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Commits on Dec 10, 2025

• Merge pull request #1120 from biojava/sym-edgecase

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Commits on Dec 8, 2025

• Merge pull request #1119 from Pasjonat90D/fix/use-isempty-instead-of-size-#1079

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• Bugfix: edge-case with no equiv residues in alignment wasn't dealt with and led to IllegalArgumentException.

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Commits on Nov 30, 2025

• Fix #1079: Use isEmpty() instead of size() == 0

  Pasjonat90D

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Commits on Nov 21, 2025

• Fix RSPEC-1940 boolean checks

  

  JasonKamsu

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Commits on Nov 8, 2025

• Fix for #1116

  josemduarte

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Commits on Mar 19, 2025

• Safeguards

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• More cleanup

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• More cleanup

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• Formatting and docs cleanup

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Commits on Mar 18, 2025

• Update biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java

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  sbittrich

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Commits on Mar 17, 2025

• Make entity type case insensitive. Also improved docs

  josemduarte

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Commits on Mar 4, 2025

• Update biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java

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  sbittrich

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Commits on Feb 28, 2025

• Deal with missing strand_id

  josemduarte

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• Revert "Dealing with struct_ref_seq_dif strand_id by referencing through struct_ref_seq and struct_ref"

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• Logging

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• Dealing with struct_ref_seq_dif strand_id by referencing through struct_ref_seq and struct_ref

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• Deal with some missing fields in IHM

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Commits on Feb 27, 2025

• Merge pull request #1106 from josemduarte/cifparsing-lenient

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Commits on Feb 22, 2025

• Review comment

  josemduarte

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• Fix: first model is model index 0

  josemduarte

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Commits on Feb 21, 2025

• Bugfix: ASA calculation was by default using all models. Now it will use model 1 by default. Added new constructor to choose model.

  josemduarte

  committed
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• Another safeguard, that applies to some PDB-IHM entries

  josemduarte

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• Lenient to missing atom_site.occupancy

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• Handle more missing fields in struct_ref_seq

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Commits on Jan 8, 2025

• Merge pull request #1103 from josemduarte/cifparser-gemmifile

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Commits on Jan 7, 2025

• Javadoc fix: remaining errors in structure module. Mostly obsolete references

  josemduarte

  committed
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• Javadoc fix: most other errors in structure module

  josemduarte

  committed
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• Javadoc fix: many errors in struct align package

  josemduarte

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• Javadoc fix: many errors in struct align package

  josemduarte

  committed
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Commits on Jan 6, 2025

• Javadoc fix: many errors in struct align package

  josemduarte

  committed
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• More lenient parsing if some fields are missing (e.g. in files output by Gemmi)

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Commits on Jan 4, 2025

• Javadoc fix: some more errors from structure module

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Commits on Jan 3, 2025

• Javadoc fix: some more errors from structure module

  josemduarte

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• Javadoc fix: a few errors from structure module

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  committed
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