diff --git a/src/main/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithms.java b/src/main/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithms.java
index 38d1a6e3cb2..d79cfcb79d1 100644
--- a/src/main/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithms.java
+++ b/src/main/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithms.java
@@ -362,7 +362,7 @@ private void clearMaps() {
      *
      */
     private void init(MolHandler Reactant, MolHandler Product, boolean removeHydrogen) throws CDKException {
-        if (Reactant instanceof IQueryAtomContainer) {
+        if (Product instanceof IQueryAtomContainer) {
             throw new CDKException(
                     "The first IAtomContainer must not be an IQueryAtomContainer");
         }
@@ -388,7 +388,7 @@ private void init(MolHandler Reactant, MolHandler Product, boolean removeHydroge
     @Override
     @TestMethod("testInit_3args_1")
     public void init(IMolecule Reactant, IMolecule Product, boolean removeHydrogen) throws CDKException {
-        if (Reactant instanceof IQueryAtomContainer) {
+        if (Product instanceof IQueryAtomContainer) {
             throw new CDKException(
                     "The first IAtomContainer must not be an IQueryAtomContainer");
         }
@@ -406,7 +406,7 @@ public void init(IMolecule Reactant, IMolecule Product, boolean removeHydrogen)
     @Override
     @TestMethod("testInit_3args_2")
     public void init(IAtomContainer Reactant, IAtomContainer Product, boolean removeHydrogen) throws CDKException {
-        if (Reactant instanceof IQueryAtomContainer) {
+        if (Product instanceof IQueryAtomContainer) {
             throw new CDKException(
                     "The first IAtomContainer must not be an IQueryAtomContainer");
         }
diff --git a/src/test/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithmsTest.java b/src/test/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithmsTest.java
index d4ef47edf27..93bca9c247b 100644
--- a/src/test/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithmsTest.java
+++ b/src/test/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithmsTest.java
@@ -25,6 +25,7 @@
 import org.junit.Test;
 import static org.junit.Assert.*;
 import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IMolecule;
@@ -58,9 +59,10 @@ public void testSubStructureSearchAlgorithms() {
     /**
      * Test of init method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testInit_3args_1() throws InvalidSmilesException {
+    public void testInit_3args_1() throws InvalidSmilesException, CDKException {
         System.out.println("init");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IMolecule target = sp.parseSmiles("C\\C=C/OCC=C");
@@ -76,9 +78,10 @@ public void testInit_3args_1() throws InvalidSmilesException {
     /**
      * Test of init method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testInit_3args_2() throws InvalidSmilesException {
+    public void testInit_3args_2() throws InvalidSmilesException, CDKException {
         System.out.println("init");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/OCC=C");
@@ -115,9 +118,10 @@ public void testInit_3args_3() throws Exception {
     /**
      * Test of setChemFilters method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testSetChemFilters() throws InvalidSmilesException {
+    public void testSetChemFilters() throws InvalidSmilesException, CDKException {
         System.out.println("setChemFilters");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/OCC=C");
@@ -132,9 +136,10 @@ public void testSetChemFilters() throws InvalidSmilesException {
     /**
      * Test of getFragmentSize method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetFragmentSize() throws InvalidSmilesException {
+    public void testGetFragmentSize() throws InvalidSmilesException, CDKException {
         System.out.println("getFragmentSize");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -150,9 +155,10 @@ public void testGetFragmentSize() throws InvalidSmilesException {
     /**
      * Test of getStereoScore method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetStereoScore() throws InvalidSmilesException {
+    public void testGetStereoScore() throws InvalidSmilesException, CDKException {
         System.out.println("getStereoScore");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/OCC=C");
@@ -167,10 +173,11 @@ public void testGetStereoScore() throws InvalidSmilesException {
 
     /**
      * Test of getEnergyScore method, of class SubStructureSearchAlgorithms.
-     * @throws InvalidSmilesException 
+     * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetEnergyScore() throws InvalidSmilesException {
+    public void testGetEnergyScore() throws InvalidSmilesException, CDKException {
         System.out.println("getEnergyScore");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -186,9 +193,10 @@ public void testGetEnergyScore() throws InvalidSmilesException {
     /**
      * Test of getFirstMapping method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetFirstMapping() throws InvalidSmilesException {
+    public void testGetFirstMapping() throws InvalidSmilesException, CDKException {
         System.out.println("getFirstMapping");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -203,10 +211,11 @@ public void testGetFirstMapping() throws InvalidSmilesException {
 
     /**
      * Test of getAllMapping method, of class SubStructureSearchAlgorithms.
-     * @throws InvalidSmilesException 
+     * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetAllMapping() throws InvalidSmilesException {
+    public void testGetAllMapping() throws InvalidSmilesException, CDKException {
         System.out.println("getAllMapping");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -222,9 +231,10 @@ public void testGetAllMapping() throws InvalidSmilesException {
     /**
      * Test of getFirstAtomMapping method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetFirstAtomMapping() throws InvalidSmilesException {
+    public void testGetFirstAtomMapping() throws InvalidSmilesException, CDKException {
         System.out.println("getFirstAtomMapping");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -240,9 +250,10 @@ public void testGetFirstAtomMapping() throws InvalidSmilesException {
     /**
      * Test of getAllAtomMapping method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetAllAtomMapping() throws InvalidSmilesException {
+    public void testGetAllAtomMapping() throws InvalidSmilesException, CDKException {
         System.out.println("getAllAtomMapping");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -258,9 +269,10 @@ public void testGetAllAtomMapping() throws InvalidSmilesException {
     /**
      * Test of getReactantMolecule method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetReactantMolecule() throws InvalidSmilesException {
+    public void testGetReactantMolecule() throws InvalidSmilesException, CDKException {
         System.out.println("getReactantMolecule");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -276,9 +288,10 @@ public void testGetReactantMolecule() throws InvalidSmilesException {
     /**
      * Test of getProductMolecule method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetProductMolecule() throws InvalidSmilesException {
+    public void testGetProductMolecule() throws InvalidSmilesException, CDKException {
         System.out.println("getProductMolecule");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -313,9 +326,10 @@ public void testGetTanimotoSimilarity() throws Exception {
     /**
      * Test of isStereoMisMatch method, of class SubStructureSearchAlgorithms.
      * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testIsStereoMisMatch() throws InvalidSmilesException {
+    public void testIsStereoMisMatch() throws InvalidSmilesException, CDKException {
         System.out.println("isStereoMisMatch");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -332,7 +346,7 @@ public void testIsStereoMisMatch() throws InvalidSmilesException {
      * @throws InvalidSmilesException
      */
     @Test
-    public void testIsSubgraph() throws InvalidSmilesException {
+    public void testIsSubgraph() throws InvalidSmilesException, CDKException {
         System.out.println("isSubgraph");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
diff --git a/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java b/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
index b1909955559..f88a58d3094 100644
--- a/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
+++ b/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
@@ -31,6 +31,7 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.smiles.SmilesParser;
@@ -89,10 +90,11 @@ public void testSortResultsByStereoAndBondMatch() throws Exception {
 
     /**
      * Test of sortResultsByFragments method, of class ChemicalFilters.
-     * @throws InvalidSmilesException 
+     * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testSortResultsByFragments() throws InvalidSmilesException {
+    public void testSortResultsByFragments() throws InvalidSmilesException, CDKException {
         System.out.println("sortResultsByFragments");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -176,10 +178,11 @@ public void testSortMapByValueInDecendingOrder() {
 
     /**
      * Test of getSortedEnergy method, of class ChemicalFilters.
-     * @throws InvalidSmilesException 
+     * @throws InvalidSmilesException
+     * @throws CDKException 
      */
     @Test
-    public void testGetSortedEnergy() throws InvalidSmilesException {
+    public void testGetSortedEnergy() throws InvalidSmilesException, CDKException {
         System.out.println("getSortedEnergy");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -195,9 +198,10 @@ public void testGetSortedEnergy() throws InvalidSmilesException {
     /**
      * Test of getSortedFragment method, of class ChemicalFilters.
      * @throws InvalidSmilesException
+     * @throws CDKException 
      */
     @Test
-    public void testGetSortedFragment() throws InvalidSmilesException {
+    public void testGetSortedFragment() throws InvalidSmilesException, CDKException {
         System.out.println("getSortedFragment");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
@@ -212,10 +216,11 @@ public void testGetSortedFragment() throws InvalidSmilesException {
 
     /**
      * Test of getStereoMatches method, of class ChemicalFilters.
-     * @throws InvalidSmilesException 
+     * @throws InvalidSmilesException
+     * @throws CDKException
      */
     @Test
-    public void testGetStereoMatches() throws InvalidSmilesException {
+    public void testGetStereoMatches() throws InvalidSmilesException, CDKException {
         System.out.println("getStereoMatches");
         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer target = sp.parseSmiles("C\\C=C/OCC=C");