diff --git a/Code/DataManip/MetricMatrixCalc/MetricFuncs.h b/Code/DataManip/MetricMatrixCalc/MetricFuncs.h
index 20e519216..31cdfb36a 100755
--- a/Code/DataManip/MetricMatrixCalc/MetricFuncs.h
+++ b/Code/DataManip/MetricMatrixCalc/MetricFuncs.h
@@ -28,13 +28,13 @@ namespace RDDataManip {
   double TanimotoDistanceMetric(const T1 &bv1, const T2 &bv2, unsigned int dim) {
     // the dim parameter is actually irrelevant here but we have to include it to deal with 
     // template version of setMetricFunc in MetricMatricCalc
-    return (1.0 - SimilarityWrapper(bv1, bv2,(const double (*)(const T1&,const T2&))TanimotoSimilarity));
+    return (1.0 - SimilarityWrapper(bv1, bv2,(double (*)(const T1&,const T2&))TanimotoSimilarity));
   };
 
   //! return the Tanimoto similarity between two bit vectors
   template <typename T1, typename T2>
   double TanimotoSimilarityMetric(const T1 &bv1, const T2 &bv2, unsigned int dim) {
-    return SimilarityWrapper(bv1,bv2,(const double (*)(const T1&,const T2&))TanimotoSimilarity);
+    return SimilarityWrapper(bv1,bv2,(double (*)(const T1&,const T2&))TanimotoSimilarity);
   };
 }
 
diff --git a/Code/DataStructs/BitOps.cpp b/Code/DataStructs/BitOps.cpp
index f957d9886..0f6849a32 100755
--- a/Code/DataStructs/BitOps.cpp
+++ b/Code/DataStructs/BitOps.cpp
@@ -210,7 +210,7 @@ NumOnBitsInCommon(const ExplicitBitVect& bv1,
 //
 // """ -------------------------------------------------------
 template <typename T1, typename T2>
-const double
+double
 TanimotoSimilarity(const T1& bv1,
                    const T2& bv2)
 {
@@ -225,7 +225,7 @@ TanimotoSimilarity(const T1& bv1,
 
 
 template <typename T1, typename T2>
-const double
+double
 TverskySimilarity(const T1& bv1,
                   const T2& bv2,
                   double a,
@@ -244,7 +244,7 @@ TverskySimilarity(const T1& bv1,
 }
 
 template <typename T1, typename T2>
-const double
+double
 CosineSimilarity(const T1& bv1,
                    const T2& bv2)
 {
@@ -262,7 +262,7 @@ CosineSimilarity(const T1& bv1,
 }
 
 template <typename T1, typename T2>
-const double
+double
 KulczynskiSimilarity(const T1& bv1,
                    const T2& bv2)
 {
@@ -281,7 +281,7 @@ KulczynskiSimilarity(const T1& bv1,
 
 
 template <typename T1, typename T2>
-const double
+double
 DiceSimilarity(const T1& bv1,
               const T2& bv2)
 {
@@ -299,7 +299,7 @@ DiceSimilarity(const T1& bv1,
 }
 
 template <typename T1, typename T2>
-const double
+double
 SokalSimilarity(const T1& bv1,
               const T2& bv2)
 {
@@ -313,7 +313,7 @@ SokalSimilarity(const T1& bv1,
 }
 
 template <typename T1, typename T2>
-const double
+double
 McConnaugheySimilarity(const T1& bv1,
                        const T2& bv2)
 {
@@ -343,7 +343,7 @@ inline T tmax(T v1,T v2) {
 }
 
 template <typename T1, typename T2>
-const double
+double
 AsymmetricSimilarity(const T1& bv1,
                      const T2& bv2)
 {
@@ -361,7 +361,7 @@ AsymmetricSimilarity(const T1& bv1,
 }
 
 template <typename T1, typename T2>
-const double
+double
 BraunBlanquetSimilarity(const T1& bv1,
                      const T2& bv2)
 {
@@ -379,7 +379,7 @@ BraunBlanquetSimilarity(const T1& bv1,
 }
 
 template <typename T1, typename T2>
-const double
+double
 RusselSimilarity(const T1& bv1,
                      const T2& bv2)
 {
@@ -405,7 +405,7 @@ RusselSimilarity(const T1& bv1,
 //
 // """ -------------------------------------------------------
 template <typename T1, typename T2>
-const double
+double
 OnBitSimilarity(const T1& bv1,
                 const T2& bv2)
 {
@@ -436,7 +436,7 @@ OnBitSimilarity(const T1& bv1,
 //
 // """ -------------------------------------------------------
 template <typename T1, typename T2>
-const int
+int
 NumBitsInCommon(const T1& bv1,
                 const T2& bv2)
 {
@@ -462,7 +462,7 @@ NumBitsInCommon(const T1& bv1,
 //
 // """ -------------------------------------------------------
 template <typename T1, typename T2>
-const double
+double
 AllBitSimilarity(const T1& bv1,
                 const T2& bv2)
 {
@@ -644,38 +644,38 @@ BitVectToText(const T1& bv1){
 
 
 
-template const double TanimotoSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double TverskySimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2,double a, double b);
-template const double CosineSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double KulczynskiSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double DiceSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double SokalSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double McConnaugheySimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double AsymmetricSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double BraunBlanquetSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double RusselSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double OnBitSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const int NumBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
-template const double AllBitSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double TanimotoSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double TverskySimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2,double a, double b);
+template double CosineSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double KulczynskiSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double DiceSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double SokalSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double McConnaugheySimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double AsymmetricSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double BraunBlanquetSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double RusselSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double OnBitSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template int NumBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template double AllBitSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
 template int NumOnBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
 template IntVect OnBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
 template IntVect OffBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
 template DoubleVect OnBitProjSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
 template DoubleVect OffBitProjSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
 
-template const double TanimotoSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double TverskySimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2,double a, double b);
-template const double CosineSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double KulczynskiSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double DiceSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double SokalSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double McConnaugheySimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double AsymmetricSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double BraunBlanquetSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double RusselSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double OnBitSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const int NumBitsInCommon(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
-template const double AllBitSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double TanimotoSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double TverskySimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2,double a, double b);
+template double CosineSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double KulczynskiSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double DiceSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double SokalSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double McConnaugheySimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double AsymmetricSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double BraunBlanquetSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double RusselSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double OnBitSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template int NumBitsInCommon(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template double AllBitSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
 template IntVect OnBitsInCommon(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
 template IntVect OffBitsInCommon(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
 template DoubleVect OnBitProjSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
diff --git a/Code/DataStructs/BitOps.h b/Code/DataStructs/BitOps.h
index f4293532a..86f1da5c3 100755
--- a/Code/DataStructs/BitOps.h
+++ b/Code/DataStructs/BitOps.h
@@ -24,7 +24,7 @@
 //! that may be of unequal size (will automatically fold as appropriate)
 template <typename T>
 double SimilarityWrapper(const T &bv1,const T &bv2,
-                         const double (*metric)(const T &,const T &),
+                         double (*metric)(const T &,const T &),
                          bool returnDistance=false){
   double res=0.0;
   if(bv1.GetNumBits()>bv2.GetNumBits()){
@@ -44,7 +44,7 @@ double SimilarityWrapper(const T &bv1,const T &bv2,
 //! \overload
 template <typename T>
 double SimilarityWrapper(const T &bv1,const T &bv2,double a,double b,
-                         const double (*metric)(const T &,const T &,double,double),
+                         double (*metric)(const T &,const T &,double,double),
                          bool returnDistance=false){
   double res=0.0;
   if(bv1.GetNumBits()>bv2.GetNumBits()){
@@ -90,7 +90,7 @@ NumOnBitsInCommon(const ExplicitBitVect & bv1,const ExplicitBitVect & bv2);
   \return <tt>(bv1&bv2)_o / [bv1_o + bv2_o - (bv1&bv2)_o]</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 TanimotoSimilarity(const T1& bv1,const T2& bv2);
 
 //! returns the Cosine similarity between two bit vects
@@ -98,7 +98,7 @@ TanimotoSimilarity(const T1& bv1,const T2& bv2);
   \return <tt>(bv1&bv2)_o / sqrt(bv1_o + bv2_o)</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 CosineSimilarity(const T1& bv1,
                  const T2& bv2);
 
@@ -107,7 +107,7 @@ CosineSimilarity(const T1& bv1,
   \return <tt>(bv1&bv2)_o * [bv1_o + bv2_o] / [2 * bv1_o * bv2_o]</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 KulczynskiSimilarity(const T1& bv1,
                      const T2& bv2);
 
@@ -116,7 +116,7 @@ KulczynskiSimilarity(const T1& bv1,
   \return <tt>2*(bv1&bv2)_o / [bv1_o + bv2_o]</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 DiceSimilarity(const T1& bv1,
                const T2& bv2);
 
@@ -131,7 +131,7 @@ DiceSimilarity(const T1& bv1,
  
 */
 template <typename T1, typename T2>
-const double
+double
 TverskySimilarity(const T1& bv1,
                   const T2& bv2,double a,double b);
 
@@ -140,7 +140,7 @@ TverskySimilarity(const T1& bv1,
   \return <tt>(bv1&bv2)_o / [2*bv1_o + 2*bv2_o - 3*(bv1&bv2)_o]</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 SokalSimilarity(const T1& bv1,
                 const T2& bv2);
 
@@ -149,7 +149,7 @@ SokalSimilarity(const T1& bv1,
   \return <tt>[(bv1&bv2)_o * (bv1_o + bv2_o) - (bv1_o * bv2_o)] / (bv1_o * bv2_o)</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 McConnaugheySimilarity(const T1& bv1,
                        const T2& bv2);
 
@@ -158,7 +158,7 @@ McConnaugheySimilarity(const T1& bv1,
   \return <tt>(bv1&bv2)_o / min(bv1_o,bv2_o)</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 AsymmetricSimilarity(const T1& bv1,
                      const T2& bv2);
 
@@ -167,7 +167,7 @@ AsymmetricSimilarity(const T1& bv1,
   \return <tt>(bv1&bv2)_o / max(bv1_o,bv2_o)</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 BraunBlanquetSimilarity(const T1& bv1,
                         const T2& bv2);
 
@@ -180,7 +180,7 @@ BraunBlanquetSimilarity(const T1& bv1,
 
 */
 template <typename T1, typename T2>
-const double
+double
 RusselSimilarity(const T1& bv1,
                  const T2& bv2);
 
@@ -190,7 +190,7 @@ RusselSimilarity(const T1& bv1,
   \return <tt>(bv1&bv2)_o / (bv1|bv2)_o </tt>
 */
 template <typename T1, typename T2>
-const double
+double
 OnBitSimilarity(const T1& bv1,const T2& bv2);
 
 //! returns the number of common bits (on and off) between two bit vects
@@ -198,7 +198,7 @@ OnBitSimilarity(const T1& bv1,const T2& bv2);
   \return <tt>bv1_n - (bv1^bv2)_o</tt>
 */
 template <typename T1, typename T2>
-const int
+int
 NumBitsInCommon(const T1& bv1,const T2& bv2);
 
 //! returns the commong-bit similarity (on and off) between two bit vects
@@ -206,7 +206,7 @@ NumBitsInCommon(const T1& bv1,const T2& bv2);
   \return <tt>[bv1_n - (bv1^bv2)_o] / bv1_n</tt>
 */
 template <typename T1, typename T2>
-const double
+double
 AllBitSimilarity(const T1& bv1,const T2& bv2);
 
 //! returns an IntVect with indices of all on bits in common between two bit vects
diff --git a/Code/DataStructs/BitVect.h b/Code/DataStructs/BitVect.h
index 7dc04ef19..e625a579e 100755
--- a/Code/DataStructs/BitVect.h
+++ b/Code/DataStructs/BitVect.h
@@ -27,11 +27,11 @@ public:
   //! returns the value of a particular bit
   virtual bool GetBit(const unsigned int which) const = 0;
   //! returns the number of bits (the length of the BitVect)
-  virtual const unsigned int GetNumBits() const = 0;
+  virtual unsigned int GetNumBits() const = 0;
   //! returns the number of on bits
-  virtual const unsigned int GetNumOnBits() const = 0;
+  virtual unsigned int GetNumOnBits() const = 0;
   //! returns the number of off bits
-  virtual const unsigned int GetNumOffBits() const =0;
+  virtual unsigned int GetNumOffBits() const =0;
   //! replaces the contents of \c v with indices of our on bits
   virtual void GetOnBits (IntVect& v) const = 0;
   //! clears (sets to off) all of our bits
diff --git a/Code/DataStructs/ExplicitBitVect.cpp b/Code/DataStructs/ExplicitBitVect.cpp
index 89f2d6e7b..9e52c43bb 100755
--- a/Code/DataStructs/ExplicitBitVect.cpp
+++ b/Code/DataStructs/ExplicitBitVect.cpp
@@ -104,13 +104,13 @@ ExplicitBitVect::ExplicitBitVect(const char *data,const unsigned int dataLen)
     return(ans);
   };
 
-  const unsigned int ExplicitBitVect::GetNumBits() const {
+  unsigned int ExplicitBitVect::GetNumBits() const {
     return d_size;
   };
-  const unsigned int ExplicitBitVect::GetNumOnBits() const {
+  unsigned int ExplicitBitVect::GetNumOnBits() const {
     return d_numOnBits;
   };
-  const unsigned int ExplicitBitVect::GetNumOffBits() const {
+  unsigned int ExplicitBitVect::GetNumOffBits() const {
     return d_size - d_numOnBits;
   };
 
diff --git a/Code/DataStructs/ExplicitBitVect.h b/Code/DataStructs/ExplicitBitVect.h
index bbe4100ee..8388d1dd0 100755
--- a/Code/DataStructs/ExplicitBitVect.h
+++ b/Code/DataStructs/ExplicitBitVect.h
@@ -41,9 +41,9 @@ public:
   ExplicitBitVect operator& (const ExplicitBitVect &other) const;
   ExplicitBitVect operator| (const ExplicitBitVect &other) const;
   ExplicitBitVect operator~ () const;
-  const unsigned int GetNumBits() const;
-  const unsigned int GetNumOnBits() const;
-  const unsigned int GetNumOffBits() const;
+  unsigned int GetNumBits() const;
+  unsigned int GetNumOnBits() const;
+  unsigned int GetNumOffBits() const;
 
   void GetOnBits (IntVect& v) const;
 
diff --git a/Code/DataStructs/SparseBitVect.h b/Code/DataStructs/SparseBitVect.h
index a3d4fdac7..a2e87b25e 100755
--- a/Code/DataStructs/SparseBitVect.h
+++ b/Code/DataStructs/SparseBitVect.h
@@ -58,7 +58,7 @@ public:
   //! returns a (const) pointer to our raw storage
   const IntSet *GetBitSet() const { return dp_bits;}
 
-  const unsigned int GetNumBits() const { return d_size; };
+  unsigned int GetNumBits() const { return d_size; };
   bool SetBit(const unsigned int which);
   bool SetBit(const IntSetIter which);
   bool UnSetBit(const unsigned int which);
@@ -66,8 +66,8 @@ public:
   bool GetBit(const IntVectIter which) const;
   bool GetBit(const IntSetIter which) const;
 
-  const unsigned int GetNumOnBits() const { return dp_bits->size(); };
-  const unsigned int GetNumOffBits() const { return d_size - dp_bits->size(); };
+  unsigned int GetNumOnBits() const { return dp_bits->size(); };
+  unsigned int GetNumOffBits() const { return d_size - dp_bits->size(); };
 
   std::string ToString() const;
 
diff --git a/Code/DataStructs/Wrap/wrap_BitOps.cpp b/Code/DataStructs/Wrap/wrap_BitOps.cpp
index d7c7e11d4..5dc2f667d 100755
--- a/Code/DataStructs/Wrap/wrap_BitOps.cpp
+++ b/Code/DataStructs/Wrap/wrap_BitOps.cpp
@@ -21,13 +21,13 @@ EBV *ff2(const EBV &ev1, int factor=2) {
 
 template <typename T>
 double SimilarityWrapper(const T &bv1,const std::string &pkl,
-                         const double (*metric)(const T &,const T &),bool returnDistance){
+                         double (*metric)(const T &,const T &),bool returnDistance){
   T bv2(pkl);
   return SimilarityWrapper(bv1,bv2,metric,returnDistance);
 }
 template <typename T>
 double SimilarityWrapper(const T &bv1,const std::string &pkl,double a,double b,
-                         const double (*metric)(const T &,const T &,double,double),bool returnDistance){
+                         double (*metric)(const T &,const T &,double,double),bool returnDistance){
   T bv2(pkl);
   return SimilarityWrapper(bv1,bv2,a,b,metric,returnDistance);
 }
@@ -35,7 +35,7 @@ double SimilarityWrapper(const T &bv1,const std::string &pkl,double a,double b,
 
 template <typename T>
 python::list BulkWrapper(const T &bv1,python::list bvs,
-                         const double (*metric)(const T &,const T &),
+                         double (*metric)(const T &,const T &),
                          bool returnDistance){
   python::list res;
   unsigned int nbvs=python::extract<unsigned int>(bvs.attr("__len__")());
@@ -48,7 +48,7 @@ python::list BulkWrapper(const T &bv1,python::list bvs,
 
 template <typename T>
 python::list BulkWrapper(const T &bv1,python::list bvs,double a,double b,
-                         const double (*metric)(const T &,const T &,double,double),
+                         double (*metric)(const T &,const T &,double,double),
                          bool returnDistance){
   python::list res;
   unsigned int nbvs=python::extract<unsigned int>(bvs.attr("__len__")());
@@ -62,53 +62,53 @@ python::list BulkWrapper(const T &bv1,python::list bvs,double a,double b,
 template <typename T1, typename T2>
 double TanimotoSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))TanimotoSimilarity,
+                           (double (*)(const T1&,const T1&))TanimotoSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkTanimotoSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))TanimotoSimilarity,
+                     (double (*)(const T&,const T&))TanimotoSimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double TverskySimilarity_w(const T1 &bv1,const T2 &bv2,double a,double b,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,a,b,
-                           (const double (*)(const T1&,const T1&,double,double))TverskySimilarity,
+                           (double (*)(const T1&,const T1&,double,double))TverskySimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkTverskySimilarity(const T &bv1,python::list bvs,double a,double b,
                                    bool returnDistance){
   return BulkWrapper(bv1,bvs,a,b,
-                     (const double (*)(const T&,const T&,double,double))TverskySimilarity,
+                     (double (*)(const T&,const T&,double,double))TverskySimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double CosineSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))CosineSimilarity,
+                           (double (*)(const T1&,const T1&))CosineSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkCosineSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))CosineSimilarity,
+                     (double (*)(const T&,const T&))CosineSimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double KulczynskiSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))KulczynskiSimilarity,
+                           (double (*)(const T1&,const T1&))KulczynskiSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkKulczynskiSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))KulczynskiSimilarity,
+                     (double (*)(const T&,const T&))KulczynskiSimilarity,
                      returnDistance);
 }
 
@@ -116,99 +116,99 @@ python::list BulkKulczynskiSimilarity(const T &bv1,python::list bvs,bool returnD
 template <typename T1, typename T2>
 double DiceSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))DiceSimilarity,
+                           (double (*)(const T1&,const T1&))DiceSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkDiceSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))DiceSimilarity,
+                     (double (*)(const T&,const T&))DiceSimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double SokalSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))SokalSimilarity,
+                           (double (*)(const T1&,const T1&))SokalSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkSokalSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))SokalSimilarity,
+                     (double (*)(const T&,const T&))SokalSimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double McConnaugheySimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))McConnaugheySimilarity,
+                           (double (*)(const T1&,const T1&))McConnaugheySimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkMcConnaugheySimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))McConnaugheySimilarity,
+                     (double (*)(const T&,const T&))McConnaugheySimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double AsymmetricSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))AsymmetricSimilarity,
+                           (double (*)(const T1&,const T1&))AsymmetricSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkAsymmetricSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))AsymmetricSimilarity,
+                     (double (*)(const T&,const T&))AsymmetricSimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double BraunBlanquetSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))BraunBlanquetSimilarity,
+                           (double (*)(const T1&,const T1&))BraunBlanquetSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkBraunBlanquetSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))BraunBlanquetSimilarity,
+                     (double (*)(const T&,const T&))BraunBlanquetSimilarity,
                      returnDistance);
 }
 
 template <typename T1, typename T2>
 double RusselSimilarity_w(const T1 &bv1,const T2 &bv2,bool returnDistance){
   return SimilarityWrapper(bv1,bv2,
-                           (const double (*)(const T1&,const T1&))RusselSimilarity,
+                           (double (*)(const T1&,const T1&))RusselSimilarity,
                            returnDistance);
 }
 template <typename T>
 python::list BulkRusselSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))RusselSimilarity,
+                     (double (*)(const T&,const T&))RusselSimilarity,
                      returnDistance);
 }
 
 template <typename T>
 python::list BulkOnBitSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))OnBitSimilarity,
+                     (double (*)(const T&,const T&))OnBitSimilarity,
                      returnDistance);
 }
 template <typename T>
 python::list BulkAllBitSimilarity(const T &bv1,python::list bvs,bool returnDistance){
   return BulkWrapper(bv1,bvs,
-                     (const double (*)(const T&,const T&))AllBitSimilarity,
+                     (double (*)(const T&,const T&))AllBitSimilarity,
                      returnDistance);
 }
 
 
 #define DBL_DEF(_funcname_,_bulkname_,_help_) { \
-  python::def( # _funcname_,(const double (*)(const SBV &,const SBV &))_funcname_,\
+  python::def( # _funcname_,(double (*)(const SBV &,const SBV &))_funcname_,\
                (python::args("v1"),python::args("v2"))); \
-  python::def( # _funcname_,(const double (*)(const EBV &,const EBV &))_funcname_,\
+  python::def( # _funcname_,(double (*)(const EBV &,const EBV &))_funcname_,\
                (python::args("v1"),python::args("v2")),_help_);\
   python::def( # _bulkname_,(python::list (*)(const EBV &,python::list,bool))_bulkname_,\
                (python::args("v1"),python::args("v2"),python::args("returnDistance")=0));\
@@ -297,9 +297,9 @@ struct BitOps_wrapper {
                 (DoubleVect (*)(const EBV&,const EBV&))OffBitProjSimilarity);
 
     python::def("NumBitsInCommon",
-                (const int (*)(const SBV&,const SBV&))NumBitsInCommon);
+                (int (*)(const SBV&,const SBV&))NumBitsInCommon);
     python::def("NumBitsInCommon",
-                (const int (*)(const EBV&,const EBV&))NumBitsInCommon,
+                (int (*)(const EBV&,const EBV&))NumBitsInCommon,
                 "Returns the total number of bits in common between the two bit vectors"
                 );
     python::def("OnBitsInCommon",
diff --git a/Code/Demos/RDKit/GettingStarted/Jamfile b/Code/Demos/RDKit/GettingStarted/Jamfile
index 808bc6081..6abd689cc 100644
--- a/Code/Demos/RDKit/GettingStarted/Jamfile
+++ b/Code/Demos/RDKit/GettingStarted/Jamfile
@@ -9,7 +9,7 @@ exe sample : sample.cpp
   ../../../GraphMol//GraphMol 
   ../../../DataStructs//DataStructs	
   ../../../RDGeneral//RDGeneral ../../../Geometry//RDGeometry
-  ../../..//vflib ../../..//lapacklibs
+ ../../..//lapacklibs
 ;
 
 
diff --git a/Code/Demos/SWIG/java_example/Jamfile b/Code/Demos/SWIG/java_example/Jamfile
index 435a987b4..a3f2ba9fe 100644
--- a/Code/Demos/SWIG/java_example/Jamfile
+++ b/Code/Demos/SWIG/java_example/Jamfile
@@ -8,7 +8,6 @@ lib RDKFuncs : RDKFuncs_wrap.cpp RDKFuncs.cpp
   ../../../GraphMol/Substruct//Substruct
   ../../../GraphMol/ChemReactions//ChemReactions
   ../../../RDGeneral//RDGeneral ../../../Geometry//RDGeometry /RDKit//lapacklibs
-  /RDKit//vflib 
   : <cflags>-fno-strict-aliasing <include>/usr/include/java <include>/usr/include/java/linux <include>. ;
 
 cpp RDKFuncs_wrap.cpp : RDKFuncs.i : <main-target-type>JAVA_WRAPPER ;
diff --git a/Code/Demos/sqlite/Jamfile b/Code/Demos/sqlite/Jamfile
index a902194c2..0f3ffbbbf 100644
--- a/Code/Demos/sqlite/Jamfile
+++ b/Code/Demos/sqlite/Jamfile
@@ -10,7 +10,7 @@ lib rdk_funcs : rdk_funcs.cpp
   ../../GraphMol//GraphMol
   /RDKit//DataStructs	
   /RDKit//RDGeneral /RDKit//Geometry
-  /RDKit//vflib /RDKit//lapacklibs
+  /RDKit//lapacklibs
  ;
 
 install lib-install : rdk_funcs : <location>. ;
diff --git a/Code/GraphMol/ChemReactions/Jamfile b/Code/GraphMol/ChemReactions/Jamfile
index 19b50d154..94fc6bf7c 100644
--- a/Code/GraphMol/ChemReactions/Jamfile
+++ b/Code/GraphMol/ChemReactions/Jamfile
@@ -11,7 +11,7 @@ install lib-install : ChemReactions : <location>$(RDBASE)/bin ;
 exe testReaction : testReaction.cpp ChemReactions 
   ../FileParsers//FileParsers ../SmilesParse//SmilesParse
   ../Substruct//Substruct ..//GraphMol ../../RDGeneral//RDGeneral 
-  ../../Geometry//RDGeometry ../..//vflib ;
+  ../../Geometry//RDGeometry ;
 
 install regrs : testReaction
   : <location>testExecs ;
diff --git a/Code/GraphMol/ChemReactions/Wrap/Jamfile b/Code/GraphMol/ChemReactions/Wrap/Jamfile
index c57c62dca..616ffe7c7 100644
--- a/Code/GraphMol/ChemReactions/Wrap/Jamfile
+++ b/Code/GraphMol/ChemReactions/Wrap/Jamfile
@@ -11,7 +11,7 @@ python-extension rdChemReactions : rdChemReactions.cpp
   ../..//GraphMol
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs ../../../RDBoost//RDBoost 
-../../..//vflib 
+ 
   ;
 
 install pymod : rdChemReactions
diff --git a/Code/GraphMol/ChemTransforms/Jamfile b/Code/GraphMol/ChemTransforms/Jamfile
index fe1d5e39b..7cd05ceb7 100644
--- a/Code/GraphMol/ChemTransforms/Jamfile
+++ b/Code/GraphMol/ChemTransforms/Jamfile
@@ -10,7 +10,7 @@ install lib-install : ChemTransforms : <location>$(RDBASE)/bin ;
 
 exe main : testChemTransforms.cpp ChemTransforms
   ../FileParsers//FileParsers ../SmilesParse//SmilesParse
-../Substruct//Substruct ..//GraphMol ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry ../..//vflib ;
+../Substruct//Substruct ..//GraphMol ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry ;
 
 install regrs : main
   : <location>testExecs ;
diff --git a/Code/GraphMol/Depictor/Jamfile b/Code/GraphMol/Depictor/Jamfile
index 5fe7e924b..0e69741ae 100644
--- a/Code/GraphMol/Depictor/Jamfile
+++ b/Code/GraphMol/Depictor/Jamfile
@@ -10,7 +10,7 @@ install lib-install : Depictor : <location>$(RDBASE)/bin ;
 
 exe testDepictor : testDepictor.cpp Depictor ../SmilesParse//SmilesParse
   ../FileParsers//FileParsers
-../Substruct//Substruct ..//GraphMol ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry ../..//vflib ;
+../Substruct//Substruct ..//GraphMol ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry ;
 
 install regrs : testDepictor
   : <location>testExecs ;
diff --git a/Code/GraphMol/Descriptors/Jamfile b/Code/GraphMol/Descriptors/Jamfile
index 02c32a825..70ab8b616 100644
--- a/Code/GraphMol/Descriptors/Jamfile
+++ b/Code/GraphMol/Descriptors/Jamfile
@@ -10,7 +10,7 @@ install lib-install : Descriptors : <location>$(RDBASE)/bin ;
 
 exe testDescriptors : test.cpp Descriptors
   ../FileParsers//FileParsers ../SmilesParse//SmilesParse ../Subgraphs//Subgraphs
-../Substruct//Substruct ..//GraphMol ../../DataStructs//DataStructs ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry ../..//lapacklibs ../..//vflib ;
+../Substruct//Substruct ..//GraphMol ../../DataStructs//DataStructs ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry ../..//lapacklibs ;
 
 install regrs : testDescriptors
   : <location>testExecs ;
diff --git a/Code/GraphMol/Descriptors/Wrap/Jamfile b/Code/GraphMol/Descriptors/Wrap/Jamfile
index 73597884c..0427776c1 100644
--- a/Code/GraphMol/Descriptors/Wrap/Jamfile
+++ b/Code/GraphMol/Descriptors/Wrap/Jamfile
@@ -11,7 +11,7 @@ python-extension rdMolDescriptors : rdMolDescriptors.cpp
   ../..//GraphMol
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs ../../../RDBoost//RDBoost 
-../../..//vflib ../../..//lapacklibs 
+ ../../..//lapacklibs 
   ;
 
 install pymod : rdMolDescriptors 
diff --git a/Code/GraphMol/DistGeomHelpers/Embedder.cpp b/Code/GraphMol/DistGeomHelpers/Embedder.cpp
index 102ebfc3f..91b21e854 100644
--- a/Code/GraphMol/DistGeomHelpers/Embedder.cpp
+++ b/Code/GraphMol/DistGeomHelpers/Embedder.cpp
@@ -73,38 +73,33 @@ namespace RDKit {
                                                                        chiralCenters,
                                                                        1.0, 0.1, 
                                                                        0,basinThresh);
-	unsigned int nPasses=0;
-	field->initialize();
-	if(field->calcEnergy() > ERROR_TOL){
-	  int needMore = 1;
-	  while(needMore){
-            //std::cerr<<"********* Minimize1 from: "<<field->calcEnergy()<<std::endl;
-	    needMore = field->minimize(200,optimizerForceTol);
-	    ++nPasses;
-	  }
-          //std::cerr<<"********* Finished1 at "<<field->calcEnergy()<<std::endl;
-	}
+        unsigned int nPasses=0;
+        field->initialize();
+        if(field->calcEnergy() > ERROR_TOL){
+          int needMore = 1;
+          while(needMore){
+            needMore = field->minimize(200,optimizerForceTol);
+            ++nPasses;
+          }
+        }
         // now redo the minimization if we have a chiral center, this
         // time removing the chiral constraints and
         // increasing the weight on the fourth dimension
         if (chiralCenters.size()>0 || useRandomCoords) {
           ForceFields::ForceField *field2 = DistGeom::constructForceField(*mmat, positions,
-                                                                         chiralCenters,
-                                                                         0.1, 1.0, 0,
-                                                                         basinThresh);
-	  field2->initialize();
-	  if(field2->calcEnergy() > ERROR_TOL){
-	    int needMore = 1;
-	    while(needMore){
-              //std::cerr<<"********* Minimize2 from: "<<field2->calcEnergy()<<std::endl;
-	      needMore = field2->minimize(200,optimizerForceTol);
-	    }
-            //std::cerr<<"********* Finished2 at "<<field2->calcEnergy()<<std::endl;
-	  }
-	  delete field2;
-          //std::cerr<<"********* Field1 again: "<<field->calcEnergy()<<std::endl;
+                                                                          chiralCenters,
+                                                                          0.1, 1.0, 0,
+                                                                          basinThresh);
+          field2->initialize();
+          if(field2->calcEnergy() > ERROR_TOL){
+            int needMore = 1;
+            while(needMore){
+              needMore = field2->minimize(200,optimizerForceTol);
+            }
+          }
+          delete field2;
         }
-	delete field;
+        delete field;
       }
       return gotCoords;
     }
@@ -121,7 +116,7 @@ namespace RDKit {
             nbrs.clear();
             nbrs.reserve(4);
             // find the neighbors of this atom and enter them into the
-	    // nbr list along with their CIPRanks
+            // nbr list along with their CIPRanks
             boost::tie(beg,end) = mol.getAtomBonds(*ati);
             while (beg != end) {
               oatom = mol[*beg]->getOtherAtom(*ati);
@@ -132,7 +127,7 @@ namespace RDKit {
               ++beg;
             }
             // if we have less than 4 heavy atoms as neighbors,
-	    // we need to include the chiral center into the mix
+            // we need to include the chiral center into the mix
             // we should at least have 3 though
             bool includeSelf = false;
             CHECK_INVARIANT(nbrs.size() >= 3, "Cannot be a chiral center");
@@ -153,18 +148,18 @@ namespace RDKit {
             if (cipCode == "S") { 
               // postive chiral volume
               DistGeom::ChiralSet *cset = new DistGeom::ChiralSet(nbrs[0].second,
-								  nbrs[1].second,
-								  nbrs[2].second,
+                                                                  nbrs[1].second,
+                                                                  nbrs[2].second,
                                                                   nbrs[3].second,
-								  5.0, 100.0);
+                                                                  5.0, 100.0);
               DistGeom::ChiralSetPtr cptr(cset);
               chiralCenters.push_back(cptr);
             } else {
               DistGeom::ChiralSet *cset = new DistGeom::ChiralSet(nbrs[0].second,
-								  nbrs[1].second,
-								  nbrs[2].second,
+                                                                  nbrs[1].second,
+                                                                  nbrs[2].second,
                                                                   nbrs[3].second,
-								  -100.0, -5.0);
+                                                                  -100.0, -5.0);
               DistGeom::ChiralSetPtr cptr(cset);
               chiralCenters.push_back(cptr);
             }
@@ -184,7 +179,7 @@ namespace RDKit {
     }
         
     bool _isConfFarFromRest(const ROMol &mol, const Conformer &conf,
-			    double threshold) {
+                            double threshold) {
       // NOTE: it is tempting to use some triangle inequality to prune
       // conformations here but some basic testing has shown very
       // little advantage and given that the time for pruning fades in
@@ -217,7 +212,7 @@ namespace RDKit {
                       bool useRandomCoords,double boxSizeMult,
                       bool randNegEig, unsigned int numZeroFail,
                       const std::map<int,RDGeom::Point3D> *coordMap,
-		      double optimizerForceTol,double basinThresh){
+                      double optimizerForceTol,double basinThresh){
       INT_VECT confIds;
       confIds=EmbedMultipleConfs(mol,1,maxIterations,seed,clearConfs,
                                  useRandomCoords,boxSizeMult,randNegEig,
diff --git a/Code/GraphMol/DistGeomHelpers/Jamfile b/Code/GraphMol/DistGeomHelpers/Jamfile
index 62b0f973d..be4226a7c 100644
--- a/Code/GraphMol/DistGeomHelpers/Jamfile
+++ b/Code/GraphMol/DistGeomHelpers/Jamfile
@@ -16,7 +16,7 @@ exe main.exe : testDgeomHelpers.cpp DistGeomHelpers ../../DistGeom//DistGeom
   ../../Numerics/Optimizer//Optimizer ../../Numerics/EigenSolvers//EigenSolvers  
   ../../Numerics/Alignment//Alignment
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
-  ../..//lapacklibs ../..//vflib ;
+  ../..//lapacklibs ;
 
 install regrs : main.exe
   : <location>testExecs ;
diff --git a/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py b/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py
index d4db7cbf7..c0b8142f3 100644
--- a/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py
+++ b/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py
@@ -254,7 +254,6 @@ class TestCase(unittest.TestCase) :
                                    conf.GetAtomPosition(3))
             self.failUnless(abs(vol-tgtVol)<1,"%s %s"%(vol,tgtVol))
 
-
         tgtVol=3.5
         expected = [-3.62, -3.67, -3.72,  3.91,  3.95,  3.98,  3.90,  3.94,  3.98,  3.91]
         nPos=0
diff --git a/Code/GraphMol/FileParsers/Jamfile b/Code/GraphMol/FileParsers/Jamfile
index 0b1415a0d..082e12e25 100644
--- a/Code/GraphMol/FileParsers/Jamfile
+++ b/Code/GraphMol/FileParsers/Jamfile
@@ -39,9 +39,6 @@ exe testMol2ToMol : testMol2ToMol.cpp FileParsers
   ../SmilesParse//SmilesParse ..//GraphMol 
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry ;
 
-lib profiler : : <name>profiler ;
-
-
 install regrs : test1 testMolSupplier testMolWriter testTplParser testMol2ToMol
   : <location>testExecs ;
 
diff --git a/Code/GraphMol/ForceFieldHelpers/Jamfile b/Code/GraphMol/ForceFieldHelpers/Jamfile
index 9642f44b3..51b4ca24f 100644
--- a/Code/GraphMol/ForceFieldHelpers/Jamfile
+++ b/Code/GraphMol/ForceFieldHelpers/Jamfile
@@ -17,7 +17,7 @@ exe testHelpers : testHelpers.cpp ForceFieldHelpers
   ../../Numerics/EigenSolvers//EigenSolvers
   ../..//Numerics/Alignment//Alignment
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
-  ../..//vflib ;
+ ;
 
 install regrs : testHelpers
   : <location>testExecs ;
diff --git a/Code/GraphMol/ForceFieldHelpers/Wrap/Jamfile b/Code/GraphMol/ForceFieldHelpers/Wrap/Jamfile
index 7eeca7477..8e0959b80 100644
--- a/Code/GraphMol/ForceFieldHelpers/Wrap/Jamfile
+++ b/Code/GraphMol/ForceFieldHelpers/Wrap/Jamfile
@@ -13,7 +13,7 @@ python-extension rdForceFieldHelpers : rdForceFields.cpp
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs 
   ../../../RDBoost//RDBoost 
-  ../../..//vflib 
+ 
   ;
 
 install pymod : rdForceFieldHelpers
diff --git a/Code/GraphMol/FragCatalog/Jamfile b/Code/GraphMol/FragCatalog/Jamfile
index ec6223620..04925511f 100644
--- a/Code/GraphMol/FragCatalog/Jamfile
+++ b/Code/GraphMol/FragCatalog/Jamfile
@@ -15,7 +15,7 @@ exe test1 : test1.cpp FragCatalog
   ../Substruct//Substruct ../FileParsers//FileParsers
   ..//GraphMol ../../DataStructs//DataStructs 
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
-  ../..//lapacklibs ../..//vflib ;
+  ../..//lapacklibs ;
 
 install regrs : test1
   : <location>testExecs ;
diff --git a/Code/GraphMol/FragCatalog/Wrap/Jamfile b/Code/GraphMol/FragCatalog/Wrap/Jamfile
index 179a51f90..b23512dfc 100644
--- a/Code/GraphMol/FragCatalog/Wrap/Jamfile
+++ b/Code/GraphMol/FragCatalog/Wrap/Jamfile
@@ -14,7 +14,7 @@ python-extension rdfragcatalog : rdfragcatalog.cpp
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs 
   ../../../RDBoost//RDBoost 
-  ../../..//vflib ../../..//lapacklibs 
+ ../../..//lapacklibs 
   ;
 
 install pymod : rdfragcatalog 
diff --git a/Code/GraphMol/Jamfile b/Code/GraphMol/Jamfile
index 213b84437..3cf7f6f52 100644
--- a/Code/GraphMol/Jamfile
+++ b/Code/GraphMol/Jamfile
@@ -21,17 +21,18 @@ exe MolOpsTest : molopstest.cpp GraphMol
   ../RDGeneral//RDGeneral ../Geometry//RDGeometry ;
 exe testCanon : testCanon.cpp GraphMol 
   ./SmilesParse//SmilesParse ./Substruct//Substruct 
-  ../RDGeneral//RDGeneral ../Geometry//RDGeometry ..//vflib ;
+  ../RDGeneral//RDGeneral ../Geometry//RDGeometry ;
 exe testChirality : testChirality.cpp GraphMol 
   ./SmilesParse//SmilesParse ./FileParsers//FileParsers
-  ../RDGeneral//RDGeneral ../Geometry//RDGeometry ..//vflib ;
+  ../RDGeneral//RDGeneral ../Geometry//RDGeometry ;
 exe testPickler : testPickler.cpp GraphMol 
   ./SmilesParse//SmilesParse ./FileParsers//FileParsers ./Substruct//Substruct 
-  ../RDGeneral//RDGeneral ../Geometry//RDGeometry ..//vflib ;
+  ../RDGeneral//RDGeneral ../Geometry//RDGeometry ;
 exe itertest : itertest.cpp GraphMol 
   ./SmilesParse//SmilesParse 
   ../RDGeneral//RDGeneral ../Geometry//RDGeometry ;
 
+alias all : all-libraries all-wrappers regrs ;
 
 install regrs : test1 cptest querytest MolOpsTest testCanon testChirality testPickler itertest
   : <location>testExecs ;
diff --git a/Code/GraphMol/MolAlign/Jamfile b/Code/GraphMol/MolAlign/Jamfile
index c771dd5a5..e2cb71b14 100644
--- a/Code/GraphMol/MolAlign/Jamfile
+++ b/Code/GraphMol/MolAlign/Jamfile
@@ -17,7 +17,7 @@ exe testMolAlign : testMolAlign.cpp MolAlign ../MolTransforms//MolTransforms
   ../..//Numerics/Alignment//Alignment
   ../Substruct//Substruct ..//GraphMol 
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
-   ../..//vflib ;
+ ;
 
 install regrs : testMolAlign
   : <location>testExecs ;
diff --git a/Code/GraphMol/MolAlign/Wrap/Jamfile b/Code/GraphMol/MolAlign/Wrap/Jamfile
index ace34b5a3..72e79c0c5 100644
--- a/Code/GraphMol/MolAlign/Wrap/Jamfile
+++ b/Code/GraphMol/MolAlign/Wrap/Jamfile
@@ -14,7 +14,7 @@ python-extension rdMolAlign : rdMolAlign.cpp
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs 
   ../../../RDBoost//RDBoost 
-  ../../..//vflib 
+ 
   ;
 
 install pymod : rdMolAlign
diff --git a/Code/GraphMol/MolChemicalFeatures/Jamfile b/Code/GraphMol/MolChemicalFeatures/Jamfile
index 05a5e4dd2..e894d1da8 100644
--- a/Code/GraphMol/MolChemicalFeatures/Jamfile
+++ b/Code/GraphMol/MolChemicalFeatures/Jamfile
@@ -14,7 +14,7 @@ exe testFeatures : testFeatures.cpp MolChemicalFeatures
   ../Substruct//Substruct
   ..//GraphMol 
   ../../DataStructs//DataStructs ../../RDGeneral//RDGeneral 
-  ../../Geometry//RDGeometry ../..//vflib
+  ../../Geometry//RDGeometry
  ;
 
 install regrs : testFeatures
diff --git a/Code/GraphMol/MolChemicalFeatures/Wrap/Jamfile b/Code/GraphMol/MolChemicalFeatures/Wrap/Jamfile
index 0aec20601..f58065e92 100644
--- a/Code/GraphMol/MolChemicalFeatures/Wrap/Jamfile
+++ b/Code/GraphMol/MolChemicalFeatures/Wrap/Jamfile
@@ -12,7 +12,7 @@ python-extension rdMolChemicalFeatures : rdMolChemicalFeatures.cpp
   ../..//GraphMol
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs ../../../RDBoost//RDBoost 
-  ../../..//vflib
+
   ;
 
 install pymod : rdMolChemicalFeatures
diff --git a/Code/GraphMol/QueryAtom.cpp b/Code/GraphMol/QueryAtom.cpp
index c6076e94b..d2a564f69 100755
--- a/Code/GraphMol/QueryAtom.cpp
+++ b/Code/GraphMol/QueryAtom.cpp
@@ -52,17 +52,106 @@ void QueryAtom::expandQuery(QUERYATOM_QUERY *what,
   }
 }
 
-// FIX: the const crap here is all mucked up.
 bool QueryAtom::Match(const Atom::ATOM_SPTR what) const {
   return Match(what.get());
 }
   
+  namespace {
+    bool localMatch(ATOM_EQUALS_QUERY const *q1,ATOM_EQUALS_QUERY const *q2){
+      if(q1->getNegation()==q2->getNegation()){
+        return q1->getVal()==q2->getVal();
+      } else {
+        return q1->getVal()!=q2->getVal();
+      }
+    }
+    bool queriesMatch(QueryAtom::QUERYATOM_QUERY const *q1,
+                      QueryAtom::QUERYATOM_QUERY const *q2){
+      PRECONDITION(q1,"no q1");
+      PRECONDITION(q2,"no q2");
+
+      static const unsigned int nQueries=18;
+      static std::string equalityQueries[nQueries]={"AtomRingBondCount","AtomRingSize","AtomMinRingSize","AtomImplicitValence",\
+                                                    "AtomExplicitValence","AtomTotalValence","AtomAtomicNum","AtomExplicitDegree",\
+                                                    "AtomTotalDegree","AtomHCount","AtomIsAromatic","AtomIsAliphatic","AtomUnsaturated",\
+                                                    "AtomMass","AtomFormalCharge","AtomHybridization","AtomInRing","AtomInNRings"};
+                                                  
+      bool res=false;
+      std::string d1=q1->getDescription();
+      std::string d2=q2->getDescription();
+      if(d1=="AtomNull"||d2=="AtomNull"){
+        res = true;
+      } else if(d1=="AtomOr"){
+        // FIX: handle negation on AtomOr and AtomAnd
+        for(QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI iter1=q1->beginChildren();iter1!=q1->endChildren();++iter1){
+          if(d2=="AtomOr"){
+            for(QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+              if(queriesMatch(iter1->get(),iter2->get())){
+                res=true;
+                break;
+              }
+            }
+          } else {
+            if(queriesMatch(iter1->get(),q2)) {
+              res=true;
+            }
+          }
+          if(res) break;
+        }
+      } else if(d1=="AtomAnd"){
+          res=true;
+          for(QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI iter1=q1->beginChildren();iter1!=q1->endChildren();++iter1){
+            bool matched=false;
+            if(d2=="AtomAnd"){
+              for(QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+                if(queriesMatch(iter1->get(),iter2->get())){
+                  matched=true;
+                  break;
+                }
+              }
+            } else {
+              matched = queriesMatch(iter1->get(),q2);
+            }
+            if(!matched){
+              res=false;
+              break;
+            }
+          }
+      // FIX : handle AtomXOr
+      } else if(d2=="AtomOr"){
+        // FIX: handle negation on AtomOr and AtomAnd
+        for(QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+          if(queriesMatch(q1,iter2->get())) {
+            res=true;
+            break;
+          }
+        }
+      } else if(d2=="AtomAnd"){
+        res=true;
+        for(QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+          if(queriesMatch(q1,iter2->get())){
+            res=false;
+            break;
+          }
+        }
+      } else if(d1==d2){
+          if(std::find(&equalityQueries[0],&equalityQueries[nQueries],d1)!= &equalityQueries[nQueries]){
+            res=localMatch(static_cast<ATOM_EQUALS_QUERY const *>(q1),
+                           static_cast<ATOM_EQUALS_QUERY const *>(q2));
+          }
+      } else {
+      }
+      return res;
+    }
+  } //end of local namespace
+
 bool QueryAtom::Match(Atom const *what) const {
   PRECONDITION(what,"bad query atom");
   PRECONDITION(dp_query,"no query set");
-  return dp_query->Match(what);
+  if(!what->hasQuery()){
+    return dp_query->Match(what);
+  } else {
+    return queriesMatch(dp_query,what->getQuery());
+  }
 }
 
-
-
 }; // end o' namespace
diff --git a/Code/GraphMol/QueryBond.cpp b/Code/GraphMol/QueryBond.cpp
index ced5b7496..fb62ad567 100755
--- a/Code/GraphMol/QueryBond.cpp
+++ b/Code/GraphMol/QueryBond.cpp
@@ -58,21 +58,13 @@ void QueryBond::setBondDir(BondDir bD) {
   //   situations, whatever those may be.
   //
   d_dirTag = bD;
+#if 0  
   if(dp_query){
     delete dp_query;
     dp_query = 0;
   }
   dp_query = makeBondDirEqualsQuery(bD);
-}
-
-
-bool QueryBond::Match(const Bond::BOND_SPTR what) const {
-  return Match(what.get());
-}
-  
-bool QueryBond::Match(Bond const *what) const {
-  PRECONDITION(dp_query,"no query set");
-  return dp_query->Match(what);
+#endif
 }
 
 void QueryBond::expandQuery(QUERYBOND_QUERY *what,
@@ -106,4 +98,105 @@ void QueryBond::expandQuery(QUERYBOND_QUERY *what,
   }
 }
 
+bool QueryBond::Match(const Bond::BOND_SPTR what) const {
+  return Match(what.get());
+}
+  
+
+  namespace {
+    bool localMatch(BOND_EQUALS_QUERY const *q1,BOND_EQUALS_QUERY const *q2){
+      if(q1->getNegation()==q2->getNegation()){
+        return q1->getVal()==q2->getVal();
+      } else {
+        return q1->getVal()!=q2->getVal();
+      }
+    }
+
+    bool queriesMatch(QueryBond::QUERYBOND_QUERY const *q1,
+                      QueryBond::QUERYBOND_QUERY const *q2){
+      PRECONDITION(q1,"no q1");
+      PRECONDITION(q2,"no q2");
+
+      static const unsigned int nQueries=6;
+      static std::string equalityQueries[nQueries]={"BondRingSize","BondMinRingSize","BondOrder","BondDir",\
+                                                    "BondInRing","BondInNRings"};
+                                                  
+      bool res=false;
+      std::string d1=q1->getDescription();
+      std::string d2=q2->getDescription();
+      if(d1=="BondNull"||d2=="BondNull"){
+        res = true;
+      } else if(d1=="BondOr"){
+        // FIX: handle negation on BondOr and BondAnd
+        for(QueryBond::QUERYBOND_QUERY::CHILD_VECT_CI iter1=q1->beginChildren();iter1!=q1->endChildren();++iter1){
+          if(d2=="BondOr"){
+            for(QueryBond::QUERYBOND_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+              if(queriesMatch(iter1->get(),iter2->get())){
+                res=true;
+                break;
+              }
+            }
+          } else {
+            if(queriesMatch(iter1->get(),q2)) {
+              res=true;
+            }
+          }
+          if(res) break;
+        }
+      } else if(d1=="BondAnd"){
+          res=true;
+          for(QueryBond::QUERYBOND_QUERY::CHILD_VECT_CI iter1=q1->beginChildren();iter1!=q1->endChildren();++iter1){
+            bool matched=false;
+            if(d2=="BondAnd"){
+              for(QueryBond::QUERYBOND_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+                if(queriesMatch(iter1->get(),iter2->get())){
+                  matched=true;
+                  break;
+                }
+              }
+            } else {
+              matched = queriesMatch(iter1->get(),q2);
+            }
+            if(!matched){
+              res=false;
+              break;
+            }
+          }
+      // FIX : handle BondXOr
+      } else if(d2=="BondOr"){
+        // FIX: handle negation on BondOr and BondAnd
+        for(QueryBond::QUERYBOND_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+          if(queriesMatch(q1,iter2->get())) {
+            res=true;
+            break;
+          }
+        }
+      } else if(d2=="BondAnd"){
+        res=true;
+        for(QueryBond::QUERYBOND_QUERY::CHILD_VECT_CI iter2=q2->beginChildren();iter2!=q2->endChildren();++iter2){
+          if(queriesMatch(q1,iter2->get())){
+            res=false;
+            break;
+          }
+        }
+      } else if(std::find(&equalityQueries[0],&equalityQueries[nQueries],d1)!= &equalityQueries[nQueries]){
+          res=localMatch(static_cast<BOND_EQUALS_QUERY const *>(q1),
+                         static_cast<BOND_EQUALS_QUERY const *>(q2));
+      } 
+      return res;
+    }
+  } //end of local namespace
+
+bool QueryBond::Match(Bond const *what) const {
+  PRECONDITION(dp_query,"no query set");
+  if(!what->hasQuery()){
+    return dp_query->Match(what);
+  } else {
+    return queriesMatch(dp_query,what->getQuery());
+  }
+}
+
+
+
+
 } // end o' namespace
diff --git a/Code/GraphMol/SLNParse/Jamfile b/Code/GraphMol/SLNParse/Jamfile
index 3f65340e1..82b81eb62 100644
--- a/Code/GraphMol/SLNParse/Jamfile
+++ b/Code/GraphMol/SLNParse/Jamfile
@@ -15,7 +15,7 @@ cpp sln.tab.cpp : sln.yy : <bison.prefix>yysln_ ;
 
 exe test : test.cpp SLNParse 
   ..//GraphMol   ../SmilesParse//SmilesParse
-  ../Substruct//Substruct ../..//vflib 
+  ../Substruct//Substruct 
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
 ;
 
diff --git a/Code/GraphMol/SLNParse/Wrap/Jamfile b/Code/GraphMol/SLNParse/Wrap/Jamfile
index a6819fdab..8034f54c0 100644
--- a/Code/GraphMol/SLNParse/Wrap/Jamfile
+++ b/Code/GraphMol/SLNParse/Wrap/Jamfile
@@ -10,7 +10,6 @@ python-extension rdSLNParse : rdSLNParse.cpp
   ../..//GraphMol
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs ../../../RDBoost//RDBoost 
-/RDKit//vflib
   ;
 
 install pymod : rdSLNParse
diff --git a/Code/GraphMol/ShapeHelpers/Jamfile b/Code/GraphMol/ShapeHelpers/Jamfile
index 5c0013dcf..f982927e4 100644
--- a/Code/GraphMol/ShapeHelpers/Jamfile
+++ b/Code/GraphMol/ShapeHelpers/Jamfile
@@ -15,7 +15,7 @@ exe main : testShapeHelpers.cpp ShapeHelpers
   ../../Numerics/Alignment//Alignment
   ..//GraphMol ../../DataStructs//DataStructs 
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
-  ../..//lapacklibs ../..//vflib
+  ../..//lapacklibs
  ;
 
 install regrs : main
diff --git a/Code/GraphMol/ShapeHelpers/Wrap/Jamfile b/Code/GraphMol/ShapeHelpers/Wrap/Jamfile
index bd2df50fa..15e9cadd2 100644
--- a/Code/GraphMol/ShapeHelpers/Wrap/Jamfile
+++ b/Code/GraphMol/ShapeHelpers/Wrap/Jamfile
@@ -11,7 +11,7 @@ python-extension rdShapeHelpers : rdShapeHelpers.cpp
   ../../../Numerics/EigenSolvers//EigenSolvers
   ../../../Geometry//RDGeometry
   ../../../RDGeneral//RDGeneral ../../../DataStructs//DataStructs ../../../RDBoost//RDBoost 
-../../..//vflib ../../..//lapacklibs 
+ ../../..//lapacklibs 
   ;
 
 install pymod : rdShapeHelpers
diff --git a/Code/GraphMol/SmilesParse/Jamfile b/Code/GraphMol/SmilesParse/Jamfile
index 24837c2cb..d6993ba02 100644
--- a/Code/GraphMol/SmilesParse/Jamfile
+++ b/Code/GraphMol/SmilesParse/Jamfile
@@ -7,7 +7,7 @@ local RDBASE = [ os.environ RDBASE ] ;
 
 
 lib SmilesParse : lex.yysmiles.cpp   smiles.tab.cpp lex.yysmarts.cpp smarts.tab.cpp InputFiller.cpp SmilesParse.cpp SmilesParseOps.cpp SmilesWrite.cpp SmartsWrite.cpp
-  ..//GraphMol ../..//RDGeneral//RDGeneral ../../Geometry//RDGeometry ../..//vflib
+  ..//GraphMol ../..//RDGeneral//RDGeneral ../../Geometry//RDGeometry
   : <include>. <toolset>msvc:<link>static 
   <toolset>msvc:<define>YY_NO_UNISTD_H 
 ;
@@ -29,7 +29,7 @@ exe test : test.cpp SmilesParse ..//GraphMol
 exe smatest : smatest.cpp SmilesParse 
    ..//GraphMol ../Substruct//Substruct 
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
-  ../..//vflib ;
+ ;
 
 install regrs : test  smatest
   : <location>testExecs ;
diff --git a/Code/GraphMol/SmilesParse/smarts.ll b/Code/GraphMol/SmilesParse/smarts.ll
index b80a092d8..3e295b700 100755
--- a/Code/GraphMol/SmilesParse/smarts.ll
+++ b/Code/GraphMol/SmilesParse/smarts.ll
@@ -262,12 +262,10 @@ A			{
 
 [\\]    { yysmarts_lval.bond = new QueryBond(Bond::SINGLE);
 	yysmarts_lval.bond->setBondDir(Bond::ENDDOWNRIGHT);
-        yysmarts_lval.bond->setQuery(makeBondDirEqualsQuery(Bond::ENDDOWNRIGHT));
 	return BOND_TOKEN;  }
 	
 [\/]    { yysmarts_lval.bond = new QueryBond(Bond::SINGLE);
 	yysmarts_lval.bond->setBondDir(Bond::ENDUPRIGHT);
-        yysmarts_lval.bond->setQuery(makeBondDirEqualsQuery(Bond::ENDUPRIGHT));
 	return BOND_TOKEN;  }
 
 
diff --git a/Code/GraphMol/SmilesParse/smatest.cpp b/Code/GraphMol/SmilesParse/smatest.cpp
index f26019be2..5e59dab59 100755
--- a/Code/GraphMol/SmilesParse/smatest.cpp
+++ b/Code/GraphMol/SmilesParse/smatest.cpp
@@ -1146,6 +1146,20 @@ void testMiscSmartsWriting(){
   BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
 }
 
+void testSmartsStereochem(){
+  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "Testing handling (or lack thereof) of stereochem in smarts (sf.net issue 2738320)" << std::endl;
+
+  _checkMatches("C/C=C/C", "CC=CC", 1, 4);
+  _checkMatches("C/C=C/C", "C/C=C/C", 1, 4);
+  _checkMatches("C/C=C/C", "C\\C=C\\C", 1, 4);
+  _checkMatches("C/C=C/C", "C/C=C\\C", 1, 4);
+  
+  BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
+}
+
+
+
 int
 main(int argc, char *argv[])
 {
@@ -1174,5 +1188,6 @@ main(int argc, char *argv[])
   testIssue1914154();
   testMiscSmartsWriting();
   //testIssue1804420();
+  testSmartsStereochem();
   return 0;
 }
diff --git a/Code/GraphMol/Substruct/Jamfile b/Code/GraphMol/Substruct/Jamfile
index 6cd3affec..0373a1b97 100644
--- a/Code/GraphMol/Substruct/Jamfile
+++ b/Code/GraphMol/Substruct/Jamfile
@@ -4,13 +4,13 @@ local RDBASE = [ os.environ RDBASE ] ;
 
 
 lib Substruct : SubstructMatch.cpp SubstructUtils.cpp
-  ..//GraphMol ../..//RDGeneral//RDGeneral  ../..//vflib
+  ..//GraphMol ../..//RDGeneral//RDGeneral
   :  <toolset>msvc:<link>static ; #<link>static ;
 install lib-install : Substruct : <location>$(RDBASE)/bin ;
 
 exe test1 : test1.cpp Substruct ..//GraphMol 
   ../../RDGeneral//RDGeneral ../../Geometry//RDGeometry 
-  ../..//vflib
+
  ; 
 
 install regrs : test1
diff --git a/Code/GraphMol/Wrap/MolOps.cpp b/Code/GraphMol/Wrap/MolOps.cpp
index 0bc5b2fbf..e77477ff8 100755
--- a/Code/GraphMol/Wrap/MolOps.cpp
+++ b/Code/GraphMol/Wrap/MolOps.cpp
@@ -13,6 +13,7 @@
 
 #include <DataStructs/ExplicitBitVect.h>
 #include <GraphMol/RDKitBase.h>
+#include <GraphMol/RDKitQueries.h>
 #include <GraphMol/Substruct/SubstructMatch.h>
 #include <GraphMol/Subgraphs/Subgraphs.h>
 #include <GraphMol/Fingerprints/Fingerprints.h>
@@ -49,6 +50,34 @@ namespace RDKit{
     return res;
   }
 
+  void addRecursiveQuery(ROMol &mol,
+                         const ROMol &query,
+                         unsigned int atomIdx,
+                         bool preserveExistingQuery){
+    if(atomIdx>=mol.getNumAtoms()){
+      throw_value_error("atom index exceeds mol.GetNumAtoms()");
+    }
+    RecursiveStructureQuery *q = new RecursiveStructureQuery(new ROMol(query));
+
+    Atom *oAt=mol.getAtomWithIdx(atomIdx);
+    if(!oAt->hasQuery()){
+      QueryAtom qAt(*oAt);
+      static_cast<RWMol &>(mol).replaceAtom(atomIdx,&qAt);
+      oAt = mol.getAtomWithIdx(atomIdx);
+    }
+
+    
+    if(!preserveExistingQuery){
+      // FIX: this leaks a query atom on oAt
+      oAt->setQuery(q);
+    } else {
+      oAt->expandQuery(q,Queries::COMPOSITE_AND);
+    }
+    
+  }
+
+
+
   void sanitizeMol(ROMol &mol) {
     RWMol &wmol = static_cast<RWMol &>(mol);
     MolOps::sanitizeMol(wmol);
@@ -370,7 +399,7 @@ namespace RDKit{
                   docString.c_str());
 
       // ------------------------------------------------------------------------
-      docString="Returns the molecule's distance matrix.\n\
+      docString="Returns the molecule's topological distance matrix.\n\
 \n\
   ARGUMENTS:\n\
 \n\
@@ -845,6 +874,28 @@ namespace RDKit{
       docString.c_str(),
       python::return_value_policy<python::manage_new_object>());
 
+      // ------------------------------------------------------------------------
+      docString="Adds a recursive query to an atom\n\
+\n\
+  ARGUMENTS:\n\
+\n\
+    - mol: the molecule to be modified\n\
+\n\
+    - query: the molecule to be used as the recursive query (this will be copied)\n\
+\n\
+    - atomIdx: the atom to modify\n\
+\n\
+    - preserveExistingQuery: (optional) if this is set, existing query information on the atom will be preserved\n\
+\n\
+  RETURNS: None\n\
+\n";
+      python::def("AddRecursiveQuery", addRecursiveQuery,
+                  (python::arg("mol"),python::arg("query"),
+                   python::arg("atomIdx"),python::arg("preserveExistingQuery")=true),
+                  docString.c_str());
+
+
+
     };
   };
 }
diff --git a/Code/GraphMol/Wrap/rough_test.py b/Code/GraphMol/Wrap/rough_test.py
index e0dcb8585..939ce7300 100755
--- a/Code/GraphMol/Wrap/rough_test.py
+++ b/Code/GraphMol/Wrap/rough_test.py
@@ -391,9 +391,9 @@ class TestCase(unittest.TestCase):
     self.failUnless(m2.GetNumAtoms()==5)
     m2 = Chem.RemoveHs(m2)
     self.failUnless(m2.GetNumAtoms()==4)
+
     m = Chem.MolFromSmiles('CC[H]',False)
     self.failUnless(m.GetNumAtoms()==3)
-    print 'merge'
     m2 = Chem.MergeQueryHs(m)
     self.failUnless(m2.GetNumAtoms()==2)
     self.failUnless(m2.GetAtomWithIdx(1).HasQuery())
@@ -1909,6 +1909,37 @@ CAS<~>
     sdSup = Chem.CompressedSDMolSupplier(fileN, 0)
     for mol in sdSup :
       self.failUnless(not mol.HasProp("numArom"))
+
+  def test57AddRecursiveQuery(self):
+    q1 = Chem.MolFromSmiles('CC')
+    q2 = Chem.MolFromSmiles('CO')
+    Chem.AddRecursiveQuery(q1,q2,1)
+
+    m1 = Chem.MolFromSmiles('OCC')
+    self.failUnless(m1.HasSubstructMatch(q2))
+    self.failUnless(m1.HasSubstructMatch(q1))
+    self.failUnless(m1.HasSubstructMatch(q1))
+    self.failUnless(m1.GetSubstructMatch(q1)==(2,1))
+
+    q3 = Chem.MolFromSmiles('CS')
+    Chem.AddRecursiveQuery(q1,q3,1)
+    
+    self.failIf(m1.HasSubstructMatch(q3))
+    self.failIf(m1.HasSubstructMatch(q1))
+
+    m2 = Chem.MolFromSmiles('OC(S)C')
+    self.failUnless(m2.HasSubstructMatch(q1))
+    self.failUnless(m2.GetSubstructMatch(q1)==(3,1))
+    
+    m3 = Chem.MolFromSmiles('SCC')
+    self.failUnless(m3.HasSubstructMatch(q3))
+    self.failIf(m3.HasSubstructMatch(q1))
+
+    q1 = Chem.MolFromSmiles('CC')
+    Chem.AddRecursiveQuery(q1,q2,1)
+    Chem.AddRecursiveQuery(q1,q3,1,False)
+    self.failUnless(m3.HasSubstructMatch(q1))
+    self.failUnless(m3.GetSubstructMatch(q1)==(2,1))
     
 if __name__ == '__main__':
   unittest.main()
diff --git a/Code/GraphMol/querytest.cpp b/Code/GraphMol/querytest.cpp
index 85c580b12..a50dc2866 100755
--- a/Code/GraphMol/querytest.cpp
+++ b/Code/GraphMol/querytest.cpp
@@ -330,7 +330,184 @@ void test6(){
   massVal=queryAtomMass(a);
   TEST_ASSERT(massVal==static_cast<int>(RDKit::round(13.000*massIntegerConversionFactor)));
   
+  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
+}
+
+
+void testQueryQueryMatches(){
+  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "Testing query--query matches" << std::endl;
+
+  // =====================================
+  // ATOMS
+  // =====================================
+  {
+    QueryAtom a1,a2;
+    a1.setQuery(makeAtomNullQuery());
+    a2.setQuery(makeAtomNullQuery());
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1,a2(6);
+    a1.setQuery(makeAtomNullQuery());
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(8);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(6);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1,a2;
+    a1.setQuery(makeAtomAromaticQuery());
+    a2.setQuery(makeAtomAromaticQuery());
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1,a2;
+    a1.setQuery(makeAtomAromaticQuery());
+    a2.setQuery(makeAtomAliphaticQuery());
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(8);
+    a1.expandQuery(makeAtomNumEqualsQuery(8),Queries::COMPOSITE_OR);
+    a2.expandQuery(makeAtomNumEqualsQuery(9),Queries::COMPOSITE_OR);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(8);
+    a1.expandQuery(makeAtomNumEqualsQuery(7),Queries::COMPOSITE_OR);
+    a2.expandQuery(makeAtomNumEqualsQuery(9),Queries::COMPOSITE_OR);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(6);
+    a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
+    a2.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(6);
+    a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
+    a2.expandQuery(makeAtomExplicitValenceQuery(4),Queries::COMPOSITE_AND);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(8);
+    a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
+    a2.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryAtom a1(6),a2(8);
+    a1.expandQuery(makeAtomNumEqualsQuery(8),Queries::COMPOSITE_OR);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  // =====================================
+  // BONDS
+  // =====================================
   
+  {
+    QueryBond a1,a2;
+    a1.setQuery(makeBondNullQuery());
+    a2.setQuery(makeBondNullQuery());
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1,a2(Bond::SINGLE);
+    a1.setQuery(makeBondNullQuery());
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::SINGLE);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
+    a1.expandQuery(makeBondOrderEqualsQuery(Bond::DOUBLE),Queries::COMPOSITE_OR);
+    a2.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
+    a1.expandQuery(makeBondOrderEqualsQuery(Bond::TRIPLE),Queries::COMPOSITE_OR);
+    a2.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
+    a1.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_OR);
+    a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_OR);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
+    a1.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
+    a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::SINGLE);
+    a1.expandQuery(makeBondMinRingSizeQuery(5),Queries::COMPOSITE_AND);
+    a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
+    TEST_ASSERT(!a1.Match(&a2));
+    TEST_ASSERT(!a2.Match(&a1));
+  }
+
+  {
+    QueryBond a1(Bond::SINGLE),a2(Bond::AROMATIC);
+    a1.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
+    TEST_ASSERT(a1.Match(&a2));
+    TEST_ASSERT(a2.Match(&a1));
+  }
 
   BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
 }
@@ -344,5 +521,8 @@ int main(){
   test4();
   test5();
   test6();
+  testQueryQueryMatches();
+
+
   return 0;
 }
diff --git a/Code/Jamroot b/Code/Jamroot
index 314c659a2..7a04f7d7f 100644
--- a/Code/Jamroot
+++ b/Code/Jamroot
@@ -17,16 +17,13 @@ use-project RDKit_Externals
 project RDKit
 	: requirements <include>.  <threading>multi
           <include>$(BOOSTHOME)
-          <include>$(RDBASE)/External/Lapack++/include
-          <include>$(RDBASE)/External/vflib-2.0/include
-          #<define>USE_VFLIB
           <toolset>gcc:<cflags>-Wno-unused-function
           <toolset>gcc:<cflags>-Wno-deprecated
           <toolset>darwin:<cflags>-Wno-unused-function
           <toolset>gcc:<cflags>-fno-strict-aliasing
           <toolset>msvc:<define>WIN32
-          <include>/usr/lib/python2.5/site-packages/numpy-1.2.1-py2.5-linux-i686.egg/numpy/core/include
-	  <address-model>64:<cflags>-fPIC
+          <include>MISSING
+          <address-model>64:<cflags>-fPIC
           # <define>RDK_USELAPACKPP #<- uncomment this to use lapack++
           <target-os>windows:<define>BOOST_NUMERIC_BINDINGS_USE_CLAPACK
           <toolset>msvc:<define>_CRT_SECURE_NO_DEPRECATE
@@ -35,7 +32,10 @@ project RDKit
 
 alias all-libraries : Catalogs DistGeom ForceField DataManip/MetricMatrixCalc DataStructs Geometry Query RDBoost RDGeneral Numerics  SimDivPickers ChemicalFeatures GraphMol
 ;
+alias all : all-libraries all-wrappers ;
 
+alias minimal : DistGeom ForceField DataStructs Geometry Query RDGeneral Numerics ChemicalFeatures GraphMol//minimal 
+;
 
 alias all-wrappers : RDBoost/Wrap 
   DataStructs/Wrap
@@ -83,6 +83,5 @@ lib blas
 # if you want to use Lapack++, use this version:
 #alias lapacklibs : /RDKit_Externals//Lapack++ lapack blas ;
 alias lapacklibs : lapack blas ;
-alias vflib : /RDKit_Externals//vflib ;
 
 
diff --git a/Code/Jamroot.in b/Code/Jamroot.in
index 3c06c4363..cbf735247 100644
--- a/Code/Jamroot.in
+++ b/Code/Jamroot.in
@@ -17,8 +17,6 @@ use-project RDKit_Externals
 project RDKit
 	: requirements <include>.  <threading>multi
           <include>$(BOOSTHOME)
-          <include>$(RDBASE)/External/vflib-2.0/include
-          #<define>USE_VFLIB
           <toolset>gcc:<cflags>-Wno-unused-function
           <toolset>gcc:<cflags>-Wno-deprecated
           <toolset>darwin:<cflags>-Wno-unused-function
@@ -34,6 +32,7 @@ project RDKit
 
 alias all-libraries : Catalogs DistGeom ForceField DataManip/MetricMatrixCalc DataStructs Geometry Query RDBoost RDGeneral Numerics  SimDivPickers ChemicalFeatures GraphMol
 ;
+alias all : all-libraries all-wrappers ;
 
 alias minimal : DistGeom ForceField DataStructs Geometry Query RDGeneral Numerics ChemicalFeatures GraphMol//minimal 
 ;
@@ -84,5 +83,4 @@ lib blas
 # if you want to use Lapack++, use this version:
 #alias lapacklibs : /RDKit_Externals//Lapack++ lapack blas ;
 alias lapacklibs : lapack blas ;
-alias vflib : /RDKit_Externals//vflib ;