BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

biojava3-structure.jar is the Structure module of BioJava 3.

JAR File Size and Download Location:

File name: biojava3-structure.jar, biojava3-structure-3.0.2.jar
File size: 724001 bytes
Date modified: 02-Sep-2011
Download: BioJava 3.0 - Structure

Manifest of the JAR:

Archiver-Version: Plexus Archiver
Built-By: andreas
Build-Jdk: 1.7.0

List of Classes in the JAR:

org/biojava/bio/structure/AminoAcid
org/biojava/bio/structure/JournalArticle
org/biojava/bio/structure/StructureTools
org/biojava/bio/structure/AtomImpl
org/biojava/bio/structure/Group
org/biojava/bio/structure/Bond
org/biojava/bio/structure/BondType
org/biojava/bio/structure/Structure
org/biojava/bio/structure/scop/ScopNode
org/biojava/bio/structure/scop/ScopDatabase
org/biojava/bio/structure/scop/ScopFactory
org/biojava/bio/structure/scop/ScopDomain
org/biojava/bio/structure/scop/RemoteScopInstallation
org/biojava/bio/structure/scop/ScopCategory
org/biojava/bio/structure/scop/ScopDescription
org/biojava/bio/structure/scop/ScopInstallation
org/biojava/bio/structure/scop/server/XMLUtil
org/biojava/bio/structure/scop/server/ScopDomains
org/biojava/bio/structure/scop/server/ScopDescriptions
org/biojava/bio/structure/scop/server/ScopNodes
org/biojava/bio/structure/GroupIterator
org/biojava/bio/structure/ResidueNumber
org/biojava/bio/structure/jama/SingularValueDecomposition
org/biojava/bio/structure/jama/Maths
org/biojava/bio/structure/jama/EigenvalueDecomposition
org/biojava/bio/structure/jama/CholeskyDecomposition
org/biojava/bio/structure/jama/LUDecomposition
org/biojava/bio/structure/jama/QRDecomposition
org/biojava/bio/structure/jama/Matrix
org/biojava/bio/structure/Calc
org/biojava/bio/structure/NucleotideImpl
org/biojava/bio/structure/StandardAminoAcid
org/biojava/bio/structure/SVDSuperimposer
org/biojava/bio/structure/UnknownPdbAminoAcidException
org/biojava/bio/structure/StructureException
org/biojava/bio/structure/Mutator
org/biojava/bio/structure/Site
org/biojava/bio/structure/DBRef
org/biojava/bio/structure/AtomIterator
org/biojava/bio/structure/ChainImpl
org/biojava/bio/structure/HetatomImpl
org/biojava/bio/structure/PDBStatus
org/biojava/bio/structure/SSBond
org/biojava/bio/structure/Author
org/biojava/bio/structure/io/FileParsingParameters
org/biojava/bio/structure/io/PDBFileReader
org/biojava/bio/structure/io/PDBSRSReader
org/biojava/bio/structure/io/MMCIFFileReader
org/biojava/bio/structure/io/LocalCacheStructureProvider
org/biojava/bio/structure/io/FileConvert
org/biojava/bio/structure/io/SandboxStyleStructureProvider
org/biojava/bio/structure/io/StructureIO
org/biojava/bio/structure/io/PDBFileParser
org/biojava/bio/structure/io/mmcif/MMcifConsumer
org/biojava/bio/structure/io/mmcif/SimpleMMcifParser
org/biojava/bio/structure/io/mmcif/DownloadChemCompProvider
org/biojava/bio/structure/io/mmcif/ReducedChemCompProvider
org/biojava/bio/structure/io/mmcif/ChemCompGroupFactory
org/biojava/bio/structure/io/mmcif/chem/ChemCompTools
org/biojava/bio/structure/io/mmcif/chem/PolymerType
org/biojava/bio/structure/io/mmcif/chem/ResidueType
org/biojava/bio/structure/io/mmcif/model/StructKeywords
org/biojava/bio/structure/io/mmcif/model/ChemCompDescriptor
org/biojava/bio/structure/io/mmcif/model/EntityPolySeq
org/biojava/bio/structure/io/mmcif/model/Refine
org/biojava/bio/structure/io/mmcif/model/AbstractBean
org/biojava/bio/structure/io/mmcif/model/AtomSite
org/biojava/bio/structure/io/mmcif/model/PdbxPolySeqScheme
org/biojava/bio/structure/io/mmcif/model/Struct
org/biojava/bio/structure/io/mmcif/model/StructAsym
org/biojava/bio/structure/io/mmcif/model/Exptl
org/biojava/bio/structure/io/mmcif/model/PdbxNonPolyScheme
org/biojava/bio/structure/io/mmcif/model/StructRefSeq
org/biojava/bio/structure/io/mmcif/model/AuditAuthor
org/biojava/bio/structure/io/mmcif/model/StructRef
org/biojava/bio/structure/io/mmcif/model/DatabasePDBremark
org/biojava/bio/structure/io/mmcif/model/PdbxEntityNonPoly
org/biojava/bio/structure/io/mmcif/model/Entity
org/biojava/bio/structure/io/mmcif/model/ChemComp
org/biojava/bio/structure/io/mmcif/model/DatabasePDBrev
org/biojava/bio/structure/io/mmcif/ChemicalComponentDictionary
org/biojava/bio/structure/io/mmcif/ChemCompConsumer
org/biojava/bio/structure/io/mmcif/AllChemCompProvider
org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer
org/biojava/bio/structure/io/mmcif/ChemCompProvider
org/biojava/bio/structure/io/mmcif/MMcifParser
org/biojava/bio/structure/io/SeqRes2AtomAligner
org/biojava/bio/structure/io/CAConverter
org/biojava/bio/structure/io/StructureIOFile
org/biojava/bio/structure/io/PDBParseException
org/biojava/bio/structure/io/StructureProvider
org/biojava/bio/structure/PDBHeader
org/biojava/bio/structure/ElementType
org/biojava/bio/structure/Compound
org/biojava/bio/structure/StructureImpl
org/biojava/bio/structure/align/ce/AbstractUserArgumentProcessor
org/biojava/bio/structure/align/ce/CeUserArgumentProcessor
org/biojava/bio/structure/align/ce/CeParameters
org/biojava/bio/structure/align/ce/GuiWrapper
org/biojava/bio/structure/align/ce/CECalculator
org/biojava/bio/structure/align/ce/CeMain
org/biojava/bio/structure/align/ce/CeSideChainUserArgumentProcessor
org/biojava/bio/structure/align/ce/UserArgumentProcessor
org/biojava/bio/structure/align/ce/MatrixListener
org/biojava/bio/structure/align/ce/CeSideChainMain
org/biojava/bio/structure/align/ce/StartupParameters
org/biojava/bio/structure/align/ce/ConfigStrucAligParams
org/biojava/bio/structure/align/ce/CeCPMain
org/biojava/bio/structure/align/events/AlignmentProgressListener
org/biojava/bio/structure/align/helper/IdxComparator
org/biojava/bio/structure/align/helper/AlignTools
org/biojava/bio/structure/align/helper/AligMatEl
org/biojava/bio/structure/align/helper/JointFragments
org/biojava/bio/structure/align/helper/IndexPair
org/biojava/bio/structure/align/helper/GapArray
org/biojava/bio/structure/align/StructureAlignmentFactory
org/biojava/bio/structure/align/BioJavaStructureAlignment
org/biojava/bio/structure/align/client/JFatCatClient
org/biojava/bio/structure/align/client/PdbPair
org/biojava/bio/structure/align/client/FarmJobRunnable
org/biojava/bio/structure/align/client/StructureName
org/biojava/bio/structure/align/client/JobKillException
org/biojava/bio/structure/align/client/CountProgressListener
org/biojava/bio/structure/align/client/FarmJobParameters
org/biojava/bio/structure/align/ClusterAltAligs
org/biojava/bio/structure/align/fatcat/FatCatUserArgumentProcessor
org/biojava/bio/structure/align/fatcat/FatCatFlexible
org/biojava/bio/structure/align/fatcat/FatCat
org/biojava/bio/structure/align/fatcat/calc/StructureAlignmentOptimizer
org/biojava/bio/structure/align/fatcat/calc/AFPCalculator
org/biojava/bio/structure/align/fatcat/calc/AFPChainer
org/biojava/bio/structure/align/fatcat/calc/FCAlignHelper
org/biojava/bio/structure/align/fatcat/calc/AFPPostProcessor
org/biojava/bio/structure/align/fatcat/calc/FatCatParameters
org/biojava/bio/structure/align/fatcat/calc/AFPOptimizer
org/biojava/bio/structure/align/fatcat/calc/SigEva
org/biojava/bio/structure/align/fatcat/calc/FatCatAligner
org/biojava/bio/structure/align/fatcat/FatCatRigid
org/biojava/bio/structure/align/AFPTwister
org/biojava/bio/structure/align/xml/AFPChainXMLConverter
org/biojava/bio/structure/align/xml/PositionInQueueXMLConverter
org/biojava/bio/structure/align/xml/AFPChainXMLParser
org/biojava/bio/structure/align/xml/AFPChainFlipper
org/biojava/bio/structure/align/xml/PdbPairXMLConverter
org/biojava/bio/structure/align/xml/RepresentativeXMLConverter
org/biojava/bio/structure/align/xml/HasResultXMLConverter
org/biojava/bio/structure/align/model/AFPChain
org/biojava/bio/structure/align/model/AFP
org/biojava/bio/structure/align/model/AfpChainWriter
org/biojava/bio/structure/align/FarmJob
org/biojava/bio/structure/align/StructureAlignment
org/biojava/bio/structure/align/pairwise/Alignable
org/biojava/bio/structure/align/pairwise/AlternativeAlignment
org/biojava/bio/structure/align/pairwise/AlignmentProgressListener
org/biojava/bio/structure/align/pairwise/FragmentPair
org/biojava/bio/structure/align/pairwise/JointFragmentsComparator
org/biojava/bio/structure/align/pairwise/Gotoh
org/biojava/bio/structure/align/pairwise/StrCompAlignment
org/biojava/bio/structure/align/pairwise/AligNPE
org/biojava/bio/structure/align/pairwise/FragmentJoiner
org/biojava/bio/structure/align/pairwise/AlignmentResult
org/biojava/bio/structure/align/pairwise/AltAligComparator
org/biojava/bio/structure/align/AbstractStructureAlignment
org/biojava/bio/structure/align/CallableStructureAlignment
org/biojava/bio/structure/align/util/SynchronizedOutFile
org/biojava/bio/structure/align/util/UserConfiguration
org/biojava/bio/structure/align/util/ResourceManager
org/biojava/bio/structure/align/util/AtomCache
org/biojava/bio/structure/align/util/AFPAlignmentDisplay
org/biojava/bio/structure/align/util/ConfigurationException
org/biojava/bio/structure/align/util/CacheFactory
org/biojava/bio/structure/align/util/HTTPConnectionTools
org/biojava/bio/structure/align/util/CollectionTools
org/biojava/bio/structure/align/util/AFPChainScorer
org/biojava/bio/structure/align/util/CliTools
org/biojava/bio/structure/align/seq/SmithWaterman3Daligner
org/biojava/bio/structure/align/seq/SmithWaterman3DParameters
org/biojava/bio/structure/align/seq/SmithWatermanUserArgumentProcessor
org/biojava/bio/structure/align/StructurePairAligner
org/biojava/bio/structure/align/StrucAligParameters
org/biojava/bio/structure/server/StructureEventImpl
org/biojava/bio/structure/server/PDBInstallation
org/biojava/bio/structure/server/StructureListener
org/biojava/bio/structure/server/StructureServer
org/biojava/bio/structure/server/StructureFetcherRunnable
org/biojava/bio/structure/server/FlatFileInstallation
org/biojava/bio/structure/server/SimpleStructureServer
org/biojava/bio/structure/server/MMCIFFileInstallation
org/biojava/bio/structure/server/StructureEvent
org/biojava/bio/structure/server/PrepareMMcifIndexFile
org/biojava/bio/structure/server/PDBFilter
org/biojava/bio/structure/server/PrepareIndexFile
org/biojava/bio/structure/PDBRecord
org/biojava/bio/structure/Atom
org/biojava/bio/structure/GroupType
org/biojava/bio/structure/AminoAcidImpl
org/biojava/bio/structure/secstruc/HBond
org/biojava/bio/structure/secstruc/SecStrucState
org/biojava/bio/structure/secstruc/SecStruc
org/biojava/bio/structure/secstruc/BigSqrt
org/biojava/bio/structure/secstruc/DistEn
org/biojava/bio/structure/secstruc/SecStrucGroup
org/biojava/bio/structure/Chain
org/biojava/bio/structure/Element
org/biojava/bio/structure/domain/pdp/Domain
org/biojava/bio/structure/domain/pdp/GetDistanceMatrix
org/biojava/bio/structure/domain/pdp/Segment
org/biojava/bio/structure/domain/pdp/SegmentComparator
org/biojava/bio/structure/domain/pdp/PDPDistanceMatrix
org/biojava/bio/structure/domain/pdp/ClusterDomains
org/biojava/bio/structure/domain/pdp/ShortSegmentRemover
org/biojava/bio/structure/domain/pdp/PDPParameters
org/biojava/bio/structure/domain/pdp/CutDomain
org/biojava/bio/structure/domain/pdp/CutSites
org/biojava/bio/structure/domain/pdp/Cut
org/biojava/bio/structure/domain/pdp/CutValues
org/biojava/bio/structure/domain/ProteinDomainParser
demo/DemoFATCAT
demo/DemoSCOP
demo/DemoMMCIFReader
demo/DemoLoadStructure
demo/DemoAtomCache
demo/ChemCompDistribution
demo/DemoChangeChemCompProvider
demo/DemoCommandLineStartup
demo/DemoCE
demo/DemoDomainsplit