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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