- AbstractBean
- AbstractScoresCache
- AbstractStructureAlignment
- AbstractUserArgumentProcessor
- AFP
- AFPAlignmentDisplay
- AFPCalculator
- AFPChain
- AFPChainer
- AFPChainFlipper
- AFPChainScorer
- AfpChainWriter
- AFPChainXMLConverter
- AFPChainXMLParser
- AFPOptimizer
- AFPPostProcessor
- AFPTwister
- AligMatEl
- Alignable
- AlignmentProgressListener
- AlignmentProgressListener
- AlignmentResult
- AlignmentTools
- AlignmentTools.IdentityMap
- AligNPE
- AlignUtils
- AllChemCompProvider
- AltAligComparator
- AlternativeAlignment
- AminoAcid
- AminoAcidImpl
- AngleOrderDetectorPlus
- AngleOutlier
- AsaCalculator
- AssignmentXMLSerializer
- Astral
- Astral.AstralSet
- Atom
- AtomCache
- AtomContact
- AtomContactSet
- AtomIdentifier
- AtomImpl
- AtomIterator
- AtomPositionMap
- AtomPositionMap.GroupMatcher
- AtomSite
- AtomSites
- AuditAuthor
- AugmentedResidueRange
- Author
- AxisAligner
- BasePairParameters
- BerkeleyScopInstallation
- BetaBridge
- BioAssemblyIdentifier
- BioAssemblyInfo
- BioAssemblyTools
- BioJavaStructureAlignment
- BiologicalAssemblyBuilder
- BiologicalAssemblyTransformation
- BlastClustReader
- Block
- BlockImpl
- BlockSet
- BlockSetImpl
- Bond
- BondImpl
- BondMaker
- BondOutlier
- BondType
- BoundingBox
- BravaisLattice
- BridgeType
- C2RotationSolver
- CachedRemoteScopInstallation
- CAConverter
- Calc
- CalcPoint
- CallableStructureAlignment
- CartesianProduct
- CathCategory
- CathDatabase
- CathDomain
- CathFactory
- CathFragment
- CathInstallation
- CathNode
- CathSegment
- CECalculator
- CeCalculatorEnhanced
- CeCPMain
- CeCPMain.CPRange
- CECPParameters
- CECPParameters.DuplicationHint
- CeCPUserArgumentProcessor
- Cell
- CeMain
- CeParameters
- CeParameters.ScoringStrategy
- CeSideChainMain
- CeSideChainUserArgumentProcessor
- CeSymm
- CeSymmIterative
- CESymmParameters
- CESymmParameters.OrderDetectorMethod
- CESymmParameters.RefineMethod
- CESymmParameters.SymmetryType
- CeSymmResult
- CeUserArgumentProcessor
- CeUserArgumentProcessor.CeStartupParams
- Chain
- ChainImpl
- ChainSignature
- ChargeAdder
- ChemComp
- ChemCompAtom
- ChemCompBond
- ChemCompConsumer
- ChemCompDescriptor
- ChemCompDistribution
- ChemCompGroupFactory
- ChemCompProvider
- ChemCompTools
- ChemicalComponentDictionary
- CholeskyDecomposition
- CIFLabel
- Clash
- CliTools
- ClusterAltAligs
- ClusterDomains
- CollectionTools
- ConfigStrucAligParams
- ConfigurationException
- Contact
- CoreSuperimposer
- CountProgressListener
- CrystalBuilder
- CrystalCell
- CrystalTransform
- Cut
- CutDomain
- CutSites
- CutValues
- DatabasePDBremark
- DatabasePDBrev
- DatabasePdbrevRecord
- DBRef
- DemoAsa
- DemoAtomCache
- DemoBerkeleyScop
- DemoBioAssemblies
- DemoCATH
- DemoCE
- DemoCeSymm
- DemoChangeChemCompProvider
- DemoCommandLineStartup
- DemoContacts
- DemoCrystalInterfaces
- DemoDomainsplit
- DemoFATCAT
- DemoLoadSecStruc
- DemoLoadStructure
- DemoMMCIFReader
- DemoMmcifToPdbConverter
- DemoMmtfReader
- DemoMmtfWriter
- DemoMultipleMC
- DemoQsAlign
- DemoSCOP
- DemoSecStrucCalc
- DemoSymmetry
- DistanceBox
- Domain
- DomainProvider
- DomainProviderFactory
- DownloadChemCompProvider
- DSSPParser
- EcodDatabase
- EcodDomain
- EcodFactory
- EcodInstallation
- EcodInstallation.EcodParser
- EigenvalueDecomposition
- Element
- ElementType
- Entity
- EntityFinder
- EntityInfo
- EntityPoly
- EntityPolySeq
- EntitySrcGen
- EntitySrcNat
- EntitySrcSyn
- EntityType
- Entry
- ExperimentalTechnique
- Exptl
- FarmJob
- FarmJobParameters
- FarmJobRunnable
- FastaAFPChainConverter
- FastaStructureParser
- FatCat
- FatCatAligner
- FatCatFlexible
- FatCatParameters
- FatCatRigid
- FatCatUserArgumentProcessor
- FCAlignHelper
- FileConvert
- FileParsingParameters
- FragmentJoiner
- FragmentPair
- GapArray
- GetDistanceMatrix
- GetRepresentatives
- Gotoh
- GraphComponentOrderDetector
- GraphComponentRefiner
- Grid
- GridCell
- Group
- GroupAsa
- GroupContact
- GroupContactSet
- GroupIterator
- GroupToSDF
- GroupType
- GuiWrapper
- HasResultXMLConverter
- HBond
- HelicalRepeatUnit
- Helix
- HelixAxisAligner
- HelixExtender
- HelixLayers
- HelixSolver
- HetatomImpl
- HetatomImpl.PerformanceBehavior
- IcosahedralSampler
- Icosahedron
- IdxComparator
- IgnoreField
- IndexPair
- JFatCatClient
- JobKillException
- JointFragments
- JournalArticle
- Ladder
- ListStringWrapper
- LocalPDBDirectory
- LocalPDBDirectory.FetchBehavior
- LocalPDBDirectory.ObsoleteBehavior
- LocalProteinDomainParser
- LocalScopDatabase
- LUDecomposition
- Maths
- Matrices
- Matrix
- MatrixListener
- MetalBondConsumer
- MetalBondDistance
- MetalBondParser
- MismatchedBasePairParameters
- MMcifConsumer
- MMCIFFileReader
- MMCIFFileTools
- MMcifParser
- MmtfActions
- MMTFFileReader
- MmtfStructureReader
- MmtfStructureWriter
- MmtfSummaryDataBean
- MmtfUtils
- Model
- ModelledSubgroup
- MogAngleOutlier
- MogBondOutlier
- MomentsOfInertia
- MomentsOfInertia.SymmetryClass
- MultipleAlignment
- MultipleAlignmentDisplay
- MultipleAlignmentEnsemble
- MultipleAlignmentEnsembleImpl
- MultipleAlignmentImpl
- MultipleAlignmentScorer
- MultipleAlignmentTools
- MultipleAlignmentWriter
- MultipleAlignmentXMLConverter
- MultipleAlignmentXMLParser
- MultipleMcMain
- MultipleMcOptimizer
- MultipleMcParameters
- MultipleStructureAligner
- MultipleSuperimposer
- MultiThreadedDBSearch
- Mutator
- NucleotideImpl
- ObjectFactory
- Octahedron
- OperatorResolver
- OptimalCECPMain
- OptimalCECPParameters
- OrderDetector
- OrderedPair
- Pair
- PassthroughIdentifier
- PDBBioAssemblyParser
- PDBCrystallographicInfo
- PDBDomainProvider
- PDBFileParser
- PDBFileReader
- PDBHeader
- PdbIdLists
- PdbPair
- PdbPairsMessage
- PdbPairXMLConverter
- PDBParseException
- PDBRecord
- PDBStatus
- PDBStatus.Status
- PDBTemporaryStorageUtils
- PDBTemporaryStorageUtils.LinkRecord
- PdbxAuditRevisionHistory
- PdbxChemCompDescriptor
- PdbxChemCompIdentifier
- PdbxDatabaseStatus
- PdbxEntityNonPoly
- PdbxNonPolyScheme
- PdbxPolySeqScheme
- PdbxStructAssembly
- PdbxStructAssemblyGen
- PdbxStructAssemblyGenXMLContainer
- PdbxStructAssemblyXMLContainer
- PdbxStructOperList
- PdbxStructOperListXMLContainer
- PDPDistanceMatrix
- PDPDomain
- PDPParameters
- PDPProvider
- PermutationGenerator
- PermutationGroup
- Polyhedron
- PolymerType
- PositionInQueueXMLConverter
- PowerSet
- Prism
- Program
- Programs
- ProteinComplexSignature
- QRDecomposition
- QsAlign
- QsAlignParameters
- QsAlignResult
- QsRelation
- QuatSuperpositionScorer
- QuatSymmetryDetector
- QuatSymmetryParameters
- QuatSymmetryResults
- QuatSymmetryScores
- QuatSymmetrySolver
- QuatSymmetrySubunits
- RCSBDescription
- RCSBDescriptionFactory
- RCSBLigand
- RCSBLigands
- RCSBLigandsFactory
- RCSBMacromolecule
- RCSBPolymer
- RCSBTaxonomy
- RCSBUpdates
- ReadUtils
- RectangularPrism
- ReducedChemCompProvider
- ReferenceSuperimposer
- Refine
- RefinerFailedException
- RemoteDomainProvider
- RemotePDPProvider
- RemoteScopInstallation
- RepresentativeXMLConverter
- ResidueGroup
- ResidueNumber
- ResidueRange
- ResidueRangeAndLength
- ResidueType
- ResourceManager
- Rotation
- RotationAxis
- RotationAxisAligner
- RotationGroup
- RotationSolver
- SandboxStyleStructureProvider
- ScopCategory
- ScopDatabase
- ScopDescription
- ScopDescriptions
- ScopDomain
- ScopDomains
- ScopFactory
- ScopInstallation
- ScopIOException
- ScopMirror
- ScopNode
- ScopNodes
- ScoresCache
- SecStrucCalc
- SecStrucElement
- SecStrucInfo
- SecStrucState
- SecStrucTools
- SecStrucType
- Segment
- SegmentComparator
- SeqMisMatch
- SeqMisMatchImpl
- SeqRes2AtomAligner
- SequenceFunctionOrderDetector
- SequenceFunctionRefiner
- SerializableCache
- ShortSegmentRemover
- SiftsChainEntry
- SiftsChainToUniprotMapping
- SiftsEntity
- SiftsMappingProvider
- SiftsResidue
- SiftsSegment
- SiftsXMLParser
- SigEva
- SimpleMMcifConsumer
- SimpleMMcifParser
- SingularValueDecomposition
- Site
- SmithWaterman3Daligner
- SmithWaterman3DParameters
- SmithWatermanUserArgumentProcessor
- SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
- SpaceGroup
- SpaceGroupMapElements
- SpaceGroupMapRoot
- SparseSquareMatrix
- SparseVector
- SphereSampler
- SSBondImpl
- StandardAminoAcid
- StartupParameters
- Stoichiometry
- Stoichiometry.StringOverflowStrategy
- StrCompAlignment
- StrucAligParameters
- Struct
- StructAsym
- StructConn
- StructKeywords
- StructNcsOper
- StructRef
- StructRefSeq
- StructRefSeqDif
- StructSite
- StructSiteGen
- Structure
- StructureAlignment
- StructureAlignmentFactory
- StructureAlignmentOptimizer
- StructureException
- StructureIdentifier
- StructureImpl
- StructureInterface
- StructureInterfaceCluster
- StructureInterfaceList
- StructureIO
- StructureIO.StructureFiletype
- StructureIOFile
- StructureName
- StructureName.Source
- StructurePairAligner
- StructureProvider
- StructureSequenceMatcher
- StructureTools
- SubstructureIdentifier
- Subunit
- SubunitCluster
- SubunitClusterer
- SubunitClustererMethod
- SubunitClustererParameters
- SubunitExtractor
- SuperPosition
- SuperPositionAbstract
- SuperPositionQCP
- SuperPositionQuat
- SuperPositions
- SuperPositionSVD
- SymbolTable
- SymmClash
- Symmetry
- SymmetryAxes
- SymmetryAxes.Axis
- SymmetryPerceptionMethod
- SymmetryRefiner
- SymmetryTools
- SymmOptimizer
- SymoplibParser
- SynchronizedOutFile
- SystematicSolver
- TertiaryBasePairParameters
- Tetrahedron
- TransfAlgebraicAdapter
- TransformType
- TreeMapSpaceGroupWrapper
- TreeSetStringWrapper
- UnitCellBoundingBox
- UnitQuaternions
- URLConnectionTools
- URLIdentifier
- UserArgumentProcessor
- UserConfiguration
- WwPDBValidationInformation
- XMLUtil
- ZipChemCompProvider