BioJava v5.4.0 Release Notes

Release Date: 2020-06-29 // almost 2 years ago
  • ๐Ÿ†• New features

    • ๐Ÿš€ 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
    • ๐Ÿ†• New switch in Subunit clusterer useEntityIdForSeqIdentityDetermination #857 #859

    ๐Ÿ”„ Changed

    • ๐Ÿ“œ Now genbank parser will allow 5'<3' for circular DNA #855

    ๐Ÿ› Bug fixes

    • Issue in bonds between atoms of different alt locs (rcsb/mmtf#44) #854
    • ๐Ÿš€ Upgrade ciftools-java dependency to latest java-8 compatible release 0.7.1

Previous changes from v5.3.0

  • ๐Ÿ†• New features

    • ๐Ÿ‘Œ Support for reading structures from binary cif format in structure module, thanks to CIFTools-java library. Thanks @JonStargaryen
    • ๐ŸŽ 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.

    ๐Ÿ› Bug fixes

    • ๐ŸŽ 8x performance increase in reading (non-gzipped) MMTF files thanks to mmtf-java dependency upgrade to 1.0.9
    • ๐Ÿ› Bug fixes in MMTF file reading, #671 #850
    • ๐Ÿ› Bug fix in OBO reading, where only one synonym was saved, #836
    • ๐Ÿ› Bug fix in Genbank LOCUS line parsing #833
    • ๐Ÿ› Bug fix in PDB file reading of MTRIX records #845
    • ๐Ÿ› Bug fix in GenbankReader #800 #829
    • โฌ†๏ธ Dependencies and maven plugin upgrades