Fixed

• Now actually runnable in a java-8 JRE. Previous release 6.0.0 had a java-11 dependency that made it incompatible. #996
• Switch JAXB to glassfish implementation for better java 15+ support. Now biojava should run under a java-15 JRE. #996

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

New features

• Minimal read support for mmCIF files with branched entities (upcoming PDB release July 2020). The new entity type is understood now but branched entities are still treated as non-polymers within BioJava. #868
• InterfaceFinder class to find interfaces of a given PDB assembly #867
• New switch in Subunit clusterer useEntityIdForSeqIdentityDetermination #857 #859

Changed

• Now genbank parser will allow 5'<3' for circular DNA #855

Bug fixes

• Issue in bonds between atoms of different alt locs (rcsb/mmtf#44) #854
• Upgrade ciftools-java dependency to latest java-8 compatible release 0.7.1

New features

• Support for reading structures from binary cif format in structure module, thanks to CIFTools-java library. Thanks @JonStargaryen
• Reading structures from mmCIF via new parser from CIFTools-java library. Much better read performance than existing parser. Both parsers still live alongside in BioJava 5.3.0, with default still being the BioJava native one.

Bug fixes

• 8x performance increase in reading (non-gzipped) MMTF files thanks to mmtf-java dependency upgrade to 1.0.9
• Bug fixes in MMTF file reading, #671 #850
• Bug fix in OBO reading, where only one synonym was saved, #836
• Bug fix in Genbank LOCUS line parsing #833
• Bug fix in PDB file reading of MTRIX records #845
• Bug fix in GenbankReader #800 #829
• Dependencies and maven plugin upgrades

Bug fixes

• 2 bugfixes in ASA calculation introduced in 5.2.0: calculation would fail when an atom had no neighbors or when supplying a 0-length atom array, #824
• Fixes in bioassembly creation, where EntityInfo objects weren't correctly cloned and wired #825
• More efficient interface ASA calculation in NCS cases #823
• Add EntityInfo to reduced structure #822

BioJava 5.2.0 runs on Java 8 or later.

New Feature

• improved algorithm for ASA computation. It is much faster on large molecules. #820

Bug fixes

• Fix broken tests #809 & ed7fb66
• Add tests for new GenBank formats (confirmed that the parser worked) #811
• Fix exceptions displaying CE-Symm results #816 #817
• Merge in bug fixes from the 4.2.x series (4.2.6 through 4.2.12)

This release contains 22 commits from 3 contributors.

Note this is the first version of BioJava that will run under 9, 10 or 11 JREs. It is still fully compatible with Java 8.

Bug fixes

• #801 - Chain identifiers for generated bioassemblies now more explicit
• #804 - Adapted BioJava to run under 9, 10 and 111 JREs

Manual Download

This release contains 55 commits from 7 contributors.

New feature

• ABI tracer ported from legacy biojava, #769, thanks @MaxGreil

Bug fixes

• Performance improvement for secondary structure calculation, #789
• #731
• Improved alt locs docs and some fixes, #778
• Jmol dep updated to 14.29.17
• #712
• #791
• #797
• #784

Manual Download

This is a bugfix release in the 4.2 branch. This branch is being maintained for use with Java 7. Applications using more recent versions of Java are encouraged to migrate to BioJava 5.

Changes:

• Fix #703: Recover from empty structure files in PDB_CACHE_DIR
• Reflect changes in external resources (#780, 0c10a2e)
• CE-Symm bug fixes (#92)

This release is associated with CE-Symm 2.0.0.

This release contains 5 commits from 2 contributors.

Requires Java 8 or newer.

Bug fixes

• Fixed issue #770
• Upgraded to latest mmtf-java 1.0.8

Manual Download