diff --git a/Code/Demos/SWIG/CMakeLists.txt b/Code/Demos/SWIG/CMakeLists.txt
index 0ff080c64..7ea640f46 100644
--- a/Code/Demos/SWIG/CMakeLists.txt
+++ b/Code/Demos/SWIG/CMakeLists.txt
@@ -13,5 +13,5 @@ Depictor SubstructMatch ChemReactions Fingerprints Subgraphs
 GraphMol DataStructs
 RDGeometryLib RDGeneral )
 
-add_subdirectory(python_example)
+#add_subdirectory(python_example)
 add_subdirectory(java_example)
diff --git a/Code/Demos/SWIG/RDKFuncs.i b/Code/Demos/SWIG/RDKFuncs.i
index 5effa02be..b8b0f5b05 100644
--- a/Code/Demos/SWIG/RDKFuncs.i
+++ b/Code/Demos/SWIG/RDKFuncs.i
@@ -80,13 +80,13 @@ SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(Match_Vect, std::vector< std::pair<int,int> >
 %extend RDKit::ROMol {
   bool hasSubstructMatch(RDKit::ROMol &query,bool useChirality=false){
     RDKit::MatchVectType mv;
-    return SubstructMatch(*($self),query,mv,true,useChirality,false);
+    return SubstructMatch(*($self),query,mv,true,useChirality);
   };
 
   std::vector<std::pair<int, int> >
   getSubstructMatch(RDKit::ROMol &query,bool useChirality=false){
     RDKit::MatchVectType mv;
-    SubstructMatch(*($self),query,mv,true,useChirality,false);
+    SubstructMatch(*($self),query,mv,true,useChirality);
     return mv;
 
   };
@@ -95,7 +95,7 @@ SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(Match_Vect, std::vector< std::pair<int,int> >
   getSubstructMatches(RDKit::ROMol &query,bool uniquify=true,
                       bool useChirality=false){
     std::vector<RDKit::MatchVectType> mv;
-    SubstructMatch(*($self),query,mv,uniquify,true,useChirality,false);
+    SubstructMatch(*($self),query,mv,uniquify,true,useChirality);
     return mv;
   };
 
@@ -165,6 +165,7 @@ SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(Match_Vect, std::vector< std::pair<int,int> >
 #include <boost/cstdint.hpp>
 #include <DataStructs/SparseIntVect.h>
 #include <GraphMol/Fingerprints/MorganFingerprints.h>
+#include <GraphMol/Fingerprints/AtomPairs.h>
 %}
 
 #if SWIGCSHARP
@@ -191,10 +192,21 @@ SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(UInt_Pair_Vect, std::vector< std::pair<unsign
 %rename(MorganFingerprintMol) RDKit::MorganFingerprints::getFingerprint;
 %include <GraphMol/Fingerprints/MorganFingerprints.h>
 
+
+%template(SparseIntVecti32) RDKit::SparseIntVect<boost::int32_t>;
+%template(SparseIntVecti64) RDKit::SparseIntVect<boost::int64_t>;
+%include <GraphMol/Fingerprints/AtomPairs.h>
+
+
 %include <DataStructs/BitOps.h>
 %template(TanimotoSimilarityEBV) TanimotoSimilarity<ExplicitBitVect,ExplicitBitVect>;
 %template(DiceSimilarityEBV) DiceSimilarity<ExplicitBitVect,ExplicitBitVect>;
 %template(DiceSimilaritySIVu32) RDKit::DiceSimilarity<boost::uint32_t>;
+%template(DiceSimilaritySIVi32) RDKit::DiceSimilarity<boost::int32_t>;
+%template(DiceSimilaritySIVi64) RDKit::DiceSimilarity<boost::int64_t>;
+%template(TanimotoSimilaritySIVu32) RDKit::TanimotoSimilarity<boost::uint32_t>;
+%template(TanimotoSimilaritySIVi32) RDKit::TanimotoSimilarity<boost::int32_t>;
+%template(TanimotoSimilaritySIVi64) RDKit::TanimotoSimilarity<boost::int64_t>;
 
 
 
diff --git a/Code/Demos/SWIG/java_example/CMakeLists.txt b/Code/Demos/SWIG/java_example/CMakeLists.txt
index 124397621..eb7cae49a 100644
--- a/Code/Demos/SWIG/java_example/CMakeLists.txt
+++ b/Code/Demos/SWIG/java_example/CMakeLists.txt
@@ -5,10 +5,10 @@ find_package(JNI REQUIRED)
 INCLUDE_DIRECTORIES(${JNI_INCLUDE_DIRS})
 
 SET_SOURCE_FILES_PROPERTIES(RDKFuncs.i PROPERTIES CPLUSPLUS ON )
-SET_SOURCE_FILES_PROPERTIES(RDKFuncs.i OBJECT_DEPENDS ../RDKFuncs.i )
 
 SET(CMAKE_SWIG_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/org/RDKit )
 SET(CMAKE_SWIG_FLAGS -package "org.RDKit")
+SET(SWIG_MODULE_RDKFuncs_EXTRA_DEPS ../RDKFuncs.i)
 SWIG_ADD_MODULE(RDKFuncs "java" RDKFuncs.i ../RDKFuncs.cpp)
 
 SWIG_LINK_LIBRARIES(RDKFuncs ${RDKit_Wrapper_Libs} )
@@ -33,5 +33,6 @@ ADD_CUSTOM_TARGET(RDKitJava ALL
   COMMENT "building jar"
 )
 
+
 INSTALL(TARGETS RDKFuncs 
               DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} )
diff --git a/Code/Demos/SWIG/java_example/WrapperTests.java b/Code/Demos/SWIG/java_example/WrapperTests.java
index d20a1f052..4c997d8c1 100644
--- a/Code/Demos/SWIG/java_example/WrapperTests.java
+++ b/Code/Demos/SWIG/java_example/WrapperTests.java
@@ -153,26 +153,68 @@ public class WrapperTests {
 	assertTrue(v2.size()>0);
 	assertTrue(v2.size()>v1.size());
     }
+    @Test public void testFingerprints3() {
+	ROMol m1,m2;
+	m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
+	m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
+	SparseIntVecti32 fp1,fp2;
+	fp1=RDKFuncs.getAtomPairFingerprint(m1,2,6);
+	fp2=RDKFuncs.getAtomPairFingerprint(m1,2,6);
+	assertTrue(RDKFuncs.DiceSimilaritySIVi32(fp1,fp2)==1.0);
+	fp2=RDKFuncs.getAtomPairFingerprint(m2,2,6);
+        assertEquals(RDKFuncs.DiceSimilaritySIVi32(fp1,fp2),0.66667,.0001);
+    }
+    @Test public void testFingerprints4() {
+	ROMol m1,m2;
+	m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
+	m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
+	SparseIntVecti64 fp1,fp2;
+	fp1=RDKFuncs.getTopologicalTorsionFingerprint(m1);
+	fp2=RDKFuncs.getTopologicalTorsionFingerprint(m1);
+	assertTrue(RDKFuncs.DiceSimilaritySIVi64(fp1,fp2)==1.0);
+	fp2=RDKFuncs.getTopologicalTorsionFingerprint(m2);
+        assertEquals(RDKFuncs.DiceSimilaritySIVi64(fp1,fp2),0.3333,.0001);
+    }
     @Test public void testErrorHandling() {
 	ROMol m1;
-	System.err.println("go");
 	m1 = RDKFuncs.MolFromSmiles("C1CC");
 	assertTrue(m1==null);
-	System.err.println("go2");
 	m1 = RDKFuncs.MolFromSmiles("c1cc1");
 	assertTrue(m1==null);
 	System.err.println("ok!");
     }
-    /*    @Test public void testMemory() {
+    /*@Test*/ public void testMemory() {
 	for(int i=0;i<1000000;i++){
-	    ROMol m1,m2;
+	    ROMol m1;
 	    m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
 	    if((i%1000)==0){
 		System.err.println("done: "+i);
 	    }
 	    m1.delete();
 	}
-	}*/
+    }
+    /*@Test*/ public void testMemory2() {
+	ChemicalReaction rxn;
+	rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
+	assertTrue(rxn.getNumReactantTemplates()==2);
+	assertTrue(rxn.getNumProductTemplates()==1);
+	ROMol r1,r2;
+	r1=RDKFuncs.MolFromSmiles("CC(=O)O");
+	r2=RDKFuncs.MolFromSmiles("ClCN");
+	assertTrue(r1.getNumAtoms()==4);
+	assertTrue(r2.getNumAtoms()==3);
+	for(int i=0;i<1000000;i++){
+            ROMol_Vect rs= new ROMol_Vect(2);
+            rs.set(0,r1);
+            rs.set(1,r2);
+            ROMol_Vect_Vect ps;
+            ps=rxn.runReactants(rs);
+	    if((i%1000)==0){
+		System.err.println("done: "+i);
+	    }
+            ps.delete();
+        }
+    }
     static {
         try {
             System.loadLibrary("RDKFuncs");
diff --git a/Code/Demos/SWIG/python_example/CMakeLists.txt b/Code/Demos/SWIG/python_example/CMakeLists.txt
index b267b830f..d57a4d0a4 100644
--- a/Code/Demos/SWIG/python_example/CMakeLists.txt
+++ b/Code/Demos/SWIG/python_example/CMakeLists.txt
@@ -2,9 +2,12 @@ FIND_PACKAGE(PythonLibs)
 INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH})
 
 SET_SOURCE_FILES_PROPERTIES(RDKFuncs.i PROPERTIES CPLUSPLUS ON)
-SET_SOURCE_FILES_PROPERTIES(RDKFuncs.i PROPERTIES SWIG_FLAGS "")
+SET_SOURCE_FILES_PROPERTIES(RDKFuncs.i PROPERTIES SWIG_FLAGS ""
+OBJECT_DEPENDS ../RDKFuncs.i )
+
 
 SET(CMAKE_SWIG_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR} )
+SET(SWIG_MODULE_pyRDKFuncs_EXTRA_DEPS ../RDKFuncs.i)
 SWIG_ADD_MODULE(pyRDKFuncs "python" RDKFuncs.i ../RDKFuncs.cpp)
 SWIG_LINK_LIBRARIES(pyRDKFuncs ${RDKit_Wrapper_Libs} ${PYTHON_LIBRARIES})