Download biojava3-structure-3.0.5-sources.jar
biojava3/biojava3-structure-3.0.5-sources.jar.zip( 713 k)
The download jar file contains the following class files or Java source files.
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
demo.ChemCompDistribution.java
demo.DemoAtomCache.java
demo.DemoBerkeleyScop.java
demo.DemoCATH.java
demo.DemoCE.java
demo.DemoChangeChemCompProvider.java
demo.DemoCommandLineStartup.java
demo.DemoDomainsplit.java
demo.DemoFATCAT.java
demo.DemoLoadStructure.java
demo.DemoMMCIFReader.java
demo.DemoSCOP.java
jfatcat.properties
org.biojava.bio.structure.AminoAcid.java
org.biojava.bio.structure.AminoAcidImpl.java
org.biojava.bio.structure.Atom.java
org.biojava.bio.structure.AtomImpl.java
org.biojava.bio.structure.AtomIterator.java
org.biojava.bio.structure.Author.java
org.biojava.bio.structure.Bond.java
org.biojava.bio.structure.BondType.java
org.biojava.bio.structure.Calc.java
org.biojava.bio.structure.Chain.java
org.biojava.bio.structure.ChainImpl.java
org.biojava.bio.structure.Compound.java
org.biojava.bio.structure.DBRef.java
org.biojava.bio.structure.Element.java
org.biojava.bio.structure.ElementType.java
org.biojava.bio.structure.Group.java
org.biojava.bio.structure.GroupIterator.java
org.biojava.bio.structure.GroupType.java
org.biojava.bio.structure.HetatomImpl.java
org.biojava.bio.structure.JournalArticle.java
org.biojava.bio.structure.Mutator.java
org.biojava.bio.structure.NucleotideImpl.java
org.biojava.bio.structure.PDBCrystallographicInfo.java
org.biojava.bio.structure.PDBHeader.java
org.biojava.bio.structure.PDBRecord.java
org.biojava.bio.structure.PDBStatus.java
org.biojava.bio.structure.ResidueNumber.java
org.biojava.bio.structure.SSBond.java
org.biojava.bio.structure.SVDSuperimposer.java
org.biojava.bio.structure.Site.java
org.biojava.bio.structure.StandardAminoAcid.java
org.biojava.bio.structure.Structure.java
org.biojava.bio.structure.StructureException.java
org.biojava.bio.structure.StructureImpl.java
org.biojava.bio.structure.StructureTools.java
org.biojava.bio.structure.UnknownPdbAminoAcidException.java
org.biojava.bio.structure.align.AFPTwister.java
org.biojava.bio.structure.align.AbstractStructureAlignment.java
org.biojava.bio.structure.align.BioJavaStructureAlignment.java
org.biojava.bio.structure.align.CallableStructureAlignment.java
org.biojava.bio.structure.align.ClusterAltAligs.java
org.biojava.bio.structure.align.FarmJob.java
org.biojava.bio.structure.align.StrucAligParameters.java
org.biojava.bio.structure.align.StructureAlignment.java
org.biojava.bio.structure.align.StructureAlignmentFactory.java
org.biojava.bio.structure.align.StructurePairAligner.java
org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor.java
org.biojava.bio.structure.align.ce.CECalculator.java
org.biojava.bio.structure.align.ce.CeCPMain.java
org.biojava.bio.structure.align.ce.CeCPUserArgumentProcessor.java
org.biojava.bio.structure.align.ce.CeCalculatorEnhanced.java
org.biojava.bio.structure.align.ce.CeMain.java
org.biojava.bio.structure.align.ce.CeParameters.java
org.biojava.bio.structure.align.ce.CeSideChainMain.java
org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor.java
org.biojava.bio.structure.align.ce.CeUserArgumentProcessor.java
org.biojava.bio.structure.align.ce.ConfigStrucAligParams.java
org.biojava.bio.structure.align.ce.GuiWrapper.java
org.biojava.bio.structure.align.ce.MatrixListener.java
org.biojava.bio.structure.align.ce.OptimalCECPMain.java
org.biojava.bio.structure.align.ce.OptimalCECPParameters.java
org.biojava.bio.structure.align.ce.StartupParameters.java
org.biojava.bio.structure.align.ce.UserArgumentProcessor.java
org.biojava.bio.structure.align.client.CountProgressListener.java
org.biojava.bio.structure.align.client.FarmJobParameters.java
org.biojava.bio.structure.align.client.FarmJobRunnable.java
org.biojava.bio.structure.align.client.JFatCatClient.java
org.biojava.bio.structure.align.client.JobKillException.java
org.biojava.bio.structure.align.client.PdbPair.java
org.biojava.bio.structure.align.client.StructureName.java
org.biojava.bio.structure.align.events.AlignmentProgressListener.java
org.biojava.bio.structure.align.fatcat.FatCat.java
org.biojava.bio.structure.align.fatcat.FatCatFlexible.java
org.biojava.bio.structure.align.fatcat.FatCatRigid.java
org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor.java
org.biojava.bio.structure.align.fatcat.calc.AFPCalculator.java
org.biojava.bio.structure.align.fatcat.calc.AFPChainer.java
org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer.java
org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor.java
org.biojava.bio.structure.align.fatcat.calc.FCAlignHelper.java
org.biojava.bio.structure.align.fatcat.calc.FatCatAligner.java
org.biojava.bio.structure.align.fatcat.calc.FatCatParameters.java
org.biojava.bio.structure.align.fatcat.calc.SigEva.java
org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer.java
org.biojava.bio.structure.align.helper.AligMatEl.java
org.biojava.bio.structure.align.helper.AlignTools.java
org.biojava.bio.structure.align.helper.GapArray.java
org.biojava.bio.structure.align.helper.IdxComparator.java
org.biojava.bio.structure.align.helper.IndexPair.java
org.biojava.bio.structure.align.helper.JointFragments.java
org.biojava.bio.structure.align.model.AFP.java
org.biojava.bio.structure.align.model.AFPChain.java
org.biojava.bio.structure.align.model.AfpChainWriter.java
org.biojava.bio.structure.align.pairwise.AligNPE.java
org.biojava.bio.structure.align.pairwise.Alignable.java
org.biojava.bio.structure.align.pairwise.AlignmentProgressListener.java
org.biojava.bio.structure.align.pairwise.AlignmentResult.java
org.biojava.bio.structure.align.pairwise.AltAligComparator.java
org.biojava.bio.structure.align.pairwise.AlternativeAlignment.java
org.biojava.bio.structure.align.pairwise.FragmentJoiner.java
org.biojava.bio.structure.align.pairwise.FragmentPair.java
org.biojava.bio.structure.align.pairwise.Gotoh.java
org.biojava.bio.structure.align.pairwise.StrCompAlignment.java
org.biojava.bio.structure.align.seq.SmithWaterman3DParameters.java
org.biojava.bio.structure.align.seq.SmithWaterman3Daligner.java
org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor.java
org.biojava.bio.structure.align.util.AFPAlignmentDisplay.java
org.biojava.bio.structure.align.util.AFPChainScorer.java
org.biojava.bio.structure.align.util.AlignmentTools.java
org.biojava.bio.structure.align.util.AtomCache.java
org.biojava.bio.structure.align.util.CacheFactory.java
org.biojava.bio.structure.align.util.CliTools.java
org.biojava.bio.structure.align.util.CollectionTools.java
org.biojava.bio.structure.align.util.ConfigurationException.java
org.biojava.bio.structure.align.util.HTTPConnectionTools.java
org.biojava.bio.structure.align.util.ResourceManager.java
org.biojava.bio.structure.align.util.SynchronizedOutFile.java
org.biojava.bio.structure.align.util.UserConfiguration.java
org.biojava.bio.structure.align.xml.AFPChainFlipper.java
org.biojava.bio.structure.align.xml.AFPChainXMLConverter.java
org.biojava.bio.structure.align.xml.AFPChainXMLParser.java
org.biojava.bio.structure.align.xml.HasResultXMLConverter.java
org.biojava.bio.structure.align.xml.PdbPairXMLConverter.java
org.biojava.bio.structure.align.xml.PdbPairsMessage.java
org.biojava.bio.structure.align.xml.PositionInQueueXMLConverter.java
org.biojava.bio.structure.align.xml.RepresentativeXMLConverter.java
org.biojava.bio.structure.cath.CathCategory.java
org.biojava.bio.structure.cath.CathDatabase.java
org.biojava.bio.structure.cath.CathDomain.java
org.biojava.bio.structure.cath.CathFragment.java
org.biojava.bio.structure.cath.CathInstallation.java
org.biojava.bio.structure.cath.CathNode.java
org.biojava.bio.structure.cath.CathSegment.java
org.biojava.bio.structure.domain.AssignmentXMLSerializer.java
org.biojava.bio.structure.domain.DomainProvider.java
org.biojava.bio.structure.domain.DomainProviderFactory.java
org.biojava.bio.structure.domain.LocalProteinDomainParser.java
org.biojava.bio.structure.domain.PDBDomainProvider.java
org.biojava.bio.structure.domain.PDPProvider.java
org.biojava.bio.structure.domain.RemoteDomainProvider.java
org.biojava.bio.structure.domain.RemotePDPProvider.java
org.biojava.bio.structure.domain.SerializableCache.java
org.biojava.bio.structure.domain.pdp.ClusterDomains.java
org.biojava.bio.structure.domain.pdp.Cut.java
org.biojava.bio.structure.domain.pdp.CutDomain.java
org.biojava.bio.structure.domain.pdp.CutSites.java
org.biojava.bio.structure.domain.pdp.CutValues.java
org.biojava.bio.structure.domain.pdp.Domain.java
org.biojava.bio.structure.domain.pdp.GetDistanceMatrix.java
org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix.java
org.biojava.bio.structure.domain.pdp.PDPParameters.java
org.biojava.bio.structure.domain.pdp.Segment.java
org.biojava.bio.structure.domain.pdp.SegmentComparator.java
org.biojava.bio.structure.domain.pdp.ShortSegmentRemover.java
org.biojava.bio.structure.io.CAConverter.java
org.biojava.bio.structure.io.FastaStructureParser.java
org.biojava.bio.structure.io.FileConvert.java
org.biojava.bio.structure.io.FileParsingParameters.java
org.biojava.bio.structure.io.LocalCacheStructureProvider.java
org.biojava.bio.structure.io.MMCIFFileReader.java
org.biojava.bio.structure.io.PDBBioAssemblyParser.java
org.biojava.bio.structure.io.PDBFileParser.java
org.biojava.bio.structure.io.PDBFileReader.java
org.biojava.bio.structure.io.PDBParseException.java
org.biojava.bio.structure.io.PDBSRSReader.java
org.biojava.bio.structure.io.SandboxStyleStructureProvider.java
org.biojava.bio.structure.io.SeqRes2AtomAligner.java
org.biojava.bio.structure.io.StructureIO.java
org.biojava.bio.structure.io.StructureIOFile.java
org.biojava.bio.structure.io.StructureProvider.java
org.biojava.bio.structure.io.StructureSequenceMatcher.java
org.biojava.bio.structure.io.mmcif.AllChemCompProvider.java
org.biojava.bio.structure.io.mmcif.ChemCompConsumer.java
org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory.java
org.biojava.bio.structure.io.mmcif.ChemCompProvider.java
org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary.java
org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider.java
org.biojava.bio.structure.io.mmcif.MMcifConsumer.java
org.biojava.bio.structure.io.mmcif.MMcifParser.java
org.biojava.bio.structure.io.mmcif.ReducedChemCompProvider.java
org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer.java
org.biojava.bio.structure.io.mmcif.SimpleMMcifParser.java
org.biojava.bio.structure.io.mmcif.chem.ChemCompTools.java
org.biojava.bio.structure.io.mmcif.chem.PolymerType.java
org.biojava.bio.structure.io.mmcif.chem.ResidueType.java
org.biojava.bio.structure.io.mmcif.model.AbstractBean.java
org.biojava.bio.structure.io.mmcif.model.AtomSite.java
org.biojava.bio.structure.io.mmcif.model.AuditAuthor.java
org.biojava.bio.structure.io.mmcif.model.ChemComp.java
org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor.java
org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark.java
org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev.java
org.biojava.bio.structure.io.mmcif.model.Entity.java
org.biojava.bio.structure.io.mmcif.model.EntityPolySeq.java
org.biojava.bio.structure.io.mmcif.model.Exptl.java
org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly.java
org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme.java
org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme.java
org.biojava.bio.structure.io.mmcif.model.PdbxStructAssembly.java
org.biojava.bio.structure.io.mmcif.model.PdbxStructAssemblyGen.java
org.biojava.bio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer.java
org.biojava.bio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer.java
org.biojava.bio.structure.io.mmcif.model.PdbxStructOperList.java
org.biojava.bio.structure.io.mmcif.model.PdbxStructOperListXMLContainer.java
org.biojava.bio.structure.io.mmcif.model.Refine.java
org.biojava.bio.structure.io.mmcif.model.Struct.java
org.biojava.bio.structure.io.mmcif.model.StructAsym.java
org.biojava.bio.structure.io.mmcif.model.StructKeywords.java
org.biojava.bio.structure.io.mmcif.model.StructRef.java
org.biojava.bio.structure.io.mmcif.model.StructRefSeq.java
org.biojava.bio.structure.io.sifts.SiftsEntity.java
org.biojava.bio.structure.io.sifts.SiftsMappingProvider.java
org.biojava.bio.structure.io.sifts.SiftsResidue.java
org.biojava.bio.structure.io.sifts.SiftsSegment.java
org.biojava.bio.structure.io.sifts.SiftsXMLParser.java
org.biojava.bio.structure.io.util.FileDownloadUtils.java
org.biojava.bio.structure.jama.CholeskyDecomposition.java
org.biojava.bio.structure.jama.EigenvalueDecomposition.java
org.biojava.bio.structure.jama.LUDecomposition.java
org.biojava.bio.structure.jama.Maths.java
org.biojava.bio.structure.jama.Matrix.java
org.biojava.bio.structure.jama.QRDecomposition.java
org.biojava.bio.structure.jama.SingularValueDecomposition.java
org.biojava.bio.structure.quaternary.BioAssemblyTools.java
org.biojava.bio.structure.quaternary.BiologicalAssemblyBuilder.java
org.biojava.bio.structure.quaternary.CartesianProduct.java
org.biojava.bio.structure.quaternary.ModelTransformationMatrix.java
org.biojava.bio.structure.quaternary.OperatorResolver.java
org.biojava.bio.structure.quaternary.OrderedPair.java
org.biojava.bio.structure.quaternary.io.BioUnitDataProvider.java
org.biojava.bio.structure.quaternary.io.BioUnitDataProviderFactory.java
org.biojava.bio.structure.quaternary.io.FileBasedPDBBioUnitDataProvider.java
org.biojava.bio.structure.quaternary.io.MmCifBiolAssemblyProvider.java
org.biojava.bio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider.java
org.biojava.bio.structure.quaternary.io.PDBBioUnitDataProvider.java
org.biojava.bio.structure.quaternary.io.RawBioUnitDataProvider.java
org.biojava.bio.structure.quaternary.io.RemoteBioUnitDataProvider.java
org.biojava.bio.structure.quaternary.io.RemoteRawBioUnitDataProvider.java
org.biojava.bio.structure.scop.BerkeleyScopInstallation.java
org.biojava.bio.structure.scop.CachedRemoteScopInstallation.java
org.biojava.bio.structure.scop.RemoteScopInstallation.java
org.biojava.bio.structure.scop.ScopCategory.java
org.biojava.bio.structure.scop.ScopDatabase.java
org.biojava.bio.structure.scop.ScopDescription.java
org.biojava.bio.structure.scop.ScopDomain.java
org.biojava.bio.structure.scop.ScopFactory.java
org.biojava.bio.structure.scop.ScopInstallation.java
org.biojava.bio.structure.scop.ScopNode.java
org.biojava.bio.structure.scop.server.ScopDescriptions.java
org.biojava.bio.structure.scop.server.ScopDomains.java
org.biojava.bio.structure.scop.server.ScopNodes.java
org.biojava.bio.structure.scop.server.TreeSetStringWrapper.java
org.biojava.bio.structure.scop.server.XMLUtil.java
org.biojava.bio.structure.secstruc.BigSqrt.java
org.biojava.bio.structure.secstruc.BridgeType.java
org.biojava.bio.structure.secstruc.DistEn.java
org.biojava.bio.structure.secstruc.HBond.java
org.biojava.bio.structure.secstruc.Ladder.java
org.biojava.bio.structure.secstruc.SecStruc.java
org.biojava.bio.structure.secstruc.SecStrucGroup.java
org.biojava.bio.structure.secstruc.SecStrucState.java
org.biojava.bio.structure.secstruc.SecStrucType.java
org.biojava.bio.structure.server.FlatFileInstallation.java
org.biojava.bio.structure.server.MMCIFFileInstallation.java
org.biojava.bio.structure.server.PDBFilter.java
org.biojava.bio.structure.server.PDBInstallation.java
org.biojava.bio.structure.server.PrepareIndexFile.java
org.biojava.bio.structure.server.PrepareMMcifIndexFile.java
org.biojava.bio.structure.server.SimpleStructureServer.java
org.biojava.bio.structure.server.StructureEvent.java
org.biojava.bio.structure.server.StructureEventImpl.java
org.biojava.bio.structure.server.StructureFetcherRunnable.java
org.biojava.bio.structure.server.StructureListener.java
org.biojava.bio.structure.server.StructureServer.java
org.biojava3.structure.StructureIO.java
org/biojava/bio/structure/align/ce/package.html
org/biojava/bio/structure/align/client/package.html
org/biojava/bio/structure/align/fatcat/package.html
org/biojava/bio/structure/align/helper/package.html
org/biojava/bio/structure/align/package.html
org/biojava/bio/structure/align/pairwise/package.html
org/biojava/bio/structure/align/xml/package.html
org/biojava/bio/structure/io/mmcif/model/package.html
org/biojava/bio/structure/io/mmcif/package.html
org/biojava/bio/structure/io/package.html
org/biojava/bio/structure/jama/README.txt
org/biojava/bio/structure/jama/package.html
org/biojava/bio/structure/package.html
org/biojava/bio/structure/scop/package.html
org/biojava/bio/structure/server/package.html
org/biojava/bio/structure/standardaminos.pdb
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