Deprecated API

Contents

• Deprecated Methods

Deprecated Methods

Method and Description
org.biojava.nbio.structure.Structure.findChain(String)
org.biojava.nbio.structure.Structure.findChain(String, int)
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.Structure.getChainByPDB(String) use Structure.getPolyChainByPDB(String) instead
org.biojava.nbio.structure.Structure.getChainByPDB(String, int) use Structure.getPolyChainByPDB(String,int) instead
org.biojava.nbio.structure.Chain.getChainID() use getId() instead
org.biojava.nbio.structure.Structure.getCompoundById(int) use Structure.getEntityById(int) instead
org.biojava.nbio.structure.contact.Grid.getContacts() use Grid.getAtomContacts() 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.ChainImpl.getParent() use getStructure instead.
org.biojava.nbio.structure.StructureImpl.getPdbId()
org.biojava.nbio.structure.Structure.getPdbId() From BioJava 4.2, use Structure.getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
org.biojava.nbio.structure.StructureTools.getPredominantGroupType(Chain) use Chain.getPredominantGroupType() instead.
org.biojava.nbio.structure.StructureImpl.getRanges()
org.biojava.nbio.structure.Structure.getRanges() From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, String) Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
org.biojava.nbio.structure.StructureImpl.getResidueRanges()
org.biojava.nbio.structure.Structure.getResidueRanges() From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()
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.genome.parsers.gff.LocIterator.main(String[])
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.setParent(Structure)
org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult(boolean)