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Deprecated ClassesClassDescriptionuse org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener insteadUse
StructureNameinstead. Deprecated in v. 4.2.0
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Deprecated MethodsMethodDescriptionreplaced with
NucleotideCompound.getConstituents()due to typographical erroruse getModification().getId()Always returns true (4.0.0)Ignored (4.0.0)use AFPAlignmentDisplay.getBlockNrForAlignPos instead...use getCoverage1() insteaduse getCoverage2() insteadRenamed toAtomCache.getBiologicalAssembly(String)in 4.2UseFileParsingParameters#getObsoleteBehavior()instead (4.0.0)UseFileParsingParameters#getObsoleteBehavior()instead (4.0.0)since 4.2UseFileParsingParameters#setObsoleteBehavior()instead (4.0.0)UseFileParsingParameters#setObsoleteBehavior()instead (4.0.0)Removed in 4.2.0This method is poorly named; useCathDomain.getThePdbId()orCathDomain.getPdbIdAndChain()insteaduse getStructure(Structure) instead.use setStructure insteaduse getStructure instead.Create a newStructureNameinstead.Use the more genericCAConverter.getRepresentativeAtomsOnly(List)insteadUse the more genericCAConverter.getRepresentativeAtomsOnly(Chain)insteadProperties which impact downloading and caching behavior have been moved to theStructureIOFileimplementations. SeeLocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)Properties which impact downloading and caching behavior have been moved to theStructureIOFileimplementations. SeeLocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)Use#setFetchBehavior()TheMMCIFFileTools.toMMCIF(List, Class)provides compile-time type safetyUseFileParsingParameters#getObsoleteBehavior()UseFileParsingParameters#getObsoleteBehavior()UseFileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)UseFileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)As of 4.0, useSpaceGroup.getMultiplicity()andStructure.size()Use the more genericBioAssemblyTools.getReducedStructure(Structure)UseScopInstallation.addMirror(java.lang.String)insteaduseAtom.getBonds()insteadFrom BioJava 4.2, useStructure.getPDBCode()orgetStructureIdentifier().toCanonical().getPdbId()From BioJava 4.2, usegetStructureIdentifier().toCanonical().getRanges()From BioJava 4.2, usegetStructureIdentifier().toCanonical().getResidueRanges()useAtom.addBond(Bond)insteadUse the better-namedStructureTools.cloneAtomArray(Atom[])insteadUseStructureTools.get1LetterCodeAmino(String)insteadUseStructureIdentifier.reduce(Structure)instead (v. 4.2.0)UseStructureIdentifier.reduce(Structure)instead (v. 4.2.0)UseStructureIdentifierinstead (4.2.0)useQuatSymmetryResults.getScores()instead.useQuatSymmetryResults.getScores()instead.UseSymmetryAxes.addAxis(Matrix4d, int, SymmetryType)instead. Repeats and Superposition are now inferred automatically.
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Deprecated ConstructorsConstructorDescriptionRetained for backwards compatability, setting
RNAToAminoAcidTranslator.stopAtStopCodonstofalseisSplit parameter is ignored (4.0.0)isSplit parameter is ignored (4.0.0)