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Don't output label_seq_id for non-polymers in mmCIF writing #1117

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Merged
josemduarte merged 1 commit into from
Nov 12, 2025
+11 −1
Merged

Don't output label_seq_id for non-polymers in mmCIF writing #1117

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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
BioJava Changelog
-----------------

BioJava 7.2.3 - future release
==============================
### Fixed
* Don't use label_seq_id in mmCIF output for non-polymers #1116

BioJava 7.2.2
==============================
### Fixed
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7 changes: 6 additions & 1 deletion ...va-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
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Expand Up @@ -308,7 +308,12 @@ public void accept(WrappedAtom wrappedAtom) {
}
}
labelEntityId.add(entityId);
labelSeqId.add(seqId);
// see https://github.com/biojava/biojava/issues/1116
if (chain.getEntityInfo().getType() == EntityType.POLYMER) {
labelSeqId.add(seqId);
} else {
labelSeqId.markNextNotPresent();
}
String insCode = "";
if (group.getResidueNumber().getInsCode() != null) {
insCode = Character.toString(group.getResidueNumber().getInsCode());
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