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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<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
- {
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 <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
- {
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
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