Deprecated API

Contents

• Methods

Methods

Method	Description
org.biojava.nbio.genome.parsers.gff.LocIterator.main(String[])
org.biojava.nbio.structure.Chain.getAtomLigands()	since biojava 5.0 this does not apply anymore. Chains contain either polymeric groups or non-polymeric groups
org.biojava.nbio.structure.Chain.getChainID()	use getId() instead
org.biojava.nbio.structure.Chain.getInternalChainID()	use Chain.getId() instead
org.biojava.nbio.structure.Chain.getParent()	use getStructure(Structure) instead.
org.biojava.nbio.structure.Chain.setChainID(String)	use Chain.setId(String asymId) instead
org.biojava.nbio.structure.Chain.setInternalChainID(String)	use #setId() instead
org.biojava.nbio.structure.Chain.setParent(Structure)	use setStructure instead
org.biojava.nbio.structure.ChainImpl.getParent()	use getStructure instead.
org.biojava.nbio.structure.ChainImpl.setParent(Structure)
org.biojava.nbio.structure.contact.Grid.getContacts()	use Grid.getAtomContacts() instead
org.biojava.nbio.structure.Structure.findChain(String)
org.biojava.nbio.structure.Structure.getChainByPDB(String)	use Structure.getPolyChainByPDB(String) instead
org.biojava.nbio.structure.Structure.getCompoundById(int)	use Structure.getEntityById(int) instead
org.biojava.nbio.structure.Structure.getPdbId()	From BioJava 4.2, use Structure.getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
org.biojava.nbio.structure.Structure.getRanges()	From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
org.biojava.nbio.structure.Structure.getResidueRanges()	From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()
org.biojava.nbio.structure.StructureImpl.getPdbId()
org.biojava.nbio.structure.StructureImpl.getRanges()
org.biojava.nbio.structure.StructureImpl.getResidueRanges()
org.biojava.nbio.structure.StructureTools.getPredominantGroupType(Chain)	use Chain.getPredominantGroupType() instead.
org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, String)	Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
org.biojava.nbio.structure.StructureTools.isChainPureNonPolymer(Chain)	use Chain.isPureNonPolymer() instead.
org.biojava.nbio.structure.StructureTools.isChainWaterOnly(Chain)	use Chain.isWaterOnly() instead.
org.biojava.nbio.structure.StructureTools.isNucleicAcid(Chain)	use Chain.isNucleicAcid() instead.
org.biojava.nbio.structure.StructureTools.isProtein(Chain)	use Chain.isProtein() instead.
org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult(boolean)