FreeBSD Bugzilla – Attachment 182702 Details for
Bug 219382
science/openbabel: Update to 2.4.1
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[patch]
patch
openbabel.patch (text/plain), 45.96 KB, created by
Yuri Victorovich
on 2017-05-18 15:04:17 UTC
(
hide
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Description:
patch
Filename:
MIME Type:
Creator:
Yuri Victorovich
Created:
2017-05-18 15:04:17 UTC
Size:
45.96 KB
patch
obsolete
>Index: science/openbabel/Makefile >=================================================================== >--- science/openbabel/Makefile (revision 439698) >+++ science/openbabel/Makefile (working copy) >@@ -2,8 +2,7 @@ > # $FreeBSD$ > > PORTNAME= openbabel >-PORTVERSION= 2.3.2 >-PORTREVISION= 2 >+PORTVERSION= 2.4.1 > CATEGORIES= science > MASTER_SITES= SF > >Index: science/openbabel/distinfo >=================================================================== >--- science/openbabel/distinfo (revision 439698) >+++ science/openbabel/distinfo (working copy) >@@ -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: science/openbabel/files/patch-doc_CMakeLists.txt >=================================================================== >--- science/openbabel/files/patch-doc_CMakeLists.txt (nonexistent) >+++ science/openbabel/files/patch-doc_CMakeLists.txt (working copy) >@@ -0,0 +1,9 @@ >+--- doc/CMakeLists.txt.orig 2017-05-18 05:46:23 UTC >++++ doc/CMakeLists.txt >+@@ -1,5 +1,5 @@ >+ file(GLOB man_1 *.1) >+-install(FILES ${man_1} DESTINATION "${BABEL_DATAROOTDIR}/man/man1") >++install(FILES ${man_1} DESTINATION "${BABEL_DATAROOTDIR}/../man/man1") >+ install(FILES splash.png DESTINATION "${BABEL_DATADIR}/${BABEL_VERSION}") >+ >+ OPTION(BUILD_DOCS "Build Open Babel documentation" OFF) > >Property changes on: science/openbabel/files/patch-doc_CMakeLists.txt >___________________________________________________________________ >Added: fbsd:nokeywords >## -0,0 +1 ## >+yes >\ No newline at end of property >Added: svn:eol-style >## -0,0 +1 ## >+native >\ No newline at end of property >Added: svn:mime-type >## -0,0 +1 ## >+text/plain >\ No newline at end of property >Index: science/openbabel/files/patch-gcc5-support >=================================================================== >--- science/openbabel/files/patch-gcc5-support (revision 439698) >+++ science/openbabel/files/patch-gcc5-support (nonexistent) >@@ -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 >- { > >Property changes on: science/openbabel/files/patch-gcc5-support >___________________________________________________________________ >Deleted: fbsd:nokeywords >## -1 +0,0 ## >-yes >\ No newline at end of property >Deleted: svn:eol-style >## -1 +0,0 ## >-native >\ No newline at end of property >Deleted: svn:mime-type >## -1 +0,0 ## >-text/plain >\ No newline at end of property >Index: science/openbabel/files/patch-git_c3abbdda >=================================================================== >--- science/openbabel/files/patch-git_c3abbdda (revision 439698) >+++ science/openbabel/files/patch-git_c3abbdda (nonexistent) >@@ -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 >- { > >Property changes on: science/openbabel/files/patch-git_c3abbdda >___________________________________________________________________ >Deleted: fbsd:nokeywords >## -1 +0,0 ## >-yes >\ No newline at end of property >Deleted: svn:eol-style >## -1 +0,0 ## >-native >\ No newline at end of property >Deleted: svn:mime-type >## -1 +0,0 ## >-text/plain >\ No newline at end of property >Index: science/openbabel/files/patch-scripts__CMakeLists.txt >=================================================================== >--- science/openbabel/files/patch-scripts__CMakeLists.txt (revision 439698) >+++ science/openbabel/files/patch-scripts__CMakeLists.txt (nonexistent) >@@ -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 > >Property changes on: science/openbabel/files/patch-scripts__CMakeLists.txt >___________________________________________________________________ >Deleted: fbsd:nokeywords >## -1 +0,0 ## >-yes >\ No newline at end of property >Deleted: svn:eol-style >## -1 +0,0 ## >-native >\ No newline at end of property >Deleted: svn:mime-type >## -1 +0,0 ## >-text/plain >\ No newline at end of property >Index: science/openbabel/pkg-plist >=================================================================== >--- science/openbabel/pkg-plist (revision 439698) >+++ science/openbabel/pkg-plist (working copy) >@@ -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 >@@ -182,10 +201,12 @@ > 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 >@@ -192,7 +213,10 @@ > 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 >-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
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: 182702