Download biojava-structure-4.2.0.jar file

• Jar

• B

• • B

  • backbone-associations

  • backbone

  • balance

  • balloontip

  • baratine

  • barchart-udt-bundle

  • base-converter

  • base64

  • batchee-jbatch

  • batik-anim

  • batik-awt-util

  • batik-bridge

  • batik-codec

  • batik-constants

  • batik-css

  • batik-dom

  • batik-ext

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  • batik-gui-util

  • batik-gvt

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  • batik-js

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  • batik-util

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  • batoo-jpa

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  • bcel-findbugs

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  • bcmail-jdk15on

  • bcpg-jdk15on

  • bcpkix-jdk15on

  • bcprov-ext-jdk15on

  • bcprov-jdk14

  • bcprov-jdk15

  • bcprov-jdk15on

  • bdg-formats

  • bdg-utils-parquet

  • beam-runners-core-java

  • beam-runners-direct-java

  • beam-runners-google-cloud-dataflow-java

  • beam-runners-spark

  • beam-sdks-java-core

  • bean-matchers

  • bean-validator

  • beanio

  • beanvalidation-tck-tests

  • bedrock-testing-support

  • beetl-core

  • beetl

  • bigdata-blueprints

  • bigdata-cache

  • bigdata-client

  • bigdata-common-util

  • bigdata-core-test

  • bigdata-core

  • bigdata-ganglia

  • bigdata-gas

  • bigdata-rdf-test

  • bigdata-runtime

  • bigdata-statics

  • bigdata-util

  • bigdime-common-test-utils

  • bigdime-commons

  • bigtable-client-core

  • bigtable-protos

  • bijection-avro_2.10

  • biojava-alignment

  • biojava-core

  • biojava-structure

  • bitcoinj-core

  • bitcoinj

  • biz.aQute.bnd.annotation

  • biz.aQute.bndlib

  • blade-kit

  • blueprints-core

  • blueprints-neo4j2-graph

  • blueprints-test

  • bndlib

  • body

  • boilerpipe

  • bonecp-provider

  • bonecp-spring

  • bonecp

  • bonita-common

  • bonita-server

  • bookkeeper-server

  • boon

  • bootbox

  • bootsfaces

  • bootstrap-datepicker

  • bootstrap-material-design

  • bootstrap-multiselect

  • bootstrap-select

  • bootstrap-switch

  • bootstrap

  • bootswatch

  • bounce

  • box-java-sdk

  • braintree-java

  • brave-apache-http-interceptors

  • brave-core

  • brave-http

  • brave-okhttp

  • brave-spancollector-http

  • brave-web-servlet-filter

  • breeze-macros_2.10

  • breeze_2.10

  • breeze_2.11

  • brooklyn-all

  • brooklyn-api

  • brooklyn-camp

  • brooklyn-cli

  • brooklyn-core

  • brooklyn-jmxmp-agent

  • brooklyn-jmxrmi-agent

  • brooklyn-launcher

  • brooklyn-locations-jclouds

  • brooklyn-logback-includes

  • brooklyn-logback-xml

  • brooklyn-policy

  • brooklyn-rest-api

  • brooklyn-rest-resources

  • brooklyn-rest-server

  • brooklyn-software-base

  • brooklyn-software-database

  • brooklyn-software-messaging

  • brooklyn-software-monitoring

  • brooklyn-software-network

  • brooklyn-software-nosql

  • brooklyn-software-osgi

  • brooklyn-software-webapp

  • brooklyn-software-winrm

  • brooklyn-test-framework

  • brooklyn-test-support

  • brooklyn-utils-common

  • brooklyn-utils-groovy

  • brooklyn-utils-rest-swagger

  • brooklyn-utils-test-support

  • brownies-collections

  • BrowserLauncher2

  • browsermob-core-littleproxy

  • browsermob-core

  • browsermob-proxy

  • browserstack-local-java

  • bsh

  • bson

  • bson4jackson

  • btf

  • btm

  • build-helper-maven-plugin

  • builder-commons

  • bundlescanner

  • bval-extras

  • bval-jsr

  • byon

  • byte-buddy

  • bytelist

  • byteman-bmunit

  • byteman-install

  • byteman-submit

  • byteman

Introduction

You can download biojava-structure-4.2.0.jar in this page.

License

GNU LGPL v2

Type List

biojava-structure-4.2.0.jar file has the following types.

META-INF/MANIFEST.MF
about.properties
blosum62.mat
ce.properties
chemcomp/2EP.cif.gz
chemcomp/2MD.cif.gz
chemcomp/6MO.cif.gz
chemcomp/A.cif.gz
chemcomp/ACY.cif.gz
chemcomp/ALA.cif.gz
chemcomp/ANS.cif.gz
chemcomp/ARG.cif.gz
chemcomp/ASN.cif.gz
chemcomp/ASP.cif.gz
chemcomp/C.cif.gz
chemcomp/CA.cif.gz
chemcomp/CMP.cif.gz
chemcomp/CSE.cif.gz
chemcomp/CYS.cif.gz
chemcomp/DA.cif.gz
chemcomp/DAR.cif.gz
chemcomp/DC.cif.gz
chemcomp/DG.cif.gz
chemcomp/DI.cif.gz
chemcomp/DOD.cif.gz
chemcomp/DT.cif.gz
chemcomp/G.cif.gz
chemcomp/GLN.cif.gz
chemcomp/GLU.cif.gz
chemcomp/GLY.cif.gz
chemcomp/GOL.cif.gz
chemcomp/HIS.cif.gz
chemcomp/HOH.cif.gz
chemcomp/I.cif.gz
chemcomp/ILE.cif.gz
chemcomp/KTH.cif.gz
chemcomp/LEU.cif.gz
chemcomp/LYS.cif.gz
chemcomp/MAL.cif.gz
chemcomp/MET.cif.gz
chemcomp/MG.cif.gz
chemcomp/MGD.cif.gz
chemcomp/MO.cif.gz
chemcomp/MSE.cif.gz
chemcomp/NA.cif.gz
chemcomp/PHE.cif.gz
chemcomp/PO4.cif.gz
chemcomp/PRO.cif.gz
chemcomp/SEC.cif.gz
chemcomp/SER.cif.gz
chemcomp/SF4.cif.gz
chemcomp/SO4.cif.gz
chemcomp/THR.cif.gz
chemcomp/TRP.cif.gz
chemcomp/TYR.cif.gz
chemcomp/TYS.cif.gz
chemcomp/U.cif.gz
chemcomp/UNX.cif.gz
chemcomp/VAL.cif.gz
chemcomp/ZN.cif.gz
jfatcat.properties
log4j2.xml
org.biojava.nbio.structure.AminoAcid.class
org.biojava.nbio.structure.AminoAcidImpl.class
org.biojava.nbio.structure.Atom.class
org.biojava.nbio.structure.AtomImpl.class
org.biojava.nbio.structure.AtomIterator.class
org.biojava.nbio.structure.AtomPositionMap.class
org.biojava.nbio.structure.AugmentedResidueRange.class
org.biojava.nbio.structure.Author.class
org.biojava.nbio.structure.BioAssemblyIdentifier.class
org.biojava.nbio.structure.Bond.class
org.biojava.nbio.structure.BondImpl.class
org.biojava.nbio.structure.BondType.class
org.biojava.nbio.structure.Calc.class
org.biojava.nbio.structure.Chain.class
org.biojava.nbio.structure.ChainImpl.class
org.biojava.nbio.structure.Compound.class
org.biojava.nbio.structure.DBRef.class
org.biojava.nbio.structure.Element.class
org.biojava.nbio.structure.ElementType.class
org.biojava.nbio.structure.ExperimentalTechnique.class
org.biojava.nbio.structure.Group.class
org.biojava.nbio.structure.GroupIterator.class
org.biojava.nbio.structure.GroupType.class
org.biojava.nbio.structure.HetatomImpl.class
org.biojava.nbio.structure.Identifier.class
org.biojava.nbio.structure.JournalArticle.class
org.biojava.nbio.structure.Mutator.class
org.biojava.nbio.structure.NucleotideImpl.class
org.biojava.nbio.structure.PDBCrystallographicInfo.class
org.biojava.nbio.structure.PDBHeader.class
org.biojava.nbio.structure.PDBRecord.class
org.biojava.nbio.structure.PDBStatus.class
org.biojava.nbio.structure.PassthroughIdentifier.class
org.biojava.nbio.structure.ResidueNumber.class
org.biojava.nbio.structure.ResidueRange.class
org.biojava.nbio.structure.ResidueRangeAndLength.class
org.biojava.nbio.structure.SVDSuperimposer.class
org.biojava.nbio.structure.SeqMisMatch.class
org.biojava.nbio.structure.SeqMisMatchImpl.class
org.biojava.nbio.structure.Site.class
org.biojava.nbio.structure.StandardAminoAcid.class
org.biojava.nbio.structure.Structure.class
org.biojava.nbio.structure.StructureException.class
org.biojava.nbio.structure.StructureIO.class
org.biojava.nbio.structure.StructureIdentifier.class
org.biojava.nbio.structure.StructureImpl.class
org.biojava.nbio.structure.StructureTools.class
org.biojava.nbio.structure.SubstructureIdentifier.class
org.biojava.nbio.structure.URLIdentifier.class
org.biojava.nbio.structure.align.AFPTwister.class
org.biojava.nbio.structure.align.AbstractStructureAlignment.class
org.biojava.nbio.structure.align.BioJavaStructureAlignment.class
org.biojava.nbio.structure.align.CallableStructureAlignment.class
org.biojava.nbio.structure.align.ClusterAltAligs.class
org.biojava.nbio.structure.align.FarmJob.class
org.biojava.nbio.structure.align.MultiThreadedDBSearch.class
org.biojava.nbio.structure.align.MultipleStructureAligner.class
org.biojava.nbio.structure.align.StrucAligParameters.class
org.biojava.nbio.structure.align.StructureAlignment.class
org.biojava.nbio.structure.align.StructureAlignmentFactory.class
org.biojava.nbio.structure.align.StructurePairAligner.class
org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor.class
org.biojava.nbio.structure.align.ce.CECPParameters.class
org.biojava.nbio.structure.align.ce.CECalculator.class
org.biojava.nbio.structure.align.ce.CeCPMain.class
org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.class
org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced.class
org.biojava.nbio.structure.align.ce.CeMain.class
org.biojava.nbio.structure.align.ce.CeParameters.class
org.biojava.nbio.structure.align.ce.CeSideChainMain.class
org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor.class
org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.class
org.biojava.nbio.structure.align.ce.ConfigStrucAligParams.class
org.biojava.nbio.structure.align.ce.GuiWrapper.class
org.biojava.nbio.structure.align.ce.MatrixListener.class
org.biojava.nbio.structure.align.ce.OptimalCECPMain.class
org.biojava.nbio.structure.align.ce.OptimalCECPParameters.class
org.biojava.nbio.structure.align.ce.StartupParameters.class
org.biojava.nbio.structure.align.ce.UserArgumentProcessor.class
org.biojava.nbio.structure.align.client.CountProgressListener.class
org.biojava.nbio.structure.align.client.FarmJobParameters.class
org.biojava.nbio.structure.align.client.FarmJobRunnable.class
org.biojava.nbio.structure.align.client.JFatCatClient.class
org.biojava.nbio.structure.align.client.JobKillException.class
org.biojava.nbio.structure.align.client.PdbPair.class
org.biojava.nbio.structure.align.client.StructureName.class
org.biojava.nbio.structure.align.events.AlignmentProgressListener.class
org.biojava.nbio.structure.align.fatcat.FatCat.class
org.biojava.nbio.structure.align.fatcat.FatCatFlexible.class
org.biojava.nbio.structure.align.fatcat.FatCatRigid.class
org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.class
org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator.class
org.biojava.nbio.structure.align.fatcat.calc.AFPChainer.class
org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer.class
org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor.class
org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper.class
org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner.class
org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters.class
org.biojava.nbio.structure.align.fatcat.calc.SigEva.class
org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer.class
org.biojava.nbio.structure.align.helper.AligMatEl.class
org.biojava.nbio.structure.align.helper.AlignTools.class
org.biojava.nbio.structure.align.helper.GapArray.class
org.biojava.nbio.structure.align.helper.IdxComparator.class
org.biojava.nbio.structure.align.helper.IndexPair.class
org.biojava.nbio.structure.align.helper.JointFragments.class
org.biojava.nbio.structure.align.model.AFP.class
org.biojava.nbio.structure.align.model.AFPChain.class
org.biojava.nbio.structure.align.model.AfpChainWriter.class
org.biojava.nbio.structure.align.multiple.AbstractScoresCache.class
org.biojava.nbio.structure.align.multiple.Block.class
org.biojava.nbio.structure.align.multiple.BlockImpl.class
org.biojava.nbio.structure.align.multiple.BlockSet.class
org.biojava.nbio.structure.align.multiple.BlockSetImpl.class
org.biojava.nbio.structure.align.multiple.MultipleAlignment.class
org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble.class
org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl.class
org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl.class
org.biojava.nbio.structure.align.multiple.ScoresCache.class
org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain.class
org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer.class
org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters.class
org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer.class
org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay.class
org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer.class
org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools.class
org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter.class
org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer.class
org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer.class
org.biojava.nbio.structure.align.pairwise.AligNPE.class
org.biojava.nbio.structure.align.pairwise.Alignable.class
org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener.class
org.biojava.nbio.structure.align.pairwise.AlignmentResult.class
org.biojava.nbio.structure.align.pairwise.AltAligComparator.class
org.biojava.nbio.structure.align.pairwise.AlternativeAlignment.class
org.biojava.nbio.structure.align.pairwise.FragmentJoiner.class
org.biojava.nbio.structure.align.pairwise.FragmentPair.class
org.biojava.nbio.structure.align.pairwise.Gotoh.class
org.biojava.nbio.structure.align.pairwise.JointFragmentsComparator.class
org.biojava.nbio.structure.align.pairwise.StrCompAlignment.class
org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters.class
org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner.class
org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.class
org.biojava.nbio.structure.align.util.AFPAlignmentDisplay.class
org.biojava.nbio.structure.align.util.AFPChainScorer.class
org.biojava.nbio.structure.align.util.AlignmentTools.class
org.biojava.nbio.structure.align.util.AtomCache.class
org.biojava.nbio.structure.align.util.CacheFactory.class
org.biojava.nbio.structure.align.util.CliTools.class
org.biojava.nbio.structure.align.util.CollectionTools.class
org.biojava.nbio.structure.align.util.ConfigurationException.class
org.biojava.nbio.structure.align.util.HTTPConnectionTools.class
org.biojava.nbio.structure.align.util.ResourceManager.class
org.biojava.nbio.structure.align.util.RotationAxis.class
org.biojava.nbio.structure.align.util.SynchronizedOutFile.class
org.biojava.nbio.structure.align.util.UserConfiguration.class
org.biojava.nbio.structure.align.xml.AFPChainFlipper.class
org.biojava.nbio.structure.align.xml.AFPChainXMLConverter.class
org.biojava.nbio.structure.align.xml.AFPChainXMLParser.class
org.biojava.nbio.structure.align.xml.HasResultXMLConverter.class
org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter.class
org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser.class
org.biojava.nbio.structure.align.xml.PdbPairXMLConverter.class
org.biojava.nbio.structure.align.xml.PdbPairsMessage.class
org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter.class
org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter.class
org.biojava.nbio.structure.asa.AsaCalculator.class
org.biojava.nbio.structure.asa.GroupAsa.class
org.biojava.nbio.structure.cath.CathCategory.class
org.biojava.nbio.structure.cath.CathDatabase.class
org.biojava.nbio.structure.cath.CathDomain.class
org.biojava.nbio.structure.cath.CathFactory.class
org.biojava.nbio.structure.cath.CathFragment.class
org.biojava.nbio.structure.cath.CathInstallation.class
org.biojava.nbio.structure.cath.CathNode.class
org.biojava.nbio.structure.cath.CathSegment.class
org.biojava.nbio.structure.contact.AtomContact.class
org.biojava.nbio.structure.contact.AtomContactSet.class
org.biojava.nbio.structure.contact.AtomIdentifier.class
org.biojava.nbio.structure.contact.BoundingBox.class
org.biojava.nbio.structure.contact.Grid.class
org.biojava.nbio.structure.contact.GridCell.class
org.biojava.nbio.structure.contact.GroupContact.class
org.biojava.nbio.structure.contact.GroupContactSet.class
org.biojava.nbio.structure.contact.Pair.class
org.biojava.nbio.structure.contact.ResidueIdentifier.class
org.biojava.nbio.structure.contact.StructureInterface.class
org.biojava.nbio.structure.contact.StructureInterfaceCluster.class
org.biojava.nbio.structure.contact.StructureInterfaceList.class
org.biojava.nbio.structure.domain.AssignmentXMLSerializer.class
org.biojava.nbio.structure.domain.DomainProvider.class
org.biojava.nbio.structure.domain.DomainProviderFactory.class
org.biojava.nbio.structure.domain.LocalProteinDomainParser.class
org.biojava.nbio.structure.domain.PDBDomainProvider.class
org.biojava.nbio.structure.domain.PDPDomain.class
org.biojava.nbio.structure.domain.PDPProvider.class
org.biojava.nbio.structure.domain.RemoteDomainProvider.class
org.biojava.nbio.structure.domain.RemotePDPProvider.class
org.biojava.nbio.structure.domain.SerializableCache.class
org.biojava.nbio.structure.domain.pdp.ClusterDomains.class
org.biojava.nbio.structure.domain.pdp.Cut.class
org.biojava.nbio.structure.domain.pdp.CutDomain.class
org.biojava.nbio.structure.domain.pdp.CutSites.class
org.biojava.nbio.structure.domain.pdp.CutValues.class
org.biojava.nbio.structure.domain.pdp.Domain.class
org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix.class
org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix.class
org.biojava.nbio.structure.domain.pdp.PDPParameters.class
org.biojava.nbio.structure.domain.pdp.Segment.class
org.biojava.nbio.structure.domain.pdp.SegmentComparator.class
org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover.class
org.biojava.nbio.structure.ecod.EcodDatabase.class
org.biojava.nbio.structure.ecod.EcodDomain.class
org.biojava.nbio.structure.ecod.EcodFactory.class
org.biojava.nbio.structure.ecod.EcodInstallation.class
org.biojava.nbio.structure.io.BondMaker.class
org.biojava.nbio.structure.io.CAConverter.class
org.biojava.nbio.structure.io.ChargeAdder.class
org.biojava.nbio.structure.io.CompoundFinder.class
org.biojava.nbio.structure.io.FastaAFPChainConverter.class
org.biojava.nbio.structure.io.FastaStructureParser.class
org.biojava.nbio.structure.io.FileConvert.class
org.biojava.nbio.structure.io.FileParsingParameters.class
org.biojava.nbio.structure.io.GroupToSDF.class
org.biojava.nbio.structure.io.LocalPDBDirectory.class
org.biojava.nbio.structure.io.MMCIFFileReader.class
org.biojava.nbio.structure.io.PDBBioAssemblyParser.class
org.biojava.nbio.structure.io.PDBFileParser.class
org.biojava.nbio.structure.io.PDBFileReader.class
org.biojava.nbio.structure.io.PDBParseException.class
org.biojava.nbio.structure.io.SSBondImpl.class
org.biojava.nbio.structure.io.SandboxStyleStructureProvider.class
org.biojava.nbio.structure.io.SeqRes2AtomAligner.class
org.biojava.nbio.structure.io.StructureIOFile.class
org.biojava.nbio.structure.io.StructureProvider.class
org.biojava.nbio.structure.io.StructureSequenceMatcher.class
org.biojava.nbio.structure.io.mmcif.AllChemCompProvider.class
org.biojava.nbio.structure.io.mmcif.ChemCompConsumer.class
org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory.class
org.biojava.nbio.structure.io.mmcif.ChemCompProvider.class
org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary.class
org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider.class
org.biojava.nbio.structure.io.mmcif.MMCIFFileTools.class
org.biojava.nbio.structure.io.mmcif.MMcifConsumer.class
org.biojava.nbio.structure.io.mmcif.MMcifParser.class
org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider.class
org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer.class
org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser.class
org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider.class
org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools.class
org.biojava.nbio.structure.io.mmcif.chem.PolymerType.class
org.biojava.nbio.structure.io.mmcif.chem.ResidueType.class
org.biojava.nbio.structure.io.mmcif.model.AbstractBean.class
org.biojava.nbio.structure.io.mmcif.model.AtomSite.class
org.biojava.nbio.structure.io.mmcif.model.AuditAuthor.class
org.biojava.nbio.structure.io.mmcif.model.Cell.class
org.biojava.nbio.structure.io.mmcif.model.ChemComp.class
org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom.class
org.biojava.nbio.structure.io.mmcif.model.ChemCompBond.class
org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor.class
org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark.class
org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev.class
org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord.class
org.biojava.nbio.structure.io.mmcif.model.Entity.class
org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq.class
org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen.class
org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat.class
org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn.class
org.biojava.nbio.structure.io.mmcif.model.Exptl.class
org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor.class
org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier.class
org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly.class
org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme.class
org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme.class
org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly.class
org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen.class
org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer.class
org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer.class
org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList.class
org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer.class
org.biojava.nbio.structure.io.mmcif.model.Refine.class
org.biojava.nbio.structure.io.mmcif.model.Struct.class
org.biojava.nbio.structure.io.mmcif.model.StructAsym.class
org.biojava.nbio.structure.io.mmcif.model.StructConn.class
org.biojava.nbio.structure.io.mmcif.model.StructKeywords.class
org.biojava.nbio.structure.io.mmcif.model.StructNcsOper.class
org.biojava.nbio.structure.io.mmcif.model.StructRef.class
org.biojava.nbio.structure.io.mmcif.model.StructRefSeq.class
org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif.class
org.biojava.nbio.structure.io.mmcif.model.StructSite.class
org.biojava.nbio.structure.io.mmcif.model.StructSiteGen.class
org.biojava.nbio.structure.io.mmcif.model.Symmetry.class
org.biojava.nbio.structure.io.sifts.SiftsChainEntry.class
org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping.class
org.biojava.nbio.structure.io.sifts.SiftsEntity.class
org.biojava.nbio.structure.io.sifts.SiftsMappingProvider.class
org.biojava.nbio.structure.io.sifts.SiftsResidue.class
org.biojava.nbio.structure.io.sifts.SiftsSegment.class
org.biojava.nbio.structure.io.sifts.SiftsXMLParser.class
org.biojava.nbio.structure.io.util.FileDownloadUtils.class
org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.class
org.biojava.nbio.structure.jama.CholeskyDecomposition.class
org.biojava.nbio.structure.jama.EigenvalueDecomposition.class
org.biojava.nbio.structure.jama.LUDecomposition.class
org.biojava.nbio.structure.jama.Maths.class
org.biojava.nbio.structure.jama.Matrix.class
org.biojava.nbio.structure.jama.QRDecomposition.class
org.biojava.nbio.structure.jama.SingularValueDecomposition.class
org.biojava.nbio.structure.math.SparseSquareMatrix.class
org.biojava.nbio.structure.math.SparseVector.class
org.biojava.nbio.structure.math.SymbolTable.class
org.biojava.nbio.structure.quaternary.BioAssemblyInfo.class
org.biojava.nbio.structure.quaternary.BioAssemblyTools.class
org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder.class
org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation.class
org.biojava.nbio.structure.quaternary.CartesianProduct.class
org.biojava.nbio.structure.quaternary.OperatorResolver.class
org.biojava.nbio.structure.quaternary.OrderedPair.class
org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider.class
org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory.class
org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider.class
org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider.class
org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider.class
org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider.class
org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider.class
org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider.class
org.biojava.nbio.structure.rcsb.GetRepresentatives.class
org.biojava.nbio.structure.rcsb.PdbIdLists.class
org.biojava.nbio.structure.rcsb.RCSBDescription.class
org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory.class
org.biojava.nbio.structure.rcsb.RCSBLigand.class
org.biojava.nbio.structure.rcsb.RCSBLigands.class
org.biojava.nbio.structure.rcsb.RCSBLigandsFactory.class
org.biojava.nbio.structure.rcsb.RCSBMacromolecule.class
org.biojava.nbio.structure.rcsb.RCSBPolymer.class
org.biojava.nbio.structure.rcsb.RCSBTaxonomy.class
org.biojava.nbio.structure.rcsb.RCSBUpdates.class
org.biojava.nbio.structure.rcsb.ReadUtils.class
org.biojava.nbio.structure.scop.Astral.class
org.biojava.nbio.structure.scop.BerkeleyScopInstallation.class
org.biojava.nbio.structure.scop.CachedRemoteScopInstallation.class
org.biojava.nbio.structure.scop.LocalScopDatabase.class
org.biojava.nbio.structure.scop.RemoteScopInstallation.class
org.biojava.nbio.structure.scop.ScopCategory.class
org.biojava.nbio.structure.scop.ScopDatabase.class
org.biojava.nbio.structure.scop.ScopDescription.class
org.biojava.nbio.structure.scop.ScopDomain.class
org.biojava.nbio.structure.scop.ScopFactory.class
org.biojava.nbio.structure.scop.ScopIOException.class
org.biojava.nbio.structure.scop.ScopInstallation.class
org.biojava.nbio.structure.scop.ScopMirror.class
org.biojava.nbio.structure.scop.ScopNode.class
org.biojava.nbio.structure.scop.server.ListStringWrapper.class
org.biojava.nbio.structure.scop.server.ScopDescriptions.class
org.biojava.nbio.structure.scop.server.ScopDomains.class
org.biojava.nbio.structure.scop.server.ScopNodes.class
org.biojava.nbio.structure.scop.server.TreeSetStringWrapper.class
org.biojava.nbio.structure.scop.server.XMLUtil.class
org.biojava.nbio.structure.secstruc.BetaBridge.class
org.biojava.nbio.structure.secstruc.BridgeType.class
org.biojava.nbio.structure.secstruc.DSSPParser.class
org.biojava.nbio.structure.secstruc.HBond.class
org.biojava.nbio.structure.secstruc.Ladder.class
org.biojava.nbio.structure.secstruc.SecStrucCalc.class
org.biojava.nbio.structure.secstruc.SecStrucElement.class
org.biojava.nbio.structure.secstruc.SecStrucGroup.class
org.biojava.nbio.structure.secstruc.SecStrucInfo.class
org.biojava.nbio.structure.secstruc.SecStrucState.class
org.biojava.nbio.structure.secstruc.SecStrucTools.class
org.biojava.nbio.structure.secstruc.SecStrucType.class
org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry.class
org.biojava.nbio.structure.symmetry.core.AxisAligner.class
org.biojava.nbio.structure.symmetry.core.C2RotationSolver.class
org.biojava.nbio.structure.symmetry.core.ChainClusterer.class
org.biojava.nbio.structure.symmetry.core.ClusterMerger.class
org.biojava.nbio.structure.symmetry.core.ClusterProteinChains.class
org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit.class
org.biojava.nbio.structure.symmetry.core.Helix.class
org.biojava.nbio.structure.symmetry.core.HelixAxisAligner.class
org.biojava.nbio.structure.symmetry.core.HelixExtender.class
org.biojava.nbio.structure.symmetry.core.HelixLayers.class
org.biojava.nbio.structure.symmetry.core.HelixSolver.class
org.biojava.nbio.structure.symmetry.core.PairwiseAlignment.class
org.biojava.nbio.structure.symmetry.core.PermutationGroup.class
org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor.class
org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer.class
org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer.class
org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector.class
org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters.class
org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults.class
org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores.class
org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver.class
org.biojava.nbio.structure.symmetry.core.Rotation.class
org.biojava.nbio.structure.symmetry.core.RotationAxisAligner.class
org.biojava.nbio.structure.symmetry.core.RotationGroup.class
org.biojava.nbio.structure.symmetry.core.RotationSolver.class
org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster.class
org.biojava.nbio.structure.symmetry.core.SubunitGraph.class
org.biojava.nbio.structure.symmetry.core.Subunits.class
org.biojava.nbio.structure.symmetry.core.SystematicSolver.class
org.biojava.nbio.structure.symmetry.core.UniqueSequenceList.class
org.biojava.nbio.structure.symmetry.geometry.DistanceBox.class
org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler.class
org.biojava.nbio.structure.symmetry.geometry.Icosahedron.class
org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.class
org.biojava.nbio.structure.symmetry.geometry.Octahedron.class
org.biojava.nbio.structure.symmetry.geometry.Permute.class
org.biojava.nbio.structure.symmetry.geometry.Polyhedron.class
org.biojava.nbio.structure.symmetry.geometry.Prism.class
org.biojava.nbio.structure.symmetry.geometry.RectangularPrism.class
org.biojava.nbio.structure.symmetry.geometry.SphereSampler.class
org.biojava.nbio.structure.symmetry.geometry.SuperPosition.class
org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP.class
org.biojava.nbio.structure.symmetry.geometry.Tetrahedron.class
org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus.class
org.biojava.nbio.structure.symmetry.internal.CESymmParameters.class
org.biojava.nbio.structure.symmetry.internal.CeSymm.class
org.biojava.nbio.structure.symmetry.internal.CeSymmIterative.class
org.biojava.nbio.structure.symmetry.internal.CeSymmResult.class
org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector.class
org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner.class
org.biojava.nbio.structure.symmetry.internal.OrderDetector.class
org.biojava.nbio.structure.symmetry.internal.RefinerFailedException.class
org.biojava.nbio.structure.symmetry.internal.ResidueGroup.class
org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector.class
org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner.class
org.biojava.nbio.structure.symmetry.internal.SymmOptimizer.class
org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.class
org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner.class
org.biojava.nbio.structure.symmetry.misc.ChainSignature.class
org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature.class
org.biojava.nbio.structure.symmetry.utils.BlastClustReader.class
org.biojava.nbio.structure.symmetry.utils.CombinationGenerator.class
org.biojava.nbio.structure.symmetry.utils.PermutationGenerator.class
org.biojava.nbio.structure.symmetry.utils.SymmetryTools.class
org.biojava.nbio.structure.validation.AngleOutlier.class
org.biojava.nbio.structure.validation.BondOutlier.class
org.biojava.nbio.structure.validation.Clash.class
org.biojava.nbio.structure.validation.Entry.class
org.biojava.nbio.structure.validation.ModelledSubgroup.class
org.biojava.nbio.structure.validation.MogAngleOutlier.class
org.biojava.nbio.structure.validation.MogBondOutlier.class
org.biojava.nbio.structure.validation.ObjectFactory.class
org.biojava.nbio.structure.validation.Program.class
org.biojava.nbio.structure.validation.Programs.class
org.biojava.nbio.structure.validation.SymmClash.class
org.biojava.nbio.structure.validation.WwPDBValidationInformation.class
org.biojava.nbio.structure.xtal.BravaisLattice.class
org.biojava.nbio.structure.xtal.CrystalBuilder.class
org.biojava.nbio.structure.xtal.CrystalCell.class
org.biojava.nbio.structure.xtal.CrystalTransform.class
org.biojava.nbio.structure.xtal.SpaceGroup.class
org.biojava.nbio.structure.xtal.SymoplibParser.class
org.biojava.nbio.structure.xtal.TransformType.class
org.biojava.nbio.structure.xtal.UnitCellBoundingBox.class
org.biojava.nbio.structure.xtal.io.SpaceGroupMapAdapter.class
org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements.class
org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot.class
org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter.class
org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper.class
org/biojava/nbio/structure/standardaminos.pdb
org/biojava/nbio/structure/xtal/spacegroups.xml

Pom

biojava-structure-4.2.0.pom file content.

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>4.2.0</version>
	</parent>
	<artifactId>biojava-structure</artifactId>
	<name>biojava-structure</name>
	<description>The protein structure modules of BioJava.</description>
	<licenses>
		<license>
			<name>GNU LGPL v2</name>
			<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

	<dependencies>

		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-alignment</artifactId>
			<version>4.2.0</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>4.2.0</version>
			<scope>compile</scope>
		</dependency>

		<dependency>
			<groupId>java3d</groupId>
			<artifactId>vecmath</artifactId>
			<version>1.3.1</version>
		</dependency>
		
		<dependency>
			<groupId>org.jgrapht</groupId>
  			<artifactId>jgrapht-core</artifactId>
  			<version>0.9.1</version>
		</dependency>

		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
		<dependency>
        	<groupId>org.slf4j</groupId>
        	<artifactId>slf4j-api</artifactId>
    	</dependency>
    	<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-slf4j-impl</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-api</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-core</artifactId>
  		</dependency>



		<!--  Testing related dependencies -->

		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>xmlunit</groupId>
			<artifactId>xmlunit</artifactId>
			<version>1.6</version>
			<scope>test</scope>
		</dependency>

	</dependencies>

	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.build.targetEncoding>UTF-8</project.build.targetEncoding>

		<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
		<timestamp>${maven.build.timestamp}</timestamp>

	</properties>
	<build>

		<plugins>

			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <excludes>
                        <exclude>demo/**</exclude>
                    </excludes>
                </configuration>
            </plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-resources-plugin</artifactId>
			</plugin>

		</plugins>
		<resources>
			<resource>
				<directory>src/main/resources</directory>
				<filtering>true</filtering>
				<includes>
					<include>**/*.properties</include>
				</includes>
			</resource>
			<resource>
				<directory>src/main/resources</directory>
				<filtering>false</filtering>
				<includes>
					<include>**/*.cif.gz</include>
					<include>**/*.pdb</include>
					<include>**/*.mat</include>
					<include>**/*.xml</include>
				</includes>
			</resource>
		</resources>

	</build>


</project>

POM Entry

<dependency>
   <groupId>org.biojava</groupId>
   <artifactId>biojava-structure</artifactId>
   <version>4.2.0</version>
</dependency>

Download

If you think the following biojava-structure-4.2.0.jar downloaded from Maven central repository is inappropriate, such as containing malicious code/tools or violating the copyright, please email , thanks.

Download biojava-structure-4.2.0.jar file

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