All Classes
AbstractRepresentationScheme
AffinityAlignment
AffinityAlignment.AtomStep
AffinityAlignment.Builder
AffinityAlignment.InputStep
AffinityAlignment.ParameterStep
AlphaCarbonRepresentationScheme
AminoAcid
AminoAcidFamily
AminoAcids
Atom
AtomContainer
AtomName
AtomToken
BetaCarbonRepresentationScheme
BondType
CentroidRepresentationScheme
Chain
ChainContainer
ChainTerminatorToken
CifFileParser
ConsensusAlignment
ConsensusBuilder
ConsensusBuilder.AtomStep
ConsensusBuilder.Builder
ConsensusBuilder.InputStep
ConsensusBuilder.ParameterStep
ConsensusContainer
ConsensusException
ElectronConfiguration
ElectronConfiguration.AtomicOrbital
Element
ElementProvider
Exchangeable
Fit3D
Fit3DAlignment
Fit3DAlignmentBatch
Fit3DBuilder
Fit3DBuilder.AtomStep
Fit3DBuilder.BatchParameterStep
Fit3DBuilder.Builder
Fit3DBuilder.ParameterStep
Fit3DBuilder.QueryStep
Fit3DBuilder.SiteConfigurationStep
Fit3DBuilder.SiteParameterConfigurationStep
Fit3DBuilder.SiteStep
Fit3DBuilder.TargetStep
Fit3DException
Fit3DMatch
Fit3DSiteAlignment
FofanovEstimation
FragmentSubstructureSuperimposer
Gyration
HalogenBond
HeaderToken
HydrogenBond
HydrophobicInteraction
Interaction
InteractionContainer
InteractionType
Justification
LastHeavySidechainRepresentationScheme
LeafIdentifier
LeafIdentifiers
LeafSkeleton
LeafSkeleton.AssignedFamily
LeafSubstructure
LeafSubstructureContainer
LeafSubstructureFactory
Ligand
LigandFamily
LigandParserService
MatcherFamily
MetalComplex
MmtfAminoAcid
MmtfAtom
MmtfChain
MmtfLeafSubstructure
MmtfLigand
MmtfModel
MmtfNucleotide
MmtfReducer
MmtfStructure
Model
ModelToken
MolarMass
MoleculeAtom
MoleculeBond
MoleculeBondType
MoleculeGraph
MoleculeGraphs
MoleculeIsomorphism
MoleculeIsomorphismFinder
MoleculeIsomorphismFinder.AtomConditions
MoleculeIsomorphismFinder.BondConditions
MoleculePathFinder
Nucleotide
NucleotideFamily
OakAminoAcid
OakAtom
OakBond
OakChain
OakLeafSubstructure
OakLigand
OakModel
OakNucleotide
OakStructure
PDBEnzymeMapper
PDBIdentifier
PDBPfamMapper
PDBRestEndpoint
PDBSequenceCluster
PDBSequenceCluster.PDBSequenceClusterIdentity
PDBSequenceClusterMember
PDBToken
PDBUniProtMapper
PfamParser
PfamParser.Builder
PfamParser.ChainStep
PfamParser.DomainStep
PfamParser.FamilyStep
PfamParser.PfamVersion
PfamParser.VersionStep
PfamToken
PfamToken.IdentifierToken
PfamToken.PDBToken
PiCation
PiStacking
PlipContentHandler
PlipParser
PlipShellGenerator
PlipShellGenerator.InteractionShell
PsScore
RepresentationScheme
RepresentationSchemeFactory
RepresentationSchemeType
ResidueMapContentHandler
SaltBridge
SideChainCentroidRepresentationScheme
SourceLocation
StarkEstimation
StatisticalModel
StructuralEntityFilter
StructuralEntityFilter.AtomFilter
StructuralEntityFilter.AtomFilterType
StructuralEntityFilter.ChainFilter
StructuralEntityFilter.LeafFilter
StructuralEntityFilter.LeafFilterType
StructuralFamily
StructuralMotif
StructuralMotif.Type
StructuralMotifs
Structure
StructureCollector
StructureParser
StructureParser.AdditionalLocalSourceStep
StructureParser.IdentifierStep
StructureParser.LocalPDB
StructureParser.LocalSourceStep
StructureParser.MultiBranchStep
StructureParser.MultiChainStep
StructureParser.MultiParser
StructureParser.Reducer
StructureParser.SingleBranchStep
StructureParser.SingleChainStep
StructureParser.SingleParser
StructureParserException
StructureParserOptions
StructureParserOptions.Setting
StructureRepresentation
Structures
StructureSelector
StructureSelector.AminoAcidAtomStep
StructureSelector.AtomContainerAtomStep
StructureSelector.AtomStep
StructureSelector.ChainStep
StructureSelector.NucleotideAtomStep
StructureSelector.ResidueStep
StructureSelector.Selector
StructureSelector.SelectStep
StructureSelector.StructuralModelStep
StructureWriter
SubstitutionMatrix
SubstructureSuperimposer
SubstructureSuperimposition
SubstructureSuperimpositionException
TerminatorTokens
TitleToken
UniProtResidueMapParser
UniqueAtomIdentifer
ValidAlignmentGenerator
ValidCandidateGenerator
WaterBridge
XieScore