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Jar File Download » b » biojava3   Download biojava3-structure-3.0.5-sources.jar Files contained in biojava3-structure-3.0.5-sources.jar:  META-INF/MANIFEST.MF demo.DemoChangeChemCompProvider.java demo.DemoMMCIFReader.java demo.DemoCATH.java demo.DemoLoadStructure.java demo.DemoFATCAT.java demo.DemoDomainsplit.java demo.DemoAtomCache.java demo.DemoSCOP.java demo.ChemCompDistribution.java demo.DemoBerkeleyScop.java demo.DemoCE.java demo.DemoCommandLineStartup.java org.biojava.bio.structure.cath.CathInstallation.java org.biojava.bio.structure.cath.CathSegment.java org.biojava.bio.structure.cath.CathFragment.java org.biojava.bio.structure.cath.CathDatabase.java org.biojava.bio.structure.cath.CathNode.java org.biojava.bio.structure.cath.CathDomain.java org.biojava.bio.structure.cath.CathCategory.java org.biojava.bio.structure.secstruc.DistEn.java org.biojava.bio.structure.secstruc.SecStrucGroup.java org.biojava.bio.structure.secstruc.HBond.java org.biojava.bio.structure.secstruc.BigSqrt.java org.biojava.bio.structure.secstruc.Ladder.java org.biojava.bio.structure.secstruc.SecStruc.java org.biojava.bio.structure.secstruc.SecStrucState.java org.biojava.bio.structure.secstruc.SecStrucType.java org.biojava.bio.structure.secstruc.BridgeType.java org.biojava.bio.structure.server.SimpleStructureServer.java org.biojava.bio.structure.server.PrepareMMcifIndexFile.java org.biojava.bio.structure.server.StructureEvent.java org.biojava.bio.structure.server.StructureEventImpl.java org.biojava.bio.structure.server.PrepareIndexFile.java org.biojava.bio.structure.server.StructureListener.java org.biojava.bio.structure.server.PDBInstallation.java org.biojava.bio.structure.server.StructureServer.java org.biojava.bio.structure.server.FlatFileInstallation.java org.biojava.bio.structure.server.StructureFetcherRunnable.java org.biojava.bio.structure.server.PDBFilter.java org.biojava.bio.structure.server.MMCIFFileInstallation.java org/biojava/bio/structure/server/package.html org.biojava.bio.structure.align.helper.AligMatEl.java org.biojava.bio.structure.align.helper.IndexPair.java org.biojava.bio.structure.align.helper.GapArray.java org.biojava.bio.structure.align.helper.JointFragments.java org.biojava.bio.structure.align.helper.AlignTools.java org.biojava.bio.structure.align.helper.IdxComparator.java org/biojava/bio/structure/align/helper/package.html org.biojava.bio.structure.align.pairwise.AligNPE.java org.biojava.bio.structure.align.pairwise.FragmentPair.java org.biojava.bio.structure.align.pairwise.Gotoh.java org.biojava.bio.structure.align.pairwise.AltAligComparator.java org.biojava.bio.structure.align.pairwise.StrCompAlignment.java org.biojava.bio.structure.align.pairwise.AlignmentProgressListener.java org.biojava.bio.structure.align.pairwise.FragmentJoiner.java org.biojava.bio.structure.align.pairwise.AlignmentResult.java org.biojava.bio.structure.align.pairwise.AlternativeAlignment.java org.biojava.bio.structure.align.pairwise.Alignable.java org/biojava/bio/structure/align/pairwise/package.html org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor.java org.biojava.bio.structure.align.ce.CECalculator.java org.biojava.bio.structure.align.ce.CeSideChainMain.java org.biojava.bio.structure.align.ce.OptimalCECPMain.java org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor.java org.biojava.bio.structure.align.ce.MatrixListener.java org.biojava.bio.structure.align.ce.CeParameters.java org.biojava.bio.structure.align.ce.CeCPUserArgumentProcessor.java org/biojava/bio/structure/align/ce/package.html org.biojava.bio.structure.align.ce.CeCPMain.java org.biojava.bio.structure.align.ce.UserArgumentProcessor.java org.biojava.bio.structure.align.ce.OptimalCECPParameters.java org.biojava.bio.structure.align.ce.GuiWrapper.java org.biojava.bio.structure.align.ce.StartupParameters.java org.biojava.bio.structure.align.ce.ConfigStrucAligParams.java org.biojava.bio.structure.align.ce.CeCalculatorEnhanced.java org.biojava.bio.structure.align.ce.CeUserArgumentProcessor.java org.biojava.bio.structure.align.ce.CeMain.java org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor.java org.biojava.bio.structure.align.seq.SmithWaterman3Daligner.java org.biojava.bio.structure.align.seq.SmithWaterman3DParameters.java org.biojava.bio.structure.align.model.AFP.java org.biojava.bio.structure.align.model.AfpChainWriter.java org.biojava.bio.structure.align.model.AFPChain.java org.biojava.bio.structure.align.xml.AFPChainXMLConverter.java org.biojava.bio.structure.align.xml.HasResultXMLConverter.java org.biojava.bio.structure.align.xml.AFPChainXMLParser.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.align.xml.PdbPairXMLConverter.java org.biojava.bio.structure.align.xml.AFPChainFlipper.java org/biojava/bio/structure/align/xml/package.html 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.StructureAlignmentOptimizer.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.AFPOptimizer.java org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor.java org.biojava.bio.structure.align.fatcat.calc.SigEva.java org.biojava.bio.structure.align.fatcat.FatCatRigid.java org.biojava.bio.structure.align.fatcat.FatCat.java org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor.java org.biojava.bio.structure.align.fatcat.FatCatFlexible.java org/biojava/bio/structure/align/fatcat/package.html org.biojava.bio.structure.align.events.AlignmentProgressListener.java org.biojava.bio.structure.align.util.AlignmentTools.java org.biojava.bio.structure.align.util.HTTPConnectionTools.java org.biojava.bio.structure.align.util.ResourceManager.java org.biojava.bio.structure.align.util.AtomCache.java org.biojava.bio.structure.align.util.ConfigurationException.java org.biojava.bio.structure.align.util.UserConfiguration.java org.biojava.bio.structure.align.util.AFPChainScorer.java org.biojava.bio.structure.align.util.SynchronizedOutFile.java org.biojava.bio.structure.align.util.CliTools.java org.biojava.bio.structure.align.util.AFPAlignmentDisplay.java org.biojava.bio.structure.align.util.CacheFactory.java org.biojava.bio.structure.align.util.CollectionTools.java org.biojava.bio.structure.align.client.PdbPair.java org.biojava.bio.structure.align.client.StructureName.java org.biojava.bio.structure.align.client.CountProgressListener.java org.biojava.bio.structure.align.client.FarmJobParameters.java org.biojava.bio.structure.align.client.JobKillException.java org.biojava.bio.structure.align.client.FarmJobRunnable.java org.biojava.bio.structure.align.client.JFatCatClient.java org/biojava/bio/structure/align/client/package.html org.biojava.bio.structure.align.StructureAlignment.java org.biojava.bio.structure.align.ClusterAltAligs.java org.biojava.bio.structure.align.StructurePairAligner.java org/biojava/bio/structure/align/package.html org.biojava.bio.structure.align.CallableStructureAlignment.java org.biojava.bio.structure.align.FarmJob.java org.biojava.bio.structure.align.StrucAligParameters.java org.biojava.bio.structure.align.AbstractStructureAlignment.java org.biojava.bio.structure.align.StructureAlignmentFactory.java org.biojava.bio.structure.align.AFPTwister.java org.biojava.bio.structure.align.BioJavaStructureAlignment.java org.biojava.bio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider.java org.biojava.bio.structure.quaternary.io.FileBasedPDBBioUnitDataProvider.java org.biojava.bio.structure.quaternary.io.PDBBioUnitDataProvider.java org.biojava.bio.structure.quaternary.io.RemoteRawBioUnitDataProvider.java org.biojava.bio.structure.quaternary.io.BioUnitDataProviderFactory.java org.biojava.bio.structure.quaternary.io.RawBioUnitDataProvider.java org.biojava.bio.structure.quaternary.io.RemoteBioUnitDataProvider.java org.biojava.bio.structure.quaternary.io.MmCifBiolAssemblyProvider.java org.biojava.bio.structure.quaternary.io.BioUnitDataProvider.java org.biojava.bio.structure.quaternary.OrderedPair.java org.biojava.bio.structure.quaternary.BioAssemblyTools.java org.biojava.bio.structure.quaternary.CartesianProduct.java org.biojava.bio.structure.quaternary.BiologicalAssemblyBuilder.java org.biojava.bio.structure.quaternary.ModelTransformationMatrix.java org.biojava.bio.structure.quaternary.OperatorResolver.java org.biojava.bio.structure.scop.server.ScopDomains.java org.biojava.bio.structure.scop.server.TreeSetStringWrapper.java org.biojava.bio.structure.scop.server.ScopDescriptions.java org.biojava.bio.structure.scop.server.ScopNodes.java org.biojava.bio.structure.scop.server.XMLUtil.java org.biojava.bio.structure.scop.RemoteScopInstallation.java org.biojava.bio.structure.scop.ScopCategory.java org.biojava.bio.structure.scop.ScopInstallation.java org.biojava.bio.structure.scop.ScopDescription.java org.biojava.bio.structure.scop.BerkeleyScopInstallation.java org.biojava.bio.structure.scop.ScopDatabase.java org.biojava.bio.structure.scop.CachedRemoteScopInstallation.java org.biojava.bio.structure.scop.ScopNode.java org.biojava.bio.structure.scop.ScopDomain.java org.biojava.bio.structure.scop.ScopFactory.java org/biojava/bio/structure/scop/package.html org.biojava.bio.structure.domain.pdp.GetDistanceMatrix.java org.biojava.bio.structure.domain.pdp.Segment.java org.biojava.bio.structure.domain.pdp.ShortSegmentRemover.java org.biojava.bio.structure.domain.pdp.CutDomain.java org.biojava.bio.structure.domain.pdp.CutSites.java org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix.java org.biojava.bio.structure.domain.pdp.Domain.java org.biojava.bio.structure.domain.pdp.PDPParameters.java org.biojava.bio.structure.domain.pdp.SegmentComparator.java org.biojava.bio.structure.domain.pdp.Cut.java org.biojava.bio.structure.domain.pdp.CutValues.java org.biojava.bio.structure.domain.pdp.ClusterDomains.java org.biojava.bio.structure.domain.LocalProteinDomainParser.java org.biojava.bio.structure.domain.DomainProvider.java org.biojava.bio.structure.domain.AssignmentXMLSerializer.java org.biojava.bio.structure.domain.PDBDomainProvider.java org.biojava.bio.structure.domain.DomainProviderFactory.java org.biojava.bio.structure.domain.RemotePDPProvider.java org.biojava.bio.structure.domain.SerializableCache.java org.biojava.bio.structure.domain.PDPProvider.java org.biojava.bio.structure.domain.RemoteDomainProvider.java org.biojava.bio.structure.io.sifts.SiftsMappingProvider.java org.biojava.bio.structure.io.sifts.SiftsEntity.java org.biojava.bio.structure.io.sifts.SiftsXMLParser.java org.biojava.bio.structure.io.sifts.SiftsResidue.java org.biojava.bio.structure.io.sifts.SiftsSegment.java org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme.java org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme.java org.biojava.bio.structure.io.mmcif.model.PdbxStructAssembly.java org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev.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.PdbxEntityNonPoly.java org.biojava.bio.structure.io.mmcif.model.Entity.java org.biojava.bio.structure.io.mmcif.model.StructKeywords.java org.biojava.bio.structure.io.mmcif.model.StructAsym.java org/biojava/bio/structure/io/mmcif/model/package.html org.biojava.bio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer.java org.biojava.bio.structure.io.mmcif.model.StructRef.java org.biojava.bio.structure.io.mmcif.model.PdbxStructOperList.java org.biojava.bio.structure.io.mmcif.model.Struct.java org.biojava.bio.structure.io.mmcif.model.AtomSite.java org.biojava.bio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer.java org.biojava.bio.structure.io.mmcif.model.EntityPolySeq.java org.biojava.bio.structure.io.mmcif.model.AuditAuthor.java org.biojava.bio.structure.io.mmcif.model.AbstractBean.java org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor.java org.biojava.bio.structure.io.mmcif.model.StructRefSeq.java org.biojava.bio.structure.io.mmcif.model.ChemComp.java org.biojava.bio.structure.io.mmcif.model.PdbxStructAssemblyGen.java org.biojava.bio.structure.io.mmcif.model.Exptl.java org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark.java org.biojava.bio.structure.io.mmcif.chem.ResidueType.java org.biojava.bio.structure.io.mmcif.chem.PolymerType.java org.biojava.bio.structure.io.mmcif.chem.ChemCompTools.java org.biojava.bio.structure.io.mmcif.AllChemCompProvider.java org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory.java org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer.java org.biojava.bio.structure.io.mmcif.ReducedChemCompProvider.java org.biojava.bio.structure.io.mmcif.SimpleMMcifParser.java org.biojava.bio.structure.io.mmcif.ChemCompProvider.java org.biojava.bio.structure.io.mmcif.ChemCompConsumer.java org.biojava.bio.structure.io.mmcif.MMcifConsumer.java org.biojava.bio.structure.io.mmcif.MMcifParser.java org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary.java org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider.java org/biojava/bio/structure/io/mmcif/package.html org.biojava.bio.structure.io.util.FileDownloadUtils.java org.biojava.bio.structure.io.SeqRes2AtomAligner.java org.biojava.bio.structure.io.LocalCacheStructureProvider.java org.biojava.bio.structure.io.StructureProvider.java org.biojava.bio.structure.io.SandboxStyleStructureProvider.java org.biojava.bio.structure.io.CAConverter.java org.biojava.bio.structure.io.PDBBioAssemblyParser.java org.biojava.bio.structure.io.MMCIFFileReader.java org/biojava/bio/structure/io/package.html org.biojava.bio.structure.io.PDBParseException.java org.biojava.bio.structure.io.PDBSRSReader.java org.biojava.bio.structure.io.FileConvert.java org.biojava.bio.structure.io.PDBFileParser.java org.biojava.bio.structure.io.FileParsingParameters.java org.biojava.bio.structure.io.StructureIOFile.java org.biojava.bio.structure.io.StructureIO.java org.biojava.bio.structure.io.PDBFileReader.java org.biojava.bio.structure.io.FastaStructureParser.java org.biojava.bio.structure.io.StructureSequenceMatcher.java org.biojava.bio.structure.jama.QRDecomposition.java org.biojava.bio.structure.jama.EigenvalueDecomposition.java org.biojava.bio.structure.jama.Matrix.java org/biojava/bio/structure/jama/README.txt org.biojava.bio.structure.jama.Maths.java org.biojava.bio.structure.jama.LUDecomposition.java org.biojava.bio.structure.jama.CholeskyDecomposition.java org.biojava.bio.structure.jama.SingularValueDecomposition.java org/biojava/bio/structure/jama/package.html org.biojava.bio.structure.Atom.java org.biojava.bio.structure.Calc.java org.biojava.bio.structure.PDBRecord.java org.biojava.bio.structure.PDBStatus.java org.biojava.bio.structure.UnknownPdbAminoAcidException.java org.biojava.bio.structure.AtomIterator.java org.biojava.bio.structure.PDBCrystallographicInfo.java org.biojava.bio.structure.NucleotideImpl.java org.biojava.bio.structure.PDBHeader.java org.biojava.bio.structure.JournalArticle.java org.biojava.bio.structure.StructureException.java org.biojava.bio.structure.StructureTools.java org.biojava.bio.structure.StructureImpl.java org.biojava.bio.structure.BondType.java org.biojava.bio.structure.Compound.java org.biojava.bio.structure.Mutator.java org.biojava.bio.structure.ElementType.java org.biojava.bio.structure.Group.java org.biojava.bio.structure.Structure.java org.biojava.bio.structure.Author.java org.biojava.bio.structure.Site.java org.biojava.bio.structure.ChainImpl.java org.biojava.bio.structure.StandardAminoAcid.java org.biojava.bio.structure.GroupIterator.java org.biojava.bio.structure.AminoAcidImpl.java org.biojava.bio.structure.ResidueNumber.java org.biojava.bio.structure.SVDSuperimposer.java org/biojava/bio/structure/package.html org.biojava.bio.structure.AtomImpl.java org.biojava.bio.structure.Bond.java org.biojava.bio.structure.Chain.java org.biojava.bio.structure.DBRef.java org.biojava.bio.structure.HetatomImpl.java org.biojava.bio.structure.AminoAcid.java org.biojava.bio.structure.SSBond.java org.biojava.bio.structure.Element.java org.biojava.bio.structure.GroupType.java org.biojava3.structure.StructureIO.java ce.properties about.properties jfatcat.properties org/biojava/bio/structure/standardaminos.pdb chemcomp/PRO.cif.gz chemcomp/PO4.cif.gz chemcomp/DOD.cif.gz chemcomp/DAR.cif.gz chemcomp/DT.cif.gz chemcomp/LYS.cif.gz chemcomp/ILE.cif.gz chemcomp/ARG.cif.gz chemcomp/CSE.cif.gz chemcomp/SEC.cif.gz chemcomp/UNX.cif.gz chemcomp/ACY.cif.gz chemcomp/HOH.cif.gz chemcomp/TYS.cif.gz chemcomp/A.cif.gz chemcomp/ANS.cif.gz chemcomp/C.cif.gz chemcomp/VAL.cif.gz chemcomp/CA.cif.gz chemcomp/DA.cif.gz chemcomp/MSE.cif.gz chemcomp/G.cif.gz chemcomp/DC.cif.gz chemcomp/GLU.cif.gz chemcomp/ZN.cif.gz chemcomp/I.cif.gz chemcomp/DG.cif.gz chemcomp/GLY.cif.gz chemcomp/DI.cif.gz chemcomp/SF4.cif.gz chemcomp/THR.cif.gz chemcomp/CYS.cif.gz chemcomp/NA.cif.gz chemcomp/6MO.cif.gz chemcomp/MG.cif.gz chemcomp/U.cif.gz chemcomp/SO4.cif.gz chemcomp/TRP.cif.gz chemcomp/MGD.cif.gz chemcomp/MAL.cif.gz chemcomp/MO.cif.gz chemcomp/PHE.cif.gz chemcomp/TYR.cif.gz chemcomp/CMP.cif.gz chemcomp/GLN.cif.gz chemcomp/GOL.cif.gz chemcomp/ASN.cif.gz chemcomp/2MD.cif.gz chemcomp/HIS.cif.gz chemcomp/ASP.cif.gz chemcomp/LEU.cif.gz chemcomp/MET.cif.gz chemcomp/KTH.cif.gz chemcomp/2EP.cif.gz chemcomp/SER.cif.gz chemcomp/ALA.cif.gz blosum62.mat                          biojava3/biojava3-structure-3.0.5-sources.jar.zip( 713 k) Related examples in the same category 1. 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