BioJava v5.4.0 Release Notes

Release Date: 2020-06-29 // over 2 years ago
  • 🆕 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

Previous changes from v5.3.0

  • 🆕 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