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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