org.biojava.nbio.alignment.io.StockholmStructure.addSequence(String, String)
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org.biojava.nbio.structure.align.ce.CECalculator.calc_rmsd(Atom[], Atom[], int, boolean, boolean)
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org.biojava.nbio.structure.StructureTools.cloneCAArray(Atom[])
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org.biojava.nbio.structure.StructureTools.convert_3code_1code(String)
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org.biojava.nbio.structure.io.PDBFileReader.downloadPDB(String) |
org.biojava.nbio.structure.align.util.UserConfiguration.getAutoFetch()
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org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults.getAverageTraceRmsd()
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org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults.getAverageTraceTmScoreMin()
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org.biojava.nbio.structure.align.util.AtomCache.getBiologicalUnit(String)
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org.biojava.nbio.structure.align.gui.DisplayAFP.getBlockNrForAlignPos(AFPChain, int)
use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
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org.biojava.nbio.structure.io.CAConverter.getCAOnly(Chain)
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org.biojava.nbio.structure.io.CAConverter.getCAOnly(List)
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org.biojava.nbio.structure.Structure.getConnections()
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org.biojava.nbio.core.sequence.compound.NucleotideCompound.getConsituents()
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org.biojava.nbio.structure.ChainImpl.getGroupsByPDB(ResidueNumber, ResidueNumber, boolean) |
org.biojava.nbio.structure.align.client.StructureName.getName()
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org.biojava.nbio.protmod.structure.ModifiedCompoundImpl.getOriginalModificationId()
use getModification().getId()
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org.biojava.nbio.structure.align.util.RotationAxis.getOtherTranslation() |
org.biojava.nbio.structure.ChainImpl.getParent()
use getStructure instead.
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org.biojava.nbio.structure.Chain.getParent()
use getStructure(Structure) instead.
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org.biojava.nbio.structure.StructureImpl.getPdbId() |
org.biojava.nbio.structure.Structure.getPdbId()
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org.biojava.nbio.structure.cath.CathDomain.getPdbId()
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org.biojava.nbio.structure.StructureImpl.getRanges() |
org.biojava.nbio.structure.Structure.getRanges()
From BioJava 4.2, use
getStructureIdentifier().toCanonical().getRanges()
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org.biojava.nbio.structure.quaternary.BioAssemblyTools.getReducedCAStructure(Structure)
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org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, int)
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org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, String)
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org.biojava.nbio.structure.StructureImpl.getResidueRanges() |
org.biojava.nbio.structure.Structure.getResidueRanges()
From BioJava 4.2, use
getStructureIdentifier().toCanonical().getResidueRanges()
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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
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org.biojava.nbio.structure.align.model.AFPChain.getSimilarity2()
use getCoverage2() instead
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org.biojava.nbio.structure.StructureTools.getSubRanges(Structure, String)
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org.biojava.nbio.structure.PDBCrystallographicInfo.getZ()
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org.biojava.nbio.structure.align.util.AtomCache.isAutoFetch()
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org.biojava.nbio.structure.io.LocalPDBDirectory.isAutoFetch()
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org.biojava.nbio.structure.align.StructurePairAligner.isDebug() |
org.biojava.nbio.structure.align.util.AtomCache.isFetchCurrent()
Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
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org.biojava.nbio.structure.io.PDBFileReader.isFetchCurrent()
Use FileParsingParameters#getObsoleteBehavior()
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org.biojava.nbio.structure.align.util.AtomCache.isFetchFileEvenIfObsolete()
Use FileParsingParameters#getObsoleteBehavior() instead (4.0.0)
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org.biojava.nbio.structure.io.PDBFileReader.isFetchFileEvenIfObsolete()
Use FileParsingParameters#getObsoleteBehavior()
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org.biojava.nbio.structure.align.ce.StartupParameters.isPdbDirSplit()
Always returns true (4.0.0)
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org.biojava.nbio.structure.align.util.AtomCache.isStrictSCOP()
since 4.2
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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)
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org.biojava.nbio.structure.Identifier.loadIdentifier(String, AtomCache)
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org.biojava.nbio.genome.parsers.gff.LocIterator.main(String[]) |
org.biojava.nbio.genome.parsers.gff.Location.main(String[]) |
org.biojava.nbio.genome.parsers.gff.Feature.main(String[]) |
org.biojava.nbio.genome.parsers.gff.FeatureList.main(String[]) |
org.biojava.nbio.structure.align.util.UserConfiguration.setAutoFetch(boolean)
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org.biojava.nbio.structure.align.util.AtomCache.setAutoFetch(boolean)
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org.biojava.nbio.structure.io.LocalPDBDirectory.setAutoFetch(boolean)
Use #setFetchBehavior()
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org.biojava.nbio.structure.Structure.setConnections(List
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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)
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org.biojava.nbio.structure.align.util.AtomCache.setFetchFileEvenIfObsolete(boolean)
Use FileParsingParameters#setObsoleteBehavior() instead (4.0.0)
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org.biojava.nbio.structure.io.PDBFileReader.setFetchFileEvenIfObsolete(boolean)
Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
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org.biojava.nbio.structure.StructureImpl.setNmr(boolean) |
org.biojava.nbio.structure.Structure.setNmr(boolean) |
org.biojava.nbio.structure.ChainImpl.setParent(Structure) |
org.biojava.nbio.structure.Chain.setParent(Structure)
use setStructure instead
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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)
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org.biojava.nbio.structure.align.util.AtomCache.setStrictSCOP(boolean)
Removed in 4.2.0
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org.biojava.nbio.structure.io.FileParsingParameters.setUpdateRemediatedFiles(boolean)
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