We will be mocking this IChemModel and so no builder will be avaliable - rewrite to avoid creating IAtomContainerSets (and a temp ChemModel).

johnmay · egonw · commit 0a99998cdd59 · 2021-12-24T09:03:56.000+01:00
diff --git a/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemModelManipulator.java b/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemModelManipulator.java
@@ -261,18 +261,24 @@ public static IReaction getRelevantReaction(IChemModel chemModel, IAtom atom) {
         return reaction;
     }
 
+    /** Local helper to add an IAtomContainerSet to a list */
+    private static void addAll(List<IAtomContainer> acList, IAtomContainerSet acSet) {
+        for (IAtomContainer ac : acSet.atomContainers())
+            acList.add(ac);
+    }
+
     /**
      * Returns all the AtomContainer's of a ChemModel.
      */
     public static List<IAtomContainer> getAllAtomContainers(IChemModel chemModel) {
-        IAtomContainerSet moleculeSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
+        List<IAtomContainer> res = new ArrayList<>();
         if (chemModel.getMoleculeSet() != null) {
-            moleculeSet.add(chemModel.getMoleculeSet());
+            addAll(res, chemModel.getMoleculeSet());
         }
         if (chemModel.getReactionSet() != null) {
-            moleculeSet.add(ReactionSetManipulator.getAllMolecules(chemModel.getReactionSet()));
+            addAll(res, ReactionSetManipulator.getAllMolecules(chemModel.getReactionSet()));
         }
-        return MoleculeSetManipulator.getAllAtomContainers(moleculeSet);
+        return res;
     }
 
     /**
diff --git a/storage/ctab/src/main/java/org/openscience/cdk/io/SDFWriter.java b/storage/ctab/src/main/java/org/openscience/cdk/io/SDFWriter.java
@@ -53,6 +53,7 @@
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
+import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
 
 /**
  * Writes MDL SD files ({@cdk.cite DAL92}). A MDL SD file contains one or more molecules,
@@ -219,11 +220,7 @@ public void write(IChemObject object) throws CDKException {
                 writeChemFile((IChemFile) object);
                 return;
             } else if (object instanceof IChemModel) {
-                IChemFile file = object.getBuilder().newInstance(IChemFile.class);
-                IChemSequence sequence = object.getBuilder().newInstance(IChemSequence.class);
-                sequence.addChemModel((IChemModel) object);
-                file.addChemSequence(sequence);
-                writeChemFile((IChemFile) file);
+                writeChemModel((IChemModel) object);
                 return;
             } else if (object instanceof IAtomContainer) {
                 writeMolecule((IAtomContainer) object);
@@ -255,6 +252,12 @@ private void writeChemFile(IChemFile file) throws Exception {
         }
     }
 
+    private void writeChemModel(IChemModel model) throws Exception {
+        for (IAtomContainer container : ChemModelManipulator.getAllAtomContainers(model)) {
+            writeMolecule(container);
+        }
+    }
+
     private static String replaceInvalidHeaderChars(String headerKey) {
         return headerKey.replaceAll("[-<>.=% ]", "_");
     }
