JAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be...

[jalview.git] / src / jalview / ext / jmol / JmolParser.java

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 309e196..c514503 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -27,7 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
@@ -186,7 +186,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           prot.add(chainseq);
         }
 
-        if (StructureViewSettings.isPredictSecondaryStructure())
+        if (StructureImportSettings.isPredictSecondaryStructure())
         {
           createAnnotation(chainseq, chain, ms.at);
         }
@@ -208,7 +208,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       // System.out.println("Seq Id : " + atom.getSeqID());
       // System.out.println("To String : " + atom.toString());
-      if (atom.isHetero())
+      if (!StructureImportSettings.isProcessHETATMs() && atom.isHetero())
       {
         continue;
       }