Skip to content

Latest commit

 

History

History
154 lines (103 loc) · 5.12 KB

CHANGELOG.md

File metadata and controls

154 lines (103 loc) · 5.12 KB
Raw

BioJava 5.0.0

unreleased

  • For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included

BioJava 4.2.5

release date: December 7th 2016 This release contains 30 commits from 7 contributors.

Bug fixes

  • 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

BioJava 4.2.4

release date: July 29th 2016 This release contains over 17 commits from 4 contributors.

Bug fixes

  • 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

BioJava 4.2.3

release date: July 28th 2016 This release contains over 13 commits from 2 contributors.

Bug fixes

  • mmCIF file writing: special fields (e.g. containing hyphens) are now correctly written
  • General improvements in mmCIF file read and write

BioJava 4.2.2

release date: June 14th 2016 This release contains over 31 commits from 5 contributors.

Bug fixes

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

BioJava 4.2.1

release date: May 3rd 2016 This release contains over 31 commits from 7 contributors.

Bug fixes

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)

BioJava 4.2.0

release date: March 10th 2016

This release contains over 750 commits from 16 contributors.

New Features

BioJava 4.2.0 offers many new features, as well several bug-fixes.

General

  • Requires Java 7
  • Better logging with SLF4J

Biojava-Core

  • New SearchIO framework including blast xml parser

Biojava-structure

  • 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

Biojava-structure-gui

  • MultipleAlignmentGUI for visualizing Multiple Structure Alignments with Jmol
  • SymmetryDisplay for visualizing internal symmetry

Biojava-Phylo

  • 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 AND
  • correct some of the tree evaluator statistics.