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.fastq is now org.biojava.nbio.genome.io.fastq
• org.biojava.nbio.structure.Compound -> org.biojava.nbio.structure.EntityInfo
• org.biojava.nbio.structure.io.util.FileDownloadUtils -> org.biojava.nbio.core.util.FileDownloadUtils
• org.biojava.nbio.structure.symmetry.core.AxisAligner -> org.biojava.nbio.structure.symmetry.axis.AxisAligner
• org.biojava.nbio.structure.symmetry.core.Subunits -> refactored into several classes in org.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.

• 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 SubstitutionMatrices in the core module (instead of imported Jalview matrices)
• use Sequence and Compound classes 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.