All Classes
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
AlignTools
AllChemCompProvider
AltAligComparator
AlternativeAlignment
AminoAcid
AminoAcidImpl
AngleOrderDetectorPlus
AngleOutlier
AsaCalculator
AssignmentXMLSerializer
Astral
Astral.AstralSet
Atom
AtomCache
AtomContact
AtomContactSet
AtomIdentifier
AtomImpl
AtomIterator
AtomPositionMap
AtomPositionMap.GroupMatcher
AtomSite
AuditAuthor
AugmentedResidueRange
Author
AxisAligner
BerkeleyScopInstallation
BetaBridge
BioAssemblyIdentifier
BioAssemblyInfo
BioAssemblyTools
BioJavaStructureAlignment
BioJavaStructureDecoder
BiologicalAssemblyBuilder
BiologicalAssemblyTransformation
BioUnitDataProvider
BioUnitDataProviderFactory
BlastClustReader
Block
BlockImpl
BlockSet
BlockSetImpl
Bond
BondImpl
BondMaker
BondOutlier
BondType
BoundingBox
BravaisLattice
BridgeType
C2RotationSolver
CachedRemoteScopInstallation
CacheFactory
CAConverter
Calc
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
ChainClusterer
ChainImpl
ChainSignature
ChargeAdder
ChemComp
ChemCompAtom
ChemCompBond
ChemCompConsumer
ChemCompDescriptor
ChemCompDistribution
ChemCompGroupFactory
ChemCompProvider
ChemCompTools
ChemicalComponentDictionary
CholeskyDecomposition
Clash
CliTools
ClusterAltAligs
ClusterDomains
ClusterMerger
ClusterProteinChains
CollectionTools
CombinationGenerator
CompoundFinder
ConfigStrucAligParams
ConfigurationException
CoreSuperimposer
CountProgressListener
CrystalBuilder
CrystalCell
CrystalTransform
Cut
CutDomain
CutSites
CutValues
DatabasePDBremark
DatabasePDBrev
DatabasePdbrevRecord
DBRef
DemoAsa
DemoAtomCache
DemoBerkeleyScop
DemoCATH
DemoCE
DemoCeSymm
DemoChangeChemCompProvider
DemoCommandLineStartup
DemoContacts
DemoCrystalInterfaces
DemoDomainsplit
DemoFATCAT
DemoLoadSecStruc
DemoLoadStructure
DemoMMCIFReader
DemoMultipleMC
DemoSCOP
DemoSecStrucCalc
DistanceBox
Domain
DomainProvider
DomainProviderFactory
DownloadChemCompProvider
DSSPParser
EcodDatabase
EcodDomain
EcodFactory
EcodInstallation
EcodInstallation.EcodParser
EigenvalueDecomposition
Element
ElementType
Entity
EntityInfo
EntityPolySeq
EntitySrcGen
EntitySrcNat
EntitySrcSyn
Entry
ExperimentalTechnique
Exptl
FarmJob
FarmJobParameters
FarmJobRunnable
FastaAFPChainConverter
FastaStructureParser
FatCat
FatCatAligner
FatCatFlexible
FatCatParameters
FatCatRigid
FatCatUserArgumentProcessor
FCAlignHelper
FileConvert
FileDownloadUtils
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
HTTPConnectionTools
IcosahedralSampler
Icosahedron
Identifier
IdxComparator
IndexPair
JFatCatClient
JobKillException
JointFragments
JournalArticle
Ladder
ListStringWrapper
LocalPDBDirectory
LocalPDBDirectory.FetchBehavior
LocalPDBDirectory.ObsoleteBehavior
LocalProteinDomainParser
LocalScopDatabase
LUDecomposition
Maths
Matrix
MatrixListener
MmCifBiolAssemblyProvider
MMcifConsumer
MMCIFFileReader
MMCIFFileTools
MMcifParser
MmCifPDBBiolAssemblyProvider
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
PairwiseAlignment
ParseUsingBioJava
PassthroughIdentifier
PDBBioAssemblyParser
PDBBioUnitDataProvider
PDBCrystallographicInfo
PDBDomainProvider
PDBFileParser
PDBFileReader
PDBHeader
PdbIdLists
PdbPair
PdbPairsMessage
PdbPairXMLConverter
PDBParseException
PDBRecord
PDBStatus
PDBStatus.Status
PDBTemporaryStorageUtils
PDBTemporaryStorageUtils.LinkRecord
PdbxChemCompDescriptor
PdbxChemCompIdentifier
PdbxEntityNonPoly
PdbxNonPolyScheme
PdbxPolySeqScheme
PdbxStructAssembly
PdbxStructAssemblyGen
PdbxStructAssemblyGenXMLContainer
PdbxStructAssemblyXMLContainer
PdbxStructOperList
PdbxStructOperListXMLContainer
PDPDistanceMatrix
PDPDomain
PDPParameters
PDPProvider
PermutationGenerator
PermutationGroup
Polyhedron
PolymerType
PositionInQueueXMLConverter
Prism
Program
Programs
ProteinChainExtractor
ProteinComplexSignature
ProteinSequenceClusterer
QRDecomposition
QuatSuperpositionScorer
QuatSymmetryDetector
QuatSymmetryParameters
QuatSymmetryResults
QuatSymmetryScores
QuatSymmetrySolver
RawBioUnitDataProvider
RCSBDescription
RCSBDescriptionFactory
RCSBLigand
RCSBLigands
RCSBLigandsFactory
RCSBMacromolecule
RCSBPolymer
RCSBTaxonomy
RCSBUpdates
ReadUtils
RectangularPrism
ReducedChemCompProvider
ReferenceSuperimposer
Refine
RefinerFailedException
RemoteBioUnitDataProvider
RemoteDomainProvider
RemotePDPProvider
RemoteRawBioUnitDataProvider
RemoteScopInstallation
RepresentativeXMLConverter
ResidueGroup
ResidueNumber
ResidueRange
ResidueRangeAndLength
ResidueType
ResourceManager
Rotation
RotationAxis
RotationAxisAligner
RotationGroup
RotationSolver
SandboxStyleStructureProvider
ScanSymmetry
ScopCategory
ScopDatabase
ScopDescription
ScopDescriptions
ScopDomain
ScopDomains
ScopFactory
ScopInstallation
ScopIOException
ScopMirror
ScopNode
ScopNodes
ScoresCache
SecStrucCalc
SecStrucElement
SecStrucInfo
SecStrucState
SecStrucTools
SecStrucType
Segment
SegmentComparator
SeqMisMatch
SeqMisMatchImpl
SeqRes2AtomAligner
SequenceAlignmentCluster
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
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
SubunitGraph
Subunits
SuperPosition
SuperPositionQCP
SVDSuperimposer
SymbolTable
SymmClash
Symmetry
SymmetryAxes
SymmetryRefiner
SymmetryTools
SymmOptimizer
SymoplibParser
SynchronizedOutFile
SystematicSolver
Tetrahedron
TransfAlgebraicAdapter
TransformType
TreeMapSpaceGroupWrapper
TreeSetStringWrapper
UniqueSequenceList
UnitCellBoundingBox
URLIdentifier
UserArgumentProcessor
UserConfiguration
WwPDBValidationInformation
XMLUtil
ZipChemCompProvider