- AbinitReader
- AboutDialog
- ActionManager
- ActionManagerMT
- AdfReader
- AFLOWReader
- AimsReader
- AlchemyReader
- AlphaMonomer
- AlphaPolymer
- AlphaPolymer.Code
- AminoMonomer
- AminoPolymer
- AmpacReader
- AnimationManager
- AnimationThread
- Annotation
- AnnotationParser
- ApbsReader
- AppConsole
- AppletConsole
- AppletConsole
- AppletWrapper
- ArrayListTransferHandler
- ASimpleJvxlWriter
- Atom
- Atom
- AtomCollection
- AtomData
- AtomDataReader
- AtomDataServer
- AtomIndexIterator
- AtomIterator
- AtomIteratorWithinModel
- AtomIteratorWithinModelSet
- AtomPropertyMapper
- AtomSetChooser
- AtomSetChooser.AtomSet
- AtomSetCollection
- AtomSetCollectionReader
- AtomSetObject
- AtomShape
- AtomType
- AviCreator
- AwtClipboard
- AwtColor
- AwtFile
- AwtFont
- AwtG2D
- AwtSwingComponent
- AwtSwingPopupHelper
- Axes
- AxesRenderer
- Backbone
- BackboneRenderer
- Balls
- BallsRenderer
- BannerFrame
- BasePair
- BasisFunctionReader
- Bbcage
- BbcageRenderer
- BilbaoReader
- BinaryDcdReader
- Binding
- BioExt
- BioMeshRenderer
- BioModel
- BioModelSet
- BioPolymer
- BioResolver
- BioShape
- BioShapeCollection
- BioShapeRenderer
- Bond
- Bond
- BondCollection
- BondIterator
- BondIterator
- BondIteratorSelected
- BondSet
- BoxInfo
- Bridge
- BS
- Bspf
- Bspt
- BSUtil
- C
- CageRenderer
- Calculation
- Calculations
- CalculationsMMFF
- CalculationsUFF
- CarbohydrateMonomer
- CarbohydratePolymer
- Cartoon
- CartoonRenderer
- CastepDensityReader
- CastepReader
- CBK
- CgdReader
- CGO
- CGOMesh
- CGORenderer
- Chain
- ChimeMessenger
- ChimePanel
- ChimeToJmol
- ChimeToJmol.ApplicationCloser
- CifReader
- CircleRenderer
- ClassPreloader
- CmdExt
- ColorEncoder
- ColorManager
- CommandHistory
- CommandWatcherThread
- Connection
- Connections
- ConsoleTextArea
- Contact
- ContactPair
- ContactRenderer
- ContextToken
- CreditsDialog
- CrystalReader
- CsfReader
- CubeIterator
- CubeReader
- CubeReader
- CylinderRenderer
- DataManager
- DefaultLogger
- DelPhiBinaryReader
- DgridReader
- Dialog
- Dialog.TypeFilter
- Dipole
- Dipoles
- DipolesRenderer
- Display
- Display
- DisplayPanel
- DmolReader
- DOMReader
- Dots
- DotsRenderer
- DragBinding
- Draw
- Draw.EnumDrawType
- DrawMesh
- DrawRenderer
- Dsn6BinaryReader
- DSSP
- DSSR0
- DSSR1
- Echo
- EchoRenderer
- Edge
- Edge.EnumBondOrder
- EfvetReader
- EigenSort
- Element
- Elements
- Ellipsoid
- Ellipsoids
- EllipsoidsRenderer
- EnterListener
- EnvelopeCalculation
- Escape
- EspressoReader
- Export3D
- FFParam
- FIL
- FileChooser
- FileDropper
- FileLoadThread
- FileManager
- FilePreview
- FilePreview.FPPanel
- FileReader
- FileReader
- FilesReader
- FileTyper
- FoldingXyzReader
- FontLineShape
- FontLineShapeRenderer
- ForceField
- ForceFieldMMFF
- ForceFieldReader
- ForceFieldUFF
- Frank
- FrankRenderer
- G3DRenderer
- GamessReader
- GamessUKReader
- GamessUSReader
- GaussianDialog
- GaussianFchkReader
- GaussianReader
- GaussianWfnReader
- GData
- GenericApplet
- GenericConsole
- GenericGraphics
- GenericSwingPopup
- GenericTextArea
- GenNBOReader
- Geodesic
- GeoSurface
- GeoSurfaceRenderer
- Gesture
- GhemicalMMReader
- GlobalSettings
- Graphics3D
- GromacsReader
- Group
- GT
- GuiMap
- GulpReader
- HallInfo
- HallRotation
- HallRotationTerm
- HallTranslation
- Halos
- HalosRenderer
- HB
- HBond
- Helix
- HelpDialog
- HermiteRenderer
- HistoryFile
- Hover
- HoverRenderer
- HoverWatcherThread
- HyperChemReader
- Image
- Image
- ImageDialog
- InputReader
- InputScannerThread
- Int2IntHash
- Int2IntHashEntry
- Interface
- InvalidSmilesException
- IsoExt
- IsoFxyReader
- IsoFxyzReader
- IsoIntersectReader
- IsoMepReader
- IsoMlpReader
- IsoMOReader
- IsoPlaneReader
- IsoShapeReader
- IsoSolventReader
- Isosurface
- IsosurfaceMesh
- IsosurfaceRenderer
- JaguarReader
- JaguarReader
- JanaReader
- JC
- JcampdxReader
- JDXMOLParser
- JmeReader
- Jmol
- Jmol
- Jmol
- JmolAbstractButton
- JmolAdapter
- JmolAdapterAtomIterator
- JmolAdapterBondIterator
- JmolAdapterStructureIterator
- JmolAnnotationParser
- JmolApp
- JmolAppAPI
- JmolAppConsoleInterface
- JmolAppletInterface
- JmolAsyncException
- JmolAwtPopup
- JmolBinding
- JmolButton
- JmolCallbackListener
- JmolChimeMessenger
- JmolConsole
- JmolData
- JmolDataManager
- JmolDataReader
- JmolDialogInterface
- JmolDomReaderInterface
- JmolEnvCalc
- JmolFilesReaderInterface
- JmolFrame
- JmolGenericPopup
- JmolGestureServerInterface
- JmolGraphicsInterface
- JmolInstance
- JmolJDXMOLParser
- JmolJDXMOLReader
- JmolJniClientAdapter
- JmolJSpecView
- JmolJSPopup
- JmolLabel
- JmolMeasurementClient
- JmolModulationSet
- JmolMolecule
- JmolMovieCreatorInterface
- JmolMultiTouchAdapter
- JmolMultiTouchClient
- JmolMultiTouchClientAdapter
- JmolNavigatorInterface
- JmolNMRInterface
- JmolObject
- JmolPanel
- JmolPanel.ActionChangedListener
- JmolParallelProcessor
- JmolPatternMatcher
- JmolPdfCreatorInterface
- JmolPropertyManager
- JmolRendererInterface
- JmolRepaintManager
- JmolResourceHandler
- JmolSceneGenerator
- JmolScriptEditorInterface
- JmolScriptEvaluator
- JmolScriptFunction
- JmolScriptManager
- JmolSelectionListener
- JmolSparshClientAdapter
- JmolStateCreator
- JmolStatusListener
- JmolSyncInterface
- JmolThread
- JmolToggleButton
- JmolToJSmolInterface
- JmolTouchSimulatorInterface
- JmolUtil
- JmolViewer
- JmolZipUtilities
- JSConsole
- JSExporter
- JSFile
- JSFont
- JsG2D
- JSModelKitPopup
- JsonNioClient
- JsonNioServer
- JsonNioService
- JSONReader
- JSpecView
- JSSwingPopupHelper
- JSVInterface
- Jvxl
- JvxlCoder
- JvxlData
- JvxlReader
- JvxlWrite
- JvxlXmlReader
- KeyJCheckBox
- KeyJCheckBoxMenuItem
- KeyJMenu
- KeyJMenuItem
- KeyJRadioButtonMenuItem
- KinemageReader
- KioskFrame
- Labels
- LabelsRenderer
- LabelToken
- Language
- LcaoCartoon
- LcaoCartoonRenderer
- Leaf
- LineRenderer
- Logger
- LoggerInterface
- LogPanel
- LoopedStreams
- MagresReader
- MainPopupResourceBundle
- MapFileReader
- MarchingCubes
- MarchingSquares
- MathExt
- MdCrdReader
- MdTopReader
- Measurement
- MeasurementData
- MeasurementPending
- MeasurementTable
- Measures
- MeasuresRenderer
- MepCalculation
- Mesh
- MeshCapper
- MeshCollection
- MeshData
- MeshData
- MeshDataServer
- MeshRenderer
- MeshRibbon
- MeshRibbonRenderer
- MeshSlicer
- MeshSurface
- MessagePackReader
- MinAngle
- MinAtom
- MinBond
- MinimizationThread
- Minimizer
- MinObject
- MinPosition
- MinTorsion
- MlpCalculation
- MMCifReader
- MMCifValidationParser
- MMFFAngleCalc
- MMFFDistanceCalc
- MMFFESCalc
- MMFFOOPCalc
- MMFFSBCalc
- MMFFTorsionCalc
- MMFFVDWCalc
- MMTFReader
- MOCalculation
- Model
- ModelKitPopup
- ModelKitPopupResourceBundle
- ModelLoader
- ModelManager
- ModelSet
- Modulation
- ModulationSet
- Mol2Reader
- Mol3DReader
- MoldenReader
- MolecularOrbital
- MolecularOrbitalRenderer
- Molecules
- MolReader
- MonitorInputStream
- Monomer
- MopacArchiveReader
- MopacGraphfReader
- MopacReader
- MopacSlaterReader
- MOReader
- MotionPoint
- Mouse
- Mouse
- MouseState
- MoveToThread
- MrcBinaryReader
- MSCifRdr
- MSInterface
- MsmsReader
- MSRdr
- Navigator
- NBO
- NBODialog
- NBODialogConfig
- NBODialogModel
- NBODialogRun
- NBODialogSearch
- NBODialogView
- NBOJob
- NBOJobQueueManager
- NBORenderer
- NBOService
- NciCalculation
- NffReader
- NMRCalculation
- Node
- Node
- Normix
- NucleicMonomer
- NucleicPolymer
- NucleicRenderer
- NWChemReader
- ObjReader
- OdysseyReader
- Orbitals
- Orientation
- OutputManager
- OutputManagerAwt
- OutputManagerJS
- P2nReader
- PAL
- Parameters
- Parser
- PatternMatcher
- PdbReader
- PeriodicVolumeFileReader
- PfaatBinding
- PhosphorusMonomer
- PhosphorusPolymer
- PickleReader
- Pixelator
- PixelatorScreened
- PixelatorShaded
- PixelatorT
- Platform
- Platform
- Platform
- Platform3D
- Plot3D
- Plot3DRenderer
- PltFormattedReader
- Pmesh
- Pmesh4Reader
- PmeshReader
- PmeshRenderer
- Point3fi
- PointGroup
- PolygonFileReader
- Polyhedra
- PolyhedraRenderer
- Polyhedron
- PolyhedronStereoSorter
- PopInJmol
- PopupHelper
- PopupResource
- PovrayDialog
- PqrReader
- PrecisionRenderer
- PreferencesDialog
- PropertyManager
- ProteinStructure
- PsiReader
- PyMOL
- PymolAtomReader
- PyMOLGroup
- PyMOLMeshReader
- PyMOLReader
- PyMOLScene
- QchemReader
- QMAtom
- QS
- QuantumCalculation
- QuantumPlaneCalculation
- RadiusData
- RadiusData.EnumType
- Ras3DReader
- RasmolBinding
- RecentFilesDialog
- Rectangle
- RepaintManager
- Resolver
- Resource
- Rgb16
- Ribbons
- RibbonsRenderer
- RocketRenderer
- Rockets
- RocketsRenderer
- Scene
- ScriptButtons
- ScriptCompiler
- ScriptContext
- ScriptDelayThread
- ScriptEditor
- ScriptError
- ScriptEval
- ScriptException
- ScriptExpr
- ScriptExt
- ScriptFlowContext
- ScriptFunction
- ScriptInterruption
- ScriptManager
- ScriptMathProcessor
- ScriptParallelProcessor
- ScriptParam
- ScriptProcess
- ScriptProcessRunnable
- ScriptQueueThread
- ScriptTokenParser
- SelectionManager
- Shader
- Shape
- ShapeManager
- ShapeRenderer
- Sheet
- ShelxReader
- SiestaReader
- SimpleMarchingCubes
- SimpleMarchingCubesOld
- SimpleUnitCell
- SinglePointGesture
- SlaterData
- SlaterReader
- Slice
- SmarterJmolAdapter
- SmilesAromatic
- SmilesAtom
- SmilesBond
- SmilesExt
- SmilesGenerator
- SmilesMatcher
- SmilesMatcherInterface
- SmilesMeasure
- SmilesParser
- SmilesRing
- SmilesRingSet
- SmilesSearch
- SmilesStereo
- SpaceGroup
- SpartanArchive
- SpartanInputReader
- SpartanReader
- SpartanSmolReader
- SpartanUtil
- SphereRenderer
- SpinThread
- Splash
- SplashInterface
- Stars
- StarsRenderer
- StateCreator
- StateManager
- StateScript
- StatusBar
- StatusListener
- StatusManager
- STER
- Sticks
- SticksRenderer
- STR
- Strands
- StrandsRenderer
- Structure
- Structure
- StructureIterator
- Subsystem
- SurfaceFileReader
- SurfaceGenerator
- SurfaceReader
- SurfaceStatus
- SurfaceTool
- SurfaceToolGUI
- SV
- Symmetry
- SymmetryDesc
- SymmetryInfo
- SymmetryInterface
- SymmetryOperation
- T
- TempArray
- Tensor
- Test
- Text
- TextRenderer
- TextRenderer
- TextShape
- TextString
- TickerThread
- TickInfo
- TimeoutThread
- TinkerReader
- TlsDataOnlyReader
- Trace
- TraceRenderer
- Trajectory
- TransformManager
- TransformManager4D
- Translator
- TriangleData
- TriangleRenderer
- Triangulator
- Turn
- TwoPointGesture
- Txt
- Uccage
- UccageRenderer
- UFFAngleCalc
- UFFDistanceCalc
- UFFOOPCalc
- UFFTorsionCalc
- UFFVDWCalc
- UhbdReader
- UnitCell
- UnitCellIterator
- UseTable
- Util
- V3000Rdr
- VaspChgcarReader
- VaspChgcarReader
- VaspOutcarReader
- VaspPoscarReader
- VDW
- Vectors
- VectorsRenderer
- VertexDataServer
- Vibration
- VibrationThread
- Viewer
- Viewer.ACCESS
- VolumeData
- VolumeDataReader
- VolumeFileReader
- VoxelDataCreator
- VTemp
- WebExport
- WebMOReader
- WebPanel
- WhatsNewDialog
- Widgets
- Wien2kReader
- WrappedApplet
- WrappedAppletLoader
- XcrysdenReader
- XmlArgusReader
- XmlChem3dReader
- XmlCmlReader
- XmlHandler
- XmlMagResReader
- XmlMolproReader
- XmlMOReader
- XmlOdysseyReader
- XmlQEReader
- XmlReader
- XmlReader
- XmlVaspReader
- XmlXsdReader
- XplorReader
- XsfReader
- XtalSymmetry
- XyzReader
- ___Exporter
- __CartesianExporter
- __RayTracerExporter
- _IdtfExporter
- _MayaExporter
- _ObjExporter
- _PovrayExporter
- _StlExporter
- _TachyonExporter
- _VrmlExporter
- _X3dExporter