Index: head/science/openbabel/Makefile =================================================================== --- head/science/openbabel/Makefile +++ head/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 @@ 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: Index: head/science/openbabel/distinfo =================================================================== --- head/science/openbabel/distinfo +++ head/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 Index: head/science/openbabel/files/patch-gcc5-support =================================================================== --- head/science/openbabel/files/patch-gcc5-support +++ head/science/openbabel/files/patch-gcc5-support @@ -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 > > SmartsTable; -+ typedef std::vector< std::pair > > 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 > _reactants; -- std::vector > _products; -- shared_ptr _ts; -- shared_ptr _agent; -+ std::vector > _reactants; -+ std::vector > _products; -+ obsharedptr _ts; -+ obsharedptr _agent; - std::string _title; - std::string _comment; - bool _reversible; -@@ -52,37 +52,37 @@ public: - int NumProducts()const - { return static_cast (_products.size()); } - -- void AddReactant(const shared_ptr sp) -+ void AddReactant(const obsharedptr sp) - { _reactants.push_back(sp); } - -- void AddProduct(const shared_ptr sp) -+ void AddProduct(const obsharedptr sp) - { _products.push_back(sp); } - -- void SetTransitionState(const shared_ptr sp) -+ void SetTransitionState(const obsharedptr sp) - { _ts = sp; } - -- void AddAgent(const shared_ptr sp) -+ void AddAgent(const obsharedptr sp) - { _agent = sp; } - -- shared_ptr GetReactant(const unsigned i) -+ obsharedptr GetReactant(const unsigned i) - { -- shared_ptr sp; -+ obsharedptr sp; - if(i<_reactants.size()) - sp = _reactants[i]; - return sp; //returns empty if out of range - } -- shared_ptr GetProduct(const unsigned i) -+ obsharedptr GetProduct(const unsigned i) - { -- shared_ptr sp; -+ obsharedptr sp; - if(i<_products.size()) - sp = _products[i]; - return sp; //returns empty if out of range - } - -- shared_ptr GetTransitionState()const -+ obsharedptr GetTransitionState()const - { return _ts; } - -- shared_ptr GetAgent()const -+ obsharedptr 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 -- #define shared_ptr boost::shared_ptr -+ #define obsharedptr boost::shared_ptr - #else - #include -- #if __GNUC__ == 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of Konstantin Tokarev -- #include -+ #if __GNUC__ >= 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of Konstantin Tokarev -+ #ifdef _LIBCPP_VERSION -+ #include -+ #else -+ #include -+ #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 - #include - #include -+#include - - 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 psp(new OBSmartsPattern); -+ obsharedptr 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 CheckSpecies(string& name, string& ln, bool MustBeKnown); -+ obsharedptr 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 > MolMap; -- typedef set > MolSet; -+ typedef map > MolMap; -+ typedef set > MolSet; - //used on input - MolMap IMols; - string ln; -@@ -215,7 +215,7 @@ void ChemKinFormat::Init() - SpeciesListed=false; - IMols.clear(); - //Special species name -- shared_ptr sp(new OBMol); -+ obsharedptr 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 sp(new OBMol); -+ obsharedptr 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 sp; -+ obsharedptr sp; - - string::size_type eqpos = ln.find('='); - -@@ -643,7 +643,7 @@ bool ChemKinFormat::ReadReactionQualifie - } - - /////////////////////////////////////////////////////////////// --shared_ptr ChemKinFormat::CheckSpecies(string& name, string& ln, bool MustBeKnown) -+obsharedptr ChemKinFormat::CheckSpecies(string& name, string& ln, bool MustBeKnown) - { - MolMap::iterator mapitr = IMols.find(name); - if(mapitr==IMols.end()) -@@ -653,14 +653,14 @@ shared_ptr ChemKinFormat::CheckSp - { - obErrorLog.ThrowError(__FUNCTION__, - name + " not recognized as a species in\n" + ln, obError); -- shared_ptr sp; -+ obsharedptr 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 sp(new OBMol); -+ obsharedptr 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 psnewmol(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(),&thmol)); -+ obsharedptr 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 psnewmol(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(),&thmol)); -+ obsharedptr 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;iNumReactants();++i) - { -- shared_ptr psMol = pReact->GetReactant(i); -+ obsharedptr psMol = pReact->GetReactant(i); - // if(strcasecmp(psMol->GetTitle(),"M")) - OMols.insert(psMol); - -@@ -954,7 +954,7 @@ bool ChemKinFormat::WriteReactionLine(OB - - for(i=0;iNumProducts();++i) - { -- shared_ptr psMol = pReact->GetProduct(i); -+ obsharedptr 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(new OBMol(*itr))); -+ pReact->AddReactant(obsharedptr(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(pAgent)); -+ pReact->AddAgent(obsharedptr(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(new OBMol(*itr))); -+ pReact->AddProduct(obsharedptr(new OBMol(*itr))); - - return true; - } -@@ -247,7 +247,7 @@ namespace OpenBabel - - ofs << '>'; - -- shared_ptr spAgent = pReact->GetAgent(); -+ obsharedptr 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 p(pmol); -+ obsharedptr p(pmol); - pReact->AddReactant(p); - } - } -@@ -189,7 +189,7 @@ bool RXNFormat::ReadMolecule(OBBase* pOb - else - { - // pReact->products.push_back(pmol); -- shared_ptr p(pmol); -+ obsharedptr 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 > MolMap; -- string AddMolToList(shared_ptr spmol, MolMap& mmap); -+ typedef map > MolMap; -+ string AddMolToList(obsharedptr spmol, MolMap& mmap); - bool WriteRateData(OBReaction* pReact, xmlChar* altprefix); - void WriteMetadataList(OBReaction& react); - - private: - OBReaction* _preact; - OBMol* pmol; -- shared_ptr _spmol; -+ obsharedptr _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 sp(new OBMol); -+ obsharedptr sp(new OBMol); - sp.get()->SetTitle("M"); - IMols["M"] = sp; - } -@@ -192,7 +192,7 @@ bool CMLReactFormat::DoElement(const str - } - else - { -- shared_ptr sp(new OBMol); -+ obsharedptr sp(new OBMol); - OBFormat* pCMLFormat = OBConversion::FindFormat("cml"); - if(!pCMLFormat) - return false; -@@ -331,7 +331,7 @@ bool CMLReactFormat::WriteChemObject(OBC - OBMol* pmol = dynamic_cast(pOb); - if(pmol!=NULL) - { -- shared_ptr sp(pmol); -+ obsharedptr 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 spmol, MolMap& mmap) -+string CMLReactFormat::AddMolToList(obsharedptr 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 spnew(OBMoleculeFormat::MakeCombinedMolecule(mapitr->second.get(), spmol.get())); -+ obsharedptr 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 > mols; -+ vector > mols; - unsigned i; - for(i=0;iNumReactants();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 OBMolPtr; -+typedef obsharedptr OBMolPtr; - - struct OBTestUtil - { Index: head/science/openbabel/files/patch-git_c3abbdda =================================================================== --- head/science/openbabel/files/patch-git_c3abbdda +++ head/science/openbabel/files/patch-git_c3abbdda @@ -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 -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 - #endif - --#if __GNUC__ == 4 && __GNUC_MINOR__ >= 1 -+#include // detect std::lib -+#ifdef _LIBCPP_VERSION -+ #include -+#elif __GNUC__ == 4 && __GNUC_MINOR__ >= 1 - #include - #elif defined(USE_BOOST) - #include -@@ -141,6 +144,8 @@ public: - - #ifdef _MSC_VER - typedef stdext::hash_map NameIndexType; -+#elif defined(_LIBCPP_VERSION) -+ typedef std::unordered_map NameIndexType; - #elif (__GNUC__ == 4 && __GNUC_MINOR__ >= 1 && !defined(__APPLE_CC__)) || defined (USE_BOOST) - typedef std::tr1::unordered_map 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 - #include - #include --#ifdef _MSC_VER -+#if defined(_MSC_VER) || defined(_LIBCPP_VERSION) - #include - #elif (__GNUC__ == 4 && __GNUC_MINOR__ >= 1 && !defined(__APPLE_CC__)) - #include -@@ -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 - { Index: head/science/openbabel/files/patch-scripts__CMakeLists.txt =================================================================== --- head/science/openbabel/files/patch-scripts__CMakeLists.txt +++ head/science/openbabel/files/patch-scripts__CMakeLists.txt @@ -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 Index: head/science/openbabel/pkg-plist =================================================================== --- head/science/openbabel/pkg-plist +++ head/science/openbabel/pkg-plist @@ -2,6 +2,7 @@ bin/obabel bin/obchiral bin/obconformer +bin/obdistgen bin/obenergy bin/obfit bin/obgen @@ -13,6 +14,9 @@ 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/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/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/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.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%%/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%%/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%%/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%%/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%%/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_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/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 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