Taken from upstream: https://github.com/openbabel/openbabel

The TR1 shared_ptr isn't supported on the latest gcc.OB

--- include/openbabel/alias.h.orig	2010-09-07 17:07:53 UTC
+++ include/openbabel/alias.h
@@ -115,7 +115,7 @@ private:
   }
   bool        FromNameLookup(OBMol& mol, const unsigned int atomindex);
 #ifdef HAVE_SHARED_POINTER
-  typedef std::vector< std::pair<std::string, shared_ptr<OBSmartsPattern> > > SmartsTable;
+  typedef std::vector< std::pair<std::string, obsharedptr<OBSmartsPattern> > > SmartsTable;
   static bool LoadFile(SmartsTable& smtable);
 #endif
 };
--- include/openbabel/reaction.h.orig	2010-10-10 02:05:12 UTC
+++ include/openbabel/reaction.h
@@ -35,10 +35,10 @@ namespace OpenBabel
 class OBReaction : public OBBase
 {
 private:
-  std::vector<shared_ptr<OBMol> > _reactants;
-  std::vector<shared_ptr<OBMol> > _products;
-  shared_ptr<OBMol> _ts;
-  shared_ptr<OBMol> _agent;
+  std::vector<obsharedptr<OBMol> > _reactants;
+  std::vector<obsharedptr<OBMol> > _products;
+  obsharedptr<OBMol> _ts;
+  obsharedptr<OBMol> _agent;
   std::string _title;
   std::string _comment;
   bool _reversible;
@@ -52,37 +52,37 @@ public:
   int NumProducts()const
   { return static_cast<int> (_products.size()); }
 
-  void AddReactant(const shared_ptr<OBMol> sp)
+  void AddReactant(const obsharedptr<OBMol> sp)
   { _reactants.push_back(sp); }
 
-  void AddProduct(const shared_ptr<OBMol> sp)
+  void AddProduct(const obsharedptr<OBMol> sp)
   { _products.push_back(sp); }
 
-  void SetTransitionState(const shared_ptr<OBMol> sp)
+  void SetTransitionState(const obsharedptr<OBMol> sp)
   { _ts = sp; }
 
-  void AddAgent(const shared_ptr<OBMol> sp)
+  void AddAgent(const obsharedptr<OBMol> sp)
   { _agent = sp; }
 
-  shared_ptr<OBMol> GetReactant(const unsigned i)
+  obsharedptr<OBMol> GetReactant(const unsigned i)
   {
-    shared_ptr<OBMol> sp;
+    obsharedptr<OBMol> sp;
     if(i<_reactants.size())
       sp = _reactants[i];
     return sp; //returns empty if out of range
   }
-  shared_ptr<OBMol> GetProduct(const unsigned i)
+  obsharedptr<OBMol> GetProduct(const unsigned i)
   {
-    shared_ptr<OBMol> sp;
+    obsharedptr<OBMol> sp;
     if(i<_products.size())
       sp = _products[i];
     return sp; //returns empty if out of range
   }
 
-  shared_ptr<OBMol> GetTransitionState()const
+  obsharedptr<OBMol> GetTransitionState()const
   { return _ts; }
 
-  shared_ptr<OBMol> GetAgent()const
+  obsharedptr<OBMol> GetAgent()const
   { return _agent; }
 
   std::string GetTitle()	const { return _title; }
--- include/openbabel/shared_ptr.h.orig	2011-10-12 20:24:02 UTC
+++ include/openbabel/shared_ptr.h
@@ -18,13 +18,21 @@ GNU General Public License for more deta
 
 #ifdef USE_BOOST
   #include <boost/shared_ptr.hpp>
-  #define shared_ptr boost::shared_ptr
+  #define obsharedptr boost::shared_ptr
 #else
   #include <memory>
-  #if __GNUC__ == 4  //&& __GNUC_MINOR__ < 3  removed at the suggestion of Konstantin Tokarev
-    #include <tr1/memory>
+  #if __GNUC__ >= 4  //&& __GNUC_MINOR__ < 3  removed at the suggestion of Konstantin Tokarev
+    #ifdef _LIBCPP_VERSION
+      #include <memory>
+    #else
+      #include <tr1/memory>
+    #endif
+  #endif
+  #ifdef _LIBCPP_VERSION
+    #define obsharedptr std::shared_ptr
+  #else
+    #define obsharedptr std::tr1::shared_ptr
   #endif
-  using std::tr1::shared_ptr;
 #endif
 
 #endif // OB_SHARED_PTR_H
--- scripts/python/openbabel-python.cpp.orig	2012-10-11 19:20:57 UTC
+++ scripts/python/openbabel-python.cpp
@@ -25531,64 +25531,64 @@ SWIGINTERN PyObject *_wrap_OBReaction_Nu
   result = (int)((OpenBabel::OBReaction const *)arg1)->NumProducts(); resultobj = SWIG_From_int(static_cast< int >(result));
   return resultobj; fail: return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_AddReactant(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0;
-  OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > arg2 ;
+  OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > arg2 ;
   void *argp1 = 0 ; int res1 = 0 ; void *argp2 ; int res2 = 0 ; PyObject *swig_obj[2] ;
   if (!SWIG_Python_UnpackTuple(args,"OBReaction_AddReactant",2,2,swig_obj)) SWIG_fail;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_AddReactant" "', argument " "1"" of type '" "OpenBabel::OBReaction *""'");  }
    arg1 = reinterpret_cast< OpenBabel::OBReaction * >(argp1); {
     res2 = SWIG_ConvertPtr(swig_obj[1], &argp2, SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t,  0  | 0); if (!SWIG_IsOK(res2)) {
-      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_AddReactant" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'");  }
+      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_AddReactant" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'");  }
        if (!argp2) {
-      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_AddReactant" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'"); }
-     else { shared_ptr< OpenBabel::OBMol > * temp = reinterpret_cast< shared_ptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
+      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_AddReactant" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'"); }
+     else { obsharedptr< OpenBabel::OBMol > * temp = reinterpret_cast< obsharedptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
       if (SWIG_IsNewObj(res2)) delete temp; }  }  (arg1)->AddReactant(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail:
   return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_AddProduct(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0;
-  OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > arg2 ;
+  OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > arg2 ;
   void *argp1 = 0 ; int res1 = 0 ; void *argp2 ; int res2 = 0 ; PyObject *swig_obj[2] ;
   if (!SWIG_Python_UnpackTuple(args,"OBReaction_AddProduct",2,2,swig_obj)) SWIG_fail;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_AddProduct" "', argument " "1"" of type '" "OpenBabel::OBReaction *""'");  }
    arg1 = reinterpret_cast< OpenBabel::OBReaction * >(argp1); {
     res2 = SWIG_ConvertPtr(swig_obj[1], &argp2, SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t,  0  | 0); if (!SWIG_IsOK(res2)) {
-      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_AddProduct" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'");  }
+      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_AddProduct" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'");  }
        if (!argp2) {
-      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_AddProduct" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'"); }
-     else { shared_ptr< OpenBabel::OBMol > * temp = reinterpret_cast< shared_ptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
+      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_AddProduct" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'"); }
+     else { obsharedptr< OpenBabel::OBMol > * temp = reinterpret_cast< obsharedptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
       if (SWIG_IsNewObj(res2)) delete temp; }  }  (arg1)->AddProduct(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail:
   return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_SetTransitionState(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
   PyObject *resultobj = 0; OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ;
-  SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > arg2 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 ; int res2 = 0 ;
+  SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > arg2 ; void *argp1 = 0 ; int res1 = 0 ; void *argp2 ; int res2 = 0 ;
   PyObject *swig_obj[2] ; if (!SWIG_Python_UnpackTuple(args,"OBReaction_SetTransitionState",2,2,swig_obj)) SWIG_fail;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_SetTransitionState" "', argument " "1"" of type '" "OpenBabel::OBReaction *""'");  }
    arg1 = reinterpret_cast< OpenBabel::OBReaction * >(argp1); {
     res2 = SWIG_ConvertPtr(swig_obj[1], &argp2, SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t,  0  | 0); if (!SWIG_IsOK(res2)) {
-      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_SetTransitionState" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'");  }
+      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_SetTransitionState" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'");  }
        if (!argp2) {
-      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_SetTransitionState" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'"); }
-     else { shared_ptr< OpenBabel::OBMol > * temp = reinterpret_cast< shared_ptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
+      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_SetTransitionState" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'"); }
+     else { obsharedptr< OpenBabel::OBMol > * temp = reinterpret_cast< obsharedptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
       if (SWIG_IsNewObj(res2)) delete temp; }  }  (arg1)->SetTransitionState(arg2); resultobj = SWIG_Py_Void();
   return resultobj; fail: return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_AddAgent(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0;
-  OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > arg2 ;
+  OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > arg2 ;
   void *argp1 = 0 ; int res1 = 0 ; void *argp2 ; int res2 = 0 ; PyObject *swig_obj[2] ;
   if (!SWIG_Python_UnpackTuple(args,"OBReaction_AddAgent",2,2,swig_obj)) SWIG_fail;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_AddAgent" "', argument " "1"" of type '" "OpenBabel::OBReaction *""'");  }
    arg1 = reinterpret_cast< OpenBabel::OBReaction * >(argp1); {
     res2 = SWIG_ConvertPtr(swig_obj[1], &argp2, SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t,  0  | 0); if (!SWIG_IsOK(res2)) {
-      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_AddAgent" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'");  }
+      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBReaction_AddAgent" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'");  }
        if (!argp2) {
-      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_AddAgent" "', argument " "2"" of type '" "shared_ptr< OpenBabel::OBMol > const""'"); }
-     else { shared_ptr< OpenBabel::OBMol > * temp = reinterpret_cast< shared_ptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
+      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBReaction_AddAgent" "', argument " "2"" of type '" "obsharedptr< OpenBabel::OBMol > const""'"); }
+     else { obsharedptr< OpenBabel::OBMol > * temp = reinterpret_cast< obsharedptr< OpenBabel::OBMol > * >(argp2); arg2 = *temp;
       if (SWIG_IsNewObj(res2)) delete temp; }  }  (arg1)->AddAgent(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail:
   return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_GetReactant(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0;
   OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; unsigned int arg2 ; void *argp1 = 0 ; int res1 = 0 ;
-  unsigned int val2 ; int ecode2 = 0 ; PyObject *swig_obj[2] ; SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > result;
+  unsigned int val2 ; int ecode2 = 0 ; PyObject *swig_obj[2] ; SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > result;
   if (!SWIG_Python_UnpackTuple(args,"OBReaction_GetReactant",2,2,swig_obj)) SWIG_fail;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_GetReactant" "', argument " "1"" of type '" "OpenBabel::OBReaction *""'");  }
@@ -25596,11 +25596,11 @@ SWIGINTERN PyObject *_wrap_OBReaction_Ge
   if (!SWIG_IsOK(ecode2)) {
     SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBReaction_GetReactant" "', argument " "2"" of type '" "unsigned int""'"); }
     arg2 = static_cast< unsigned int >(val2); result = (arg1)->GetReactant(arg2);
-  resultobj = SWIG_NewPointerObj((new shared_ptr< OpenBabel::OBMol >(static_cast< const shared_ptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
+  resultobj = SWIG_NewPointerObj((new obsharedptr< OpenBabel::OBMol >(static_cast< const obsharedptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
   return resultobj; fail: return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_GetProduct(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0;
   OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; unsigned int arg2 ; void *argp1 = 0 ; int res1 = 0 ;
-  unsigned int val2 ; int ecode2 = 0 ; PyObject *swig_obj[2] ; SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > result;
+  unsigned int val2 ; int ecode2 = 0 ; PyObject *swig_obj[2] ; SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > result;
   if (!SWIG_Python_UnpackTuple(args,"OBReaction_GetProduct",2,2,swig_obj)) SWIG_fail;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_GetProduct" "', argument " "1"" of type '" "OpenBabel::OBReaction *""'");  }
@@ -25608,24 +25608,24 @@ SWIGINTERN PyObject *_wrap_OBReaction_Ge
   if (!SWIG_IsOK(ecode2)) {
     SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBReaction_GetProduct" "', argument " "2"" of type '" "unsigned int""'"); }
     arg2 = static_cast< unsigned int >(val2); result = (arg1)->GetProduct(arg2);
-  resultobj = SWIG_NewPointerObj((new shared_ptr< OpenBabel::OBMol >(static_cast< const shared_ptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
+  resultobj = SWIG_NewPointerObj((new obsharedptr< OpenBabel::OBMol >(static_cast< const obsharedptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
   return resultobj; fail: return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_GetTransitionState(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {
   PyObject *resultobj = 0; OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; void *argp1 = 0 ; int res1 = 0 ;
-  PyObject *swig_obj[1] ; SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > result; if (!args) SWIG_fail; swig_obj[0] = args;
+  PyObject *swig_obj[1] ; SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > result; if (!args) SWIG_fail; swig_obj[0] = args;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_GetTransitionState" "', argument " "1"" of type '" "OpenBabel::OBReaction const *""'");  }
    arg1 = reinterpret_cast< OpenBabel::OBReaction * >(argp1);
   result = ((OpenBabel::OBReaction const *)arg1)->GetTransitionState();
-  resultobj = SWIG_NewPointerObj((new shared_ptr< OpenBabel::OBMol >(static_cast< const shared_ptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
+  resultobj = SWIG_NewPointerObj((new obsharedptr< OpenBabel::OBMol >(static_cast< const obsharedptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
   return resultobj; fail: return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_GetAgent(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0;
   OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; void *argp1 = 0 ; int res1 = 0 ; PyObject *swig_obj[1] ;
-  SwigValueWrapper< shared_ptr< OpenBabel::OBMol > > result; if (!args) SWIG_fail; swig_obj[0] = args;
+  SwigValueWrapper< obsharedptr< OpenBabel::OBMol > > result; if (!args) SWIG_fail; swig_obj[0] = args;
   res1 = SWIG_ConvertPtr(swig_obj[0], &argp1,SWIGTYPE_p_OpenBabel__OBReaction, 0 |  0 ); if (!SWIG_IsOK(res1)) {
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBReaction_GetAgent" "', argument " "1"" of type '" "OpenBabel::OBReaction const *""'");  }
    arg1 = reinterpret_cast< OpenBabel::OBReaction * >(argp1); result = ((OpenBabel::OBReaction const *)arg1)->GetAgent();
-  resultobj = SWIG_NewPointerObj((new shared_ptr< OpenBabel::OBMol >(static_cast< const shared_ptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
+  resultobj = SWIG_NewPointerObj((new obsharedptr< OpenBabel::OBMol >(static_cast< const obsharedptr< OpenBabel::OBMol >& >(result))), SWIGTYPE_p_shared_ptrT_OpenBabel__OBMol_t, SWIG_POINTER_OWN |  0 );
   return resultobj; fail: return NULL; }
 SWIGINTERN PyObject *_wrap_OBReaction_GetTitle(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0;
   OpenBabel::OBReaction *arg1 = (OpenBabel::OBReaction *) 0 ; void *argp1 = 0 ; int res1 = 0 ; PyObject *swig_obj[1] ;
@@ -56173,7 +56173,7 @@ static swig_type_info _swigt__p_p_double
 static swig_type_info _swigt__p_p_int = {"_p_p_int", "int **", 0, 0, (void*)0, 0};
 static swig_type_info _swigt__p_reference = {"_p_reference", "reference *", 0, 0, (void*)0, 0};
 static swig_type_info _swigt__p_second_type = {"_p_second_type", "second_type *", 0, 0, (void*)0, 0};
-static swig_type_info _swigt__p_shared_ptrT_OpenBabel__OBMol_t = {"_p_shared_ptrT_OpenBabel__OBMol_t", "shared_ptr< OpenBabel::OBMol > *", 0, 0, (void*)0, 0};
+static swig_type_info _swigt__p_shared_ptrT_OpenBabel__OBMol_t = {"_p_shared_ptrT_OpenBabel__OBMol_t", "obsharedptr< OpenBabel::OBMol > *", 0, 0, (void*)0, 0};
 static swig_type_info _swigt__p_size_type = {"_p_size_type", "size_type *", 0, 0, (void*)0, 0};
 static swig_type_info _swigt__p_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t = {"_p_std__allocatorT_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__allocatorT_std__pairT_unsigned_int_unsigned_int_t_t_t_t", "std::allocator< std::vector< std::pair< unsigned int,unsigned int >,std::allocator< std::pair< unsigned int,unsigned int > > > > *|std::vector< std::vector< std::pair< unsigned int,unsigned int > > >::allocator_type *", 0, 0, (void*)0, 0};
 static swig_type_info _swigt__p_std__binary_functionT_char_const_p_char_const_p_bool_t = {"_p_std__binary_functionT_char_const_p_char_const_p_bool_t", "std::binary_function< char const *,char const *,bool > *", 0, 0, (void*)0, 0};
--- src/alias.cpp.orig	2012-10-05 20:17:36 UTC
+++ src/alias.cpp
@@ -21,6 +21,7 @@ GNU General Public License for more deta
 #include <openbabel/parsmart.h>
 #include <openbabel/mcdlutil.h>
 #include <openbabel/atomclass.h>
+#include <openbabel/shared_ptr.h>
 
 using namespace std;
 namespace OpenBabel
@@ -270,7 +271,7 @@ bool AliasData::LoadFile(SmartsTable& sm
         //OBSmartsPattern objects are not copyable without complications,
         //so reference semantics used.
 
-        shared_ptr<OBSmartsPattern> psp(new OBSmartsPattern);
+        obsharedptr<OBSmartsPattern> psp(new OBSmartsPattern);
         psp->Init(ssmarts.str());
         smtable.push_back(make_pair(vec[0], psp));
       }
--- src/formats/chemkinformat.cpp.orig	2012-10-03 19:08:14 UTC
+++ src/formats/chemkinformat.cpp
@@ -78,7 +78,7 @@ private:
   bool              ReadHeader(istream& ifs, OBConversion* pConv);
   bool              ParseReactionLine(OBReaction* pReact, OBConversion* pConv);
   bool              ReadReactionQualifierLines(istream& ifs, OBReaction* pReact);
-  shared_ptr<OBMol> CheckSpecies(string& name, string& ln, bool MustBeKnown);
+  obsharedptr<OBMol> CheckSpecies(string& name, string& ln, bool MustBeKnown);
   bool              ReadThermo(OBConversion* pConv);
   bool              ReadStdThermo(const string& datafilename);
   OBFormat*         GetThermoFormat();
@@ -86,8 +86,8 @@ private:
   bool              WriteReactionLine(OBReaction* pReact, OBConversion* pConv);
   bool              WriteHeader(OBConversion* pConv);
 private:
-  typedef map<string,shared_ptr<OBMol> > MolMap;
-  typedef set<shared_ptr<OBMol> > MolSet;
+  typedef map<string,obsharedptr<OBMol> > MolMap;
+  typedef set<obsharedptr<OBMol> > MolSet;
   //used on input
   MolMap IMols;
   string ln;
@@ -215,7 +215,7 @@ void ChemKinFormat::Init()
     SpeciesListed=false;
     IMols.clear();
     //Special species name
-    shared_ptr<OBMol> sp(new OBMol);
+    obsharedptr<OBMol> sp(new OBMol);
     sp.get()->SetTitle("M");
     IMols["M"] = sp;
 }
@@ -280,7 +280,7 @@ bool ChemKinFormat::ReadHeader(istream&
           break;
         }
         //Add all species to IMols
-        shared_ptr<OBMol> sp(new OBMol);
+        obsharedptr<OBMol> sp(new OBMol);
         sp.get()->SetTitle(*itr);
         IMols[*itr] = sp;
       }
@@ -346,7 +346,7 @@ bool ChemKinFormat::ParseReactionLine(OB
   OBRateData* pRD = new OBRateData; //to store rate constant data. Attach only if rate data found
 
   int n=0;
-  shared_ptr<OBMol> sp;
+  obsharedptr<OBMol> sp;
 
   string::size_type eqpos = ln.find('=');
 
@@ -643,7 +643,7 @@ bool ChemKinFormat::ReadReactionQualifie
 }
 
 ///////////////////////////////////////////////////////////////
-shared_ptr<OBMol> ChemKinFormat::CheckSpecies(string& name, string& ln, bool MustBeKnown)
+obsharedptr<OBMol> ChemKinFormat::CheckSpecies(string& name, string& ln, bool MustBeKnown)
 {
   MolMap::iterator mapitr = IMols.find(name);
   if(mapitr==IMols.end())
@@ -653,14 +653,14 @@ shared_ptr<OBMol> ChemKinFormat::CheckSp
     {
       obErrorLog.ThrowError(__FUNCTION__,
         name + " not recognized as a species in\n" + ln, obError);
-      shared_ptr<OBMol> sp;
+      obsharedptr<OBMol> sp;
       return sp; //empty
     }
     else
     {
       // There was no REACTIONS section in input file and probably no SPECIES section.
       // Unknown species that appear in a reaction can be made here with just a name.
-      shared_ptr<OBMol> sp(new OBMol);
+      obsharedptr<OBMol> sp(new OBMol);
       sp->SetTitle(name.c_str());
       return sp;
     }
@@ -697,7 +697,7 @@ bool ChemKinFormat::ReadThermo(OBConvers
       MolMap::iterator mapitr = IMols.find(thmol.GetTitle());
       if(mapitr!=IMols.end())
       {
-        shared_ptr<OBMol> psnewmol(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(),&thmol));
+        obsharedptr<OBMol> psnewmol(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(),&thmol));
         IMols.erase(mapitr);
         IMols[thmol.GetTitle()] = psnewmol;
       }
@@ -743,7 +743,7 @@ bool ChemKinFormat::ReadStdThermo(const
       OBMol thmol;
       stdthermo.seekg(itr->second);
       StdThermConv.Read(&thmol);
-      shared_ptr<OBMol> psnewmol(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(),&thmol));
+      obsharedptr<OBMol> psnewmol(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(),&thmol));
       IMols[thmol.GetTitle()] = psnewmol;
     }
     else
@@ -915,7 +915,7 @@ bool ChemKinFormat::WriteReactionLine(OB
   int i;
   for(i=0;i<pReact->NumReactants();++i)
   {
-    shared_ptr<OBMol> psMol = pReact->GetReactant(i);
+    obsharedptr<OBMol> psMol = pReact->GetReactant(i);
 //    if(strcasecmp(psMol->GetTitle(),"M"))
     OMols.insert(psMol);
 
@@ -954,7 +954,7 @@ bool ChemKinFormat::WriteReactionLine(OB
 
   for(i=0;i<pReact->NumProducts();++i)
   {
-    shared_ptr<OBMol> psMol = pReact->GetProduct(i);
+    obsharedptr<OBMol> psMol = pReact->GetProduct(i);
     if(strcasecmp(psMol->GetTitle(),"M"))
       OMols.insert(psMol);
 
--- src/formats/rsmiformat.cpp.orig	2012-10-03 19:08:14 UTC
+++ src/formats/rsmiformat.cpp
@@ -181,7 +181,7 @@ namespace OpenBabel
     }
     mols = jreactants.Separate();
     for(itr=mols.begin();itr!=mols.end();++itr)
-      pReact->AddReactant(shared_ptr<OBMol>(new OBMol(*itr)));
+      pReact->AddReactant(obsharedptr<OBMol>(new OBMol(*itr)));
 
     pos2 = rsmiles.find('>', pos+1);
     if(pos2==string::npos)
@@ -201,7 +201,7 @@ namespace OpenBabel
         delete pAgent;
         return false;
       }
-      pReact->AddAgent(shared_ptr<OBMol>(pAgent));
+      pReact->AddAgent(obsharedptr<OBMol>(pAgent));
     }
 
     //Extract products and split into separate molecules
@@ -215,7 +215,7 @@ namespace OpenBabel
     mols.clear();
     mols = jproducts.Separate();
     for(itr=mols.begin();itr!=mols.end();++itr)
-      pReact->AddProduct(shared_ptr<OBMol>(new OBMol(*itr)));
+      pReact->AddProduct(obsharedptr<OBMol>(new OBMol(*itr)));
 
     return true;
   }
@@ -247,7 +247,7 @@ namespace OpenBabel
 
     ofs << '>';
 
-    shared_ptr<OBMol> spAgent = pReact->GetAgent();
+    obsharedptr<OBMol> spAgent = pReact->GetAgent();
     if(spAgent.get())
       if(!pSmiFormat->WriteMolecule(spAgent.get(), pConv))
         return false;
--- src/formats/rxnformat.cpp.orig	2012-10-03 19:08:14 UTC
+++ src/formats/rxnformat.cpp
@@ -175,7 +175,7 @@ bool RXNFormat::ReadMolecule(OBBase* pOb
         obErrorLog.ThrowError(__FUNCTION__, "Failed to read a reactant", obWarning);
       else
       {
-        shared_ptr<OBMol> p(pmol);
+        obsharedptr<OBMol> p(pmol);
         pReact->AddReactant(p);
       }
     }
@@ -189,7 +189,7 @@ bool RXNFormat::ReadMolecule(OBBase* pOb
       else
       {
         //        pReact->products.push_back(pmol);
-        shared_ptr<OBMol> p(pmol);
+        obsharedptr<OBMol> p(pmol);
         pReact->AddProduct(p);
       }
     }
--- src/formats/xml/cmlreactformat.cpp.orig	2012-10-03 19:08:13 UTC
+++ src/formats/xml/cmlreactformat.cpp
@@ -91,15 +91,15 @@ public:
   };
 
 private:
-  typedef map<string,shared_ptr<OBMol> > MolMap;
-  string AddMolToList(shared_ptr<OBMol> spmol, MolMap& mmap);
+  typedef map<string,obsharedptr<OBMol> > MolMap;
+  string AddMolToList(obsharedptr<OBMol> spmol, MolMap& mmap);
   bool WriteRateData(OBReaction* pReact, xmlChar* altprefix);
   void WriteMetadataList(OBReaction& react);
 
 private:
   OBReaction* _preact;
   OBMol* pmol;
-  shared_ptr<OBMol> _spmol;
+  obsharedptr<OBMol> _spmol;
   MolMap IMols; //used on input
   MolMap OMols; //used on output
   int nextmol;
@@ -123,7 +123,7 @@ bool CMLReactFormat::ReadChemObject(OBCo
   {
     IMols.clear();
     //add special species
-    shared_ptr<OBMol> sp(new OBMol);
+    obsharedptr<OBMol> sp(new OBMol);
     sp.get()->SetTitle("M");
     IMols["M"] = sp;
   }
@@ -192,7 +192,7 @@ bool CMLReactFormat::DoElement(const str
     }
     else
     {
-      shared_ptr<OBMol> sp(new OBMol);
+      obsharedptr<OBMol> sp(new OBMol);
       OBFormat* pCMLFormat = OBConversion::FindFormat("cml");
       if(!pCMLFormat)
         return false;
@@ -331,7 +331,7 @@ bool CMLReactFormat::WriteChemObject(OBC
     OBMol* pmol = dynamic_cast<OBMol*>(pOb);
     if(pmol!=NULL)
     {
-      shared_ptr<OBMol> sp(pmol);
+      obsharedptr<OBMol> sp(pmol);
       AddMolToList(sp, OMols);
       pConv->SetOutputIndex(-1); //Signals that molecules have been added
 
@@ -624,7 +624,7 @@ bool CMLReactFormat::WriteMolecule(OBBas
   return true;
 }
 
-string CMLReactFormat::AddMolToList(shared_ptr<OBMol> spmol, MolMap& mmap)
+string CMLReactFormat::AddMolToList(obsharedptr<OBMol> spmol, MolMap& mmap)
 {
   //Adds a molecule to the map
   string id = spmol->GetTitle();
@@ -664,7 +664,7 @@ string CMLReactFormat::AddMolToList(shar
     {
       //already in map.
       //Get a molecule with the best bits of both old and new molecules and immediately make a shared_ ptr
-      shared_ptr<OBMol> spnew(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(), spmol.get()));
+      obsharedptr<OBMol> spnew(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(), spmol.get()));
       if(spnew)
       {
         spmol.swap(spnew);
--- src/obmolecformat.cpp.orig	2012-10-03 19:08:15 UTC
+++ src/obmolecformat.cpp
@@ -439,7 +439,7 @@ namespace OpenBabel
     //Output all the constituent molecules of the reaction
 
     //Collect the molecules first, just for convenience
-    vector<shared_ptr<OBMol> > mols;
+    vector<obsharedptr<OBMol> > mols;
     unsigned i;
     for(i=0;i<pReact->NumReactants();i++)
       mols.push_back(pReact->GetReactant(i));
--- test/obtest.h.orig	2010-09-22 04:05:05 UTC
+++ test/obtest.h
@@ -40,7 +40,7 @@ const char* ob_expr(const char *expr) {
 
 
 // some utility functions
-typedef shared_ptr<OpenBabel::OBMol> OBMolPtr;
+typedef obsharedptr<OpenBabel::OBMol> OBMolPtr;
 
 struct OBTestUtil
 {