3.2.0

Breaking changes

The PdbParser no longer accepts a strictMode boolean parameter. The parser is always robust and effectively interprets the provided data.

What's Changed

• build: bump nexus-staging-maven-plugin from 1.6.7 to 1.6.13 by @dependabot in #7
• build: bump slf4j-api from 1.7.36 to 2.0.0 by @dependabot in #8
• build: bump sortpom-maven-plugin from 2.12.0 to 3.2.0 by @dependabot in #9
• build: bump jackson-databind from 2.13.2 to 2.13.3 by @dependabot in #10
• build: bump maven-gpg-plugin from 1.5 to 3.0.1 by @dependabot in #15
• build: bump maven-source-plugin from 3.2.0 to 3.2.1 by @dependabot in #14
• build: bump jackson-annotations from 2.13.2 to 2.13.3 by @dependabot in #16
• build: bump value from 2.9.0 to 2.9.1 by @dependabot in #13
• build: bump versions-maven-plugin from 2.8.1 to 2.11.0 by @dependabot in #12
• feat: replace BioJava dependency by @tzok in #17
• build: bump maven-compiler-plugin from 3.8.1 to 3.10.1 by @dependabot in #24
• build: bump maven-dependency-plugin from 3.1.2 to 3.3.0 by @dependabot in #25
• build: bump maven-javadoc-plugin from 3.2.0 to 3.4.1 by @dependabot in #23
• build: bump actions/checkout from 2 to 3 by @dependabot in #22
• build: bump actions/setup-java from 1 to 3 by @dependabot in #20
• build: bump logback-classic from 1.2.11 to 1.4.0 by @dependabot in #21
• build: bump jackson-annotations from 2.13.3 to 2.13.4 by @dependabot in #28
• build: bump jackson-databind from 2.13.3 to 2.13.4 by @dependabot in #27
• build: bump value from 2.9.1 to 2.9.2 by @dependabot in #30
• build: bump versions-maven-plugin from 2.11.0 to 2.12.0 by @dependabot in #29
• feat: add spotless plugin by @tzok in #31
• feat: make bpseq class more robust by @tzok in #32
• Fix git history by @tzok in #34
• build: bump logback-classic from 1.4.0 to 1.4.1 by @dependabot in #36
• build: bump batik-svggen from 1.14 to 1.15 by @dependabot in #39
• build: bump batik-codec from 1.14 to 1.15 by @dependabot in #38
• build: bump spotless-maven-plugin from 2.25.0 to 2.27.0 by @dependabot in #40
• build: bump slf4j-api from 2.0.0 to 2.0.2 by @dependabot in #41
• build: bump batik-anim from 1.14 to 1.15 by @dependabot in #42
• build: bump batik-transcoder from 1.14 to 1.15 by @dependabot in #43
• build: bump batik-awt-util from 1.14 to 1.15 by @dependabot in #44
• build: bump batik-util from 1.14 to 1.15 by @dependabot in #45
• build: bump batik-bridge from 1.14 to 1.15 by @dependabot in #46
• build: bump batik-gvt from 1.14 to 1.15 by @dependabot in #47
• feat: remove isolated base pairs from dot-bracket by @tzok in #48
• fix: usage of modified residues in base pair parsing by @tzok in #49
• feat: release 3.1.1, remove isolated base pairs from dot-bracket (#48), fix usage of modified residues in base pair parsing (#49) by @tzok in #50
• build: bump jackson-databind from 2.13.4 to 2.13.4.1 by @dependabot in #58
• release: 3.1.2 by @tzok in #62
• release: 3.1.3 by @tzok in #64
• release: 3.1.4 by @tzok in #85
• release: 3.1.5 by @tzok in #94
• release: 3.1.6 by @tzok in #102
• release: 3.1.7 by @tzok in #103
• release: 3.1.8 by @tzok in #106
• release: 3.1.9 by @tzok in #115
• build: bump spotless-maven-plugin from 2.35.0 to 2.36.0 by @dependabot in #116
• build: bump jackson-databind from 2.14.2 to 2.15.0 by @dependabot in #118
• build: bump jackson-annotations from 2.14.2 to 2.15.0 by @dependabot in #117
• build: bump logback-classic from 1.4.6 to 1.4.7 by @dependabot in #119
• build: bump maven-gpg-plugin from 3.0.1 to 3.1.0 by @dependabot in #120
• build: bump commons-io from 2.11.0 to 2.12.0 by @dependabot in #121
• build: bump jackson-databind from 2.15.0 to 2.15.1 by @dependabot in #122
• build: bump ciftools-java from 5.0.0 to 5.0.1 by @dependabot in #124
• build: bump spotless-maven-plugin from 2.36.0 to 2.37.0 by @dependabot in #126
• build: bump jackson-annotations from 2.15.0 to 2.15.2 by @dependabot in #128
• build: bump jackson-databind from 2.15.1 to 2.15.2 by @dependabot in #129
• build: bump commons-io from 2.12.0 to 2.13.0 by @dependabot in #130
• build: bump logback-classic from 1.4.7 to 1.4.8 by @dependabot in #131
• build: bump com.diffplug.spotless:spotless-maven-plugin from 2.37.0 to 2.38.0 by @dependabot in #132
• build: bump org.apache.commons:commons-lang3 from 3.12.0 to 3.13.0 by @dependabot in #133
• build: bump com.github.ekryd.sortpom:sortpom-maven-plugin from 3.2.1 to 3.3.0 by @dependabot in #134
• build: bump ch.qos.logback:logback-classic from 1.4.8 to 1.4.9 by @dependabot in #135
• build: bump ch.qos.logback:logback-classic from 1.4.9 to 1.4.11 by @dependabot in #136
• build: bump org.apache.xmlgraphics:batik-bridge from 1.16 to 1.17 by @dependabot in #137
• build: bump org.apache.xmlgraphics:batik-transcoder from 1.16 to 1.17 by @dependabot in #138
• build: bump org.apache.xmlgraphics:batik-anim from 1.16 to 1.17 by @dependabot in #140
• build: bump org.apache.xmlgraphics:batik-awt-util from 1.16 to 1.17 by @dependabot in #139
• build: bump org.apache.xmlgraphics:batik-gvt from 1.16 to 1.17 by @dependabot in #141
• build: bump org.apache.xmlgraphics:batik-svggen from 1.16 to 1.17 by @dependabot in #144
• build: bump org.apache.xmlgraphics:fop from 2.8 to 2.9 by @dependabot in #142
• build: bump org.apache.xmlgraphics:batik-util from 1.16 to 1.17 by @dependabot in #146
• build: bump com.diffplug.spotless:spotless-maven-plugin from 2.38.0 to 2.39.0 by @dependabot in #147
• build: bump org.apache.maven.plugins:maven-javadoc-plugin from 3.5.0 to 3.6.0 by @dependabot in #148
• build: bump org.slf4j:slf4j-api from 2.0.7 to 2.0.9 by @dependabot in #149
• build: bump commons-io:commons-io from 2.13.0 to 2.14.0 by @dependabot in #150
• build: bump com.diffplug.spotless:spotless-maven-plugin from 2.39.0 to 2.40.0 by @dependabot in #151
• build: bump org.rcsb:ciftools-java from 5.0.1 to 5.0.2 by @dependabot in #152
• build: bump org.immutables:value from 2.9.3 to 2.10.0 by @dependabot in #153
• build: bump com.fasterxml.jackson.core:jackson-annotations from 2.15.2 to 2.15.3 by @dependabot in #155
• build: bump actions/checkout from 3 to 4 by @dependabot in #145
• build: bump org.apache.xmlgraphics:batik-codec from 1.16 to 1.17 by @dependabot in #143
• build: bump com.fasterxml.jackson.core:jackson-databind from 2.15.2 to 2.15.3 by @dependabot in #154
• build: bump org.apache.maven.plugins:maven-dependency-plugin from 3.5.0 to 3.6.1 by @dependabot in #156
• build: bump maven-source-plugin from 3.2.1 to 3.3.0 by @dependabot in #123
• build: bump commons-io:commons-io from 2.14.0 to 2.15.0 by @dependabot in https://github.com/tz...

BioCommons 3.1.1

What's Changed

• feat: remove isolated base pairs from dot-bracket (#50)
• fix: usage of modified residues in base pair parsing (#49)

Full Changelog: 3.1.0...3.1.1

BioCommons 3.1.0

What's Changed

• Replace BioJava with ciftools
• Make BPSEQ more robust

Full Changelog: 3.0...3.1.0

BioCommons 3.0

Changelog:

• Chain reordering for nucleic acid structures
• Better detection of nucleic acids' canonical base pairs
• Much improved documentation
• Much improved testing
• Full replacement of Lombok with Immutables
• Lots of improvements and bugfixes
• Merged tzok/Circular
• Merged tzok/TzokCommons

BioCommons v2.2

Changelog:

• Improved test suite
• Added parsing of structure title
• Redesigned strand to allow combining of virtual and real strand on either canonical or non-canonical base pairs
• Improved description of non-canonical base pairs
• Introduced torsion angle ranges and comparison based on them
• Lots of minor bugfixes and refactorings

BioCommons v2.1

Changelog:

• Better support for mmCIF format
• Speed improvements (map lookups instead of list traversals)
• Switch to Java 8
• Support for base-phosphate (BPh) and base-ribose (BR) notations for RNAs
• New dynamic programming from @Delgon95
• Bugfixes

BioCommons v2.0 - support for parsing of files in mmCIF format and extended support for RNA secondary structure (pseudoknot removal)

The major release v2.0 brings a working mmCIF parser. Additionally, RNA secondary structure is handled much better. Many algorithms to work with pseudoknots are added and now BioCommons on its own allows to extract canonical secondary structure from PDB/mmCIF and also annotate it with pseudoknot level.

See:

• Antczak, M.; Zok, T. et al., 2014. RNApdbee - A webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Research, 42(W1), pp.368–372.
• Smit, S. et al., 2008. From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal. RNA, 14, pp.410–416.