From 274a36abf39908eb0eb27c3da6d8e47ae875a83d Mon Sep 17 00:00:00 2001
From: Jose Duarte <jose.m.duarte@gmail.com>
Date: Fri, 7 Nov 2025 21:53:06 -0800
Subject: [PATCH] Fix for #1116

---
 CHANGELOG.md                                               | 5 +++++
 .../nbio/structure/io/cif/AbstractCifFileSupplier.java     | 7 ++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 74b52303b0..07be3a5172 100644
--- 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
index 826d9588ef..7e9d8ad7ac 100644
--- 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());