- AAindexFactory
- AAIndexFileParser
- AAIndexProvider
- ABITrace
- ABITracerCompoundSet
- AboutDialog
- AbstractAlignmentJmol
- AbstractAnnotation
- AbstractCifFileSupplier
- AbstractCifFileSupplier.WrappedAtom
- AbstractCompound
- AbstractCompoundSet
- AbstractCompoundTranslator
- AbstractFeature
- AbstractLocation
- AbstractMatrixAligner
- AbstractNucleotideCompoundSet
- AbstractPairwiseSequenceAligner
- AbstractProfileProfileAligner
- AbstractReference
- AbstractScorer
- AbstractScoresCache
- AbstractSequence
- AbstractSequence.AnnotationType
- AbstractStructureAlignment
- AbstractTerm
- AbstractUserArgumentProcessor
- AccesionedLocation
- Accessioned
- AccessionID
- AFP
- AFPAlignmentDisplay
- AFPCalculator
- AFPChain
- AFPChainCoordManager
- AFPChainer
- AFPChainFlipper
- AFPChainScorer
- AfpChainWriter
- AFPChainXMLConverter
- AFPChainXMLParser
- AFPFromFasta
- AFPOptimizer
- AFPPostProcessor
- AFPTwister
- AgScore
- AligMatEl
- Alignable
- AlignedPosition
- AlignedSequence
- AlignedSequence.Step
- Aligner
- AlignerHelper
- AlignerHelper.Anchor
- AlignerHelper.Anchor.QueryIndexComparator
- AlignerHelper.Cut
- AlignerHelper.Last
- AlignerHelper.Subproblem
- AlignmentCalc
- AlignmentCalc
- AlignmentCalculationRunnable
- AlignmentGui
- AlignmentGuiDemo
- AlignmentPositionListener
- AlignmentProgressListener
- AlignmentResult
- Alignments
- Alignments.PairInProfileScorerType
- Alignments.PairwiseSequenceAlignerType
- Alignments.PairwiseSequenceScorerType
- Alignments.ProfileProfileAlignerType
- Alignments.RefinerType
- AlignmentTextPanel
- AlignmentTools
- AlignmentTools.IdentityMap
- AligNPE
- AlignUtils
- AligPanel
- AligPanelMouseMotionListener
- AligUIManager
- AllChemCompProvider
- AlreadyExistsException
- AltAligComparator
- AlternativeAlignment
- AlternativeAlignmentFrame
- AmbiguityDNACompoundSet
- AmbiguityDNARNAHybridCompoundSet
- AmbiguityRNACompoundSet
- AminoAcid
- AminoAcidComposition
- AminoAcidCompositionTable
- AminoAcidCompound
- AminoAcidCompoundSet
- AminoAcidImpl
- AminoAcidProperties
- AnchoredPairwiseSequenceAligner
- AngleOrderDetectorPlus
- Annotatable
- Annotation
- App
- App
- ArrayListProxySequenceReader
- ArrayListSequenceReader
- AsaCalculator
- AssertionFailure
- Astral
- Astral.AstralSet
- Atom
- AtomCache
- AtomContact
- AtomContactSet
- AtomIdentifier
- AtomImpl
- AtomInfo
- AtomInfoParser
- AtomIterator
- AtomPositionMap
- AtomPositionMap.GroupMatcher
- AugmentedResidueRange
- Author
- AutoSuggestProvider
- AxisAligner
- BasePairParameters
- BasicSequence
- BcifFileReader
- BerkeleyScopInstallation
- BetaBridge
- BioAssemblyIdentifier
- BioAssemblyInfo
- BioAssemblyTools
- BioJavaAADemo
- BiojavaJmol
- BioJavaStructureAlignment
- BiologicalAssemblyBuilder
- BiologicalAssemblyTransformation
- BitSequenceReader
- BitSequenceReader.BitArrayWorker
- BlastAlignmentParameterEnum
- BlastClustReader
- BlastHitBuilder
- BlastHomologyHits
- BlastHspBuilder
- BlastJob
- BlastMatrixEnum
- BlastOutputAlignmentFormatEnum
- BlastOutputFormatEnum
- BlastOutputParameterEnum
- BlastProgramEnum
- BlastResult
- BlastResultBuilder
- BlastTabularParser
- BlastXMLParser
- BlastXMLQuery
- Block
- BlockImpl
- BlockSet
- BlockSetImpl
- Bond
- BondImpl
- BondMaker
- BondType
- BoundingBox
- BravaisLattice
- BridgeType
- BrowserOpener
- BufferedReaderBytesRead
- C2RotationSolver
- CAConverter
- Calc
- CalcPoint
- CallablePairwiseSequenceAligner
- CallablePairwiseSequenceScorer
- CallableProfileProfileAligner
- CallableStructureAlignment
- CartesianProduct
- CaseFreeAminoAcidCompoundSet
- CaseInsensitiveCompound
- CasePreservingProteinSequenceCreator
- CathCategory
- CathDatabase
- CathDomain
- CathFactory
- CathFragment
- CathInstallation
- CathNode
- CathSegment
- CDSComparator
- CDSSequence
- CECalculator
- CeCalculatorEnhanced
- CeCPMain
- CeCPMain.CPRange
- CECPParameters
- CECPParameters.DuplicationHint
- CeCPUserArgumentProcessor
- CeMain
- CensorStatus
- CensorStatusSelect
- CeParameters
- CeParameters.ScoringStrategy
- CeSideChainMain
- CeSideChainUserArgumentProcessor
- CeSymm
- CeSymmIterative
- CESymmParameters
- CESymmParameters.OrderDetectorMethod
- CESymmParameters.RefineMethod
- CESymmParameters.SymmetryType
- CeSymmResult
- CeUserArgumentProcessor
- CeUserArgumentProcessor.CeStartupParams
- Chain
- ChainImpl
- ChainSignature
- ChangeValue
- ChargeAdder
- ChemComp
- ChemCompAtom
- ChemCompBond
- ChemCompConsumer
- ChemCompConsumerImpl
- ChemCompConverter
- ChemCompDescriptor
- ChemCompDistribution
- ChemCompGroupFactory
- ChemCompProvider
- ChemCompTools
- ChemicalComponentDictionary
- ChiSq
- Cholesky2
- CholeskyDecomposition
- ChooseDirAction
- ChromosomeMappingTools
- ChromosomeSequence
- ChromPos
- Chsolve2
- CifBean
- CifChainSupplierImpl
- CifFileConsumer
- CifFileReader
- CifFileSupplier
- CifStructureConsumer
- CifStructureConsumerImpl
- CifStructureConverter
- CifStructureSupplierImpl
- ClasspathResource
- ClinicalMetaDataOutcome
- CliTools
- ClusterAltAligs
- ClusterDomains
- CodonCompound
- CollectionTools
- ColorConverter
- ColorInterpolator
- ColorUtils
- CommandPrompt
- CommandPrompt.PropertyName
- CompactCharSequence
- Comparison
- ComplementCompound
- ComplementSequenceView
- Component
- ComponentXMLConverter
- Compound
- CompoundNotFoundException
- CompoundSet
- CompoundTranslator
- ConcurrencyTools
- ConfigPDBInstallPanel
- ConfigStrucAligParams
- ConfigurationException
- ConfigXMLHandler
- Constraints
- Contact
- ContinuousColorMapper
- ContinuousColorMapperTransform
- Convert2Charge
- Convert2Hydrophobicity
- Convert2NormalizedVanDerWaalsVolume
- Convert2Polarity
- Convert2Polarizability
- Convert2SecondaryStructure
- Convert2SolventAccessibility
- Convertor
- CookBook
- CookbookMSA
- CoordManager
- CoreSuperimposer
- CoxCC
- CoxCoefficient
- CoxComparatorInterface
- CoxHelper
- CoxInfo
- CoxMart
- CoxMethod
- CoxR
- CoxScore
- CoxVariables
- CoxVariablesOverallModelFitComparator
- CoxVariablesVariableComparator
- CRC64Checksum
- CrystalBuilder
- CrystalCell
- CrystalTransform
- Cut
- CutDomain
- CutSites
- CutValues
- Cytoband
- CytobandParser
- DatabasePDBRevRecord
- DatabaseReferenceInterface
- Dataset
- DataSource
- DBRef
- DBReferenceInfo
- DefaultAAIndexProvider
- DefaultAutoSuggestProvider
- DefaultMatrixMapper
- DefaultOps
- DemoAlignmentFromFasta
- DemoAlignProteins
- DemoAsa
- DemoAtomCache
- DemoBerkeleyScop
- DemoBioAssemblies
- DemoCATH
- DemoCE
- DemoCeSymm
- DemoChangeChemCompProvider
- DemoCommandLineStartup
- DemoContacts
- DemoCrystalInterfaces
- DemoDistanceTree
- DemoDomainsplit
- DemoFATCAT
- DemoLoadSecStruc
- DemoLoadStructure
- DemoLoadSubstMax
- DemoMMCIFReader
- DemoMmcifToPdbConverter
- DemoMmtfReader
- DemoMmtfWriter
- DemoMultipleMC
- DemoNWALignment
- DemoQsAlign
- DemoQuatSymmetryJmol
- DemoRotationAxis
- DemoSCOP
- DemoSecStrucCalc
- DemoShowBiolAssembly
- DemoShowCATHDomain
- DemoShowLargeAssembly
- DemoSixFrameTranslation
- DemoStructureFromFasta
- DemoSW3DAligner
- DemoSymmetry
- DiscreteQuantizerInterface
- DisplayAFP
- DistanceBox
- DistanceMatrixCalculator
- DistanceTreeEvaluator
- DNACompoundSet
- DNASequence
- DNASequence.DNAType
- DNASequenceCreator
- DNAToRNATranslator
- Domain
- DomainProvider
- DotPlotPanel
- DownloadChemCompProvider
- DSSPParser
- EcodDatabase
- EcodDomain
- EcodFactory
- EcodInstallation
- EcodInstallation.EcodParser
- Edit
- Edit.AbstractEdit
- Edit.Delete
- Edit.Insert
- Edit.Substitute
- EigenvalueDecomposition
- Element
- Element
- ElementTable
- ElementType
- EmblId
- EmblReader
- EmblRecord
- EmblReference
- EntityFinder
- EntityInfo
- EntityType
- Equals
- ExonComparator
- ExonSequence
- ExperimentalTechnique
- ExpressionFigure
- FastaAFPChainConverter
- FastaGeneWriter
- FastaHeaderFormatInterface
- FastaReader
- FastaReaderHelper
- FastaSequence
- FastaSequenceParser
- FastaStructureParser
- FastaWriter
- FastaWriterHelper
- Fastq
- FastqBuilder
- FastqReader
- FastqTools
- FastqVariant
- FastqWriter
- FatCat
- FatCatAligner
- FatCatFlexible
- FatCatParameters
- FatCatRigid
- FatCatUserArgumentProcessor
- FCAlignHelper
- Feature
- FeatureDbReferenceInfo
- FeatureHelper
- FeatureI
- FeatureInterface
- FeatureList
- FeatureRetriever
- FeaturesKeyWordInterface
- FileConvert
- FileDownloadUtils
- FileParsingParameters
- FileProxyDNASequenceCreator
- FileProxyProteinSequenceCreator
- FileProxyRNASequenceCreator
- FlatFileCache
- ForesterWrapper
- FourBitSequenceReader
- FourBitSequenceReader.FourBitArrayWorker
- FractionalIdentityInProfileScorer
- FractionalIdentityScorer
- FractionalSimilarityInProfileScorer
- FractionalSimilarityScorer
- FragmentJoiner
- FragmentPair
- Frame
- FuzzyPoint
- GapArray
- GapPenalty
- GapPenalty.Type
- GCStats
- GenbankHeaderFormatInterface
- GenbankProxySequenceReader
- GenbankReader
- GenbankReaderHelper
- GenbankReference
- GenbankSequenceParser
- GenbankWriter
- GenbankWriterHelper
- GeneChromosomePosition
- GeneChromosomePositionParser
- GeneFeatureHelper
- GeneIDGFF2Reader
- GeneIDXMLReader
- GeneMarkGTFReader
- GeneName
- GeneNamesParser
- GenericFastaHeaderFormat
- GenericFastaHeaderParser
- GenericGenbankHeaderFormat
- GenericGenbankHeaderParser
- GenericInsdcHeaderFormat
- GeneSequence
- GetDistanceMatrix
- GFF3FromUniprotBlastHits
- GFF3Reader
- GFF3Writer
- GOParser
- Gotoh
- GradientMapper
- GradientPanel
- GraphComponentOrderDetector
- GraphComponentRefiner
- Grid
- GridCell
- Group
- GroupAsa
- GroupContact
- GroupContactSet
- GroupIterator
- GroupResults
- GroupToSDF
- GroupType
- GuanUberbacher
- GuideTree
- GuideTreeNode
- GuiWrapper
- Hashcoder
- HBond
- HeaderInfo
- HelicalRepeatUnit
- Helix
- HelixAxisAligner
- HelixExtender
- HelixLayers
- HelixSolver
- HelloWorld
- HelpDialog
- HetatomImpl
- HetatomImpl.PerformanceBehavior
- HierarchicalClusterer
- Hit
- HmmerDemo
- HmmerDomain
- HmmerResult
- HmmerScan
- Hsp
- HSVColorSpace
- IcosahedralSampler
- Icosahedron
- IdxComparator
- IlluminaFastqReader
- IlluminaFastqWriter
- IndexPair
- InputStreamProvider
- InsdcLocations
- InsdcLocations.BondLocation
- InsdcLocations.GroupLocation
- InsdcLocations.OneOfLocation
- InsdcLocations.OrderLocation
- InsdcParser
- IntegerOntology
- InterfaceFinder
- IntronSequence
- InvalidTermException
- IOUtils
- IOUtils.ReaderProcessor
- IPeptideProperties
- IProfeatProperties
- IProfeatProperties.ATTRIBUTE
- IProfeatProperties.DISTRIBUTION
- IProfeatProperties.GROUPING
- IProfeatProperties.TRANSITION
- Isotope
- IUPACParser
- IUPACParser.IUPACTable
- JAutoSuggest
- JMatrixPanel
- JmolAlignedPositionListener
- JmolPanel
- JmolPanel.JmolLoggerAdapter
- JmolSymmetryScriptGenerator
- JmolSymmetryScriptGeneratorC1
- JmolSymmetryScriptGeneratorCn
- JmolSymmetryScriptGeneratorDn
- JmolSymmetryScriptGeneratorH
- JmolSymmetryScriptGeneratorI
- JmolSymmetryScriptGeneratorO
- JmolSymmetryScriptGeneratorPointGroup
- JmolSymmetryScriptGeneratorT
- JmolTools
- JmolViewerImpl
- JNLPProxy
- JoiningSequenceReader
- JointFragments
- JournalArticle
- JPrintPanel
- Jronn
- Jronn.Range
- KaplanMeierFigure
- KeyedWeakReference
- KMFigureInfo
- Ladder
- LightweightProfile
- LightweightProfile.StringFormat
- LinearColorInterpolator
- LinearColorInterpolator.InterpolationDirection
- LocalPDBDirectory
- LocalPDBDirectory.FetchBehavior
- LocalPDBDirectory.ObsoleteBehavior
- LocalProteinDomainParser
- LocalScopDatabase
- Location
- Location
- Location.Tools
- LocationHelper
- LocIterator
- LogColorMapper
- LUDecomposition
- MapToStringTransformer
- Maths
- Matrices
- Matrix
- Matrix
- MatrixAligner
- MatrixListener
- MeanModelComparator
- MeanQuantizer
- MemoryMonitor
- MenuCreator
- MenuCreator
- MenuCreator.DotPlotListener
- Messages
- MetaDataInfo
- MetalBondConsumer
- MetalBondConsumerImpl
- MetalBondConverter
- MetalBondDistance
- MismatchedBasePairParameters
- MmtfActions
- MMTFFileReader
- MmtfStructureReader
- MmtfStructureWriter
- MmtfSummaryDataBean
- MmtfUtils
- Model
- ModelLoader
- ModelLoader.Model
- ModelLoader.Threshold
- ModificationCategory
- ModificationCondition
- ModificationConditionImpl
- ModificationLinkage
- ModificationOccurrenceType
- ModifiedAminoAcidCompoundSet
- ModifiedCompound
- ModifiedCompoundImpl
- ModifiedCompoundXMLConverter
- MomentsOfInertia
- MomentsOfInertia.SymmetryClass
- MultipleAlignment
- MultipleAlignmentCalc
- MultipleAlignmentCoordManager
- MultipleAlignmentDisplay
- MultipleAlignmentEnsemble
- MultipleAlignmentEnsembleImpl
- MultipleAlignmentGUI
- MultipleAlignmentImpl
- MultipleAlignmentJmol
- MultipleAlignmentJmolDisplay
- MultipleAlignmentScorer
- MultipleAlignmentTools
- MultipleAlignmentWriter
- MultipleAlignmentXMLConverter
- MultipleAlignmentXMLParser
- MultipleAligPanel
- MultipleAligPanelMouseMotionListener
- MultipleMcMain
- MultipleMcOptimizer
- MultipleMcParameters
- MultipleSequenceAlignment
- MultipleStatusDisplay
- MultipleStructureAligner
- MultipleSuperimposer
- MutableAlignedSequence
- MutableProfile
- MutableProfilePair
- MutableSequencePair
- Mutator
- MyAlignmentLoadListener
- MyDistMaxListener
- MyExportListener
- MyJmolStatusListener
- MyOpenPdbFileListener
- MySaveFileListener
- MyTableRowSorter
- MyValidationEventHandler
- Name2Count
- NCBIQBlastAlignmentProperties
- NCBIQBlastOutputProperties
- NCBIQBlastService
- NCBIQBlastServiceDemo
- NeedlemanWunsch
- NucleotideCompound
- NucleotideImpl
- NullOutputStream
- NumbersAtRiskPanel
- OboFileEventListener
- OboFileHandler
- OboFileParser
- OboFileParser.SOPair
- OboParser
- Octahedron
- Ontology
- Ontology.Impl
- OntologyException
- OntologyFactory
- OntologyOps
- OntologyTerm
- OntologyTerm.Impl
- OntoTools
- OperatorResolver
- OptimalCECPMain
- OptimalCECPParameters
- OrderDetector
- OrderedPair
- ORonn
- ORonnModel
- OutputHitsGFF
- Pair
- PairInProfileScorer
- PairwiseSequenceAligner
- PairwiseSequenceScorer
- ParameterGUI
- ParseFastaFileDemo
- ParseGO
- ParseListener
- ParserException
- PartitionRefiner
- PassthroughIdentifier
- PDBBioAssemblyParser
- PDBCrystallographicInfo
- PDBDirPanel
- PDBFileParser
- PDBFileReader
- PDBHeader
- PdbId
- PdbPair
- PdbPairsMessage
- PdbPairXMLConverter
- PDBParseException
- PDBRecord
- PDBServerPanel
- PDBStatus
- PDBStatus.Status
- PDBTemporaryStorageUtils
- PDBTemporaryStorageUtils.LinkRecord
- PDBUploadPanel
- PDPDistanceMatrix
- PDPParameters
- PeptideProperties
- PeptideProperties.SingleLetterAACode
- PeptidePropertiesImpl
- PermutationGenerator
- PermutationGroup
- PlainFastaHeaderParser
- Point
- Point.Resolver
- Polyhedron
- PolymerType
- PowerSet
- PredictDisorder
- PrettyXMLWriter
- Prism
- ProfeatProperties
- ProfeatPropertiesImpl
- Profile
- Profile.StringFormat
- ProfilePair
- ProfileProfileAligner
- ProfileProfileScorer
- ProfileView
- ProteinComplexSignature
- ProteinMappingTools
- ProteinModification
- ProteinModificationIdentifier
- ProteinModificationImpl
- ProteinModificationImpl.Builder
- ProteinModificationRegistry
- ProteinModificationXmlReader
- ProteinSequence
- ProteinSequenceCreator
- ProxySequenceReader
- QRDecomposition
- QsAlign
- QsAlignParameters
- QsAlignResult
- QsRelation
- Qualifier
- QualityFeature
- QuantityFeature
- QuatSuperpositionScorer
- QuatSymmetryDetector
- QuatSymmetryParameters
- QuatSymmetryResults
- QuatSymmetryScores
- QuatSymmetrySolver
- QuatSymmetrySubunits
- RasmolCommandListener
- RectangularPrism
- ReducedChemCompProvider
- ReferenceInterface
- ReferenceSuperimposer
- RefinerFailedException
- RemoteHmmerScan
- RemotePairwiseAlignmentOutputProperties
- RemotePairwiseAlignmentProperties
- RemotePairwiseAlignmentService
- RemoteTerm
- RemoteTerm.Impl
- RenderStyle
- RescoreRefiner
- ResidualsCoxph
- ResidualsCoxph.Type
- ResidueGroup
- ResidueNumber
- ResidueRange
- ResidueRangeAndLength
- ResidueType
- ResourceManager
- Result
- ResultFactory
- ReversedSequenceView
- RiskInfo
- RNACompoundSet
- RNASequence
- RNASequenceCreator
- RnaSequenceView
- RNAToAminoAcidTranslator
- RonnConstraint
- RonnConstraint.Threshold
- Rotation
- RotationAxis
- RotationAxisAligner
- RotationGroup
- RotationSolver
- SangerFastqReader
- SangerFastqWriter
- ScaleableMatrixPanel
- ScaledSubstitutionMatrix
- SchemaGenerator
- SCOPAutoSuggestProvider
- ScopCategory
- ScopDatabase
- ScopDescription
- ScopDomain
- ScopFactory
- ScopInstallation
- ScopInstallationInstance
- ScopIOException
- ScopMirror
- ScopNode
- ScopSelectPanel
- Scorer
- ScoresCache
- SearchIO
- SecStrucCalc
- SecStrucElement
- SecStrucInfo
- SecStrucState
- SecStrucTools
- SecStrucType
- Segment
- SegmentComparator
- Selection
- SelectionImpl
- SelectMultiplePanel
- SelectPDBPanel
- SeqMisMatch
- SeqMisMatchImpl
- SeqRes2AtomAligner
- Sequence
- SequenceAsStringHelper
- SequenceComparator
- SequenceCreatorInterface
- SequenceDisplay
- SequenceFileProxyLoader
- SequenceFunctionOrderDetector
- SequenceFunctionRefiner
- SequenceHeaderParserInterface
- SequenceLocation
- SequenceMixin
- SequenceMixin.SequenceIterator
- SequenceMouseListener
- SequenceOptimizationHints
- SequenceOptimizationHints.SequenceCollection
- SequenceOptimizationHints.SequenceUsage
- SequencePair
- SequenceParserInterface
- SequenceProxyView
- SequenceReader
- SequenceScalePanel
- SequenceTools
- SequenceUtil
- SequenceView
- SerializableCache
- ShortSegmentRemover
- ShowPDBIDListener
- ShowStructureInJmol
- SiftsChainEntry
- SiftsChainToUniprotMapping
- SiftsEntity
- SiftsMappingProvider
- SiftsResidue
- SiftsSegment
- SiftsXMLParser
- SigEva
- SimpleAlignedSequence
- SimpleGapPenalty
- SimpleLocation
- SimplePoint
- SimpleProfile
- SimpleProfilePair
- SimpleProfileProfileAligner
- SimpleSequencePair
- SimpleSubstitutionMatrix
- SingleCompoundSequenceReader
- SingleLinkageClusterer
- SingularValueDecomposition
- Site
- Site
- SmallAnnotation
- SmallMap
- SmithWaterman
- SmithWaterman3Daligner
- SmithWaterman3DParameters
- SmithWatermanUserArgumentProcessor
- SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
- SoftHashMap
- SolexaFastqReader
- SolexaFastqWriter
- SpaceGroup
- SpaceGroupMapElements
- SpaceGroupMapRoot
- SparseSquareMatrix
- SparseVector
- SphereSampler
- SplitFasta
- SqrtColorMapper
- SSBondImpl
- StainType
- StandardAminoAcid
- StandardRescoreRefiner
- StartCodonSequence
- StartupParameters
- StaticMemberPlaceHolder
- StatusDisplay
- StdArrayIO
- StockholmFileAnnotation
- StockholmFileAnnotation.StockholmFileAnnotationReference
- StockholmFileParser
- StockholmStructure
- StockholmStructure.DatabaseReference
- Stoichiometry
- Stoichiometry.StringOverflowStrategy
- StopCodonSequence
- Strand
- StrataInfo
- StrCompAlignment
- StreamListener
- StringManipulationHelper
- StringProxySequenceReader
- StrucAligParameters
- Structure
- StructureAlignment
- StructureAlignmentDisplay
- StructureAlignmentFactory
- StructureAlignmentJmol
- StructureAlignmentOptimizer
- StructureAtom
- StructureAtomLinkage
- StructureAtomXMLConverter
- StructureException
- StructureFiletype
- StructureGroup
- StructureGroupXMLConverter
- StructureIdentifier
- StructureImpl
- StructureInterface
- StructureInterfaceCluster
- StructureInterfaceList
- StructureIO
- StructureIOFile
- StructureLoaderThread
- StructureName
- StructureName.Source
- StructurePairAligner
- StructurePairSelector
- StructureProvider
- StructureSequenceMatcher
- StructureTools
- StructureUtil
- StructureViewer
- SubstitutionMatrix
- SubstitutionMatrixHelper
- SubstitutionMatrixScorer
- SubstructureIdentifier
- Subunit
- SubunitCluster
- SubunitClusterer
- SubunitClustererMethod
- SubunitClustererParameters
- SubunitExtractor
- SuperPosition
- SuperPositionAbstract
- SuperPositionQCP
- SuperPositionQuat
- SuperPositions
- SuperPositionSVD
- SurvFitInfo
- SurvFitKM
- SurvFitKM.ConfLower
- SurvFitKM.ConfType
- SurvFitKM.Error
- SurvFitKM.Method
- SurvivalInfo
- SurvivalInfoComparator
- SurvivalInfoHelper
- SurvivalInfoIndex
- SurvivalInfoValueComparator
- SymbolTable
- SymmetryAxes
- SymmetryAxes.Axis
- SymmetryCalc
- SymmetryDisplay
- SymmetryGui
- SymmetryListener
- SymmetryPerceptionMethod
- SymmetryRefiner
- SymmetryTools
- SymmOptimizer
- SymoplibParser
- SynchronizedOutFile
- Synonym
- SystematicSolver
- SystemInfo
- TabDelimParser
- Table
- Table.CaseInsensitiveTriplet
- Table.Codon
- TaxonomyID
- Term
- Term.Impl
- TertiaryBasePairParameters
- TestDNANeedlemanWunsch
- Tetrahedron
- TextFeature
- Timer
- TranscriptionEngine
- TranscriptionEngine.Builder
- TranscriptSequence
- TransfAlgebraicAdapter
- TransformType
- TranslationException
- TreeConstructor
- TreeConstructorType
- TreeMapSpaceGroupWrapper
- TreeType
- Triple
- Triple.Impl
- TwoBitFacade
- TwoBitParser
- TwoBitSequenceReader
- TwoBitSequenceReader.TwoBitArrayWorker
- UncompressFile
- UncompressInputStream
- UniprotProxySequenceReader
- UniprotToFasta
- UnitCellBoundingBox
- UnitQuaternions
- URLConnectionTools
- URLIdentifier
- UserArgumentProcessor
- UserConfiguration
- Utils
- Variable
- Variable.Impl
- WaldTest
- WaldTestInfo
- WeakValueHashMap
- WebStartClientDemo
- WebStartMain
- WindowedSequence
- WorkSheet
- WrapLayout
- XMLHelper
- XMLWriter
- ZipChemCompProvider