Hierarchy For All Packages

Package Hierarchies:

• demo,
• org.biojava.nbio.structure,
• org.biojava.nbio.structure.align,
• org.biojava.nbio.structure.align.ce,
• org.biojava.nbio.structure.align.client,
• org.biojava.nbio.structure.align.events,
• org.biojava.nbio.structure.align.fatcat,
• org.biojava.nbio.structure.align.fatcat.calc,
• org.biojava.nbio.structure.align.helper,
• org.biojava.nbio.structure.align.model,
• org.biojava.nbio.structure.align.multiple,
• org.biojava.nbio.structure.align.multiple.mc,
• org.biojava.nbio.structure.align.multiple.util,
• org.biojava.nbio.structure.align.pairwise,
• org.biojava.nbio.structure.align.seq,
• org.biojava.nbio.structure.align.util,
• org.biojava.nbio.structure.align.xml,
• org.biojava.nbio.structure.asa,
• org.biojava.nbio.structure.cath,
• org.biojava.nbio.structure.contact,
• org.biojava.nbio.structure.domain,
• org.biojava.nbio.structure.domain.pdp,
• org.biojava.nbio.structure.ecod,
• org.biojava.nbio.structure.io,
• org.biojava.nbio.structure.io.mmcif,
• org.biojava.nbio.structure.io.mmcif.chem,
• org.biojava.nbio.structure.io.mmcif.model,
• org.biojava.nbio.structure.io.sifts,
• org.biojava.nbio.structure.io.util,
• org.biojava.nbio.structure.jama,
• org.biojava.nbio.structure.math,
• org.biojava.nbio.structure.quaternary,
• org.biojava.nbio.structure.quaternary.io,
• org.biojava.nbio.structure.rcsb,
• org.biojava.nbio.structure.scop,
• org.biojava.nbio.structure.scop.server,
• org.biojava.nbio.structure.secstruc,
• org.biojava.nbio.structure.symmetry.analysis,
• org.biojava.nbio.structure.symmetry.core,
• org.biojava.nbio.structure.symmetry.geometry,
• org.biojava.nbio.structure.symmetry.internal,
• org.biojava.nbio.structure.symmetry.misc,
• org.biojava.nbio.structure.symmetry.utils,
• org.biojava.nbio.structure.validation,
• org.biojava.nbio.structure.xtal,
• org.biojava.nbio.structure.xtal.io

Class Hierarchy

• java.lang.Object
  • org.biojava.nbio.structure.io.mmcif.model.AbstractBean
    • org.biojava.nbio.structure.io.mmcif.model.AtomSite
    • org.biojava.nbio.structure.io.mmcif.model.AtomSites
    • org.biojava.nbio.structure.io.mmcif.model.Cell
    • org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
    • org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
    • org.biojava.nbio.structure.io.mmcif.model.Exptl
    • org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
    • org.biojava.nbio.structure.io.mmcif.model.StructAsym
    • org.biojava.nbio.structure.io.mmcif.model.StructConn
    • org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
    • org.biojava.nbio.structure.io.mmcif.model.StructRef
    • org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
    • org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
    • org.biojava.nbio.structure.io.mmcif.model.Symmetry
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap<K>
  • org.biojava.nbio.structure.align.multiple.AbstractScoresCache (implements org.biojava.nbio.structure.align.multiple.ScoresCache)
    • org.biojava.nbio.structure.align.multiple.BlockImpl (implements org.biojava.nbio.structure.align.multiple.Block, java.lang.Cloneable, java.io.Serializable)
    • org.biojava.nbio.structure.align.multiple.BlockSetImpl (implements org.biojava.nbio.structure.align.multiple.BlockSet, java.lang.Cloneable, java.io.Serializable)
    • org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble, java.io.Serializable)
    • org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.MultipleAlignment, java.io.Serializable)
  • org.biojava.nbio.structure.align.AbstractStructureAlignment (implements org.biojava.nbio.structure.align.StructureAlignment)
    • org.biojava.nbio.structure.align.ce.CeMain (implements org.biojava.nbio.structure.align.StructureAlignment)
      • org.biojava.nbio.structure.align.ce.CeCPMain
      • org.biojava.nbio.structure.align.ce.CeSideChainMain (implements org.biojava.nbio.structure.align.StructureAlignment)
      • org.biojava.nbio.structure.align.ce.OptimalCECPMain
    • org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner (implements org.biojava.nbio.structure.align.StructureAlignment)
  • org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor (implements org.biojava.nbio.structure.align.ce.UserArgumentProcessor)
    • org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
      • org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
      • org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
    • org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
    • org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
  • org.biojava.nbio.structure.align.model.AFP (implements java.io.Serializable)
  • org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
  • org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
  • org.biojava.nbio.structure.align.model.AFPChain (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
  • org.biojava.nbio.structure.align.xml.AFPChainFlipper
  • org.biojava.nbio.structure.align.util.AFPChainScorer
  • org.biojava.nbio.structure.align.model.AfpChainWriter
  • org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
  • org.biojava.nbio.structure.align.xml.AFPChainXMLParser
  • org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
  • org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
  • org.biojava.nbio.structure.align.AFPTwister
  • org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
  • org.biojava.nbio.structure.align.pairwise.AlignmentResult (implements java.io.Serializable)
  • org.biojava.nbio.structure.align.util.AlignmentTools
  • org.biojava.nbio.structure.align.pairwise.AligNPE
  • org.biojava.nbio.structure.align.helper.AlignTools
  • org.biojava.nbio.structure.io.mmcif.AllChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider, java.lang.Runnable)
  • org.biojava.nbio.structure.align.pairwise.AltAligComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.align.pairwise.AlternativeAlignment (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
  • org.biojava.nbio.structure.validation.AngleOutlier
  • org.biojava.nbio.structure.asa.AsaCalculator
  • org.biojava.nbio.structure.domain.AssignmentXMLSerializer
  • org.biojava.nbio.structure.scop.Astral
  • org.biojava.nbio.structure.align.util.AtomCache
  • org.biojava.nbio.structure.contact.AtomContact (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.AtomContactSet (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.contact.AtomIdentifier (implements java.io.Serializable)
  • org.biojava.nbio.structure.AtomImpl (implements org.biojava.nbio.structure.Atom, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.AtomIterator (implements java.util.Iterator<E>)
  • org.biojava.nbio.structure.AtomPositionMap
  • org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
  • org.biojava.nbio.structure.Author (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.AxisAligner
    • org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
    • org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
  • org.biojava.nbio.structure.secstruc.BetaBridge
  • org.biojava.nbio.structure.BioAssemblyIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.quaternary.BioAssemblyInfo (implements java.io.Serializable)
  • org.biojava.nbio.structure.quaternary.BioAssemblyTools
  • org.biojava.nbio.structure.align.BioJavaStructureAlignment (implements org.biojava.nbio.structure.align.StructureAlignment)
  • org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
  • org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
  • org.biojava.nbio.structure.symmetry.utils.BlastClustReader (implements java.io.Serializable)
  • org.biojava.nbio.structure.BondImpl (implements org.biojava.nbio.structure.Bond, java.io.Serializable)
  • org.biojava.nbio.structure.io.BondMaker
  • org.biojava.nbio.structure.validation.BondOutlier
  • org.biojava.nbio.structure.contact.BoundingBox (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.C2RotationSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
  • org.biojava.nbio.structure.align.util.CacheFactory
  • org.biojava.nbio.structure.io.CAConverter
  • org.biojava.nbio.structure.Calc
  • org.biojava.nbio.structure.align.CallableStructureAlignment (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.structure.quaternary.CartesianProduct<T>
  • org.biojava.nbio.structure.cath.CathDomain (implements java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.cath.CathFactory
  • org.biojava.nbio.structure.cath.CathFragment (implements java.io.Serializable)
  • org.biojava.nbio.structure.cath.CathInstallation (implements org.biojava.nbio.structure.cath.CathDatabase)
  • org.biojava.nbio.structure.cath.CathNode (implements java.io.Serializable)
  • org.biojava.nbio.structure.cath.CathSegment (implements java.io.Serializable)
  • org.biojava.nbio.structure.align.ce.CECalculator
  • org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
  • org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
  • org.biojava.nbio.structure.align.ce.CeParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
    • org.biojava.nbio.structure.align.ce.CECPParameters
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters
    • org.biojava.nbio.structure.align.ce.OptimalCECPParameters
  • org.biojava.nbio.structure.symmetry.internal.CeSymm
  • org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
  • org.biojava.nbio.structure.symmetry.internal.CeSymmResult
  • org.biojava.nbio.structure.symmetry.core.ChainClusterer
  • org.biojava.nbio.structure.ChainImpl (implements org.biojava.nbio.structure.Chain, java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.misc.ChainSignature (implements java.lang.Comparable<T>)
  • org.biojava.nbio.structure.io.ChargeAdder
  • org.biojava.nbio.structure.io.mmcif.model.ChemComp (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.ChemCompBond (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.ChemCompConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
  • org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor (implements java.io.Serializable)
  • demo.ChemCompDistribution
  • org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
  • org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
  • org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
  • org.biojava.nbio.structure.jama.CholeskyDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.structure.validation.Clash
  • org.biojava.nbio.structure.align.util.CliTools
  • org.biojava.nbio.structure.align.ClusterAltAligs
  • org.biojava.nbio.structure.domain.pdp.ClusterDomains
  • org.biojava.nbio.structure.symmetry.core.ClusterMerger
  • org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
  • org.biojava.nbio.structure.align.util.CollectionTools
  • org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
  • org.biojava.nbio.structure.Compound (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.CompoundFinder
  • org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer (implements org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer)
  • org.biojava.nbio.structure.align.client.CountProgressListener (implements org.biojava.nbio.structure.align.events.AlignmentProgressListener)
  • org.biojava.nbio.structure.xtal.CrystalBuilder
  • org.biojava.nbio.structure.xtal.CrystalCell (implements java.io.Serializable)
  • org.biojava.nbio.structure.xtal.CrystalTransform (implements java.io.Serializable)
  • org.biojava.nbio.structure.domain.pdp.Cut
  • org.biojava.nbio.structure.domain.pdp.CutDomain
  • org.biojava.nbio.structure.domain.pdp.CutSites
  • org.biojava.nbio.structure.domain.pdp.CutValues
  • org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
  • org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord (implements java.io.Serializable)
  • org.biojava.nbio.structure.DBRef (implements org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • demo.DemoAsa
  • demo.DemoAtomCache
  • demo.DemoBerkeleyScop
  • demo.DemoCATH
  • demo.DemoCE
  • demo.DemoCeSymm
  • demo.DemoChangeChemCompProvider
  • demo.DemoCommandLineStartup
  • demo.DemoContacts
  • demo.DemoCrystalInterfaces
  • demo.DemoDomainsplit
  • demo.DemoFATCAT
  • demo.DemoLoadSecStruc
  • demo.DemoLoadStructure
  • demo.DemoMMCIFReader
  • demo.DemoMultipleMC
  • demo.DemoSCOP
  • demo.DemoSecStrucCalc
  • org.biojava.nbio.structure.symmetry.geometry.DistanceBox<T>
  • org.biojava.nbio.structure.domain.pdp.Domain (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.domain.DomainProviderFactory
  • org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)
  • org.biojava.nbio.structure.secstruc.DSSPParser
  • org.biojava.nbio.structure.ecod.EcodDomain (implements java.lang.Cloneable, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.ecod.EcodFactory
  • org.biojava.nbio.structure.ecod.EcodInstallation (implements org.biojava.nbio.structure.ecod.EcodDatabase)
  • org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
  • org.biojava.nbio.structure.jama.EigenvalueDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.Entity
  • org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
  • org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
  • org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
  • org.biojava.nbio.structure.validation.Entry
  • org.biojava.nbio.structure.align.FarmJob (implements java.lang.Runnable)
  • org.biojava.nbio.structure.align.client.FarmJobParameters
  • org.biojava.nbio.structure.align.client.FarmJobRunnable (implements java.lang.Runnable)
  • org.biojava.nbio.structure.io.FastaAFPChainConverter
  • org.biojava.nbio.structure.io.FastaStructureParser
  • org.biojava.nbio.structure.align.fatcat.FatCat
    • org.biojava.nbio.structure.align.fatcat.FatCatFlexible (implements org.biojava.nbio.structure.align.StructureAlignment)
    • org.biojava.nbio.structure.align.fatcat.FatCatRigid (implements org.biojava.nbio.structure.align.StructureAlignment)
  • org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
  • org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
  • org.biojava.nbio.structure.io.FileConvert
  • org.biojava.nbio.structure.io.util.FileDownloadUtils
  • org.biojava.nbio.structure.io.FileParsingParameters (implements java.io.Serializable)
  • org.biojava.nbio.structure.align.pairwise.FragmentJoiner
  • org.biojava.nbio.structure.align.pairwise.FragmentPair
  • org.biojava.nbio.structure.align.helper.GapArray
  • org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
  • org.biojava.nbio.structure.rcsb.GetRepresentatives
  • org.biojava.nbio.structure.align.pairwise.Gotoh
  • org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
  • org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner (implements org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner)
  • org.biojava.nbio.structure.contact.Grid
  • org.biojava.nbio.structure.contact.GridCell
  • org.biojava.nbio.structure.asa.GroupAsa (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.GroupContact (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.GroupContactSet (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.GroupIterator (implements java.util.Iterator<E>)
  • org.biojava.nbio.structure.io.GroupToSDF
  • org.biojava.nbio.structure.align.ce.GuiWrapper
  • org.biojava.nbio.structure.align.xml.HasResultXMLConverter
  • org.biojava.nbio.structure.secstruc.HBond
  • org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
  • org.biojava.nbio.structure.symmetry.core.Helix
  • org.biojava.nbio.structure.symmetry.core.HelixExtender
  • org.biojava.nbio.structure.symmetry.core.HelixLayers
  • org.biojava.nbio.structure.symmetry.core.HelixSolver
  • org.biojava.nbio.structure.HetatomImpl (implements org.biojava.nbio.structure.Group, java.io.Serializable)
    • org.biojava.nbio.structure.AminoAcidImpl (implements org.biojava.nbio.structure.AminoAcid, java.io.Serializable)
    • org.biojava.nbio.structure.NucleotideImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.Group, java.io.Serializable)
  • org.biojava.nbio.structure.align.util.HTTPConnectionTools
  • org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
  • org.biojava.nbio.structure.symmetry.geometry.Icosahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.structure.Identifier
  • org.biojava.nbio.structure.align.helper.IdxComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.align.helper.IndexPair (implements java.io.Serializable)
    • org.biojava.nbio.structure.align.helper.AligMatEl
  • org.biojava.nbio.structure.align.client.JFatCatClient
  • org.biojava.nbio.structure.align.helper.JointFragments
  • org.biojava.nbio.structure.JournalArticle (implements java.io.Serializable)
  • org.biojava.nbio.structure.secstruc.Ladder
  • org.biojava.nbio.structure.scop.server.ListStringWrapper (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.LocalPDBDirectory (implements org.biojava.nbio.structure.io.StructureIOFile)
    • org.biojava.nbio.structure.io.MMCIFFileReader
    • org.biojava.nbio.structure.io.PDBFileReader
  • org.biojava.nbio.structure.domain.LocalProteinDomainParser
  • org.biojava.nbio.structure.jama.LUDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.structure.jama.Maths
  • org.biojava.nbio.structure.jama.Matrix (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.MetalBondConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
  • org.biojava.nbio.structure.io.mmcif.chem.MetalBondDistance
  • org.biojava.nbio.structure.io.mmcif.MetalBondParser
  • org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
  • org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
  • org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider (implements org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider)
  • org.biojava.nbio.structure.validation.ModelledSubgroup
  • org.biojava.nbio.structure.validation.MogAngleOutlier
  • org.biojava.nbio.structure.validation.MogBondOutlier
  • org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
  • org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
  • org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
  • org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain (implements org.biojava.nbio.structure.align.MultipleStructureAligner)
  • org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava.nbio.structure.align.MultiThreadedDBSearch
  • org.biojava.nbio.structure.Mutator
  • org.biojava.nbio.structure.validation.ObjectFactory
  • org.biojava.nbio.structure.symmetry.geometry.Octahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.structure.quaternary.OperatorResolver
  • org.biojava.nbio.structure.quaternary.OrderedPair<T>
  • org.biojava.nbio.structure.contact.Pair<T> (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
  • org.biojava.nbio.structure.PassthroughIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.io.PDBBioAssemblyParser
  • org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
  • org.biojava.nbio.structure.PDBCrystallographicInfo (implements java.io.Serializable)
  • org.biojava.nbio.structure.domain.PDBDomainProvider (implements org.biojava.nbio.structure.domain.DomainProvider)
  • org.biojava.nbio.structure.io.PDBFileParser
  • org.biojava.nbio.structure.PDBHeader (implements org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.rcsb.PdbIdLists
  • org.biojava.nbio.structure.align.client.PdbPair (implements java.lang.Comparable<T>)
  • org.biojava.nbio.structure.align.xml.PdbPairsMessage
  • org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
  • org.biojava.nbio.structure.PDBStatus
  • org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils
  • org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
  • org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
  • org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
  • org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
  • org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
  • org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
  • org.biojava.nbio.structure.domain.PDPDomain (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.domain.pdp.PDPParameters
  • org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
  • org.biojava.nbio.structure.symmetry.core.PermutationGroup (implements java.lang.Iterable<T>)
  • org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
  • org.biojava.nbio.structure.symmetry.geometry.Prism (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.structure.validation.Program
  • org.biojava.nbio.structure.validation.Programs
  • org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
  • org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
  • org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
  • org.biojava.nbio.structure.jama.QRDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
  • org.biojava.nbio.structure.rcsb.RCSBDescription
  • org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
  • org.biojava.nbio.structure.rcsb.RCSBLigand
  • org.biojava.nbio.structure.rcsb.RCSBLigands
  • org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
  • org.biojava.nbio.structure.rcsb.RCSBMacromolecule
  • org.biojava.nbio.structure.rcsb.RCSBPolymer
  • org.biojava.nbio.structure.rcsb.RCSBTaxonomy
  • org.biojava.nbio.structure.rcsb.RCSBUpdates
  • org.biojava.nbio.structure.rcsb.ReadUtils
  • org.biojava.nbio.structure.symmetry.geometry.RectangularPrism (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)
  • org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer (implements org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer)
  • org.biojava.nbio.structure.io.mmcif.model.Refine
  • org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
  • org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider)
  • org.biojava.nbio.structure.scop.RemoteScopInstallation (implements org.biojava.nbio.structure.scop.ScopDatabase)
  • org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter
  • org.biojava.nbio.structure.symmetry.internal.ResidueGroup
  • org.biojava.nbio.structure.ResidueNumber (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.ResidueRange
    • org.biojava.nbio.structure.ResidueRangeAndLength
      • org.biojava.nbio.structure.AugmentedResidueRange
  • org.biojava.nbio.structure.align.util.ResourceManager
  • org.biojava.nbio.structure.symmetry.core.Rotation
  • org.biojava.nbio.structure.align.util.RotationAxis
  • org.biojava.nbio.structure.symmetry.core.RotationGroup (implements java.lang.Iterable<T>)
  • org.biojava.nbio.structure.symmetry.core.RotationSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
  • org.biojava.nbio.structure.io.SandboxStyleStructureProvider (implements org.biojava.nbio.structure.io.StructureProvider)
  • org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry (implements java.lang.Runnable)
  • org.biojava.nbio.structure.scop.ScopDescription (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.structure.scop.server.ScopDescriptions (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.ScopDomain (implements java.lang.Cloneable, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.scop.server.ScopDomains (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.ScopFactory
  • org.biojava.nbio.structure.scop.ScopInstallation (implements org.biojava.nbio.structure.scop.LocalScopDatabase)
    • org.biojava.nbio.structure.scop.BerkeleyScopInstallation
  • org.biojava.nbio.structure.scop.ScopMirror
  • org.biojava.nbio.structure.scop.ScopNode (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.server.ScopNodes (implements java.io.Serializable)
  • org.biojava.nbio.structure.secstruc.SecStrucCalc
  • org.biojava.nbio.structure.secstruc.SecStrucElement
  • org.biojava.nbio.structure.secstruc.SecStrucInfo
    • org.biojava.nbio.structure.secstruc.SecStrucState
  • org.biojava.nbio.structure.secstruc.SecStrucTools
  • org.biojava.nbio.structure.domain.pdp.Segment (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.domain.pdp.SegmentComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.SeqMisMatchImpl (implements org.biojava.nbio.structure.SeqMisMatch, java.io.Serializable)
  • org.biojava.nbio.structure.io.SeqRes2AtomAligner
  • org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster (implements java.lang.Cloneable)
  • org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
  • org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner (implements org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner)
  • org.biojava.nbio.structure.domain.SerializableCache<K,V>
    • org.biojava.nbio.structure.scop.CachedRemoteScopInstallation (implements org.biojava.nbio.structure.scop.ScopDatabase)
    • org.biojava.nbio.structure.domain.RemoteDomainProvider (implements org.biojava.nbio.structure.domain.DomainProvider)
    • org.biojava.nbio.structure.domain.RemotePDPProvider (implements org.biojava.nbio.structure.domain.PDPProvider)
  • org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
  • org.biojava.nbio.structure.io.sifts.SiftsChainEntry
  • org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
  • org.biojava.nbio.structure.io.sifts.SiftsEntity (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
  • org.biojava.nbio.structure.io.sifts.SiftsResidue (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.sifts.SiftsSegment (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.sifts.SiftsXMLParser
  • org.biojava.nbio.structure.align.fatcat.calc.SigEva
  • org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
  • org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser (implements org.biojava.nbio.structure.io.mmcif.MMcifParser)
  • org.biojava.nbio.structure.jama.SingularValueDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.structure.Site (implements java.lang.Comparable<T>, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava.nbio.structure.xtal.SpaceGroup (implements java.io.Serializable)
  • org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
  • org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
  • org.biojava.nbio.structure.math.SparseSquareMatrix (implements java.io.Serializable)
  • org.biojava.nbio.structure.math.SparseVector (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.geometry.SphereSampler
  • org.biojava.nbio.structure.io.SSBondImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.StandardAminoAcid
  • org.biojava.nbio.structure.align.ce.StartupParameters
    • org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
      • org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
    • org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
    • org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
  • org.biojava.nbio.structure.align.pairwise.StrCompAlignment (implements org.biojava.nbio.structure.align.pairwise.Alignable)
  • org.biojava.nbio.structure.align.StrucAligParameters
  • org.biojava.nbio.structure.io.mmcif.model.Struct
  • org.biojava.nbio.structure.io.mmcif.model.StructKeywords
  • org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
  • org.biojava.nbio.structure.io.mmcif.model.StructSite
  • org.biojava.nbio.structure.align.StructureAlignmentFactory
  • org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
  • org.biojava.nbio.structure.StructureImpl (implements java.io.Serializable, org.biojava.nbio.structure.Structure)
  • org.biojava.nbio.structure.contact.StructureInterface (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.contact.StructureInterfaceCluster (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.StructureInterfaceList (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.StructureIO
  • org.biojava.nbio.structure.align.client.StructureName (implements java.lang.Comparable<T>, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.align.StructurePairAligner
  • org.biojava.nbio.structure.io.StructureSequenceMatcher
  • org.biojava.nbio.structure.StructureTools
  • org.biojava.nbio.structure.SubstructureIdentifier (implements java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.symmetry.core.SubunitGraph
  • org.biojava.nbio.structure.symmetry.core.Subunits
  • org.biojava.nbio.structure.symmetry.geometry.SuperPosition
  • org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
  • org.biojava.nbio.structure.SVDSuperimposer
  • org.biojava.nbio.structure.math.SymbolTable<Key,Value> (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.validation.SymmClash
  • org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
  • org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.Axis
  • org.biojava.nbio.structure.symmetry.utils.SymmetryTools
  • org.biojava.nbio.structure.symmetry.internal.SymmOptimizer
  • org.biojava.nbio.structure.xtal.SymoplibParser
  • org.biojava.nbio.structure.align.util.SynchronizedOutFile
  • org.biojava.nbio.structure.symmetry.core.SystematicSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
  • org.biojava.nbio.structure.symmetry.geometry.Tetrahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.biojava.nbio.structure.align.util.ConfigurationException
      • org.biojava.nbio.structure.align.client.JobKillException
      • org.biojava.nbio.structure.io.PDBParseException
      • org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
      • java.lang.RuntimeException
        • org.biojava.nbio.structure.scop.ScopIOException
      • org.biojava.nbio.structure.StructureException
  • org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.server.TreeSetStringWrapper (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.UniqueSequenceList (implements java.lang.Cloneable)
  • org.biojava.nbio.structure.xtal.UnitCellBoundingBox
  • org.biojava.nbio.structure.URLIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.align.util.UserConfiguration
  • org.biojava.nbio.structure.validation.WwPDBValidationInformation (implements java.io.Serializable)
  • javax.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
    • org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
  • org.biojava.nbio.structure.scop.server.XMLUtil
  • org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)

Interface Hierarchy

• org.biojava.nbio.structure.align.pairwise.Alignable
• org.biojava.nbio.structure.align.events.AlignmentProgressListener
• org.biojava.nbio.structure.AtomPositionMap.GroupMatcher
• org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
• org.biojava.nbio.structure.Bond
• org.biojava.nbio.structure.cath.CathDatabase
• org.biojava.nbio.structure.Chain
• org.biojava.nbio.structure.io.mmcif.ChemCompProvider
• java.lang.Cloneable
  • org.biojava.nbio.structure.Atom (also extends org.biojava.nbio.structure.PDBRecord)
  • org.biojava.nbio.structure.Structure
• org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
• org.biojava.nbio.structure.domain.DomainProvider
• org.biojava.nbio.structure.ecod.EcodDatabase
• org.biojava.nbio.structure.Group
  • org.biojava.nbio.structure.AminoAcid
• org.biojava.nbio.structure.align.ce.MatrixListener
• org.biojava.nbio.structure.io.mmcif.MMcifConsumer
• org.biojava.nbio.structure.io.mmcif.MMcifParser
• org.biojava.nbio.structure.align.MultipleStructureAligner
• org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer
• org.biojava.nbio.structure.symmetry.internal.OrderDetector
• org.biojava.nbio.structure.PDBRecord
  • org.biojava.nbio.structure.Atom (also extends java.lang.Cloneable)
• org.biojava.nbio.structure.domain.PDPProvider
• org.biojava.nbio.structure.symmetry.geometry.Polyhedron
• org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
• org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
• org.biojava.nbio.structure.scop.ScopDatabase
  • org.biojava.nbio.structure.scop.LocalScopDatabase
• org.biojava.nbio.structure.align.multiple.ScoresCache
  • org.biojava.nbio.structure.align.multiple.Block
  • org.biojava.nbio.structure.align.multiple.BlockSet
  • org.biojava.nbio.structure.align.multiple.MultipleAlignment
  • org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
• org.biojava.nbio.structure.SeqMisMatch
• org.biojava.nbio.structure.align.StructureAlignment
• org.biojava.nbio.structure.StructureIdentifier
• org.biojava.nbio.structure.io.StructureProvider
  • org.biojava.nbio.structure.io.StructureIOFile
• org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner
• org.biojava.nbio.structure.align.ce.UserArgumentProcessor

Annotation Type Hierarchy

• org.biojava.nbio.structure.io.mmcif.model.IgnoreField (implements java.lang.annotation.Annotation)
• org.biojava.nbio.structure.io.mmcif.model.CIFLabel (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
    • org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
    • org.biojava.nbio.structure.align.client.StructureName.Source
    • org.biojava.nbio.structure.StructureIO.StructureFiletype
    • org.biojava.nbio.structure.PDBStatus.Status
    • org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
    • org.biojava.nbio.structure.GroupType
    • org.biojava.nbio.structure.ExperimentalTechnique
    • org.biojava.nbio.structure.ElementType (implements java.io.Serializable)
    • org.biojava.nbio.structure.Element (implements java.io.Serializable)
    • org.biojava.nbio.structure.BondType
    • org.biojava.nbio.structure.cath.CathCategory
    • org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
    • org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
    • org.biojava.nbio.structure.io.mmcif.chem.ResidueType (implements java.io.Serializable)
    • org.biojava.nbio.structure.io.mmcif.chem.PolymerType (implements java.io.Serializable)
    • org.biojava.nbio.structure.scop.ScopCategory (implements java.io.Serializable)
    • org.biojava.nbio.structure.scop.Astral.AstralSet
    • org.biojava.nbio.structure.secstruc.SecStrucType
    • org.biojava.nbio.structure.secstruc.BridgeType
    • org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
    • org.biojava.nbio.structure.xtal.TransformType
    • org.biojava.nbio.structure.xtal.BravaisLattice