Lenient to missing atom_site.occupancy

josemduarte · josemduarte · commit 65d3dcde9a49 · 2025-02-21T11:24:49.000-08:00
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
@@ -333,7 +333,7 @@ public void consumeAtomSite(AtomSite atomSite) {
             atom.setY(cartnY.get(atomIndex));
             atom.setZ(cartnZ.get(atomIndex));
 
-            atom.setOccupancy((float) occupancy.get(atomIndex));
+            atom.setOccupancy((float) (occupancy.isDefined()? occupancy.get(atomIndex) : 1.0));
             atom.setTempFactor((float) bIsoOrEquiv.get(atomIndex));
 
             if (altLocation == null || altLocation.isEmpty() || ".".equals(altLocation)) {
