- 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.
- 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
- 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
- new algorithm for ASA computation. It is much faster on large molecules. #820
- 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)
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.
- Chain identifiers for generated bioassemblies now more explicit, #801
- Adapted BioJava to run under 9, 10 and 111 JREs, #804
- ABI tracer ported from legacy biojava, #769, thanks @MaxGreil
- Performance improvement for secondary structure calculation, #789
- Fixed issue #731
- Improved alt locs docs and some fixes, #778
- Jmol dep updated to 14.29.17
- Fixed issue #712
- Fixed issue #791
- Fixed issue #797
- Fixed issue #784
- Fixed issue #770
- Upgraded to latest mmtf-java 1.0.8
- Fixed issue #767
- Fixed issue #761
- Pom fixes for mvn site
- Some logging fixes
This release contains 1,170 commits from 19 contributors.
Requires Java 8 or newer.
- New utlity methods for sequence alignment objects (gap, similarity and coverage).
- 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.
- For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included
- 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).
- 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.AxisAlignerorg.biojava.nbio.structure.symmetry.core.Subunits-> refactored into several classes inorg.biojava.nbio.structure.cluster: Subunit, SubunitCluster, SubunitClustererorg.biojava.nbio.structure.align.helper.AlignTools->org.biojava.nbio.structure.align.helper.AlignUtils- All deprecations introduced in 4.0.0 or before were removed.
- Javadocs improvements across the board.
- All tests are now Junit4.
- Updated dependency versions (guava, slf4j, and log4j).
A very long list.
release date: January 11th 2018 This release contains 3 commits from 1 contributor.
- Updated hmmer scan web service URL to https.
release date: December 11th 2017 This release contains 7 commits from 2 contributors.
- Fixed issue #659
- Fixed issue #715
release date: October 19th 2017 This release contains 15 commits from 2 contributors.
- Some fixes to PDB file parsing CONECT/LINK records
- Updated URLs for external resources
release date: July 6th 2017 This release contains 15 commits from 3 contributors.
- Small additions to AlignedSequence in core module to better support pipelines that use 4.2.x
- URLs adapted to latest RCSB PDB convention #682
release date: March 7th 2017 This release contains 8 commits from 4 contributors.
- Fix for hmmer web service in biojava-ws #640
- Fix in chromosome mapping tool #636
release date: February 17th 2017 This release contains 12 commits from 4 contributors.
- Fix for problem in chain cloning, #631
- Several bug fixes and better error check in quaternary symmetry detection code
release date: December 7th 2016 This release contains 30 commits from 7 contributors.
- Fix for new phosphositeplus.org format, #610
- org.biojava.nbio.genome.parsers.gff.Location union() and intersect() now work correctly, #355
- Minor addition of crystallographic metadata fields to handle legacy PDB entries
- Jmol interchange format is now mmCIF, allowing for multiletter chain ids
- Update to latest jmol 14.6.2_2016.08.28
- A few minor bug fixes
release date: July 29th 2016 This release contains over 17 commits from 4 contributors.
- NCBI links now using https (see NCBI's announcement )
- CATH links redirected to new server http://release.cathdb.info/
- SCOP default location now points to the Berkeley server after demise of Scop at MRC LMB
- Fixed important bug in mmCIF writing where structures with multiple models were written with identical coordinates
- Fixed bug in Group cloning where chemical components weren't cloned
- Added utility class for Chromosome mapping
release date: July 28th 2016 This release contains over 13 commits from 2 contributors.
- mmCIF file writing: special fields (e.g. containing hyphens) are now correctly written
- General improvements in mmCIF file read and write
release date: June 14th 2016 This release contains over 31 commits from 5 contributors.
This is a bug-fix release
- CE-Symm features and bug fixes
- Better data structures for symmetry axes (particularly for hierarchical symmetry)
- Fix bug with symmetry axis positioning
- Optimization includes all symmetry repeats for hierarchical symmetry
- Update of protein modifications to latest version,
- including new glycans and chromophores
- Updating naming definitions to latest conventions
release date: May 3rd 2016 This release contains over 31 commits from 7 contributors.
Biojava-structure
- Nucleotide bonds are now generated
- BIO: identifiers are now correctly handled
- Several fixes for CE-Symm
- Substructures now contain seqres groups (isse #449)
- Structures containing insertion codes are now written correctly to mmCIF
- AtomCache now uses the correct default parsing parameters (issue #455)
- Fixed problem with some atom charges that weren't being added
- CATH updated to 4.0.0
- Better ECOD javadocs (issue #452)
Biojava-structure-gui
- Removed javaws dependency (issue #459)
release date: March 10th 2016
This release contains over 750 commits from 16 contributors.
BioJava 4.2.0 offers many new features, as well several bug-fixes.
- Requires Java 7
- Better logging with SLF4J
- New SearchIO framework including blast xml parser
- Secondary structure assignment (DSSP compatible)
- Multiple Structure Alignments
- New MultipleStructureAlignment datastructure supporting flexible and order-independent alignments
- MultipleMC algorithm
- Can use any pairwise StructureAlignment implementation
- serialize and parse multiple structure alignments as XML files, output as Text, FatCat, FASTA, Rotation Matrices, etc.
- More complete mmCIF and cif parsing
- Parse bonds, sites, charges
- Better support for non-deposited pdb and mmcif files
- Include CE-Symm algorithm for finding internal symmetry (Myers-Turnbull, 2014)
- Replaced internal graph datastructures with Jgraph
- Unified StructureIdentifier framework
- Improved chemical component framework, now by default providing full chemical description by using DownloadChemCompProvider
- Optimised memory usage of Residue/Atoms
- MultipleAlignmentGUI for visualizing Multiple Structure Alignments with Jmol
- SymmetryDisplay for visualizing internal symmetry
- Use
Forester 1.038 - Significant bug fixes
- use
SubstitutionMatricesin the core module (instead of imported Jalview matrices) - use
SequenceandCompoundclasses from the alignment module - provide some Wrapper methods to communicate with forester
- decouple distance matrix calculation from tree constructor
- provide methods for common distance matrix calculations and framework for user-defined distances
- update the forester version to have the correct NJ tree constructor
- correct some of the tree evaluator statistics.
release date: June 24th 2015
- New algorithm for multiple structure alignments
- Improved visualization of structural alignments in Jmol
- Support for the ECOD protein classification
- Better mmCIF support: limited write support, better parsing
release date: January 30th 2015
- General
- Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations. (many contributors, including @benjamintboyle and @josemduarte)
- Improved handling of exceptions (@dmyersturnbull)
- Removed deprecated methods
- Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and @sbliven)
- Updated dependencies where applicable
- Available on Maven Central (@andreasprlic and @heuermh)
- biojava3-core
- Improved Genbank parser, including support for feature records, qualifiers, and nested locations. (@paolopavan and @jgrzebyta)
- biojava3-structure
- Better support for crystallographic information, including crystallographic operators, unit cells, and protein-protein interfaces. (@josemduarte)
- Better organization of downloaded structure files (set using the PDB_DIR and PDB_CACHE_DIR environmental variables) (@sbliven)
- Better command-line tools for structure alignment (@sbliven)
- New algorithm for symmetry detection in biological assemblies (@pwrose)
- New algorithm for fast contact calculation, both intra-chain and inter-chain (@josemduarte)
- Support for Accessible Surface Area (ASA) calculation through and implementation of the Shrake & Rupley algorithm, both single-thread and parallel (memory permitting) (@josemduarte)
- Support for large structures (memory permitting) and multi-character chain IDs.
- Default to mmCIF file format, as recommended by the wwPDB
This version is compatible with Java 6, 7, and 8.
Since we renamed all package names to be consistent across the whole project, there will be import errors when upgrading to this version. These can automatically get resolved by IDEs such as Eclipse or IntelliJ by selecting the Optimize Import menu item.
release date: August 25th 2014
While most development is going towards the upcoming 4.0.0 release, this release provides bug fixes and a few new features:
- CE-CP version 1.4, with additional parameters
- Update to SCOPe 2.04
- Improvements in FASTQ parsing
- Fix bugs in PDB parsing
- Minor fixes in structure alignments
This version is compatible with Java 6 and 7.
release date: March 25th 2014
New Features:
- New Genbank writer
- New parser for Karyotype file from UCSC
- New parser for Gene locations from UCSC
- New parser for Gene names file from genenames.org
- New module for Cox regression code for survival analysis
- New calculation of accessible surface area (ASA)
- New module for parsing .OBO files (ontologies)
- Improved representation of SCOP and Berkeley-SCOP classifications
release date: September 23rd 2013
New features:
- added a basic genbank parser
- fixed a problem when translating codons with N
- now can infer bonds in protein structures
- added support to parse mmcif records for organism and expression system
- many small bug fixes and improvements