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META-INF/MANIFEST.MF
META-INF/maven/org.biojava/biojava3-structure/pom.properties
META-INF/maven/org.biojava/biojava3-structure/pom.xml
blosum62.mat
ce.properties
chemcomp/2EP.cif.gz
chemcomp/2MD.cif.gz
chemcomp/6MO.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/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/DOD.cif.gz
chemcomp/DT.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/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/UNX.cif.gz
chemcomp/VAL.cif.gz
chemcomp/ZN.cif.gz
demo.ChemCompDistribution.class
demo.DemoAtomCache.class
demo.DemoCE.class
demo.DemoChangeChemCompProvider.class
demo.DemoCommandLineStartup.class
demo.DemoFATCAT.class
demo.DemoLoadStructure.class
demo.DemoMMCIFReader.class
demo.DemoSCOP.class
jfatcat.properties
org.biojava.bio.structure.AminoAcid.class
org.biojava.bio.structure.AminoAcidImpl.class
org.biojava.bio.structure.Atom.class
org.biojava.bio.structure.AtomImpl.class
org.biojava.bio.structure.AtomIterator.class
org.biojava.bio.structure.Author.class
org.biojava.bio.structure.Calc.class
org.biojava.bio.structure.Chain.class
org.biojava.bio.structure.ChainImpl.class
org.biojava.bio.structure.Compound.class
org.biojava.bio.structure.DBRef.class
org.biojava.bio.structure.Element.class
org.biojava.bio.structure.ElementType.class
org.biojava.bio.structure.Group.class
org.biojava.bio.structure.GroupIterator.class
org.biojava.bio.structure.GroupType.class
org.biojava.bio.structure.HetatomImpl.class
org.biojava.bio.structure.JournalArticle.class
org.biojava.bio.structure.Mutator.class
org.biojava.bio.structure.NucleotideImpl.class
org.biojava.bio.structure.PDBHeader.class
org.biojava.bio.structure.PDBRecord.class
org.biojava.bio.structure.ResidueNumber.class
org.biojava.bio.structure.SSBond.class
org.biojava.bio.structure.SVDSuperimposer.class
org.biojava.bio.structure.Site.class
org.biojava.bio.structure.StandardAminoAcid.class
org.biojava.bio.structure.Structure.class
org.biojava.bio.structure.StructureException.class
org.biojava.bio.structure.StructureImpl.class
org.biojava.bio.structure.StructureTools.class
org.biojava.bio.structure.UnknownPdbAminoAcidException.class
org.biojava.bio.structure.align.AFPTwister.class
org.biojava.bio.structure.align.AbstractStructureAlignment.class
org.biojava.bio.structure.align.BioJavaStructureAlignment.class
org.biojava.bio.structure.align.CallableStructureAlignment.class
org.biojava.bio.structure.align.ClusterAltAligs.class
org.biojava.bio.structure.align.FarmJob.class
org.biojava.bio.structure.align.StrucAligParameters.class
org.biojava.bio.structure.align.StructureAlignment.class
org.biojava.bio.structure.align.StructureAlignmentFactory.class
org.biojava.bio.structure.align.StructurePairAligner.class
org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor.class
org.biojava.bio.structure.align.ce.CECalculator.class
org.biojava.bio.structure.align.ce.CeCPMain.class
org.biojava.bio.structure.align.ce.CeMain.class
org.biojava.bio.structure.align.ce.CeParameters.class
org.biojava.bio.structure.align.ce.CeSideChainMain.class
org.biojava.bio.structure.align.ce.CeSideChainUserArgumentProcessor.class
org.biojava.bio.structure.align.ce.CeUserArgumentProcessor.class
org.biojava.bio.structure.align.ce.ConfigStrucAligParams.class
org.biojava.bio.structure.align.ce.GuiWrapper.class
org.biojava.bio.structure.align.ce.StartupParameters.class
org.biojava.bio.structure.align.ce.UserArgumentProcessor.class
org.biojava.bio.structure.align.client.CountProgressListener.class
org.biojava.bio.structure.align.client.FarmJobParameters.class
org.biojava.bio.structure.align.client.FarmJobRunnable.class
org.biojava.bio.structure.align.client.JFatCatClient.class
org.biojava.bio.structure.align.client.JobKillException.class
org.biojava.bio.structure.align.client.PdbPair.class
org.biojava.bio.structure.align.events.AlignmentProgressListener.class
org.biojava.bio.structure.align.fatcat.FatCat.class
org.biojava.bio.structure.align.fatcat.FatCatFlexible.class
org.biojava.bio.structure.align.fatcat.FatCatRigid.class
org.biojava.bio.structure.align.fatcat.FatCatUserArgumentProcessor.class
org.biojava.bio.structure.align.fatcat.calc.AFPCalculator.class
org.biojava.bio.structure.align.fatcat.calc.AFPChainer.class
org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer.class
org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor.class
org.biojava.bio.structure.align.fatcat.calc.FCAlignHelper.class
org.biojava.bio.structure.align.fatcat.calc.FatCatAligner.class
org.biojava.bio.structure.align.fatcat.calc.FatCatParameters.class
org.biojava.bio.structure.align.fatcat.calc.SigEva.class
org.biojava.bio.structure.align.fatcat.calc.StructureAlignmentOptimizer.class
org.biojava.bio.structure.align.helper.AligMatEl.class
org.biojava.bio.structure.align.helper.AlignTools.class
org.biojava.bio.structure.align.helper.GapArray.class
org.biojava.bio.structure.align.helper.IdxComparator.class
org.biojava.bio.structure.align.helper.IndexPair.class
org.biojava.bio.structure.align.helper.JointFragments.class
org.biojava.bio.structure.align.model.AFP.class
org.biojava.bio.structure.align.model.AFPChain.class
org.biojava.bio.structure.align.model.AfpChainWriter.class
org.biojava.bio.structure.align.pairwise.AligNPE.class
org.biojava.bio.structure.align.pairwise.Alignable.class
org.biojava.bio.structure.align.pairwise.AlignmentProgressListener.class
org.biojava.bio.structure.align.pairwise.AlignmentResult.class
org.biojava.bio.structure.align.pairwise.AltAligComparator.class
org.biojava.bio.structure.align.pairwise.AlternativeAlignment.class
org.biojava.bio.structure.align.pairwise.FragmentJoiner.class
org.biojava.bio.structure.align.pairwise.FragmentPair.class
org.biojava.bio.structure.align.pairwise.Gotoh.class
org.biojava.bio.structure.align.pairwise.JointFragmentsComparator.class
org.biojava.bio.structure.align.pairwise.StrCompAlignment.class
org.biojava.bio.structure.align.seq.SmithWaterman3DParameters.class
org.biojava.bio.structure.align.seq.SmithWaterman3Daligner.class
org.biojava.bio.structure.align.seq.SmithWatermanUserArgumentProcessor.class
org.biojava.bio.structure.align.util.AFPAlignmentDisplay.class
org.biojava.bio.structure.align.util.AFPChainScorer.class
org.biojava.bio.structure.align.util.AtomCache.class
org.biojava.bio.structure.align.util.CacheFactory.class
org.biojava.bio.structure.align.util.CliTools.class
org.biojava.bio.structure.align.util.CollectionTools.class
org.biojava.bio.structure.align.util.ConfigurationException.class
org.biojava.bio.structure.align.util.HTTPConnectionTools.class
org.biojava.bio.structure.align.util.ResourceManager.class
org.biojava.bio.structure.align.util.SynchronizedOutFile.class
org.biojava.bio.structure.align.util.UserConfiguration.class
org.biojava.bio.structure.align.xml.AFPChainFlipper.class
org.biojava.bio.structure.align.xml.AFPChainXMLConverter.class
org.biojava.bio.structure.align.xml.AFPChainXMLParser.class
org.biojava.bio.structure.align.xml.HasResultXMLConverter.class
org.biojava.bio.structure.align.xml.PdbPairXMLConverter.class
org.biojava.bio.structure.align.xml.PositionInQueueXMLConverter.class
org.biojava.bio.structure.align.xml.RepresentativeXMLConverter.class
org.biojava.bio.structure.domain.ProteinDomainParser.class
org.biojava.bio.structure.domain.pdp.ClusterDomains.class
org.biojava.bio.structure.domain.pdp.Cut.class
org.biojava.bio.structure.domain.pdp.CutDomain.class
org.biojava.bio.structure.domain.pdp.CutSites.class
org.biojava.bio.structure.domain.pdp.CutValues.class
org.biojava.bio.structure.domain.pdp.Domain.class
org.biojava.bio.structure.domain.pdp.GetDistanceMatrix.class
org.biojava.bio.structure.domain.pdp.PDPDistanceMatrix.class
org.biojava.bio.structure.domain.pdp.PDPParameters.class
org.biojava.bio.structure.domain.pdp.Segment.class
org.biojava.bio.structure.domain.pdp.SegmentComparator.class
org.biojava.bio.structure.domain.pdp.ShortSegmentRemover.class
org.biojava.bio.structure.io.CAConverter.class
org.biojava.bio.structure.io.FileConvert.class
org.biojava.bio.structure.io.FileParsingParameters.class
org.biojava.bio.structure.io.MMCIFFileReader.class
org.biojava.bio.structure.io.PDBFileParser.class
org.biojava.bio.structure.io.PDBFileReader.class
org.biojava.bio.structure.io.PDBParseException.class
org.biojava.bio.structure.io.PDBSRSReader.class
org.biojava.bio.structure.io.SeqRes2AtomAligner.class
org.biojava.bio.structure.io.StructureIO.class
org.biojava.bio.structure.io.StructureIOFile.class
org.biojava.bio.structure.io.mmcif.AllChemCompProvider.class
org.biojava.bio.structure.io.mmcif.ChemCompConsumer.class
org.biojava.bio.structure.io.mmcif.ChemCompGroupFactory.class
org.biojava.bio.structure.io.mmcif.ChemCompProvider.class
org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary.class
org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider.class
org.biojava.bio.structure.io.mmcif.MMcifConsumer.class
org.biojava.bio.structure.io.mmcif.MMcifParser.class
org.biojava.bio.structure.io.mmcif.ReducedChemCompProvider.class
org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer.class
org.biojava.bio.structure.io.mmcif.SimpleMMcifParser.class
org.biojava.bio.structure.io.mmcif.chem.ChemCompTools.class
org.biojava.bio.structure.io.mmcif.chem.PolymerType.class
org.biojava.bio.structure.io.mmcif.chem.ResidueType.class
org.biojava.bio.structure.io.mmcif.model.AbstractBean.class
org.biojava.bio.structure.io.mmcif.model.AtomSite.class
org.biojava.bio.structure.io.mmcif.model.AuditAuthor.class
org.biojava.bio.structure.io.mmcif.model.ChemComp.class
org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark.class
org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev.class
org.biojava.bio.structure.io.mmcif.model.Entity.class
org.biojava.bio.structure.io.mmcif.model.EntityPolySeq.class
org.biojava.bio.structure.io.mmcif.model.Exptl.class
org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly.class
org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme.class
org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme.class
org.biojava.bio.structure.io.mmcif.model.Refine.class
org.biojava.bio.structure.io.mmcif.model.Struct.class
org.biojava.bio.structure.io.mmcif.model.StructAsym.class
org.biojava.bio.structure.io.mmcif.model.StructKeywords.class
org.biojava.bio.structure.io.mmcif.model.StructRef.class
org.biojava.bio.structure.io.mmcif.model.StructRefSeq.class
org.biojava.bio.structure.jama.CholeskyDecomposition.class
org.biojava.bio.structure.jama.EigenvalueDecomposition.class
org.biojava.bio.structure.jama.LUDecomposition.class
org.biojava.bio.structure.jama.Maths.class
org.biojava.bio.structure.jama.Matrix.class
org.biojava.bio.structure.jama.QRDecomposition.class
org.biojava.bio.structure.jama.SingularValueDecomposition.class
org.biojava.bio.structure.scop.ScopCategory.class
org.biojava.bio.structure.scop.ScopDescription.class
org.biojava.bio.structure.scop.ScopDomain.class
org.biojava.bio.structure.scop.ScopInstallation.class
org.biojava.bio.structure.scop.ScopNode.class
org.biojava.bio.structure.secstruc.BigSqrt.class
org.biojava.bio.structure.secstruc.DistEn.class
org.biojava.bio.structure.secstruc.HBond.class
org.biojava.bio.structure.secstruc.SecStruc.class
org.biojava.bio.structure.secstruc.SecStrucGroup.class
org.biojava.bio.structure.secstruc.SecStrucState.class
org.biojava.bio.structure.server.DemoStructureServer.class
org.biojava.bio.structure.server.FlatFileInstallation.class
org.biojava.bio.structure.server.MMCIFFileInstallation.class
org.biojava.bio.structure.server.PDBFilter.class
org.biojava.bio.structure.server.PDBInstallation.class
org.biojava.bio.structure.server.PrepareIndexFile.class
org.biojava.bio.structure.server.PrepareMMcifIndexFile.class
org.biojava.bio.structure.server.SimpleStructureServer.class
org.biojava.bio.structure.server.StructureEvent.class
org.biojava.bio.structure.server.StructureEventImpl.class
org.biojava.bio.structure.server.StructureFetcherRunnable.class
org.biojava.bio.structure.server.StructureListener.class
org.biojava.bio.structure.server.StructureServer.class
org/biojava/bio/structure/standardaminos.pdb