- AbstractCifFileSupplier
- AbstractCifFileSupplier.WrappedAtom
- AbstractScoresCache
- AbstractStructureAlignment
- AbstractUserArgumentProcessor
- AFP
- AFPAlignmentDisplay
- AFPCalculator
- AFPChain
- AFPChainer
- AFPChainFlipper
- AFPChainScorer
- AfpChainWriter
- AFPChainXMLConverter
- AFPChainXMLParser
- AFPOptimizer
- AFPPostProcessor
- AFPTwister
- AligMatEl
- Alignable
- AlignmentProgressListener
- AlignmentResult
- AlignmentTools
- AlignmentTools.IdentityMap
- AligNPE
- AlignUtils
- AllChemCompProvider
- AltAligComparator
- AlternativeAlignment
- AminoAcid
- AminoAcidImpl
- AngleOrderDetectorPlus
- AsaCalculator
- Astral
- Astral.AstralSet
- Atom
- AtomCache
- AtomContact
- AtomContactSet
- AtomIdentifier
- AtomImpl
- AtomIterator
- AtomPositionMap
- AtomPositionMap.GroupMatcher
- AugmentedResidueRange
- Author
- AxisAligner
- BasePairParameters
- BcifFileReader
- BerkeleyScopInstallation
- BetaBridge
- BioAssemblyIdentifier
- BioAssemblyInfo
- BioAssemblyTools
- BioJavaStructureAlignment
- BiologicalAssemblyBuilder
- BiologicalAssemblyTransformation
- BlastClustReader
- Block
- BlockImpl
- BlockSet
- BlockSetImpl
- Bond
- BondImpl
- BondMaker
- BondType
- BoundingBox
- BravaisLattice
- BridgeType
- C2RotationSolver
- CAConverter
- Calc
- CalcPoint
- CallableStructureAlignment
- CartesianProduct
- CathCategory
- CathDatabase
- CathDomain
- CathFactory
- CathFragment
- CathInstallation
- CathNode
- CathSegment
- CECalculator
- CeCalculatorEnhanced
- CeCPMain
- CeCPMain.CPRange
- CECPParameters
- CECPParameters.DuplicationHint
- CeCPUserArgumentProcessor
- 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
- ChemCompConsumerImpl
- ChemCompConverter
- ChemCompDescriptor
- ChemCompDistribution
- ChemCompGroupFactory
- ChemCompProvider
- ChemCompTools
- ChemicalComponentDictionary
- CholeskyDecomposition
- CifBean
- CifChainSupplierImpl
- CifFileConsumer
- CifFileReader
- CifFileSupplier
- CifStructureConsumer
- CifStructureConsumerImpl
- CifStructureConverter
- CifStructureSupplierImpl
- CliTools
- ClusterAltAligs
- ClusterDomains
- CollectionTools
- ConfigStrucAligParams
- ConfigurationException
- Contact
- CoreSuperimposer
- CrystalBuilder
- CrystalCell
- CrystalTransform
- Cut
- CutDomain
- CutSites
- CutValues
- 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
- DownloadChemCompProvider
- DSSPParser
- EcodDatabase
- EcodDomain
- EcodFactory
- EcodInstallation
- EcodInstallation.EcodParser
- EigenvalueDecomposition
- Element
- ElementType
- EntityFinder
- EntityInfo
- EntityType
- ExperimentalTechnique
- FastaAFPChainConverter
- FastaStructureParser
- FatCat
- FatCatAligner
- FatCatFlexible
- FatCatParameters
- FatCatRigid
- FatCatUserArgumentProcessor
- FCAlignHelper
- FileConvert
- FileParsingParameters
- FragmentJoiner
- FragmentPair
- GapArray
- GetDistanceMatrix
- Gotoh
- GraphComponentOrderDetector
- GraphComponentRefiner
- Grid
- GridCell
- Group
- GroupAsa
- GroupContact
- GroupContactSet
- GroupIterator
- GroupToSDF
- GroupType
- GuiWrapper
- HBond
- HelicalRepeatUnit
- Helix
- HelixAxisAligner
- HelixExtender
- HelixLayers
- HelixSolver
- HetatomImpl
- HetatomImpl.PerformanceBehavior
- IcosahedralSampler
- Icosahedron
- IdxComparator
- IndexPair
- InterfaceFinder
- JointFragments
- JournalArticle
- Ladder
- LocalPDBDirectory
- LocalPDBDirectory.FetchBehavior
- LocalPDBDirectory.ObsoleteBehavior
- LocalProteinDomainParser
- LocalScopDatabase
- LUDecomposition
- Maths
- Matrices
- Matrix
- MatrixListener
- MetalBondConsumer
- MetalBondConsumerImpl
- MetalBondConverter
- MetalBondDistance
- MismatchedBasePairParameters
- MmtfActions
- MMTFFileReader
- MmtfStructureReader
- MmtfStructureWriter
- MmtfSummaryDataBean
- MmtfUtils
- Model
- MomentsOfInertia
- MomentsOfInertia.SymmetryClass
- MultipleAlignment
- MultipleAlignmentDisplay
- MultipleAlignmentEnsemble
- MultipleAlignmentEnsembleImpl
- MultipleAlignmentImpl
- MultipleAlignmentScorer
- MultipleAlignmentTools
- MultipleAlignmentWriter
- MultipleAlignmentXMLConverter
- MultipleAlignmentXMLParser
- MultipleMcMain
- MultipleMcOptimizer
- MultipleMcParameters
- MultipleStructureAligner
- MultipleSuperimposer
- Mutator
- NucleotideImpl
- Octahedron
- OperatorResolver
- OptimalCECPMain
- OptimalCECPParameters
- OrderDetector
- OrderedPair
- Pair
- PassthroughIdentifier
- PDBBioAssemblyParser
- PDBCrystallographicInfo
- PDBFileParser
- PDBFileReader
- PDBHeader
- PdbId
- PdbPair
- PdbPairsMessage
- PdbPairXMLConverter
- PDBParseException
- PDBRecord
- PDBStatus
- PDBStatus.Status
- PDBTemporaryStorageUtils
- PDBTemporaryStorageUtils.LinkRecord
- PDPDistanceMatrix
- PDPParameters
- PermutationGenerator
- PermutationGroup
- Polyhedron
- PolymerType
- PowerSet
- Prism
- ProteinComplexSignature
- QRDecomposition
- QsAlign
- QsAlignParameters
- QsAlignResult
- QsRelation
- QuatSuperpositionScorer
- QuatSymmetryDetector
- QuatSymmetryParameters
- QuatSymmetryResults
- QuatSymmetryScores
- QuatSymmetrySolver
- QuatSymmetrySubunits
- RectangularPrism
- ReducedChemCompProvider
- ReferenceSuperimposer
- RefinerFailedException
- ResidueGroup
- ResidueNumber
- ResidueRange
- ResidueRangeAndLength
- ResidueType
- ResourceManager
- Rotation
- RotationAxis
- RotationAxisAligner
- RotationGroup
- RotationSolver
- ScopCategory
- ScopDatabase
- ScopDescription
- ScopDomain
- ScopFactory
- ScopInstallation
- ScopIOException
- ScopMirror
- ScopNode
- ScoresCache
- SecStrucCalc
- SecStrucElement
- SecStrucInfo
- SecStrucState
- SecStrucTools
- SecStrucType
- Segment
- SegmentComparator
- SeqMisMatch
- SeqMisMatchImpl
- SeqRes2AtomAligner
- SequenceFunctionOrderDetector
- SequenceFunctionRefiner
- SerializableCache
- ShortSegmentRemover
- SiftsChainEntry
- SiftsChainToUniprotMapping
- SiftsEntity
- SiftsMappingProvider
- SiftsResidue
- SiftsSegment
- SiftsXMLParser
- SigEva
- SingularValueDecomposition
- Site
- SmithWaterman3Daligner
- SmithWaterman3DParameters
- SmithWatermanUserArgumentProcessor
- SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
- SpaceGroup
- SpaceGroupMapElements
- SpaceGroupMapRoot
- SparseSquareMatrix
- SparseVector
- SphereSampler
- SSBondImpl
- StandardAminoAcid
- StartupParameters
- Stoichiometry
- Stoichiometry.StringOverflowStrategy
- StrCompAlignment
- StrucAligParameters
- Structure
- StructureAlignment
- StructureAlignmentFactory
- StructureAlignmentOptimizer
- StructureException
- StructureFiletype
- StructureIdentifier
- StructureImpl
- StructureInterface
- StructureInterfaceCluster
- StructureInterfaceList
- StructureIO
- StructureIOFile
- StructureName
- StructureName.Source
- StructurePairAligner
- StructureProvider
- StructureSequenceMatcher
- StructureTools
- SubstructureIdentifier
- Subunit
- SubunitCluster
- SubunitClusterer
- SubunitClustererMethod
- SubunitClustererParameters
- SubunitExtractor
- SuperPosition
- SuperPositionAbstract
- SuperPositionQCP
- SuperPositionQuat
- SuperPositions
- SuperPositionSVD
- SymbolTable
- SymmetryAxes
- SymmetryAxes.Axis
- SymmetryPerceptionMethod
- SymmetryRefiner
- SymmetryTools
- SymmOptimizer
- SymoplibParser
- SynchronizedOutFile
- SystematicSolver
- TertiaryBasePairParameters
- Tetrahedron
- TransfAlgebraicAdapter
- TransformType
- TreeMapSpaceGroupWrapper
- UnitCellBoundingBox
- UnitQuaternions
- URLConnectionTools
- URLIdentifier
- UserArgumentProcessor
- UserConfiguration
- ZipChemCompProvider