Releases · biojava/biojava · GitHub

8000 Releases · biojava/biojava · GitHub

10 Dec 22:17

josemduarte

BioJava 7.2.4 Latest

Latest

Fixed

Edge case in quaternary symmetry calculation #1120

Assets 2

13 Nov 01:26

josemduarte

BioJava 7.2.3

Fixed

Don't use label_seq_id in mmCIF output for non-polymers #1116

Assets 2

20 Mar 20:31

josemduarte

BioJava 7.2.2

Fixed

mmCIF parsing: entity type should be case insensitive #1109
Upgraded to latest version of ciftools-java, fixes mmCIF parsing performance issues in some edge cases rcsb/ciftools-java#13
Added safeguards for Structure.get*Chain*() methods #1111

Assets 2

05 Mar 21:09

josemduarte

BioJava 7.2.1

Fixed

More lenient mmCIF parsing to be able to parse PDB-IHM entries, some more edge cases #1108

Assets 2

27 Feb 19:36

josemduarte

BioJava 7.2.0

Fixed

More lenient mmCIF parsing to be able to parse PDB-IHM entries #1106
Now AsaCalculator main constructor will use first model only instead of all #1107

Added

New constructor for AsaCalculator to provide Structure and model #1107

Assets 2

08 Jan 23:30

josemduarte

BioJava 7.1.4

Fixed

More lenient mmCIF parsing, now can read files produced by Gemmi #1103
Javadocs: all javadoc lint errors fixed
Plugin updates and fixed issues in maven release process

Assets 2

06 Sep 22:24

josemduarte

BioJava 7.1.3

Fixed

Bug in symmetry detection #1101 and rcsb/symmetry#118

Assets 2

09 Aug 18:08

josemduarte

BioJava 7.1.2

Fixed

Brought back a command line argument for protein comparison tool #1096
Upgraded the log facade framework to slf4j2 #1094
Code smell fixes (Sonar issues S2293, S1319) #1095 #1091
Various small fixes

Removed

Removed capability of automatic download/caching of PDB archive files in MMTF format, following deprecation
by RCSB PDB. Code to encode/decode in MMTF format is still in place #1099

Assets 2

06 Mar 18:58

josemduarte

BioJava 7.1.1

Fixed

Now mmCIF files that have no author fields in atom_site can be read (e.g. from PyMol or ESMAtlas) #775 #1083
No evaluations of arguments in debug level log statements #1086 #789

Removed

Minor removal from biojava-core: FileDownloadUtils::copy, replaced by Files::copy

Assets 2

23 Feb 19:47

josemduarte

BioJava 7.1.0

Added

Class FastaStreamer to read FASTA-formatted files using Java streams

Fixed

Various minor fixes for code smells
Some dependency upgrades
Now using Jakarta as the JAXB implementation #1076
Fixed SCOP URL #1077

Assets 2

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