Fix for entity_src_nat category parsing, when some items missing

josemduarte · josemduarte · commit b0a1da5a3864 · 2023-01-29T09:43:51.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1403,8 +1403,8 @@ private void addInformationFromEntitySrcSyn(int rowIndex, EntityInfo entityInfo)
     }
 
     private void addInformationFromEntitySrcNat(int rowIndex, EntityInfo entityInfo) {
-        entityInfo.setAtcc(entitySrcNat.getPdbxAtcc().get(rowIndex));
-        entityInfo.setCell(entitySrcNat.getPdbxCell().get(rowIndex));
+        entityInfo.setAtcc(entitySrcNat.getPdbxAtcc().values().skip(rowIndex).findFirst().orElse(""));
+        entityInfo.setCell(entitySrcNat.getPdbxCell().values().skip(rowIndex).findFirst().orElse(""));
         entityInfo.setOrganismCommon(entitySrcNat.getCommonName().get(rowIndex));
         entityInfo.setOrganismScientific(entitySrcNat.getPdbxOrganismScientific().get(rowIndex));
         entityInfo.setOrganismTaxId(entitySrcNat.getPdbxNcbiTaxonomyId().get(rowIndex));
