Deprecated List

Deprecated Classes
Class	Description
org.biojava.nbio.structure.Identifier	Use `StructureName` instead. Deprecated in v. 4.2.0
org.biojava.nbio.structure.gui.RasmolCommandListener	use org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener instead

Deprecated Methods
Method	Description
org.biojava.nbio.structure.symmetry.internal.SymmetryAxes.addAxis(Matrix4d, List<List<Integer>>, List<Integer>, Integer)	Use `SymmetryAxes.addAxis(Matrix4d, int, SymmetryType)` instead. Repeats and Superposition are now inferred automatically.
org.biojava.nbio.alignment.io.StockholmStructure.addSequence(String, String)	Use `StockholmStructure.appendToSequence(String,String)` instead
org.biojava.nbio.structure.align.ce.CECalculator.calc_rmsd(Atom[], Atom[], int, boolean, boolean)	Use `CECalculator.calc_rmsd(Atom[],Atom[],int,boolean)` instead
org.biojava.nbio.structure.StructureTools.cloneCAArray(Atom[])	Use the better-named `StructureTools.cloneAtomArray(Atom[])` instead
org.biojava.nbio.structure.StructureTools.convert_3code_1code(String)	Use `StructureTools.get1LetterCodeAmino(String)` instead
org.biojava.nbio.structure.io.PDBFileReader.downloadPDB(String)
org.biojava.nbio.structure.symmetry.utils.SymmetryTools.equivalentAxes(Matrix4d, Matrix4d, double)
org.biojava.nbio.structure.align.util.UserConfiguration.getAutoFetch()	Use `UserConfiguration.getFetchBehavior()`
org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults.getAverageTraceRmsd()	use `QuatSymmetryResults.getScores()` instead.
org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults.getAverageTraceTmScoreMin()	use `QuatSymmetryResults.getScores()` instead.
org.biojava.nbio.structure.align.util.AtomCache.getBiologicalUnit(String)	Renamed to `AtomCache.getBiologicalAssembly(String)` in 4.2
org.biojava.nbio.structure.align.gui.DisplayAFP.getBlockNrForAlignPos(AFPChain, int)	use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
org.biojava.nbio.structure.io.CAConverter.getCAOnly(List<Chain>)	Use the more generic `CAConverter.getRepresentativeAtomsOnly(List)` instead
org.biojava.nbio.structure.io.CAConverter.getCAOnly(Chain)	Use the more generic `CAConverter.getRepresentativeAtomsOnly(Chain)` instead
org.biojava.nbio.structure.Structure.getConnections()	use `Atom.getBonds()` instead
org.biojava.nbio.core.sequence.compound.NucleotideCompound.getConsituents()	replaced with `NucleotideCompound.getConstituents()` due to typographical error
org.biojava.nbio.structure.ChainImpl.getGroupsByPDB(ResidueNumber, ResidueNumber, boolean)
org.biojava.nbio.structure.align.client.StructureName.getName()	use `StructureName.getIdentifier()`
org.biojava.nbio.protmod.structure.ModifiedCompoundImpl.getOriginalModificationId()	use getModification().getId()
org.biojava.nbio.structure.align.util.RotationAxis.getOtherTranslation()
org.biojava.nbio.structure.Chain.getParent()	use getStructure(Structure) instead.
org.biojava.nbio.structure.ChainImpl.getParent()	use getStructure instead.
org.biojava.nbio.structure.cath.CathDomain.getPdbId()	This method is poorly named; use `CathDomain.getThePdbId()` or `CathDomain.getPdbIdAndChain()` instead
org.biojava.nbio.structure.Structure.getPdbId()	From BioJava 4.2, use `Structure.getPDBCode()` or `getStructureIdentifier().toCanonical().getPdbId()`
org.biojava.nbio.structure.StructureImpl.getPdbId()
org.biojava.nbio.structure.Structure.getRanges()	From BioJava 4.2, use `getStructureIdentifier().toCanonical().getRanges()`
org.biojava.nbio.structure.StructureImpl.getRanges()
org.biojava.nbio.structure.quaternary.BioAssemblyTools.getReducedCAStructure(Structure)	Use the more generic `BioAssemblyTools.getReducedStructure(Structure)`
org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, int)	Use `StructureIdentifier.reduce(Structure)` instead (v. 4.2.0)
org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, String)	Use `StructureIdentifier.reduce(Structure)` instead (v. 4.2.0)
org.biojava.nbio.structure.Structure.getResidueRanges()	From BioJava 4.2, use `getStructureIdentifier().toCanonical().getResidueRanges()`
org.biojava.nbio.structure.StructureImpl.getResidueRanges()
org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry.getRotationGroup()
org.biojava.nbio.structure.gui.JMatrixPanel.getSaturation()
org.biojava.nbio.structure.gui.JMatrixPanel.getScalevalue()
org.biojava.nbio.structure.scop.ScopInstallation.getScopDownloadURL()
org.biojava.nbio.structure.align.model.AFPChain.getSimilarity1()	use getCoverage1() instead
org.biojava.nbio.structure.align.model.AFPChain.getSimilarity2()	use getCoverage2() instead
org.biojava.nbio.structure.StructureTools.getSubRanges(Structure, String)	Use `StructureIdentifier` instead (4.2.0)
org.biojava.nbio.structure.PDBCrystallographicInfo.getZ()	As of 4.0, use `SpaceGroup.getMultiplicity()` and `Structure.size()`
org.biojava.nbio.structure.align.util.AtomCache.isAutoFetch()	Use `AtomCache.getFetchBehavior()`
org.biojava.nbio.structure.io.LocalPDBDirectory.isAutoFetch()	Use `LocalPDBDirectory.getFetchBehavior()`
org.biojava.nbio.structure.align.StructurePairAligner.isDebug()
org.biojava.nbio.structure.align.util.AtomCache.isFetchCurrent()	Use `FileParsingParameters#getObsoleteBehavior()` instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.isFetchCurrent()	Use `FileParsingParameters#getObsoleteBehavior()`
org.biojava.nbio.structure.align.util.AtomCache.isFetchFileEvenIfObsolete()	Use `FileParsingParameters#getObsoleteBehavior()` instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.isFetchFileEvenIfObsolete()	Use `FileParsingParameters#getObsoleteBehavior()`
org.biojava.nbio.structure.align.ce.StartupParameters.isPdbDirSplit()	Always returns true (4.0.0)
org.biojava.nbio.structure.symmetry.utils.SymmetryTools.isRefined(MultipleAlignment)
org.biojava.nbio.structure.symmetry.utils.SymmetryTools.isSignificant(MultipleAlignment, double)
org.biojava.nbio.structure.align.util.AtomCache.isStrictSCOP()	since 4.2
org.biojava.nbio.structure.io.FileParsingParameters.isUpdateRemediatedFiles()	Properties which impact downloading and caching behavior have been moved to the `StructureIOFile` implementations. See `LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)`
org.biojava.nbio.structure.Identifier.loadIdentifier(String, AtomCache)	Create a new `StructureName` instead.
org.biojava.nbio.genome.parsers.gff.Feature.main(String[])
org.biojava.nbio.genome.parsers.gff.FeatureList.main(String[])
org.biojava.nbio.genome.parsers.gff.Location.main(String[])
org.biojava.nbio.genome.parsers.gff.LocIterator.main(String[])
org.biojava.nbio.structure.align.util.AtomCache.setAutoFetch(boolean)	Use `AtomCache.getFetchBehavior()`
org.biojava.nbio.structure.align.util.UserConfiguration.setAutoFetch(boolean)	Use `UserConfiguration.getFetchBehavior()`
org.biojava.nbio.structure.io.LocalPDBDirectory.setAutoFetch(boolean)	Use `#setFetchBehavior()`
org.biojava.nbio.structure.Structure.setConnections(List<Map<String, Integer>>)	use `Atom.addBond(Bond)` instead
org.biojava.nbio.structure.align.StructurePairAligner.setDebug(boolean)
org.biojava.nbio.structure.align.util.AtomCache.setFetchCurrent(boolean)	Use `FileParsingParameters#setObsoleteBehavior()` instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.setFetchCurrent(boolean)	Use `FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)`
org.biojava.nbio.structure.align.util.AtomCache.setFetchFileEvenIfObsolete(boolean)	Use `FileParsingParameters#setObsoleteBehavior()` instead (4.0.0)
org.biojava.nbio.structure.io.PDBFileReader.setFetchFileEvenIfObsolete(boolean)	Use `FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)`
org.biojava.nbio.structure.io.StructureProvider.setFileParsingParameters(FileParsingParameters)
org.biojava.nbio.structure.Structure.setNmr(boolean)
org.biojava.nbio.structure.StructureImpl.setNmr(boolean)
org.biojava.nbio.structure.Chain.setParent(Structure)	use setStructure instead
org.biojava.nbio.structure.ChainImpl.setParent(Structure)
org.biojava.nbio.structure.align.ce.StartupParameters.setPdbDirSplit(boolean)	Ignored (4.0.0)
org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult(boolean)
org.biojava.nbio.structure.gui.JMatrixPanel.setSaturation(float)
org.biojava.nbio.structure.gui.JMatrixPanel.setScalevalue(float)
org.biojava.nbio.structure.scop.ScopInstallation.setScopDownloadURL(String)	Use `ScopInstallation.addMirror(java.lang.String)` instead
org.biojava.nbio.structure.align.util.AtomCache.setStrictSCOP(boolean)	Removed in 4.2.0
org.biojava.nbio.structure.io.FileParsingParameters.setUpdateRemediatedFiles(boolean)	Properties which impact downloading and caching behavior have been moved to the `StructureIOFile` implementations. See `LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)`
org.biojava.nbio.structure.io.mmcif.MMCIFFileTools.toMMCIF(List<T>)	The `MMCIFFileTools.toMMCIF(List, Class)` provides compile-time type safety

Deprecated Constructors
Constructor	Description
org.biojava.nbio.structure.align.model.AFPChain()
org.biojava.nbio.structure.align.util.AtomCache(String, boolean)	isSplit parameter is ignored (4.0.0)
org.biojava.nbio.structure.align.util.AtomCache(String, String, boolean)	isSplit parameter is ignored (4.0.0)
org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean)	Retained for backwards compatability, setting `RNAToAminoAcidTranslator.stopAtStopCodons` to `false`
org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound>, CompoundSet<NucleotideCompound>, CompoundSet<Table.Codon>, CompoundSet<AminoAcidCompound>, Table, boolean, boolean, boolean, boolean)

Deprecated API

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