All Versions
10
Latest Version
Avg Release Cycle
111 days
Latest Release
1391 days ago
Changelog History
Changelog History
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v5.4.0 Changes
June 29, 2020🆕 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
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v5.3.0 Changes
September 06, 2019🆕 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
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v5.2.1 Changes
February 05, 2019🐛 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
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v5.2.0 Changes
January 03, 2019BioJava 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
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v5.1.1 Changes
September 28, 2018🚀 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
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v5.1.0 Changes
August 30, 2018🚀 This release contains 55 commits from 7 contributors.
🆕 New feature
🐛 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
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v5.0.2 Changes
May 22, 2018🚀 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
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v5.0.1 Changes
May 11, 2018🚀 This release contains 13 commits from 2 contributors.
Requires Java 8 or newer.
🐛 Bug fixes
Manual Download
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v5.0.0 Changes
March 24, 2018🚀 This release contains 1,170 commits from 19 contributors.
Requires Java 8 or newer.
🆕 New features
biojava-alignment
- 🆕 New utlity methods for sequence alignment objects (gap, similarity and coverage).
biojava-structure
- The data structures to represent 3D macromolecules now follow the mmCIF data model.
- 👍 MMTF format support.
- 👍 Symmetry detection algorithms overhaul: better symmetry detection for tertiary and quaternary structure levels.
- 🆕 New method and data structures for the clustering of protein subunits at the sequence and structure levels.
- 🆕 New method to align biological assemblies, see
org.biojava.nbio.structure.align.quaternary.QsAlign. - 🆕 New algorithms for base-pair geometry in nucleic acids.
- 🆕 New SuperPosition interface for different 3D-structure superposition algorithms, see
org.biojava.nbio.structure.geometry.SuperPosition. - Geometry-related API now more consistently based on vecmath interfaces.
🔄 Changed
- For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included
- 0️⃣ Symmetry expansion for bioassembly creation is now by default happening via adding new chains instead of new models.
- 👉 Make objects serializable for compatibility with big data frameworks (e.g. Spark).
💥 Breaking API changes
- 📦 module biojava-phylo merged into biojava-alignment. The package namespace stays the same (
org.biojava.nbio.phylo). - 📦 module biojava-sequencing merged into biojava-genome. Package
org.biojava.nbio.sequencing.io.fastqis noworg.biojava.nbio.genome.io.fastq org.biojava.nbio.structure.Compound->org.biojava.nbio.structure.EntityInfoorg.biojava.nbio.structure.io.util.FileDownloadUtils->org.biojava.nbio.core.util.FileDownloadUtilsorg.biojava.nbio.structure.symmetry.core.AxisAligner->org.biojava.nbio.structure.symmetry.axis.AxisAligner- 🔨
org.biojava.nbio.structure.symmetry.core.Subunits-> refactored into several classes inorg.biojava.nbio.structure.cluster: Subunit, SubunitCluster, SubunitClusterer org.biojava.nbio.structure.align.helper.AlignTools->org.biojava.nbio.structure.align.helper.AlignUtils- 🚚 All deprecations introduced in 4.0.0 or before were removed.
General
- Javadocs improvements across the board.
- ✅ All tests are now Junit4.
- ⚡️ Updated dependency versions (guava, slf4j, and log4j).
🐛 Bug fixes
A very long list.
Manual Download
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v4.2.12 Changes
July 02, 2018🛠 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.