Hierarchy For All Packages

Package Hierarchies:

Acme, Acme.JPM.Encoders, cformat, com.obrador, joelib, joelib.algo, joelib.algo.contribution, joelib.algo.datamining.weka, joelib.algo.morgan, joelib.algo.morgan.types, joelib.data, joelib.desc, joelib.desc.data, joelib.desc.result, joelib.desc.types, joelib.desc.types.atompair, joelib.desc.util, joelib.ext, joelib.gui.molviewer.java3d, joelib.gui.molviewer.java3d.graphics3D, joelib.gui.molviewer.java3d.math.geometry, joelib.gui.molviewer.java3d.math.util, joelib.gui.molviewer.java3d.molecule, joelib.gui.molviewer.java3d.util, joelib.gui.render, joelib.gui.test, joelib.gui.util, joelib.io, joelib.io.types, joelib.io.types.cml, joelib.io.types.cml.elements, joelib.jcamp, joelib.math, joelib.math.similarity, joelib.math.symmetry, joelib.molecule, joelib.molecule.charge, joelib.molecule.fragmentation, joelib.molecule.generation, joelib.molecule.types, joelib.process, joelib.process.filter, joelib.process.types, joelib.ring, joelib.smarts, joelib.smarts.atomexpr, joelib.smarts.bondexpr, joelib.smarts.test, joelib.smarts.types, joelib.smiles, joelib.sort, joelib.test, joelib.util, joelib.util.cdk, joelib.util.database, joelib.util.ghemical, joelib.util.iterator, joelib.util.types, jtt.docbook, jtt.util, wsi.ra.database, wsi.ra.image, wsi.ra.io, wsi.ra.text, wsi.ra.tool

Class Hierarchy

• class java.lang.Object
  • class java.util.AbstractCollection (implements java.util.Collection)
    • class java.util.AbstractList (implements java.util.List)
      • class java.util.Vector (implements java.lang.Cloneable, java.util.List, java.util.RandomAccess, java.io.Serializable)
        • class wsi.ra.tool.SortedVector
        • class joelib.gui.molviewer.java3d.molecule.ViewerAtoms
        • class joelib.gui.molviewer.java3d.molecule.ViewerBonds
  • class joelib.util.database.AbstractDatabase (implements joelib.util.database.DatabaseInterface)
    • class joelib.util.database.SimpleJOELibDatabase
  • class joelib.io.types.Amber (implements joelib.io.MoleculeFileType)
  • class joelib.process.filter.ANDFilter (implements joelib.process.filter.Filter)
  • class joelib.gui.molviewer.java3d.math.geometry.Angle
  • class joelib.algo.APropertyBFS (implements joelib.desc.Descriptor)
  • class joelib.desc.types.APropertyDistanceMatrix (implements joelib.desc.Descriptor)
  • class joelib.algo.datamining.weka.APWekaHelper
  • class wsi.ra.tool.ArrayBinning (implements java.io.Serializable)
  • class joelib.io.types.cml.elements.ArrayCML (implements joelib.io.types.cml.elements.ElementCML)
  • class joelib.util.ArrayHelper
  • class joelib.sort.ArraySizeComparator (implements java.util.Comparator)
  • class wsi.ra.tool.ArrayStatistic (implements java.io.Serializable)
  • class joelib.gui.render.Arrows
  • class joelib.util.types.AtomArrayInt (implements java.io.Serializable)
  • class joelib.algo.morgan.AtomDouble
  • class joelib.algo.morgan.AtomDoubleComparator (implements java.util.Comparator)
  • class joelib.algo.morgan.AtomDoubleParent
  • class joelib.smarts.atomexpr.AtomExpr (implements java.io.Serializable)
    • class joelib.smarts.atomexpr.BinAtomExpr (implements java.io.Serializable)
    • class joelib.smarts.atomexpr.LeafAtomExpr (implements java.io.Serializable)
    • class joelib.smarts.atomexpr.MonAtomExpr (implements java.io.Serializable)
    • class joelib.smarts.atomexpr.RecurAtomExpr (implements java.io.Serializable)
  • class joelib.util.types.AtomHCount (implements java.io.Serializable)
  • class joelib.util.types.AtomIntInt (implements java.io.Serializable)
  • class joelib.desc.types.atompair.AtomPair
  • class joelib.desc.types.atompair.AtomPairAtomType
  • class joelib.desc.types.atompair.AtomPairTypeComparator (implements java.util.Comparator)
  • class joelib.desc.types.atompair.AtomPairTypeHolder
  • class joelib.molecule.types.AtomPropertyColoring
  • class joelib.desc.util.AtomPropertyDescriptors
  • class joelib.process.types.AtomPropertyMatrix (implements joelib.process.JOEProcess)
  • class joelib.desc.AtomsCounter (implements joelib.desc.Descriptor)
    • class joelib.desc.types.NumberOfB
    • class joelib.desc.types.NumberOfBr
    • class joelib.desc.types.NumberOfC
    • class joelib.desc.types.NumberOfCl
    • class joelib.desc.types.NumberOfF
    • class joelib.desc.types.NumberOfHal
    • class joelib.desc.types.NumberOfI
    • class joelib.desc.types.NumberOfN
    • class joelib.desc.types.NumberOfO
    • class joelib.desc.types.NumberOfP
    • class joelib.desc.types.NumberOfS
  • class joelib.smarts.AtomSpec (implements java.io.Serializable)
  • class joelib.desc.types.atompair.AtomTypePair
  • class joelib.util.types.AtomZPos (implements java.io.Serializable)
  • class joelib.molecule.AtomZPosComparator (implements java.util.Comparator)
  • class joelib.desc.types.Autocorrelation (implements joelib.desc.Descriptor)
  • class joelib.desc.types.atompair.BasicAPDistanceMetric (implements joelib.math.similarity.DistanceMetric)
  • class joelib.util.types.BasicFactoryInfo (implements java.io.Serializable)
    • class joelib.desc.DescriptorInfo
    • class joelib.process.filter.FilterInfo
    • class joelib.process.ProcessInfo
      • class joelib.ext.ExternalInfo
  • class joelib.algo.morgan.types.BasicTieResolver (implements joelib.algo.morgan.TieResolver)
  • class wsi.ra.io.BatchScriptReplacer
  • class joelib.desc.types.BCUT (implements joelib.desc.Descriptor)
  • class joelib.algo.BFS (implements joelib.desc.Descriptor)
  • class joelib.util.BitSet14 (implements java.lang.Cloneable, java.io.Serializable)
    • class joelib.util.JOEBitVec (implements java.io.Serializable)
  • class joelib.molecule.BondComparator (implements java.util.Comparator)
  • class joelib.smarts.bondexpr.BondExpr (implements java.io.Serializable)
    • class joelib.smarts.bondexpr.BinBondExpr (implements java.io.Serializable)
    • class joelib.smarts.bondexpr.LeafBondExpr (implements java.io.Serializable)
    • class joelib.smarts.bondexpr.MonBondExpr (implements java.io.Serializable)
  • class joelib.util.types.BondInt (implements java.io.Serializable)
  • class joelib.smarts.BondSpec (implements java.io.Serializable)
  • class joelib.desc.types.BurdenEigenvalues (implements joelib.desc.Descriptor)
  • class joelib.desc.types.BurdenModifiedEigenvalues (implements joelib.desc.Descriptor)
  • class joelib.util.cdk.CDKTools
  • class joelib.io.types.cml.CDOAcceptedObjects
  • class joelib.gui.molviewer.java3d.util.CentralLookup
  • class joelib.io.types.ChemicalMarkupLanguage (implements joelib.io.types.cml.CMLWriterProperties, joelib.io.MoleculeFileType, joelib.io.PropertyWriter)
  • class joelib.io.types.ClearTextFormat (implements joelib.io.MoleculeFileType)
  • class joelib.smiles.ClosureBond (implements java.io.Serializable)
  • class joelib.io.types.cml.CMLCoreModule (implements joelib.io.types.cml.ModuleInterface)
    • class joelib.io.types.cml.CDKConvention
    • class joelib.io.types.cml.CMLReactionModule
  • class joelib.io.types.cml.CMLErrorHandler (implements org.xml.sax.ErrorHandler)
  • class joelib.io.types.cml.CMLIDCreator
  • class joelib.io.types.cml.CMLMoleculeWriterBase (implements joelib.io.types.cml.CMLMoleculeWriter)
    • class joelib.io.types.cml.MoleculeArray
    • class joelib.io.types.cml.MoleculeAttributeArray
    • class joelib.io.types.cml.MoleculeHuge
    • class joelib.io.types.cml.MoleculeLarge
  • class joelib.io.types.cml.CMLPropertyWriter
  • class joelib.io.types.cml.CMLResolver (implements org.xml.sax.EntityResolver)
  • class joelib.io.types.cml.CMLSequentialSAXReader
  • class joelib.io.types.cml.CMLStack
  • class joelib.io.types.cml.CMLSymmetryWriter
  • class joelib.test.Combine
  • class joelib.test.Comparison
  • class joelib.util.ComparisonHelper
  • class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • class wsi.ra.image.BMPFile
    • class java.awt.Container
      • class javax.swing.JComponent (implements java.io.Serializable)
        • class javax.swing.JPanel (implements javax.accessibility.Accessible)
          • class joelib.gui.test.ConvertPanel
          • class joelib.gui.util.JLog4JPanel
          • class joelib.gui.molviewer.java3d.graphics3D.JPanel3D
          • class joelib.gui.render.MoleculeViewer2D (implements joelib.gui.render.Renderer2DChangeListener)
          • class joelib.gui.test.SelectionPanel
          • class joelib.gui.test.StatisticPanel
        • class javax.swing.JTabbedPane (implements javax.accessibility.Accessible, java.io.Serializable, javax.swing.SwingConstants)
          • class joelib.gui.test.InfoPanel
        • class javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • class javax.swing.JEditorPane
            • class joelib.gui.util.JEditorPaneAndPagePrinter (implements java.awt.print.Printable)
      • class java.awt.Window (implements javax.accessibility.Accessible)
        • class java.awt.Dialog
          • class javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class joelib.gui.molviewer.java3d.ViewerUsage (implements java.awt.event.ActionListener)
        • class java.awt.Frame (implements java.awt.MenuContainer)
          • class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class joelib.gui.test.JOELibTestGUI
            • class joelib.gui.molviewer.java3d.ViewerFrame
          • class com.obrador.JpegEncoder
  • class joelib.desc.types.ConjElectroTopolState (implements joelib.desc.Descriptor)
  • class joelib.gui.render.ConjugatedRing
  • class joelib.gui.render.ConjugatedRings
  • class joelib.molecule.fragmentation.ContiguousFragments
  • class joelib.test.Convert (implements joelib.io.MoleculeCallback)
  • class joelib.test.ConvertSkip
  • class joelib.process.types.CreateFileName (implements joelib.process.JOEProcess)
  • class joelib.math.CrystalGeometryTools
  • class joelib.gui.molviewer.java3d.graphics3D.Cylinder
  • class wsi.ra.database.DatabaseConnection
  • class wsi.ra.text.DecimalFormatHelper (implements wsi.ra.text.DecimalFormatter)
  • class org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • class joelib.io.types.cml.CMLHandler
  • class wsi.ra.tool.Deque
  • class wsi.ra.tool.DequeIterator (implements java.util.Iterator)
  • class wsi.ra.tool.DequeNode
  • class joelib.desc.DescDescription
  • class joelib.desc.Description
  • class joelib.test.DescriptorCalculation
  • class joelib.desc.DescriptorFactory
  • class joelib.process.filter.DescriptorFilter (implements joelib.process.filter.Filter)
  • class joelib.desc.DescriptorHelper
  • class joelib.test.DescriptorSelection
  • class joelib.test.DescriptorStatistic
  • class joelib.algo.DFS (implements joelib.desc.Descriptor)
  • class java.util.Dictionary
    • class Acme.IntHashtable (implements java.lang.Cloneable)
  • class joelib.desc.types.DistanceDistanceMatrix (implements joelib.desc.Descriptor)
  • class joelib.desc.types.DistanceMatrix (implements joelib.desc.Descriptor)
  • class joelib.math.similarity.DistanceMetricHelper
  • class jtt.docbook.DocBookArticles
  • class jtt.docbook.DocBookEquations
  • class jtt.docbook.DocBookMolecules
  • class joelib.util.types.DoubleInt (implements java.io.Serializable)
  • class joelib.util.types.DoubleType (implements java.io.Serializable)
  • class joelib.desc.types.ElectrogeometricalState (implements joelib.desc.Descriptor)
  • class joelib.desc.types.ElectrotopologicalState (implements joelib.desc.Descriptor)
  • class joelib.molecule.Element
  • class joelib.test.EuklidianComparison
  • class java.util.EventObject (implements java.io.Serializable)
    • class joelib.gui.molviewer.java3d.util.MolViewerEvent
  • class jtt.util.Executable
  • class joelib.ext.ExternalFactory
  • class joelib.ext.ExternalHelper
  • class javax.swing.filechooser.FileFilter
    • class joelib.gui.util.MolFileFilter
  • class wsi.ra.io.FileUtilities
  • class joelib.process.filter.FilterFactory
  • class joelib.io.types.Flat (implements joelib.io.MoleculeFileType)
  • class joelib.gui.render.FromToAtoms
    • class joelib.gui.render.Arrow
    • class joelib.gui.render.OrthoLine
  • class joelib.molecule.charge.GasteigerState (implements java.io.Serializable)
  • class joelib.io.types.Gaussian (implements joelib.io.MoleculeFileType)
  • class joelib.algo.contribution.GCPredictor
  • class joelib.molecule.GenericDataHolder (implements java.io.Serializable)
  • class joelib.util.iterator.GenericDataIterator (implements java.util.Iterator)
  • class joelib.desc.types.GeomDistanceMatrix (implements joelib.desc.Descriptor)
  • class joelib.gui.molviewer.java3d.math.geometry.Geometry
  • class joelib.gui.molviewer.java3d.math.geometry.GeoVector3D
  • class joelib.util.ghemical.GhemicalInterface
  • class joelib.test.GhemicalTest
  • class joelib.desc.types.GlobalTopologicalChargeIndex (implements joelib.desc.Descriptor)
  • class Acme.JPM.Encoders.GrayJPEG
  • class joelib.algo.contribution.GroupContributions
  • class joelib.test.GroupContributionTest
  • class org.xml.sax.HandlerBase (implements org.xml.sax.DocumentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • class joelib.io.types.cml.XMLHandler
  • class joelib.process.filter.HasAllDataFilter (implements joelib.process.filter.Filter)
  • class joelib.process.filter.HasDataFilter (implements joelib.process.filter.Filter)
  • class joelib.desc.types.HeavyBonds (implements joelib.desc.Descriptor)
  • class joelib.desc.types.HeteroCycles (implements joelib.desc.Descriptor)
  • class joelib.io.types.HIN (implements joelib.io.MoleculeFileType)
  • class joelib.gui.molviewer.java3d.graphics3D.IcoSphere
  • class Acme.JPM.Encoders.ImageEncoder (implements java.awt.image.ImageConsumer)
    • class Acme.JPM.Encoders.GifEncoder
    • class Acme.JPM.Encoders.PpmEncoder
  • class joelib.gui.molviewer.java3d.graphics3D.IndexedCylinder
  • class Instance
    • class joelib.algo.datamining.weka.MolInstance
      • class joelib.algo.datamining.weka.MolSparseInstance
  • class Instances
    • class joelib.algo.datamining.weka.MolInstancesCache (implements joelib.desc.data.MoleculeCache)
  • class Instances
    • class joelib.algo.datamining.weka.MolInstances
  • class joelib.algo.datamining.weka.InstancesHelper
  • class joelib.util.types.Int (implements java.io.Serializable)
  • class joelib.util.types.IntInt (implements java.io.Serializable)
  • class joelib.util.types.IntIntInt (implements java.io.Serializable)
  • class joelib.io.IOHelper
  • class joelib.io.IOType (implements java.io.Serializable)
  • class joelib.io.IOTypeHolder
  • class joelib.util.IsomerismDetection
  • class jtt.docbook.Jade
  • class joelib.gui.molviewer.java3d.util.Java3DHelper
  • class joelib.io.types.JCAMP (implements joelib.io.MoleculeFileType)
  • class joelib.jcamp.JCAMPData
  • class joelib.jcamp.JCAMPDataBlock
  • class joelib.jcamp.JCAMPParser
  • class joelib.util.JHM
  • class joelib.JOE
  • class joelib.molecule.JOEAtom (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.molecule.JOEBond (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.data.JOEChemTransformation
  • class joelib.math.JOECoordTrans (implements java.io.Serializable)
  • class joelib.data.JOEDataType (implements java.io.Serializable)
  • class joelib.molecule.JOEElement (implements java.io.Serializable)
  • class joelib.data.JOEExternalBond
  • class joelib.io.JOEFileFormat
  • class joelib.molecule.charge.JOEGastChrg (implements java.io.Serializable)
  • class joelib.data.JOEGenericData (implements java.io.Serializable)
    • class joelib.data.JOECommentData
    • class joelib.data.JOEExternalBondData
    • class joelib.data.JOEPairData (implements java.io.Serializable)
      • class joelib.desc.result.APropDoubleArrResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NumberFormatDescResult, java.io.Serializable)
      • class joelib.desc.result.APropDoubleResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NativeValue, joelib.desc.NumberFormatDescResult, java.io.Serializable)
      • class joelib.desc.result.APropIntResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NativeValue, java.io.Serializable)
      • class joelib.desc.types.atompair.AtomPairResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.DistanceMetricValue)
      • class joelib.algo.BFSResult (implements java.lang.Cloneable, joelib.desc.DescResult, java.io.Serializable)
      • class joelib.desc.result.BitArrayResult (implements joelib.desc.BinaryValue, java.lang.Cloneable, joelib.desc.DescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.desc.result.BitResult (implements joelib.desc.BinaryValue, java.lang.Cloneable, joelib.desc.DescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.desc.result.BooleanResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NativeValue, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.algo.DFSResult (implements joelib.desc.DescResult, java.io.Serializable)
      • class joelib.desc.result.DoubleArrayResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NumberFormatDescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
        • class joelib.desc.result.AtomDoubleResult (implements joelib.molecule.types.AtomProperties, java.io.Serializable)
        • class joelib.desc.result.BondDoubleResult (implements joelib.molecule.types.BondProperties, java.io.Serializable)
      • class joelib.desc.result.DoubleMatrixResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NumberFormatDescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.desc.result.DoubleResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NativeValue, joelib.desc.NumberFormatDescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.desc.result.DynamicArrayResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NumberFormatDescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
        • class joelib.desc.result.AtomDynamicResult (implements joelib.molecule.types.AtomProperties, java.io.Serializable)
        • class joelib.desc.result.BondDynamicResult (implements joelib.molecule.types.BondProperties, java.io.Serializable)
      • class joelib.desc.result.FloatMatrixResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NumberFormatDescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.desc.result.IntArrayResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
        • class joelib.desc.result.AtomIntResult (implements joelib.molecule.types.AtomProperties, java.io.Serializable)
        • class joelib.desc.result.BondIntResult (implements joelib.molecule.types.BondProperties, java.io.Serializable)
      • class joelib.desc.result.IntBitArrayResult (implements joelib.desc.BinaryValue, joelib.desc.DescResult, java.io.Serializable)
      • class joelib.desc.result.IntMatrixResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.desc.result.IntResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.desc.NativeValue, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
      • class joelib.desc.result.StringArrayResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
        • class joelib.desc.result.AtomStringResult (implements joelib.molecule.types.AtomProperties, java.io.Serializable)
      • class joelib.desc.result.StringResult (implements java.lang.Cloneable, joelib.desc.DescResult, joelib.io.types.cml.ResultCMLProperties, java.io.Serializable)
    • class joelib.data.JOERgroupData
    • class joelib.ring.JOERingData (implements java.io.Serializable)
    • class joelib.data.JOEVirtualBond
  • class joelib.util.JOEHelper
  • class joelib.util.types.JOEInternalCoord (implements java.io.Serializable)
  • class joelib.data.JOEKernel
  • class joelib.molecule.JOEMol (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.smiles.JOEMol2Smi (implements java.io.Serializable)
  • class joelib.molecule.JOEMolVector (implements java.io.Serializable)
  • class joelib.util.JOEProperty
  • class joelib.util.JOEPropertyHelper
  • class joelib.util.JOERandom
  • class joelib.molecule.JOEResidue (implements java.io.Serializable)
  • class joelib.ring.JOERing (implements java.io.Serializable)
  • class joelib.ring.JOERingSearch (implements java.io.Serializable)
  • class joelib.molecule.JOERTree (implements java.io.Serializable)
  • class joelib.smarts.JOESmartsPattern (implements java.io.Serializable)
  • class joelib.smiles.JOESmilesParser (implements java.io.Serializable)
  • class joelib.smiles.JOESmiNode (implements java.io.Serializable)
  • class joelib.math.JOESqrtTbl (implements java.io.Serializable)
  • class joelib.smarts.JOESSMatch (implements java.io.Serializable)
  • class com.obrador.Jpeg
  • class joelib.jcamp.LabelData
  • class joelib.gui.molviewer.java3d.math.geometry.Line
  • class joelib.util.LineArrayHelper
  • class joelib.util.LineMatrixHelper
  • class joelib.math.MathHelper
  • class joelib.gui.molviewer.java3d.math.util.MathUtils
  • class joelib.io.types.Matlab (implements joelib.io.MoleculeFileType)
  • class joelib.gui.molviewer.java3d.molecule.Matrix3D (implements java.lang.Cloneable)
  • class joelib.math.Matrix3x3 (implements java.io.Serializable)
  • class joelib.io.types.cml.elements.MatrixCML (implements joelib.io.types.cml.elements.ElementCML)
  • class joelib.util.MatrixHelper
  • class joelib.io.types.MDLSD (implements joelib.io.MoleculeFileType, joelib.io.PropertyWriter)
  • class joelib.gui.render.Mol2Image
  • class joelib.io.types.MolconnZ (implements joelib.io.MoleculeFileType)
  • class joelib.desc.data.MolDescCounter (implements java.io.Serializable)
  • class joelib.gui.molviewer.java3d.graphics3D.MolecularScene
  • class joelib.util.MoleculeDataCacheHolder
  • class joelib.io.types.cml.MoleculeFileCDO (implements joelib.io.types.cml.CDOInterface)
  • class joelib.process.types.MoleculeFileCreation (implements joelib.process.JOEProcess)
  • class joelib.process.types.MoleculeFileDeletion (implements joelib.process.JOEProcess, java.io.Serializable)
  • class joelib.desc.data.MoleculesDescriptorMatrix (implements joelib.desc.data.MoleculeCache, java.io.Serializable)
  • class joelib.gui.util.MolFileChooser
  • class joelib.molecule.generation.MolGenerationHelper
  • class joelib.gui.molviewer.java3d.util.MolViewerEventAdapter (implements joelib.gui.molviewer.java3d.util.MolViewerEventListener)
    • class joelib.gui.molviewer.java3d.util.CentralDisplayAdapter
  • class joelib.io.types.Mopac (implements joelib.io.MoleculeFileType)
  • class joelib.algo.morgan.Morgan
  • class joelib.algo.morgan.MorganTest
  • class joelib.process.filter.NativeValueFilter (implements joelib.process.filter.Filter)
  • class joelib.util.iterator.NativeValueIterator (implements java.util.Iterator)
  • class joelib.process.filter.NOTFilter (implements joelib.process.filter.Filter)
  • class joelib.process.filter.ORFilter (implements joelib.process.filter.Filter)
  • class joelib.gui.render.OrthoLines
  • class java.io.OutputStream
    • class java.io.FilterOutputStream
      • class java.io.PrintStream
        • class cformat.PrintfStream
  • class joelib.smarts.ParseSmart (implements java.io.Serializable)
  • class joelib.smarts.ParseState (implements java.io.Serializable)
  • class joelib.smarts.Pattern (implements java.io.Serializable)
  • class joelib.smarts.Patty (implements java.io.Serializable)
  • class joelib.io.types.PDB (implements joelib.io.MoleculeFileType)
  • class joelib.io.types.PDF (implements joelib.io.MoleculeFileType, joelib.io.PropertyWriter)
  • class joelib.gui.molviewer.java3d.math.geometry.Point3D
  • class joelib.math.symmetry.PointGroup
  • class joelib.math.symmetry.PointGroups
  • class joelib.io.types.POVRay (implements joelib.io.MoleculeFileType)
  • class cformat.PrintfFormat
  • class cformat.PrintfFormatTest
  • class joelib.process.ProcessFactory
  • class joelib.process.ProcessPipe (implements joelib.process.JOEProcess)
  • class joelib.process.ProcessPipeEntry
  • class wsi.ra.tool.PropertyHolder
  • class joelib.desc.types.RadialDistributionFunction (implements joelib.desc.Descriptor)
  • class java.io.Reader
    • class cformat.ScanfReader
  • class wsi.ra.io.RegExpFilenameFilter (implements java.io.FilenameFilter)
  • class joelib.gui.render.RenderAtom
  • class joelib.gui.render.Renderer2D
  • class joelib.gui.render.Renderer2DModel (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.gui.render.RenderHelper
  • class joelib.gui.render.RenderingAtoms (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.gui.molviewer.java3d.graphics3D.RenderTable
  • class wsi.ra.tool.ResourceLoader
  • class joelib.ring.RingSizeComparator (implements java.util.Comparator)
  • class joelib.sort.RotorComparator (implements java.util.Comparator)
  • class joelib.smarts.RSCacheEntry (implements java.io.Serializable)
  • class joelib.process.filter.RuleOf5Filter (implements joelib.process.filter.Filter)
  • class joelib.io.types.cml.elements.ScalarCML (implements joelib.io.types.cml.elements.ElementCML)
  • class cformat.ScanfFormat
  • class cformat.ScanfFormatTest
  • class cformat.ScanfReaderTest
  • class javax.media.j3d.SceneGraphObject
    • class javax.media.j3d.Node
      • class javax.media.j3d.Group
        • class javax.media.j3d.BranchGroup
          • class joelib.gui.molviewer.java3d.graphics3D.AtomNode
          • class joelib.gui.molviewer.java3d.graphics3D.BondNode
          • class joelib.gui.molviewer.java3d.graphics3D.MoleculeNode (implements joelib.gui.molviewer.java3d.graphics3D.RenderStyle)
        • class javax.media.j3d.SharedGroup
          • class joelib.gui.molviewer.java3d.graphics3D.SharedAtomGroup (implements joelib.gui.molviewer.java3d.graphics3D.RenderStyle)
          • class joelib.gui.molviewer.java3d.graphics3D.SharedBondGroup (implements joelib.gui.molviewer.java3d.graphics3D.RenderStyle)
      • class javax.media.j3d.Leaf
        • class javax.media.j3d.Behavior
          • class joelib.gui.molviewer.java3d.graphics3D.DragBehavior
          • class com.sun.j3d.utils.behaviors.mouse.MouseBehavior (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
            • class com.sun.j3d.utils.behaviors.mouse.MouseRotate
              • class joelib.gui.molviewer.java3d.graphics3D.MouseFastRotate
          • class com.sun.j3d.utils.picking.behaviors.PickMouseBehavior
            • class joelib.gui.molviewer.java3d.graphics3D.PickHighlightBehavior
  • class joelib.process.filter.SelectionFilter (implements joelib.process.filter.Filter)
  • class joelib.desc.SimpleBooleanDesc (implements joelib.desc.Descriptor)
  • class joelib.desc.SimpleDoubleAtomProperty (implements joelib.desc.Descriptor)
    • class joelib.molecule.charge.GasteigerMarsili
    • class joelib.desc.types.GraphPotentials
  • class joelib.desc.SimpleDoubleDesc (implements joelib.desc.Descriptor)
    • class joelib.desc.types.FractionRotatableBonds
    • class joelib.desc.types.GeometricalDiameter
    • class joelib.desc.types.GeometricalRadius
    • class joelib.desc.types.GeometricalShapeCoefficient
    • class joelib.desc.types.GraphShapeCoefficient
    • class joelib.desc.types.KierShape1
    • class joelib.desc.types.KierShape2
    • class joelib.desc.types.KierShape3
    • class joelib.desc.types.LogP
    • class joelib.desc.types.MolarRefractivity
    • class joelib.desc.types.MolecularWeight
    • class joelib.desc.types.PolarSurfaceArea
    • class joelib.desc.types.ZagrebIndex1
    • class joelib.desc.types.ZagrebIndex2
  • class joelib.desc.SimpleDynamicAtomProperty (implements joelib.desc.Descriptor)
    • class joelib.desc.types.AtomInAcceptor
    • class joelib.desc.types.AtomInAromaticSystem
    • class joelib.desc.types.AtomInConjEnvironment
    • class joelib.desc.types.AtomInDonAcc
    • class joelib.desc.types.AtomInDonor
    • class joelib.desc.types.AtomInRing
    • class joelib.desc.types.AtomInTerminalCarbon
    • class joelib.desc.types.AtomIsNegative
    • class joelib.desc.types.AtomIsPositive
    • class joelib.desc.types.AtomMass
    • class joelib.desc.types.AtomValence
    • class joelib.desc.types.AtomVanDerWaalsVolume
    • class joelib.desc.types.ConjugatedTopologicalDistance
    • class joelib.desc.types.ElectronAffinity
    • class joelib.desc.types.ElectronegativityPauling
    • class joelib.desc.types.IntrinsicState
  • class joelib.ext.SimpleExternalProcess (implements joelib.ext.External)
    • class joelib.ext.Title2Data
  • class joelib.io.SimpleImageWriter (implements joelib.io.MoleculeFileType)
    • class joelib.io.types.BMP
    • class joelib.io.types.GIF
    • class joelib.io.types.JPEG
    • class joelib.io.types.PNG
    • class joelib.io.types.PPM
  • class joelib.desc.SimpleIntDesc (implements joelib.desc.Descriptor)
    • class joelib.desc.types.AromaticBonds
    • class joelib.desc.types.NumberOfAtoms
    • class joelib.desc.types.NumberOfBonds
    • class joelib.desc.types.RotatableBonds
    • class joelib.desc.types.TopologicalDiameter
    • class joelib.desc.types.TopologicalRadius
  • class joelib.process.SimpleProcess (implements joelib.process.JOEProcess, java.io.Serializable)
    • class joelib.process.types.DescBinning (implements java.io.Serializable)
    • class joelib.process.types.DescSelectionWriter
    • class joelib.process.types.DescStatistic (implements java.lang.Cloneable, java.io.Serializable)
    • class joelib.process.types.DescVarianceNorm
    • class joelib.process.types.DistanceCalculation
  • class joelib.io.SimpleReader
  • class joelib.io.SimpleReaderWriterPipe
  • class joelib.desc.SimpleStringAtomProperty (implements joelib.desc.Descriptor)
    • class joelib.desc.types.AtomType
  • class joelib.io.SimpleWriter
  • class joelib.algo.morgan.types.SingleTieResolverBO (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverDistance (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverElectrons (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverElement (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverENGrad (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverGraphPot (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverImpVal (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverImpValGrad (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.algo.morgan.types.SingleTieResolverPartCh (implements joelib.algo.morgan.SingleTieResolver)
  • class joelib.desc.SMARTSCounter (implements joelib.desc.Descriptor)
    • class joelib.desc.types.AcidicGroups
    • class joelib.desc.types.AliphaticOHGroups
    • class joelib.desc.types.AromaticOHGroups
    • class joelib.desc.types.BasicGroups
    • class joelib.desc.types.HBA1
    • class joelib.desc.types.HBA2
    • class joelib.desc.types.HBD1
    • class joelib.desc.types.HBD2
    • class joelib.desc.types.HydrophobicGroups
    • class joelib.desc.types.NO2Groups
    • class joelib.desc.types.OSOGroups
    • class joelib.desc.types.SO2Groups
    • class joelib.desc.types.SOGroups
  • class joelib.desc.util.SMARTSDescriptors
  • class joelib.smarts.test.SMARTSEvaluation
  • class joelib.process.filter.SMARTSFilter (implements joelib.process.filter.Filter)
  • class joelib.molecule.fragmentation.SMARTSFragmentation
  • class joelib.smarts.types.SMARTSPatternFVec (implements java.io.Serializable)
  • class joelib.smarts.types.SMARTSPatternInt (implements java.io.Serializable)
  • class joelib.smarts.types.SMARTSPatternIntInt (implements java.io.Serializable)
  • class joelib.smarts.types.SMARTSPatternString (implements java.io.Serializable)
  • class joelib.io.types.Smiles (implements joelib.io.MoleculeFileType)
  • class joelib.data.SoftCodedKernelBase (implements joelib.data.SoftCodedKernel)
    • class joelib.data.JOEGlobalDataBase
      • class joelib.data.JOEAromaticTyper (implements joelib.data.HardCodedKernel)
      • class joelib.data.JOEAtomTyper (implements joelib.data.HardCodedKernel)
      • class joelib.data.JOEElementTable (implements joelib.data.HardCodedKernel)
      • class joelib.data.JOEIsotopeTable (implements joelib.data.HardCodedKernel)
      • class joelib.data.JOEPhModel (implements joelib.data.HardCodedKernel)
      • class joelib.data.JOEResidueData (implements joelib.data.HardCodedKernel)
      • class joelib.data.JOETypeTable (implements joelib.data.HardCodedKernel)
      • class joelib.desc.ResultFactory
    • class joelib.data.JOEGroupContribution (implements joelib.data.HardCodedKernel)
  • class joelib.sort.Sorter
    • class joelib.sort.InsertSort
    • class joelib.sort.QuickInsertSort
  • class joelib.gui.molviewer.java3d.graphics3D.Sphere
  • class joelib.desc.types.SSKey3DS (implements joelib.desc.Descriptor)
  • class joelib.util.types.StackType (implements java.io.Serializable)
  • class wsi.ra.tool.Statistics
  • class wsi.ra.tool.StatisticUtils
  • class wsi.ra.tool.StopWatch
  • class joelib.util.types.StringInt (implements java.io.Serializable)
  • class joelib.util.types.StringObject (implements java.io.Serializable)
  • class joelib.util.types.StringPattern (implements java.io.Serializable)
  • class joelib.util.types.StringString (implements java.io.Serializable)
  • class joelib.io.types.SybylMol2 (implements joelib.io.MoleculeFileType)
  • class joelib.math.symmetry.SymAxesComparator (implements java.util.Comparator)
  • class joelib.math.symmetry.SymCoordinates
    • class joelib.math.symmetry.SymAtom
  • class joelib.math.symmetry.Symmetry
  • class joelib.math.symmetry.SymmetryElement
  • class joelib.math.symmetry.SymStatistic
  • class joelib.util.types.Template (implements java.io.Serializable)
  • class joelib.test.TestDescriptor
  • class joelib.util.ghemical.TestInterface
  • class joelib.test.TestMolecule
  • class joelib.test.TestPatty
  • class joelib.test.TestSmarts
  • class joelib.test.TestSMILES
    • class joelib.util.cdk.TestLayout
  • class joelib.test.TestSSSR
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class joelib.desc.DescriptorException
      • class joelib.ext.ExternalException
      • class joelib.process.filter.FilterException
      • class joelib.util.ghemical.GhemicalException
      • class java.io.IOException
        • class cformat.ScanfMatchException
      • class joelib.util.iterator.IteratorException
      • class joelib.jcamp.JCAMPException
      • class joelib.process.JOEProcessException
      • class joelib.util.JOEPropertyException
      • class joelib.io.MoleculeIOException
      • class joelib.math.symmetry.SymmetryException
  • class joelib.io.types.Tinker (implements joelib.io.MoleculeFileType)
  • class joelib.test.Title2DataTest
  • class joelib.desc.types.atompair.TopologicalAtomPair (implements joelib.desc.Descriptor)
  • class joelib.math.symmetry.TransformationAtom
  • class joelib.io.types.Undefined (implements joelib.io.MoleculeFileType)
  • class joelib.util.iterator.VectorIterator (implements java.lang.Cloneable, java.util.Iterator)
    • class joelib.util.iterator.AtomIterator (implements java.lang.Cloneable)
    • class joelib.util.iterator.BondIterator
    • class joelib.util.iterator.ConformerIterator
    • class joelib.util.iterator.NbrAtomIterator
    • class joelib.util.iterator.ResidueIterator
    • class joelib.util.iterator.RingIterator
    • class joelib.util.iterator.RotamerIterator
    • class joelib.util.iterator.RotorIterator
  • class joelib.sort.VectorSizeComparator (implements java.util.Comparator)
  • class joelib.gui.molviewer.java3d.Viewer
  • class joelib.gui.molviewer.java3d.molecule.ViewerAtom
  • class joelib.gui.molviewer.java3d.molecule.ViewerBond
  • class joelib.gui.molviewer.java3d.molecule.ViewerMolecule
  • class joelib.desc.types.WeightedBurdenEigenvalues (implements joelib.desc.Descriptor)
  • class joelib.desc.types.WeightedBurdenModifiedEigenvalues (implements joelib.desc.Descriptor)
  • class java.io.Writer
    • class java.io.PrintWriter
      • class cformat.PrintfWriter
  • class joelib.io.types.cml.XMLSpecialCharacter
  • class joelib.sort.XYDoubleArray (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.sort.XYIntArray (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.io.types.XYZ (implements joelib.io.MoleculeFileType)
  • class joelib.math.XYZVector (implements java.lang.Cloneable, java.io.Serializable)
  • class joelib.io.types.ZIP (implements joelib.io.MoleculeFileType)

Interface Hierarchy

• interface joelib.molecule.types.AtomProperties
  • interface joelib.molecule.types.AtomAtomProperties
• interface joelib.desc.BinaryValue
• interface joelib.molecule.types.BondProperties
• interface joelib.io.types.cml.CDOInterface
• interface joelib.io.types.cml.CMLMoleculeWriter
• interface joelib.io.types.cml.CMLWriterProperties
• interface joelib.util.database.DatabaseInterface
• interface wsi.ra.text.DecimalFormatter
• interface joelib.desc.DescResult
• interface joelib.math.similarity.DistanceMetric
• interface joelib.desc.DistanceMetricValue
• interface joelib.io.types.cml.elements.ElementCML
• interface java.util.EventListener
  • interface joelib.gui.molviewer.java3d.util.MolViewerEventListener
  • interface joelib.gui.render.Renderer2DChangeListener
• interface joelib.process.filter.Filter
• interface joelib.molecule.fragmentation.Fragmentation
• interface joelib.data.HardCodedKernel
• interface joelib.io.types.cml.ModuleInterface
  • interface joelib.io.types.cml.ConventionInterface
• interface joelib.desc.data.MoleculeCache
• interface joelib.io.MoleculeCallback
• interface joelib.io.MoleculeFileType
• interface joelib.desc.NativeValue
• interface joelib.desc.NumberFormatDescResult
• interface joelib.util.PropertyAcceptor
  • interface joelib.desc.Descriptor
  • interface joelib.ext.External
  • interface joelib.process.JOEProcess
    • interface joelib.ext.External
• interface joelib.io.PropertyWriter
• interface joelib.gui.molviewer.java3d.graphics3D.RenderStyle
• interface joelib.io.types.cml.ResultCMLProperties
• interface joelib.algo.morgan.SingleTieResolver
• interface joelib.data.SoftCodedKernel
• interface joelib.algo.morgan.TieResolver
• interface joelib.util.ToolTipInfo