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

A

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

B

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

C

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

D

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

E

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

F

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

G

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

H

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

I

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

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

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

J

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

K

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

L

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

M

MATRIX - Static variable in class joelib.io.types.cml.CMLCoreModule
 
MATRIX_TYPE - Static variable in class joelib.io.types.cml.elements.MatrixCML
 
MAX - Static variable in class joelib.io.types.cml.elements.ScalarCML
 
MAXOPT_STEP_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
 
MAX_AXIS_ORDER_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
 
MAX_OPT_CYCLES_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
 
MAX_SPHERICAL_VOLUME - Static variable in class joelib.desc.types.RadialDistributionFunction
 
MAX_SPHERICAL_VOLUME_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
 
MAX_VALUES - Static variable in class joelib.io.types.cml.elements.ArrayCML
 
MDLSD - class joelib.io.types.MDLSD.
Reader/Writer for SDF files.
MDLSD() - Constructor for class joelib.io.types.MDLSD
Constructor for the MDLSD object
MIN - Static variable in class joelib.io.types.cml.elements.ScalarCML
 
MINOPT_STEP_DEFAULT - Static variable in class joelib.math.symmetry.Symmetry
 
MIN_SPHERICAL_VOLUME - Static variable in class joelib.desc.types.RadialDistributionFunction
 
MIN_SPHERICAL_VOLUME_PROPERTY - Static variable in class joelib.desc.types.RadialDistributionFunction
 
MIN_VALUES - Static variable in class joelib.io.types.cml.elements.ArrayCML
 
MOLECULE - Static variable in class joelib.io.types.cml.CMLCoreModule
 
MOL_AND_DESCRIPTORS - Static variable in class joelib.process.types.DescSelectionWriter
Description of the Field
MX_GASTEIGER_DAMP - Static variable in class joelib.molecule.charge.GasteigerState
Damping factor.
MX_GASTEIGER_DENOM - Static variable in class joelib.molecule.charge.GasteigerState
Default denominator for hydrogen atoms.
MX_GASTEIGER_ITERS - Static variable in class joelib.molecule.charge.GasteigerState
Number of iterations.
MathHelper - class joelib.math.MathHelper.
Mathematical helper methods.
MathHelper() - Constructor for class joelib.math.MathHelper
 
MathUtils - class joelib.gui.molviewer.java3d.math.util.MathUtils.
This class provides some math utility methods.
MathUtils() - Constructor for class joelib.gui.molviewer.java3d.math.util.MathUtils
 
Matlab - class joelib.io.types.Matlab.
Reader/Writer for Matlab files.
Matlab() - Constructor for class joelib.io.types.Matlab
 
Matrix3D - class joelib.gui.molviewer.java3d.molecule.Matrix3D.
A fairly conventional 3D matrix object that can transform sets of 3D points and perform a variety of manipulations on the transform.
Matrix3D() - Constructor for class joelib.gui.molviewer.java3d.molecule.Matrix3D
Create a new unit matrix
Matrix3x3 - class joelib.math.Matrix3x3.
3x3 Matrix.
Matrix3x3() - Constructor for class joelib.math.Matrix3x3
Constructor for the Matrix3x3 object
Matrix3x3(XYZVector, XYZVector, XYZVector) - Constructor for class joelib.math.Matrix3x3
Constructor for the Matrix3x3 object
Matrix3x3(double[][]) - Constructor for class joelib.math.Matrix3x3
 
MatrixCML - class joelib.io.types.cml.elements.MatrixCML.
Scalar CML element.
MatrixCML(Vector) - Constructor for class joelib.io.types.cml.elements.MatrixCML
Constructor for the StringString object
MatrixHelper - class joelib.util.MatrixHelper.
Helper methods for wrinting and loading matrices.
ModuleInterface - interface joelib.io.types.cml.ModuleInterface.
This interface describes the procedures classes must implement to be plugable into the CMLHandler.
Mol2Image - class joelib.gui.render.Mol2Image.
Image creation with options.
MolDescCounter - class joelib.desc.data.MolDescCounter.
Counts the number of descriptors and molecules in a molecule file.
MolDescCounter() - Constructor for class joelib.desc.data.MolDescCounter
Constructor for the IntResult object
MolDescCounter(int, int) - Constructor for class joelib.desc.data.MolDescCounter
Constructor for the MolDescCounter object
MolDescCounter(IOType, String) - Constructor for class joelib.desc.data.MolDescCounter
Constructor for the MolDescCounter object
MolDescCounter(int, int, IOType, String) - Constructor for class joelib.desc.data.MolDescCounter
Constructor for the MolDescCounter object
MolFileChooser - class joelib.gui.util.MolFileChooser.
 
MolFileFilter - class joelib.gui.util.MolFileFilter.
A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
MolFileFilter(IOType, MoleculeFileType, boolean, boolean) - Constructor for class joelib.gui.util.MolFileFilter
Creates a file filter.
MolFileFilter() - Constructor for class joelib.gui.util.MolFileFilter
Creates a file filter.
MolFileFilter(String) - Constructor for class joelib.gui.util.MolFileFilter
Creates a file filter that accepts files with the given extension.
MolFileFilter(String, String) - Constructor for class joelib.gui.util.MolFileFilter
Creates a file filter that accepts the given file type.
MolFileFilter(String[]) - Constructor for class joelib.gui.util.MolFileFilter
Creates a file filter from the given string array.
MolFileFilter(String[], String) - Constructor for class joelib.gui.util.MolFileFilter
Creates a file filter from the given string array and description.
MolGenerationHelper - class joelib.molecule.generation.MolGenerationHelper.
Helper class for molecule generation.
MolGenerationHelper() - Constructor for class joelib.molecule.generation.MolGenerationHelper
 
MolInstance - class joelib.algo.datamining.weka.MolInstance.
Molecule Weka instance.
MolInstance(MolInstance) - Constructor for class joelib.algo.datamining.weka.MolInstance
Constructor that copies the attribute values and the weight from the given instance.
MolInstance(JOEMol, double, double[]) - Constructor for class joelib.algo.datamining.weka.MolInstance
Constructor that inititalizes instance variable with given values.
MolInstance(int) - Constructor for class joelib.algo.datamining.weka.MolInstance
Constructor of an instance that sets weight to one, all values to be missing, and the reference to the dataset to null.
MolInstances - class joelib.algo.datamining.weka.MolInstances.
Molecule Weka instances.
MolInstances(MolInstances) - Constructor for class joelib.algo.datamining.weka.MolInstances
Constructor copying all instances and references to the header information from the given set of instances.
MolInstances(MolInstances, int) - Constructor for class joelib.algo.datamining.weka.MolInstances
Constructor creating an empty set of instances.
MolInstances(MolInstances, int, int) - Constructor for class joelib.algo.datamining.weka.MolInstances
Creates a new set of instances by copying a subset of another set.
MolInstances(String, FastVector, int) - Constructor for class joelib.algo.datamining.weka.MolInstances
Creates an empty set of instances.
MolInstances(Reader) - Constructor for class joelib.algo.datamining.weka.MolInstances
Reads a Descriptor ARFF file from a reader, and assigns a weight of one to each instance.
MolInstances(Reader, int) - Constructor for class joelib.algo.datamining.weka.MolInstances
Reads the header of a Descriptor ARFF file from a reader and reserves space for the given number of instances.
MolInstancesCache - class joelib.algo.datamining.weka.MolInstancesCache.
Molecule caching class for Weka data mining instances.
MolInstancesCache() - Constructor for class joelib.algo.datamining.weka.MolInstancesCache
 
MolInstancesCache(IOType, String, boolean) - Constructor for class joelib.algo.datamining.weka.MolInstancesCache
 
MolInstancesCache(IOType, String) - Constructor for class joelib.algo.datamining.weka.MolInstancesCache
 
MolSparseInstance - class joelib.algo.datamining.weka.MolSparseInstance.
Class for storing an instance as a sparse vector.
MolSparseInstance(MolInstance) - Constructor for class joelib.algo.datamining.weka.MolSparseInstance
Constructor that generates a sparse instance from the given instance.
MolSparseInstance(MolSparseInstance) - Constructor fo