rendered paste bodydiff -u -r -N openbabel-2.1.1-msys/CMakeLists.txt openbabel-2.1.1/CMakeLists.txt
--- openbabel-2.1.1-msys/CMakeLists.txt 1970-01-01 01:00:00.000000000 +0100
+++ openbabel-2.1.1/CMakeLists.txt 2007-11-03 14:06:16.186625000 +0100
@@ -0,0 +1,60 @@
+project(openabel)
+set(BABEL_MAJ_VER 2)
+set(BABEL_MIN_VER 1)
+set(BABEL_PATCH_VER 1)
+set(BABEL_VERSION "${BABEL_MAJ_VER}.${BABEL_MIN_VER}.${BABEL_PATCH_VER}")
+set(BABEL_DATADIR "{CMAKE_INSTALL_PREFIX}/share/openbabel")
+
+option(WITH_INCHI "build inchi lib" ON)
+option(BUILD_SHARED "enable static build support" ON)
+if(BUILD_SHARED)
+ set(BUILD_TYPE SHARED)
+else(BUILD_SHARED)
+ set(BUILD_TYPE STATIC)
+endif(BUILD_SHARED)
+
+if(WIN32)
+ set(MODULE_EXTENSION ".dll")
+else(WIN32)
+ set(MODULE_EXTENSION ".so")
+endif(WIN32)
+
+# configure checks
+find_package(LibXml2)
+find_package(ZLIB)
+if(ZLIB_FOUND)
+ add_definitions(-DHAVE_LIBZ)
+ include_directories(${ZLIB_INCLUDE_DIR})
+endif(ZLIB_FOUND)
+
+include(CheckIncludeFile)
+include(CheckIncludeFileCXX)
+include(CheckSymbolExists)
+include(CheckTypeSize)
+
+check_include_file(conio.h HAVE_CONIO_H)
+check_include_file(sys/time.h HAVE_SYS_TIME_H)
+check_include_file(time.h HAVE_TIME_H)
+check_include_file_cxx(sstream HAVE_SSTREAM)
+
+check_symbol_exists(rint "math.h" HAVE_RINT)
+check_symbol_exists(snprintf "stdio.h" HAVE_SNPRINTF)
+check_symbol_exists(sranddev "stdlib.h" HAVE_SRANDDEV)
+check_symbol_exists(strcasecmp "string.h" HAVE_STRCASECMP)
+check_symbol_exists(strncasecmp "string.h" HAVE_STRNCASECMP)
+
+set(CMAKE_EXTRA_INCLUDE_FILES time.h)
+check_type_size(clock_t CLOCK_T)
+
+configure_file(${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_BINARY_DIR}/include/openbabel/babelconfig.h)
+install(FILES ${CMAKE_BINARY_DIR}/include/openbabel/babelconfig.h DESTINATION include/openbabel-2.0/openbabel)
+
+include_directories(${CMAKE_SOURCE_DIR}/include
+ ${CMAKE_SOURCE_DIR}/data
+ ${CMAKE_BINARY_DIR}/include
+)
+
+add_subdirectory(include)
+add_subdirectory(data)
+add_subdirectory(src)
+
diff -u -r -N openbabel-2.1.1-msys/data/CMakeLists.txt openbabel-2.1.1/data/CMakeLists.txt
--- openbabel-2.1.1-msys/data/CMakeLists.txt 1970-01-01 01:00:00.000000000 +0100
+++ openbabel-2.1.1/data/CMakeLists.txt 2007-11-03 13:35:54.253000000 +0100
@@ -0,0 +1,11 @@
+
+set(to_install
+ aromatic.txt bondtyp.txt isotope.txt resdata.txt
+ atomtyp.txt element.txt isotope-small.txt phmodel.txt
+ patterns.txt torlib.txt types.txt
+ SMARTS_InteLigand.txt
+ ghemical.prm
+ logp.txt psa.txt mr.txt
+)
+
+install(FILES ${to_install} DESTINATION share/openbabel/${BABEL_VERSION})
diff -u -r -N openbabel-2.1.1-msys/include/CMakeLists.txt openbabel-2.1.1/include/CMakeLists.txt
--- openbabel-2.1.1-msys/include/CMakeLists.txt 1970-01-01 01:00:00.000000000 +0100
+++ openbabel-2.1.1/include/CMakeLists.txt 2007-11-03 13:23:40.852625000 +0100
@@ -0,0 +1,7 @@
+
+file(GLOB openbabel_headers openbabel/*.h)
+file(GLOB math_headers openbabel/math/*.h)
+
+install(FILES inchi_api.h DESTINATION include/inchi)
+install(FILES ${openbabel_headers} DESTINATION include/openbabel-2.0/openbabel)
+install(FILES ${math_headers} DESTINATION include/openbabel-2.0/openbabel/math)
diff -u -r -N openbabel-2.1.1-msys/Makefile.in openbabel-2.1.1/Makefile.in
--- openbabel-2.1.1-msys/Makefile.in 2007-11-03 13:27:41.383875000 +0100
+++ openbabel-2.1.1/Makefile.in 2007-07-01 22:11:22.000000000 +0200
@@ -69,7 +69,7 @@
distclean-recursive maintainer-clean-recursive
ETAGS = etags
CTAGS = ctags
-DIST_SUBDIRS = data src include
+DIST_SUBDIRS = data src test tools doc include scripts
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
top_distdir = $(distdir)
@@ -207,7 +207,7 @@
# only build in the scripts subdirectory if possible (perl, python, swig, etc.)
@BUILD_SCRIPTS_TRUE@SCRIPT_DIR = scripts
-SUBDIRS = data src include
+SUBDIRS = data src test tools doc include $(SCRIPT_DIR)
EXTRA_DIST = Doxyfile windows-vc2005
AUTOMAKE_OPTIONS = foreign
pkgconfigdir = $(libdir)/pkgconfig
diff -u -r -N openbabel-2.1.1-msys/src/CMakeLists.txt openbabel-2.1.1/src/CMakeLists.txt
--- openbabel-2.1.1-msys/src/CMakeLists.txt 1970-01-01 01:00:00.000000000 +0100
+++ openbabel-2.1.1/src/CMakeLists.txt 2007-11-03 17:49:07.653500000 +0100
@@ -0,0 +1,172 @@
+if(WITH_INCHI)
+ add_definitions(-DINCHI_LINK_AS_DLL)
+ add_subdirectory(formats/inchi)
+endif(WITH_INCHI)
+
+set(fingerprints_srcs
+ fingerprints/finger2.cpp
+ fingerprints/finger3.cpp
+)
+
+set(forcefields_srcs
+ forcefields/forcefieldghemical.cpp
+)
+
+set(formats_srcs
+ formats/APIInterface.cpp
+ formats/obmolecformat.cpp
+ formats/CSRformat.cpp
+ formats/PQSformat.cpp
+ formats/alchemyformat.cpp
+ formats/acrformat.cpp
+ formats/amberformat.cpp
+ formats/balstformat.cpp
+ formats/bgfformat.cpp
+ formats/boxformat.cpp
+ formats/cacaoformat.cpp
+ formats/cacheformat.cpp
+ formats/carformat.cpp
+ formats/cccformat.cpp
+ formats/chem3dformat.cpp
+ formats/chemdrawct.cpp
+ formats/chemdrawcdx.cpp
+ formats/chemtoolformat.cpp
+ formats/cifformat.cpp
+ formats/copyformat.cpp
+ formats/crkformat.cpp
+ formats/cssrformat.cpp
+ formats/dmolformat.cpp
+ formats/fastsearchformat.cpp
+ formats/fastaformat.cpp
+ formats/fchkformat.cpp
+ formats/featformat.cpp
+ formats/fhformat.cpp
+ formats/fingerprintformat.cpp
+ formats/freefracformat.cpp
+ formats/gamessformat.cpp
+ formats/gaussformat.cpp
+ formats/ghemicalformat.cpp
+ formats/gromos96format.cpp
+ formats/hinformat.cpp
+ formats/jaguarformat.cpp
+ formats/mdlformat.cpp
+ formats/mmodformat.cpp
+ formats/mol2format.cpp
+ formats/molreport.cpp
+ formats/mopacformat.cpp
+ formats/mpdformat.cpp
+ formats/mpqcformat.cpp
+ formats/nwchemformat.cpp
+ formats/pcmodelformat.cpp
+ formats/pdbformat.cpp
+ formats/povrayformat.cpp
+ formats/qchemformat.cpp
+ formats/reportformat.cpp
+ formats/rxnformat.cpp
+ formats/shelxformat.cpp
+ formats/smilesformat.cpp
+ formats/thermoformat.cpp
+ formats/tinkerformat.cpp
+ formats/titleformat.cpp
+ formats/turbomoleformat.cpp
+ formats/unichemformat.cpp
+ formats/viewmolformat.cpp
+ formats/xedformat.cpp
+ formats/xyzformat.cpp
+ formats/yasaraformat.cpp
+ formats/zindoformat.cpp
+)
+
+if(WITH_INCHI)
+ set(formats_srcs
+ ${formats_srcs}
+ formats/getinchi.cpp
+ formats/inchiformat.cpp
+ )
+ set(libs ${libs} inchi)
+endif(WITH_INCHI)
+
+if(LIBXML2_FOUND)
+ include_directories(${LIBXML2_INCLUDE_DIR})
+ set(xml_srcs
+ formats/xml/cdxmlformat.cpp
+ formats/xml/cmlformat.cpp
+ formats/xml/cmlreactlformat.cpp
+ formats/xml/pubchem.cpp
+ formats/xml/xmlformat.cpp
+ formats/xml/xml.cpp
+ )
+endif(LIBXML2_FOUND)
+
+set(math_srcs
+ math/matrix3x3.cpp
+ math/vector3.cpp
+)
+
+set(openbabel_srcs
+ atom.cpp
+ base.cpp
+ bitvec.cpp
+ bond.cpp
+ bondtyper.cpp
+ canon.cpp
+ chains.cpp
+ chiral.cpp
+ data.cpp
+ fingerprint.cpp
+ forcefield.cpp
+ generic.cpp
+ grid.cpp
+ kekulize.cpp
+ matrix.cpp
+ mol.cpp
+ molchrg.cpp
+ obconversion.cpp
+ oberror.cpp
+ obiter.cpp
+ obutil.cpp
+ parsmart.cpp
+ patty.cpp
+ phmodel.cpp
+ rand.cpp
+ residue.cpp
+ ring.cpp
+ rotor.cpp
+ rotamer.cpp
+ tokenst.cpp
+ typer.cpp
+ transform.cpp
+ groupcontrib.cpp
+)
+
+if(BUILD_SHARED)
+ if(WIN32)
+ set(openbabel_srcs ${openbabel_srcs}
+ dlhandler_win32.cpp
+ )
+ else(WIN32)
+ set(openbabel_srcs ${openbabel_srcs}
+ dlhandler_unix.cpp
+ )
+ endif(WIN32)
+endif(BUILD_SHARED)
+
+add_library(openbabel-2 ${BUILD_TYPE}
+ ${openbabel_srcs}
+ ${fingerprints_srcs}
+ ${forcefields_srcs}
+ ${formats_srcs}
+ ${xml_srcs}
+ ${math_srcs}
+)
+
+if(NOT WIN32)
+ set(libs ${libs} m)
+endif(NOT WIN32)
+
+target_link_libraries(openbabel-2 ${libs} ${LIBXML2_LIBRARIES} ${ZLIB_LIBRARY})
+install(TARGETS openbabel-2
+ RUNTIME DESTINATION bin
+ LIBRARY DESTINATION lib
+ ARCHIVE DESTINATION lib
+)
diff -u -r -N openbabel-2.1.1-msys/src/config.h.cmake openbabel-2.1.1/src/config.h.cmake
--- openbabel-2.1.1-msys/src/config.h.cmake 1970-01-01 01:00:00.000000000 +0100
+++ openbabel-2.1.1/src/config.h.cmake 2007-11-03 17:38:27.101000000 +0100
@@ -0,0 +1,151 @@
+/* src/config.h.in. Generated from configure.in by autoheader. */
+
+/* Where the data files are located */
+#define BABEL_DATADIR "@BABEL_DATADIR@"
+
+/* The version of Open Babel */
+#define BABEL_VERSION "@BABEL_VERSION@"
+
+/* Used to export symbols for DLL / shared library builds */
+#if defined(WIN32)
+ #if defined(USING_OBDLL) // e.g. in src/main.cpp
+ #define EXTERN __declspec(dllimport) extern
+ #else
+ #define EXTERN __declspec(dllexport) extern
+ #endif
+#else //Everything else (behaviour as original)
+ #define EXTERN extern
+#endif
+
+/* The file extension used for shared modules */
+#define MODULE_EXTENSION "@MODULE_EXTENSION@"
+
+/* Used to export symbols for DLL / shared library builds */
+#if defined(WIN32)
+ #if defined(USING_OBDLL) // e.g. in src/main.cpp
+ #define OBAPI __declspec(dllimport)
+ #else
+ #define OBAPI __declspec(dllexport)
+ #endif
+#else //Everything else (behaviour as original)
+ #define OBAPI
+#endif
+
+
+/* Used to export symbols for DLL / shared library builds */
+#if defined(WIN32)
+ #if defined(USING_OBDLL) // e.g. in src/main.cpp
+ #define OBCOMMON __declspec(dllimport)
+ #else
+ #define OBCOMMON __declspec(dllexport)
+ #endif
+#else //Everything else (behaviour as original)
+ #define OBCOMMON
+#endif
+
+
+/* Used to export symbols for DLL / shared library builds */
+#if defined(WIN32)
+ #if defined(USING_OBDLL) // e.g. in src/main.cpp
+ #define OBCONV __declspec(dllimport)
+ #else
+ #define OBCONV __declspec(dllexport)
+ #endif
+#else //Everything else (behaviour as original)
+ #define OBCONV
+#endif
+
+
+/* Used to export symbols for DLL / shared library builds */
+#if defined(WIN32)
+ #if defined(USING_OBDLL) // e.g. in src/main.cpp
+ #define OBERROR __declspec(dllimport)
+ #else
+ #define OBERROR __declspec(dllexport)
+ #endif
+#else //Everything else (behaviour as original)
+ #define OBERROR
+#endif
+
+
+/* Used to export symbols for DLL / shared library builds */
+#if defined(WIN32)
+ #if defined(USING_OBDLL) // e.g. in src/main.cpp
+ #define OBFPTR __declspec(dllimport)
+ #else
+ #define OBFPTR __declspec(dllexport)
+ #endif
+#else //Everything else (behaviour as original)
+ #define OBFPTR
+#endif
+
+#ifdef _MSC_VER
+ // Supress warning on deprecated functions
+ #pragma warning(disable : 4996)
+ // Supress warning that compiler is ignoring C++ exception specification
+ #pragma warning( disable : 4290 )
+ // Supress warning on signed/unsigned comparison with < or > (harmless, but maybe should be fixed)
+ #pragma warning( disable : 4018 )
+ // Supress warning on unreferenced formal parameter
+ #pragma warning( disable : 4100 )
+ //
+ #pragma warning( disable : 4251 )
+
+
+ #include <crtdbg.h>
+
+ #ifdef _DEBUG
+ #define DEBUG_NEW new(_NORMAL_BLOCK, THIS_FILE, __LINE__)
+ #else
+ #define DEBUG_NEW new
+ #endif
+#endif // _MSC_VER
+/* have <conio.h> */
+#cmakedefine HAVE_CONIO_H 1
+
+/* have <sys/time.h> */
+#cmakedefine HAVE_SYS_TIME_H 1
+
+/* have <time.h> */
+#cmakedefine HAVE_TIME_H 1
+
+/* have <sstream> */
+#cmakedefine HAVE_SSTREAM 1
+
+/* have symbol clock_t */
+#cmakedefine HAVE_CLOCK_T 1
+
+/* have symbol rint */
+#cmakedefine HAVE_RINT 1
+
+/* have symbol snprintf */
+#cmakedefine HAVE_SNPRINTF 1
+
+/* have symbol sranddev */
+#cmakedefine HAVE_SRANDDEV 1
+
+/* have symbol strcasecmp */
+#cmakedefine HAVE_STRCASECMP 1
+
+/* have symbol strncasecmp */
+#cmakedefine HAVE_STRNCASECMP 1
+
+/* have struct clock_t */
+#cmakedefine HAVE_CLOCK_T 1
+
+#if defined(WIN32)
+ #ifndef HAVE_SNPRINTF
+ #define snprintf _snprintf
+ #define HAVE_SNPRINTF 1
+ #endif
+
+ #ifndef HAVE_STRCASECMP
+ #define strcasecmp _stricmp
+ #define HAVE_STRCASECMP 1
+ #endif
+
+ #ifndef HAVE_STRNCASECMP
+ #define strncasecmp _strnicmp
+ #define HAVE_STRNCASECMP 1
+ #endif
+#endif // WIN32
diff -u -r -N openbabel-2.1.1-msys/src/fingerprints/finger3.cpp openbabel-2.1.1/src/fingerprints/finger3.cpp
--- openbabel-2.1.1-msys/src/fingerprints/finger3.cpp 2007-07-05 06:26:18.000000000 +0200
+++ openbabel-2.1.1/src/fingerprints/finger3.cpp 2007-11-02 21:37:02.540500000 +0100
@@ -18,6 +18,11 @@
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
+#ifdef HAVE_SSTREAM
+#include <sstream>
+#else
+#include <strstream>
+#endif
#include <fstream>
#include <map>
#include <string>
diff -u -r -N openbabel-2.1.1-msys/src/formats/inchi/CMakeLists.txt openbabel-2.1.1/src/formats/inchi/CMakeLists.txt
--- openbabel-2.1.1-msys/src/formats/inchi/CMakeLists.txt 1970-01-01 01:00:00.000000000 +0100
+++ openbabel-2.1.1/src/formats/inchi/CMakeLists.txt 2007-11-03 17:48:40.887875000 +0100
@@ -0,0 +1,17 @@
+set(inchi_srcs
+ ichi_bns.c ichican2.c ichicano.c ichicans.c ichiisot.c
+ ichilnct.c ichimak2.c ichimake.c ichimap1.c ichimap2.c
+ ichimap4.c ichinorm.c ichiparm.c ichiprt1.c ichiprt2.c
+ ichiprt3.c ichiqueu.c ichiread.c ichiring.c ichirvr1.c
+ ichirvr2.c ichirvr3.c ichirvr4.c ichirvr5.c ichirvr6.c
+ ichirvr7.c ichisort.c ichister.c ichitaut.c inchi_dll.c
+ inchi_dll_main.c runichi.c strutil.c util.c
+)
+include_directories(${CMAKE_SOURCE_DIR}/include/inchi)
+add_library(inchi SHARED ${inchi_srcs})
+set_target_properties(inchi PROPERTIES DEFINE_SYMBOL _USRDLL)
+install(TARGETS inchi
+ inchi DESTINATION bin
+ LIBRARY DESTINATION lib
+ ARCHIVE DESTINATION lib
+)
diff -u -r -N openbabel-2.1.1-msys/src/formats/inchiformat.cpp openbabel-2.1.1/src/formats/inchiformat.cpp
--- openbabel-2.1.1-msys/src/formats/inchiformat.cpp 2007-07-07 08:35:54.000000000 +0200
+++ openbabel-2.1.1/src/formats/inchiformat.cpp 2007-11-02 21:44:30.842000000 +0100
@@ -21,7 +21,11 @@
#include <openbabel/obmolecformat.h>
#include "inchi_api.h"
+#ifdef HAVE_SSTREAM
#include <sstream>
+#else
+#include <strstream>
+#endif
#include <set>
#include <vector>
#include "openbabel/chiral.h"
diff -u -r -N openbabel-2.1.1-msys/src/formats/xml/cmlformat.cpp openbabel-2.1.1/src/formats/xml/cmlformat.cpp
--- openbabel-2.1.1-msys/src/formats/xml/cmlformat.cpp 2007-04-14 02:34:14.000000000 +0200
+++ openbabel-2.1.1/src/formats/xml/cmlformat.cpp 2007-11-02 21:45:26.607625000 +0100
@@ -23,6 +23,11 @@
#ifdef WIN32
#pragma warning (disable : 4800)
#endif
+#ifdef HAVE_SSTREAM
+#include <sstream>
+#else
+#include <strstream>
+#endif
using namespace std;
namespace OpenBabel