All Classes
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
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
RepresentativeXMLConverter
ResidueGroup
ResidueNumber
ResidueRange
ResidueRangeAndLength
ResidueType
ResourceManager
Rotation
RotationAxis
RotationAxisAligner
RotationGroup
RotationSolver
SandboxStyleStructureProvider
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