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

Fixed

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

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

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

Fixed

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

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

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

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

Added

• Some more categories related to entity are now written in mmCIF writer #1063

Fixed

• Not declaring anymore unchecked exceptions in signatures #1062

Fixed

• The jar packages now contain pom.properties files #1057
• Some minor improvements in a few biojava-structure methods #1058