Merge pull request #1117 from biojava/jd/issue1116

josemduarte · web-flow · commit c7261dfdefe2 · 2025-11-12T09:42:54.000-08:00
Don't output label_seq_id for non-polymers in mmCIF writing
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
@@ -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());

Original file line number	Diff line number	Diff line change
`@@ -308,7 +308,12 @@ public void accept(WrappedAtom wrappedAtom) {`
`308`	`308`	`}`
`309`	`309`	`}`
`310`	`310`	`labelEntityId.add(entityId);`
`311`		`- labelSeqId.add(seqId);`
	`311`	`+ // see https://github.com/biojava/biojava/issues/1116`
	`312`	`+ if (chain.getEntityInfo().getType() == EntityType.POLYMER) {`
	`313`	`+ labelSeqId.add(seqId);`
	`314`	`+ } else {`
	`315`	`+ labelSeqId.markNextNotPresent();`
	`316`	`+ }`
`312`	`317`	`String insCode = "";`
`313`	`318`	`if (group.getResidueNumber().getInsCode() != null) {`
`314`	`319`	`insCode = Character.toString(group.getResidueNumber().getInsCode());`