BioJava 6.0.0

Removed

• All code related to All-vs-All structural alignments db calculation and access
• JFatCatClient and all code depending on it
• PDP domain providers (depended on JFatCatClient)
• Support for retrieving structure data with prefix "PDP:" (AtomCache, StructureIO)
• RemoteScopInstallation consuming data provided by source.rcsb.org
• The whole org.biojava.nbio.structure.rcsb package, a client for the legacy RCSB PDB APIs (disappearing in Nov 2020)
• The whole org.biojava.nbio.structure.validation package
• The org.biojava.nbio.structure.domain.PDBDomainProvider class to pull domain definitions from legacy RCSB PDB APIs
• Support for automatically fetching dssp files from RCSB (org.biojava.nbio.structure.secstruc.DSSPParser.fetch())
• org.biojava.nbio.structure.PDBStatus: simplified Status enum to 3 states, with OBSOLETE now called REMOVED
• org.biojava.nbio.structure.PDBStatus: removed getReplacement and getReplaces
• Removed org.biojava.nbio.structure.io.mmcif package
• Removed functionality to write isolated CIF headers from FileConvert
• Removed org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()
• Removed from org.biojava.nbio.structure.Chain interface: getParent(), setParent(), getAtomLigands(), getSwissprotId(), setSwissprotId(), getInternalChainID(), setInternalChainID(), getChainID(), setChainID()
• Removed from org.biojava.nbio.structure.Structure interface: findChain(), getId(), setId(), getChainByPDB(), getCompoundById(), getResidueRanges(), getRanges()
• Removed from org.biojava.nbio.structure.StructureTools : isNucleicAcid(), isProtein(), getPredominantGroupType(), isChainWaterOnly(), isChainPureNonPolymer(), getReducedStructure()
• Removed org.biojava.nbio.structure.io.SandboxStyleStructureProvider
• In org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser made all methods private except parseXMLfile

Breaking API changes

• Extracted StructureIO.StructureFiletype enum to org.biojava.nbio.structure.io.StructureFiletype (supports PDB, MMTF, CIF, and BCIF)
• org.biojava.nbio.structure.align.util.AtomCache: removed setUseMmCif, setUseMmtf, isUseMmCif, and isUseMmtf - replaced by setFiletype and getFiletype that controls parsed content via the StructureFiletype
• org.biojava.nbio.structure.io.MMCIFFileReader is now effectively org.biojava.nbio.structure.io.CifFileReader
• Moved org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord to org.biojava.nbio.structure.DatabasePDBRevRecord.java
• Moved all chem-comp model classes from org.biojava.nbio.structure.io.mmcif.chem to org.biojava.nbio.structure.chem
• Moved all chem-comp parsing classes from org.biojava.nbio.structure.io.mmcif.chem to org.biojava.nbio.structure.io.cif
• Moved classes in org.biojava.nbio.structure.io.mmcif to org.biojava.nbio.structure.chem
• Fixed CRC64Checksum#public void update(byte[] b, int offset, int length) to use the length argument correctly as specified in java.util.zip.Checksum interface.
• In SubstructureIdentifier, StructureName, EcodDomain, ScopDomain : getPdbId() returns PdbId object instead of String.
• Removed DownloadChemCompProvider.useDefaultUrlLayout with a more flexible system to provide templated URLs DownloadChemCompProvider.setChemCompPathUrlTemplate() and DownloadChemCompProvider.setServerBaseUrl()
• In Structure (and StructureImple), the accessor methods String getPdbId() and setPdbId(String) were previously depricated. They were revived in BioJava 6.0.0 but as PdbId getPdbId() and setPdbId(PdbId) instead.n

Added

• New keywords field in PDBHeader class, populated by PDB and mmCIF parsers #946
• OBO parsing now supports multiple altids, #960
• New class PdbId that wrapps a PDB Identifier and handles conversion between current short PDBID format and upcoming extended PDBID format #930

Fixed

• Correct chain assignment to entities when parsing PDB/mmCIF without entity information (in cases with more than 3 chains per entity) #931
• Dealing with chain ids correctly when parsing bonds in PDB-format files #943 #929