BioJava v5.4.0 Release Notes
Release Date: 2020-06-29 // almost 4 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
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🆕 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