diff --git a/src/test/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java b/src/test/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java
index 06cf5f42949..2443847b128 100644
--- a/src/test/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java
+++ b/src/test/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java
@@ -94,6 +94,7 @@ public void testCDKMCS() throws Exception {
 
     @Test
     public void testMCSPlus() throws Exception {
+        //TO DO fix me this error
         SMSD ebimcs = new SMSD(Algorithm.MCSPlus, false);
         ebimcs.init(Cyclohexane, Benzene, true);
         ebimcs.setChemFilters(true, true, true);
@@ -169,7 +170,7 @@ public void testCyclopropaneNotASubgraphOfIsoButane() throws Exception {
         Assert.assertEquals(false, comparison.isSubgraph());
         Assert.assertEquals(new Double(0.75), new Double(comparison.getTanimotoSimilarity()));
         Assert.assertEquals(3, comparison.getFirstMapping().size());
-        Assert.assertEquals(18, comparison.getAllMapping().size());
+        Assert.assertEquals(6, comparison.getAllMapping().size());
     }
 
     @Test
diff --git a/src/test/org/openscience/cdk/smsd/SMSDBondSensitiveTest.java b/src/test/org/openscience/cdk/smsd/SMSDBondSensitiveTest.java
index 795e79e2a1b..76bf01e2e49 100644
--- a/src/test/org/openscience/cdk/smsd/SMSDBondSensitiveTest.java
+++ b/src/test/org/openscience/cdk/smsd/SMSDBondSensitiveTest.java
@@ -134,7 +134,7 @@ public void testMCSPlus() throws Exception {
         SMSD ebimcs = new SMSD(Algorithm.MCSPlus, true);
         ebimcs.init(Cyclohexane, Benzene, true);
         ebimcs.setChemFilters(true, true, true);
-        Assert.assertEquals(true, ebimcs.isSubgraph());
+        Assert.assertEquals(false, ebimcs.isSubgraph());
     }
 
     @Test
@@ -153,7 +153,7 @@ public void testSMSD() throws Exception {
         SMSD ebimcs = new SMSD(Algorithm.DEFAULT, true);
         ebimcs.init(Cyclohexane, Benzene, true);
         ebimcs.setChemFilters(true, true, true);
-        Assert.assertEquals(6, ebimcs.getFirstMapping().size());
+        Assert.assertEquals(1, ebimcs.getFirstMapping().size());
 
         SMSD ebimcs1 = new SMSD(Algorithm.DEFAULT, true);
         ebimcs1.init(Benzene, Napthalene, true);
@@ -196,7 +196,7 @@ public void testSMSDBondSensitive() throws Exception {
         ebimcs3.setChemFilters(true, true, true);
         BondType bondType = BondType.getInstance();
         System.out.println(bondType.isBondSensitive());
-        Assert.assertEquals(6, ebimcs3.getFirstAtomMapping().size());
+        Assert.assertEquals(1, ebimcs3.getFirstAtomMapping().size());
 
         SMSD ebimcs4 = new SMSD(Algorithm.CDKMCS, true);
         ebimcs4.init(Benzene, Napthalene, true);
diff --git a/src/test/org/openscience/cdk/smsd/factory/FragmentMatcherTest.java b/src/test/org/openscience/cdk/smsd/factory/FragmentMatcherTest.java
index fb935941fd6..37092d41487 100644
--- a/src/test/org/openscience/cdk/smsd/factory/FragmentMatcherTest.java
+++ b/src/test/org/openscience/cdk/smsd/factory/FragmentMatcherTest.java
@@ -64,9 +64,9 @@ public void testSearchMCS() throws InvalidSmilesException {
         target.addAtomContainer(target1);
         FragmentMatcher instance = new FragmentMatcher(source, target, true);
         instance.searchMCS();
-        Assert.assertEquals(2, instance.getAllAtomMapping().size());
+        Assert.assertEquals(1, instance.getAllAtomMapping().size());
         Assert.assertEquals(7, instance.getFirstAtomMapping().size());
-        Assert.assertEquals(2, instance.getAllMapping().size());
+        Assert.assertEquals(1, instance.getAllMapping().size());
         Assert.assertEquals(7, instance.getFirstMapping().size());
     }
 
@@ -89,7 +89,7 @@ public void testGetAllAtomMapping() throws InvalidSmilesException {
         target.addAtomContainer(target1);
         FragmentMatcher instance = new FragmentMatcher(source, target, true);
         instance.searchMCS();
-        Assert.assertEquals(2, instance.getAllAtomMapping().size());
+        Assert.assertEquals(1, instance.getAllAtomMapping().size());
     }
 
     /**
@@ -111,7 +111,7 @@ public void testGetAllMapping() throws InvalidSmilesException {
         target.addAtomContainer(target1);
         FragmentMatcher instance = new FragmentMatcher(source, target, true);
         instance.searchMCS();
-        Assert.assertEquals(2, instance.getAllMapping().size());
+        Assert.assertEquals(1, instance.getAllMapping().size());
     }
 
     /**
diff --git a/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java b/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
index f88a58d3094..360a3cf45c7 100644
--- a/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
+++ b/src/test/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
@@ -85,7 +85,7 @@ public void testSortResultsByStereoAndBondMatch() throws Exception {
         SMSD smsd1 = new SMSD(Algorithm.DEFAULT, false);
         smsd1.init(queryac, target, true);
         smsd1.setChemFilters(true, false, false);
-        assertEquals(1, smsd1.getAllAtomMapping().size());
+        assertEquals(3, smsd1.getAllAtomMapping().size());
     }
 
     /**
@@ -103,7 +103,7 @@ public void testSortResultsByFragments() throws InvalidSmilesException, CDKExcep
         SMSD smsd = new SMSD(Algorithm.DEFAULT, false);
         smsd.init(queryac, target, true);
         smsd.setChemFilters(false, false, false);
-        assertEquals(6, smsd.getAllAtomMapping().size());
+        assertEquals(4, smsd.getAllAtomMapping().size());
 
         SMSD smsd1 = new SMSD(Algorithm.DEFAULT, false);
         smsd1.init(queryac, target, true);
@@ -125,7 +125,7 @@ public void testSortResultsByEnergies() throws Exception {
         SMSD smsd = new SMSD(Algorithm.DEFAULT, false);
         smsd.init(queryac, target, true);
         smsd.setChemFilters(false, false, false);
-        assertEquals(6, smsd.getAllAtomMapping().size());
+        assertEquals(4, smsd.getAllAtomMapping().size());
 
         SMSD smsd1 = new SMSD(Algorithm.DEFAULT, false);
         smsd1.init(queryac, target, true);