybridisation perceived.
JOE_H_ADDED_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: H atoms added molecule.
JOE_IMPVAL_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: implicit valences perceived.
JOE_KDOUBLE_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is double bond
JOE_KEKULE_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: kekulization perceived.
JOE_KSINGLE_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is single bond
JOE_KTRIPLE_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is triple bond
JOE_PAIR_DATA - Static variable in class joelib.data.JOEDataType: Pair data (descriptor data).
JOE_PCHARGE_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: partitial charges perceived.
JOE_PH_CORRECTED_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: PH value perceived.
JOE_RGROUP_DATA - Static variable in class joelib.data.JOEDataType: Rgroup data.
JOE_RINGFLAGS_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: rings perceived.
JOE_RING_ATOM - Static variable in class joelib.molecule.JOEAtom: Atom flag: is in a ring.
JOE_RING_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is ring bond
JOE_RING_DATA - Static variable in class joelib.data.JOEDataType: Ring data.
JOE_ROTAMER_LIST - Static variable in class joelib.data.JOEDataType: Description of the Field
JOE_SPECTRA_DATA - Static variable in class joelib.data.JOEDataType: Description of the Field
JOE_SSSR_MOL - Static variable in class joelib.molecule.JOEMol: Molecule flag: SSSR calculated.
JOE_TORDOWN_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is tordown bond
JOE_TORUP_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is torup bond
JOE_UNDEFINED_DATA - Static variable in class joelib.data.JOEDataType: Description of the Field
JOE_VIRTUAL_BOND_DATA - Static variable in class joelib.data.JOEDataType: Description of the Field
JOE_WEDGE_BOND - Static variable in class joelib.molecule.JOEBond: Bond flag: is wedge bond
JPEG - class joelib.io.types.JPEG.: Atom representation.
JPEG() - Constructor for class joelib.io.types.JPEG
JPanel3D - class joelib.gui.molviewer.java3d.graphics3D.JPanel3D.: JPanel for Java3D molecule viewer.
JPanel3D() - Constructor for class joelib.gui.molviewer.java3d.graphics3D.JPanel3D: Constructor for the Panel3D object
Jade - class jtt.docbook.Jade.: Calls corina to create 3D structures.
Jade() - Constructor for class jtt.docbook.Jade: Constructor for the Corina object
Java3DHelper - class joelib.gui.molviewer.java3d.util.Java3DHelper.: Test class for the Java3D configuration.
Java3DHelper() - Constructor for class joelib.gui.molviewer.java3d.util.Java3DHelper
Jpeg - class com.obrador.Jpeg.: DOCUMENT ME!
Jpeg() - Constructor for class com.obrador.Jpeg
JpegEncoder - class com.obrador.JpegEncoder.
JpegEncoder(Image, int, OutputStream) - Constructor for class com.obrador.JpegEncoder
jMenuAddDescriptors_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame
jMenuAddHydrogens_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
jMenuAddPolarHydrogens_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame
jMenuAtomColoring_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
jMenuBallStick_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
jMenuFileExit_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: File | Exit action performed
jMenuFileOpen_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: File | Open action performed
jMenuFileSave_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: File | Save action performed
jMenuHelpAbout_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method Help | About action performed
jMenuRemoveDescriptors_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame
jMenuRemoveHydrogens_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
jMenuRemoveNonPolarHydrogens_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
jMenuSpacefill_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame
jMenuStick_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
jMenuWire_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
jacobi3x3(double[][], double[][]) - Static method in class joelib.math.MathHelper
joelib - package joelib: Provides classes for processing, converting molecular chemical data and calculate chemical properties (descriptors).
joelib.algo - package joelib.algo: Provides classes for calculating Depth First Search (DFS) [clr98dfs] Breadth First Search (BFS) [clr98bfs] on molecular graphs.
joelib.algo.contribution - package joelib.algo.contribution: Provides classes for value prediction based on group contribution models.
joelib.algo.datamining.weka - package joelib.algo.datamining.weka: Provides classes for an interface to the Weka Data Mining library.
joelib.algo.morgan - package joelib.algo.morgan: Provides classes for Morgan number generation and unique molecule numbering.
joelib.algo.morgan.types - package joelib.algo.morgan.types
joelib.data - package joelib.data: These classes are the chemical heart of JOELib.
joelib.desc - package joelib.desc: Provides classes for defining molecular properties (descriptors).
joelib.desc.data - package joelib.desc.data: Provides classes for building descriptor matrices.
joelib.desc.result - package joelib.desc.result: Provides representating classes for molecular properties (descriptors).
joelib.desc.types - package joelib.desc.types: Provides representating classes for the calculation of molecular properties (descriptors).
joelib.desc.types.atompair - package joelib.desc.types.atompair
joelib.desc.util - package joelib.desc.util
joelib.ext - package joelib.ext: Provides classes for defining external molecular processing modules.
joelib.gui.molviewer.java3d - package joelib.gui.molviewer.java3d: Provides classes for a simple Java3D visualization of molecules.
joelib.gui.molviewer.java3d.graphics3D - package joelib.gui.molviewer.java3d.graphics3D: Provides core Java3D elements for the molecule visualization.
joelib.gui.molviewer.java3d.math.geometry - package joelib.gui.molviewer.java3d.math.geometry: Provides geometrical element classes for the Java3D visualization.
joelib.gui.molviewer.java3d.math.util - package joelib.gui.molviewer.java3d.math.util: Provides mathematical utilities for the Java3D visualization.
joelib.gui.molviewer.java3d.molecule - package joelib.gui.molviewer.java3d.molecule: Provides atoms, bonds and the molecule for the Java3D visualization.
joelib.gui.molviewer.java3d.util - package joelib.gui.molviewer.java3d.util: Provides event and adapter classes/patterns for the Java3D visualization.
joelib.gui.render - package joelib.gui.render
joelib.gui.test - package joelib.gui.test
joelib.gui.util - package joelib.gui.util
joelib.io - package joelib.io: Provides classes for defining molecular import and export methods.
joelib.io.types - package joelib.io.types: Provides representating classes for the molecular import and export methods.
joelib.io.types.cml - package joelib.io.types.cml: Provides helper classes for processing the Chemical Markup Language (CML) [rr99b, mr01, gmrw01, wil01, mr03, mrww04].
joelib.io.types.cml.elements - package joelib.io.types.cml.elements
joelib.jcamp - package joelib.jcamp: Provides helper classes for processing spectroscopic data defined by the Joint Commitee on Atomic and Molecular Physical Data (JCAMP) [dl93, dw88, ghhjs91, lhdl94, dhl90].
joelib.math - package joelib.math: Provides mathematical oriented helper classes for molecular data processing.
joelib.math.similarity - package joelib.math.similarity
joelib.math.symmetry - package joelib.math.symmetry
joelib.molecule - package joelib.molecule: Provides classes for molecular data structures.
joelib.molecule.charge - package joelib.molecule.charge: Provides classes for the calculation of the partitial charge.
joelib.molecule.fragmentation - package joelib.molecule.fragmentation: Provides classes for fragmenting molecules.
joelib.molecule.generation - package joelib.molecule.generation: Provides classes for generating molecules.
joelib.molecule.types - package joelib.molecule.types: Provides classes for atom and bond properties.
joelib.process - package joelib.process: Provides classes for defining molecular processing modules.
joelib.process.filter - package joelib.process.filter: Provides representating classes for the specialized filter options for molecular processing methods.
joelib.process.types - package joelib.process.types: Provides representating classes for the molecular processing methods.
joelib.ring - package joelib.ring: Provides classes for finding the Smallest Set of Smallest Rings (SSSR) [fig96].
joelib.smarts - package joelib.smarts: Provides classes for searching substructures in chemical structures based on the Smiles ARbitrary Target Specification (SMARTS) standard [smarts].
joelib.smarts.atomexpr - package joelib.smarts.atomexpr: Provides classes for SMARTS atom types.
joelib.smarts.bondexpr - package joelib.smarts.bondexpr: Provides classes for SMARTS bond types.
joelib.smarts.test - package joelib.smarts.test
joelib.smarts.types - package joelib.smarts.types: Provides classes for SMARTS special types.
joelib.smiles - package joelib.smiles: Provides classes for building molecules using the Simplified Molecular Input Line Entry System (SMILES) [smilesFormat, wei88, www89].
joelib.sort - package joelib.sort: Provides classes for sorting data.
joelib.test - package joelib.test: Provides testing classes for processing molecular data.
joelib.util - package joelib.util: Provides all kind of additional technical/molecular helper classes.
joelib.util.cdk - package joelib.util.cdk: Provides classes for an interface to the Chemical Development Kit (CDK).
joelib.util.database - package joelib.util.database
joelib.util.ghemical - package joelib.util.ghemical: Provides classes for an interface to the (Lib)Ghemical library.
joelib.util.iterator - package joelib.util.iterator: Provides iterator classes specialized for molecular operations.
joelib.util.types - package joelib.util.types: Provides special data types.
jpegNaturalOrder - Static variable in class com.obrador.JpegEncoder
jtt.docbook - package jtt.docbook
jtt.util - package jtt.util

K

KBOSum() - Method in class joelib.molecule.JOEAtom: Returns the K bond order sum of this atom.
KierShape1 - class joelib.desc.types.KierShape1.: Calculates the Kier Shape for paths with length one.
KierShape1() - Constructor for class joelib.desc.types.KierShape1: Constructor for the KierShape1 object
KierShape2 - class joelib.desc.types.KierShape2.: Calculates the Kier Shape for paths with length two.
KierShape2() - Constructor for class joelib.desc.types.KierShape2: Constructor for the KierShape2 object
KierShape3 - class joelib.desc.types.KierShape3.: Calculates the Kier Shape for paths with length three.
KierShape3() - Constructor for class joelib.desc.types.KierShape3: Constructor for the KierShape3 object
kekulePropagate(JOEAtom, Vector, Vector, int) - Static method in class joelib.util.JHM
kekulize() - Method in class joelib.molecule.JOEMol: Kekulizes the molecule.
key - Variable in class wsi.ra.tool.DequeNode
keys() - Method in class Acme.IntHashtable

L

LINK - Static variable in class joelib.io.types.cml.CMLCoreModule
LINK - Static variable in class joelib.jcamp.JCAMPParser: data representation: LINK definition
LINK_TYPE - Static variable in class joelib.jcamp.JCAMPDataBlock
LIST - Static variable in class joelib.io.types.cml.CMLCoreModule
LabelData - class joelib.jcamp.LabelData.: Label/Data entry for JCAMP format.
LabelData() - Constructor for class joelib.jcamp.LabelData
LabelData(String, String) - Constructor for class joelib.jcamp.LabelData
LeafAtomExpr - class joelib.smarts.atomexpr.LeafAtomExpr.: Leaf node of atom expression.
LeafAtomExpr() - Constructor for class joelib.smarts.atomexpr.LeafAtomExpr: Constructor for the LeafAtomExpr object
LeafAtomExpr(int) - Constructor for class joelib.smarts.atomexpr.LeafAtomExpr: Constructor for the LeafAtomExpr object
LeafBondExpr - class joelib.smarts.bondexpr.LeafBondExpr.: Leaf bond node for SMARTS.
LeafBondExpr() - Constructor for class joelib.smarts.bondexpr.LeafBondExpr: Constructor for the LeafBondExpr object
LeafBondExpr(int) - Constructor for class joelib.smarts.bondexpr.LeafBondExpr: Constructor for the LeafBondExpr object
Line - class joelib.gui.molviewer.java3d.math.geometry.Line.: A class that defines geometric straight line in 3D space
Line() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Line: Default constructor
Line(Point3D, Point3D) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Line: Full constructor
LineArrayHelper - class joelib.util.LineArrayHelper.: Helper methods for writing and loading line arrays.
LineMatrixHelper - class joelib.util.LineMatrixHelper.: Helper methods for writing and loading line matrices.
LogP - class joelib.desc.types.LogP.: Calculates the Octanol/Water partition coefficient (logP) or hydrophobicity.
LogP() - Constructor for class joelib.desc.types.LogP
label - Variable in class joelib.gui.render.OrthoLine
label - Variable in class joelib.jcamp.LabelData
labelEndString - Static variable in class joelib.jcamp.JCAMPDataBlock
labelStartString - Static variable in class joelib.jcamp.JCAMPDataBlock
lastElement() - Method in class wsi.ra.tool.SortedVector: Returns the last component of the vector.
lastIndexOf(Object, int) - Method in class wsi.ra.tool.SortedVector: Searches backwards for the specified object, starting from the specified index, and returns an index to it.
length() - Method in class joelib.desc.result.AtomDynamicResult
length() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: calculate the length of the vector
length() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Retrun the length of this bond
length() - Method in class joelib.math.XYZVector: Description of the Method
length() - Method in class joelib.util.BitSet14: Returns the "logical size" of this BitSet14: the index of the highest set bit in the BitSet14 plus one.
length_2() - Method in class joelib.math.XYZVector: Description of the Method
lexPtr - Variable in class joelib.smarts.ParseSmart: Description of the Field
lexPtrIndex - Variable in class joelib.smarts.ParseSmart: Description of the Field
lft - Variable in class joelib.smarts.atomexpr.BinAtomExpr: Description of the Field
lft - Variable in class joelib.smarts.bondexpr.BinBondExpr: Description of the Field
lnFactorial(double) - Static method in class wsi.ra.tool.Statistics: Returns natural logarithm of factorial using gamma methodName.
lnGamma(double) - Static method in class wsi.ra.tool.Statistics: Returns natural logarithm of gamma methodName.
lo - Variable in class joelib.util.types.DoubleType: Description of the Field
loadDefaultMetric() - Method in interface joelib.desc.DistanceMetricValue
loadDefaultMetric() - Method in class joelib.desc.types.atompair.AtomPairResult
loadMatrix(IOType, String, boolean) - Method in class joelib.algo.datamining.weka.MolInstancesCache
loadMatrix(IOType, String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
loadMatrix(IOType, String) - Method in interface joelib.desc.data.MoleculeCache
loadMatrix(IOType, String, boolean) - Method in interface joelib.desc.data.MoleculeCache
loadMatrix(IOType, String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
loadMatrix(IOType, String, boolean) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
loadMetric(String) - Method in interface joelib.desc.DistanceMetricValue
loadMetric(String) - Method in class joelib.desc.types.atompair.AtomPairResult
loadMolFromFile(String, String) - Static method in class joelib.io.IOHelper: Loads a single molecule from a file.
loadMolFromFile(MoleculeFileType[], JOEMol, String, String) - Static method in class joelib.io.IOHelper: Loads a single molecule from a file.
loadParameters() - Method in class jtt.docbook.DocBookArticles: Description of the Method
loadParameters() - Method in class jtt.docbook.DocBookEquations: Description of the Method
loadParameters() - Method in class jtt.docbook.DocBookMolecules: Description of the Method
loadParameters() - Method in class jtt.docbook.Jade: Description of the Method
loadedMolecule() - Method in class joelib.io.SimpleReaderWriterPipe: Returns the last loaded molecule.
locateIndex(int) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Locates the greatest index that is not greater than the given index.
log2 - Static variable in class wsi.ra.tool.StatisticUtils: The natural logarithm of 2.
log2(double) - Static method in class wsi.ra.tool.StatisticUtils: Returns the logarithm of a for base 2.
lookAheadCharValid() - Method in class cformat.ScanfReader: Returns whether or not a look-ahead character is currently begin stored.
lookupBO(String) - Method in class joelib.data.JOEResidueData
lookupBO(String, String) - Method in class joelib.data.JOEResidueData
lookupType(String) - Method in class joelib.data.JOEResidueData

M

MATRIX - Static variable in class joelib.io.types.cml.CMLCoreModule
MATRIX_TYPE - Static variable in class joelib.io.types.cml.elements.MatrixCML
MAX - Static variable in class joelib.io.types.cml.elements.ScalarCML
MAXOPT_STEP_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
MAX_AXIS_ORDER_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
MAX_OPT_CYCLES_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
MAX_SPHERICAL_VOLUME - Static variable in class joelib.desc.types.RadialDistributionFunction
MAX_SPHERICAL_VOLUME_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
MAX_VALUES - Static variable in class joelib.io.types.cml.elements.ArrayCML
MDLSD - class joelib.io.types.MDLSD.: Reader/Writer for SDF files.
MDLSD() - Constructor for class joelib.io.types.MDLSD: Constructor for the MDLSD object
MIN - Static variable in class joelib.io.types.cml.elements.ScalarCML
MINOPT_STEP_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
MIN_SPHERICAL_VOLUME - Static variable in class joelib.desc.types.RadialDistributionFunction
MIN_SPHERICAL_VOLUME_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
MIN_VALUES - Static variable in class joelib.io.types.cml.elements.ArrayCML
MOLECULE - Static variable in class joelib.io.types.cml.CMLCoreModule
MOL_AND_DESCRIPTORS - Static variable in class joelib.process.types.DescSelectionWriter: Description of the Field
MX_GASTEIGER_DAMP - Static variable in class joelib.molecule.charge.GasteigerState: Damping factor.
MX_GASTEIGER_DENOM - Static variable in class joelib.molecule.charge.GasteigerState: Default denominator for hydrogen atoms.
MX_GASTEIGER_ITERS - Static variable in class joelib.molecule.charge.GasteigerState: Number of iterations.
MathHelper - class joelib.math.MathHelper.: Mathematical helper methods.
MathHelper() - Constructor for class joelib.math.MathHelper
MathUtils - class joelib.gui.molviewer.java3d.math.util.MathUtils.: This class provides some math utility methods.
MathUtils() - Constructor for class joelib.gui.molviewer.java3d.math.util.MathUtils
Matlab - class joelib.io.types.Matlab.: Reader/Writer for Matlab files.
Matlab() - Constructor for class joelib.io.types.Matlab
Matrix3D - class joelib.gui.molviewer.java3d.molecule.Matrix3D.: A fairly conventional 3D matrix object that can transform sets of 3D points and perform a variety of manipulations on the transform.
Matrix3D() - Constructor for class joelib.gui.molviewer.java3d.molecule.Matrix3D: Create a new unit matrix
Matrix3x3 - class joelib.math.Matrix3x3.: 3x3 Matrix.
Matrix3x3() - Constructor for class joelib.math.Matrix3x3: Constructor for the Matrix3x3 object
Matrix3x3(XYZVector, XYZVector, XYZVector) - Constructor for class joelib.math.Matrix3x3: Constructor for the Matrix3x3 object
Matrix3x3(double[][]) - Constructor for class joelib.math.Matrix3x3
MatrixCML - class joelib.io.types.cml.elements.MatrixCML.: Scalar CML element.
MatrixCML(Vector) - Constructor for class joelib.io.types.cml.elements.MatrixCML: Constructor for the StringString object
MatrixHelper - class joelib.util.MatrixHelper.: Helper methods for wrinting and loading matrices.
ModuleInterface - interface joelib.io.types.cml.ModuleInterface.: This interface describes the procedures classes must implement to be plugable into the CMLHandler.
Mol2Image - class joelib.gui.render.Mol2Image.: Image creation with options.
MolDescCounter - class joelib.desc.data.MolDescCounter.: Counts the number of descriptors and molecules in a molecule file.
MolDescCounter() - Constructor for class joelib.desc.data.MolDescCounter: Constructor for the IntResult object
MolDescCounter(int, int) - Constructor for class joelib.desc.data.MolDescCounter: Constructor for the MolDescCounter object
MolDescCounter(IOType, String) - Constructor for class joelib.desc.data.MolDescCounter: Constructor for the MolDescCounter object
MolDescCounter(int, int, IOType, String) - Constructor for class joelib.desc.data.MolDescCounter: Constructor for the MolDescCounter object
MolFileChooser - class joelib.gui.util.MolFileChooser.
MolFileFilter - class joelib.gui.util.MolFileFilter.: A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
MolFileFilter(IOType, MoleculeFileType, boolean, boolean) - Constructor for class joelib.gui.util.MolFileFilter: Creates a file filter.
MolFileFilter() - Constructor for class joelib.gui.util.MolFileFilter: Creates a file filter.
MolFileFilter(String) - Constructor for class joelib.gui.util.MolFileFilter: Creates a file filter that accepts files with the given extension.
MolFileFilter(String, String) - Constructor for class joelib.gui.util.MolFileFilter: Creates a file filter that accepts the given file type.
MolFileFilter(String[]) - Constructor for class joelib.gui.util.MolFileFilter: Creates a file filter from the given string array.
MolFileFilter(String[], String) - Constructor for class joelib.gui.util.MolFileFilter: Creates a file filter from the given string array and description.
MolGenerationHelper - class joelib.molecule.generation.MolGenerationHelper.: Helper class for molecule generation.
MolGenerationHelper() - Constructor for class joelib.molecule.generation.MolGenerationHelper
MolInstance - class joelib.algo.datamining.weka.MolInstance.: Molecule Weka instance.
MolInstance(MolInstance) - Constructor for class joelib.algo.datamining.weka.MolInstance: Constructor that copies the attribute values and the weight from the given instance.
MolInstance(JOEMol, double, double[]) - Constructor for class joelib.algo.datamining.weka.MolInstance: Constructor that inititalizes instance variable with given values.
MolInstance(int) - Constructor for class joelib.algo.datamining.weka.MolInstance: Constructor of an instance that sets weight to one, all values to be missing, and the reference to the dataset to null.
MolInstances - class joelib.algo.datamining.weka.MolInstances.: Molecule Weka instances.
MolInstances(MolInstances) - Constructor for class joelib.algo.datamining.weka.MolInstances: Constructor copying all instances and references to the header information from the given set of instances.
MolInstances(MolInstances, int) - Constructor for class joelib.algo.datamining.weka.MolInstances: Constructor creating an empty set of instances.
MolInstances(MolInstances, int, int) - Constructor for class joelib.algo.datamining.weka.MolInstances: Creates a new set of instances by copying a subset of another set.
MolInstances(String, FastVector, int) - Constructor for class joelib.algo.datamining.weka.MolInstances: Creates an empty set of instances.
MolInstances(Reader) - Constructor for class joelib.algo.datamining.weka.MolInstances: Reads a Descriptor ARFF file from a reader, and assigns a weight of one to each instance.
MolInstances(Reader, int) - Constructor for class joelib.algo.datamining.weka.MolInstances: Reads the header of a Descriptor ARFF file from a reader and reserves space for the given number of instances.
MolInstancesCache - class joelib.algo.datamining.weka.MolInstancesCache.: Molecule caching class for Weka data mining instances.
MolInstancesCache() - Constructor for class joelib.algo.datamining.weka.MolInstancesCache
MolInstancesCache(IOType, String, boolean) - Constructor for class joelib.algo.datamining.weka.MolInstancesCache
MolInstancesCache(IOType, String) - Constructor for class joelib.algo.datamining.weka.MolInstancesCache
MolSparseInstance - class joelib.algo.datamining.weka.MolSparseInstance.: Class for storing an instance as a sparse vector.
MolSparseInstance(MolInstance) - Constructor for class joelib.algo.datamining.weka.MolSparseInstance: Constructor that generates a sparse instance from the given instance.
MolSparseInstance(MolSparseInstance) - Constructor for class joelib.algo.datamining.weka.MolSparseInstance: Constructor that copies the info from the given instance.
MolSparseInstance(double, double[]) - Constructor for class joelib.algo.datamining.weka.MolSparseInstance: Constructor that generates a sparse instance from the given parameters.
MolSparseInstance(double, double[], int[], int) - Constructor for class joelib.algo.datamining.weka.MolSparseInstance: Constructor that inititalizes instance variable with given values.
MolSparseInstance(int) - Constructor for class joelib.algo.datamining.weka.MolSparseInstance: Constructor of an instance that sets weight to one, all values to be missing, and the reference to the dataset to null.
MolViewerEvent - class joelib.gui.molviewer.java3d.util.MolViewerEvent.: Description of the Class
MolViewerEvent(Object, int, JOEMol) - Constructor for class joelib.gui.molviewer.java3d.util.MolViewerEvent: Constructor for the MolViewerEvent object
MolViewerEvent(Object, int, JOEAtom) - Constructor for class joelib.gui.molviewer.java3d.util.MolViewerEvent
MolViewerEvent(Object, int, JOEBond) - Constructor for class joelib.gui.molviewer.java3d.util.MolViewerEvent
MolViewerEvent(Object, int) - Constructor for class joelib.gui.molviewer.java3d.util.MolViewerEvent: Constructor for the MolViewerEvent object
MolViewerEventAdapter - class joelib.gui.molviewer.java3d.util.MolViewerEventAdapter.: Description of the Class
MolViewerEventAdapter() - Constructor for class joelib.gui.molviewer.java3d.util.MolViewerEventAdapter: Constructor for the MolViewerEventAdapter object
MolViewerEventListener - interface joelib.gui.molviewer.java3d.util.MolViewerEventListener.: Description of the Interface
MolarRefractivity - class joelib.desc.types.MolarRefractivity.: Calculates the molar refractivity (MR).
MolarRefractivity() - Constructor for class joelib.desc.types.MolarRefractivity
MolconnZ - class joelib.io.types.MolconnZ.: Molconn-Z file format support.
MolconnZ() - Constructor for class joelib.io.types.MolconnZ: Constructor for the Smiles object
MolecularScene - class joelib.gui.molviewer.java3d.graphics3D.MolecularScene.: Description of the Class
MolecularScene(Canvas3D) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Constructor for the MolecularScene object
MolecularWeight - class joelib.desc.types.MolecularWeight.: Calculates the molecular weight.
MolecularWeight() - Constructor for class joelib.desc.types.MolecularWeight: Constructor for the KierShape1 object
MoleculeArray - class joelib.io.types.cml.MoleculeArray.: CML molecule array writer.
MoleculeArray(PrintStream, CMLWriterProperties) - Constructor for class joelib.io.types.cml.MoleculeArray
MoleculeAttributeArray - class joelib.io.types.cml.MoleculeAttributeArray.: CML molecule array writer.
MoleculeAttributeArray(PrintStream, CMLWriterProperties) - Constructor for class joelib.io.types.cml.MoleculeAttributeArray
MoleculeCache - interface joelib.desc.data.MoleculeCache.: Molecule caching interface for data mining classes.
MoleculeCallback - interface joelib.io.MoleculeCallback.: Molecule callback.
MoleculeDataCacheHolder - class joelib.util.MoleculeDataCacheHolder.: Molecule-Data matrix cache.
MoleculeFileCDO - class joelib.io.types.cml.MoleculeFileCDO.: CDO object needed as interface with the JCFL library for reading CML encoded data.
MoleculeFileCDO() - Constructor for class joelib.io.types.cml.MoleculeFileCDO
MoleculeFileCreation - class joelib.process.types.MoleculeFileCreation.: Calling processor classes if the filter rule fits.
MoleculeFileCreation() - Constructor for class joelib.process.types.MoleculeFileCreation: Constructor for the DescSelectionWriter object
MoleculeFileDeletion - class joelib.process.types.MoleculeFileDeletion.: Calling processor classes if the filter rule fits.
MoleculeFileDeletion() - Constructor for class joelib.process.types.MoleculeFileDeletion: Constructor for the DescSelectionWriter object
MoleculeFileType - interface joelib.io.MoleculeFileType.: Interface for implementing molecule reader/writer classes.
MoleculeHuge - class joelib.io.types.cml.MoleculeHuge.: CML molecule writing all informations explicitely.
MoleculeHuge(PrintStream, CMLWriterProperties) - Constructor for class joelib.io.types.cml.MoleculeHuge
MoleculeIOException - exception joelib.io.MoleculeIOException.: Molecule IO exception, which will be thrown if the molecule entry is corrupt.
MoleculeIOException() - Constructor for class joelib.io.MoleculeIOException: Constructor for the MoleculeIOException object
MoleculeIOException(String) - Constructor for class joelib.io.MoleculeIOException: Constructor for the MoleculeIOException object
MoleculeLarge - class joelib.io.types.cml.MoleculeLarge.: CML molecule writer which uses some arrays to avoid overhead.
MoleculeLarge(PrintStream, CMLWriterProperties) - Constructor for class joelib.io.types.cml.MoleculeLarge
MoleculeNode - class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode.: Description of the Class
MoleculeNode() - Constructor for class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode: Constructor for the MoleculeNode object
MoleculeViewer2D - class joelib.gui.render.MoleculeViewer2D.: A 2D renderer for viewing molecules.
MoleculeViewer2D(RenderingAtoms, Renderer2DModel) - Constructor for class joelib.gui.render.MoleculeViewer2D: Constructs a MoleculeViewer with a molecule to display and a Renderer2DModel containing the information on how to display it.
MoleculeViewer2D(RenderingAtoms) - Constructor for class joelib.gui.render.MoleculeViewer2D: Constructs a MoleculeViewer with a molecule to display
MoleculeViewer2D() - Constructor for class joelib.gui.render.MoleculeViewer2D: Constructs a MoleculeViewer with a molecule to display
MoleculesDescriptorMatrix - class joelib.desc.data.MoleculesDescriptorMatrix.: Purpose: Holds all native value descriptors as double matrix for all known molecules.
MoleculesDescriptorMatrix() - Constructor for class joelib.desc.data.MoleculesDescriptorMatrix: Constructor for the MoleculesDescriptorMatrix object
MoleculesDescriptorMatrix(IOType, String) - Constructor for class joelib.desc.data.MoleculesDescriptorMatrix: Constructor for the IntResult object
MonAtomExpr - class joelib.smarts.atomexpr.MonAtomExpr.: Single atom expression for atom expression.
MonAtomExpr() - Constructor for class joelib.smarts.atomexpr.MonAtomExpr: Constructor for the MonAtomExpr object
MonAtomExpr(int) - Constructor for class joelib.smarts.atomexpr.MonAtomExpr: Constructor for the MonAtomExpr object
MonBondExpr - class joelib.smarts.bondexpr.MonBondExpr.: Single bond expression for SMARTS.
MonBondExpr() - Constructor for class joelib.smarts.bondexpr.MonBondExpr: Constructor for the MonBondExpr object
MonBondExpr(int) - Constructor for class joelib.smarts.bondexpr.MonBondExpr: Constructor for the MonBondExpr object
Mopac - class joelib.io.types.Mopac.: Reader for MopacOut format.
Mopac() - Constructor for class joelib.io.types.Mopac
Morgan - class joelib.algo.morgan.Morgan.: Morgan number generation and unique molecule numbering.
Morgan(TieResolver) - Constructor for class joelib.algo.morgan.Morgan: Constructor for the Morgan object
MorganTest - class joelib.algo.morgan.MorganTest.: Unique molecule numbering test.
MorganTest() - Constructor for class joelib.algo.morgan.MorganTest
MouseFastRotate - class joelib.gui.molviewer.java3d.graphics3D.MouseFastRotate.: MouseFastRotate.java
MouseFastRotate(TransformGroup, MolecularScene) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.MouseFastRotate: Constructor for the MouseFastRotate object
m_maxNumPage - Variable in class joelib.gui.util.JEditorPaneAndPagePrinter
main(String[]) - Static method in class cformat.PrintfFormatTest: Tests the class PrintfFormat.
main(String[]) - Static method in class cformat.ScanfFormatTest: Tests the class ScanfFormat.
main(String[]) - Static method in class cformat.ScanfReaderTest: Tests the class ScanfReader.
main(String[]) - Static method in class com.obrador.Jpeg
main(String[]) - Static method in class joelib.JOE: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.algo.datamining.weka.MolSparseInstance: Main method for testing this class.
main(String[]) - Static method in class joelib.algo.morgan.MorganTest: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.data.JOEKernel
main(String[]) - Static method in class joelib.gui.molviewer.java3d.Viewer: Main method
main(String[]) - Static method in class joelib.gui.molviewer.java3d.graphics3D.Sphere: Description of the Method
main(String[]) - Static method in class joelib.gui.render.MoleculeViewer2D: The main method.
main(String[]) - Static method in class joelib.gui.test.JOELibTestGUI: The main program for the ConvertSkip class
main(String[]) - Static method in class joelib.math.symmetry.Symmetry: The main program for the symmetry class.
main(String[]) - Static method in class joelib.smarts.test.SMARTSEvaluation: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.Combine: The main program for the ConvertSkip class
main(String[]) - Static method in class joelib.test.Comparison: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.Convert: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.ConvertSkip: The main program for the ConvertSkip class
main(String[]) - Static method in class joelib.test.DescriptorCalculation: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.DescriptorSelection: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.DescriptorStatistic: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.EuklidianComparison: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.GhemicalTest: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.GroupContributionTest
main(String[]) - Static method in class joelib.test.TestDescriptor: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.TestMolecule: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.TestPatty: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.TestSMILES: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.TestSSSR: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.TestSmarts: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.test.Title2DataTest: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.util.cdk.TestLayout: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.util.database.SimpleJOELibDatabase: The main program for the TestSmarts class
main(String[]) - Static method in class joelib.util.ghemical.TestInterface: The main method creates an instance of the main program class 'TestInterface'.
main(String[]) - Static method in class jtt.docbook.DocBookArticles: The main program for the TestSmarts class
main(String[]) - Static method in class jtt.docbook.DocBookEquations: The main program for the TestSmarts class
main(String[]) - Static method in class jtt.docbook.DocBookMolecules: The main program for the TestSmarts class
main(String[]) - Static method in class jtt.docbook.Jade: The main program for the TestSmarts class
main(String[]) - Static method in class jtt.util.Executable: The main program for the TestSmarts class
main(String[]) - Static method in class wsi.ra.tool.ArrayStatistic: Tests the paired stats object from the command line.
main(String[]) - Static method in class wsi.ra.tool.StatisticUtils: Main method for testing this class.
main(String[]) - Static method in class wsi.ra.tool.Statistics: Main method for testing this class.
mainPtr - Variable in class joelib.smarts.ParseSmart: Description of the Field
mainPtrIndex - Variable in class joelib.smarts.ParseSmart: Description of the Field
markGrowBonds(Pattern) - Static method in class joelib.smarts.ParseSmart: Description of the Method
match(Vector) - Method in class joelib.smarts.JOESSMatch
match(JOEMol) - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
match(JOEMol, boolean) - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
match(JOEMol, Pattern, Vector) - Method in class joelib.smarts.ParseSmart
match(JOEMol, Pattern, Vector, boolean) - Method in class joelib.smarts.ParseSmart
matrix2instances(double[][], String[], int[]) - Static method in class joelib.algo.datamining.weka.InstancesHelper
matrixToString(Matrix) - Static method in class joelib.math.MathHelper
matrixToString(Matrix, int, int) - Static method in class joelib.math.MathHelper
max - Variable in class wsi.ra.tool.ArrayStatistic: The maximum value seen, or Double.NaN if no values seen
maxBitSize - Variable in class joelib.desc.result.BitResult
maxIndex(double[]) - Static method in class wsi.ra.tool.StatisticUtils: Returns index of maximum element in a given array of doubles.
maxIndex(int[]) - Static method in class wsi.ra.tool.StatisticUtils: Returns index of maximum element in a given array of integers.
maxType - Static variable in class joelib.desc.Description: Description of the Field
maxdev - Variable in class joelib.math.symmetry.SymmetryElement: Larges error associated with the element.
mean - Variable in class wsi.ra.tool.ArrayStatistic: The mean of values at the last calculateDerived() call
mean(double[]) - Static method in class wsi.ra.tool.StatisticUtils: Computes the mean for an array of doubles.
memberOfRingCount() - Method in class joelib.molecule.JOEAtom: Returns the number of rings in which this atom is contained.
mergeInstance(MolInstance) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Merges this instance with the given instance and returns the result.
method - Variable in class joelib.math.symmetry.TransformationAtom
min - Variable in class wsi.ra.tool.ArrayStatistic: The minimum value seen, or Double.NaN if no values seen
minIndex(int[]) - Static method in class wsi.ra.tool.StatisticUtils: Returns index of minimum element in a given array of integers.
minIndex(double[]) - Static method in class wsi.ra.tool.StatisticUtils: Returns index of minimum element in a given array of doubles.
minimumPairRMS(JOEMol, double[], double[], boolean[]) - Static method in class joelib.util.JHM: Description of the Method
minus(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: subtract a vector from this vector
mol - Variable in class joelib.gui.render.RenderAtom
mol2image(JOEMol) - Method in class joelib.gui.render.Mol2Image
mol2image(JOEMol, StringString[]) - Method in class joelib.gui.render.Mol2Image
mol2image(JOEMol, String) - Method in class joelib.gui.render.Mol2Image
mol2image(JOEMol, JOESmartsPattern) - Method in class joelib.gui.render.Mol2Image
mol2image(JOEMol, String, JOESmartsPattern, String, String, String, String) - Method in class joelib.gui.render.Mol2Image
molDescriptors(JOEMol) - Method in class joelib.desc.DescriptorHelper: Returns all descriptor values in the molecule as JOEGenericData elements.
molecule - Variable in class joelib.gui.render.Arrows
molecule - Variable in class joelib.gui.render.ConjugatedRings
molecule - Variable in class joelib.gui.render.OrthoLines
molecule2handle(JOEMol) - Method in class joelib.io.SimpleReaderWriterPipe: The molecule which should be handled when SimpleReaderWriterPipe.readWriteNext() is called.
moleculeToFile(String, JOEMol, IOType, boolean) - Static method in class joelib.util.JHM
moleculesLoaded() - Method in class joelib.io.SimpleReader: Returns the number of loaded molecules.
moleculesLoaded() - Method in class joelib.io.SimpleReaderWriterPipe: Returns the number of loaded molecules.
moleculesWritten() - Method in class joelib.io.SimpleReaderWriterPipe: Returns the number of written molecules.
moleculesWritten() - Method in class joelib.io.SimpleWriter: Returns the number of written molecules.
morgan - Variable in class joelib.util.database.AbstractDatabase
mul(XYZVector, Matrix3x3) - Method in class joelib.math.Matrix3x3: Description of the Method
mul(Matrix3x3, XYZVector) - Method in class joelib.math.Matrix3x3: Description of the Method
mul(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
mul(XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
mul(XYZVector, Matrix3x3) - Static method in class joelib.math.XYZVector: Description of the Method
mul(XYZVector, XYZVector, Matrix3x3) - Static method in class joelib.math.XYZVector: Description of the Method
mul(XYZVector, Matrix3x3, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
mul(int) - Method in class joelib.math.XYZVector: Description of the Method
mul(XYZVector, int) - Static method in class joelib.math.XYZVector: Description of the Method
mul(XYZVector, XYZVector, double) - Static method in class joelib.math.XYZVector: Description of the Method
mul(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
muling(double) - Method in class joelib.math.XYZVector: Description of the Method
muling(Matrix3x3) - Method in class joelib.math.XYZVector: Description of the Method
mult(Matrix3D) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Multiply this matrix by a second: M = M*R

N

NAME - Static variable in class joelib.io.types.cml.CMLCoreModule
NATIVE_DESCRIPTORS - Static variable in class joelib.desc.data.MolDescCounter: Description of the Field
NO2Groups - class joelib.desc.types.NO2Groups.: Number of NO2 groups.
NO2Groups() - Constructor for class joelib.desc.types.NO2Groups
NONE - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
NOTFilter - class joelib.process.filter.NOTFilter.: Molecule process filter NOT condition.
NOTFilter() - Constructor for class joelib.process.filter.NOTFilter: Constructor for the DescriptorFilter object
NOTFilter(Filter) - Constructor for class joelib.process.filter.NOTFilter: Constructor for the DescriptorFilter object
NOT_EQUAL - Static variable in class joelib.process.filter.NativeValueFilter
NOT_EQUAL - Static variable in class joelib.process.filter.SMARTSFilter
NativeValue - interface joelib.desc.NativeValue.: Interface to have a fast method to getting native descriptor values.
NativeValueFilter - class joelib.process.filter.NativeValueFilter.: Molecule process filter for native value descriptor entries.
NativeValueFilter() - Constructor for class joelib.process.filter.NativeValueFilter: Constructor for the DescriptorFilter object
NativeValueFilter(String, int, double) - Constructor for class joelib.process.filter.NativeValueFilter: Constructor for the DescriptorFilter object
NativeValueIterator - class joelib.util.iterator.NativeValueIterator.: Gets an iterator over native descriptor values (int or double) of this molecule.
NativeValueIterator(JOEMol, GenericDataIterator) - Constructor for class joelib.util.iterator.NativeValueIterator: Constructor for the GenericDataIterator object
NbrAtomIterator - class joelib.util.iterator.NbrAtomIterator.: Gets an iterator over all neighbour atoms in a atom.
NbrAtomIterator(Vector, JOEAtom) - Constructor for class joelib.util.iterator.NbrAtomIterator: Constructor for the NbrAtomIterator object
NumberFormatDescResult - interface joelib.desc.NumberFormatDescResult.: Interface definition for descriptor results which use number formats.
NumberOfAtoms - class joelib.desc.types.NumberOfAtoms.: Number of atoms.
NumberOfAtoms() - Constructor for class joelib.desc.types.NumberOfAtoms: Constructor for the KierShape1 object
NumberOfB - class joelib.desc.types.NumberOfB.: Number of bor atoms.
NumberOfB() - Constructor for class joelib.desc.types.NumberOfB
NumberOfBonds - class joelib.desc.types.NumberOfBonds.: Number of bonds.
NumberOfBonds() - Constructor for class joelib.desc.types.NumberOfBonds: Constructor for the KierShape1 object
NumberOfBr - class joelib.desc.types.NumberOfBr.: Number of brom atoms.
NumberOfBr() - Constructor for class joelib.desc.types.NumberOfBr
NumberOfC - class joelib.desc.types.NumberOfC.: Number of carbon atoms.
NumberOfC() - Constructor for class joelib.desc.types.NumberOfC
NumberOfCl - class joelib.desc.types.NumberOfCl.: Number of chlor atoms.
NumberOfCl() - Constructor for class joelib.desc.types.NumberOfCl
NumberOfF - class joelib.desc.types.NumberOfF.: Number of fluor atoms.
NumberOfF() - Constructor for class joelib.desc.types.NumberOfF
NumberOfHal - class joelib.desc.types.NumberOfHal.: Number of halogen atoms.
NumberOfHal() - Constructor for class joelib.desc.types.NumberOfHal
NumberOfI - class joelib.desc.types.NumberOfI.: Number of iod atoms.
NumberOfI() - Constructor for class joelib.desc.types.NumberOfI
NumberOfN - class joelib.desc.types.NumberOfN.: Number of nitrogen atoms.
NumberOfN() - Constructor for class joelib.desc.types.NumberOfN
NumberOfO - class joelib.desc.types.NumberOfO.: Number of oxygen atoms.
NumberOfO() - Constructor for class joelib.desc.types.NumberOfO
NumberOfP - class joelib.desc.types.NumberOfP.: Number of phospor atoms.
NumberOfP() - Constructor for class joelib.desc.types.NumberOfP
NumberOfS - class joelib.desc.types.NumberOfS.: Number of sulfur atoms.
NumberOfS() - Constructor for class joelib.desc.types.NumberOfS
n1 - Variable in class joelib.util.types.Template: Description of the Field
n2 - Variable in class joelib.util.types.Template: Description of the Field
n3 - Variable in class joelib.util.types.Template: Description of the Field
n4 - Variable in class joelib.util.types.Template: Description of the Field
nativeValueIterator() - Method in class joelib.molecule.JOEMol: Gets an iterator over native descriptor values (int or double) of this molecule.
nbrAtomIterator() - Method in class joelib.molecule.JOEAtom: Returns a NbrAtomIterator for all neighbour atoms in this atom.
needDisplay() - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Return true if the atom need to be display
needExplicitAnd(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
needExplicitAnd2(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
neededProperties() - Method in class joelib.process.types.DescBinning: Description of the Method
neededProperties() - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
neededProperties() - Method in class joelib.process.types.DescStatistic: Description of the Method
neededProperties() - Method in class joelib.process.types.DescVarianceNorm: Description of the Method
neededProperties() - Method in class joelib.process.types.DistanceCalculation: Description of the Method
negate() - Method in class joelib.util.JOEBitVec: Description of the Method
newAtom() - Method in class joelib.molecule.JOEMol: Creates a new atom and adds it to molecule.
newResidue() - Method in class joelib.molecule.JOEAtom
newResidue() - Method in class joelib.molecule.JOEMol: Returns and adds new residue informations for this molecule.
next() - Method in class joelib.util.iterator.GenericDataIterator: Description of the Method
next() - Method in class joelib.util.iterator.NativeValueIterator: Description of the Method
next() - Method in class joelib.util.iterator.NbrAtomIterator: Description of the Method
next() - Method in class joelib.util.iterator.VectorIterator: Description of the Method
next() - Method in class wsi.ra.tool.DequeIterator
next - Variable in class wsi.ra.tool.DequeNode
nextAtom() - Method in class joelib.util.iterator.AtomIterator: Description of the Method
nextBit(int) - Method in class joelib.util.JOEBitVec: Returns the index of the first bit that is set to true that occurs on or after the specified starting index.
nextBond() - Method in class joelib.util.iterator.BondIterator: Description of the Method
nextButton_actionPerformed(ActionEvent) - Method in class joelib.gui.molviewer.java3d.ViewerFrame: Description of the Method
nextClearBit(int) - Method in class joelib.util.BitSet14: Returns the index of the first bit that is set to false that occurs on or after the specified starting index.
nextConformer() - Method in class joelib.util.iterator.ConformerIterator
nextDouble() - Method in class joelib.util.iterator.NativeValueIterator
nextFloat() - Method in class joelib.util.JOERandom: Description of the Method
nextGenericData() - Method in class joelib.util.iterator.GenericDataIterator: Description of the Method
nextInt() - Method in class joelib.util.JOERandom: Description of the Method
nextInt() - Method in class joelib.util.iterator.NativeValueIterator
nextNativeValue() - Method in class joelib.util.iterator.NativeValueIterator: Description of the Method
nextNbrAtom() - Method in class joelib.util.iterator.NbrAtomIterator: Description of the Method
nextResidue() - Method in class joelib.util.iterator.ResidueIterator
nextRing() - Method in class joelib.util.iterator.RingIterator: Description of the Method
nextRotamer() - Method in class joelib.util.iterator.RotamerIterator: Description of the Method
nextRotor() - Method in class joelib.util.iterator.RotorIterator: Description of the Method
nextSetBit(int) - Method in class joelib.util.BitSet14: Returns the index of the first bit that is set to true that occurs on or after the specified starting index.
nextString() - Method in class joelib.util.iterator.NativeValueIterator
normal - Variable in class joelib.math.symmetry.SymmetryElement
normalInverse(double) - Static method in class wsi.ra.tool.Statistics: Returns the value, x, for which the area under the Normal (Gaussian) probability density methodName (integrated from minus infinity to x) is equal to the argument y (assumes mean is zero, variance is one).
normalProbability(double) - Static method in class wsi.ra.tool.Statistics: Returns the area under the Normal (Gaussian) probability density methodName, integrated from minus infinity to x (assumes mean is zero, variance is one).
normalize() - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: change the vector's length so that it becomes a unit vector
normalize() - Method in class joelib.math.XYZVector: Description of the Method
normalize(double[]) - Static method in class wsi.ra.tool.StatisticUtils: Normalizes the doubles in the array by their sum.
normalize(double[], double) - Static method in class wsi.ra.tool.StatisticUtils: Normalizes the doubles in the array using the given value.
notAtomExpr(AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
notBondExpr(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
notEquals(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
notEquals(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
notionalToCartesian(double, double, double, double, double, double) - Static method in class joelib.math.CrystalGeometryTools: Calculates cartesian vectors for unit cell axes from axes lengths and angles between axes.
nparam - Variable in class joelib.math.symmetry.SymmetryElement: 4 for inversion and planes, 7 for axes.
numAtoms() - Method in class joelib.molecule.JOEMol: Returns the number of atoms.
numAtoms() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
numAttributes() - Method in class joelib.algo.datamining.weka.MolSparseInstance: Returns the number of attributes.
numBonds() - Method in class joelib.molecule.JOEMol: Returns the number of bonds.
numBonds() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
numConformers() - Method in class joelib.molecule.JOEMol: Returns the number of conformers of this molecule.
numHvyAtoms() - Method in class joelib.molecule.JOEMol: Returns the number of heavy atoms.
numMatches() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
numResidues() - Method in class joelib.molecule.JOEMol: Returns the number of residues.
numRotors() - Method in class joelib.molecule.JOEMol: Returns the number of rotatable bonds.
numValues() - Method in class joelib.algo.datamining.weka.MolSparseInstance: Returns the number of values in the sparse vector.
numberDescriptors() - Method in class joelib.desc.data.MolDescCounter: Gets the numberDescriptors attribute of the MolDescCounter object
numberMolecules() - Method in class joelib.desc.data.MolDescCounter: Gets the numberMolecules attribute of the MolDescCounter object
numberOfBins - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
numberOfDescriptors() - Method in class joelib.algo.datamining.weka.MolInstancesCache
numberOfDescriptors() - Method in interface joelib.desc.data.MoleculeCache
numberOfDescriptors() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
numberOfDescriptors() - Method in class joelib.process.types.DescBinning: Description of the Method
numberOfDescs() - Method in class joelib.desc.DescriptorHelper: Gets the number of descriptors that are available.
numberOfGOAtoms() - Method in class joelib.util.ghemical.GhemicalInterface
numberOfMolecules() - Method in class joelib.algo.datamining.weka.MolInstancesCache
numberOfMolecules() - Method in interface joelib.desc.data.MoleculeCache
numberOfMolecules() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method

O

OELipoGrid - Static variable in class joelib.util.JOEHelper: Description of the Field
OEPolarGrid - Static variable in class joelib.util.JOEHelper: Description of the Field
OE_EVAL_STACKSIZE - Static variable in class joelib.smarts.ParseSmart: Description of the Field
OLDCODE - Static variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
OPTCHANGE_THRESHOLD_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
OPT_CHANGE_HITS_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
ORFilter - class joelib.process.filter.ORFilter.: Molecule process filter OR condition.
ORFilter() - Constructor for class joelib.process.filter.ORFilter: Constructor for the DescriptorFilter object
ORFilter(Filter, Filter) - Constructor for class joelib.process.filter.ORFilter: Constructor for the DescriptorFilter object
ORIG - Static variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field
OSOGroups - class joelib.desc.types.OSOGroups.: Number of OSO groups.
OSOGroups() - Constructor for class joelib.desc.types.OSOGroups
OS_LINUX - Static variable in class joelib.ext.ExternalHelper
OS_SOLARIS - Static variable in class joelib.ext.ExternalHelper
OS_WINDOWS - Static variable in class joelib.ext.ExternalHelper
OUTPUT_ARRAY - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OUTPUT_ARRAY_S - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OUTPUT_ATTRIBUTE_ARRAY - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OUTPUT_ATTRIBUTE_ARRAY_S - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OUTPUT_HUGE - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OUTPUT_HUGE_S - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OUTPUT_LARGE - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OUTPUT_LARGE_S - Static variable in class joelib.io.types.ChemicalMarkupLanguage
OrthoLine - class joelib.gui.render.OrthoLine.: Holding single orthogonal line informations.
OrthoLine() - Constructor for class joelib.gui.render.OrthoLine
OrthoLines - class joelib.gui.render.OrthoLines.: Holding multiple orthogonal line informations.
OrthoLines(JOEMol, String) - Constructor for class joelib.gui.render.OrthoLines
o - Variable in class joelib.util.types.StringObject: Description of the Field
or(BitSet14) - Method in class joelib.util.BitSet14: Performs a logical OR of this bit set with the bit set argument.
or(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
or(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec: Description of the Method
orAtomExpr(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
orAtomExprLeaf(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
orSet(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
order - Variable in class joelib.math.symmetry.SymmetryElement: Applying transformation this many times is identity.
order - Variable in class joelib.smiles.ClosureBond: Order.
orderAtomExpr(AtomExpr, AtomExpr) - Static method in class joelib.smarts.atomexpr.AtomExpr: Description of the Method
organic - Variable in class joelib.molecule.Element: Description of the Field
orthoLines - Variable in class joelib.gui.render.OrthoLines
out(OutputStream) - Method in class joelib.util.JOEBitVec: Description of the Method
outputDescription() - Method in interface joelib.io.MoleculeFileType: Description of the Method
outputDescription() - Method in class joelib.io.types.Amber
outputDescription() - Method in class joelib.io.types.BMP
outputDescription() - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
outputDescription() - Method in class joelib.io.types.ClearTextFormat: Description of the Method
outputDescription() - Method in class joelib.io.types.Flat: Description of the Method
outputDescription() - Method in class joelib.io.types.GIF
outputDescription() - Method in class joelib.io.types.Gaussian
outputDescription() - Method in class joelib.io.types.HIN
outputDescription() - Method in class joelib.io.types.JCAMP: Description of the Method
outputDescription() - Method in class joelib.io.types.JPEG
outputDescription() - Method in class joelib.io.types.MDLSD: Description of the Method
outputDescription() - Method in class joelib.io.types.Matlab: Description of the Method
outputDescription() - Method in class joelib.io.types.MolconnZ: Description of the Method
outputDescription() - Method in class joelib.io.types.Mopac
outputDescription() - Method in class joelib.io.types.PDB: Description of the Method
outputDescription() - Method in class joelib.io.types.PDF
outputDescription() - Method in class joelib.io.types.PNG
outputDescription() - Method in class joelib.io.types.POVRay: Description of the Method
outputDescription() - Method in class joelib.io.types.PPM
outputDescription() - Method in class joelib.io.types.Smiles: Description of the Method
outputDescription() - Method in class joelib.io.types.SybylMol2: Description of the Method
outputDescription() - Method in class joelib.io.types.Tinker: Description of the Method
outputDescription() - Method in class joelib.io.types.Undefined: Description of the Method
outputDescription() - Method in class joelib.io.types.XYZ: Description of the Method
outputDescription() - Method in class joelib.io.types.ZIP: Description of the Method
outputFileExtensions() - Method in interface joelib.io.MoleculeFileType: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.Amber
outputFileExtensions() - Method in class joelib.io.types.BMP
outputFileExtensions() - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.ClearTextFormat: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.Flat: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.GIF
outputFileExtensions() - Method in class joelib.io.types.Gaussian
outputFileExtensions() - Method in class joelib.io.types.HIN
outputFileExtensions() - Method in class joelib.io.types.JCAMP: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.JPEG
outputFileExtensions() - Method in class joelib.io.types.MDLSD: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.Matlab: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.MolconnZ: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.Mopac
outputFileExtensions() - Method in class joelib.io.types.PDB: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.PDF
outputFileExtensions() - Method in class joelib.io.types.PNG
outputFileExtensions() - Method in class joelib.io.types.POVRay: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.PPM
outputFileExtensions() - Method in class joelib.io.types.Smiles: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.SybylMol2: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.Tinker: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.Undefined: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.XYZ: Description of the Method
outputFileExtensions() - Method in class joelib.io.types.ZIP: Description of the Method

P

PDB - class joelib.io.types.PDB.: Reader/Writer for Protein DataBank (PDB) files.
PDB() - Constructor for class joelib.io.types.PDB: Constructor for the Undefined object
PDF - class joelib.io.types.PDF.: Writer for Portable Adobe Document Format (PDF) format with native descriptors (scalars).
PDF() - Constructor for class joelib.io.types.PDF
PEAK_ASSIGNMENTS - Static variable in class joelib.jcamp.JCAMPParser: data representation: PEAK ASSIGNMENTS definition
PEAK_TABLE - Static variable in class joelib.jcamp.JCAMPParser: data representation: PEAK TABLE definition
PNG - class joelib.io.types.PNG.: Writer for a Portable Network Graphics (PNG) image.
PNG() - Constructor for class joelib.io.types.PNG
POVRay - class joelib.io.types.POVRay.: Writer for Persistance Of Vision Raytracer (POVRay) files.
POVRay() - Constructor for class joelib.io.types.POVRay
PPM - class joelib.io.types.PPM.: Writer for a Portable Pixelmap (PPM) image.
PPM() - Constructor for class joelib.io.types.PPM
PT_ACCEPTOR - Static variable in class joelib.util.JOEHelper: Description of the Field
PT_ANION - Static variable in class joelib.util.JOEHelper: Description of the Field
PT_CATION - Static variable in class joelib.util.JOEHelper: Description of the Field
PT_DONOR - Static variable in class joelib.util.JOEHelper: Description of the Field
PT_HYDROPHOBIC - Static variable in class joelib.util.JOEHelper: Description of the Field
PT_METAL - Static variable in class joelib.util.JOEHelper: Description of the Field
PT_OTHER - Static variable in class joelib.util.JOEHelper: Description of the Field
PT_POLAR - Static variable in class joelib.util.JOEHelper: Description of the Field
ParseSmart - class joelib.smarts.ParseSmart.: Contains methods for SMARTS parsing.
ParseSmart() - Constructor for class joelib.smarts.ParseSmart
ParseState - class joelib.smarts.ParseState.: Holds closure bond informations.
ParseState() - Constructor for class joelib.smarts.ParseState
Pattern - class joelib.smarts.Pattern.: SMARTS pattern representation.
Pattern() - Constructor for class joelib.smarts.Pattern
Patty - class joelib.smarts.Patty.: PATtern TYper (PATTY) using SMARTS patterns.
Patty() - Constructor for class joelib.smarts.Patty: Constructor for the PATTY object.
PickHighlightBehavior - class joelib.gui.molviewer.java3d.graphics3D.PickHighlightBehavior.: DOCUMENT ME!
PickHighlightBehavior(MolecularScene, Canvas3D, BranchGroup, Bounds) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.PickHighlightBehavior
Point3D - class joelib.gui.molviewer.java3d.math.geometry.Point3D.: A class that provides mathematical definition of and utility for 3D geometric points
Point3D() - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Point3D: default constructor: coordinates are all 0.0;
Point3D(double, double, double) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Point3D: full constructor
Point3D(Point3D) - Constructor for class joelib.gui.molviewer.java3d.math.geometry.Point3D: copy constructor
PointGroup - class joelib.math.symmetry.PointGroup.: PointGroup.
PointGroup(String, String, boolean) - Constructor for class joelib.math.symmetry.PointGroup: Constructor for the PointGroup object
PointGroups - class joelib.math.symmetry.PointGroups.: PointGroups.
PointGroups() - Constructor for class joelib.math.symmetry.PointGroups: Constructor for the AtomIntInt object
PolarSurfaceArea - class joelib.desc.types.PolarSurfaceArea.: Calculates the polar surface area (PSA).
PolarSurfaceArea() - Constructor for class joelib.desc.types.PolarSurfaceArea
PpmEncoder - class Acme.JPM.Encoders.PpmEncoder.: Write out an image as a PPM.
PpmEncoder(Image, OutputStream) - Constructor for class Acme.JPM.Encoders.PpmEncoder
PpmEncoder(ImageProducer, OutputStream) - Constructor for class Acme.JPM.Encoders.PpmEncoder
PrintfFormat - class cformat.PrintfFormat.: Object for formatting output in the same way as the C printf methodName.
PrintfFormat(String) - Constructor for class cformat.PrintfFormat: Creates a new instance of PrintfFormat from the supplied format string.
PrintfFormatTest - class cformat.PrintfFormatTest.: Testing class for PrintfFormat.
PrintfFormatTest() - Constructor for class cformat.PrintfFormatTest
PrintfStream - class cformat.PrintfStream.: PrintStream which outputs primitive types using C printf style formatting.
PrintfStream(OutputStream) - Constructor for class cformat.PrintfStream: Creates a PrintfStream, without automatic line flushing, from an existing OutputStream.
PrintfStream(OutputStream, boolean) - Constructor for class cformat.PrintfStream: Creates a PrintfStream from an existing OutputStream.
PrintfWriter - class cformat.PrintfWriter.: Writer class to output primitive types using C printf style formatting.
PrintfWriter(OutputStream) - Constructor for class cformat.PrintfWriter: Creates a PrintfWriter, without automatic line flushing, from an existing OutputStream.
PrintfWriter(OutputStream, boolean) - Constructor for class cformat.PrintfWriter: Creates a PrintfWriter from an existing OutputStream.
PrintfWriter(Writer) - Constructor for class cformat.PrintfWriter: Creates a PrintfWriter, without automatic line flushing, from an existing Writer.
PrintfWriter(Writer, boolean) - Constructor for class cformat.PrintfWriter: Creates a PrintfWriter from an existing Writer.
ProcessFactory - class joelib.process.ProcessFactory.: Factory class to get molecule processing classes.
ProcessInfo - class joelib.process.ProcessInfo.: Processing informations.
ProcessInfo(String, String, String) - Constructor for class joelib.process.ProcessInfo: Constructor for the DescriptorInfo object
ProcessPipe - class joelib.process.ProcessPipe.: Processing pipe for appending multiple processes combined with Filter functionality.
ProcessPipe() - Constructor for class joelib.process.ProcessPipe: Constructor for the SimpleReader object
ProcessPipeEntry - class joelib.process.ProcessPipeEntry.: Processing pipe entry.
ProcessPipeEntry(JOEProcess, Filter, Hashtable) - Constructor for class joelib.process.ProcessPipeEntry: Constructor for the ProcessPipeEntry object
PropertyAcceptor - interface joelib.util.PropertyAcceptor.: Descriptor base class.
PropertyHolder - class wsi.ra.tool.PropertyHolder.: Singleton class to hold java properties.
PropertyWriter - interface joelib.io.PropertyWriter.: Interface for molecule file formats, which accepts descriptor values.
p - Variable in class joelib.util.types.StringPattern: Description of the Field
paint(Graphics) - Method in class joelib.gui.render.MoleculeViewer2D: Paints the molecule onto the JPanel
paintBoundingBox(RenderingAtoms, String, int, Graphics) - Method in class joelib.gui.render.Renderer2D
paintBoundingBox(RenderingAtoms, String, int, Graphics, boolean, boolean) - Method in class joelib.gui.render.Renderer2D
paintMolecule(RenderingAtoms, Graphics) - Method in class joelib.gui.render.Renderer2D: triggers the methods to make the molecule fit into the frame and to paint it.
paintReaction(JOEMol[], JOEMol[], String, Graphics) - Method in class joelib.gui.render.Renderer2D
parent - Variable in class joelib.algo.BFSResult: Description of the Field
parent - Variable in class joelib.algo.DFSResult: Description of the Field
parent - Variable in class joelib.algo.morgan.AtomDoubleParent: Parent atom index of the atom.
parseAtomExpr(int) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseBondExpr(int) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseBondPrimitive() - Method in class joelib.smarts.ParseSmart: Description of the Method
parseCRing(String) - Method in class joelib.gui.render.ConjugatedRing: Parse from-option-to string, where from and to are colon delimited atom indices and option is a colon delimited option string which must start with a non-digit character.
parseCRing(JOEMol, String) - Method in class joelib.gui.render.ConjugatedRings: Parse entries which start with a non-digit.
parseCommandLine(String[]) - Method in class joelib.test.Combine: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.Comparison: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.Convert: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.ConvertSkip: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.DescriptorCalculation: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.DescriptorSelection: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.DescriptorStatistic: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.EuklidianComparison: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.GhemicalTest: Description of the Method
parseCommandLine(String[]) - Method in class joelib.test.Title2DataTest: Description of the Method
parseComplex(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
parseComplexAtomPrimitive() - Method in class joelib.smarts.ParseSmart: Description of the Method
parseEquation(String) - Method in class jtt.docbook.DocBookEquations
parseExternalBond(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
parseFirstLineReadNext(String) - Method in class joelib.io.types.Flat
parseFromToAtom(String) - Method in class joelib.gui.render.FromToAtoms: Parse from-option-to string, where from and to are colon delimited atom indices and option is a colon delimited option string which must start with a non-digit character.
parseFromToAtoms(JOEMol, String) - Method in class joelib.gui.render.Arrows: Parse entries which start with a non-digit.
parseFromToAtoms(JOEMol, String) - Method in class joelib.gui.render.OrthoLines: Parse entries which start with a non-digit.
parseLine(String) - Method in class joelib.data.JOEAromaticTyper: Parses the atom typer definition line to initialize the aromatic typer.
parseLine(String) - Method in class joelib.data.JOEAtomTyper: Description of the Method
parseLine(String) - Method in class joelib.data.JOEElementTable: Description of the Method
parseLine(String) - Method in class joelib.data.JOEGlobalDataBase: Description of the Method
parseLine(String) - Method in class joelib.data.JOEGroupContribution: Description of the Method
parseLine(String) - Method in class joelib.data.JOEIsotopeTable: Description of the Method
parseLine(String) - Method in class joelib.data.JOEPhModel: Description of the Method
parseLine(String) - Method in class joelib.data.JOEResidueData
parseLine(String) - Method in class joelib.data.JOETypeTable: Description of the Method
parseLine(String) - Method in class joelib.data.SoftCodedKernelBase: Description of the Method
parseLine(String) - Method in class joelib.desc.ResultFactory: Description of the Method
parseMolStruct(String) - Method in class jtt.docbook.DocBookMolecules
parseOption(String) - Method in class joelib.gui.render.Arrow: Parse entries which start with a non-digit.
parseOption(String) - Method in class joelib.gui.render.ConjugatedRing: Parse entries which start with a non-digit.
parseOption(String) - Method in class joelib.gui.render.FromToAtoms: Parse entries which start with a non-digit.
parseOption(String) - Method in class joelib.gui.render.OrthoLine: Parse entries which start with a non-digit.
parseOptions(String) - Static method in class joelib.gui.render.Mol2Image
parsePairData(JOEMol, String, JOEGenericData) - Method in class joelib.desc.ResultFactory: Description of the Method
parseRingBond(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
parseSMARTSError(Pattern, BondExpr) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSMARTSPart(Pattern, int) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSMARTSPattern() - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSMARTSRecord(char[], int, int) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSMARTSString(String) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSMARTSString(char[]) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSMARTSString(char[], int, int) - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSimple(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
parseSimpleAtomPrimitive() - Method in class joelib.smarts.ParseSmart: Description of the Method
parseSmiles(JOEMol) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
part - Variable in class joelib.smarts.AtomSpec: Part number of this atom expression in the SMARTS pattern.
parts - Variable in class joelib.smarts.Pattern: Description of the Field
pathSize() - Method in class joelib.ring.JOERing: Returns the size of the ring.
pathToRoot(Vector) - Method in class joelib.molecule.JOERTree: Adds this atom to the given path.
pattern - Variable in class joelib.smarts.RSCacheEntry: Description of the Field
perceiveKekuleBonds() - Method in class joelib.molecule.JOEMol: Description of the Method
performTests(boolean) - Method in class joelib.util.ghemical.TestInterface: Performs a number of test methodName calls to determine if everything is ok.
pickAtomMapping - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule
pickBondMapping - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule
pop() - Method in class joelib.io.types.cml.CMLStack: Retrieves and deletes to last added entry.
popBack() - Method in class wsi.ra.tool.Deque: Returns the back DequeNode and removes it from this stack.
popFront() - Method in class wsi.ra.tool.Deque: Returns the front DequeNode and removes it from this stack.
predict(GroupContributions, JOEMol) - Static method in class joelib.algo.contribution.GCPredictor
prev - Variable in class joelib.util.types.StackType: Description of the Field
prev - Variable in class wsi.ra.tool.DequeNode
previous - Variable in class joelib.smiles.ClosureBond: Index of the previous atom.
print(Graphics, PageFormat, int) - Method in class joelib.gui.util.JEditorPaneAndPagePrinter: The method print must be implemented for Printable interface.
printMatrix(Matrix, OutputStream, int, int) - Static method in class joelib.math.MathHelper: Description of the Method
printPassedTime(String) - Method in class wsi.ra.tool.StopWatch: Prints the passed time since last 'reset stop watch' call in millis to 'stdout'.
printf(String, double) - Method in class cformat.PrintfStream: Prints a double in accordance with the supplied format string.
printf(String, float) - Method in class cformat.PrintfStream: Prints a float in accordance with the supplied format string.
printf(String, long) - Method in class cformat.PrintfStream: Prints a long in accordance with the supplied format string.
printf(String, int) - Method in class cformat.PrintfStream: Prints an int in accordance with the supplied format string.
printf(String, String) - Method in class cformat.PrintfStream: Prints a String in accordance with the supplied format string.
printf(String, char) - Method in class cformat.PrintfStream: Prints a char in accordance with the supplied format string.
printf(PrintfFormat, double) - Method in class cformat.PrintfStream: Prints a double in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, float) - Method in class cformat.PrintfStream: Prints a float in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, long) - Method in class cformat.PrintfStream: Prints a long in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, int) - Method in class cformat.PrintfStream: Prints an int in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, String) - Method in class cformat.PrintfStream: Prints a String in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, char) - Method in class cformat.PrintfStream: Prints a char in accordance with the supplied PrintfFormat object.
printf(String, double) - Method in class cformat.PrintfWriter: Prints a double in accordance with the supplied format string.
printf(String, float) - Method in class cformat.PrintfWriter: Prints a float in accordance with the supplied format string.
printf(String, long) - Method in class cformat.PrintfWriter: Prints a long in accordance with the supplied format string.
printf(String, int) - Method in class cformat.PrintfWriter: Prints an int in accordance with the supplied format string.
printf(String, String) - Method in class cformat.PrintfWriter: Prints a String in accordance with the supplied format string.
printf(String, char) - Method in class cformat.PrintfWriter: Prints a char in accordance with the supplied format string.
printf(PrintfFormat, double) - Method in class cformat.PrintfWriter: Prints a double in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, float) - Method in class cformat.PrintfWriter: Prints a float in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, long) - Method in class cformat.PrintfWriter: Prints a long in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, int) - Method in class cformat.PrintfWriter: Prints an int in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, String) - Method in class cformat.PrintfWriter: Prints a String in accordance with the supplied PrintfFormat object.
printf(PrintfFormat, char) - Method in class cformat.PrintfWriter: Prints a char in accordance with the supplied PrintfFormat object.
proceed() - Method in class wsi.ra.tool.StopWatch: Resets the time to the time when the stop watch was suspended.
process(JOEMol, Map) - Method in class joelib.ext.SimpleExternalProcess: Description of the Method
process(JOEMol, Hashtable) - Method in class joelib.ext.Title2Data: Description of the Method
process(JOEMol, Map) - Method in interface joelib.process.JOEProcess: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.ProcessPipe: Process single molecule entry.
process(JOEMol, Map) - Method in class joelib.process.SimpleProcess: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.AtomPropertyMatrix: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.CreateFileName: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.DescBinning: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.DescSelectionWriter: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.DescStatistic: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.DescVarianceNorm: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.DistanceCalculation: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.MoleculeFileCreation: Description of the Method
process(JOEMol, Map) - Method in class joelib.process.types.MoleculeFileDeletion: Description of the Method
processMouseEvent(MouseEvent) - Method in class joelib.gui.molviewer.java3d.graphics3D.MouseFastRotate: Description of the Method
processStimulus(Enumeration) - Method in class joelib.gui.molviewer.java3d.graphics3D.DragBehavior: Description of the Method
processes() - Method in class joelib.process.ProcessFactory: Description of the Method
project(GeoVector3D, GeoVector3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: return the projection of va on vb
prop - Variable in class joelib.smarts.atomexpr.LeafAtomExpr: Description of the Field
prop - Variable in class joelib.smarts.bondexpr.LeafBondExpr: Description of the Field
propagatePotentialAromatic(JOEAtom) - Method in class joelib.data.JOEAromaticTyper: Description of the Method
propertyCML - Variable in class joelib.util.database.SimpleJOELibDatabase
propertyHASH - Variable in class joelib.util.database.AbstractDatabase
propertyID - Variable in class joelib.util.database.AbstractDatabase
propertyNAME - Variable in class joelib.util.database.AbstractDatabase
propertySDF - Variable in class joelib.util.database.SimpleJOELibDatabase
propertySHASH - Variable in class joelib.util.database.AbstractDatabase
propertySMILES - Variable in class joelib.util.database.SimpleJOELibDatabase
push(String) - Method in class joelib.io.types.cml.CMLStack: Adds an entry to the stack.
pushBack(Object) - Method in class wsi.ra.tool.Deque: Adds the DequeNode to the back of this stack.
pushFront(Object) - Method in class wsi.ra.tool.Deque: Adds the DequeNode to the front of this stack.
pushFront(Deque) - Method in class wsi.ra.tool.Deque
put(int, Object) - Method in class Acme.IntHashtable
put(Object, Object) - Method in class Acme.IntHashtable
put(String, Object) - Method in class joelib.util.MoleculeDataCacheHolder
putArrayStatistic(String, ArrayStatistic) - Method in class joelib.process.types.DescStatistic: Description of the Method

Q

QuickInsertSort - class joelib.sort.QuickInsertSort.: Quick Sort combined with Insert Sort.
QuickInsertSort() - Constructor for class joelib.sort.QuickInsertSort: Constructor for the mixed sorting algorithm.
QuickInsertSort(boolean) - Constructor for class joelib.sort.QuickInsertSort: Constructor for the mixed sorting algorithm.
q - Variable in class joelib.molecule.charge.GasteigerState: Description of the Field

R

RADATA - Static variable in class joelib.jcamp.JCAMPParser: data representation: RADATA definition
RAD_TO_DEG - Static variable in class joelib.math.Matrix3x3: Description of the Field
RAD_TO_DEG - Static variable in class joelib.math.XYZVector: Description of the Field
RAD_TO_DEG - Static variable in class joelib.util.JHM: Description of the Field
RDF_SMOOTHINGFACTORS - Static variable in class joelib.desc.util.AtomPropertyDescriptors
REACTION - Static variable in class joelib.io.types.cml.CMLCoreModule
REMOVE_HYDROGENS - Static variable in class joelib.desc.types.RadialDistributionFunction
REMOVE_HYDROGENS_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
REPLACE_MOLECULE - Static variable in class joelib.gui.molviewer.java3d.util.MolViewerEvent: Description of the Field
REQUIRED_DIMENSION_ENERGETIC - Static variable in class joelib.desc.DescriptorInfo
REQUIRED_DIMENSION_GEOMETRICAL - Static variable in class joelib.desc.DescriptorInfo
REQUIRED_DIMENSION_NO_COORDINATES - Static variable in class joelib.desc.DescriptorInfo
REQUIRED_DIMENSION_TOPOLOGICAL - Static variable in class joelib.desc.DescriptorInfo
REQUIRED_DIMENSION_UNKNOWN - Static variable in class joelib.desc.DescriptorInfo
ROWS - Static variable in class joelib.io.types.cml.elements.MatrixCML
RSCacheEntry - class joelib.smarts.RSCacheEntry.: Pattern chache entry.
RSCacheEntry(Pattern, boolean[]) - Constructor for class joelib.smarts.RSCacheEntry: Constructor for the RSCacheEntry object
RadialDistributionFunction - class joelib.desc.types.RadialDistributionFunction.: Radial Basis Function (RDF).
RadialDistributionFunction() - Constructor for class joelib.desc.types.RadialDistributionFunction
RecurAtomExpr - class joelib.smarts.atomexpr.RecurAtomExpr.: Recurrent atom expression for SMARTS.
RecurAtomExpr() - Constructor for class joelib.smarts.atomexpr.RecurAtomExpr: Constructor for the RecurAtomExpr object
RecurAtomExpr(int) - Constructor for class joelib.smarts.atomexpr.RecurAtomExpr: Constructor for the RecurAtomExpr object
RegExpFilenameFilter - class wsi.ra.io.RegExpFilenameFilter.: Regular expression filter for files.
RegExpFilenameFilter(String) - Constructor for class wsi.ra.io.RegExpFilenameFilter
RenderAtom - class joelib.gui.render.RenderAtom.: Holding original atom and render atom.
RenderAtom() - Constructor for class joelib.gui.render.RenderAtom
RenderHelper - class joelib.gui.render.RenderHelper.: A set of static utility classes for geometric calculations and operations.
RenderHelper() - Constructor for class joelib.gui.render.RenderHelper
RenderStyle - interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle.: Description of the Interface
RenderTable - class joelib.gui.molviewer.java3d.graphics3D.RenderTable.: Description of the Class
Renderer2D - class joelib.gui.render.Renderer2D.: A Renderer class which draws 2D representations of molecules onto a given graphics objects using information from a Renderer2DModel.
Renderer2D() - Constructor for class joelib.gui.render.Renderer2D: Constructs a Renderer2D with a default settings model.
Renderer2D(Renderer2DModel) - Constructor for class joelib.gui.render.Renderer2D
Renderer2DChangeListener - interface joelib.gui.render.Renderer2DChangeListener.: A ChangeListener for the 2D layout.
Renderer2DModel - class joelib.gui.render.Renderer2DModel.: Model for Renderer2D that contains settings for drawing objects.
RenderingAtoms - class joelib.gui.render.RenderingAtoms.: Rendering atoms.
RenderingAtoms() - Constructor for class joelib.gui.render.RenderingAtoms
ResidueIterator - class joelib.util.iterator.ResidueIterator.: Gets an iterator over all residue informations.
ResidueIterator(Vector) - Constructor for class joelib.util.iterator.ResidueIterator
ResourceLoader - class wsi.ra.tool.ResourceLoader.: Loads resource file from directory OR jar file.
ResultCMLProperties - interface joelib.io.types.cml.ResultCMLProperties.: Interface for a CML molecule writer.
ResultFactory - class joelib.desc.ResultFactory.: Factory class to get descriptor results and faciliate the parsing of descriptor entries.
RingIterator - class joelib.util.iterator.RingIterator.: Gets an iterator over all rings in a molecule.
RingIterator(Vector) - Constructor for class joelib.util.iterator.RingIterator: Constructor for the RingIterator object
RingSizeComparator - class joelib.ring.RingSizeComparator.: Comparator for ring size.
RingSizeComparator() - Constructor for class joelib.ring.RingSizeComparator: Initializes the RingSizeComparator-Comparator.
RotamerIterator - class joelib.util.iterator.RotamerIterator.: Iterator over rotamers.
RotamerIterator(Vector) - Constructor for class joelib.util.iterator.RotamerIterator: Constructor for the RotamerIterator object
RotatableBonds - class joelib.desc.types.RotatableBonds.: Number of rotatable bonds.
RotatableBonds() - Constructor for class joelib.desc.types.RotatableBonds: Constructor for the KierShape1 object
RotorComparator - class joelib.sort.RotorComparator.: Comparator for ring size.
RotorComparator() - Constructor for class joelib.sort.RotorComparator: Initializes the RingSizeComparator-Comparator.
RotorIterator - class joelib.util.iterator.RotorIterator.: Iterator over rotors.
RotorIterator(Vector) - Constructor for class joelib.util.iterator.RotorIterator: Constructor for the RotorIterator object
RuleOf5Filter - class joelib.process.filter.RuleOf5Filter.: Filter to avoid molecules with a 'poor absorption or permeability'.
RuleOf5Filter() - Constructor for class joelib.process.filter.RuleOf5Filter: Constructor for the DescriptorFilter object
radValue() - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Return angle value in rad unit
randomRotation(JOERandom) - Method in class joelib.math.Matrix3x3: Description of the Method
randomUnitXYZVector() - Method in class joelib.math.XYZVector: Description of the Method
randomUnitXYZVector(JOERandom) - Method in class joelib.math.XYZVector: Description of the Method
reHash() - Method in class joelib.desc.types.atompair.AtomPair
reHash() - Method in class joelib.desc.types.atompair.AtomPairAtomType
reHash() - Method in class joelib.molecule.JOEAtom
reHash() - Method in class joelib.molecule.JOEBond
reHash() - Method in class joelib.molecule.JOEMol
read(char[], int, int) - Method in class cformat.ScanfReader: Reads characters into a portion of a character array.
read() - Method in interface joelib.io.MoleculeFileType: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in interface joelib.io.MoleculeFileType: Reads an molecule entry from the initialized molecule reader.
read(JOEMol, String) - Method in interface joelib.io.MoleculeFileType: Reads an molecule entry from the initialized molecule reader.
read() - Method in class joelib.io.SimpleImageWriter: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.SimpleImageWriter: Description of the Method
read(JOEMol, String) - Method in class joelib.io.SimpleImageWriter: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.Amber: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Amber: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Amber: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.ChemicalMarkupLanguage: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.ChemicalMarkupLanguage: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.ClearTextFormat: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.ClearTextFormat: Loads a ClearTextFile.
read(JOEMol, String) - Method in class joelib.io.types.ClearTextFormat: Loads an molecule in ClearTextFile format and sets the title.
read() - Method in class joelib.io.types.Flat: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Flat: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Flat: Loads an molecule in SMILES format and sets the title.
read() - Method in class joelib.io.types.Gaussian: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Gaussian: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Gaussian: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.HIN: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.HIN: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.HIN: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.JCAMP: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.JCAMP: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.JCAMP: Description of the Method
read() - Method in class joelib.io.types.MDLSD: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.MDLSD: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.MDLSD: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.Matlab: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Matlab: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Matlab: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.MolconnZ: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.MolconnZ: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.MolconnZ: Loads an molecule in SMILES format and sets the title.
read() - Method in class joelib.io.types.Mopac: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Mopac: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Mopac: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.PDB: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.PDB: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.PDB: Description of the Method
read() - Method in class joelib.io.types.PDF: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.PDF: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.PDF: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.POVRay: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.POVRay: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.POVRay: Loads an molecule in MDL SD-MOL format and sets the title.
read() - Method in class joelib.io.types.Smiles: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Smiles: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Smiles: Loads an molecule in SMILES format and sets the title.
read() - Method in class joelib.io.types.SybylMol2: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.SybylMol2: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.SybylMol2: Description of the Method
read() - Method in class joelib.io.types.Tinker: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Tinker: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Tinker: Description of the Method
read() - Method in class joelib.io.types.Undefined: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.Undefined: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.Undefined: Description of the Method
read() - Method in class joelib.io.types.XYZ: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.XYZ: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.XYZ: Description of the Method
read() - Method in class joelib.io.types.ZIP: Reads an molecule entry as (unparsed) String representation.
read(JOEMol) - Method in class joelib.io.types.ZIP: Description of the Method
read(JOEMol, String) - Method in class joelib.io.types.ZIP: Description of the Method
read(JOEMol) - Method in class joelib.io.types.cml.CMLSequentialSAXReader
read(InputStream, IOType, IOType, int) - Method in class joelib.molecule.JOEMolVector: Read all molecules from a file into a Vector of JOEMol.
readCoordinates(JOEMol) - Method in class joelib.math.symmetry.Symmetry: Read coordinates from a single molecule.
readFile(String) - Method in class jtt.docbook.DocBookEquations
readFile(String) - Method in class jtt.docbook.DocBookMolecules
readLines(String) - Static method in class wsi.ra.tool.ResourceLoader: Description of the Method
readLines(String, boolean) - Static method in class wsi.ra.tool.ResourceLoader: Description of the Method
readNext(JOEMol) - Method in class joelib.io.SimpleReader: Read next molecule.
readRules(String) - Method in class joelib.smarts.Patty: Loads patty rules from file at resource loacation resourceURL.
readRules(InputStream) - Method in class joelib.smarts.Patty: Loads patty rules from input stream.
readWriteNext() - Method in class joelib.io.SimpleReaderWriterPipe: Reads/writes the next molecule and calls SimpleReaderWriterPipe.molecule2handle(JOEMol).
readable() - Method in interface joelib.io.MoleculeFileType: Returns true if this molecule data type is readable.
readable() - Method in class joelib.io.SimpleImageWriter
readable() - Method in class joelib.io.types.Amber
readable() - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
readable() - Method in class joelib.io.types.ClearTextFormat: Description of the Method
readable() - Method in class joelib.io.types.Flat: Description of the Method
readable() - Method in class joelib.io.types.Gaussian
readable() - Method in class joelib.io.types.HIN
readable() - Method in class joelib.io.types.JCAMP: Description of the Method
readable() - Method in class joelib.io.types.MDLSD: Description of the Method
readable() - Method in class joelib.io.types.Matlab: Description of the Method
readable() - Method in class joelib.io.types.MolconnZ: Description of the Method
readable() - Method in class joelib.io.types.Mopac
readable() - Method in class joelib.io.types.PDB: Description of the Method
readable() - Method in class joelib.io.types.PDF
readable() - Method in class joelib.io.types.POVRay: Description of the Method
readable() - Method in class joelib.io.types.Smiles: Description of the Method
readable() - Method in class joelib.io.types.SybylMol2: Description of the Method
readable() - Method in class joelib.io.types.Tinker: Description of the Method
readable() - Method in class joelib.io.types.Undefined: Description of the Method
readable() - Method in class joelib.io.types.XYZ: Description of the Method
readable() - Method in class joelib.io.types.ZIP: Description of the Method
recur - Variable in class joelib.smarts.atomexpr.RecurAtomExpr: Description of the Field
registerConvention(String, ModuleInterface) - Method in class joelib.io.types.cml.CMLHandler
remove(int) - Method in class Acme.IntHashtable
remove(Object) - Method in class Acme.IntHashtable
remove() - Method in class joelib.util.iterator.GenericDataIterator: Description of the Method
remove() - Method in class joelib.util.iterator.NativeValueIterator: Description of the Method
remove() - Method in class joelib.util.iterator.VectorIterator: Description of the Method
remove(DequeNode) - Method in class wsi.ra.tool.Deque
remove() - Method in class wsi.ra.tool.DequeIterator
remove(int) - Method in class wsi.ra.tool.SortedVector: Removes the element at the specified position in this Vector.
removeAll() - Method in class wsi.ra.tool.Deque
removeAll(Collection) - Method in class wsi.ra.tool.SortedVector: Removes from this Vector all of its elements that are contained in the specified Collection.
removeAtom(JOEAtom) - Method in class joelib.molecule.JOEResidue
removeChangeListener(Renderer2DChangeListener) - Method in class joelib.gui.render.Renderer2DModel: Removes a change listener from the list of listeners
removeCommentsInLine(String) - Static method in class joelib.jcamp.JCAMPDataBlock: Removes the comments from the actual line.
removeElementAt(int) - Method in class wsi.ra.tool.SortedVector: Deletes the component at the specified index.
removeMolViewerEventListener(MolViewerEventListener) - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D: Remove an answer listener from our list of interested listeners
removeMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.ViewerFrame
removeMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D
removeMolecule(JOEMol) - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Description of the Method
removeMolecule(ViewerMolecule) - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene
removeProcess(JOEProcess) - Method in class joelib.process.ProcessPipe
removeProcess(int) - Method in class joelib.process.ProcessPipe
removeRedundant(int) - Method in class joelib.ring.JOERingSearch: Description of the Method
removeUsedClosures() - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
removedDuplicates - Variable in class joelib.math.symmetry.SymStatistic
removedInitialMating - Variable in class joelib.math.symmetry.SymStatistic
removedUnsuccOpt - Variable in class joelib.math.symmetry.SymStatistic
removedWrongTransOrder - Variable in class joelib.math.symmetry.SymStatistic
renumber(JOEMol) - Method in class joelib.algo.morgan.Morgan: Renumber a molecule and use the calulated morgan numbers and try to resolve renumbering ties.
renumberAtoms(Vector) - Method in class joelib.molecule.JOEMol
replaceMissingValues(double[]) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Replaces all missing values in the instance with the values contained in the given array.
reportErrors - Variable in class joelib.io.types.cml.CMLErrorHandler
reportSymmetryElementsVerbose() - Method in class joelib.math.symmetry.Symmetry: Report symmetry elements.
reserveAtoms(int) - Method in class joelib.molecule.JOEMol: Reserves a initial capacity of atoms.
reset() - Method in class joelib.util.iterator.VectorIterator: Description of the Method
resetMoleculeEntryNumber() - Method in class joelib.io.types.HIN
resetTime() - Method in class wsi.ra.tool.StopWatch: Saves the current system time in a local variable.
resetVisit(JOEMol, Vector, int) - Static method in class joelib.util.JHM
residueIterator() - Method in class joelib.molecule.JOEMol: Description of the Method
resolveEntity(String, String, String, String) - Method in class joelib.io.types.cml.CMLResolver: Not implemented, but uses resolveEntity(String publicId, String systemId) instead.
resolveEntity(String, String) - Method in class joelib.io.types.cml.CMLResolver: Resolves SYSTEM and PUBLIC identifiers for CML DTDs.
restrictedMatch(JOEMol, Vector) - Method in class joelib.smarts.JOESmartsPattern
restrictedMatch(JOEMol, Vector, boolean) - Method in class joelib.smarts.JOESmartsPattern
restrictedMatch(JOEMol, JOEBitVec) - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
restrictedMatch(JOEMol, JOEBitVec, boolean) - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
retainAll(Collection) - Method in class wsi.ra.tool.SortedVector: Retains only the elements in this Vector that are contained in the specified Collection.
returnCDO() - Method in class joelib.io.types.cml.CDKConvention
returnCDO() - Method in class joelib.io.types.cml.CMLCoreModule
returnCDO() - Method in class joelib.io.types.cml.CMLHandler
returnCDO() - Method in class joelib.io.types.cml.CMLReactionModule
returnCDO() - Method in interface joelib.io.types.cml.ModuleInterface
returnCDO() - Method in class joelib.io.types.cml.XMLHandler
rgt - Variable in class joelib.smarts.atomexpr.BinAtomExpr: Description of the Field
rgt - Variable in class joelib.smarts.bondexpr.BinBondExpr: Description of the Field
ring - Variable in class joelib.gui.render.ConjugatedRing
rmsError(double[], double[]) - Static method in class wsi.ra.tool.StatisticUtils: returns root mean square error.
rotAboutAxisByAngle(XYZVector, double) - Method in class joelib.math.Matrix3x3: Description of the Method
rotate(RenderingAtoms, Point2d, double) - Static method in class joelib.gui.render.RenderHelper: Rotates a molecule around a given center by a given angle
rotate(double[][]) - Method in class joelib.molecule.JOEMol
rotate(double[]) - Method in class joelib.molecule.JOEMol
rotate(double[], int) - Method in class joelib.molecule.JOEMol
rotateCoords(double[], int) - Method in class joelib.math.Matrix3x3: Description of the Method
rsCache - Variable in class joelib.smarts.ParseSmart: of type RSCacheEntry

S

SCALAR - Static variable in class joelib.io.types.cml.CMLCoreModule
SEQUENCE - Static variable in class joelib.io.types.cml.CMLCoreModule
SINGLE - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Single bond type
SIZE - Static variable in class joelib.io.types.cml.elements.ArrayCML
SMALL - Static variable in class wsi.ra.tool.StatisticUtils: The small deviation allowed in double comparisons
SMALLER - Static variable in class joelib.process.filter.NativeValueFilter
SMALLER - Static variable in class joelib.process.filter.SMARTSFilter
SMALLER_EQUAL - Static variable in class joelib.process.filter.NativeValueFilter
SMALLER_EQUAL - Static variable in class joelib.process.filter.SMARTSFilter
SMARTS - Static variable in class joelib.desc.SMARTSCounter
SMARTSCounter - class joelib.desc.SMARTSCounter.: Representation for a simple SMARTS counter descriptor.
SMARTSCounter() - Constructor for class joelib.desc.SMARTSCounter: Initializes descriptor class for calculating the number of SMARTS patterns.
SMARTSDescriptors - class joelib.desc.util.SMARTSDescriptors.: Example for loading molecules and get atom properties.
SMARTSDescriptors() - Constructor for class joelib.desc.util.SMARTSDescriptors
SMARTSError(Pattern) - Method in class joelib.smarts.ParseSmart: Description of the Method
SMARTSEvaluation - class joelib.smarts.test.SMARTSEvaluation.: Test SMARTS matching in batch mode allowing different rules, molecules, etc.
SMARTSEvaluation() - Constructor for class joelib.smarts.test.SMARTSEvaluation
SMARTSFilter - class joelib.process.filter.SMARTSFilter.: Molecule process filter for SMARTS patterns.
SMARTSFilter() - Constructor for class joelib.process.filter.SMARTSFilter: Constructor for the DescriptorFilter object
SMARTSFilter(String, int, int, boolean) - Constructor for class joelib.process.filter.SMARTSFilter: Constructor for the DescriptorFilter object
SMARTSFragmentation - class joelib.molecule.fragmentation.SMARTSFragmentation.: Fragmentation implementation based on SMARTS patterns for a molecule.
SMARTSFragmentation() - Constructor for class joelib.molecule.fragmentation.SMARTSFragmentation
SMARTSParser(Pattern, ParseState, int, int) - Method in class joelib.smarts.ParseSmart: Description of the Method
SMARTSPatternFVec - class joelib.smarts.types.SMARTSPatternFVec.: Atom representation.
SMARTSPatternFVec(JOESmartsPattern, double[]) - Constructor for class joelib.smarts.types.SMARTSPatternFVec
SMARTSPatternInt - class joelib.smarts.types.SMARTSPatternInt.: Atom representation.
SMARTSPatternInt(JOESmartsPattern, int) - Constructor for class joelib.smarts.types.SMARTSPatternInt: Constructor for the SMARTSPatternInt object
SMARTSPatternIntInt - class joelib.smarts.types.SMARTSPatternIntInt.: Atom representation.
SMARTSPatternIntInt(JOESmartsPattern, IntInt) - Constructor for class joelib.smarts.types.SMARTSPatternIntInt: Constructor for the SMARTSPatternIntInt object
SMARTSPatternIntInt(JOESmartsPattern, int, int) - Constructor for class joelib.smarts.types.SMARTSPatternIntInt: Constructor for the SMARTSPatternIntInt object
SMARTSPatternString - class joelib.smarts.types.SMARTSPatternString.: Atom representation.
SMARTSPatternString(JOESmartsPattern, String) - Constructor for class joelib.smarts.types.SMARTSPatternString: Constructor for the SMARTSPatternString object
SMOOTHING_FACTOR - Static variable in class joelib.desc.types.RadialDistributionFunction
SMOOTHING_FACTOR_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
SO2Groups - class joelib.desc.types.SO2Groups.: Number of SO2 groups.
SO2Groups() - Constructor for class joelib.desc.types.SO2Groups
SOGroups - class joelib.desc.types.SOGroups.: Number of SO groups.
SOGroups() - Constructor for class joelib.desc.types.SOGroups
SPHERE - Static variable in class joelib.io.types.Matlab: Description of the Field
SPHERE - Static variable in class joelib.io.types.POVRay: Description of the Field
SPHERES2CALCULATE - Static variable in class joelib.process.types.AtomPropertyMatrix
SPHERE_S - Static variable in class joelib.io.types.POVRay
SPHERICAL_VOLUME_RESOLUTION - Static variable in class joelib.desc.types.RadialDistributionFunction
SPHERICAL_VOLUME_RESOLUTION_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
SQUARE(double) - Static method in class joelib.util.JOEHelper: Description of the Method
SSKey3DS - class joelib.desc.types.SSKey3DS.: Pharmacophore fingerprint.
SSKey3DS() - Constructor for class joelib.desc.types.SSKey3DS: Constructor for the KierShape2 object
STARTING_ATOM - Static variable in class joelib.algo.APropertyBFS
STARTING_ATOM - Static variable in class joelib.algo.BFS
STARTING_ATOM - Static variable in class joelib.algo.DFS
STICK - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
STICK - Static variable in class joelib.io.types.Matlab: Description of the Field
STICK - Static variable in class joelib.io.types.POVRay: Description of the Field
STICK_RADIUS - Static variable in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: The Radius of the sticks *
STICK_S - Static variable in class joelib.io.types.POVRay
STOP - Static variable in class joelib.test.Convert
STOP - Static variable in class joelib.test.ConvertSkip
STOP - Static variable in class joelib.test.DescriptorCalculation
STOP - Static variable in class joelib.test.DescriptorStatistic
STOP_USAGE - Static variable in class joelib.test.Convert
STOP_USAGE - Static variable in class joelib.test.ConvertSkip
STOP_USAGE - Static variable in class joelib.test.DescriptorCalculation
STOP_USAGE - Static variable in class joelib.test.DescriptorStatistic
STRING - Static variable in class joelib.io.types.cml.CMLCoreModule
STRINGARRAY - Static variable in class joelib.io.types.cml.CMLCoreModule
SYMMETRY - Static variable in class joelib.io.types.cml.CMLCoreModule
ScalarCML - class joelib.io.types.cml.elements.ScalarCML.: Scalar CML element.
ScalarCML(Vector) - Constructor for class joelib.io.types.cml.elements.ScalarCML: Constructor for the StringString object
ScanfFormat - class cformat.ScanfFormat.: Format object for scanning input in the same way as the C scanf methodName.
ScanfFormat(String) - Constructor for class cformat.ScanfFormat: Constructs a ScanfFormat class from a format string.
ScanfFormatTest - class cformat.ScanfFormatTest.: Testing class for ScanfFormat.
ScanfFormatTest() - Constructor for class cformat.ScanfFormatTest
ScanfMatchException - exception cformat.ScanfMatchException.: Exception class used by the scan methods within ScanfReader when the input does not match the specified format.
ScanfMatchException(String) - Constructor for class cformat.ScanfMatchException: Creates a new ScanfMatchException with the given message.
ScanfReader - class cformat.ScanfReader.: A Reader which implements C scanf functionality.
ScanfReader(Reader) - Constructor for class cformat.ScanfReader: Create a new ScanfReader from the given reader.
ScanfReaderTest - class cformat.ScanfReaderTest.: Testing class for ScanfReader.
SelectionFilter - class joelib.process.filter.SelectionFilter.: Interface definition for calling external programs from JOELib.
SelectionFilter() - Constructor for class joelib.process.filter.SelectionFilter: Constructor for the DescriptorFilter object
SelectionPanel - class joelib.gui.test.SelectionPanel.
SelectionPanel() - Constructor for class joelib.gui.test.SelectionPanel
SharedAtomGroup - class joelib.gui.molviewer.java3d.graphics3D.SharedAtomGroup.: SharedAtomGroup.java Created: Sat Nov 28 20:22:12 1998
SharedAtomGroup(ViewerAtom) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.SharedAtomGroup: Constructor for the SharedAtomGroup object
SharedBondGroup - class joelib.gui.molviewer.java3d.graphics3D.SharedBondGroup.: SharedBondGroup.java Created: Sat Nov 28 20:46:06 1998
SharedBondGroup(ViewerAtom, float) - Constructor for class joelib.gui.molviewer.java3d.graphics3D.SharedBondGroup: Constructor for the SharedBondGroup object
SimpleBooleanDesc - class joelib.desc.SimpleBooleanDesc.: Representation for a simple integer value descriptor.
SimpleBooleanDesc() - Constructor for class joelib.desc.SimpleBooleanDesc: Initializes descriptor class for calculating a boolean value.
SimpleDoubleAtomProperty - class joelib.desc.SimpleDoubleAtomProperty.: Descriptor class for calculating an atom property which are double values.
SimpleDoubleAtomProperty() - Constructor for class joelib.desc.SimpleDoubleAtomProperty: Initializes descriptor class for calculating an atom property which are double values.
SimpleDoubleDesc - class joelib.desc.SimpleDoubleDesc.: Representation for a simple double value descriptor.
SimpleDoubleDesc() - Constructor for class joelib.desc.SimpleDoubleDesc: Initializes descriptor class for calculating a double value.
SimpleDynamicAtomProperty - class joelib.desc.SimpleDynamicAtomProperty.: Descriptor class for calculating an atom property (dynamic value type definition).
SimpleDynamicAtomProperty() - Constructor for class joelib.desc.SimpleDynamicAtomProperty: Initializes descriptor class for calculating an atom property (dynamic value type definition).
SimpleExternalProcess - class joelib.ext.SimpleExternalProcess.: Simple external process representation.
SimpleExternalProcess() - Constructor for class joelib.ext.SimpleExternalProcess: Constructor for the Corina object
SimpleImageWriter - class joelib.io.SimpleImageWriter.: Atom representation.
SimpleImageWriter() - Constructor for class joelib.io.SimpleImageWriter
SimpleIntDesc - class joelib.desc.SimpleIntDesc.: Representation for a simple integer value descriptor.
SimpleIntDesc() - Constructor for class joelib.desc.SimpleIntDesc: Initializes descriptor class for calculating a integer value.
SimpleJOELibDatabase - class joelib.util.database.SimpleJOELibDatabase.: Helper class to access and store molecules.
SimpleJOELibDatabase() - Constructor for class joelib.util.database.SimpleJOELibDatabase
SimpleProcess - class joelib.process.SimpleProcess.: Simple process represenation.
SimpleProcess() - Constructor for class joelib.process.SimpleProcess: Constructor for the DescSelectionWriter object
SimpleReader - class joelib.io.SimpleReader.: Simple reader implementation.
SimpleReader(String) - Constructor for class joelib.io.SimpleReader: Creates a simple reader where the file type is resolved by the file extension.
SimpleReader(String, String) - Constructor for class joelib.io.SimpleReader: Creates a simple reader.
SimpleReader(InputStream, String) - Constructor for class joelib.io.SimpleReader: Creates a simple reader.
SimpleReader(InputStream, IOType) - Constructor for class joelib.io.SimpleReader: Creates a simple reader.
SimpleReaderWriterPipe - class joelib.io.SimpleReaderWriterPipe.: Simple reader/writer pipe implementation.
SimpleReaderWriterPipe(String[]) - Constructor for class joelib.io.SimpleReaderWriterPipe: Creates a simple reader/writer pipe where the file types are resolved by the file extensions.
SimpleReaderWriterPipe(String, String) - Constructor for class joelib.io.SimpleReaderWriterPipe: Creates a simple reader/writer pipe where the file types are resolved by the file extensions.
SimpleReaderWriterPipe(String, String, String, String) - Constructor for class joelib.io.SimpleReaderWriterPipe: Creates a simple reader/writer pipe.
SimpleReaderWriterPipe(InputStream, String, OutputStream, String) - Constructor for class joelib.io.SimpleReaderWriterPipe: Creates a simple reader/writer pipe.
SimpleReaderWriterPipe(InputStream, IOType, OutputStream, IOType) - Constructor for class joelib.io.SimpleReaderWriterPipe: Creates a simple reader/writer pipe.
SimpleStringAtomProperty - class joelib.desc.SimpleStringAtomProperty.: Descriptor class for calculating an atom property which are String values.
SimpleStringAtomProperty() - Constructor for class joelib.desc.SimpleStringAtomProperty: Initializes descriptor class for calculating an atom property which are double values.
SimpleWriter - class joelib.io.SimpleWriter.: Simple writer implementation.
SimpleWriter(String) - Constructor for class joelib.io.SimpleWriter: Creates a simple writer where the file type is resolved by the file extension.
SimpleWriter(String, String) - Constructor for class joelib.io.SimpleWriter: Creates a simple writer.
SimpleWriter(OutputStream, String) - Constructor for class joelib.io.SimpleWriter: Creates a simple writer.
SimpleWriter(OutputStream, IOType) - Constructor for class joelib.io.SimpleWriter: Creates a simple writer.
SingleTieResolver - interface joelib.algo.morgan.SingleTieResolver.: Interface for resolving renumbering ties.
SingleTieResolverBO - class joelib.algo.morgan.types.SingleTieResolverBO.: Interface for resolving renumbering ties.
SingleTieResolverBO() - Constructor for class joelib.algo.morgan.types.SingleTieResolverBO
SingleTieResolverDistance - class joelib.algo.morgan.types.SingleTieResolverDistance.: Interface for resolving renumbering ties.
SingleTieResolverDistance() - Constructor for class joelib.algo.morgan.types.SingleTieResolverDistance
SingleTieResolverENGrad - class joelib.algo.morgan.types.SingleTieResolverENGrad.: Interface for resolving renumbering ties.
SingleTieResolverENGrad() - Constructor for class joelib.algo.morgan.types.SingleTieResolverENGrad
SingleTieResolverElectrons - class joelib.algo.morgan.types.SingleTieResolverElectrons.: Interface for resolving renumbering ties.
SingleTieResolverElectrons() - Constructor for class joelib.algo.morgan.types.SingleTieResolverElectrons
SingleTieResolverElement - class joelib.algo.morgan.types.SingleTieResolverElement.: Interface for resolving renumbering ties.
SingleTieResolverElement() - Constructor for class joelib.algo.morgan.types.SingleTieResolverElement
SingleTieResolverGraphPot - class joelib.algo.morgan.types.SingleTieResolverGraphPot.: Interface for resolving renumbering ties.
SingleTieResolverGraphPot() - Constructor for class joelib.algo.morgan.types.SingleTieResolverGraphPot
SingleTieResolverImpVal - class joelib.algo.morgan.types.SingleTieResolverImpVal.: Interface for resolving renumbering ties.
SingleTieResolverImpVal() - Constructor for class joelib.algo.morgan.types.SingleTieResolverImpVal
SingleTieResolverImpValGrad - class joelib.algo.morgan.types.SingleTieResolverImpValGrad.: Interface for resolving renumbering ties.
SingleTieResolverImpValGrad() - Constructor for class joelib.algo.morgan.types.SingleTieResolverImpValGrad
SingleTieResolverPartCh - class joelib.algo.morgan.types.SingleTieResolverPartCh.: Interface for resolving renumbering ties.
SingleTieResolverPartCh() - Constructor for class joelib.algo.morgan.types.SingleTieResolverPartCh
Smiles - class joelib.io.types.Smiles.: Reader/Writer for Simplified Molecular Input Line Entry System (SMILES) files.
Smiles() - Constructor for class joelib.io.types.Smiles: Constructor for the Smiles object
SoftCodedKernel - interface joelib.data.SoftCodedKernel.: Interface for defining a hard coded kernel part.
SoftCodedKernelBase - class joelib.data.SoftCodedKernelBase.: Interface for defining a hard coded kernel part.
SoftCodedKernelBase() - Constructor for class joelib.data.SoftCodedKernelBase
SortedVector - class wsi.ra.tool.SortedVector.: Sorted Vector.
SortedVector(Comparator, int) - Constructor for class wsi.ra.tool.SortedVector
SortedVector(Comparator, int, int) - Constructor for class wsi.ra.tool.SortedVector
SortedVector(Comparator) - Constructor for class wsi.ra.tool.SortedVector
SortedVector(Collection) - Constructor for class wsi.ra.tool.SortedVector: Constructs a vector containing the elements of the specified collection, in the order they are returned by the collection's iterator.
Sorter - class joelib.sort.Sorter.: The basic class for sort classes.
Sorter() - Constructor for class joelib.sort.Sorter
Sphere - class joelib.gui.molviewer.java3d.graphics3D.Sphere.: Description of the Class
Sphere() - Constructor for class joelib.gui.molviewer.java3d.graphics3D.Sphere: Constructor for the Sphere object
StackType - class joelib.util.types.StackType.: Atom, bond and integer.
StackType() - Constructor for class joelib.util.types.StackType
StandardUsage() - Static method in class com.obrador.Jpeg: Jpeg("Imagefile", Quality, "OutFileName") According to JAVA virtual machine, the files which can be read are jpeg, tiff and gif files
StatisticPanel - class joelib.gui.test.StatisticPanel.: DOCUMENT ME!
StatisticPanel() - Constructor for class joelib.gui.test.StatisticPanel
StatisticUtils - class wsi.ra.tool.StatisticUtils.: Statistic utils.
StatisticUtils() - Constructor for class wsi.ra.tool.StatisticUtils
Statistics - class wsi.ra.tool.Statistics.: Class implementing some distributions, tests, etc.
Statistics() - Constructor for class wsi.ra.tool.Statistics
StopWatch - class wsi.ra.tool.StopWatch.: Implements a very simple 'stop watch' which returns the passed time since last reset.
StopWatch() - Constructor for class wsi.ra.tool.StopWatch
StringArrayResult - class joelib.desc.result.StringArrayResult.: String array results of variable size.
StringArrayResult() - Constructor for class joelib.desc.result.StringArrayResult: Constructor for the IntArrayResult object
StringInt - class joelib.util.types.StringInt.: String and integer value.
StringInt(String, int) - Constructor for class joelib.util.types.StringInt: Constructor for the StringString object
StringObject - class joelib.util.types.StringObject.: Two String values.
StringObject(String, Object) - Constructor for class joelib.util.types.StringObject: Constructor for the StringString object
StringPattern - class joelib.util.types.StringPattern.: String and regular expression Pattern.
StringPattern(String, Pattern) - Constructor for class joelib.util.types.StringPattern: Constructor for the StringString object
StringResult - class joelib.desc.result.StringResult.: String result.
StringResult() - Constructor for class joelib.desc.result.StringResult: Constructor for the IntResult object
StringString - class joelib.util.types.StringString.: Two String values.
StringString(String, String) - Constructor for class joelib.util.types.StringString: Constructor for the StringString object
SybylMol2 - class joelib.io.types.SybylMol2.: Reader/Writer for Sybyl mol2 files.
SybylMol2() - Constructor for class joelib.io.types.SybylMol2: Constructor for the Undefined object
SymAtom - class joelib.math.symmetry.SymAtom.: SymmetryElement.
SymAtom() - Constructor for class joelib.math.symmetry.SymAtom: Constructor for the AtomIntInt object
SymAxesComparator - class joelib.math.symmetry.SymAxesComparator.: Comparator for ring size.
SymAxesComparator() - Constructor for class joelib.math.symmetry.SymAxesComparator: Initializes the SymAxesComparator-Comparator.
SymCoordinates - class joelib.math.symmetry.SymCoordinates.: SymmetryElement.
SymCoordinates() - Constructor for class joelib.math.symmetry.SymCoordinates: Constructor for the AtomIntInt object
SymStatistic - class joelib.math.symmetry.SymStatistic.: SymStatistic.
SymStatistic() - Constructor for class joelib.math.symmetry.SymStatistic: Constructor for the AtomIntInt object
Symmetry - class joelib.math.symmetry.Symmetry.: Brute force symmetry analyzer.
Symmetry() - Constructor for class joelib.math.symmetry.Symmetry: Brute force symmetry analyzer.
SymmetryElement - class joelib.math.symmetry.SymmetryElement.: SymmetryElement.
SymmetryElement(int) - Constructor for class joelib.math.symmetry.SymmetryElement: Constructor for the AtomIntInt object
SymmetryException - exception joelib.math.symmetry.SymmetryException.: JOELib property exception.
SymmetryException() - Constructor for class joelib.math.symmetry.SymmetryException: Constructor for the DescriptorException object
SymmetryException(String) - Constructor for class joelib.math.symmetry.SymmetryException: Constructor for the DescriptorException object
s - Variable in class joelib.smarts.types.SMARTSPatternString: Description of the Field
s - Variable in class joelib.util.types.StringInt: Description of the Field
s - Variable in class joelib.util.types.StringObject: Description of the Field
s - Variable in class joelib.util.types.StringPattern: Description of the Field
s1 - Variable in class joelib.util.types.StringString: Description of the Field
s2 - Variable in class joelib.util.types.StringString: Description of the Field
saveBitmap(OutputStream, Image) - Method in class wsi.ra.image.BMPFile
saveBitmap(String, Image, int, int) - Method in class wsi.ra.image.BMPFile
saveMolFromFile(JOEMol, String, String) - Static method in class joelib.io.IOHelper: Write a molecule to file.
saveMolToFile(MoleculeFileType[], JOEMol, String, String) - Static method in class joelib.io.IOHelper: Write a molecule to file.
saveUniqueRing(Deque, Deque) - Method in class joelib.ring.JOERingSearch
scale(AtomProperties, double, int) - Static method in class joelib.desc.types.WeightedBurdenEigenvalues
scale(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: scale the vector by a factor
scale(float) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Scale by f in all dimensions
scale(float, float, float) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Scale along each axis independently
scale(double) - Method in class wsi.ra.tool.ArrayStatistic: Scales the input variables so that they have interval [0,1].
scale2(AtomProperties, double, int) - Static method in class joelib.desc.types.WeightedBurdenEigenvalues
scaleMolecule(RenderingAtoms, double) - Static method in class joelib.gui.render.RenderHelper: Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
scaleMolecule(RenderingAtoms, Dimension, double) - Static method in class joelib.gui.render.RenderHelper: Scales a molecule such that it fills a given percentage of a given dimension
scanChar(String) - Method in class cformat.ScanfReader: Scan and return a single character.
scanChar() - Method in class cformat.ScanfReader: Scan and return a single character, using the default format string "%c".
scanChar(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a single character, using a pre-allocated ScanfFormat object.
scanChars(String) - Method in class cformat.ScanfReader: Scan and return a character array, whose size is determined by the field width specified in the format string (with a default width of 1 being assumed if no width is specified).
scanChars(int) - Method in class cformat.ScanfReader: Scan and return a character array, using the default format string "%c", with the field width (number of characters to read) supplanted by the argument n.
scanChars(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a character array, using a pre-allocated ScanfFormat object.
scanDec(String) - Method in class cformat.ScanfReader: Scan and return a signed decimal (long) integer.
scanDec() - Method in class cformat.ScanfReader: Scan and return a signed decimal (long) integer, using the default format string "%d".
scanDec(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a signed decimal (long) integer, using a pre-allocated ScanfFormat object.
scanDouble(String) - Method in class cformat.ScanfReader: Scan and return a double.
scanDouble() - Method in class cformat.ScanfReader: Scan and return a double, using the default format string "%f".
scanDouble(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a double, using a pre-allocated ScanfFormat object.
scanFloat(String) - Method in class cformat.ScanfReader: Scan and return a float.
scanFloat() - Method in class cformat.ScanfReader: Scan and return a float, using the default format string "%f".
scanFloat(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a float, using a pre-allocated ScanfFormat object.
scanHex(String) - Method in class cformat.ScanfReader: Scan and return a hex (long) integer.
scanHex() - Method in class cformat.ScanfReader: Scan and return a hex (long) integer, using the default format string "%x".
scanHex(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a hex (long) integer, using a pre-allocated ScanfFormat object.
scanInt(String) - Method in class cformat.ScanfReader: Scan and return a signed integer.
scanInt() - Method in class cformat.ScanfReader: Scan and return a signed integer, using the default format string "%i".
scanInt(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a signed integer, using a pre-allocated ScanfFormat object.
scanLong(String) - Method in class cformat.ScanfReader: Scan and return a signed (long) integer.
scanLong() - Method in class cformat.ScanfReader: Scan and return a signed (long) integer, using the default format string "%i".
scanLong(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a signed (long) integer, using a pre-allocated ScanfFormat object.
scanOct(String) - Method in class cformat.ScanfReader: Scan and return an octal (long) integer.
scanOct() - Method in class cformat.ScanfReader: Scan and return an octal (long) integer, using the default format string "%o".
scanOct(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return an octal (long) integer, using a pre-allocated ScanfFormat object.
scanString(String) - Method in class cformat.ScanfReader: Scan and return a String.
scanString() - Method in class cformat.ScanfReader: Scan and return a String, using the default format string "%s".
scanString(ScanfFormat) - Method in class cformat.ScanfReader: Scan and return a String, using a pre-allocated ScanfFormat object.
seedCharge - Variable in class joelib.smarts.types.SMARTSPatternFVec
select(ViewerAtom) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Flags specified atom as selected
selectBy(String, String, String, String) - Method in class joelib.util.database.AbstractDatabase
selectBy(String, String, String, String) - Method in interface joelib.util.database.DatabaseInterface
selectSMARTSPatterns(JOEMol, RenderingAtoms, JOESmartsPattern) - Method in class joelib.gui.render.Renderer2D
selectSMARTSPatterns(RenderingAtoms, JOESmartsPattern) - Method in class joelib.gui.render.Renderer2D
set(String) - Method in class cformat.PrintfFormat: Sets the format characteristics according to the supplied String.
set(String) - Method in class cformat.ScanfFormat: Sets the contents of the object according to the information provided in the format string.
set(ViewerBond, int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Set a bond at specified index; bond at index is replaced
set(JOECoordTrans) - Method in class joelib.math.JOECoordTrans: Assignment.
set(int, int, double) - Method in class joelib.math.Matrix3x3: Description of the Method
set(double, double, double) - Method in class joelib.math.XYZVector: Description of the Method
set(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
set(double[]) - Method in class joelib.math.XYZVector: Description of the Method
set(double[], int) - Method in class joelib.math.XYZVector: Description of the Method
set(int, JOEAtom, JOEAtom, int, int) - Method in class joelib.molecule.JOEBond: Description of the Method
set(JOEMol) - Method in class joelib.molecule.JOEMol: Clones molecule without additional data (e.g.
set(JOEMol, boolean, String[]) - Method in class joelib.molecule.JOEMol: Clones molecule.
set(JOEMol, boolean, String[], boolean) - Method in class joelib.molecule.JOEMol: Clones molecule.
set(int) - Method in class joelib.util.BitSet14: Sets the bit at the specified index to true.
set(int, boolean) - Method in class joelib.util.BitSet14: Sets the bit at the specified index to the specified value.
set(int, int) - Method in class joelib.util.BitSet14: Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to true.
set(int, int, boolean) - Method in class joelib.util.BitSet14: Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the specified value.
set(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
set(int, Object) - Method in class wsi.ra.tool.SortedVector: Replaces the element at the specified position in this Vector with the specified element.
setActualIndex(int) - Method in class joelib.util.iterator.VectorIterator: Sets the actual index.
setAdd(JOEMol) - Method in class joelib.molecule.JOEMol: Sets the add attribute of the JOEMol object
setAddingPolicy(boolean) - Method in class joelib.desc.DescriptorHelper
setAntiClockwiseStereo() - Method in class joelib.molecule.JOEAtom: Sets the 'anti clockwise stereo' flag of the JOEAtom .
setAromatic() - Method in class joelib.molecule.JOEAtom: Sets the aromatic attribute of the JOEAtom object
setAromatic() - Method in class joelib.molecule.JOEBond: Sets the aromatic flag for this bond.
setAromaticCorrected() - Method in class joelib.molecule.JOEMol: Sets the aromaticCorrected attribute of the JOEMol object
setAromaticPerceived() - Method in class joelib.molecule.JOEMol: Sets the aromaticPerceived attribute of the JOEMol object
setArray(Object) - Method in class joelib.desc.result.DynamicArrayResult: Sets the array attribute of the DynamicArrayResult object
setArrowColor(Color) - Method in class joelib.gui.render.Renderer2DModel
setArrowOffset(int) - Method in class joelib.gui.render.Renderer2DModel
setArrowSize(int) - Method in class joelib.gui.render.Renderer2DModel
setArrows(Arrows) - Method in class joelib.gui.render.Renderer2DModel
setAtom(JOEAtom) - Method in class joelib.data.JOEExternalBond: Sets the atom attribute of the JOEExternalBond object
setAtomContainer(RenderingAtoms) - Method in class joelib.gui.render.MoleculeViewer2D: Sets the AtomContainer to be displayed
setAtomID(JOEAtom, String) - Method in class joelib.molecule.JOEResidue
setAtomIdToIndex(Hashtable) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set atomIdToIndex
setAtomRadius(int) - Method in class joelib.gui.render.Renderer2DModel: XXX No idea what this is about
setAtomTypesPerceived() - Method in class joelib.molecule.JOEMol: Sets the atomTypesPerceived attribute of the JOEMol object
setAtomicNum(int) - Method in class joelib.molecule.JOEAtom: Sets the atomic number of the JOEAtom object.
setAttribute(String) - Method in class joelib.data.JOEGenericData: Sets the attribute attribute of the JOEGenericData object
setAutomaticFormalCharge(boolean) - Method in class joelib.molecule.JOEMol: Sets the flag if the automatic calculation of the formal charge of the atoms is allowed.
setAutomaticPartialCharge(boolean) - Method in class joelib.molecule.JOEMol: Sets the automaticPartialCharge attribute of the JOEMol object
setBO(int) - Method in class joelib.molecule.JOEBond: Sets the bond order for this bond.
setBackColor(Color) - Method in class joelib.gui.render.Renderer2DModel: Sets the background color
setBadOptimization(boolean) - Method in class joelib.math.symmetry.Symmetry
setBegin(JOEAtom) - Method in class joelib.molecule.JOEBond: Sets the begin attribute of the JOEBond object
setBitOff(int) - Method in class joelib.util.JOEBitVec: Clears the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
setBitOn(int) - Method in class joelib.util.JOEBitVec: Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
setBits(JOEBitVec) - Method in class joelib.desc.result.BitArrayResult: Sets the double attribute of the DoubleResult object
setBits(JOEBitVec, int) - Method in class joelib.desc.result.BitResult: Sets the double attribute of the DoubleResult object
setBits(JOEBitVec) - Method in class joelib.desc.result.IntBitArrayResult: Sets the double attribute of the DoubleResult object
setBlockData(String, int) - Method in class joelib.jcamp.JCAMPDataBlock: Sets the data of this JCAMP block.
setBlockID(int) - Method in class joelib.jcamp.JCAMPDataBlock: Sets the ID of this JCAMP block.
setBlockType(int) - Method in class joelib.jcamp.JCAMPDataBlock: Sets the type of this JCAMP block.
setBond(JOEBond) - Method in class joelib.data.JOEExternalBond: Sets the bond attribute of the JOEExternalBond object
setBondDistance(double) - Method in class joelib.gui.render.Renderer2DModel: Sets the distance between two lines in a double or triple bond
setBondLength(double) - Method in class joelib.gui.render.Renderer2DModel: Sets the length of a bond line.
setBondWidth(double) - Method in class joelib.gui.render.Renderer2DModel: Sets the thickness of a bond line.
setBoolean(boolean) - Method in class joelib.desc.result.BooleanResult: Sets the double attribute of the DoubleResult object
setCRings(ConjugatedRings) - Method in class joelib.gui.render.Renderer2DModel
setChain(String) - Method in class joelib.molecule.JOEResidue
setChainNum(int) - Method in class joelib.molecule.JOEResidue
setChainsPerceived() - Method in class joelib.molecule.JOEMol: Sets the chainsPerceived attribute of the JOEMol object
setCharNumber(int) - Method in class cformat.ScanfReader: Sets the current character number.
setChiral() - Method in class joelib.molecule.JOEAtom: Sets the chiral flag of the JOEAtom .
setChiralityPerceived() - Method in class joelib.molecule.JOEMol: Sets the chiralityPerceived attribute of the JOEMol object
setCisTransBond(JOEBond, int) - Static method in class joelib.util.IsomerismDetection: Sets up/down informations for cis/trans isomerism of a double bond.
Cases:
E/trans -- bondUP/doubleBond/bondUP
Z/cis -- bondDOWN/doubleBond/bondUP

The method gets two heavy atoms with the highest atomic number and sets the corresponding up/down bond flags for cis/trans isomeres.
setClockwiseStereo() - Method in class joelib.molecule.JOEAtom: Sets the 'clockwise stereo' flag of the JOEAtom .
setClosure() - Method in class joelib.molecule.JOEBond: Sets the closure attribute of the JOEBond object
setClosureBondsPerceived() - Method in class joelib.molecule.JOEMol: Sets the closureBondsPerceived attribute of the JOEMol object
setColorModel(ColorModel) - Method in class Acme.JPM.Encoders.ImageEncoder
setComment(String) - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Set comment
setComment(String) - Method in class joelib.process.types.DescSelectionWriter: Sets the comment attribute of the DescSelectionWriter object
setComparisonDescriptor(String) - Method in class joelib.util.ComparisonHelper: Sets the comparisonDescriptor attribute of the ComparisonHelper object
setComparisonDescriptors(String[]) - Method in class joelib.util.ComparisonHelper: Sets the comparisonDescriptors attribute of the ComparisonHelper object
setConformer(int) - Method in class joelib.molecule.JOEMol: Sets the conformer attribute of the JOEMol object
setConformers(Vector) - Method in class joelib.molecule.JOEMol: Sets the conformers attribute of the JOEMol object
setCoordPtr(double[]) - Method in class joelib.molecule.JOEAtom: Sets the coordPtr attribute of the JOEAtom object
setCorrectedForPH() - Method in class joelib.molecule.JOEMol: Sets the correctedForPH attribute of the JOEMol object
setData(String) - Method in class joelib.data.JOECommentData: Sets the data attribute of the JOECommentData object
setData(JOEAtom, JOEBond, int) - Method in class joelib.data.JOEExternalBondData: Sets the data attribute of the JOEExternalBondData object
setData(Vector) - Method in class joelib.data.JOERgroupData: Set all atom-Rgroup entries.
setData(String) - Method in class joelib.jcamp.LabelData
setData(Vector) - Method in class joelib.ring.JOERingData
setDataDescription(String) - Method in class joelib.desc.result.DynamicArrayResult: Sets the dataDescription attribute of the DynamicArrayResult object
setDataUnit(String) - Method in class joelib.desc.result.DynamicArrayResult: Sets the dataUnit attribute of the DynamicArrayResult object
setDefaultHeight(int) - Method in class joelib.gui.render.Mol2Image
setDefaultProperty(Object) - Method in class joelib.util.JOEProperty
setDefaultWidth(int) - Method in class joelib.gui.render.Mol2Image
setDelimiter(String) - Method in class joelib.process.types.DescSelectionWriter: Sets the delimiter attribute of the DescSelectionWriter object
setDescription(String) - Method in class joelib.gui.util.MolFileFilter: Sets the human readable description of this filter.
setDescriptionFile(String) - Method in class joelib.desc.DescDescription: Sets base file to the descriptor description files.
setDescriptionFile(String) - Method in class joelib.util.types.BasicFactoryInfo: Sets base directory for the descriptorion for the class.
setDescriptors2Calculate(String[]) - Method in class joelib.desc.util.AtomPropertyDescriptors: Set descriptors which accept the 'ATOM_PROPERTY' initializer property.
setDimensions(int, int) - Method in class Acme.JPM.Encoders.ImageEncoder
setDisplay(boolean) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the state to indicate whether the atom is to be formally displayed
setDocumentProperty(String, Object) - Method in interface joelib.io.types.cml.CDOInterface: Sets a property for this document.
setDocumentProperty(String, Object) - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
setDouble(double) - Method in class joelib.desc.result.APropDoubleResult: Sets the double attribute of the DoubleResult object
setDouble(double) - Method in class joelib.desc.result.DoubleResult: Sets the double attribute of the DoubleResult object
setDoubleArray(double[]) - Method in class joelib.desc.result.DoubleArrayResult: Sets the double attribute of the IntArrayResult object
setDoubleNV(double) - Method in interface joelib.desc.NativeValue
setDoubleNV(double) - Method in class joelib.desc.result.APropDoubleResult: Sets the doubleNV attribute of the APropDoubleResult object
setDoubleNV(double) - Method in class joelib.desc.result.APropIntResult: Sets the doubleNV attribute of the APropIntResult object
setDoubleNV(double) - Method in class joelib.desc.result.BooleanResult: Sets the doubleNV attribute of the IntResult object
setDoubleNV(double) - Method in class joelib.desc.result.DoubleResult: Sets the doubleNV attribute of the DoubleResult object
setDoubleNV(double) - Method in class joelib.desc.result.IntResult: Sets the doubleNV attribute of the IntResult object
setDoubleValue(int, double) - Method in class joelib.desc.result.APropDoubleArrResult
setDoubleValue(int, double) - Method in class joelib.desc.result.AtomDoubleResult
setDoubleValue(int, double) - Method in class joelib.desc.result.AtomDynamicResult: Sets the doubleValue attribute of the AtomDynamicResult object
setDoubleValue(int, double) - Method in class joelib.desc.result.AtomIntResult: Sets the doubleValue attribute of the AtomIntResult object
setDoubleValue(int, double) - Method in class joelib.desc.result.AtomStringResult: Sets the doubleValue attribute of the AtomIntResult object
setDoubleValue(int, double) - Method in class joelib.desc.result.BondDoubleResult
setDoubleValue(int, double) - Method in class joelib.desc.result.BondDynamicResult: Sets the doubleValue attribute of the AtomDynamicResult object
setDoubleValue(int, double) - Method in class joelib.desc.result.BondIntResult
setDoubleValue(int, int, double) - Method in interface joelib.molecule.types.AtomAtomProperties
setDoubleValue(int, double) - Method in interface joelib.molecule.types.AtomProperties: Sets the doubleValue attribute of the AtomProperties object
setDoubleValue(int, double) - Method in interface joelib.molecule.types.BondProperties
setDown() - Method in class joelib.molecule.JOEBond: Sets the down attribute of the JOEBond object
setDrawCarbonAtoms(boolean) - Method in class joelib.gui.render.Renderer2DModel
setDrawNumbers(boolean) - Method in class joelib.gui.render.Renderer2DModel: Sets if the drawing of atom numbers is switched on for this model
setElementAt(Object, int) - Method in class wsi.ra.tool.SortedVector: Sets the component at the specified index of this vector to be the specified object.
setEnd(JOEAtom) - Method in class joelib.molecule.JOEBond: Sets the end attribute of the JOEBond object
setEnergy(double) - Method in class joelib.molecule.JOEMol: Sets the energy attribute of the JOEMol object
setExtensionListInDescription(boolean) - Method in class joelib.gui.util.MolFileFilter: Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
setExternalInfo(ExternalInfo) - Method in interface joelib.ext.External
setExternalInfo(ExternalInfo) - Method in class joelib.ext.SimpleExternalProcess: Sets the externalInfo attribute of the Corina object
setFast() - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Sets the fast attribute of the MolecularScene object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.ANDFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.DescriptorFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in interface joelib.process.filter.Filter
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.HasAllDataFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.HasDataFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.NOTFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.NativeValueFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.ORFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.RuleOf5Filter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.SMARTSFilter: Sets the filterInfo attribute of the DescriptorFilter object
setFilterInfo(FilterInfo) - Method in class joelib.process.filter.SelectionFilter: Sets the filterInfo attribute of the DescriptorFilter object
setForeColor(Color) - Method in class joelib.gui.render.Renderer2DModel: Sets the foreground color with which bonds and atoms are drawn
setFormalCharge(int) - Method in class joelib.molecule.JOEAtom: Sets the formal charge of the JOEAtom object.
setFormat(String) - Method in class joelib.gui.util.JLog4JPanel: Method declaration
setFrame(JFrame) - Method in class joelib.gui.render.MoleculeViewer2D: Sets the Frame attribute of the MoleculeViewer2D object
setFreeElectrons(int) - Method in class joelib.molecule.JOEAtom: Set the number of free electrons.
setFromType(String) - Method in class joelib.data.JOETypeTable: Sets the fromType attribute of the JOETypeTable object
setGOAtomPosX(int, double) - Method in class joelib.util.ghemical.GhemicalInterface
setGOAtomPosY(int, double) - Method in class joelib.util.ghemical.GhemicalInterface
setGOAtomPosZ(int, double) - Method in class joelib.util.ghemical.GhemicalInterface
setGradientStep(double) - Method in class joelib.math.symmetry.Symmetry: Finite step used in numeric gradient evaluation.
setHetAtom(JOEAtom, boolean) - Method in class joelib.molecule.JOEResidue
setHighlight(boolean) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the state to indicate whether the atom is hightlighted
setHighlightAtoms(ViewerAtoms) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set highlighted atoms vector
setHighlightColor(Color) - Method in class joelib.gui.render.Renderer2DModel: Sets the color used for highlighting things in this model
setHighlightRadius(double) - Method in class joelib.gui.render.Renderer2DModel: Sets the radius around an atoms, for which the atom is marked highlighted if a pointer device is placed within this radius
setHighlightedAtom(JOEAtom) - Method in class joelib.gui.render.Renderer2DModel: Sets the atom currently highlighted
setHighlightedAtoms(JOEAtom[]) - Method in class joelib.gui.render.Renderer2DModel: Sets the atom currently highlighted
setHighlightedBond(JOEBond) - Method in class joelib.gui.render.Renderer2DModel: Sets the Bond currently highlighted
setHighlightedBonds(JOEBond[]) - Method in class joelib.gui.render.Renderer2DModel: Sets the Bond currently highlighted
setHints(int) - Method in class Acme.JPM.Encoders.ImageEncoder
setHyb(int) - Method in class joelib.molecule.JOEAtom: Sets the hybridisation of the JOEAtom object.
setHybAndGeom(int) - Method in class joelib.molecule.JOEAtom: Sets hybridization and geometry of this atom.
setHybridizationPerceived() - Method in class joelib.molecule.JOEMol: Sets the hybridizationPerceived attribute of the JOEMol object
setHydrogensAdded() - Method in class joelib.molecule.JOEMol: Sets the hydrogensAdded attribute of the JOEMol object
setId(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set id of this molecule
setIdx(int) - Method in class joelib.data.JOEExternalBond: Sets the idx attribute of the JOEExternalBond object
setIdx(int) - Method in class joelib.molecule.JOEAtom: Sets the index number of the JOEAtom object.
setIdx(int) - Method in class joelib.molecule.JOEBond: Sets the idx attribute of the JOEBond object
setIdx(int) - Method in class joelib.molecule.JOEResidue
setImplicitValence(int) - Method in class joelib.molecule.JOEAtom: Sets the implicit valence of the JOEAtom .
setImplicitValencePerceived() - Method in class joelib.molecule.JOEMol: Sets the implicitValencePerceived attribute of the JOEMol object
setInRing() - Method in class joelib.molecule.JOEAtom: Sets the 'in ring' flag of the JOEAtom object.
setInRing() - Method in class joelib.molecule.JOEBond: Sets the inRing attribute of the JOEBond object
setInputType(IOType) - Method in class joelib.molecule.JOEMol: Sets the inputType attribute of the JOEMol object
setInt(int) - Method in class joelib.desc.result.APropIntResult: Sets the double attribute of the DoubleResult object
setInt(int) - Method in class joelib.desc.result.IntResult: Sets the double attribute of the DoubleResult object
setIntArray(int[]) - Method in class joelib.desc.result.IntArrayResult: Sets the double attribute of the IntArrayResult object
setIntNV(int) - Method in interface joelib.desc.NativeValue
setIntNV(int) - Method in class joelib.desc.result.APropDoubleResult: Sets the intNV attribute of the APropDoubleResult object
setIntNV(int) - Method in class joelib.desc.result.APropIntResult: Sets the intNV attribute of the APropIntResult object
setIntNV(int) - Method in class joelib.desc.result.BooleanResult: Sets the intNV attribute of the IntResult object
setIntNV(int) - Method in class joelib.desc.result.DoubleResult: Sets the intNV attribute of the DoubleResult object
setIntNV(int) - Method in class joelib.desc.result.IntResult: Sets the intNV attribute of the IntResult object
setIntValue(int, int) - Method in class joelib.desc.result.APropDoubleArrResult
setIntValue(int, int) - Method in class joelib.desc.result.AtomDoubleResult
setIntValue(int, int) - Method in class joelib.desc.result.AtomDynamicResult: Sets the intValue attribute of the AtomDynamicResult object
setIntValue(int, int) - Method in class joelib.desc.result.AtomIntResult: Sets the intValue attribute of the AtomIntResult object
setIntValue(int, int) - Method in class joelib.desc.result.AtomStringResult: Sets the intValue attribute of the AtomIntResult object
setIntValue(int, int) - Method in class joelib.desc.result.BondDoubleResult
setIntValue(int, int) - Method in class joelib.desc.result.BondDynamicResult: Sets the intValue attribute of the AtomDynamicResult object
setIntValue(int, int) - Method in class joelib.desc.result.BondIntResult
setIntValue(int, int, int) - Method in interface joelib.molecule.types.AtomAtomProperties
setIntValue(int, int) - Method in interface joelib.molecule.types.AtomProperties: Sets the intValue attribute of the AtomProperties object
setIntValue(int, int) - Method in interface joelib.molecule.types.BondProperties
setIntVectorToValue(Vector, int) - Static method in class joelib.util.JHM
setIsotope(int) - Method in class joelib.molecule.JOEAtom: Set isotpe value for this atom.
setKDouble() - Method in class joelib.molecule.JOEBond: Assign double-bond-Kekule-flag to this bond.
setKSingle() - Method in class joelib.molecule.JOEBond: Assign single to this bond.
setKTriple() - Method in class joelib.molecule.JOEBond: Assign triple-bond-Kekule-flag to this bond.
setKekulePerceived() - Method in class joelib.molecule.JOEMol: Sets the kekulePerceived attribute of the JOEMol object
setKekuleStructure(boolean) - Method in class joelib.gui.render.Renderer2DModel
setLabel(String) - Method in class joelib.jcamp.LabelData
setLength(JOEAtom, double) - Method in class joelib.molecule.JOEBond: Sets the length attribute of the JOEBond object
setLibraryName(String) - Static method in class joelib.util.ghemical.GhemicalInterface: Sets the name of the OElib interface dynamic library.
setLibraryPath(String) - Static method in class joelib.util.ghemical.GhemicalInterface: Sets the path to the OElib interface dynamic library.
setLineNumber(int) - Method in class cformat.ScanfReader: Sets the current line number.
setMatrix3D(Matrix3D) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set property table Set 3D transformation matrix
setMaxAxisOrder(int) - Method in class joelib.math.symmetry.Symmetry: Maximum order of rotation axis to look for.
setMaxOptCycles(int) - Method in class joelib.math.symmetry.Symmetry: Maximum allowed number of cycles in symmetry element optimization.
setMaxOptStep(double) - Method in class joelib.math.symmetry.Symmetry: Maximum allowed number of cycles in symmetry element optimization.
setMinOptStep(double) - Method in class joelib.math.symmetry.Symmetry: Termination criterion in symmetry element optimization.
setMol(int, JOEMol) - Method in class joelib.molecule.JOEMolVector: Sets the molecule at position i of this molecule vector.
setMolIdentifier(String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
setMolIdentifier(String) - Method in class joelib.desc.data.MolDescCounter: Sets the molIdentifier attribute of the MolDescCounter object
setMolIdentifier(String) - Method in interface joelib.desc.data.MoleculeCache
setMolIdentifier(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Sets the molIdentifier attribute of the MoleculesDescriptorMatrix object
setMolecule(JOEMol) - Method in class joelib.algo.datamining.weka.MolInstance: Sets molecule.
setMolecule(JOEMol) - Method in class joelib.io.types.cml.MoleculeFileCDO
setMoleculeCallback(MoleculeCallback) - Method in class joelib.io.types.cml.MoleculeFileCDO
setMoleculeDescriptors(JOEMol, int) - Method in class joelib.algo.datamining.weka.MolInstancesCache
setMoleculeDescriptors(JOEMol, int) - Method in interface joelib.desc.data.MoleculeCache
setMoleculeDescriptors(JOEMol, int) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Sets descriptors for given molecule entry.
setMoleculeSetOfMolecules(JOEMolVector) - Method in class joelib.io.types.cml.MoleculeFileCDO
setMyAtoms(ViewerAtoms) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set atom vector
setMyBonds(ViewerBonds) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set bond vector
setName(String) - Method in class joelib.molecule.JOEResidue
setName(String) - Method in class joelib.util.types.BasicFactoryInfo
setNextNode(JOESmiNode, JOEBond) - Method in class joelib.smiles.JOESmiNode: Sets the nextNode attribute of the JOESmiNode object
setNice() - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Sets the nice attribute of the MolecularScene object
setNum(int) - Method in class joelib.molecule.JOEResidue
setNumAtoms(int) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set ring vector Set number of atoms
setNumberColor(Color) - Method in class joelib.gui.render.Renderer2DModel
setOLines(OrthoLines) - Method in class joelib.gui.render.Renderer2DModel
setObjectProperty(String, String, Object) - Method in interface joelib.io.types.cml.CDOInterface: Sets a property of the object being added.
setObjectProperty(String, String, Object) - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
setOptChangeHits(int) - Method in class joelib.math.symmetry.Symmetry: Number of minchange cycles before optimization stops
setOptChangeThreshold(double) - Method in class joelib.math.symmetry.Symmetry: Minimum allowed change in target methodName.
setOrthoLineColor(Color) - Method in class joelib.gui.render.Renderer2DModel
setOrthoLineOffset(int) - Method in class joelib.gui.render.Renderer2DModel
setOutputType(int) - Method in class joelib.io.types.Matlab: Sets the outputType attribute of the POVRay object
setOutputType(int) - Method in class joelib.io.types.POVRay: Sets the outputType attribute of the POVRay object
setOutputType(IOType) - Method in class joelib.molecule.JOEMol: Sets the outputType attribute of the JOEMol object
setParameter(LabelData[]) - Method in class joelib.jcamp.JCAMPParser: Set some LDR's (data label records).
setParameter(LabelData) - Method in class joelib.jcamp.JCAMPParser: Set one LDR (data label record).
setParent(JOEMol) - Method in class joelib.molecule.JOEAtom: Sets the parent molecule for this JOEAtom .
setParent(JOEMol) - Method in class joelib.molecule.JOEBond: Sets the parent attribute of the JOEBond object
setParent(JOEMol) - Method in class joelib.ring.JOERing: Sets the parent attribute of the JOERing object
setParent(JOEAtom) - Method in class joelib.smiles.JOESmiNode: Sets the parent attribute of the JOESmiNode object
setPartialCharge(double) - Method in class joelib.molecule.JOEAtom: Sets the partial charge of the JOEAtom object.
setPartialChargeVendor(String) - Method in class joelib.molecule.JOEMol
setPartialChargesPerceived() - Method in class joelib.molecule.JOEMol: Sets the partialChargesPerceived attribute of the JOEMol object
setPattySMARTS(String) - Method in class joelib.molecule.fragmentation.SMARTSFragmentation
setPattySMARTS(Vector) - Method in class joelib.molecule.fragmentation.SMARTSFragmentation
setPixels(int, int, int, int, ColorModel, byte[], int, int) - Method in class Acme.JPM.Encoders.ImageEncoder
setPixels(int, int, int, int, ColorModel, int[], int, int) - Method in class Acme.JPM.Encoders.ImageEncoder
setPointerVectorEnd(Point) - Method in class joelib.gui.render.Renderer2DModel: Sets the end of a pointer vector
setPointerVectorStart(Point) - Method in class joelib.gui.render.Renderer2DModel: Sets the start point of a pointer vector
setPrefix(String) - Method in class cformat.PrintfFormat: Sets the prefix string associated with the format.
setProcessInfo(ProcessInfo) - Method in class joelib.ext.SimpleExternalProcess: Sets the processInfo attribute of the ProcessPipe object
setProcessInfo(ProcessInfo) - Method in interface joelib.process.JOEProcess
setProcessInfo(ProcessInfo) - Method in class joelib.process.ProcessPipe: Sets the processInfo attribute of the ProcessPipe object
setProcessInfo(ProcessInfo) - Method in class joelib.process.SimpleProcess: Sets the processInfo attribute of the ProcessPipe object
setProcessInfo(ProcessInfo) - Method in class joelib.process.types.AtomPropertyMatrix: Sets the processInfo attribute of the ProcessPipe object
setProcessInfo(ProcessInfo) - Method in class joelib.process.types.CreateFileName: Sets the processInfo attribute of the ProcessPipe object
setProcessInfo(ProcessInfo) - Method in class joelib.process.types.MoleculeFileCreation: Sets the processInfo attribute of the ProcessPipe object
setProcessInfo(ProcessInfo) - Method in class joelib.process.types.MoleculeFileDeletion: Sets the processInfo attribute of the ProcessPipe object
setProperties(Hashtable) - Method in class Acme.JPM.Encoders.ImageEncoder
setProperty(String, Map, Object) - Static method in class joelib.util.JOEPropertyHelper: Sets the property attribute of the JOEPropertyHelper class
setPropertyType(String) - Method in class joelib.desc.result.DynamicArrayResult: Sets the propertyType attribute of the DynamicArrayResult object
setQuality(int) - Method in class com.obrador.JpegEncoder
setQuoteCharacter(char) - Method in class wsi.ra.io.BatchScriptReplacer: Sets the quoteCharacter attribute of the BatchScriptReplacer object
setRDFSmoothings(double[]) - Method in class joelib.desc.util.AtomPropertyDescriptors
setRangeOff(int, int) - Method in class joelib.util.JOEBitVec: Clears the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
setRangeOn(int, int) - Method in class joelib.util.JOEBitVec: Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(inclusive) to false.
setRenderAtomLabel(int, String) - Method in class joelib.gui.render.RenderingAtoms
setRenderAtomLabels(JOEMol, String, String, String) - Method in class joelib.gui.render.RenderingAtoms
setRenderStyle(int) - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D: Sets the renderStyle attribute of the Panel3D object
setRenderStyle(int) - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene: Sets the renderStyle attribute of the MolecularScene object
setRenderer2DModel(Renderer2DModel) - Method in class joelib.gui.render.MoleculeViewer2D: Sets a Renderer2DModel which determins the way a molecule is displayed
setRepresentation(String) - Method in class joelib.io.IOType: Sets the representation attribute of the IOType object
setRepresentation(String) - Method in class joelib.util.types.BasicFactoryInfo
setResName(String) - Method in class joelib.data.JOEResidueData
setResidue(JOEResidue) - Method in class joelib.molecule.JOEAtom
setRingAtomsAndBondsPerceived() - Method in class joelib.molecule.JOEMol: Sets the ringAtomsAndBondsPerceived attribute of the JOEMol object
setRotorToAngle(double[], JOEAtom[], double, Vector) - Static method in class joelib.util.JHM: This methodName will rotate the coordinates of 'atoms' such that tor == ang - atoms in 'tor' should be ordered such that the 3rd atom is the pivot around which atoms rotate ang is in degrees.
setSMARTS2Calculate(String[]) - Method in class joelib.desc.util.SMARTSDescriptors
setSMARTS2Calculate(String[], String[]) - Method in class joelib.desc.util.SMARTSDescriptors
setSSSRPerceived() - Method in class joelib.molecule.JOEMol: Sets the sSSRPerceived attribute of the JOEMol object
setScaleFactor(double) - Method in class joelib.gui.render.Renderer2DModel: Returns the scale factor for the drawing
setSelect(boolean) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the state to indicate whether the atom is selected
setSelectAtoms(ViewerAtoms) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set selected atoms vector
setSelectRect(Polygon) - Method in class joelib.gui.render.Renderer2DModel: Sets a selected region
setSeparator(String) - Method in class joelib.util.ArrayHelper: Sets the separator attribute of the ArrayHelper object
setSeparator(String) - Method in class joelib.util.MatrixHelper: Sets the separator attribute of the MatrixHelper object
setSerialNum(JOEAtom, int) - Method in class joelib.molecule.JOEResidue
setShowEndCarbons(boolean) - Method in class joelib.gui.render.Renderer2DModel
setSkipStream(OutputStream, IOType) - Method in class joelib.process.types.DescSelectionWriter: Sets the skipStream attribute of the DescSelectionWriter object
setStoreDescriptors(int) - Method in class joelib.desc.data.MolDescCounter: Sets the storeDescriptors attribute of the MolDescCounter object
setStoreLineInfo(boolean) - Method in class joelib.io.types.Flat: Sets the storeLineInfo attribute of the Smiles object
setStoreLineInfo(boolean) - Method in class joelib.io.types.Smiles: Sets the storeLineInfo attribute of the Smiles object
setStringArray(String[]) - Method in class joelib.desc.result.StringArrayResult: Sets the double attribute of the IntArrayResult object
setStringNV(String) - Method in interface joelib.desc.NativeValue
setStringNV(String) - Method in class joelib.desc.result.APropDoubleResult: Sets the stringNV attribute of the APropDoubleResult object
setStringNV(String) - Method in class joelib.desc.result.APropIntResult: Sets the stringNV attribute of the APropIntResult object
setStringNV(String) - Method in class joelib.desc.result.BooleanResult: Sets the stringNV attribute of the IntResult object
setStringNV(String) - Method in class joelib.desc.result.DoubleResult: Sets the stringNV attribute of the DoubleResult object
setStringNV(String) - Method in class joelib.desc.result.IntResult: Sets the stringNV attribute of the IntResult object
setStringValue(int, String) - Method in class joelib.desc.result.APropDoubleArrResult
setStringValue(int, String) - Method in class joelib.desc.result.AtomDoubleResult
setStringValue(int, String) - Method in class joelib.desc.result.AtomDynamicResult: Sets the stringValue attribute of the AtomDynamicResult object
setStringValue(int, String) - Method in class joelib.desc.result.AtomIntResult: Sets the stringValue attribute of the AtomIntResult object
setStringValue(int, String) - Method in class joelib.desc.result.AtomStringResult: Sets the stringValue attribute of the AtomIntResult object
setStringValue(int, String) - Method in class joelib.desc.result.BondDoubleResult
setStringValue(int, String) - Method in class joelib.desc.result.BondDynamicResult: Sets the stringValue attribute of the AtomDynamicResult object
setStringValue(int, String) - Method in class joelib.desc.result.BondIntResult
setStringValue(int, int, String) - Method in interface joelib.molecule.types.AtomAtomProperties
setStringValue(int, String) - Method in interface joelib.molecule.types.AtomProperties: Sets the stringValue attribute of the AtomProperties object
setStringValue(int, String) - Method in interface joelib.molecule.types.BondProperties
setStyle(int) - Method in class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode: Sets the style attribute of the MoleculeNode object
setStyle(int) - Method in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Sets the style attribute of the RenderStyle object
setStyle(int) - Method in class joelib.gui.molviewer.java3d.graphics3D.RenderTable: Set the current rendering style *
setStyle(int) - Method in class joelib.gui.molviewer.java3d.graphics3D.SharedAtomGroup: Sets the style attribute of the SharedAtomGroup object
setStyle(int) - Method in class joelib.gui.molviewer.java3d.graphics3D.SharedBondGroup: Sets the style attribute of the SharedBondGroup object
setSuffix(String) - Method in class cformat.PrintfFormat: Sets the suffix string associated with the format.
setTitle(String) - Method in class joelib.molecule.JOEMol: Sets the title attribute of the JOEMol object
setTo(XYZVector) - Method in class joelib.math.XYZVector: Copy this vector to the vector v.
setToType(String) - Method in class joelib.data.JOETypeTable: Sets the toType attribute of the JOETypeTable object
setToleranceFinal(double) - Method in class joelib.math.symmetry.Symmetry: Final criterion for atom equivalence.
setTolerancePrimary(double) - Method in class joelib.math.symmetry.Symmetry: Initial loose criterion for atom equivalence.
setToleranceSame(double) - Method in class joelib.math.symmetry.Symmetry: Atoms are colliding if distance falls below this value.
setTorsion(JOEAtom, JOEAtom, JOEAtom, JOEAtom, double) - Method in class joelib.molecule.JOEMol: Sets the torsion attribute of the JOEMol object
setTx(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the transformed x coordinate of the atom
setTy(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the transformed y coordinate of the atom
setType(String) - Method in class joelib.molecule.JOEAtom: Sets the type of the JOEAtom object.
setTz(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the transformed z coordinate of the atom
setUp() - Method in class joelib.molecule.JOEBond: The JUnit setup method
setUseUnixStyle(boolean) - Method in class joelib.io.types.Tinker
setValue(int, double) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Sets a specific value in the instance to the given value (internal floating-point format).
setValue(Object) - Method in class joelib.data.JOEPairData: Sets the value attribute of the JOEPairData object
setValue(int, Object) - Method in class joelib.desc.result.APropDoubleArrResult
setValue(int, Object) - Method in class joelib.desc.result.AtomDoubleResult
setValue(int, Object) - Method in class joelib.desc.result.AtomDynamicResult: Sets the value attribute of the AtomDynamicResult object
setValue(int, Object) - Method in class joelib.desc.result.AtomIntResult: Sets the value attribute of the AtomIntResult object
setValue(int, Object) - Method in class joelib.desc.result.AtomStringResult: Sets the value attribute of the AtomIntResult object
setValue(int, Object) - Method in class joelib.desc.result.BondDoubleResult
setValue(int, Object) - Method in class joelib.desc.result.BondDynamicResult: Sets the value attribute of the AtomDynamicResult object
setValue(int, Object) - Method in class joelib.desc.result.BondIntResult
setValue(double, boolean) - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Set value of the angle
setValue(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Set value of the angle
setValue(int, int, Object) - Method in interface joelib.molecule.types.AtomAtomProperties
setValue(int, Object) - Method in interface joelib.molecule.types.AtomProperties: Sets the value attribute of the AtomProperties object
setValue(int, Object) - Method in interface joelib.molecule.types.BondProperties
setValueSparse(int, double) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Sets a specific value in the instance to the given value (internal floating-point format).
setValues(double, double, double, double) - Method in class joelib.molecule.charge.GasteigerState: Sets the values attribute of the GasteigerState object
setVector() - Method in class joelib.molecule.JOEAtom: Sets the vector of the JOEAtom object.
setVector(XYZVector) - Method in class joelib.molecule.JOEAtom: Sets the new vector values of the JOEAtom object to the given values from .
setVector(double, double, double) - Method in class joelib.molecule.JOEAtom: Sets the vector attribute of the JOEAtom object
setX(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Set component x
setX(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Set X coordinate
setX(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the atom id Set the x coordinate of the atom
setX(double) - Method in class joelib.math.XYZVector: Sets the x attribute of the XYZVector object
setXmax(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set maxmum of X-coordinate
setXmin(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set minimum of X-coordinate of this molecule
setY(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Set component y
setY(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Set Y coordinate
setY(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the y coordinate of the atom
setY(double) - Method in class joelib.math.XYZVector: Sets the y attribute of the XYZVector object
setYmax(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set maxmum of Y-coordinate
setYmin(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set minimum of Y-coordinate
setZ(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D: Set component z
setZ(double) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: Set Z coordinate
setZ(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Set the z coordinate of the atom
setZ(double) - Method in class joelib.math.XYZVector: Sets the z attribute of the XYZVector object
setZmax(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set maxmum of Z-coordinate
setZmin(float) - Method in class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Set minimum of Z-coordinate
setZoomFactor(double) - Method in class joelib.gui.render.Renderer2DModel: Returns the zoom factor for the drawing
setup(double[]) - Method in class joelib.math.JOECoordTrans: Core function to setup the coordinate transformation.
setup(double[], double[], int) - Method in class joelib.math.JOECoordTrans: Sets up a coordinate transformation from an arbitrary set of coordinates in the initial and final reference frame.
setupAtomMatchTable(Vector, Pattern, JOEMol) - Method in class joelib.smarts.ParseSmart
setupEulerTranslation(double[], double[]) - Method in class joelib.math.JOECoordTrans: Sets up this objects transformation based on a specified \b rotation and \b translation (applied in that order).
This member methodName is distinct from setupTranslationEuler .
setupRmatrixTranslation(double[], double[]) - Method in class joelib.math.JOECoordTrans: Sets up this objects transformation based on a specified \b rotation and \b translation (applied in that order).
setupRmatrixTranslation(Matrix3x3, XYZVector) - Method in class joelib.math.JOECoordTrans: Sets up this objects transformation based on a specified \b rotation and \b translation (applied in that order).
setupRotMat(double, double, double) - Method in class joelib.math.Matrix3x3: Description of the Method
setupTranslationEuler(double[], double[]) - Method in class joelib.math.JOECoordTrans: Sets up this objects transformation based on a specified \b translation and \b rotation (applied in that order).
setupTranslationRmatrix(double[], double[]) - Method in class joelib.math.JOECoordTrans: Sets up this objects transformation based on a specified \b translation and \b rotation (applied in that order).
setupTranslationRmatrix(XYZVector, Matrix3x3) - Method in class joelib.math.JOECoordTrans: Sets up this objects transformation based on a specified \b translation and \b rotation (applied in that order).
shannon(int[], int) - Static method in class wsi.ra.tool.StatisticUtils: Computes shannon entropy for an array of integers.
shannonEntropy - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
shapes - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerAtom
shapes - Variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond
showDescriptorStatistic(String) - Method in class joelib.process.types.DescStatistic: Description of the Method
showUsage() - Method in class joelib.io.SimpleReaderWriterPipe: Shows usage.
signedVolume(XYZVector, XYZVector, XYZVector, XYZVector) - Static method in class joelib.util.JHM: Calculate the signed volume for an atom.
size() - Method in class Acme.IntHashtable
size() - Method in class joelib.molecule.GenericDataHolder: Description of the Method
size() - Method in class joelib.ring.JOERing: Returns the size of this ring.
size() - Method in class joelib.smiles.JOESmiNode: Description of the Method
size() - Method in class joelib.util.BitSet14: Returns the number of bits of space actually in use by this BitSet14 to represent bit values.
size() - Method in class wsi.ra.tool.Deque: Gets the size of this stack.
skipReaderEntry() - Method in interface joelib.io.MoleculeFileType: Skips an molecule or the rest of a molecule entry to grant the next read(JOEMol mol) invocation a proper starting position.
skipReaderEntry() - Method in class joelib.io.SimpleImageWriter: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.Amber: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.ChemicalMarkupLanguage
skipReaderEntry() - Method in class joelib.io.types.ClearTextFormat
skipReaderEntry() - Method in class joelib.io.types.Flat: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.Gaussian: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.HIN: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.JCAMP
skipReaderEntry(int) - Method in class joelib.io.types.JCAMP: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.MDLSD: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.Matlab: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.MolconnZ: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.Mopac: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.PDB: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.PDF: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.POVRay
skipReaderEntry() - Method in class joelib.io.types.Smiles: Description of the Method
skipReaderEntry() - Method in class joelib.io.types.SybylMol2
skipReaderEntry() - Method in class joelib.io.types.Tinker
skipReaderEntry() - Method in class joelib.io.types.Undefined
skipReaderEntry() - Method in class joelib.io.types.XYZ
skipReaderEntry() - Method in class joelib.io.types.ZIP
sm(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is smaller than b.
smOrEq(double, double) - Static method in class wsi.ra.tool.StatisticUtils: Tests if a is smaller or equal to b.
smallestBondAngle() - Method in class joelib.molecule.JOEAtom
smartsLexReplace(String, Vector) - Method in class joelib.smarts.ParseSmart
smiToMol(JOEMol, String, String) - Static method in class joelib.smiles.JOESmilesParser: Description of the Method
smiToMol(JOEMol, String) - Method in class joelib.smiles.JOESmilesParser: Description of the Method
sort(int[]) - Method in class joelib.sort.InsertSort: Description of the Method
sort(double[]) - Method in class joelib.sort.InsertSort: Description of the Method
sort(long[]) - Method in class joelib.sort.InsertSort: Description of the Method
sort(Object[], Comparator) - Method in class joelib.sort.InsertSort: Description of the Method
sort(Vector, Comparator) - Method in class joelib.sort.InsertSort: Description of the Method
sort(int[]) - Method in class joelib.sort.QuickInsertSort: Sorts an array in ascending order.
sort(double[]) - Method in class joelib.sort.QuickInsertSort: Sorts an array in ascending order.
sort(long[]) - Method in class joelib.sort.QuickInsertSort: Sorts an array in ascending order.
sort(Object[], Comparator) - Method in class joelib.sort.QuickInsertSort: Sorts an array in ascending order.
sort(Vector, Comparator) - Method in class joelib.sort.QuickInsertSort: Sorts an array in ascending order.
sort(int[]) - Method in class joelib.sort.Sorter: Description of the Method
sort(double[]) - Method in class joelib.sort.Sorter: Description of the Method
sort(long[]) - Method in class joelib.sort.Sorter: Description of the Method
sort(Object[], Comparator) - Method in class joelib.sort.Sorter: Description of the Method
sortBonds() - Method in class joelib.molecule.JOEMol: Description of the Method
sortRings() - Method in class joelib.ring.JOERingSearch: Description of the Method
sortX(XYDoubleArray) - Method in class joelib.sort.InsertSort: Description of the Method
sortX(XYIntArray) - Method in class joelib.sort.InsertSort: Description of the Method
sortX(XYDoubleArray) - Method in class joelib.sort.QuickInsertSort: Sorts an XYDoubleArray in decreasing order of the x values.
sortX(XYIntArray) - Method in class joelib.sort.QuickInsertSort: Sorts an XYDoubleArray in decreasing order of the x values.
sortX(XYDoubleArray) - Method in class joelib.sort.Sorter: Description of the Method
sortX(XYIntArray) - Method in class joelib.sort.Sorter: Description of the Method
sortX() - Method in class joelib.sort.XYDoubleArray: Description of the Method
sortX() - Method in class joelib.sort.XYIntArray: Description of the Method
sortY(XYDoubleArray) - Method in class joelib.sort.InsertSort: Description of the Method
sortY(XYIntArray) - Method in class joelib.sort.InsertSort: Description of the Method
sortY(XYDoubleArray) - Method in class joelib.sort.QuickInsertSort: Sorts an XYDoubleArray in decreasing order of the y values.
sortY(XYIntArray) - Method in class joelib.sort.QuickInsertSort: Sorts an XYDoubleArray in decreasing order of the y values.
sortY(XYDoubleArray) - Method in class joelib.sort.Sorter: Description of the Method
sortY(XYIntArray) - Method in class joelib.sort.Sorter: Description of the Method
sortY() - Method in class joelib.sort.XYDoubleArray: Description of the Method
sortY() - Method in class joelib.sort.XYIntArray: Description of the Method
sp - Variable in class joelib.smarts.types.SMARTSPatternFVec: Description of the Field
sp - Variable in class joelib.smarts.types.SMARTSPatternInt: Description of the Field
sp - Variable in class joelib.smarts.types.SMARTSPatternIntInt: Description of the Field
sp - Variable in class joelib.smarts.types.SMARTSPatternString: Description of the Field
sqrt(double) - Method in class joelib.math.JOESqrtTbl: Description of the Method
src - Variable in class joelib.smarts.BondSpec: Index of the SMARTS atom expression which is the source of this bond expression.
startAtomIndex - Variable in class joelib.algo.BFSResult: Description of the Field
startAtomIndex - Variable in class joelib.algo.DFSResult: Description of the Field
startConvert(String, String) - Method in class joelib.gui.test.ConvertPanel
startDocument() - Method in class joelib.io.types.cml.CDKConvention
startDocument() - Method in interface joelib.io.types.cml.CDOInterface: Called just before XML parsing is started.
startDocument() - Method in class joelib.io.types.cml.CMLCoreModule
startDocument() - Method in class joelib.io.types.cml.CMLHandler
startDocument() - Method in class joelib.io.types.cml.CMLReactionModule
startDocument() - Method in interface joelib.io.types.cml.ModuleInterface
startDocument() - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
startDocument() - Method in class joelib.io.types.cml.XMLHandler
startElement(String, String, String, Attributes) - Method in class joelib.io.types.cml.CDKConvention
startElement(CMLStack, String, String, String, Attributes) - Method in class joelib.io.types.cml.CMLCoreModule
startElement(String, String, String, Attributes) - Method in class joelib.io.types.cml.CMLHandler
startElement(String, String, String, Attributes) - Method in class joelib.io.types.cml.CMLReactionModule
startElement(CMLStack, String, String, String, Attributes) - Method in interface joelib.io.types.cml.ModuleInterface
startElement(String, AttributeList) - Method in class joelib.io.types.cml.XMLHandler
startElement(String, String) - Method in class joelib.io.types.cml.elements.ArrayCML
startElement(String, String) - Method in interface joelib.io.types.cml.elements.ElementCML
startElement(String, String) - Method in class joelib.io.types.cml.elements.MatrixCML
startElement(String, String) - Method in class joelib.io.types.cml.elements.ScalarCML
startObject(String) - Method in interface joelib.io.types.cml.CDOInterface: Start the process of adding a new object to the CDO of a certain type.
startObject(String) - Method in class joelib.io.types.cml.MoleculeFileCDO: Procedure required by the CDOInterface.
startSelection(String, String) - Method in class joelib.gui.test.SelectionPanel
startStatistic(String, String) - Method in class joelib.gui.test.StatisticPanel
stateChanged(EventObject) - Method in class joelib.gui.render.MoleculeViewer2D: Method to notify this CDKChangeListener if something has changed in another object
stateChanged(EventObject) - Method in interface joelib.gui.render.Renderer2DChangeListener: Invoked when the target of the listener has changed its state.
stdDev - Variable in class wsi.ra.tool.ArrayStatistic: The std deviation of values at the last calculateDerived() call
store(String, String) - Method in class wsi.ra.tool.PropertyHolder
storeChemistryKernelInfo() - Method in class joelib.io.types.ChemicalMarkupLanguage
storeChemistryKernelInfo() - Method in interface joelib.io.types.cml.CMLWriterProperties
storeMolsInDatabase(String, IOType) - Method in class joelib.util.database.SimpleJOELibDatabase
stringArrayFromSimpleString(String, String) - Static method in class joelib.util.ArrayHelper: Loads String array from String .
stringArrayFromString(String) - Method in class joelib.util.ArrayHelper: Loads String array from String .
stringArrayFromString(String, String, int) - Static method in class joelib.util.ArrayHelper: Loads double array from String .
stringArrayFromString(String) - Static method in class joelib.util.LineArrayHelper: Description of the Method
stringArrayFromString(Reader) - Static method in class joelib.util.LineArrayHelper: Description of the Method
stringArrayFromString(String, int) - Static method in class joelib.util.LineArrayHelper: Description of the Method
stringArrayFromString(Reader, int) - Static method in class joelib.util.LineArrayHelper: Gets int arrays from a Reader.
stripSalts() - Method in class joelib.molecule.JOEMol: Deletes all atoms except for the largest contiguous fragment.
sub(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
sub(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
sub(XYZVector, XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
sub(int) - Method in class joelib.math.XYZVector: Description of the Method
sub(XYZVector, int) - Static method in class joelib.math.XYZVector: Description of the Method
sub(XYZVector, XYZVector, int) - Static method in class joelib.math.XYZVector: Description of the Method
sub(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
sub(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec: Description of the Method
subList(int, int) - Method in class wsi.ra.tool.SortedVector: Returns a view of the portion of this List between fromIndex, inclusive, and toIndex, exclusive.
subSet(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
subing(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
subing(double[]) - Method in class joelib.math.XYZVector: Description of the Method
subtract(GeoVector3D, GeoVector3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: Return a geometric vector that is the result of subtracting second input geometric vector from the first one.
subtract(double) - Method in class wsi.ra.tool.ArrayStatistic: Removes a value to the observed values (no checking is done that the value being removed was actually added).
subtract(double, int) - Method in class wsi.ra.tool.ArrayStatistic: Subtracts a value that has been seen n times from the observed values
sum(GeoVector3D, GeoVector3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: Return a geometric vector that is the result of summation of two input geometric vectors
sum - Variable in class wsi.ra.tool.ArrayBinning: Description of the Field
sum - Variable in class wsi.ra.tool.ArrayStatistic: The sum of values seen
sum(double[]) - Static method in class wsi.ra.tool.StatisticUtils: Computes the sum of the elements of an array of doubles.
sum(int[]) - Static method in class wsi.ra.tool.StatisticUtils: Computes the sum of the elements of an array of integers.
sumSq - Variable in class wsi.ra.tool.ArrayStatistic: The sum of values squared seen
suspend() - Method in class wsi.ra.tool.StopWatch: Freezes the time when the stop watch is suspended.
swap(int[], int, int) - Static method in class joelib.sort.Sorter: Description of the Method
swap(double[], int, int) - Static method in class joelib.sort.Sorter: Description of the Method
swap(long[], int, int) - Static method in class joelib.sort.Sorter: Description of the Method
swap(Object[], int, int) - Static method in class joelib.sort.Sorter: Description of the Method
swap(Vector, int, int) - Static method in class joelib.sort.Sorter: Description of the Method
swap(XYDoubleArray, int, int) - Static method in class joelib.sort.Sorter: Description of the Method
swap(XYIntArray, int, int) - Static method in class joelib.sort.Sorter: Description of the Method
swap(int, int) - Method in class joelib.sort.XYDoubleArray: Description of the Method
swap(int, int) - Method in class joelib.sort.XYIntArray: Description of the Method
symbol - Variable in class joelib.molecule.Element: Description of the Field

T

TEXT - Static variable in class joelib.desc.Description: Description of the Field
TITLE - Static variable in class joelib.io.types.cml.elements.ArrayCML
TITLE - Static variable in class joelib.io.types.cml.elements.MatrixCML
TITLE - Static variable in class joelib.io.types.cml.elements.ScalarCML
TOLERANCE_FINAL_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
TOLERANCE_PRIMARY_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
TOLERANCE_SAME_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
TORSION - Static variable in class joelib.io.types.cml.CMLCoreModule
TRANS_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
TRIPLE - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Triple bond type
TYPE_ENERGETIC - Static variable in class joelib.desc.DescriptorInfo
TYPE_GEOMETRICAL - Static variable in class joelib.desc.DescriptorInfo
TYPE_NO_COORDINATES - Static variable in class joelib.desc.DescriptorInfo
TYPE_TOPOLOGICAL - Static variable in class joelib.desc.DescriptorInfo
TYPE_UNKNOWN - Static variable in class joelib.desc.DescriptorInfo
TYPE_UNKNOWN - Static variable in class joelib.smarts.Patty
Template - class joelib.util.types.Template.: Template values.
Template() - Constructor for class joelib.util.types.Template
TestDescriptor - class joelib.test.TestDescriptor.: Example for loading molecules and get atom properties.
TestDescriptor() - Constructor for class joelib.test.TestDescriptor
TestInterface - class joelib.util.ghemical.TestInterface.: Small self-running class used to test the native methods of the 'oelib' interface.
TestInterface(GhemicalInterface) - Constructor for class joelib.util.ghemical.TestInterface
TestInterface() - Constructor for class joelib.util.ghemical.TestInterface: Gets an instance of the oelib JNI interface class.
TestLayout - class joelib.util.cdk.TestLayout.: Example for generating 2D coordinates from SMILES.
TestLayout() - Constructor for class joelib.util.cdk.TestLayout
TestMolecule - class joelib.test.TestMolecule.: Example for loading molecules and get atom properties.
TestMolecule() - Constructor for class joelib.test.TestMolecule
TestPatty - class joelib.test.TestPatty.: Example for the pattern assignment of SMARTS pattern.
TestPatty() - Constructor for class joelib.test.TestPatty
TestSMILES - class joelib.test.TestSMILES.: Example for generating a molecule using SMILES.
TestSMILES() - Constructor for class joelib.test.TestSMILES
TestSSSR - class joelib.test.TestSSSR.: Example for getting the 'Smallest Set of Smallest Rings' (SSSR).
TestSSSR() - Constructor for class joelib.test.TestSSSR
TestSmarts - class joelib.test.TestSmarts.: 'SMiles ARbitrary Target Specification' (SMARTS) example for finding substructures.
TestSmarts() - Constructor for class joelib.test.TestSmarts
TieResolver - interface joelib.algo.morgan.TieResolver.: Interface for resolving renumbering ties.
Tinker - class joelib.io.types.Tinker.: Reader/Writer for Tinker files.
Tinker() - Constructor for class joelib.io.types.Tinker
Title2Data - class joelib.ext.Title2Data.: Simple example for calling external programs.
Title2Data() - Constructor for class joelib.ext.Title2Data: Constructor for the Corina object
Title2DataTest - class joelib.test.Title2DataTest.: Example for converting molecules.
Title2DataTest() - Constructor for class joelib.test.Title2DataTest
ToolTipInfo - interface joelib.util.ToolTipInfo.: Tool tip information for chart visualisations.
TopologicalAtomPair - class joelib.desc.types.atompair.TopologicalAtomPair.: Calculates topological atom type pair (depends on atom properties used).
TopologicalAtomPair() - Constructor for class joelib.desc.types.atompair.TopologicalAtomPair: Constructor for the KierShape1 object
TopologicalDiameter - class joelib.desc.types.TopologicalDiameter.: Calculates the topological diameter.
TopologicalDiameter() - Constructor for class joelib.desc.types.TopologicalDiameter
TopologicalRadius - class joelib.desc.types.TopologicalRadius.: Calculates the topological radius.
TopologicalRadius() - Constructor for class joelib.desc.types.TopologicalRadius
TransformationAtom - class joelib.math.symmetry.TransformationAtom.: TransformationAtom.
TransformationAtom(String) - Constructor for class joelib.math.symmetry.TransformationAtom: Constructor for the TransformationAtom object
tail - Variable in class wsi.ra.tool.Deque
takeCGStep() - Method in class joelib.util.ghemical.GhemicalInterface
takeCGStep(int) - Method in class joelib.util.ghemical.GhemicalInterface
tanimoto(BitSet14) - Method in class joelib.util.JOEBitVec: Returns the tanimoto similarity coefficient between this BitSet14 with the BitSet14 b.
test(String, IOType, IOType) - Method in class joelib.algo.morgan.MorganTest: A unit test for JUnit
test(String, String, String, String) - Method in class joelib.smarts.test.SMARTSEvaluation: A unit test for JUnit
test() - Method in class joelib.test.Combine
test() - Method in class joelib.test.Comparison: A unit test for JUnit
test() - Method in class joelib.test.DescriptorSelection: A unit test for JUnit
test() - Method in class joelib.test.DescriptorStatistic: A unit test for JUnit
test() - Method in class joelib.test.EuklidianComparison: A unit test for JUnit
test() - Method in class joelib.test.GhemicalTest: A unit test for JUnit
test(String, IOType, IOType) - Method in class joelib.test.TestDescriptor: A unit test for JUnit
test(String, IOType, IOType) - Method in class joelib.test.TestMolecule: A unit test for JUnit
test(String, String, IOType, IOType) - Method in class joelib.test.TestPatty: A unit test for JUnit
test(String, IOType, IOType) - Method in class joelib.test.TestSMILES: A unit test for JUnit
test(String, IOType, IOType) - Method in class joelib.test.TestSSSR: A unit test for JUnit
test(String, String, IOType, IOType) - Method in class joelib.test.TestSmarts: A unit test for JUnit
test() - Method in class joelib.test.Title2DataTest: A unit test for JUnit
testDescriptor() - Method in class joelib.algo.APropertyBFS: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.algo.BFS: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.algo.DFS: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.AtomsCounter: Test the implementation of this descriptor.
testDescriptor() - Method in interface joelib.desc.Descriptor: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.SMARTSCounter: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.SimpleBooleanDesc: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.SimpleDoubleAtomProperty: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.SimpleDoubleDesc: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.SimpleDynamicAtomProperty: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.SimpleIntDesc: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.SimpleStringAtomProperty: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.APropertyDistanceMatrix: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.Autocorrelation: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.BCUT: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.BurdenEigenvalues: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.BurdenModifiedEigenvalues: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.ConjElectroTopolState: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.DistanceDistanceMatrix: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.DistanceMatrix: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.ElectrogeometricalState: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.ElectrotopologicalState: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.GeomDistanceMatrix: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.GlobalTopologicalChargeIndex: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.HeavyBonds: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.HeteroCycles: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.RadialDistributionFunction: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.SSKey3DS: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.WeightedBurdenEigenvalues: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Test the implementation of this descriptor.
testDescriptor() - Method in class joelib.desc.types.atompair.TopologicalAtomPair: Test the implementation of this descriptor.
tie - Variable in class joelib.algo.morgan.AtomDoubleParent: Renumbering tie flag.
tieResolvingProblem() - Method in class joelib.algo.morgan.Morgan
timeSeed() - Method in class joelib.util.JOERandom: Description of the Method
tmpAtomIdx - Variable in class joelib.algo.morgan.AtomDouble: Temporary and new atom index stored as double value to handle huge temporary values.
tmpAtomIdx - Variable in class joelib.algo.morgan.AtomDoubleParent: Temporary and new atom index stored as double value to handle huge temporary values.
to - Variable in class joelib.gui.render.FromToAtoms
toArray() - Method in class wsi.ra.tool.SortedVector: Returns an array containing all of the elements in this Vector in the correct order.
toArray(Object[]) - Method in class wsi.ra.tool.SortedVector: Returns an array containing all of the elements in this Vector in the correct order; the runtime type of the returned array is that of the specified array.
toBoolArr(int) - Method in class joelib.util.JOEBitVec
toBoolArray() - Method in class joelib.util.JOEBitVec
toDoubleArray() - Method in class joelib.algo.datamining.weka.MolSparseInstance: Returns the values of each attribute as an array of doubles.
toInertialFrame(int, double[]) - Method in class joelib.molecule.JOEMol: Description of the Method
toInertialFrame() - Method in class joelib.molecule.JOEMol: Description of the Method
toIntArray() - Method in class joelib.util.JOEBitVec
toNativeArff() - Method in class joelib.algo.datamining.weka.MolInstances
toRectangleString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toRectangleString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper: Description of the Method
toRectangleString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toRectangleString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toRectangleString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toRectangleString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper: Description of the Method
toRectangleString(StringBuffer, byte[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toRectangleString(StringBuffer, byte[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, int[]) - Method in class joelib.util.ArrayHelper: Write integer array to String .
toSimpleString(StringBuffer, double[]) - Method in class joelib.util.ArrayHelper: Write integer array to String .
toSimpleString(StringBuffer, double[], DecimalFormatter) - Method in class joelib.util.ArrayHelper: Write integer array to String .
toSimpleString(StringBuffer, boolean[]) - Method in class joelib.util.ArrayHelper: Write boolean array to String .
toSimpleString(StringBuffer, int[], String) - Static method in class joelib.util.ArrayHelper: Write integer array to String .
toSimpleString(StringBuffer, String[], String) - Static method in class joelib.util.ArrayHelper: Write String array to String .
toSimpleString(StringBuffer, double[], String) - Static method in class joelib.util.ArrayHelper: Write integer array to String .
toSimpleString(StringBuffer, double[], String, DecimalFormatter) - Static method in class joelib.util.ArrayHelper: Write integer array to String .
toSimpleString(StringBuffer, boolean[], String) - Static method in class joelib.util.ArrayHelper: Write boolean array to String .
toSimpleString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, boolean[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toSimpleString(StringBuffer, boolean[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toSmilesString(JOESmiNode, StringBuffer) - Method in class joelib.smiles.JOEMol2Smi: Description of the Method
toString() - Method in class Acme.IntHashtable
toString(IOType) - Method in class joelib.algo.BFSResult: Description of the Method
toString(IOType) - Method in class joelib.algo.DFSResult: Description of the Method
toString(Hashtable) - Static method in class joelib.algo.datamining.weka.APWekaHelper
toString() - Method in class joelib.algo.datamining.weka.MolInstance: Returns the description of one instance.
toString() - Method in class joelib.algo.datamining.weka.MolSparseInstance: Returns the description of one instance in sparse format.
toString() - Method in class joelib.algo.morgan.AtomDouble
toString() - Method in class joelib.algo.morgan.AtomDoubleParent
toString() - Method in class joelib.data.JOEDataType
toString() - Method in class joelib.data.JOEGenericData
toString(IOType) - Method in class joelib.data.JOEPairData: Description of the Method
toString() - Method in class joelib.data.JOEPairData
toString(IOType) - Method in interface joelib.desc.DescResult
toString() - Method in class joelib.desc.DescriptorInfo: Gets the descriptor informations.
toString(IOType, DecimalFormatter) - Method in interface joelib.desc.NumberFormatDescResult
toString() - Method in interface joelib.desc.data.MoleculeCache
toString() - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
toString(IOType) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
toString(IOType, DecimalFormatter) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
toString(IOType, DecimalFormatter) - Method in class joelib.desc.result.APropDoubleResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.APropIntResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.BitArrayResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.BitResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.BooleanResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.DoubleArrayResult: Description of the Method
toString(IOType, DecimalFormatter) - Method in class joelib.desc.result.DoubleArrayResult
toString(IOType) - Method in class joelib.desc.result.DoubleMatrixResult: Description of the Method
toString(IOType, DecimalFormatter) - Method in class joelib.desc.result.DoubleMatrixResult
toString(IOType) - Method in class joelib.desc.result.DoubleResult: Description of the Method
toString(IOType, DecimalFormatter) - Method in class joelib.desc.result.DoubleResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
toString(IOType, DecimalFormatter) - Method in class joelib.desc.result.DynamicArrayResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.FloatMatrixResult: Description of the Method
toString(IOType, DecimalFormatter) - Method in class joelib.desc.result.FloatMatrixResult
toString(IOType) - Method in class joelib.desc.result.IntArrayResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.IntBitArrayResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.IntMatrixResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.IntResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.StringArrayResult: Description of the Method
toString(IOType) - Method in class joelib.desc.result.StringResult: Description of the Method
toString() - Method in class joelib.desc.types.atompair.AtomPair
toString(IOType) - Method in class joelib.desc.types.atompair.AtomPair
toString() - Method in class joelib.desc.types.atompair.AtomPairAtomType
toString(IOType) - Method in class joelib.desc.types.atompair.AtomPairAtomType
toString(IOType) - Method in class joelib.desc.types.atompair.AtomPairResult: Description of the Method
toString() - Method in class joelib.ext.ExternalInfo: Description of the Method
toString() - Method in class joelib.gui.molviewer.java3d.math.geometry.Angle: Return string representation of angle
toString() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Method
toString() - Method in class joelib.gui.render.Arrow
toString() - Method in class joelib.gui.render.ConjugatedRing
toString() - Method in class joelib.gui.render.OrthoLine
toString() - Method in class joelib.io.IOType
toString() - Method in class joelib.io.IOTypeHolder: Shows a table of all available input/output types.
toString() - Method in class joelib.io.types.cml.CMLStack: Returns a String representation of the stack.
toString() - Method in class joelib.jcamp.JCAMPParser: Returns a string of all LDR's (label data records.
toString() - Method in class joelib.math.Matrix3x3: Description of the Method
toString(Matrix3x3) - Method in class joelib.math.Matrix3x3: Description of the Method
toString() - Method in class joelib.math.XYZVector: Description of the Method
toString(XYZVector) - Method in class joelib.math.XYZVector: Description of the Method
toString() - Method in class joelib.molecule.JOEAtom: Description of the Method
toString() - Method in class joelib.molecule.JOEBond
toString() - Method in class joelib.molecule.JOEMol: Description of the Method
toString(IOType) - Method in class joelib.molecule.JOEMol: Description of the Method
toString(boolean) - Method in class joelib.molecule.JOEMol: Description of the Method
toString(IOType, boolean) - Method in class joelib.molecule.JOEMol: Description of the Method
toString() - Method in class joelib.process.filter.NativeValueFilter
toString() - Method in class joelib.process.filter.SMARTSFilter
toString() - Method in class joelib.process.types.DescBinning: Description of the Method
toString() - Method in class joelib.process.types.DescStatistic: Description of the Method
toString() - Method in class joelib.process.types.DescVarianceNorm: Description of the Method
toString() - Method in class joelib.ring.JOERing
toString() - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
toString() - Method in class joelib.smarts.Pattern
toString(String) - Method in class joelib.smarts.Pattern
toString() - Method in class joelib.smarts.atomexpr.AtomExpr
toString() - Method in class joelib.smarts.bondexpr.BondExpr
toString(StringBuffer, int[]) - Method in class joelib.util.ArrayHelper: Write integer array to String .
toString(StringBuffer, int[], String, boolean) - Static method in class joelib.util.ArrayHelper: Write integer array to String .
toString(StringBuffer, String[]) - Method in class joelib.util.ArrayHelper: Write String array to String .
toString(StringBuffer, String[], String, boolean) - Static method in class joelib.util.ArrayHelper: Write String array to String .
toString(StringBuffer, double[]) - Method in class joelib.util.ArrayHelper: Description of the Method
toString(StringBuffer, double[], DecimalFormatter) - Method in class joelib.util.ArrayHelper: Description of the Method
toString(StringBuffer, double[], String, boolean) - Static method in class joelib.util.ArrayHelper: Description of the Method
toString(StringBuffer, double[], String, boolean, DecimalFormatter) - Static method in class joelib.util.ArrayHelper: Description of the Method
toString(StringBuffer, boolean[]) - Method in class joelib.util.ArrayHelper: Description of the Method
toString(StringBuffer, boolean[], String, boolean) - Static method in class joelib.util.ArrayHelper: Description of the Method
toString() - Method in class joelib.util.BitSet14: Returns a string representation of this bit set.
toString() - Method in class joelib.util.JOEBitVec: Writes this bit vector to a String.
toString(StringBuffer, int[]) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, int[], boolean) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, String[]) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, String[], boolean) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, double[]) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, double[], DecimalFormatter) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, double[], boolean) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, double[], boolean, DecimalFormatter) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, boolean[]) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, boolean[], boolean) - Static method in class joelib.util.LineArrayHelper: Description of the Method
toString(StringBuffer, int[][]) - Static method in class joelib.util.LineMatrixHelper: Description of the Method
toString(StringBuffer, double[][]) - Static method in class joelib.util.LineMatrixHelper: Description of the Method
toString(StringBuffer, double[][], DecimalFormatter) - Static method in class joelib.util.LineMatrixHelper: Description of the Method
toString(StringBuffer, byte[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toString(StringBuffer, byte[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper: Description of the Method
toString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper: Description of the Method
toString() - Method in class joelib.util.types.BasicFactoryInfo: Gets informations for a class which can be get by a factory class.
toString() - Method in class joelib.util.types.Int
toString() - Method in class joelib.util.types.IntInt
toString() - Method in class joelib.util.types.IntIntInt
toString() - Method in class joelib.util.types.StringInt
toString() - Method in class joelib.util.types.StringString
toString() - Method in class wsi.ra.tool.ArrayBinning: Returns a string summarising the stats so far.
toString() - Method in class wsi.ra.tool.ArrayStatistic: Returns a string summarising the stats so far.
toTranspRectString(StringBuffer, int[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toTranspRectString(StringBuffer, int[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toTranspRectString(StringBuffer, double[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toTranspRectString(StringBuffer, double[][], DecimalFormatter) - Method in class joelib.util.MatrixHelper: Description of the Method
toTranspRectString(StringBuffer, byte[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toTranspRectString(StringBuffer, byte[][]) - Method in class joelib.util.MatrixHelper: Description of the Method
toTranspRectString(StringBuffer, double[][], String) - Static method in class joelib.util.MatrixHelper: Description of the Method
toTranspRectString(StringBuffer, double[][], String, DecimalFormatter) - Static method in class joelib.util.MatrixHelper: Description of the Method
toTrueFalseString(StringBuffer, boolean[], String) - Static method in class joelib.util.ArrayHelper: Write boolean array to String .
toVectorWithIntArray(Vector) - Method in class joelib.util.JOEBitVec
tokenize(Vector, String, String, int) - Static method in class joelib.util.JHM
tokenize(Vector, String) - Static method in class joelib.util.JHM
tokenize(Vector, String, String) - Static method in class joelib.util.JHM
torsionAngle(Point3D, Point3D, Point3D, Point3D) - Static method in class joelib.gui.molviewer.java3d.math.geometry.Geometry: calculate angle among three points in 3D space note: calling Point3D.distSquare() is more efficient than calling Point3D.distance().
tostr(float) - Method in class cformat.PrintfFormat: Formats a float into a string.
tostr(double) - Method in class cformat.PrintfFormat: Formats a double into a string.
tostr(int) - Method in class cformat.PrintfFormat: Formats an int into a string.
tostr(long) - Method in class cformat.PrintfFormat: Formats a long into a string.
tostr(char) - Method in class cformat.PrintfFormat: Formats a char into a string.
tostr(String) - Method in class cformat.PrintfFormat: Formats a String into a string.
totalExaminedCandidates - Variable in class joelib.math.symmetry.SymStatistic
transform(float[], int[], int) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Transform last nvert points from v into tv.
transform(float[], float[], int) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Transform last nvert points from v into tv.
transform(double[], double[], double[], double[], double[], double[], int) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Transform first nvert points from x,y and z into tx,ty and tz.
transform(float[], float[], float[], float[], float[], float[], int) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Transform first nvert points from x,y and z into tx,ty and tz.
transform(ViewerAtoms, int) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Transform first nvert Atoms in AtomVector
transform(ViewerMolecule) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Transform everything appropriate in the molecule
transform(double[], int) - Method in class joelib.math.JOECoordTrans: Applies this objects transformation to a set of coordinates
transform - Variable in class joelib.math.symmetry.SymmetryElement: Correspondence table for the transformation.
transformAtom(Symmetry, SymmetryElement, SymAtom, SymAtom) - Method in class joelib.math.symmetry.SymmetryElement
transformAtomMethod - Variable in class joelib.math.symmetry.SymmetryElement
transformBondExpr(BondExpr) - Static method in class joelib.smarts.bondexpr.BondExpr: Description of the Method
transformCVStag(String) - Static method in class joelib.data.JOEKernel
translate(char[]) - Method in class joelib.data.JOETypeTable: Description of the Method
translate(String) - Method in class joelib.data.JOETypeTable: Description of the Method
translate(GeoVector3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: move(translate) this point along with the input geometric vector
translate(double, double, double) - Method in class joelib.gui.molviewer.java3d.math.geometry.Point3D: move(translate) this point by the input quantity along the 3 axises
translate(float, float, float) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Translate the origin
translate(XYZVector) - Method in class joelib.molecule.JOEMol: Description of the Method
translate(XYZVector, int) - Method in class joelib.molecule.JOEMol: Description of the Method
translate2D(RenderingAtoms, double, double) - Static method in class joelib.gui.render.RenderHelper: Translates the given molecule by the given Vector.
translate2D(RenderingAtoms, Vector2d) - Static method in class joelib.gui.render.RenderHelper: Translates a molecule from the origin to a new point denoted by a vector.
translate2DCentreOfMassTo(RenderingAtoms, Point2d) - Static method in class joelib.gui.render.RenderHelper: Translates a molecule from the origin to a new point denoted by a vector.
translateAllPositive(RenderingAtoms) - Static method in class joelib.gui.render.RenderHelper: Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.
traverse - Variable in class joelib.algo.BFSResult: Description of the Field
traverseSMARTS(Pattern, int) - Static method in class joelib.smarts.ParseSmart: Description of the Method
type - Variable in class joelib.math.symmetry.SymAtom
type - Variable in class joelib.smarts.atomexpr.AtomExpr: Description of the Field
type - Variable in class joelib.smarts.bondexpr.BondExpr: Description of the Field

U

UNDEFINED - Static variable in class joelib.desc.Description
UNDEFINED_TYPE - Static variable in class joelib.jcamp.JCAMPDataBlock
UNITS - Static variable in class joelib.io.types.cml.elements.ArrayCML
UNITS - Static variable in class joelib.io.types.cml.elements.MatrixCML
UNITS - Static variable in class joelib.io.types.cml.elements.ScalarCML
UNKNOWN - Static variable in class joelib.io.types.cml.CMLCoreModule
UP_BOND_FLAG - Static variable in class joelib.smiles.JOESmilesParser
Undefined - class joelib.io.types.Undefined.: Reader/Writer for Undefined files.
Undefined() - Constructor for class joelib.io.types.Undefined: Constructor for the Undefined object
unit() - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Reinitialize to the unit matrix
unsetAromatic() - Method in class joelib.molecule.JOEAtom: Clears the aromatic flag of this atom.
unsetAromatic() - Method in class joelib.molecule.JOEBond: Description of the Method
unsetAromaticPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
unsetImplicitValencePerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
unsetPartialChargesPerceived() - Method in class joelib.molecule.JOEMol: Description of the Method
unsetStereo() - Method in class joelib.molecule.JOEAtom: Clears the stereo flag of this atom.
updateScene(int, int) - Method in class joelib.gui.molviewer.java3d.graphics3D.PickHighlightBehavior
usage() - Method in class joelib.algo.morgan.MorganTest: Description of the Method
usage() - Method in class joelib.math.symmetry.Symmetry
usage() - Method in class joelib.smarts.test.SMARTSEvaluation: Description of the Method
usage() - Method in class joelib.test.Combine: Description of the Method
usage() - Method in class joelib.test.Comparison: Description of the Method
usage() - Method in class joelib.test.Convert: Description of the Method
usage() - Method in class joelib.test.ConvertSkip: Description of the Method
usage() - Method in class joelib.test.DescriptorCalculation: Description of the Method
usage() - Method in class joelib.test.DescriptorSelection: Description of the Method
usage() - Method in class joelib.test.DescriptorStatistic: Description of the Method
usage() - Method in class joelib.test.EuklidianComparison: Description of the Method
usage() - Method in class joelib.test.GhemicalTest: Description of the Method
usage() - Method in class joelib.test.TestDescriptor: Description of the Method
usage() - Method in class joelib.test.TestMolecule: Description of the Method
usage() - Method in class joelib.test.TestPatty: Description of the Method
usage() - Method in class joelib.test.TestSMILES: Description of the Method
usage() - Method in class joelib.test.TestSSSR: Description of the Method
usage() - Method in class joelib.test.TestSmarts: Description of the Method
usage() - Method in class joelib.test.Title2DataTest: Description of the Method
usage() - Method in class jtt.docbook.DocBookArticles: Description of the Method
usage() - Method in class jtt.docbook.DocBookEquations: Description of the Method
usage() - Method in class jtt.docbook.DocBookMolecules: Description of the Method
useAtomPropertyColoring(String) - Method in class joelib.gui.molviewer.java3d.ViewerFrame
useAtomPropertyColoring(String) - Method in class joelib.gui.molviewer.java3d.graphics3D.JPanel3D
useAtomPropertyColoring(String) - Method in class joelib.gui.molviewer.java3d.graphics3D.MolecularScene
useAtomPropertyColoring(JOEMol, String) - Method in class joelib.io.types.Matlab
useAtomPropertyColoring(JOEMol, String) - Method in class joelib.molecule.types.AtomPropertyColoring
useCstandard(boolean) - Method in class cformat.ScanfReader: White spaces are skipped at the beginning of a line if flag is true otherwise spaces are counted as valid characters.
useCstandard() - Method in class cformat.ScanfReader: White spaces are skipped at the beginning of a line if flag is true otherwise spaces are counted as valid characters.
useNamespace() - Method in class joelib.io.types.ChemicalMarkupLanguage
useNamespace() - Method in interface joelib.io.types.cml.CMLWriterProperties
usePlainColoring() - Method in class joelib.molecule.types.AtomPropertyColoring

V

VERSION - Static variable in class joelib.io.types.cml.CMLMoleculeWriterBase
VectorIterator - class joelib.util.iterator.VectorIterator.: Iterator for the standard Vector.
VectorIterator(Vector) - Constructor for class joelib.util.iterator.VectorIterator: Constructor for the VectorIterator object
VectorSizeComparator - class joelib.sort.VectorSizeComparator.: Comparator for Vector size.
VectorSizeComparator() - Constructor for class joelib.sort.VectorSizeComparator: Initializes the Vector-Comparator.
Viewer - class joelib.gui.molviewer.java3d.Viewer.: Description of the Class
Viewer() - Constructor for class joelib.gui.molviewer.java3d.Viewer: Construct the application
Viewer(String) - Constructor for class joelib.gui.molviewer.java3d.Viewer
Viewer(String, String) - Constructor for class joelib.gui.molviewer.java3d.Viewer: Constructor for the Viewer object
ViewerAtom - class joelib.gui.molviewer.java3d.molecule.ViewerAtom.: Atom class for Java3D viewer.
ViewerAtom(ViewerMolecule, JOEAtom) - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerAtom: Constructor for the ViewerAtom object
ViewerAtoms - class joelib.gui.molviewer.java3d.molecule.ViewerAtoms.: Atom vector class for Java3D viewer.
ViewerAtoms() - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerAtoms: Default constructor
ViewerAtoms(int) - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerAtoms: Capacity constructor
ViewerAtoms(int, int) - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerAtoms: Capacity and increment constructor
ViewerBond - class joelib.gui.molviewer.java3d.molecule.ViewerBond.: Bond class for Java3D viewer.
ViewerBond(ViewerMolecule, JOEBond, ViewerAtom, ViewerAtom) - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerBond: Constructor without Properties
ViewerBonds - class joelib.gui.molviewer.java3d.molecule.ViewerBonds.: Bond vector class for Java3D viewer.
ViewerBonds() - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Default constructor
ViewerBonds(int) - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Capacity constructor
ViewerBonds(int, int) - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerBonds: Capacity & increment constructor
ViewerFrame - class joelib.gui.molviewer.java3d.ViewerFrame.: Description of the Class
ViewerFrame(String, String) - Constructor for class joelib.gui.molviewer.java3d.ViewerFrame: Construct the frame
ViewerMolecule - class joelib.gui.molviewer.java3d.molecule.ViewerMolecule.: Molecule class for Java3D viewer.
ViewerMolecule(JOEMol) - Constructor for class joelib.gui.molviewer.java3d.molecule.ViewerMolecule: Default constructor
ViewerUsage - class joelib.gui.molviewer.java3d.ViewerUsage.: Description of the Class
ViewerUsage(Frame) - Constructor for class joelib.gui.molviewer.java3d.ViewerUsage: Constructor for the ViewerUsage object
vX - Static variable in class joelib.math.XYZVector: Description of the Field
vY - Static variable in class joelib.math.XYZVector: Description of the Field
vZ - Static variable in class joelib.math.XYZVector: Description of the Field
vZero - Static variable in class joelib.math.XYZVector: Description of the Field
valence - Variable in class joelib.smiles.ClosureBond: Valence of the previous atom.
valenceSum(JOEAtom) - Static method in class joelib.util.JHM: Description of the Method
value(int) - Method in class joelib.algo.datamining.weka.MolSparseInstance: Returns an instance's attribute value in internal format.
value - Variable in class joelib.desc.result.APropDoubleArrResult: Description of the Field
value - Variable in class joelib.desc.result.APropDoubleResult: Description of the Field
value - Variable in class joelib.desc.result.APropIntResult: Description of the Field
value - Variable in class joelib.desc.result.BitArrayResult: Description of the Field
value - Variable in class joelib.desc.result.BitResult: Description of the Field
value - Variable in class joelib.desc.result.BooleanResult: Description of the Field
value - Variable in class joelib.desc.result.DoubleMatrixResult: Description of the Field
value - Variable in class joelib.desc.result.DoubleResult: Description of the Field
value - Variable in class joelib.desc.result.FloatMatrixResult: Description of the Field
value - Variable in class joelib.desc.result.IntBitArrayResult: Description of the Field
value - Variable in class joelib.desc.result.IntMatrixResult: Description of the Field
value - Variable in class joelib.desc.result.StringResult: Description of the Field
value - Variable in class joelib.smarts.atomexpr.LeafAtomExpr: Description of the Field
value - Variable in class joelib.smarts.bondexpr.LeafBondExpr: Description of the Field
variance(double[]) - Static method in class wsi.ra.tool.StatisticUtils: Computes the variance for an array of doubles.
varianceDeNormalization(double) - Method in class wsi.ra.tool.ArrayStatistic
varianceNormalization(double) - Method in class wsi.ra.tool.ArrayStatistic: Scales the input variables so that they have similar magnitudes.
vb - Variable in class joelib.smarts.AtomSpec: Vector binding.
vectorTo(Point3D) - Method in class joelib.gui.molviewer.java3d.math.geometry.Line: Return the geometric vector from some point on the line to the given point so that the vector is perpendicular to the line.
viewer - Static variable in class joelib.gui.molviewer.java3d.Viewer: Description of the Field
visit - Variable in class joelib.smarts.AtomSpec: Visited flag.
visit - Variable in class joelib.smarts.BondSpec: Visited flag.

W

WEDGE - Static variable in class joelib.gui.molviewer.java3d.molecule.ViewerBond: Wedge up bond type
WIRE - Static variable in interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle: Description of the Field
WeightedBurdenEigenvalues - class joelib.desc.types.WeightedBurdenEigenvalues.
WeightedBurdenEigenvalues() - Constructor for class joelib.desc.types.WeightedBurdenEigenvalues: Constructor for the BCUT object
WeightedBurdenModifiedEigenvalues - class joelib.desc.types.WeightedBurdenModifiedEigenvalues.
WeightedBurdenModifiedEigenvalues() - Constructor for class joelib.desc.types.WeightedBurdenModifiedEigenvalues: Constructor for the BCUT object
WriteCompressedData(BufferedOutputStream) - Method in class com.obrador.JpegEncoder
WriteEOI(BufferedOutputStream) - Method in class com.obrador.JpegEncoder
WriteHeaders(BufferedOutputStream) - Method in class com.obrador.JpegEncoder
warning(SAXParseException) - Method in class joelib.io.types.cml.CMLErrorHandler: Outputs a SAXParseException warning to the logger.
weight - Variable in class joelib.molecule.Element: Description of the Field
write(JOEMol) - Method in interface joelib.io.MoleculeFileType: Reads an molecule entry from the initialized molecule reader.
write(JOEMol, String) - Method in interface joelib.io.MoleculeFileType: Reads an molecule entry from the initialized molecule reader.
write(JOEMol, String, boolean, Vector) - Method in interface joelib.io.PropertyWriter: Writes a molecule with his JOEPairData.
write(JOEMol) - Method in class joelib.io.SimpleImageWriter: Description of the Method
write(JOEMol, String) - Method in class joelib.io.SimpleImageWriter: Description of the Method
write(JOEMol) - Method in class joelib.io.types.Amber: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Amber: Description of the Method
write(JOEMol) - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
write(JOEMol, String, boolean, Vector) - Method in class joelib.io.types.ChemicalMarkupLanguage: Writes a molecule with his JOEPairData .
write(JOEMol) - Method in class joelib.io.types.ClearTextFormat: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.ClearTextFormat: Description of the Method
write(JOEMol) - Method in class joelib.io.types.Flat: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Flat: Description of the Method
write(JOEMol) - Method in class joelib.io.types.Gaussian: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Gaussian: Description of the Method
write(JOEMol) - Method in class joelib.io.types.HIN: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.HIN: Description of the Method
write(JOEMol) - Method in class joelib.io.types.JCAMP: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.JCAMP: Description of the Method
write(JOEMol) - Method in class joelib.io.types.MDLSD: Writes a molecule with his JOEPairData .
write(JOEMol, String) - Method in class joelib.io.types.MDLSD: Writes a molecule with his JOEPairData .
write(JOEMol, String, boolean, Vector) - Method in class joelib.io.types.MDLSD: Writes a molecule with his JOEPairData .
write(JOEMol) - Method in class joelib.io.types.Matlab: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Matlab: Description of the Method
write(JOEMol) - Method in class joelib.io.types.MolconnZ: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.MolconnZ: Description of the Method
write(JOEMol) - Method in class joelib.io.types.Mopac: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Mopac: Description of the Method
write(JOEMol) - Method in class joelib.io.types.PDB: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.PDB: Description of the Method
write(JOEMol) - Method in class joelib.io.types.PDF: Description of the Method
write(JOESmartsPattern, JOEMol) - Method in class joelib.io.types.PDF
write(JOEMol, String) - Method in class joelib.io.types.PDF: Description of the Method
write(JOEMol, String, boolean, Vector) - Method in class joelib.io.types.PDF: Writes a molecule with his JOEPairData .
write(JOEMol, String, boolean, Vector, JOESmartsPattern) - Method in class joelib.io.types.PDF: Writes a molecule with his JOEPairData .
write(JOEMol) - Method in class joelib.io.types.POVRay: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.POVRay: Description of the Method
write(JOEMol) - Method in class joelib.io.types.Smiles: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Smiles: Description of the Method
write(JOEMol) - Method in class joelib.io.types.SybylMol2: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.SybylMol2: Description of the Method
write(JOEMol) - Method in class joelib.io.types.Tinker: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Tinker: Description of the Method
write(JOEMol) - Method in class joelib.io.types.Undefined: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.Undefined: Description of the Method
write(JOEMol) - Method in class joelib.io.types.XYZ: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.XYZ: Description of the Method
write(JOEMol) - Method in class joelib.io.types.ZIP: Description of the Method
write(JOEMol, String) - Method in class joelib.io.types.ZIP: Description of the Method
write(PrintStream, double[]) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
write(PrintStream, String) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
write(OutputStream) - Method in class joelib.molecule.JOEMolVector: Write a OEMolVector to a file.
write(OutputStream, IOType) - Method in class joelib.molecule.JOEMolVector: Write a OEMolVector to a file.
write(JOEMol, String, IOType) - Method in class joelib.test.TestSMILES
writeAxes(PrintStream, String, SymmetryElement[]) - Static method in class joelib.io.types.cml.CMLSymmetryWriter
writeAxisTypeScalar(PrintStream, String, int) - Static method in class joelib.io.types.cml.CMLSymmetryWriter
writeBinningFileFor(String) - Method in class joelib.process.types.DescBinning
writeCloseTag(PrintStream, CMLWriterProperties, String) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writeDoubleArray(PrintStream, String, double[]) - Static method in class joelib.io.types.cml.CMLSymmetryWriter
writeDoubleScalar(PrintStream, String, double) - Static method in class joelib.io.types.cml.CMLSymmetryWriter
writeElementName(PrintStream, CMLWriterProperties, String) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writeEmptyElement(PrintStream, CMLWriterProperties, String, Hashtable) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writeHash(Hashtable, File) - Static method in class joelib.algo.datamining.weka.APWekaHelper
writeImage(Image, OutputStream) - Method in class joelib.io.SimpleImageWriter
writeImage(Image, OutputStream) - Method in class joelib.io.types.BMP
writeImage(Image, OutputStream) - Method in class joelib.io.types.GIF
writeImage(Image, OutputStream) - Method in class joelib.io.types.JPEG
writeImage(Image, OutputStream) - Method in class joelib.io.types.PNG
writeImage(Image, OutputStream) - Method in class joelib.io.types.PPM
writeImpliciteHydrogens() - Method in class joelib.io.types.ChemicalMarkupLanguage
writeImpliciteHydrogens() - Method in interface joelib.io.types.cml.CMLWriterProperties
writeInversionCenter(PrintStream, SymmetryElement) - Static method in class joelib.io.types.cml.CMLSymmetryWriter
writeMapList(OutputStream) - Method in class joelib.smarts.JOESmartsPattern: Description of the Method
writeMatrixFileFor(String) - Method in class joelib.algo.datamining.weka.MolInstancesCache
writeMatrixFileFor(String) - Method in interface joelib.desc.data.MoleculeCache
writeMatrixFileFor(String) - Method in class joelib.desc.data.MoleculesDescriptorMatrix: Description of the Method
writeMolecule(JOEMol, boolean, Vector) - Method in interface joelib.io.types.cml.CMLMoleculeWriter
writeMolecule(JOEMol, boolean, Vector) - Method in class joelib.io.types.cml.CMLMoleculeWriterBase: Description of the Method
writeNext(JOEMol) - Method in class joelib.io.SimpleWriter: Writes next molecule.
writeOpenTag(PrintStream, CMLWriterProperties, String) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writeOpenTag(PrintStream, CMLWriterProperties, String, boolean) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writeOpenTag(PrintStream, CMLWriterProperties, String, Hashtable) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writeOpenTag(PrintStream, CMLWriterProperties, String, Hashtable, boolean) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writeOpenTagAtts(PrintStream, Hashtable) - Static method in class joelib.io.types.cml.CMLMoleculeWriterBase
writePairData(CMLWriterProperties, PrintStream, JOEPairData) - Static method in class joelib.io.types.cml.CMLPropertyWriter
writePartialCharge() - Method in class joelib.io.types.ChemicalMarkupLanguage
writePartialCharge() - Method in interface joelib.io.types.cml.CMLWriterProperties
writePlanes(PrintStream, SymmetryElement[]) - Static method in class joelib.io.types.cml.CMLSymmetryWriter
writeProperties(CMLWriterProperties, PrintStream, JOEMol, boolean, Vector) - Static method in class joelib.io.types.cml.CMLPropertyWriter
writeRings() - Method in class joelib.ring.JOERingSearch: Description of the Method
writeSingleResults(JOEMol, String) - Method in class joelib.desc.result.APropDoubleArrResult: Write APropDoubleResult entries for every array index entry.
writeSingleResults(JOEMol, String, PrintStream, Hashtable) - Method in class joelib.desc.result.APropDoubleArrResult: Write APropDoubleResult entries for every array index entry.
writeSingleResults(JOEMol, String, boolean, boolean, PrintStream, Hashtable, boolean) - Method in class joelib.desc.result.APropDoubleArrResult: Description of the Method
writeStatisticFileFor(String) - Method in class joelib.process.types.DescStatistic
writeSymmetry(PrintStream, JOEMol) - Static method in class joelib.io.types.cml.CMLSymmetryWriter
writeSymmetryInformations() - Method in class joelib.io.types.ChemicalMarkupLanguage
writeSymmetryInformations() - Method in interface joelib.io.types.cml.CMLWriterProperties
writeTitles(OutputStream, JOEMol) - Method in class joelib.util.JHM: Description of the Method
writeable() - Method in interface joelib.io.MoleculeFileType: Returns true if this molecule data type is writeable.
writeable() - Method in class joelib.io.SimpleImageWriter
writeable() - Method in class joelib.io.types.Amber
writeable() - Method in class joelib.io.types.ChemicalMarkupLanguage: Description of the Method
writeable() - Method in class joelib.io.types.ClearTextFormat: Description of the Method
writeable() - Method in class joelib.io.types.Flat: Description of the Method
writeable() - Method in class joelib.io.types.Gaussian
writeable() - Method in class joelib.io.types.HIN
writeable() - Method in class joelib.io.types.JCAMP: Description of the Method
writeable() - Method in class joelib.io.types.MDLSD: Description of the Method
writeable() - Method in class joelib.io.types.Matlab: Description of the Method
writeable() - Method in class joelib.io.types.MolconnZ: Description of the Method
writeable() - Method in class joelib.io.types.Mopac
writeable() - Method in class joelib.io.types.PDB: Description of the Method
writeable() - Method in class joelib.io.types.PDF: Description of the Method
writeable() - Method in class joelib.io.types.POVRay: Description of the Method
writeable() - Method in class joelib.io.types.Smiles: Description of the Method
writeable() - Method in class joelib.io.types.SybylMol2: Description of the Method
writeable() - Method in class joelib.io.types.Tinker: Description of the Method
writeable() - Method in class joelib.io.types.Undefined: Description of the Method
writeable() - Method in class joelib.io.types.XYZ: Description of the Method
writeable() - Method in class joelib.io.types.ZIP: Description of the Method
wsi.ra.database - package wsi.ra.database
wsi.ra.image - package wsi.ra.image
wsi.ra.io - package wsi.ra.io: Provides simple helper classes for input/output routines.
wsi.ra.text - package wsi.ra.text
wsi.ra.tool - package wsi.ra.tool: Provides some miscellaneous helper methods.

X

XML - Static variable in class joelib.desc.Description: Description of the Field
XMLHandler - class joelib.io.types.cml.XMLHandler.: Basic XML handler for the Chemical Markup Language (CML).
XMLHandler(CDOInterface) - Constructor for class joelib.io.types.cml.XMLHandler
XMLSpecialCharacter - class joelib.io.types.cml.XMLSpecialCharacter.: Checks and converts XML special characters.
XMLSpecialCharacter() - Constructor for class joelib.io.types.cml.XMLSpecialCharacter
XYDATA_X_YY - Static variable in class joelib.jcamp.JCAMPParser: data representation: XYDATA=(X++(Y..Y)) definition
XYDoubleArray - class joelib.sort.XYDoubleArray.: Defines two double[] arrays.
XYDoubleArray(int) - Constructor for class joelib.sort.XYDoubleArray: Constructor for the XYDoubleArray object
XYDoubleArray(double[], double[]) - Constructor for class joelib.sort.XYDoubleArray: Constructor for the XYDoubleArray object
XYIntArray - class joelib.sort.XYIntArray.: Defines two int[] arrays.
XYIntArray(int) - Constructor for class joelib.sort.XYIntArray: Constructor for the XYDoubleArray object
XYIntArray(int[], int[]) - Constructor for class joelib.sort.XYIntArray: Constructor for the XYDoubleArray object
XYPAIRS - Static variable in class joelib.jcamp.JCAMPParser: data representation: XYPAIRS definition
XYPOINTS - Static variable in class joelib.jcamp.JCAMPParser: data representation: XYPOINTS definition
XYZ - class joelib.io.types.XYZ.: Reader/Writer for XYZ files.
XYZ() - Constructor for class joelib.io.types.XYZ: Constructor for the XYZ object
XYZVector - class joelib.math.XYZVector.: Vector to represent x,y,z coordinates.
XYZVector() - Constructor for class joelib.math.XYZVector: Constructor for the XYZVector object
XYZVector(double, double, double) - Constructor for class joelib.math.XYZVector: Constructor for the XYZVector object
XYZVector(XYZVector) - Constructor for class joelib.math.XYZVector: Constructor for the XYZVector object
x() - Method in class joelib.math.XYZVector: Description of the Method
x() - Method in class joelib.molecule.JOEAtom: Gets the x coordinate of the JOEAtom .
x - Variable in class joelib.sort.XYDoubleArray: Description of the Field
x - Variable in class joelib.sort.XYIntArray: Description of the Field
xlogx(int) - Static method in class wsi.ra.tool.StatisticUtils: Returns c*log2(c) for a given integer value c.
xlogx(double) - Static method in class wsi.ra.tool.StatisticUtils: Returns c*log2(c) for a given value c.
xo - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
xor(BitSet14) - Method in class joelib.util.BitSet14: Performs a logical XOR of this bit set with the bit set argument.
xor(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
xor(JOEBitVec, JOEBitVec) - Static method in class joelib.util.JOEBitVec: Description of the Method
xorSet(JOEBitVec) - Method in class joelib.util.JOEBitVec: Description of the Method
xrot(double) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Rotate theta degrees about the x axis
xscale - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
xx - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
xy - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
xyzVectorAngle(XYZVector, XYZVector) - Static method in class joelib.math.XYZVector: Description of the Method
xz - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field

Y

y() - Method in class joelib.math.XYZVector: Description of the Method
y() - Method in class joelib.molecule.JOEAtom: Gets the y coordinate of the JOEAtom .
y - Variable in class joelib.sort.XYDoubleArray: Description of the Field
y - Variable in class joelib.sort.XYIntArray: Description of the Field
yo - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
yrot(double) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Rotate theta degrees about the y axis
yscale - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
yx - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
yy - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
yz - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field

Z

ZIP - class joelib.io.types.ZIP.: Reader/Writer for compressed ZIP files.
ZIP() - Constructor for class joelib.io.types.ZIP: Constructor for the ZIP object
Z_ISOMERISM - Static variable in class joelib.util.IsomerismDetection
ZagrebIndex1 - class joelib.desc.types.ZagrebIndex1.: Calculates the Zagreb Group Index 1.
ZagrebIndex1() - Constructor for class joelib.desc.types.ZagrebIndex1: Constructor for the ZagrebIndex1 object
ZagrebIndex2 - class joelib.desc.types.ZagrebIndex2.: Calculates the Zagreb Group Index 2.
ZagrebIndex2() - Constructor for class joelib.desc.types.ZagrebIndex2: Constructor for the ZagrebIndex2 object
z() - Method in class joelib.math.XYZVector: Description of the Method
z() - Method in class joelib.molecule.JOEAtom: Gets the z coordinate of the JOEAtom .
z - Variable in class joelib.util.types.AtomZPos: Description of the Field
zo - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
zrot(double) - Method in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Rotate theta degrees about the z axis
zscale - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
zx - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
zy - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field
zz - Variable in class joelib.gui.molviewer.java3d.molecule.Matrix3D: Description of the Field

_

_a - Variable in class joelib.util.types.JOEInternalCoord
_ang - Variable in class joelib.util.types.JOEInternalCoord
_b - Variable in class joelib.util.types.JOEInternalCoord
_c - Variable in class joelib.util.types.JOEInternalCoord
_dst - Variable in class joelib.util.types.JOEInternalCoord
_path - Variable in class joelib.ring.JOERing: Vector of int[1]
_pathset - Variable in class joelib.ring.JOERing: Description of the Field
_tor - Variable in class joelib.util.types.JOEInternalCoord
_vx - Variable in class joelib.math.XYZVector: Description of the Field
_vy - Variable in class joelib.math.XYZVector: Description of the Field
_vz - Variable in class joelib.math.XYZVector: Description of the Field

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

Overview

Package

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Help

JOELib
Computational Chemistry Package
Comments and Questions? mail to J.K.Wegner

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