6 files changed, 91 insertions, 659 deletions

diff --git a/science/openbabel/Makefile b/science/openbabel/Makefile
index 8dc548351601..8e641bab8494 100644
--- a/science/openbabel/Makefile
+++ b/science/openbabel/Makefile
@@ -2,15 +2,17 @@
 # $FreeBSD$
 
 PORTNAME=	openbabel
-PORTVERSION=	2.3.2
-PORTREVISION=	2
+PORTVERSION=	2.4.1
 CATEGORIES=	science
 MASTER_SITES=	SF
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Chemistry file translation program
 
-BUILD_DEPENDS=	${LOCALBASE}/include/eigen3/Eigen/Eigen:math/eigen3
+LICENSE=	GPLv2+
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+BUILD_DEPENDS=	eigen>=0:math/eigen3
 
 BROKEN_powerpc64=	Does not build: relocation truncated to fit: R_PPC64_TOC16_DS
 
@@ -38,7 +40,7 @@ PYTHON_CMAKE_ON=	-DPYTHON_BINDINGS=on
 post-patch:
 	${REINPLACE_CMD} -e '/pkgconfig/s,$${LIB_INSTALL_DIR},libdata,' \
 		${WRKSRC}/CMakeLists.txt
-	${REINPLACE_CMD} -e 's,share/man,man,' \
+	${REINPLACE_CMD} -e 's,man/man1,../man/man1,' \
 		${WRKSRC}/doc/CMakeLists.txt
 
 post-patch-CAIRO-off:
diff --git a/science/openbabel/distinfo b/science/openbabel/distinfo
index 084378dc32a9..99f6cf54c1d8 100644
--- a/science/openbabel/distinfo
+++ b/science/openbabel/distinfo
@@ -1,2 +1,3 @@
-SHA256 (openbabel-2.3.2.tar.gz) = 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188
-SIZE (openbabel-2.3.2.tar.gz) = 20509105
+TIMESTAMP = 1495085400
+SHA256 (openbabel-2.4.1.tar.gz) = 204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc
+SIZE (openbabel-2.4.1.tar.gz) = 11618304
diff --git a/science/openbabel/files/patch-gcc5-support b/science/openbabel/files/patch-gcc5-support
deleted file mode 100644
index 48236d8ee1ca..000000000000
--- a/science/openbabel/files/patch-gcc5-support
+++ /dev/null
@@ -1,521 +0,0 @@
-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
- {
diff --git a/science/openbabel/files/patch-git_c3abbdda b/science/openbabel/files/patch-git_c3abbdda
deleted file mode 100644
index 71bdd6812ba5..000000000000
--- a/science/openbabel/files/patch-git_c3abbdda
+++ /dev/null
@@ -1,62 +0,0 @@
-This is the git commit below, with the change to include/openbabel/shared_ptr.h
-properly adapted since it originally depends on commit ce178cbb.
-
-The include/openbabel/shared_ptr.h patch was moved to patch-gcc5-support
-
-commit c3abbddae78e654df9322ad1020ff79dd6332946
-Author: Matt Swain <m.swain@me.com>
-Date:   Thu Oct 31 15:25:53 2013 +0000
-
-    Detect libc++ as this is now the default in OS X Mavericks
-
-diff --git a/include/openbabel/obmolecformat.h b/include/openbabel/obmolecformat.h
-index 46ec724..c004313 100644
---- include/openbabel/obmolecformat.h
-+++ include/openbabel/obmolecformat.h
-@@ -23,7 +23,10 @@ GNU General Public License for more details.
-   #include <hash_map>
- #endif
- 
--#if __GNUC__ == 4 && __GNUC_MINOR__ >= 1
-+#include <ciso646>  // detect std::lib
-+#ifdef _LIBCPP_VERSION
-+  #include <unordered_map>
-+#elif __GNUC__ == 4 && __GNUC_MINOR__ >= 1
-   #include <tr1/unordered_map>
- #elif defined(USE_BOOST)
-   #include <boost/tr1/unordered_map.hpp>
-@@ -141,6 +144,8 @@ public:
- 
- #ifdef _MSC_VER
-   typedef stdext::hash_map<std::string, unsigned> NameIndexType;
-+#elif defined(_LIBCPP_VERSION)
-+  typedef std::unordered_map<std::string, unsigned> NameIndexType;
- #elif (__GNUC__ == 4 && __GNUC_MINOR__ >= 1 && !defined(__APPLE_CC__)) || defined (USE_BOOST)
-   typedef std::tr1::unordered_map<std::string, unsigned> NameIndexType;
- #else
-diff --git a/src/ops/unique.cpp b/src/ops/unique.cpp
-index 5f7714f..8527fba 100644
---- src/ops/unique.cpp
-+++ src/ops/unique.cpp
-@@ -21,7 +21,7 @@ GNU General Public License for more details.
- #include <openbabel/obconversion.h>
- #include <openbabel/descriptor.h>
- #include <openbabel/inchiformat.h>
--#ifdef _MSC_VER
-+#if defined(_MSC_VER) || defined(_LIBCPP_VERSION)
-   #include <unordered_map>
- #elif (__GNUC__ == 4 && __GNUC_MINOR__ >= 1 && !defined(__APPLE_CC__))
-   #include <tr1/unordered_map>
-@@ -36,7 +36,11 @@ GNU General Public License for more details.
- 
- using namespace std;
- #ifndef NO_UNORDERED_MAP
--using std::tr1::unordered_map;
-+  #ifdef _LIBCPP_VERSION
-+    using std::unordered_map;
-+  #else
-+    using std::tr1::unordered_map;
-+  #endif
- #endif
- namespace OpenBabel
- {
diff --git a/science/openbabel/files/patch-scripts__CMakeLists.txt b/science/openbabel/files/patch-scripts__CMakeLists.txt
deleted file mode 100644
index eaf5df494a63..000000000000
--- a/science/openbabel/files/patch-scripts__CMakeLists.txt
+++ /dev/null
@@ -1,23 +0,0 @@
---- ./scripts/CMakeLists.txt.orig	2012-10-03 19:08:52.000000000 +0000
-+++ ./scripts/CMakeLists.txt	2012-10-29 23:15:24.219796263 +0000
-@@ -50,6 +50,7 @@
- 
-     if(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
-       set(DO_PYTHON_BINDINGS ON BOOL)
-+      set(PYTHON_SITE_PACKAGES_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages CACHE PATH "The directory where python modules will be installed to.")
-       message(STATUS "Python bindings will be compiled")
-     endif(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
- 
-@@ -91,9 +92,9 @@
-             PREFIX ""
-             SUFFIX .so )
-         add_dependencies(bindings_python openbabel)
--        install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR})
--        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR})
--        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR})
-+        install(TARGETS bindings_python LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES_INSTALL_DIR})
-+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${PYTHON_SITE_PACKAGES_INSTALL_DIR})
-+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${PYTHON_SITE_PACKAGES_INSTALL_DIR})
-     else(NOT WIN32)
-         set_target_properties(bindings_python PROPERTIES
-             OUTPUT_NAME _openbabel
diff --git a/science/openbabel/pkg-plist b/science/openbabel/pkg-plist
index 4cc8f5b1e1ec..284689c5f9db 100644
--- a/science/openbabel/pkg-plist
+++ b/science/openbabel/pkg-plist
@@ -2,6 +2,7 @@ bin/babel
 bin/obabel
 bin/obchiral
 bin/obconformer
+bin/obdistgen
 bin/obenergy
 bin/obfit
 bin/obgen
@@ -13,6 +14,9 @@ bin/obrms
 bin/obrotamer
 bin/obrotate
 bin/obspectrophore
+bin/obsym
+bin/obtautomer
+bin/obthermo
 bin/roundtrip
 include/inchi/inchi_api.h
 include/openbabel-2.0/openbabel/alias.h
@@ -31,7 +35,9 @@ include/openbabel-2.0/openbabel/chemdrawcdx.h
 include/openbabel-2.0/openbabel/chiral.h
 include/openbabel-2.0/openbabel/conformersearch.h
 include/openbabel-2.0/openbabel/data.h
+include/openbabel-2.0/openbabel/data_utilities.h
 include/openbabel-2.0/openbabel/descriptor.h
+include/openbabel-2.0/openbabel/distgeom.h
 include/openbabel-2.0/openbabel/dlhandler.h
 include/openbabel-2.0/openbabel/fingerprint.h
 include/openbabel-2.0/openbabel/forcefield.h
@@ -44,6 +50,9 @@ include/openbabel-2.0/openbabel/groupcontrib.h
 include/openbabel-2.0/openbabel/inchiformat.h
 include/openbabel-2.0/openbabel/internalcoord.h
 include/openbabel-2.0/openbabel/isomorphism.h
+include/openbabel-2.0/openbabel/json/customwriter.h
+include/openbabel-2.0/openbabel/json/json-forwards.h
+include/openbabel-2.0/openbabel/json/json.h
 include/openbabel-2.0/openbabel/kinetics.h
 include/openbabel-2.0/openbabel/lineend.h
 include/openbabel-2.0/openbabel/locale.h
@@ -85,6 +94,7 @@ include/openbabel-2.0/openbabel/stereo/stereo.h
 include/openbabel-2.0/openbabel/stereo/tetrahedral.h
 include/openbabel-2.0/openbabel/stereo/tetranonplanar.h
 include/openbabel-2.0/openbabel/stereo/tetraplanar.h
+include/openbabel-2.0/openbabel/tautomer.h
 include/openbabel-2.0/openbabel/text.h
 include/openbabel-2.0/openbabel/tokenst.h
 include/openbabel-2.0/openbabel/typer.h
@@ -97,8 +107,8 @@ lib/libinchi.so
 lib/libinchi.so.0
 lib/libinchi.so.0.4.1
 lib/libopenbabel.so
-lib/libopenbabel.so.4
-lib/libopenbabel.so.4.0.2
+lib/libopenbabel.so.5
+lib/libopenbabel.so.5.0.0
 lib/openbabel/%%VERSION%%/APIInterface.so
 lib/openbabel/%%VERSION%%/CSRformat.so
 lib/openbabel/%%VERSION%%/MCDLformat.so
@@ -110,6 +120,7 @@ lib/openbabel/%%VERSION%%/acrformat.so
 lib/openbabel/%%VERSION%%/adfformat.so
 lib/openbabel/%%VERSION%%/alchemyformat.so
 lib/openbabel/%%VERSION%%/amberformat.so
+lib/openbabel/%%VERSION%%/aoforceformat.so
 lib/openbabel/%%VERSION%%/asciiformat.so
 lib/openbabel/%%VERSION%%/balstformat.so
 lib/openbabel/%%VERSION%%/bgfformat.so
@@ -121,6 +132,7 @@ lib/openbabel/%%VERSION%%/castepformat.so
 lib/openbabel/%%VERSION%%/cccformat.so
 lib/openbabel/%%VERSION%%/cdxmlformat.so
 lib/openbabel/%%VERSION%%/chem3dformat.so
+lib/openbabel/%%VERSION%%/chemdoodlejsonformat.so
 lib/openbabel/%%VERSION%%/chemdrawcdx.so
 lib/openbabel/%%VERSION%%/chemdrawct.so
 lib/openbabel/%%VERSION%%/chemkinformat.so
@@ -128,12 +140,15 @@ lib/openbabel/%%VERSION%%/chemtoolformat.so
 lib/openbabel/%%VERSION%%/cifformat.so
 lib/openbabel/%%VERSION%%/cmlformat.so
 lib/openbabel/%%VERSION%%/cmlreactformat.so
+lib/openbabel/%%VERSION%%/confabreport.so
 lib/openbabel/%%VERSION%%/copyformat.so
 lib/openbabel/%%VERSION%%/crkformat.so
 lib/openbabel/%%VERSION%%/crystal09format.so
 lib/openbabel/%%VERSION%%/cssrformat.so
+lib/openbabel/%%VERSION%%/daltonformat.so
 lib/openbabel/%%VERSION%%/dlpolyformat.so
 lib/openbabel/%%VERSION%%/dmolformat.so
+lib/openbabel/%%VERSION%%/exyzformat.so
 lib/openbabel/%%VERSION%%/fastaformat.so
 lib/openbabel/%%VERSION%%/fastsearchformat.so
 lib/openbabel/%%VERSION%%/fchkformat.so
@@ -156,6 +171,8 @@ lib/openbabel/%%VERSION%%/hinformat.so
 lib/openbabel/%%VERSION%%/inchiformat.so
 lib/openbabel/%%VERSION%%/jaguarformat.so
 lib/openbabel/%%VERSION%%/lmpdatformat.so
+lib/openbabel/%%VERSION%%/lpmdformat.so
+lib/openbabel/%%VERSION%%/mdffformat.so
 lib/openbabel/%%VERSION%%/mdlformat.so
 lib/openbabel/%%VERSION%%/mmcifformat.so
 lib/openbabel/%%VERSION%%/mmodformat.so
@@ -171,7 +188,9 @@ lib/openbabel/%%VERSION%%/msmsformat.so
 lib/openbabel/%%VERSION%%/nulformat.so
 lib/openbabel/%%VERSION%%/nwchemformat.so
 lib/openbabel/%%VERSION%%/opendxformat.so
+lib/openbabel/%%VERSION%%/orcaformat.so
 lib/openbabel/%%VERSION%%/outformat.so
+lib/openbabel/%%VERSION%%/painterformat.so
 lib/openbabel/%%VERSION%%/pcmodelformat.so
 lib/openbabel/%%VERSION%%/pdbformat.so
 lib/openbabel/%%VERSION%%/pdbqtformat.so
@@ -182,17 +201,22 @@ lib/openbabel/%%VERSION%%/plugin_forcefields.so
 lib/openbabel/%%VERSION%%/plugin_ops.so
 %%CAIRO%%lib/openbabel/%%VERSION%%/png2format.so
 lib/openbabel/%%VERSION%%/pngformat.so
+lib/openbabel/%%VERSION%%/pointcloudformat.so
 lib/openbabel/%%VERSION%%/posformat.so
 lib/openbabel/%%VERSION%%/povrayformat.so
 lib/openbabel/%%VERSION%%/pqrformat.so
 lib/openbabel/%%VERSION%%/pubchem.so
+lib/openbabel/%%VERSION%%/pubchemjsonformat.so
 lib/openbabel/%%VERSION%%/pwscfformat.so
 lib/openbabel/%%VERSION%%/qchemformat.so
 lib/openbabel/%%VERSION%%/reportformat.so
 lib/openbabel/%%VERSION%%/rsmiformat.so
 lib/openbabel/%%VERSION%%/rxnformat.so
 lib/openbabel/%%VERSION%%/shelxformat.so
+lib/openbabel/%%VERSION%%/siestaformat.so
 lib/openbabel/%%VERSION%%/smilesformat.so
+lib/openbabel/%%VERSION%%/smileyformat.so
+lib/openbabel/%%VERSION%%/stlformat.so
 lib/openbabel/%%VERSION%%/svgformat.so
 lib/openbabel/%%VERSION%%/textformat.so
 lib/openbabel/%%VERSION%%/thermoformat.so
@@ -228,48 +252,59 @@ man/man1/obrotamer.1.gz
 man/man1/obrotate.1.gz
 man/man1/obspectrophore.1.gz
 man/man1/roundtrip.1.gz
-share/openbabel/%%VERSION%%/MACCS.txt
-share/openbabel/%%VERSION%%/SMARTS_InteLigand.txt
-share/openbabel/%%VERSION%%/UFF.prm
-share/openbabel/%%VERSION%%/aromatic.txt
-share/openbabel/%%VERSION%%/atomtyp.txt
-share/openbabel/%%VERSION%%/babel_povray3.inc
-share/openbabel/%%VERSION%%/bondtyp.txt
-share/openbabel/%%VERSION%%/element.txt
-share/openbabel/%%VERSION%%/fragments.txt
-share/openbabel/%%VERSION%%/gaff.dat
-share/openbabel/%%VERSION%%/gaff.prm
-share/openbabel/%%VERSION%%/ghemical.prm
-share/openbabel/%%VERSION%%/isotope-small.txt
-share/openbabel/%%VERSION%%/isotope.txt
-share/openbabel/%%VERSION%%/logp.txt
-share/openbabel/%%VERSION%%/mmff94.ff
-share/openbabel/%%VERSION%%/mmff94s.ff
-share/openbabel/%%VERSION%%/mmffang.par
-share/openbabel/%%VERSION%%/mmffbndk.par
-share/openbabel/%%VERSION%%/mmffbond.par
-share/openbabel/%%VERSION%%/mmffchg.par
-share/openbabel/%%VERSION%%/mmffdef.par
-share/openbabel/%%VERSION%%/mmffdfsb.par
-share/openbabel/%%VERSION%%/mmffoop.par
-share/openbabel/%%VERSION%%/mmffpbci.par
-share/openbabel/%%VERSION%%/mmffprop.par
-share/openbabel/%%VERSION%%/mmffs_oop.par
-share/openbabel/%%VERSION%%/mmffs_tor.par
-share/openbabel/%%VERSION%%/mmffstbn.par
-share/openbabel/%%VERSION%%/mmfftor.par
-share/openbabel/%%VERSION%%/mmffvdw.par
-share/openbabel/%%VERSION%%/mr.txt
-share/openbabel/%%VERSION%%/patterns.txt
-share/openbabel/%%VERSION%%/phmodel.txt
-share/openbabel/%%VERSION%%/plugindefines.txt
-share/openbabel/%%VERSION%%/psa.txt
-share/openbabel/%%VERSION%%/qeq.txt
-share/openbabel/%%VERSION%%/resdata.txt
-share/openbabel/%%VERSION%%/ringtyp.txt
-share/openbabel/%%VERSION%%/space-groups.txt
-share/openbabel/%%VERSION%%/splash.png
-share/openbabel/%%VERSION%%/superatom.txt
-share/openbabel/%%VERSION%%/svgformat.script
-share/openbabel/%%VERSION%%/torlib.txt
-share/openbabel/%%VERSION%%/types.txt
+%%DATADIR%%/%%VERSION%%/MACCS.txt
+%%DATADIR%%/%%VERSION%%/SMARTS_InteLigand.txt
+%%DATADIR%%/%%VERSION%%/UFF.prm
+%%DATADIR%%/%%VERSION%%/aromatic.txt
+%%DATADIR%%/%%VERSION%%/atomization-energies.txt
+%%DATADIR%%/%%VERSION%%/atomtyp.txt
+%%DATADIR%%/%%VERSION%%/babel_povray3.inc
+%%DATADIR%%/%%VERSION%%/bondtyp.txt
+%%DATADIR%%/%%VERSION%%/eem.txt
+%%DATADIR%%/%%VERSION%%/eem2015ba.txt
+%%DATADIR%%/%%VERSION%%/eem2015bm.txt
+%%DATADIR%%/%%VERSION%%/eem2015bn.txt
+%%DATADIR%%/%%VERSION%%/eem2015ha.txt
+%%DATADIR%%/%%VERSION%%/eem2015hm.txt
+%%DATADIR%%/%%VERSION%%/eem2015hn.txt
+%%DATADIR%%/%%VERSION%%/element.txt
+%%DATADIR%%/%%VERSION%%/eqeqIonizations.txt
+%%DATADIR%%/%%VERSION%%/fragments.txt
+%%DATADIR%%/%%VERSION%%/gaff.dat
+%%DATADIR%%/%%VERSION%%/gaff.prm
+%%DATADIR%%/%%VERSION%%/ghemical.prm
+%%DATADIR%%/%%VERSION%%/isotope-small.txt
+%%DATADIR%%/%%VERSION%%/isotope.txt
+%%DATADIR%%/%%VERSION%%/logp.txt
+%%DATADIR%%/%%VERSION%%/mpC.txt
+%%DATADIR%%/%%VERSION%%/mmff94.ff
+%%DATADIR%%/%%VERSION%%/mmff94s.ff
+%%DATADIR%%/%%VERSION%%/mmffang.par
+%%DATADIR%%/%%VERSION%%/mmffbndk.par
+%%DATADIR%%/%%VERSION%%/mmffbond.par
+%%DATADIR%%/%%VERSION%%/mmffchg.par
+%%DATADIR%%/%%VERSION%%/mmffdef.par
+%%DATADIR%%/%%VERSION%%/mmffdfsb.par
+%%DATADIR%%/%%VERSION%%/mmffoop.par
+%%DATADIR%%/%%VERSION%%/mmffpbci.par
+%%DATADIR%%/%%VERSION%%/mmffprop.par
+%%DATADIR%%/%%VERSION%%/mmffs_oop.par
+%%DATADIR%%/%%VERSION%%/mmffs_tor.par
+%%DATADIR%%/%%VERSION%%/mmffstbn.par
+%%DATADIR%%/%%VERSION%%/mmfftor.par
+%%DATADIR%%/%%VERSION%%/mmffvdw.par
+%%DATADIR%%/%%VERSION%%/mr.txt
+%%DATADIR%%/%%VERSION%%/patterns.txt
+%%DATADIR%%/%%VERSION%%/phmodel.txt
+%%DATADIR%%/%%VERSION%%/plugindefines.txt
+%%DATADIR%%/%%VERSION%%/psa.txt
+%%DATADIR%%/%%VERSION%%/qeq.txt
+%%DATADIR%%/%%VERSION%%/resdata.txt
+%%DATADIR%%/%%VERSION%%/ringtyp.txt
+%%DATADIR%%/%%VERSION%%/space-groups.txt
+%%DATADIR%%/%%VERSION%%/splash.png
+%%DATADIR%%/%%VERSION%%/superatom.txt
+%%DATADIR%%/%%VERSION%%/svgformat.script
+%%DATADIR%%/%%VERSION%%/templates.sdf
+%%DATADIR%%/%%VERSION%%/torlib.txt
+%%DATADIR%%/%%VERSION%%/types.txt