tag:github.com,2008:https://github.com/biojava/biojava/releasesRelease notes from biojava2026-07-30T10:17:16Ztag:github.com,2008:Repository/9199359/biojava-7.2.62026-07-30T10:17:16Zbiojava-7.2.6<p>[maven-release-plugin] copy for tag biojava-7.2.6</p>josemduartetag:github.com,2008:Repository/9199359/biojava-7.2.52026-05-05T22:39:21ZBioJava 7.2.5<h3>Fixed</h3>
<ul>
<li>Fix NPE in Structure.toMMCIF() for some PDB entries (e.g. 2G10)</li>
<li>Maven plugin duplication in main pom.xml</li>
<li>Fixes for SonarQube S1155</li>
<li>Some library upgrades</li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.2.42025-12-10T22:17:29ZBioJava 7.2.4<h3>Fixed</h3>
<ul>
<li>Edge case in quaternary symmetry calculation <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3708434445" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1120" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1120/hovercard" href="https://github.com/biojava/biojava/pull/1120">#1120</a></li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.2.32025-11-13T01:26:22ZBioJava 7.2.3<h3>Fixed</h3>
<ul>
<li>Don't use label_seq_id in mmCIF output for non-polymers <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3596241160" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1116" data-hovercard-type="issue" data-hovercard-url="/biojava/biojava/issues/1116/hovercard" href="https://github.com/biojava/biojava/issues/1116">#1116</a></li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.2.22025-03-20T20:31:30ZBioJava 7.2.2<h3>Fixed</h3>
<ul>
<li>mmCIF parsing: entity type should be case insensitive <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2927124344" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1109" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1109/hovercard" href="https://github.com/biojava/biojava/pull/1109">#1109</a></li>
<li>Upgraded to latest version of ciftools-java, fixes mmCIF parsing performance issues in some edge cases <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2927113133" data-permission-text="Title is private" data-url="https://github.com/rcsb/ciftools-java/issues/13" data-hovercard-type="issue" data-hovercard-url="/rcsb/ciftools-java/issues/13/hovercard" href="https://github.com/rcsb/ciftools-java/issues/13">rcsb/ciftools-java#13</a></li>
<li>Added safeguards for <code>Structure.get*Chain*()</code> methods <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2933018730" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1111" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1111/hovercard" href="https://github.com/biojava/biojava/pull/1111">#1111</a></li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.2.12025-03-05T21:09:39ZBioJava 7.2.1<h3>Fixed</h3>
<ul>
<li>More lenient mmCIF parsing to be able to parse <a href="https://pdb-ihm.org/" rel="nofollow">PDB-IHM</a> entries, some more edge cases <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2888096454" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1108" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1108/hovercard" href="https://github.com/biojava/biojava/pull/1108">#1108</a></li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.2.02025-02-27T19:36:19ZBioJava 7.2.0<h3>Fixed</h3>
<ul>
<li>More lenient mmCIF parsing to be able to parse <a href="https://pdb-ihm.org/" rel="nofollow">PDB-IHM</a> entries <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2869857879" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1106" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1106/hovercard" href="https://github.com/biojava/biojava/pull/1106">#1106</a></li>
<li>Now AsaCalculator main constructor will use first model only instead of all <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2870244327" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1107" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1107/hovercard" href="https://github.com/biojava/biojava/pull/1107">#1107</a></li>
</ul>
<h3>Added</h3>
<ul>
<li>New constructor for AsaCalculator to provide Structure and model <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2870244327" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1107" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1107/hovercard" href="https://github.com/biojava/biojava/pull/1107">#1107</a></li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.1.42025-01-08T23:30:25ZBioJava 7.1.4<h3>Fixed</h3>
<ul>
<li>More lenient mmCIF parsing, now can read files produced by <a href="https://gemmi.readthedocs.io/en/latest/" rel="nofollow">Gemmi</a> <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2771601996" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1103" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1103/hovercard" href="https://github.com/biojava/biojava/pull/1103">#1103</a></li>
<li>Javadocs: all javadoc lint errors fixed</li>
<li>Plugin updates and fixed issues in maven release process</li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.1.32024-09-06T22:24:22ZBioJava 7.1.3<h3>Fixed</h3>
<ul>
<li>Bug in symmetry detection <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2497613049" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1101" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1101/hovercard" href="https://github.com/biojava/biojava/pull/1101">#1101</a> and <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2461264532" data-permission-text="Title is private" data-url="https://github.com/rcsb/symmetry/issues/118" data-hovercard-type="issue" data-hovercard-url="/rcsb/symmetry/issues/118/hovercard" href="https://github.com/rcsb/symmetry/issues/118">rcsb/symmetry#118</a></li>
</ul>josemduartetag:github.com,2008:Repository/9199359/biojava-7.1.22024-08-09T18:08:20ZBioJava 7.1.2<h3>Fixed</h3>
<ul>
<li>Brought back a command line argument for protein comparison tool <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2387678163" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1096" data-hovercard-type="issue" data-hovercard-url="/biojava/biojava/issues/1096/hovercard" href="https://github.com/biojava/biojava/issues/1096">#1096</a></li>
<li>Upgraded the log facade framework to slf4j2 <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2264644028" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1094" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1094/hovercard" href="https://github.com/biojava/biojava/pull/1094">#1094</a></li>
<li>Code smell fixes (Sonar issues S2293, S1319) <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2298328759" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1095" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1095/hovercard" href="https://github.com/biojava/biojava/pull/1095">#1095</a> <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2249969918" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1091" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1091/hovercard" href="https://github.com/biojava/biojava/pull/1091">#1091</a></li>
<li>Various small fixes</li>
</ul>
<h3>Removed</h3>
<ul>
<li>Removed capability of automatic download/caching of PDB archive files in MMTF format, following deprecation<br>
by RCSB PDB. Code to encode/decode in MMTF format is still in place <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2423363038" data-permission-text="Title is private" data-url="https://github.com/biojava/biojava/issues/1099" data-hovercard-type="pull_request" data-hovercard-url="/biojava/biojava/pull/1099/hovercard" href="https://github.com/biojava/biojava/pull/1099">#1099</a></li>
</ul>josemduarte