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biojava
biojava
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Commits on Sep 19, 2026
[maven-release-plugin] prepare for next development iteration
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[maven-release-plugin] prepare release biojava-7.3.0
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Merge pull request #1155 from josemduarte/jd/interf-clustering
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Sort by number of contacts for a more deterministic clustering result.
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Sort by number of contacts for a more deterministic clustering result.
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Guard against empty clusters
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Commits on Sep 17, 2026
Further fix: don't add empty groups or chains in parseCAOnly
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Commits on Sep 14, 2026
Bugfix: setParseCAOnly wasn't correctly filtering CA-only in CIF implementation
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Docs
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Use a greedy approach (leader algorithm) for a much more scalable interface clustering
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Commits on Sep 4, 2026
Merge pull request #1142 from aalhossary/aa/bump-7.3.0-snapshot
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Merge pull request #1134 from aalhossary/aa/electron-density-maps
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Merge pull request #1147 from biojava/jd/contact-perf
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Commits on Sep 3, 2026
Docs
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Commits on Sep 1, 2026
Merge pull request #1150 from aalhossary/aa/ecod-lock-on-failure
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Commits on Aug 30, 2026
Address map coefficients by name, not by a constructed path
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Convert the density tests to JUnit 5
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Use a definition list rather than a table in UrlTemplates javadoc
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Test the density fetching, offline and against the live services
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Display density maps in the Jmol panel
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Add electron density and cryo-EM map fetching with a fallback chain
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Bump the development version to 7.3.0-SNAPSHOT
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Keep the ECOD read lock balanced when loading fails
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Commits on Aug 28, 2026
Merge branch 'master' into jd/asa-perf
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Presize the AtomContactSet HashMap. Performance gain is ~ 1.2x
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Commits on Aug 27, 2026
Logging for resolution parsing: warn only when they are actually different
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Logging cosmetics
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Merge pull request #1145 from biojava/jd/cath-fixes
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Test fix suggested by AI: test was failing when download was too slow
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Use int arrays for performance. Gain is ~ 1.5x
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Avoiding sqrt when unnecessary. About 8% performance gain
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Demoting
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Merge pull request #1130 from biojava/dependabot/maven/biojava-structure/com.fasterxml.jackson.core-jackson-databind-2.18.9
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Commits on Aug 26, 2026
Logging
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Safeguard for case of nothing parseable in file
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