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@josemduarte josemduarte released this Jun 29, 2020 · 120 commits to master since this release

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
Assets 2

@josemduarte josemduarte released this Sep 6, 2019 · 207 commits to master since this release

New features

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
Assets 2

@josemduarte josemduarte released this Feb 5, 2019 · 308 commits to master since this release

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
Assets 2

@sbliven sbliven released this Jan 3, 2019 · 334 commits to master since this release

BioJava 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

  • 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)
Assets 2

@josemduarte josemduarte released this Sep 28, 2018 · 439 commits to master since this release

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.1.1.jar biojava-core-5.1.1-sources.jar biojava-core-5.1.1-javadoc.jar
biojava-alignment biojava-alignment-5.1.1.jar biojava-alignment-5.1.1-sources.jar biojava-alignment-5.1.1-javadoc.jar
biojava-genome biojava-genome-5.1.1.jar biojava-genome-5.1.1-sources.jar biojava-genome-5.1.1-javadoc.jar
biojava-structure biojava-structure-5.1.1.jar biojava-structure-5.1.1-sources.jar biojava-structure-5.1.1-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.1.1.jar biojava-structure-gui-5.1.1-sources.jar biojava-structure-gui-5.1.1-javadoc.jar
biojava-phylo biojava-phylo-5.1.1.jar biojava-phylo-5.1.1-sources.jar biojava-phylo-5.1.1-javadoc.jar
biojava-modfinder biojava-modfinder-5.1.1.jar biojava-modfinder-5.1.1-sources.jar biojava-modfinder-5.1.1-javadoc.jar
biojava-ws biojava-ws-5.1.1.jar biojava-ws-5.1.1-sources.jar biojava-ws-5.1.1-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.1.1.jar biojava-aa-prop-5.1.1-sources.jar biojava-aa-prop-5.1.1-javadoc.jar
biojava-ontology biojava-ontology-5.1.1.jar biojava-ontology-5.1.1-sources.jar biojava-ontology-5.1.1-javadoc.jar
biojava-survival biojava-survival-5.1.1.jar biojava-survival-5.1.1-sources.jar biojava-survival-5.1.1-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.1.1.jar biojava-protein-disorder-5.1.1-sources.jar biojava-protein-disorder-5.1.1-javadoc.jar
biojava-sequencing biojava-sequencing-5.1.1.jar biojava-sequencing-5.1.1-sources.jar biojava-sequencing-5.1.1-javadoc.jar
Assets 2

@josemduarte josemduarte released this Aug 30, 2018 · 461 commits to master since this release

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.1.0.jar biojava-core-5.1.0-sources.jar biojava-core-5.1.0-javadoc.jar
biojava-alignment biojava-alignment-5.1.0.jar biojava-alignment-5.1.0-sources.jar biojava-alignment-5.1.0-javadoc.jar
biojava-genome biojava-genome-5.1.0.jar biojava-genome-5.1.0-sources.jar biojava-genome-5.1.0-javadoc.jar
biojava-structure biojava-structure-5.1.0.jar biojava-structure-5.1.0-sources.jar biojava-structure-5.1.0-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.1.0.jar biojava-structure-gui-5.1.0-sources.jar biojava-structure-gui-5.1.0-javadoc.jar
biojava-phylo biojava-phylo-5.1.0.jar biojava-phylo-5.1.0-sources.jar biojava-phylo-5.1.0-javadoc.jar
biojava-modfinder biojava-modfinder-5.1.0.jar biojava-modfinder-5.1.0-sources.jar biojava-modfinder-5.1.0-javadoc.jar
biojava-ws biojava-ws-5.1.0.jar biojava-ws-5.1.0-sources.jar biojava-ws-5.1.0-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.1.0.jar biojava-aa-prop-5.1.0-sources.jar biojava-aa-prop-5.1.0-javadoc.jar
biojava-ontology biojava-ontology-5.1.0.jar biojava-ontology-5.1.0-sources.jar biojava-ontology-5.1.0-javadoc.jar
biojava-survival biojava-survival-5.1.0.jar biojava-survival-5.1.0-sources.jar biojava-survival-5.1.0-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.1.0.jar biojava-protein-disorder-5.1.0-sources.jar biojava-protein-disorder-5.1.0-javadoc.jar
biojava-sequencing biojava-sequencing-5.1.0.jar biojava-sequencing-5.1.0-sources.jar biojava-sequencing-5.1.0-javadoc.jar
Assets 2

@sbliven sbliven released this Jul 2, 2018 · 1646 commits to master since this release

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.

Assets 2

@josemduarte josemduarte released this May 22, 2018 · 516 commits to master since this release

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.0.2.jar biojava-core-5.0.2-sources.jar biojava-core-5.0.2-javadoc.jar
biojava-alignment biojava-alignment-5.0.2.jar biojava-alignment-5.0.2-sources.jar biojava-alignment-5.0.2-javadoc.jar
biojava-genome biojava-genome-5.0.2.jar biojava-genome-5.0.2-sources.jar biojava-genome-5.0.2-javadoc.jar
biojava-structure biojava-structure-5.0.2.jar biojava-structure-5.0.2-sources.jar biojava-structure-5.0.2-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.0.2.jar biojava-structure-gui-5.0.2-sources.jar biojava-structure-gui-5.0.2-javadoc.jar
biojava-phylo biojava-phylo-5.0.2.jar biojava-phylo-5.0.2-sources.jar biojava-phylo-5.0.2-javadoc.jar
biojava-modfinder biojava-modfinder-5.0.2.jar biojava-modfinder-5.0.2-sources.jar biojava-modfinder-5.0.2-javadoc.jar
biojava-ws biojava-ws-5.0.2.jar biojava-ws-5.0.2-sources.jar biojava-ws-5.0.2-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.0.2.jar biojava-aa-prop-5.0.2-sources.jar biojava-aa-prop-5.0.2-javadoc.jar
biojava-ontology biojava-ontology-5.0.2.jar biojava-ontology-5.0.2-sources.jar biojava-ontology-5.0.2-javadoc.jar
biojava-survival biojava-survival-5.0.2.jar biojava-survival-5.0.2-sources.jar biojava-survival-5.0.2-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.0.2.jar biojava-protein-disorder-5.0.2-sources.jar biojava-protein-disorder-5.0.2-javadoc.jar
biojava-sequencing [biojava-sequencing-5.0.2.
Assets 2

@josemduarte josemduarte released this May 11, 2018 · 520 commits to master since this release

This release contains 13 commits from 2 contributors.

Requires Java 8 or newer.

Bug fixes

  • Fixed issue #767
  • Fixed issue #761
  • Pom fixes for mvn site
  • Some logging fixes

Manual Download

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.0.1.jar biojava-core-5.0.1-sources.jar biojava-core-5.0.1-javadoc.jar
biojava-alignment biojava-alignment-5.0.1.jar biojava-alignment-5.0.1-sources.jar biojava-alignment-5.0.1-javadoc.jar
biojava-genome biojava-genome-5.0.1.jar biojava-genome-5.0.1-sources.jar biojava-genome-5.0.1-javadoc.jar
biojava-structure biojava-structure-5.0.1.jar biojava-structure-5.0.1-sources.jar biojava-structure-5.0.1-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.0.1.jar biojava-structure-gui-5.0.1-sources.jar biojava-structure-gui-5.0.1-javadoc.jar
biojava-phylo biojava-phylo-5.0.1.jar biojava-phylo-5.0.1-sources.jar biojava-phylo-5.0.1-javadoc.jar
biojava-modfinder biojava-modfinder-5.0.1.jar biojava-modfinder-5.0.1-sources.jar biojava-modfinder-5.0.1-javadoc.jar
biojava-ws biojava-ws-5.0.1.jar biojava-ws-5.0.1-sources.jar biojava-ws-5.0.1-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.0.1.jar biojava-aa-prop-5.0.1-sources.jar biojava-aa-prop-5.0.1-javadoc.jar
biojava-ontology biojava-ontology-5.0.1.jar biojava-ontology-5.0.1-sources.jar biojava-ontology-5.0.1-javadoc.jar
biojava-survival biojava-survival-5.0.1.jar biojava-survival-5.0.1-sources.jar biojava-survival-5.0.1-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.0.1.jar biojava-protein-disorder-5.0.1-sources.jar biojava-protein-disorder-5.0.1-javadoc.jar
biojava-sequencing biojava-sequencing-5.0.1.jar biojava-sequencing-5.0.1-sources.jar biojava-sequencing-5.0.1-javadoc.jar
Assets 2

@josemduarte josemduarte released this Mar 24, 2018 · 533 commits to master since this release

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
  • 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.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.

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

Module Binary Jar Source Jar Javadoc Jar
biojava-core biojava-core-5.0.0.jar biojava-core-5.0.0-sources.jar biojava-core-5.0.0-javadoc.jar
biojava-alignment biojava-alignment-5.0.0.jar biojava-alignment-5.0.0-sources.jar biojava-alignment-5.0.0-javadoc.jar
biojava-genome biojava-genome-5.0.0.jar biojava-genome-5.0.0-sources.jar biojava-genome-5.0.0-javadoc.jar
biojava-structure biojava-structure-5.0.0.jar biojava-structure-5.0.0-sources.jar biojava-structure-5.0.0-javadoc.jar
biojava-structure-gui biojava-structure-gui-5.0.0.jar biojava-structure-gui-5.0.0-sources.jar biojava-structure-gui-5.0.0-javadoc.jar
biojava-phylo biojava-phylo-5.0.0.jar biojava-phylo-5.0.0-sources.jar biojava-phylo-5.0.0-javadoc.jar
biojava-modfinder biojava-modfinder-5.0.0.jar biojava-modfinder-5.0.0-sources.jar biojava-modfinder-5.0.0-javadoc.jar
biojava-ws biojava-ws-5.0.0.jar biojava-ws-5.0.0-sources.jar biojava-ws-5.0.0-javadoc.jar
biojava-aa-prop biojava-aa-prop-5.0.0.jar biojava-aa-prop-5.0.0-sources.jar biojava-aa-prop-5.0.0-javadoc.jar
biojava-ontology biojava-ontology-5.0.0.jar biojava-ontology-5.0.0-sources.jar biojava-ontology-5.0.0-javadoc.jar
biojava-survival biojava-survival-5.0.0.jar biojava-survival-5.0.0-sources.jar biojava-survival-5.0.0-javadoc.jar
biojava-protein-disorder biojava-protein-disorder-5.0.0.jar biojava-protein-disorder-5.0.0-sources.jar biojava-protein-disorder-5.0.0-javadoc.jar
biojava-sequencing biojava-sequencing-5.0.0.jar biojava-sequencing-5.0.0-sources.jar biojava-sequencing-5.0.0-javadoc.jar
Assets 2