- AbstractDepictor
- AbstractDepictor.DepictorDot
- AbstractDepictor.DepictorLine
- AbstractDescriptorHandlerFP
- AbstractDescriptorHandlerLongFP
- AbstractDrawingObject
- AbstractExtendedDepictor
- AbstractForceField
- AbstractParser
- AbstractScoringEngine
- AcceptorPoint
- Action
- AddRingAction
- AMemorizedObject
- AminoAcidLabeled
- AminoAcidsLabeledContainer
- Angle
- Angle
- Angle
- AngleBend
- AngleConstraint
- AromaticityResolver
- AromRingPoint
- ArrayUtils
- ArrayUtilsCalc
- Arrow
- ArrowAction
- Atom
- Atom
- AtomAssembler
- AtomComparator
- AtomFunctionAnalyzer
- AtomHighlightAction
- AtomicFloat
- AtomicGaussian
- AtomIndexLinkerId
- AtomMapAction
- AtomRecord
- AtomTypeCalculator
- AtomTypeList
- AtomTypeMap
- AutoMapper
- AxialStereoRule
- BadAtomTypeException
- BadRingAromException
- BinaryDecoder
- BitArray128
- BitArray128Factory
- BitUtils
- Bndk
- BOMSkipper
- Bond
- Bond
- BondAngleSet
- BondBaseAction
- BondConstraint
- BondHighlightAction
- BondLengthSet
- BondRotationHelper
- BondsCalculator
- BondStretch
- BondVector2IdCode
- BurtleHasher
- BurtleHasherABC
- ByteArray
- ByteArrayComparator
- ByteVec
- Canonizer
- CanonizerBaseValue
- CanonizerMesoHelper
- CanonizerUtil
- CanonizerUtil.IDCODE_TYPE
- CanonizerUtil.StrongHasher
- CDXConstants
- ChangeAtomAction
- ChangeAtomPropertiesAction
- ChangeChargeAction
- Charge
- Charge
- ChargePoint
- ChemDrawCDX
- ChemistryDataFormats
- ChemistryFlavors
- ChemistryHelper
- ChemPLP
- ClassificationData
- CleanAction
- ClearAction
- ClipboardHandler
- ClipboardHelper
- CLogPPredictor
- ClusterNode
- ColorHelper
- ColorUtils
- CombinationGenerator
- CommandAction
- CommandLineParser
- CommonSubGraphHelper
- CompleteGraphMatcher
- CompoundCollectionListener
- CompoundCollectionModel
- CompoundCollectionPane
- CompoundFileFilter
- CompoundFileHelper
- CompoundFileParser
- CompoundTableConstants
- ConformationRule
- ConformationSelfOrganizer
- Conformer
- ConformerGenerator
- ConformerSet
- ConformerSetGenerator
- Constants
- ConstantsAminoAcidsLabeled
- ConstantsDWAR
- ConstantsFlexophore
- ConstantsFlexophoreGenerator
- ConstantsFlexophoreHardPPPoints
- ConstantsHistogram
- ContainerBitArray
- ContainerFragBondsSolutions
- ContainerListWithIntVec
- ContainerMemory
- CoordinateInventor
- Coordinates
- CopyAction
- CorrelationCalculator
- CovRad
- CreatorMolDistHistViz
- Csv
- CursorHelper
- CutAction
- DataProcessor
- DateAnalysis
- Def
- DefaultCompoundCollectionModel
- DefaultCompoundCollectionModel.IDCode
- DefaultCompoundCollectionModel.IDCodeWithName
- DefaultCompoundCollectionModel.Molecule
- DefaultCompoundCollectionModel.Native
- Delegator
- DeleteAction
- Depictor
- Depictor2D
- DepictorTransformation
- DescriptorConstants
- DescriptorEncoder
- DescriptorHandler
- DescriptorHandlerFactory
- DescriptorHandlerFFP512
- DescriptorHandlerFlexophore
- DescriptorHandlerFunctionalGroups
- DescriptorHandlerHashedCFp
- DescriptorHandlerHashedPharmSphere
- DescriptorHandlerLongCFP
- DescriptorHandlerLongFFP512
- DescriptorHandlerLongPFP512
- DescriptorHandlerPFP512
- DescriptorHandlerPharmPath
- DescriptorHandlerPTree
- DescriptorHandlerReactionFP
- DescriptorHandlerShape
- DescriptorHandlerShapeOneConf
- DescriptorHandlerSkeletonSpheres
- DescriptorHandlerStandard2DFactory
- DescriptorHandlerStandardFactory
- DescriptorHelper
- DescriptorInfo
- Dfsb
- DialogResult
- DiastereoIDTest
- DiastereotopicAtomID
- DistanceRule
- DistHist
- DistHistEncoder
- DistHistHelper
- DistHistHelper.RangeStatistics
- DiversitySelector
- Dockable
- DockableHeader
- DockingEngine
- DockingEngine.DockingResult
- DockingEngine.ScoringFunction
- DockingEngine.StartPosition
- DockingFailedException
- DockingUtils
- DonorPoint
- DoubleArray
- DoubleFormat
- DoubleVec
- DownBondAction
- DragGlassPane
- DrawAction
- DrawAreaEvent
- DrawAreaListener
- DrawConfig
- DrawingObject
- DrawingObjectFactory
- DrawingObjectList
- DruglikenessPredictor
- DrugScoreCalculator
- DWARFileCreator
- DWARFileParser
- Electrostatic
- Element
- EmpiricalLigandStrain
- EncodeFunctions
- EncoderFloatingPointNumbers
- EncoderIntegerNumbers
- EnergyTerm
- ErrorHashMap
- Evaluable
- EvaluableFlexibleOverlap
- EvaluableOverlap
- ExceptionConformationGenerationFailed
- ExhaustiveFragmentGeneratorAtoms
- ExhaustiveFragmentGeneratorBonds
- ExhaustiveFragmentGeneratorParallizer
- ExhaustiveFragmentsStatistics
- ExhaustiveMCSGeneratorParallel
- ExitVectorPoint
- ExtendedDepictor
- ExtendedMolecule
- ExtendedMoleculeFunctions
- FactorySolution
- FastSpline
- FastSpline.Polynome
- FeatureCalculator
- FileHelper
- FingerPrintGenerator
- FingerPrintGeneratorPharmGraph
- FlexibleShapeAlignment
- FlexophoreCreateFunctions
- FlexophorePoint
- ForceField
- ForceFieldChangeListener
- ForceFieldMMFF94
- Formatter
- Formatter.LocaleFormat
- FormulaParser
- FractalDimensionMolecule
- FractalDimensionMoleculeMain
- Fragment
- Fragment3D
- FragmentAssociation
- FragmentDefinedByBondsHasher
- FragmentDefinedByBondsIdCode
- Fragmenter3D
- FunctionalGroupClassifier
- Gaussian3D
- GeometryCalculator
- GeometryCalculator
- GeomFactory
- GhostPreview
- Graph
- GraphicsContextImpl
- HashSetInt
- HBTerm
- HeaderMouseAdapter
- HeaderPaintHelper
- HerschbachLaurie
- HetNameParser
- HetSynonymParser
- HiDPIHelper
- HiDPIIcon
- HiDPIIconButton
- HiDPIToggleButton
- HiDPIUtil
- Histogram
- HistogramMatchCalculator
- HoseCodeCreator
- HungarianAlgorithm
- HydrogenHandler
- IArrow
- IAtomPropertiesDialog
- IAtomQueryFeaturesDialog
- IBitArray
- IBitArrayFactory
- IBondQueryFeaturesDialog
- IChangeListener
- IClipboardHandler
- IColor
- ICompleteGraph
- ICursor
- IDCodeCoord
- IDCodeParser
- IDCodeParserWithoutCoordinateInvention
- IdentifiedObject
- IDepictor
- IDescriptorHandlerFlexophore
- IDialog
- IdoScore
- IDrawContext
- IDrawingObject
- IFactory
- IIdentifiedObject
- IKeyCode
- IKeyEvent
- ImageClipboardHandler
- ImageClipboardHandler.ImageSelection
- ImageProvider
- IMolDistHist
- IMoleculeView
- IMouseEvent
- IncrementTable
- IndexCoordinates
- IndexHash
- InputObjectFracDimCalc
- IntArray
- IntArrayComparator
- IntegerDouble
- InteractionAtomTypeCalculator
- InteractionAtomTypeCalculator.AtomFlagCount
- InteractionAtomTypeCalculator.AtomPropertyMask
- InteractionAtomTypeCalculator.AtomPropertyShift
- InteractionAtomTypeCalculator.FunctionalGroup
- InteractionDistanceStatistics
- InteractionSimilarityTable
- InteractionSimilarityTable.InteractionDescriptor
- InteractionTerm
- InteractionTypeMap
- IntQueue
- IntQueue
- IntVec
- INumericalDataColumn
- InventorAngle
- InventorChain
- InventorCharge
- InventorDefaultTemplateList
- InventorFragment
- InventorTemplate
- IO
- IObjectiveCompleteGraph
- IonizableGroupDetector
- IonizableGroupDetector2D
- IPharmacophorePoint
- IPharmacophorePoint.Functionality
- IPipeline
- IPolygon
- IPPNode
- IPPNodeSimilarity
- IReactionArrow
- IReactionMapper
- IRectangle2D
- ISimilarityCalculator
- ISimilarityHandlerFactory
- IsomericSmilesCreator
- IsotopeHelper
- IStructureNameResolver
- IValidationListener
- JAtomLabelDialog
- JAtomQueryFeatureDialog
- JBondQueryFeatureDialog
- JBrowseButtons
- JChemistryView
- JDockingPanel
- JDrawArea
- JDrawDialog
- JDrawPanel
- JDrawToolbar
- JEditableChemistryView
- JEditableStructureView
- JFileChooserOverwrite
- JFXCanvasDepictor
- JMessageBar
- JStructureView
- JTextDrawingObjectDialog
- KabschAlignment
- LigandPose
- LinearRegression
- Linker
- ListInteger
- ListWithIntVec
- ListWithIntVecIdCode
- LittleEndianDataInputStream
- LittleEndianDataOutputStream
- Logarithm
- LookAndFeelHelper
- LUDecomposition
- MarkushStructure
- MatchFlexophoreNodesMain
- MathHelper
- Matrix
- MatrixBasedHistogram
- MCS
- MCSFast
- MCSFunctions
- MCSReactionMapper
- MDHIndexTables
- MedianStatisticFunctions
- MetaFile
- MetalTerm
- MetropolisMonteCarloHelper
- MinimumSpanningTree
- MMFFMolecule
- Model
- Model.AtomHighlightCallback
- Model.BondHighlightCallback
- ModelExhaustiveStatistics
- ModelMedianDouble
- ModelMedianFloat
- ModelMedianInteger
- ModelMedianLong
- ModelParser
- ModelSampleFragments
- ModelSolutionSimilarity
- Mol2FileParser
- MolDistHist
- MolDistHistEncoder
- MolDistHistViz
- MolDistHistVizEncoder
- MolDistHistVizFrag
- MolecularComplexityCalculator
- MolecularFormula
- MolecularVolume
- Molecule
- Molecule3D
- Molecule3DFunctions
- MoleculeAutoMapper
- MoleculeDataFormats
- MoleculeDragAdapter
- MoleculeDropAdapter
- MoleculeFilter
- MoleculeGrid
- MoleculeNeutralizer
- MoleculeStandardizer
- MoleculeTransferable
- MoleculeView
- MoleculeViewSkin
- MolfileCreator
- MolfileParser
- MolfileV3Creator
- MultCoordFragIndex
- MultipleNonOverlapSolution
- Mutation
- MutationBiasProvider
- Mutator
- NamedSubstituents
- NativeClipboardAccessor
- NewBondAction
- NewChainAction
- ObjectiveBlurFlexophoreHardMatchUncovered
- ObjectiveExhaustiveStatistics
- ODEFileParser
- OptimizerLBFGS
- OutOfPlane
- OutOfPlane
- ParameterizedStringList
- PasteAction
- PDBCoordEntryFile
- PDBFileParser
- PeriodicTable
- PeriodicTable
- PharmacophoreCalculator
- PharmacophoreNode
- PharmacophorePointFactory
- PharmacophoreTree
- PharmacophoreTree.BiGramInt
- PharmacophoreTreeGenerator
- PharmGraphGenerator
- PheSAAlignment
- PheSAAlignment.axis
- PheSAAlignment.PheSAResult
- PheSAAlignmentOptimizer
- PheSABindingHypothesis
- PheSAMolecule
- Pipeline
- PlaneRule
- Platform
- PLPTerm
- PointDouble
- PointUtils
- PolarSurfaceAreaPredictor
- Polygon
- PopupProvider
- PositionConstraint
- PotentialEnergyTerm
- PPGaussian
- PPNode
- PPNodeRGroup
- PPNodeSimilarity
- PPNodeViz
- PPNodeVizTriangle
- PPTriangle
- PPTriangleCreator
- PPTriangleMatcher
- PPTriangleMatcher.AlignmentResult
- ProgressController
- ProgressListener
- PropertyCalculator
- ProteinSynthesizer
- Quaternion
- QuickMathCalculator
- RDFileParser
- Reaction
- ReactionArrow
- ReactionDragAdapter
- ReactionDropAdapter
- ReactionEncoder
- ReactionSearch
- ReactionSearchDataSource
- ReactionSearchSpecification
- ReactionTransferable
- Reactor
- RemarkParser
- REPTerm
- Residue
- ResultFracDimCalc
- ResultFragmentsStatistic
- ResultObjective
- RigidFragment
- RigidFragmentCache
- RigidFragmentCache.CacheEntry
- RigidFragmentProvider
- RingBoolean
- RingCollection
- RotatableBond
- RunBondVector2IdCode
- RXNFileCreator
- RXNFileParser
- RXNFileV3Creator
- ScaffoldHelper
- ScaledEditorKit
- ScaledHTML
- ScaledStyleSheet
- ScorePoint
- ScrollPaneAutoScrollerWhenDragging
- Sdf
- Sdf.OnMolecule
- SDFileMolecule
- SDFileMoleculeDropAdapter
- SDFileMoleculeTransferable
- SDFileParser
- Search
- Searchable
- SelectionAction
- Selector
- SelfOrganizedConformer
- Separation
- Separation.Relation
- ShadowBorder
- SimilarityCalculatorInfo
- SimpleCanonizer
- SimpleMetalTerm
- SimplePPGaussian
- SingularValueDecomposition
- SiteParser
- SizeOf
- Sketch
- SlidingWindow
- SlidingWindowDistHist
- SmilesCreator
- SmilesParser
- SmoothingSplineInterpolator
- SolubilityPredictor
- SolutionCompleteGraph
- SortedList
- SortedPair
- SortedStringList
- SplineFunction
- SRSearcher
- SSSearcher
- SSSearcherWithIndex
- StatisticalTorsionPotential
- StatisticalTorsionTerm
- Stbn
- StereoMolecule
- StraightLineRule
- StrainTerm
- StretchBend
- String2DoubleArray
- StringFunctions
- StringReadChannel
- StrokeLineCap
- StrokeLineJoin
- StructureAssembler
- StructureCalculator
- StructureInfo
- StructureListener
- StructureNameResolver
- StructureSearch
- StructureSearchController
- StructureSearchDataSource
- StructureSearchSpecification
- StructureTransferData
- SubFlexophoreGenerator
- SubFlexophoreGenerator.ViolatedConditionsCount
- SubGraphExtractor
- SubGraphIndices
- SubStructSearchBondIndex
- SubStructSearchExhaustiveTreeWalker
- SummaryFragments
- SVGDepictor
- SymmetryCalculator
- SymmetryCorrectedRMSDCalculator
- TableModelString
- Tables
- TautomerHelper
- testChiralDia
- testDiaID
- testHoses
- TetrahedralStereoRule
- TextClipboardHandler
- TextDrawingObject
- ThreadMaster
- ToolbarSelectionChange
- Torsion
- Torsion
- TorsionAngle
- TorsionConstraint
- TorsionDB
- TorsionDescriptor
- TorsionDescriptorHelper
- TorsionDetail
- TorsionPrediction
- TorsionRelevanceHelper
- TorsionRule
- TorsionSet
- TorsionSetEliminationRule
- TorsionSetStrategy
- TorsionSetStrategyAdaptiveRandom
- TorsionSetStrategyLikelySystematic
- TorsionSetStrategyRandom
- ToxicityPredictor
- TreeContainer
- TreeElement
- TreeFork
- TreeLeaf
- TreeMatcher
- TreeMatcher.FeatureMatch
- TreeMatcher.TreeMatching
- TreeRoot
- TreeUtils
- Triangle
- UndoAction
- UniqueFragmentEstimator
- UniqueList
- UniqueStringList
- UnknownParityAction
- UnparametrizedAtomTypeException
- UpBondAction
- VanDerWaals
- VanDerWaals
- VDWRadii
- Vector3
- VectorSimilarity
- VerticalFlowLayout
- VolumeGaussian
- WMF
- WMFConstants
- WMFGraphics
- WMFGraphics2D
- ZoomRotateAction