diff --git a/ChangeLog b/ChangeLog index 475b2831a..a8f701d7d 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,9 +1,17 @@ +2006-12-10 Geoffrey Hutchison + + * include/openbabel: New directory for public headers. Ensures + internal and external code use the same + #include syntax. + + Also, all related UNIX-based build changes. + 2006-12-04 Vincent Favre-Nicolin * src/format/ciffformat.cpp: Added new OBFormat-derived class to - handle Crystallographic Information Files. Initial implementation - handles reading & writing atomic coordinates, reading unit cell - and spacegroup name but no interpretation of symmetry is done. + handle Crystallographic Information Files. Initial implementation + handles reading & writing atomic coordinates, reading unit cell + and spacegroup name but no interpretation of symmetry is done. 2006-12-04 Benoit Jacob @@ -12,10 +20,20 @@ 2006-12-08 Geoffrey Hutchison * src/generic.h, src/generic.cpp (OBRingData): Add new methods for - iterating over rings. + iterating over rings. (OBAngleData): Modifications from Tim + Vandermeersch to facilitate iteration over angles in an OBMol. - * src/obiter.h, src/obiter.cpp: New class OBMolRingIter and - FOR_RINGS_OF_MOL macro. + * src/mol.h, src/mol.cpp (FindAngles()): New method to parallel + FindTorsions() for filling an OBAngleData record in an OBMol, + contributed by Tim. + + * src/obiter.h, src/obiter.cpp: New classes and macros, including + FOR_RINGS_OF_MOL, FOR_ANGLES_OF_MOL, FOR_TORSIONS_OF_MOL + FOR_PAIRS_OF_MOL, contributed by Tim. + + * src/forcefield.h, src/forcefield.cpp, src/Makefile.am, + src/Makefile.in: New classes for mol. mechanics force fields + contributed by Tim Vandermeersch. 2006-12-07 Geoffrey Hutchison diff --git a/Doxyfile b/Doxyfile index 8bfe966ad..baa03b064 100644 --- a/Doxyfile +++ b/Doxyfile @@ -459,9 +459,8 @@ WARN_LOGFILE = # directories like "/usr/src/myproject". Separate the files or directories # with spaces. -INPUT = src/ \ - src/formats/obmolecformat.h \ - src/math/ +INPUT = include/openbabel include/openbabel/math \ + src/ src/math # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp diff --git a/configure b/configure index 4945b473b..726d89454 100755 --- a/configure +++ b/configure @@ -23422,10 +23422,10 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext { echo "$as_me:$LINENO: result: $scandirconst_cast" >&5 echo "${ECHO_T}$scandirconst_cast" >&6; } -ac_config_commands="$ac_config_commands src/babelconfig.h" +ac_config_commands="$ac_config_commands include/openbabel/babelconfig.h" -ac_config_files="$ac_config_files Makefile data/Makefile src/Makefile src/math/Makefile src/formats/Makefile src/fingerprints/Makefile src/formats/xml/Makefile src/formats/inchi/Makefile src/GUI/Makefile test/Makefile test/cmltest/Makefile tools/Makefile doc/Makefile scripts/Makefile openbabel-2.0.pc" +ac_config_files="$ac_config_files Makefile data/Makefile src/Makefile src/math/Makefile src/formats/Makefile src/fingerprints/Makefile src/formats/xml/Makefile src/formats/inchi/Makefile src/GUI/Makefile include/Makefile include/openbabel/Makefile test/Makefile test/cmltest/Makefile tools/Makefile doc/Makefile scripts/Makefile openbabel-2.0.pc" cat >confcache <<\_ACEOF # This file is a shell script that caches the results of configure @@ -24083,7 +24083,7 @@ do case $ac_config_target in "src/config.h") CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;; "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "src/babelconfig.h") CONFIG_COMMANDS="$CONFIG_COMMANDS src/babelconfig.h" ;; + "include/openbabel/babelconfig.h") CONFIG_COMMANDS="$CONFIG_COMMANDS include/openbabel/babelconfig.h" ;; "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; "data/Makefile") CONFIG_FILES="$CONFIG_FILES data/Makefile" ;; "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;; @@ -24093,6 +24093,8 @@ do "src/formats/xml/Makefile") CONFIG_FILES="$CONFIG_FILES src/formats/xml/Makefile" ;; "src/formats/inchi/Makefile") CONFIG_FILES="$CONFIG_FILES src/formats/inchi/Makefile" ;; "src/GUI/Makefile") CONFIG_FILES="$CONFIG_FILES src/GUI/Makefile" ;; + "include/Makefile") CONFIG_FILES="$CONFIG_FILES include/Makefile" ;; + "include/openbabel/Makefile") CONFIG_FILES="$CONFIG_FILES include/openbabel/Makefile" ;; "test/Makefile") CONFIG_FILES="$CONFIG_FILES test/Makefile" ;; "test/cmltest/Makefile") CONFIG_FILES="$CONFIG_FILES test/cmltest/Makefile" ;; "tools/Makefile") CONFIG_FILES="$CONFIG_FILES tools/Makefile" ;; @@ -24906,7 +24908,7 @@ echo "$as_me: error: cannot create directory $as_dir" >&2;} done done ;; - "src/babelconfig.h":C) grep -v PACKAGE src/config.h >src/babelconfig.h ;; + "include/openbabel/babelconfig.h":C) grep -v PACKAGE src/config.h >include/openbabel/babelconfig.h ;; esac done # for ac_tag diff --git a/configure.in b/configure.in index 81f9b3b0f..a9e8c9c49 100644 --- a/configure.in +++ b/configure.in @@ -257,13 +257,13 @@ scandirconst_cast=yes]) AC_MSG_RESULT([$scandirconst_cast], [set if scandir needs a const]) -AC_CONFIG_COMMANDS([src/babelconfig.h], - [grep -v PACKAGE src/config.h >src/babelconfig.h]) +AC_CONFIG_COMMANDS([include/openbabel/babelconfig.h], + [grep -v PACKAGE src/config.h >include/openbabel/babelconfig.h]) AC_OUTPUT(Makefile data/Makefile src/Makefile src/math/Makefile \ src/formats/Makefile src/fingerprints/Makefile \ src/formats/xml/Makefile src/formats/inchi/Makefile \ - src/GUI/Makefile \ + src/GUI/Makefile include/Makefile include/openbabel/Makefile \ test/Makefile test/cmltest/Makefile tools/Makefile \ doc/Makefile scripts/Makefile openbabel-2.0.pc) diff --git a/src/atom.h b/include/openbabel/atom.h similarity index 99% rename from src/atom.h rename to include/openbabel/atom.h index a38751a14..1eb950228 100644 --- a/src/atom.h +++ b/include/openbabel/atom.h @@ -21,7 +21,7 @@ GNU General Public License for more details. #ifndef OB_ATOM_H #define OB_ATOM_H -#include "babelconfig.h" +#include #ifndef EXTERN # define EXTERN extern @@ -30,8 +30,8 @@ GNU General Public License for more details. #include #include -#include "base.h" -#include "residue.h" +#include +#include namespace OpenBabel { diff --git a/src/base.h b/include/openbabel/base.h similarity index 98% rename from src/base.h rename to include/openbabel/base.h index 1d1e8ce30..da47cd6b7 100644 --- a/src/base.h +++ b/include/openbabel/base.h @@ -20,14 +20,14 @@ GNU General Public License for more details. #ifndef OB_BASE_H #define OB_BASE_H -#include "babelconfig.h" +#include #include #include #include -#include "generic.h" +#include namespace OpenBabel { diff --git a/src/bitvec.h b/include/openbabel/bitvec.h similarity index 99% rename from src/bitvec.h rename to include/openbabel/bitvec.h index 761457226..56d8af724 100644 --- a/src/bitvec.h +++ b/include/openbabel/bitvec.h @@ -20,7 +20,7 @@ GNU General Public License for more details. #ifndef OB_BITVEC_H #define OB_BITVEC_H -#include "babelconfig.h" +#include #ifdef WIN32 #pragma warning (disable : 4786) diff --git a/src/bond.h b/include/openbabel/bond.h similarity index 99% rename from src/bond.h rename to include/openbabel/bond.h index 9d243ba22..fcfa91c78 100644 --- a/src/bond.h +++ b/include/openbabel/bond.h @@ -21,14 +21,14 @@ GNU General Public License for more details. #ifndef OB_BOND_H #define OB_BOND_H -#include "babelconfig.h" +#include #ifndef EXTERN # define EXTERN extern #endif -#include "base.h" -#include "atom.h" +#include +#include namespace OpenBabel { diff --git a/src/bondtyper.h b/include/openbabel/bondtyper.h similarity index 96% rename from src/bondtyper.h rename to include/openbabel/bondtyper.h index 9c33c926e..46ef8d690 100644 --- a/src/bondtyper.h +++ b/include/openbabel/bondtyper.h @@ -19,8 +19,8 @@ GNU General Public License for more details. #ifndef OB_BONDTYPER_H #define OB_BONDTYPER_H -#include "parsmart.h" -#include "data.h" +#include +#include namespace OpenBabel { diff --git a/src/chains.h b/include/openbabel/chains.h similarity index 100% rename from src/chains.h rename to include/openbabel/chains.h diff --git a/src/chiral.h b/include/openbabel/chiral.h similarity index 98% rename from src/chiral.h rename to include/openbabel/chiral.h index 3effc3cc6..051c5794a 100644 --- a/src/chiral.h +++ b/include/openbabel/chiral.h @@ -21,7 +21,7 @@ GNU General Public License for more details. #define OB_CHIRAL_H #include -#include "matrix.h" +#include namespace OpenBabel { diff --git a/src/data.h b/include/openbabel/data.h similarity index 99% rename from src/data.h rename to include/openbabel/data.h index f6e8d6082..494a4d84b 100644 --- a/src/data.h +++ b/include/openbabel/data.h @@ -20,7 +20,7 @@ GNU General Public License for more details. #ifndef OB_DATA_H #define OB_DATA_H -#include "babelconfig.h" +#include #include diff --git a/src/dlhandler.h b/include/openbabel/dlhandler.h similarity index 98% rename from src/dlhandler.h rename to include/openbabel/dlhandler.h index 3f6ae3f68..9f85264da 100644 --- a/src/dlhandler.h +++ b/include/openbabel/dlhandler.h @@ -19,7 +19,7 @@ GNU General Public License for more details. #ifndef OB_DLHANDLER_H #define OB_DLHANDLER_H -#include "babelconfig.h" +#include #include #include diff --git a/src/fingerprint.h b/include/openbabel/fingerprint.h similarity index 100% rename from src/fingerprint.h rename to include/openbabel/fingerprint.h diff --git a/src/forcefield.h b/include/openbabel/forcefield.h similarity index 99% rename from src/forcefield.h rename to include/openbabel/forcefield.h index acf204088..67ee672d9 100644 --- a/src/forcefield.h +++ b/include/openbabel/forcefield.h @@ -24,8 +24,8 @@ GNU General Public License for more details. #include #include -#include "base.h" -#include "mol.h" +#include +#include namespace OpenBabel { diff --git a/src/generic.h b/include/openbabel/generic.h similarity index 99% rename from src/generic.h rename to include/openbabel/generic.h index 7d13eb115..2949136b9 100644 --- a/src/generic.h +++ b/include/openbabel/generic.h @@ -20,14 +20,14 @@ GNU General Public License for more details. #ifndef OB_GENERIC_H #define OB_GENERIC_H -#include "babelconfig.h" +#include #include #include #include -#include "math/vector3.h" -#include "obutil.h" +#include +#include namespace OpenBabel { diff --git a/src/grid.h b/include/openbabel/grid.h similarity index 99% rename from src/grid.h rename to include/openbabel/grid.h index 0dfe5517a..d88fefa5b 100644 --- a/src/grid.h +++ b/include/openbabel/grid.h @@ -20,7 +20,7 @@ GNU General Public License for more details. #ifndef OB_GRID_H #define OB_GRID_H -#include "babelconfig.h" +#include #include #include diff --git a/src/internalcoord.h b/include/openbabel/internalcoord.h similarity index 98% rename from src/internalcoord.h rename to include/openbabel/internalcoord.h index 930525b19..88855c889 100644 --- a/src/internalcoord.h +++ b/include/openbabel/internalcoord.h @@ -21,7 +21,7 @@ GNU General Public License for more details. #ifndef OB_INTERNALCOORD_H #define OB_INTERNALCOORD_H -#include "babelconfig.h" +#include #ifndef EXTERN # define EXTERN extern diff --git a/src/kinetics.h b/include/openbabel/kinetics.h similarity index 99% rename from src/kinetics.h rename to include/openbabel/kinetics.h index f70025b83..147f2dd28 100644 --- a/src/kinetics.h +++ b/include/openbabel/kinetics.h @@ -16,7 +16,7 @@ GNU General Public License for more details. #ifndef OB_KINETICS_H #define OB_KINETICS_H -#include "generic.h" +#include namespace OpenBabel { diff --git a/include/openbabel/math/Makefile.am b/include/openbabel/math/Makefile.am new file mode 100644 index 000000000..ca31d9ca3 --- /dev/null +++ b/include/openbabel/math/Makefile.am @@ -0,0 +1,3 @@ +libmathincludedir = $(includedir)/openbabel-2.0/openbabel/math +libmathinclude_HEADERS = \ + matrix3x3.h vector3.h diff --git a/src/matrix.h b/include/openbabel/matrix.h similarity index 98% rename from src/matrix.h rename to include/openbabel/matrix.h index bc39dcbd3..ee90bfa31 100644 --- a/src/matrix.h +++ b/include/openbabel/matrix.h @@ -19,7 +19,7 @@ GNU General Public License for more details. #ifndef OB_MATRIX_H #define OB_MATRIX_H -#include "babelconfig.h" +#include #include #include diff --git a/src/math/matrix3x3.h b/include/openbabel/matrix3x3.h similarity index 98% rename from src/math/matrix3x3.h rename to include/openbabel/matrix3x3.h index e2a850761..8feca07ed 100644 --- a/src/math/matrix3x3.h +++ b/include/openbabel/matrix3x3.h @@ -23,8 +23,8 @@ GNU General Public License for more details. #include -#include "math/vector3.h" // includes rand.h, which includes -#include "oberror.h" +#include // includes rand.h, which includes +#include #ifndef RAD_TO_DEG #define RAD_TO_DEG (180.0/M_PI) diff --git a/src/mol.h b/include/openbabel/mol.h similarity index 98% rename from src/mol.h rename to include/openbabel/mol.h index 7a8d3d4f8..660ab2fa6 100644 --- a/src/mol.h +++ b/include/openbabel/mol.h @@ -22,7 +22,7 @@ GNU General Public License for more details. #ifndef OB_MOL_H #define OB_MOL_H -#include "babelconfig.h" +#include #ifndef EXTERN # define EXTERN extern @@ -36,20 +36,20 @@ GNU General Public License for more details. // Currently includes many headers for 2.x backwards compatibility // \deprecated -- this will be cleaned up in 3.0 efforts (improving compile time) -#include "atom.h" -#include "bond.h" -#include "base.h" -#include "data.h" -#include "chains.h" -#include "math/vector3.h" -#include "bitvec.h" -#include "residue.h" -#include "ring.h" -#include "generic.h" -#include "typer.h" -#include "oberror.h" -#include "obiter.h" -#include "internalcoord.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include namespace OpenBabel { diff --git a/src/molchrg.h b/include/openbabel/molchrg.h similarity index 100% rename from src/molchrg.h rename to include/openbabel/molchrg.h diff --git a/src/newlinebuf.h b/include/openbabel/newlinebuf.h similarity index 98% rename from src/newlinebuf.h rename to include/openbabel/newlinebuf.h index 5c68fda7b..6db0fccf3 100644 --- a/src/newlinebuf.h +++ b/include/openbabel/newlinebuf.h @@ -19,7 +19,7 @@ General Public License for more details. #ifndef OB_NEWLINEBUF_H #define OB_NEWLINEBUF_H -#include "babelconfig.h" +#include #include #include diff --git a/src/obconversion.h b/include/openbabel/obconversion.h similarity index 99% rename from src/obconversion.h rename to include/openbabel/obconversion.h index 1814596ba..d4974de50 100644 --- a/src/obconversion.h +++ b/include/openbabel/obconversion.h @@ -19,7 +19,7 @@ GNU General Public License for more details. #ifndef OB_CONV_H #define OB_CONV_H -#include "babelconfig.h" +#include #include #include @@ -29,8 +29,8 @@ GNU General Public License for more details. #include #include -#include "dlhandler.h" -#include "oberror.h" +#include +#include // These macros are used in DLL builds. If they have not // been set in babelconfig.h, define them as nothing. diff --git a/src/oberror.h b/include/openbabel/oberror.h similarity index 99% rename from src/oberror.h rename to include/openbabel/oberror.h index 03e763786..8aa50aa94 100644 --- a/src/oberror.h +++ b/include/openbabel/oberror.h @@ -20,7 +20,7 @@ General Public License for more details. #ifndef OB_ERROR_H #define OB_ERROR_H -#include "babelconfig.h" +#include #include #include diff --git a/src/obiter.h b/include/openbabel/obiter.h similarity index 99% rename from src/obiter.h rename to include/openbabel/obiter.h index d084d203e..f5cf7a83b 100644 --- a/src/obiter.h +++ b/include/openbabel/obiter.h @@ -20,9 +20,9 @@ GNU General Public License for more details. #ifndef OB_OBITER_H #define OB_OBITER_H -#include "babelconfig.h" -#include "base.h" -#include "bitvec.h" +#include +#include +#include #include #include diff --git a/src/formats/obmolecformat.h b/include/openbabel/obmolecformat.h similarity index 98% rename from src/formats/obmolecformat.h rename to include/openbabel/obmolecformat.h index 4ed36d53d..e4c185992 100644 --- a/src/formats/obmolecformat.h +++ b/include/openbabel/obmolecformat.h @@ -22,8 +22,9 @@ GNU General Public License for more details. #ifdef _WIN32 #include #endif -#include "mol.h" -#include "obconversion.h" + +#include +#include namespace OpenBabel { diff --git a/src/obutil.h b/include/openbabel/obutil.h similarity index 99% rename from src/obutil.h rename to include/openbabel/obutil.h index 7fa91bddc..cd609ec28 100644 --- a/src/obutil.h +++ b/include/openbabel/obutil.h @@ -20,7 +20,7 @@ GNU General Public License for more details. #ifndef OB_UTIL_H #define OB_UTIL_H -#include "babelconfig.h" +#include #include #include @@ -43,7 +43,7 @@ GNU General Public License for more details. #endif // For backwards compatibility. Will be removed in the future -#include "rand.h" +#include namespace OpenBabel { diff --git a/src/parsmart.h b/include/openbabel/parsmart.h similarity index 99% rename from src/parsmart.h rename to include/openbabel/parsmart.h index 33d209bb8..e8a4db259 100644 --- a/src/parsmart.h +++ b/include/openbabel/parsmart.h @@ -23,7 +23,7 @@ GNU General Public License for more details. #include #include -#include "mol.h" +#include /*==========================*/ /* SMARTS Data Structures */ diff --git a/src/patty.h b/include/openbabel/patty.h similarity index 100% rename from src/patty.h rename to include/openbabel/patty.h diff --git a/src/phmodel.h b/include/openbabel/phmodel.h similarity index 97% rename from src/phmodel.h rename to include/openbabel/phmodel.h index 60f5c7bf7..f41bafdaf 100644 --- a/src/phmodel.h +++ b/include/openbabel/phmodel.h @@ -20,8 +20,8 @@ GNU General Public License for more details. #ifndef OB_PHMODEL_H #define OB_PHMODEL_H -#include "parsmart.h" -#include "data.h" +#include +#include namespace OpenBabel { diff --git a/src/rand.h b/include/openbabel/rand.h similarity index 98% rename from src/rand.h rename to include/openbabel/rand.h index becf10526..b11cf0f61 100644 --- a/src/rand.h +++ b/include/openbabel/rand.h @@ -20,7 +20,7 @@ GNU General Public License for more details. #ifndef RAND_H #define RAND_H -#include "babelconfig.h" +#include namespace OpenBabel { diff --git a/src/reaction.h b/include/openbabel/reaction.h similarity index 100% rename from src/reaction.h rename to include/openbabel/reaction.h diff --git a/src/residue.h b/include/openbabel/residue.h similarity index 99% rename from src/residue.h rename to include/openbabel/residue.h index 1ab9a7744..60e297f81 100644 --- a/src/residue.h +++ b/include/openbabel/residue.h @@ -25,12 +25,12 @@ obtained in part or whole from RasMol2 by Roger Sayle. #ifndef OB_RESIDUE_H #define OB_RESIDUE_H -#include "babelconfig.h" +#include #include #include -#include "base.h" +#include namespace OpenBabel { diff --git a/src/ring.h b/include/openbabel/ring.h similarity index 100% rename from src/ring.h rename to include/openbabel/ring.h diff --git a/src/rotamer.h b/include/openbabel/rotamer.h similarity index 98% rename from src/rotamer.h rename to include/openbabel/rotamer.h index 6aa3a4ae8..3baa38097 100644 --- a/src/rotamer.h +++ b/include/openbabel/rotamer.h @@ -23,9 +23,9 @@ GNU General Public License for more details. #include #include -#include "mol.h" -#include "rotor.h" -#include "generic.h" +#include +#include +#include namespace OpenBabel { diff --git a/src/rotor.h b/include/openbabel/rotor.h similarity index 99% rename from src/rotor.h rename to include/openbabel/rotor.h index ac1409407..95b45de69 100644 --- a/src/rotor.h +++ b/include/openbabel/rotor.h @@ -20,8 +20,8 @@ GNU General Public License for more details. #ifndef OB_ROTOR_H #define OB_ROTOR_H -#include "parsmart.h" -#include "typer.h" +#include +#include namespace OpenBabel { diff --git a/src/typer.h b/include/openbabel/typer.h similarity index 98% rename from src/typer.h rename to include/openbabel/typer.h index 83265fced..663fbf915 100644 --- a/src/typer.h +++ b/include/openbabel/typer.h @@ -20,8 +20,8 @@ GNU General Public License for more details. #ifndef OB_TYPER_H #define OB_TYPER_H -#include "parsmart.h" -#include "data.h" +#include +#include namespace OpenBabel { diff --git a/src/math/vector3.h b/include/openbabel/vector3.h similarity index 99% rename from src/math/vector3.h rename to include/openbabel/vector3.h index 8b1fc3dfe..13831a3ac 100644 --- a/src/math/vector3.h +++ b/include/openbabel/vector3.h @@ -24,7 +24,7 @@ GNU General Public License for more details. #include #include -#include "rand.h" +#include #ifndef RAD_TO_DEG #define RAD_TO_DEG (180.0/M_PI) diff --git a/scripts/Makefile.am b/scripts/Makefile.am index 307adeae1..320bf2549 100644 --- a/scripts/Makefile.am +++ b/scripts/Makefile.am @@ -19,15 +19,20 @@ if BUILD_SWIG BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \ java/openbabel_java.cpp -perl/openbabel_perl.cpp: openbabel-perl.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h +script_includes = $(top_srcdir)/include/openbabel +script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \ + $(script_includes)/atom.h $(script_includes)/bond.h \ + $(script_includes)/residue.h + +perl/openbabel_perl.cpp: openbabel-perl.i $(script_headers) $(SWIG) -perl5 -c++ -naturalvar -o $@ \ - -I$(top_srcdir)/src $<; + -I$(top_srcdir)/include $<; sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" perl/OpenBabel.new; mv perl/OpenBabel.new perl/OpenBabel.pm; -python/openbabel_python.cpp: openbabel-python.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h +python/openbabel_python.cpp: openbabel-python.i $(script_headers) $(SWIG) -python -modern -naturalvar -fastinit \ - -c++ -o $@ -I$(top_srcdir)/src $<; + -c++ -o $@ -I$(top_srcdir)/include $<; echo "import sys" >python/ob.py; echo "if sys.platform.find(\"linux\") != -1:" >>python/ob.py; echo " import dl" >>python/ob.py; @@ -36,8 +41,8 @@ python/openbabel_python.cpp: openbabel-python.i $(top_srcdir)/src/mol.h $(top_s cat python/openbabel.py >>python/ob.py; mv python/ob.py python/openbabel.py; -java/openbabel_java.cpp: openbabel-java.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h - $(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<; +java/openbabel_java.cpp: openbabel-java.i $(script_headers) + $(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/include $<; (cd java; \ for file in SWIGTYPE_p_*; \ do tgt=$$(echo $${file} | sed -e "s/SWIGTYPE_p_//" | sed -e "s/std__//g" | sed -e "s/OpenBabel__//g" | sed -e "s/p_/p/g"); \ @@ -46,8 +51,8 @@ java/openbabel_java.cpp: openbabel-java.i $(top_srcdir)/src/mol.h $(top_srcdir) if BUILD_RUBY BUILT_SOURCES += ruby/openbabel_ruby.cpp -ruby/openbabel_ruby.cpp: openbabel-ruby.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h - $(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<; +ruby/openbabel_ruby.cpp: openbabel-ruby.i $(script_headers) + $(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/include $<; (cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) ) endif # BUILD_RUBY diff --git a/scripts/Makefile.in b/scripts/Makefile.in index fbb457949..865389b57 100644 --- a/scripts/Makefile.in +++ b/scripts/Makefile.in @@ -203,6 +203,11 @@ EXTRA_DIST = openbabel-perl.i perl \ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ python/openbabel_python.cpp \ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ java/openbabel_java.cpp \ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(am__append_1) +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_includes = $(top_srcdir)/include/openbabel +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \ +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(script_includes)/atom.h $(script_includes)/bond.h \ +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(script_includes)/residue.h + all: $(BUILT_SOURCES) $(MAKE) $(AM_MAKEFLAGS) all-am @@ -379,15 +384,15 @@ dist-hook: (cd $(distdir)/python; rm -rf build; rm -rf *.pyc *.so) (cd $(distdir)/ruby; $(MAKE) distclean) -@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@perl/openbabel_perl.cpp: openbabel-perl.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@perl/openbabel_perl.cpp: openbabel-perl.i $(script_headers) @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -perl5 -c++ -naturalvar -o $@ \ -@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -I$(top_srcdir)/src $<; +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -I$(top_srcdir)/include $<; @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" perl/OpenBabel.new; @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ mv perl/OpenBabel.new perl/OpenBabel.pm; -@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/openbabel_python.cpp: openbabel-python.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/openbabel_python.cpp: openbabel-python.i $(script_headers) @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -python -modern -naturalvar -fastinit \ -@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -c++ -o $@ -I$(top_srcdir)/src $<; +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -c++ -o $@ -I$(top_srcdir)/include $<; @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo "import sys" >python/ob.py; @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo "if sys.platform.find(\"linux\") != -1:" >>python/ob.py; @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo " import dl" >>python/ob.py; @@ -396,15 +401,15 @@ dist-hook: @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ cat python/openbabel.py >>python/ob.py; @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ mv python/ob.py python/openbabel.py; -@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@java/openbabel_java.cpp: openbabel-java.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h -@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<; +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@java/openbabel_java.cpp: openbabel-java.i $(script_headers) +@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/include $<; @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ (cd java; \ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ for file in SWIGTYPE_p_*; \ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ do tgt=$$(echo $${file} | sed -e "s/SWIGTYPE_p_//" | sed -e "s/std__//g" | sed -e "s/OpenBabel__//g" | sed -e "s/p_/p/g"); \ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ mv $$file $$tgt; done) -@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ruby/openbabel_ruby.cpp: openbabel-ruby.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h -@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<; +@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ruby/openbabel_ruby.cpp: openbabel-ruby.i $(script_headers) +@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/include $<; @BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ (cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) ) # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. diff --git a/scripts/java/OBAngleData.java b/scripts/java/OBAngleData.java index 693c1eba5..aea4bdb9e 100644 --- a/scripts/java/OBAngleData.java +++ b/scripts/java/OBAngleData.java @@ -42,7 +42,11 @@ public class OBAngleData extends OBGenericData { } public long FillAngleArray(SWIGTYPE_p_p_int angles, SWIGTYPE_p_unsigned_int size) { - return openbabelJNI.OBAngleData_FillAngleArray(swigCPtr, this, SWIGTYPE_p_p_int.getCPtr(angles), SWIGTYPE_p_unsigned_int.getCPtr(size)); + return openbabelJNI.OBAngleData_FillAngleArray__SWIG_0(swigCPtr, this, SWIGTYPE_p_p_int.getCPtr(angles), SWIGTYPE_p_unsigned_int.getCPtr(size)); + } + + public boolean FillAngleArray(SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t angles) { + return openbabelJNI.OBAngleData_FillAngleArray__SWIG_1(swigCPtr, this, SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t.getCPtr(angles)); } public void SetData(OBAngle arg0) { diff --git a/scripts/java/OBMol.java b/scripts/java/OBMol.java index 4a97a517a..aa22bd2d8 100644 --- a/scripts/java/OBMol.java +++ b/scripts/java/OBMol.java @@ -562,6 +562,10 @@ public class OBMol extends OBBase { openbabelJNI.OBMol_PerceiveBondOrders(swigCPtr, this); } + public void FindAngles() { + openbabelJNI.OBMol_FindAngles(swigCPtr, this); + } + public void FindTorsions() { openbabelJNI.OBMol_FindTorsions(swigCPtr, this); } diff --git a/scripts/java/OBMolAngleIter.java b/scripts/java/OBMolAngleIter.java new file mode 100644 index 000000000..91f681c36 --- /dev/null +++ b/scripts/java/OBMolAngleIter.java @@ -0,0 +1,51 @@ +/* ---------------------------------------------------------------------------- + * This file was automatically generated by SWIG (http://www.swig.org). + * Version 1.3.30 + * + * Do not make changes to this file unless you know what you are doing--modify + * the SWIG interface file instead. + * ----------------------------------------------------------------------------- */ + + +public class OBMolAngleIter { + private long swigCPtr; + protected boolean swigCMemOwn; + + protected OBMolAngleIter(long cPtr, boolean cMemoryOwn) { + swigCMemOwn = cMemoryOwn; + swigCPtr = cPtr; + } + + protected static long getCPtr(OBMolAngleIter obj) { + return (obj == null) ? 0 : obj.swigCPtr; + } + + protected void finalize() { + delete(); + } + + public synchronized void delete() { + if(swigCPtr != 0 && swigCMemOwn) { + swigCMemOwn = false; + openbabelJNI.delete_OBMolAngleIter(swigCPtr); + } + swigCPtr = 0; + } + + public OBMolAngleIter() { + this(openbabelJNI.new_OBMolAngleIter__SWIG_0(), true); + } + + public OBMolAngleIter(OBMol mol) { + this(openbabelJNI.new_OBMolAngleIter__SWIG_1(OBMol.getCPtr(mol), mol), true); + } + + public OBMolAngleIter(OBMolAngleIter ai) { + this(openbabelJNI.new_OBMolAngleIter__SWIG_3(OBMolAngleIter.getCPtr(ai), ai), true); + } + + public SWIGTYPE_p_std__vectorTunsigned_int_t __ref__() { + return new SWIGTYPE_p_std__vectorTunsigned_int_t(openbabelJNI.OBMolAngleIter___ref__(swigCPtr, this), true); + } + +} diff --git a/scripts/java/OBMolPairIter.java b/scripts/java/OBMolPairIter.java new file mode 100644 index 000000000..0a4e27e5a --- /dev/null +++ b/scripts/java/OBMolPairIter.java @@ -0,0 +1,56 @@ +/* ---------------------------------------------------------------------------- + * This file was automatically generated by SWIG (http://www.swig.org). + * Version 1.3.30 + * + * Do not make changes to this file unless you know what you are doing--modify + * the SWIG interface file instead. + * ----------------------------------------------------------------------------- */ + + +public class OBMolPairIter { + private long swigCPtr; + protected boolean swigCMemOwn; + + protected OBMolPairIter(long cPtr, boolean cMemoryOwn) { + swigCMemOwn = cMemoryOwn; + swigCPtr = cPtr; + } + + protected static long getCPtr(OBMolPairIter obj) { + return (obj == null) ? 0 : obj.swigCPtr; + } + + protected void finalize() { + delete(); + } + + public synchronized void delete() { + if(swigCPtr != 0 && swigCMemOwn) { + swigCMemOwn = false; + openbabelJNI.delete_OBMolPairIter(swigCPtr); + } + swigCPtr = 0; + } + + public OBMolPairIter() { + this(openbabelJNI.new_OBMolPairIter__SWIG_0(), true); + } + + public OBMolPairIter(OBMol mol) { + this(openbabelJNI.new_OBMolPairIter__SWIG_1(OBMol.getCPtr(mol), mol), true); + } + + public OBMolPairIter(OBMolPairIter ai) { + this(openbabelJNI.new_OBMolPairIter__SWIG_3(OBMolPairIter.getCPtr(ai), ai), true); + } + + public SWIGTYPE_p_std__pairTint_int_t __deref__() { + long cPtr = openbabelJNI.OBMolPairIter___deref__(swigCPtr, this); + return (cPtr == 0) ? null : new SWIGTYPE_p_std__pairTint_int_t(cPtr, false); + } + + public SWIGTYPE_p_std__pairTint_int_t __ref__() { + return new SWIGTYPE_p_std__pairTint_int_t(openbabelJNI.OBMolPairIter___ref__(swigCPtr, this), false); + } + +} diff --git a/scripts/java/OBMolRingIter.java b/scripts/java/OBMolRingIter.java new file mode 100644 index 000000000..4f6f63820 --- /dev/null +++ b/scripts/java/OBMolRingIter.java @@ -0,0 +1,109 @@ +/* ---------------------------------------------------------------------------- + * This file was automatically generated by SWIG (http://www.swig.org). + * Version 1.3.30 + * + * Do not make changes to this file unless you know what you are doing--modify + * the SWIG interface file instead. + * ----------------------------------------------------------------------------- */ + + +public class OBMolRingIter { + private long swigCPtr; + protected boolean swigCMemOwn; + + protected OBMolRingIter(long cPtr, boolean cMemoryOwn) { + swigCMemOwn = cMemoryOwn; + swigCPtr = cPtr; + } + + protected static long getCPtr(OBMolRingIter obj) { + return (obj == null) ? 0 : obj.swigCPtr; + } + + protected void finalize() { + delete(); + } + + public synchronized void delete() { + if(swigCPtr != 0 && swigCMemOwn) { + swigCMemOwn = false; + openbabelJNI.delete_OBMolRingIter(swigCPtr); + } + swigCPtr = 0; + } + + public OBMolRingIter() { + this(openbabelJNI.new_OBMolRingIter__SWIG_0(), true); + } + + public OBMolRingIter(OBMol mol) { + this(openbabelJNI.new_OBMolRingIter__SWIG_1(OBMol.getCPtr(mol), mol), true); + } + + public OBMolRingIter(OBMolRingIter ri) { + this(openbabelJNI.new_OBMolRingIter__SWIG_3(OBMolRingIter.getCPtr(ri), ri), true); + } + + public OBRing __deref__() { + long cPtr = openbabelJNI.OBMolRingIter___deref__(swigCPtr, this); + return (cPtr == 0) ? null : new OBRing(cPtr, false); + } + + public OBRing __ref__() { + return new OBRing(openbabelJNI.OBMolRingIter___ref__(swigCPtr, this), false); + } + + public void set_path(vectorInt value) { + openbabelJNI.OBMolRingIter__path_set(swigCPtr, this, vectorInt.getCPtr(value), value); + } + + public vectorInt get_path() { + return new vectorInt(openbabelJNI.OBMolRingIter__path_get(swigCPtr, this), false); + } + + public void set_pathset(OBBitVec value) { + openbabelJNI.OBMolRingIter__pathset_set(swigCPtr, this, OBBitVec.getCPtr(value), value); + } + + public OBBitVec get_pathset() { + return new OBBitVec(openbabelJNI.OBMolRingIter__pathset_get(swigCPtr, this), false); + } + + public boolean findCenterAndNormal(vector3 center, vector3 norm1, vector3 norm2) { + return openbabelJNI.OBMolRingIter_findCenterAndNormal(swigCPtr, this, vector3.getCPtr(center), center, vector3.getCPtr(norm1), norm1, vector3.getCPtr(norm2), norm2); + } + + public int Size() { + return openbabelJNI.OBMolRingIter_Size(swigCPtr, this); + } + + public int PathSize() { + return openbabelJNI.OBMolRingIter_PathSize(swigCPtr, this); + } + + public boolean IsMember(OBAtom a) { + return openbabelJNI.OBMolRingIter_IsMember__SWIG_0(swigCPtr, this, OBAtom.getCPtr(a), a); + } + + public boolean IsMember(OBBond b) { + return openbabelJNI.OBMolRingIter_IsMember__SWIG_1(swigCPtr, this, OBBond.getCPtr(b), b); + } + + public boolean IsAromatic() { + return openbabelJNI.OBMolRingIter_IsAromatic(swigCPtr, this); + } + + public boolean IsInRing(int i) { + return openbabelJNI.OBMolRingIter_IsInRing(swigCPtr, this, i); + } + + public void SetParent(OBMol m) { + openbabelJNI.OBMolRingIter_SetParent(swigCPtr, this, OBMol.getCPtr(m), m); + } + + public OBMol GetParent() { + long cPtr = openbabelJNI.OBMolRingIter_GetParent(swigCPtr, this); + return (cPtr == 0) ? null : new OBMol(cPtr, false); + } + +} diff --git a/scripts/java/OBMolTorsionIter.java b/scripts/java/OBMolTorsionIter.java new file mode 100644 index 000000000..348c509ed --- /dev/null +++ b/scripts/java/OBMolTorsionIter.java @@ -0,0 +1,51 @@ +/* ---------------------------------------------------------------------------- + * This file was automatically generated by SWIG (http://www.swig.org). + * Version 1.3.30 + * + * Do not make changes to this file unless you know what you are doing--modify + * the SWIG interface file instead. + * ----------------------------------------------------------------------------- */ + + +public class OBMolTorsionIter { + private long swigCPtr; + protected boolean swigCMemOwn; + + protected OBMolTorsionIter(long cPtr, boolean cMemoryOwn) { + swigCMemOwn = cMemoryOwn; + swigCPtr = cPtr; + } + + protected static long getCPtr(OBMolTorsionIter obj) { + return (obj == null) ? 0 : obj.swigCPtr; + } + + protected void finalize() { + delete(); + } + + public synchronized void delete() { + if(swigCPtr != 0 && swigCMemOwn) { + swigCMemOwn = false; + openbabelJNI.delete_OBMolTorsionIter(swigCPtr); + } + swigCPtr = 0; + } + + public OBMolTorsionIter() { + this(openbabelJNI.new_OBMolTorsionIter__SWIG_0(), true); + } + + public OBMolTorsionIter(OBMol mol) { + this(openbabelJNI.new_OBMolTorsionIter__SWIG_1(OBMol.getCPtr(mol), mol), true); + } + + public OBMolTorsionIter(OBMolTorsionIter ai) { + this(openbabelJNI.new_OBMolTorsionIter__SWIG_3(OBMolTorsionIter.getCPtr(ai), ai), true); + } + + public SWIGTYPE_p_std__vectorTunsigned_int_t __ref__() { + return new SWIGTYPE_p_std__vectorTunsigned_int_t(openbabelJNI.OBMolTorsionIter___ref__(swigCPtr, this), true); + } + +} diff --git a/scripts/java/OBRingData.java b/scripts/java/OBRingData.java index 0e9141a96..9ab92552e 100644 --- a/scripts/java/OBRingData.java +++ b/scripts/java/OBRingData.java @@ -57,4 +57,22 @@ public class OBRingData extends OBGenericData { return new SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t(openbabelJNI.OBRingData_GetData(swigCPtr, this), false); } + public SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator BeginRings() { + return new SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator(openbabelJNI.OBRingData_BeginRings(swigCPtr, this), true); + } + + public SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator EndRings() { + return new SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator(openbabelJNI.OBRingData_EndRings(swigCPtr, this), true); + } + + public OBRing BeginRing(SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator i) { + long cPtr = openbabelJNI.OBRingData_BeginRing(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator.getCPtr(i)); + return (cPtr == 0) ? null : new OBRing(cPtr, false); + } + + public OBRing NextRing(SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator i) { + long cPtr = openbabelJNI.OBRingData_NextRing(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator.getCPtr(i)); + return (cPtr == 0) ? null : new OBRing(cPtr, false); + } + } diff --git a/scripts/java/openbabelJNI.java b/scripts/java/openbabelJNI.java index 97b14b80e..abe4dc56b 100644 --- a/scripts/java/openbabelJNI.java +++ b/scripts/java/openbabelJNI.java @@ -329,6 +329,10 @@ class openbabelJNI { public final static native void OBRingData_SetData(long jarg1, OBRingData jarg1_, long jarg2); public final static native void OBRingData_PushBack(long jarg1, OBRingData jarg1_, long jarg2, OBRing jarg2_); public final static native long OBRingData_GetData(long jarg1, OBRingData jarg1_); + public final static native long OBRingData_BeginRings(long jarg1, OBRingData jarg1_); + public final static native long OBRingData_EndRings(long jarg1, OBRingData jarg1_); + public final static native long OBRingData_BeginRing(long jarg1, OBRingData jarg1_, long jarg2); + public final static native long OBRingData_NextRing(long jarg1, OBRingData jarg1_, long jarg2); public final static native long new_OBUnitCell__SWIG_0(); public final static native long new_OBUnitCell__SWIG_1(long jarg1, OBUnitCell jarg1_); public final static native long OBUnitCell_Clone(long jarg1, OBUnitCell jarg1_, long jarg2, OBBase jarg2_); @@ -413,7 +417,8 @@ class openbabelJNI { public final static native void OBAngle_SetAtoms__SWIG_1(long jarg1, OBAngle jarg1_, long jarg2); public final static native long OBAngleData_Clone(long jarg1, OBAngleData jarg1_, long jarg2, OBBase jarg2_); public final static native void OBAngleData_Clear(long jarg1, OBAngleData jarg1_); - public final static native long OBAngleData_FillAngleArray(long jarg1, OBAngleData jarg1_, long jarg2, long jarg3); + public final static native long OBAngleData_FillAngleArray__SWIG_0(long jarg1, OBAngleData jarg1_, long jarg2, long jarg3); + public final static native boolean OBAngleData_FillAngleArray__SWIG_1(long jarg1, OBAngleData jarg1_, long jarg2); public final static native void OBAngleData_SetData(long jarg1, OBAngleData jarg1_, long jarg2, OBAngle jarg2_); public final static native long OBAngleData_GetSize(long jarg1, OBAngleData jarg1_); public final static native void delete_OBAngleData(long jarg1); @@ -1106,6 +1111,7 @@ class openbabelJNI { public final static native void OBMol_Align(long jarg1, OBMol jarg1_, long jarg2, OBAtom jarg2_, long jarg3, OBAtom jarg3_, long jarg4, vector3 jarg4_, long jarg5, vector3 jarg5_); public final static native void OBMol_ConnectTheDots(long jarg1, OBMol jarg1_); public final static native void OBMol_PerceiveBondOrders(long jarg1, OBMol jarg1_); + public final static native void OBMol_FindAngles(long jarg1, OBMol jarg1_); public final static native void OBMol_FindTorsions(long jarg1, OBMol jarg1_); public final static native boolean OBMol_GetGTDVector(long jarg1, OBMol jarg1_, long jarg2, vectorInt jarg2_); public final static native void OBMol_GetGIVector(long jarg1, OBMol jarg1_, long jarg2); @@ -2276,6 +2282,41 @@ class openbabelJNI { public final static native long OBResidueAtomIter_GetData__SWIG_3(long jarg1, OBResidueAtomIter jarg1_); public final static native long OBResidueAtomIter_BeginData(long jarg1, OBResidueAtomIter jarg1_); public final static native long OBResidueAtomIter_EndData(long jarg1, OBResidueAtomIter jarg1_); + public final static native long new_OBMolAngleIter__SWIG_0(); + public final static native long new_OBMolAngleIter__SWIG_1(long jarg1, OBMol jarg1_); + public final static native long new_OBMolAngleIter__SWIG_3(long jarg1, OBMolAngleIter jarg1_); + public final static native long OBMolAngleIter___ref__(long jarg1, OBMolAngleIter jarg1_); + public final static native void delete_OBMolAngleIter(long jarg1); + public final static native long new_OBMolTorsionIter__SWIG_0(); + public final static native long new_OBMolTorsionIter__SWIG_1(long jarg1, OBMol jarg1_); + public final static native long new_OBMolTorsionIter__SWIG_3(long jarg1, OBMolTorsionIter jarg1_); + public final static native long OBMolTorsionIter___ref__(long jarg1, OBMolTorsionIter jarg1_); + public final static native void delete_OBMolTorsionIter(long jarg1); + public final static native long new_OBMolPairIter__SWIG_0(); + public final static native long new_OBMolPairIter__SWIG_1(long jarg1, OBMol jarg1_); + public final static native long new_OBMolPairIter__SWIG_3(long jarg1, OBMolPairIter jarg1_); + public final static native long OBMolPairIter___deref__(long jarg1, OBMolPairIter jarg1_); + public final static native long OBMolPairIter___ref__(long jarg1, OBMolPairIter jarg1_); + public final static native void delete_OBMolPairIter(long jarg1); + public final static native long new_OBMolRingIter__SWIG_0(); + public final static native long new_OBMolRingIter__SWIG_1(long jarg1, OBMol jarg1_); + public final static native long new_OBMolRingIter__SWIG_3(long jarg1, OBMolRingIter jarg1_); + public final static native long OBMolRingIter___deref__(long jarg1, OBMolRingIter jarg1_); + public final static native long OBMolRingIter___ref__(long jarg1, OBMolRingIter jarg1_); + public final static native void delete_OBMolRingIter(long jarg1); + public final static native void OBMolRingIter__path_set(long jarg1, OBMolRingIter jarg1_, long jarg2, vectorInt jarg2_); + public final static native long OBMolRingIter__path_get(long jarg1, OBMolRingIter jarg1_); + public final static native void OBMolRingIter__pathset_set(long jarg1, OBMolRingIter jarg1_, long jarg2, OBBitVec jarg2_); + public final static native long OBMolRingIter__pathset_get(long jarg1, OBMolRingIter jarg1_); + public final static native boolean OBMolRingIter_findCenterAndNormal(long jarg1, OBMolRingIter jarg1_, long jarg2, vector3 jarg2_, long jarg3, vector3 jarg3_, long jarg4, vector3 jarg4_); + public final static native int OBMolRingIter_Size(long jarg1, OBMolRingIter jarg1_); + public final static native int OBMolRingIter_PathSize(long jarg1, OBMolRingIter jarg1_); + public final static native boolean OBMolRingIter_IsMember__SWIG_0(long jarg1, OBMolRingIter jarg1_, long jarg2, OBAtom jarg2_); + public final static native boolean OBMolRingIter_IsMember__SWIG_1(long jarg1, OBMolRingIter jarg1_, long jarg2, OBBond jarg2_); + public final static native boolean OBMolRingIter_IsAromatic(long jarg1, OBMolRingIter jarg1_); + public final static native boolean OBMolRingIter_IsInRing(long jarg1, OBMolRingIter jarg1_, int jarg2); + public final static native void OBMolRingIter_SetParent(long jarg1, OBMolRingIter jarg1_, long jarg2, OBMol jarg2_); + public final static native long OBMolRingIter_GetParent(long jarg1, OBMolRingIter jarg1_); public final static native long SWIGOBElementTableUpcast(long jarg1); public final static native long SWIGOBIsotopeTableUpcast(long jarg1); public final static native long SWIGOBTypeTableUpcast(long jarg1); diff --git a/scripts/java/openbabel_java.cpp b/scripts/java/openbabel_java.cpp index a3caafcf6..054335641 100644 --- a/scripts/java/openbabel_java.cpp +++ b/scripts/java/openbabel_java.cpp @@ -196,21 +196,21 @@ static void SWIGUNUSED SWIG_JavaThrowException(JNIEnv *jenv, SWIG_JavaExceptionC #include -#include "obutil.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include #include @@ -5509,6 +5509,78 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBRingData_1GetData(JNIEnv *jenv, jcl } +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBRingData_1BeginRings(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper::iterator > result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBRingData **)&jarg1; + result = (arg1)->BeginRings(); + *(std::vector::iterator **)&jresult = new std::vector::iterator((std::vector::iterator &)result); + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBRingData_1EndRings(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper::iterator > result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBRingData **)&jarg1; + result = (arg1)->EndRings(); + *(std::vector::iterator **)&jresult = new std::vector::iterator((std::vector::iterator &)result); + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBRingData_1BeginRing(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) { + jlong jresult = 0 ; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBRingData **)&jarg1; + arg2 = *(std::vector::iterator **)&jarg2; + if(!arg2) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "std::vector::iterator & reference is null"); + return 0; + } + result = (OpenBabel::OBRing *)(arg1)->BeginRing(*arg2); + *(OpenBabel::OBRing **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBRingData_1NextRing(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) { + jlong jresult = 0 ; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBRingData **)&jarg1; + arg2 = *(std::vector::iterator **)&jarg2; + if(!arg2) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "std::vector::iterator & reference is null"); + return 0; + } + result = (OpenBabel::OBRing *)(arg1)->NextRing(*arg2); + *(OpenBabel::OBRing **)&jresult = result; + return jresult; +} + + SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBUnitCell_1_1SWIG_10(JNIEnv *jenv, jclass jcls) { jlong jresult = 0 ; OpenBabel::OBUnitCell *result = 0 ; @@ -6912,7 +6984,7 @@ SWIGEXPORT void JNICALL Java_openbabelJNI_OBAngleData_1Clear(JNIEnv *jenv, jclas } -SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBAngleData_1FillAngleArray(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jlong jarg3) { +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBAngleData_1FillAngleArray_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jlong jarg3) { jlong jresult = 0 ; OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; int **arg2 = (int **) 0 ; @@ -6935,6 +7007,27 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBAngleData_1FillAngleArray(JNIEnv *j } +SWIGEXPORT jboolean JNICALL Java_openbabelJNI_OBAngleData_1FillAngleArray_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) { + jboolean jresult = 0 ; + OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; + std::vector > *arg2 = 0 ; + bool result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBAngleData **)&jarg1; + arg2 = *(std::vector > **)&jarg2; + if(!arg2) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "std::vector > & reference is null"); + return 0; + } + result = (bool)(arg1)->FillAngleArray(*arg2); + jresult = (jboolean)result; + return jresult; +} + + SWIGEXPORT void JNICALL Java_openbabelJNI_OBAngleData_1SetData(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) { OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; OpenBabel::OBAngle *arg2 = 0 ; @@ -17389,6 +17482,17 @@ SWIGEXPORT void JNICALL Java_openbabelJNI_OBMol_1PerceiveBondOrders(JNIEnv *jenv } +SWIGEXPORT void JNICALL Java_openbabelJNI_OBMol_1FindAngles(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMol **)&jarg1; + (arg1)->FindAngles(); +} + + SWIGEXPORT void JNICALL Java_openbabelJNI_OBMol_1FindTorsions(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; @@ -35459,6 +35563,567 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBResidueAtomIter_1EndData(JNIEnv *je } +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolAngleIter_1_1SWIG_10(JNIEnv *jenv, jclass jcls) { + jlong jresult = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + + (void)jenv; + (void)jcls; + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(); + *(OpenBabel::OBMolAngleIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolAngleIter_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMol **)&jarg1; + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(arg1); + *(OpenBabel::OBMolAngleIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolAngleIter_1_1SWIG_13(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolAngleIter *arg1 = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolAngleIter **)&jarg1; + if(!arg1) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::OBMolAngleIter const & reference is null"); + return 0; + } + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter((OpenBabel::OBMolAngleIter const &)*arg1); + *(OpenBabel::OBMolAngleIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolAngleIter_1_1_1ref_1_1(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + SwigValueWrapper > result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolAngleIter **)&jarg1; + result = ((OpenBabel::OBMolAngleIter const *)arg1)->operator *(); + *(std::vector **)&jresult = new std::vector((std::vector &)result); + return jresult; +} + + +SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1OBMolAngleIter(JNIEnv *jenv, jclass jcls, jlong jarg1) { + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + + (void)jenv; + (void)jcls; + arg1 = *(OpenBabel::OBMolAngleIter **)&jarg1; + delete arg1; + +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolTorsionIter_1_1SWIG_10(JNIEnv *jenv, jclass jcls) { + jlong jresult = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + + (void)jenv; + (void)jcls; + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(); + *(OpenBabel::OBMolTorsionIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolTorsionIter_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMol **)&jarg1; + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(arg1); + *(OpenBabel::OBMolTorsionIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolTorsionIter_1_1SWIG_13(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolTorsionIter *arg1 = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolTorsionIter **)&jarg1; + if(!arg1) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::OBMolTorsionIter const & reference is null"); + return 0; + } + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter((OpenBabel::OBMolTorsionIter const &)*arg1); + *(OpenBabel::OBMolTorsionIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolTorsionIter_1_1_1ref_1_1(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + SwigValueWrapper > result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolTorsionIter **)&jarg1; + result = ((OpenBabel::OBMolTorsionIter const *)arg1)->operator *(); + *(std::vector **)&jresult = new std::vector((std::vector &)result); + return jresult; +} + + +SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1OBMolTorsionIter(JNIEnv *jenv, jclass jcls, jlong jarg1) { + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + + (void)jenv; + (void)jcls; + arg1 = *(OpenBabel::OBMolTorsionIter **)&jarg1; + delete arg1; + +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolPairIter_1_1SWIG_10(JNIEnv *jenv, jclass jcls) { + jlong jresult = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + + (void)jenv; + (void)jcls; + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(); + *(OpenBabel::OBMolPairIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolPairIter_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMol **)&jarg1; + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(arg1); + *(OpenBabel::OBMolPairIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolPairIter_1_1SWIG_13(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolPairIter *arg1 = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolPairIter **)&jarg1; + if(!arg1) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::OBMolPairIter const & reference is null"); + return 0; + } + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter((OpenBabel::OBMolPairIter const &)*arg1); + *(OpenBabel::OBMolPairIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolPairIter_1_1_1deref_1_1(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolPairIter **)&jarg1; + result = (std::pair *)((OpenBabel::OBMolPairIter const *)arg1)->operator ->(); + *(std::pair **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolPairIter_1_1_1ref_1_1(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolPairIter **)&jarg1; + { + std::pair &_result_ref = ((OpenBabel::OBMolPairIter const *)arg1)->operator *(); + result = (std::pair *) &_result_ref; + } + *(std::pair **)&jresult = result; + return jresult; +} + + +SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1OBMolPairIter(JNIEnv *jenv, jclass jcls, jlong jarg1) { + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + + (void)jenv; + (void)jcls; + arg1 = *(OpenBabel::OBMolPairIter **)&jarg1; + delete arg1; + +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolRingIter_1_1SWIG_10(JNIEnv *jenv, jclass jcls) { + jlong jresult = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + + (void)jenv; + (void)jcls; + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(); + *(OpenBabel::OBMolRingIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolRingIter_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMol **)&jarg1; + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(arg1); + *(OpenBabel::OBMolRingIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBMolRingIter_1_1SWIG_13(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + if(!arg1) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::OBMolRingIter const & reference is null"); + return 0; + } + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter((OpenBabel::OBMolRingIter const &)*arg1); + *(OpenBabel::OBMolRingIter **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolRingIter_1_1_1deref_1_1(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + result = (OpenBabel::OBRing *)((OpenBabel::OBMolRingIter const *)arg1)->operator ->(); + *(OpenBabel::OBRing **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolRingIter_1_1_1ref_1_1(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + { + OpenBabel::OBRing &_result_ref = ((OpenBabel::OBMolRingIter const *)arg1)->operator *(); + result = (OpenBabel::OBRing *) &_result_ref; + } + *(OpenBabel::OBRing **)&jresult = result; + return jresult; +} + + +SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1OBMolRingIter(JNIEnv *jenv, jclass jcls, jlong jarg1) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + + (void)jenv; + (void)jcls; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + delete arg1; + +} + + +SWIGEXPORT void JNICALL Java_openbabelJNI_OBMolRingIter_1_1path_1set(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector *arg2 = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + (void)jarg2_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + arg2 = *(std::vector **)&jarg2; + if(!arg2) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "std::vector const & reference is null"); + return ; + } + if (arg1) (*arg1)->_path = *arg2; + +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolRingIter_1_1path_1get(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + { + std::vector const &_result_ref = ((*arg1)->_path); + result = (std::vector *) &_result_ref; + } + *(std::vector **)&jresult = result; + return jresult; +} + + +SWIGEXPORT void JNICALL Java_openbabelJNI_OBMolRingIter_1_1pathset_1set(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *arg2 = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + (void)jarg2_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + arg2 = *(OpenBabel::OBBitVec **)&jarg2; + if(!arg2) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::OBBitVec const & reference is null"); + return ; + } + if (arg1) (*arg1)->_pathset = *arg2; + +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolRingIter_1_1pathset_1get(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + { + OpenBabel::OBBitVec const &_result_ref = ((*arg1)->_pathset); + result = (OpenBabel::OBBitVec *) &_result_ref; + } + *(OpenBabel::OBBitVec **)&jresult = result; + return jresult; +} + + +SWIGEXPORT jboolean JNICALL Java_openbabelJNI_OBMolRingIter_1findCenterAndNormal(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_, jlong jarg3, jobject jarg3_, jlong jarg4, jobject jarg4_) { + jboolean jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::vector3 *arg2 = 0 ; + OpenBabel::vector3 *arg3 = 0 ; + OpenBabel::vector3 *arg4 = 0 ; + bool result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + (void)jarg2_; + (void)jarg3_; + (void)jarg4_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + arg2 = *(OpenBabel::vector3 **)&jarg2; + if(!arg2) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::vector3 & reference is null"); + return 0; + } + arg3 = *(OpenBabel::vector3 **)&jarg3; + if(!arg3) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::vector3 & reference is null"); + return 0; + } + arg4 = *(OpenBabel::vector3 **)&jarg4; + if(!arg4) { + SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "OpenBabel::vector3 & reference is null"); + return 0; + } + result = (bool)(*arg1)->findCenterAndNormal(*arg2,*arg3,*arg4); + jresult = (jboolean)result; + return jresult; +} + + +SWIGEXPORT jint JNICALL Java_openbabelJNI_OBMolRingIter_1Size(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jint jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + result = (int)(*arg1)->Size(); + jresult = (jint)result; + return jresult; +} + + +SWIGEXPORT jint JNICALL Java_openbabelJNI_OBMolRingIter_1PathSize(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jint jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + result = (int)(*arg1)->PathSize(); + jresult = (jint)result; + return jresult; +} + + +SWIGEXPORT jboolean JNICALL Java_openbabelJNI_OBMolRingIter_1IsMember_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) { + jboolean jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBAtom *arg2 = (OpenBabel::OBAtom *) 0 ; + bool result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + (void)jarg2_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + arg2 = *(OpenBabel::OBAtom **)&jarg2; + result = (bool)(*arg1)->IsMember(arg2); + jresult = (jboolean)result; + return jresult; +} + + +SWIGEXPORT jboolean JNICALL Java_openbabelJNI_OBMolRingIter_1IsMember_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) { + jboolean jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBond *arg2 = (OpenBabel::OBBond *) 0 ; + bool result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + (void)jarg2_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + arg2 = *(OpenBabel::OBBond **)&jarg2; + result = (bool)(*arg1)->IsMember(arg2); + jresult = (jboolean)result; + return jresult; +} + + +SWIGEXPORT jboolean JNICALL Java_openbabelJNI_OBMolRingIter_1IsAromatic(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jboolean jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + bool result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + result = (bool)(*arg1)->IsAromatic(); + jresult = (jboolean)result; + return jresult; +} + + +SWIGEXPORT jboolean JNICALL Java_openbabelJNI_OBMolRingIter_1IsInRing(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jint jarg2) { + jboolean jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int arg2 ; + bool result; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + arg2 = (int)jarg2; + result = (bool)(*arg1)->IsInRing(arg2); + jresult = (jboolean)result; + return jresult; +} + + +SWIGEXPORT void JNICALL Java_openbabelJNI_OBMolRingIter_1SetParent(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *arg2 = (OpenBabel::OBMol *) 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + (void)jarg2_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + arg2 = *(OpenBabel::OBMol **)&jarg2; + (*arg1)->SetParent(arg2); +} + + +SWIGEXPORT jlong JNICALL Java_openbabelJNI_OBMolRingIter_1GetParent(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) { + jlong jresult = 0 ; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *result = 0 ; + + (void)jenv; + (void)jcls; + (void)jarg1_; + arg1 = *(OpenBabel::OBMolRingIter **)&jarg1; + result = (OpenBabel::OBMol *)(*arg1)->GetParent(); + *(OpenBabel::OBMol **)&jresult = result; + return jresult; +} + + SWIGEXPORT jlong JNICALL Java_openbabelJNI_SWIGOBElementTableUpcast(JNIEnv *jenv, jclass jcls, jlong jarg1) { jlong baseptr = 0; (void)jenv; diff --git a/scripts/java/pairTint_int_t.java b/scripts/java/pairTint_int_t.java new file mode 100644 index 000000000..d7c898bd4 --- /dev/null +++ b/scripts/java/pairTint_int_t.java @@ -0,0 +1,25 @@ +/* ---------------------------------------------------------------------------- + * This file was automatically generated by SWIG (http://www.swig.org). + * Version 1.3.30 + * + * Do not make changes to this file unless you know what you are doing--modify + * the SWIG interface file instead. + * ----------------------------------------------------------------------------- */ + + +public class SWIGTYPE_p_std__pairTint_int_t { + private long swigCPtr; + + protected SWIGTYPE_p_std__pairTint_int_t(long cPtr, boolean futureUse) { + swigCPtr = cPtr; + } + + protected SWIGTYPE_p_std__pairTint_int_t() { + swigCPtr = 0; + } + + protected static long getCPtr(SWIGTYPE_p_std__pairTint_int_t obj) { + return (obj == null) ? 0 : obj.swigCPtr; + } +} + diff --git a/scripts/openbabel-java.i b/scripts/openbabel-java.i index 86638f3a5..493d3c229 100644 --- a/scripts/openbabel-java.i +++ b/scripts/openbabel-java.i @@ -8,21 +8,21 @@ #include -#include "obutil.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include %} %include "std_map.i" @@ -42,30 +42,30 @@ namespace std { %template (vectorData) vector; } -%import "babelconfig.h" +%import %apply std::string &OUTPUT { std::string &to }; -%include "data.h" -%include "obutil.h" -%include "math/vector3.h" -%import "math/matrix3x3.h" -%include "generic.h" +%include +%include +%include +%import +%include -%include "base.h" +%include -%import "chains.h" -%import "bitvec.h" -%import "typer.h" +%import +%import +%import -%include "oberror.h" -%include "obconversion.h" -%include "residue.h" -%include "atom.h" -%include "bond.h" -%include "mol.h" -%include "ring.h" -%include "parsmart.h" -%include "fingerprint.h" +%include +%include +%include +%include +%include +%include +%include +%include +%include %rename(inc) OpenBabel::OBMolAtomIter::operator++; %rename(inc) OpenBabel::OBMolBondIter::operator++; @@ -88,4 +88,4 @@ namespace std { %rename(deref) OpenBabel::OBResidueAtomIter::operator->; %rename(deref) OpenBabel::OBResidueBondIter::operator->; -%include "obiter.h" +%include diff --git a/scripts/openbabel-perl.i b/scripts/openbabel-perl.i index cd1cee2b3..740576430 100644 --- a/scripts/openbabel-perl.i +++ b/scripts/openbabel-perl.i @@ -8,27 +8,27 @@ #endif -#include "obutil.h" -#include "rand.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "atom.h" -#include "bond.h" -#include "residue.h" -#include "internalcoord.h" +#include +#include +#include +#include +#include +#include -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include %} %include "std_list.i" @@ -49,32 +49,32 @@ namespace std { %template (vectorData) vector; } -%import "babelconfig.h" +%import %apply std::string &OUTPUT { std::string &to }; -%include "data.h" -%include "rand.h" -%include "obutil.h" -%include "math/vector3.h" -%import "math/matrix3x3.h" -%include "generic.h" +%include +%include +%include +%include +%import +%include -%include "base.h" +%include -%import "chains.h" -%import "bitvec.h" -%import "typer.h" +%import +%import +%import -%include "oberror.h" -%include "obconversion.h" -%include "residue.h" -%include "internalcoord.h" -%include "atom.h" -%include "bond.h" -%include "mol.h" -%include "ring.h" -%include "parsmart.h" -%include "fingerprint.h" +%include +%include +%include +%include +%include +%include +%include +%include +%include +%include %rename(inc) OpenBabel::OBMolAtomIter::operator++; %rename(inc) OpenBabel::OBMolBondIter::operator++; @@ -97,4 +97,4 @@ namespace std { %rename(deref) OpenBabel::OBResidueAtomIter::operator->; %rename(deref) OpenBabel::OBResidueBondIter::operator->; -%include "obiter.h" +%include diff --git a/scripts/openbabel-python.i b/scripts/openbabel-python.i index bb07cee19..51ccaf240 100644 --- a/scripts/openbabel-python.i +++ b/scripts/openbabel-python.i @@ -7,27 +7,27 @@ #endif -#include "obutil.h" -#include "rand.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "atom.h" -#include "bond.h" -#include "residue.h" -#include "internalcoord.h" +#include +#include +#include +#include +#include +#include -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include %} %include "std_list.i" @@ -48,32 +48,32 @@ namespace std { %template (vectorData) vector; } -%import "babelconfig.h" +%import %apply std::string &OUTPUT { std::string &to }; -%include "data.h" -%include "rand.h" -%include "obutil.h" -%include "math/vector3.h" -%import "math/matrix3x3.h" -%include "generic.h" +%include +%include +%include +%include +%import +%include -%include "base.h" +%include -%import "chains.h" -%import "bitvec.h" -%import "typer.h" +%import +%import +%import -%include "oberror.h" -%include "obconversion.h" -%include "residue.h" -%include "internalcoord.h" -%include "atom.h" -%include "bond.h" -%include "mol.h" -%include "ring.h" -%include "parsmart.h" -%include "fingerprint.h" +%include +%include +%include +%include +%include +%include +%include +%include +%include +%include %rename(inc) OpenBabel::OBMolAtomIter::operator++; %rename(inc) OpenBabel::OBMolBondIter::operator++; @@ -96,7 +96,7 @@ namespace std { %rename(deref) OpenBabel::OBResidueAtomIter::operator->; %rename(deref) OpenBabel::OBResidueBondIter::operator->; -%include "obiter.h" +%include %include "carrays.i" %array_class(double, doubleArray) diff --git a/scripts/openbabel-ruby.i b/scripts/openbabel-ruby.i index a6241feb0..51a5310c9 100644 --- a/scripts/openbabel-ruby.i +++ b/scripts/openbabel-ruby.i @@ -8,27 +8,27 @@ #include -#include "obutil.h" -#include "rand.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "atom.h" -#include "bond.h" -#include "residue.h" -#include "internalcoord.h" +#include +#include +#include +#include +#include +#include -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include %} %include "std_map.i" @@ -48,32 +48,32 @@ namespace std { %template (vectorData) vector; } -%import "babelconfig.h" +%import %apply std::string &OUTPUT { std::string &to }; -%include "data.h" -%include "rand.h" -%include "obutil.h" -%include "math/vector3.h" -%import "math/matrix3x3.h" -%include "generic.h" +%include +%include +%include +%include +%import +%include -%include "base.h" +%include -%import "chains.h" -%import "bitvec.h" -%import "typer.h" +%import +%import +%import -%include "oberror.h" -%include "obconversion.h" -%include "residue.h" -%include "internalcoord.h" -%include "atom.h" -%include "bond.h" -%include "mol.h" -%include "ring.h" -%include "parsmart.h" -%include "fingerprint.h" +%include +%include +%include +%include +%include +%include +%include +%include +%include +%include %rename(inc) OpenBabel::OBMolAtomIter::operator++; %rename(inc) OpenBabel::OBMolBondIter::operator++; @@ -96,4 +96,4 @@ namespace std { %rename(deref) OpenBabel::OBResidueAtomIter::operator->; %rename(deref) OpenBabel::OBResidueBondIter::operator->; -%include "obiter.h" +%include diff --git a/scripts/perl/Makefile.PL b/scripts/perl/Makefile.PL index f7bcfbbd4..b8f6f2f51 100644 --- a/scripts/perl/Makefile.PL +++ b/scripts/perl/Makefile.PL @@ -17,6 +17,6 @@ WriteMakefile( 'LDFROM' => $ldfrom, 'CC' => $CC, 'LD' => '$(CC)', - 'INC' => '-I../../src', + 'INC' => '-I../../include', 'OBJECT' => 'openbabel_perl.o' ); diff --git a/scripts/perl/OpenBabel.pm b/scripts/perl/OpenBabel.pm index a789df093..67f2c04ad 100644 --- a/scripts/perl/OpenBabel.pm +++ b/scripts/perl/OpenBabel.pm @@ -1282,6 +1282,10 @@ sub DESTROY { *SetData = *Chemistry::OpenBabelc::OBRingData_SetData; *PushBack = *Chemistry::OpenBabelc::OBRingData_PushBack; *GetData = *Chemistry::OpenBabelc::OBRingData_GetData; +*BeginRings = *Chemistry::OpenBabelc::OBRingData_BeginRings; +*EndRings = *Chemistry::OpenBabelc::OBRingData_EndRings; +*BeginRing = *Chemistry::OpenBabelc::OBRingData_BeginRing; +*NextRing = *Chemistry::OpenBabelc::OBRingData_NextRing; sub DISOWN { my $self = shift; my $ptr = tied(%$self); @@ -2564,6 +2568,7 @@ sub DESTROY { *Align = *Chemistry::OpenBabelc::OBMol_Align; *ConnectTheDots = *Chemistry::OpenBabelc::OBMol_ConnectTheDots; *PerceiveBondOrders = *Chemistry::OpenBabelc::OBMol_PerceiveBondOrders; +*FindAngles = *Chemistry::OpenBabelc::OBMol_FindAngles; *FindTorsions = *Chemistry::OpenBabelc::OBMol_FindTorsions; *GetGTDVector = *Chemistry::OpenBabelc::OBMol_GetGTDVector; *GetGIVector = *Chemistry::OpenBabelc::OBMol_GetGIVector; @@ -4252,6 +4257,188 @@ sub ACQUIRE { } +############# Class : Chemistry::OpenBabel::OBMolAngleIter ############## + +package Chemistry::OpenBabel::OBMolAngleIter; +use overload + "++" => sub { $_[0]->__plusplus__()}, + "fallback" => 1; +use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS); +@ISA = qw( Chemistry::OpenBabel ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = Chemistry::OpenBabelc::new_OBMolAngleIter(@_); + bless $self, $pkg if defined($self); +} + +*__plusplus__ = *Chemistry::OpenBabelc::OBMolAngleIter___plusplus__; +*__ref__ = *Chemistry::OpenBabelc::OBMolAngleIter___ref__; +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + Chemistry::OpenBabelc::delete_OBMolAngleIter($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : Chemistry::OpenBabel::OBMolTorsionIter ############## + +package Chemistry::OpenBabel::OBMolTorsionIter; +use overload + "++" => sub { $_[0]->__plusplus__()}, + "fallback" => 1; +use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS); +@ISA = qw( Chemistry::OpenBabel ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = Chemistry::OpenBabelc::new_OBMolTorsionIter(@_); + bless $self, $pkg if defined($self); +} + +*__plusplus__ = *Chemistry::OpenBabelc::OBMolTorsionIter___plusplus__; +*__ref__ = *Chemistry::OpenBabelc::OBMolTorsionIter___ref__; +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + Chemistry::OpenBabelc::delete_OBMolTorsionIter($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : Chemistry::OpenBabel::OBMolPairIter ############## + +package Chemistry::OpenBabel::OBMolPairIter; +use overload + "++" => sub { $_[0]->__plusplus__()}, + "fallback" => 1; +use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS); +@ISA = qw( Chemistry::OpenBabel ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = Chemistry::OpenBabelc::new_OBMolPairIter(@_); + bless $self, $pkg if defined($self); +} + +*__plusplus__ = *Chemistry::OpenBabelc::OBMolPairIter___plusplus__; +*__deref__ = *Chemistry::OpenBabelc::OBMolPairIter___deref__; +*__ref__ = *Chemistry::OpenBabelc::OBMolPairIter___ref__; +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + Chemistry::OpenBabelc::delete_OBMolPairIter($self); + delete $OWNER{$self}; + } +} + +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + +############# Class : Chemistry::OpenBabel::OBMolRingIter ############## + +package Chemistry::OpenBabel::OBMolRingIter; +use overload + "++" => sub { $_[0]->__plusplus__()}, + "fallback" => 1; +use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS); +@ISA = qw( Chemistry::OpenBabel ); +%OWNER = (); +%ITERATORS = (); +sub new { + my $pkg = shift; + my $self = Chemistry::OpenBabelc::new_OBMolRingIter(@_); + bless $self, $pkg if defined($self); +} + +*__plusplus__ = *Chemistry::OpenBabelc::OBMolRingIter___plusplus__; +*__deref__ = *Chemistry::OpenBabelc::OBMolRingIter___deref__; +*__ref__ = *Chemistry::OpenBabelc::OBMolRingIter___ref__; +sub DESTROY { + return unless $_[0]->isa('HASH'); + my $self = tied(%{$_[0]}); + return unless defined $self; + delete $ITERATORS{$self}; + if (exists $OWNER{$self}) { + Chemistry::OpenBabelc::delete_OBMolRingIter($self); + delete $OWNER{$self}; + } +} + +*swig__path_get = *Chemistry::OpenBabelc::OBMolRingIter__path_get; +*swig__path_set = *Chemistry::OpenBabelc::OBMolRingIter__path_set; +*swig__pathset_get = *Chemistry::OpenBabelc::OBMolRingIter__pathset_get; +*swig__pathset_set = *Chemistry::OpenBabelc::OBMolRingIter__pathset_set; +*findCenterAndNormal = *Chemistry::OpenBabelc::OBMolRingIter_findCenterAndNormal; +*Size = *Chemistry::OpenBabelc::OBMolRingIter_Size; +*PathSize = *Chemistry::OpenBabelc::OBMolRingIter_PathSize; +*IsMember = *Chemistry::OpenBabelc::OBMolRingIter_IsMember; +*IsAromatic = *Chemistry::OpenBabelc::OBMolRingIter_IsAromatic; +*IsInRing = *Chemistry::OpenBabelc::OBMolRingIter_IsInRing; +*SetParent = *Chemistry::OpenBabelc::OBMolRingIter_SetParent; +*GetParent = *Chemistry::OpenBabelc::OBMolRingIter_GetParent; +sub DISOWN { + my $self = shift; + my $ptr = tied(%$self); + delete $OWNER{$ptr}; +} + +sub ACQUIRE { + my $self = shift; + my $ptr = tied(%$self); + $OWNER{$ptr} = 1; +} + + # ------- VARIABLE STUBS -------- package Chemistry::OpenBabel; diff --git a/scripts/perl/openbabel_perl.cpp b/scripts/perl/openbabel_perl.cpp index 91e52fbb3..0c99c9c46 100644 --- a/scripts/perl/openbabel_perl.cpp +++ b/scripts/perl/openbabel_perl.cpp @@ -1461,98 +1461,103 @@ SWIG_Perl_SetModule(swig_module_info *module) { #define SWIGTYPE_p_OpenBabel__OBIsotopeTable swig_types[32] #define SWIGTYPE_p_OpenBabel__OBMessageHandler swig_types[33] #define SWIGTYPE_p_OpenBabel__OBMol swig_types[34] -#define SWIGTYPE_p_OpenBabel__OBMolAtomBFSIter swig_types[35] -#define SWIGTYPE_p_OpenBabel__OBMolAtomDFSIter swig_types[36] -#define SWIGTYPE_p_OpenBabel__OBMolAtomIter swig_types[37] -#define SWIGTYPE_p_OpenBabel__OBMolBondIter swig_types[38] -#define SWIGTYPE_p_OpenBabel__OBPairData swig_types[39] -#define SWIGTYPE_p_OpenBabel__OBPairTemplateTdouble_t swig_types[40] -#define SWIGTYPE_p_OpenBabel__OBPairTemplateTint_t swig_types[41] -#define SWIGTYPE_p_OpenBabel__OBRTree swig_types[42] -#define SWIGTYPE_p_OpenBabel__OBRandom swig_types[43] -#define SWIGTYPE_p_OpenBabel__OBResidue swig_types[44] -#define SWIGTYPE_p_OpenBabel__OBResidueAtomIter swig_types[45] -#define SWIGTYPE_p_OpenBabel__OBResidueData swig_types[46] -#define SWIGTYPE_p_OpenBabel__OBResidueIter swig_types[47] -#define SWIGTYPE_p_OpenBabel__OBRing swig_types[48] -#define SWIGTYPE_p_OpenBabel__OBRingData swig_types[49] -#define SWIGTYPE_p_OpenBabel__OBRingSearch swig_types[50] -#define SWIGTYPE_p_OpenBabel__OBSSMatch swig_types[51] -#define SWIGTYPE_p_OpenBabel__OBSerialNums swig_types[52] -#define SWIGTYPE_p_OpenBabel__OBSetData swig_types[53] -#define SWIGTYPE_p_OpenBabel__OBSmartsPattern swig_types[54] -#define SWIGTYPE_p_OpenBabel__OBSqrtTbl swig_types[55] -#define SWIGTYPE_p_OpenBabel__OBStopwatch swig_types[56] -#define SWIGTYPE_p_OpenBabel__OBSymmetryData swig_types[57] -#define SWIGTYPE_p_OpenBabel__OBTorsion swig_types[58] -#define SWIGTYPE_p_OpenBabel__OBTorsionData swig_types[59] -#define SWIGTYPE_p_OpenBabel__OBTypeTable swig_types[60] -#define SWIGTYPE_p_OpenBabel__OBUnitCell swig_types[61] -#define SWIGTYPE_p_OpenBabel__OBVirtualBond swig_types[62] -#define SWIGTYPE_p_OpenBabel__Pattern swig_types[63] -#define SWIGTYPE_p_OpenBabel__Template swig_types[64] -#define SWIGTYPE_p_OpenBabel__matrix3x3 swig_types[65] -#define SWIGTYPE_p_OpenBabel__obLogBuf swig_types[66] -#define SWIGTYPE_p_OpenBabel__quadTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[67] -#define SWIGTYPE_p_OpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[68] -#define SWIGTYPE_p_OpenBabel__vector3 swig_types[69] -#define SWIGTYPE_p_a_3__double swig_types[70] -#define SWIGTYPE_p_a_4__char swig_types[71] -#define SWIGTYPE_p_char swig_types[72] -#define SWIGTYPE_p_double swig_types[73] -#define SWIGTYPE_p_int swig_types[74] -#define SWIGTYPE_p_p_OpenBabel__OBFingerprint swig_types[75] -#define SWIGTYPE_p_p_OpenBabel__OBFormat swig_types[76] -#define SWIGTYPE_p_p_double swig_types[77] -#define SWIGTYPE_p_p_int swig_types[78] -#define SWIGTYPE_p_std__dequeTint_t swig_types[79] -#define SWIGTYPE_p_std__ifstream swig_types[80] -#define SWIGTYPE_p_std__istream swig_types[81] -#define SWIGTYPE_p_std__mapTchar_const_p_OpenBabel__OBFormat_p_OpenBabel__CharPtrLess_t swig_types[82] -#define SWIGTYPE_p_std__mapTint_OpenBabel__OBAtom_p_t swig_types[83] -#define SWIGTYPE_p_std__mapTstd__string_std__string_t swig_types[84] -#define SWIGTYPE_p_std__multimapTdouble_unsigned_int_t swig_types[85] -#define SWIGTYPE_p_std__ostream swig_types[86] -#define SWIGTYPE_p_std__out_of_range swig_types[87] -#define SWIGTYPE_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[88] -#define SWIGTYPE_p_std__streampos swig_types[89] -#define SWIGTYPE_p_std__string swig_types[90] -#define SWIGTYPE_p_std__type_info swig_types[91] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t swig_types[92] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator swig_types[93] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t swig_types[94] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator swig_types[95] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_t swig_types[96] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBExternalBond_t swig_types[97] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t swig_types[98] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator swig_types[99] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t swig_types[100] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator swig_types[101] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_t swig_types[102] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator swig_types[103] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_t swig_types[104] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t swig_types[105] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator swig_types[106] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_t swig_types[107] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBTorsion_t swig_types[108] -#define SWIGTYPE_p_std__vectorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_t swig_types[109] -#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_t swig_types[110] -#define SWIGTYPE_p_std__vectorTdouble_p_t swig_types[111] -#define SWIGTYPE_p_std__vectorTdouble_p_t__iterator swig_types[112] -#define SWIGTYPE_p_std__vectorTdouble_t swig_types[113] -#define SWIGTYPE_p_std__vectorTint_t swig_types[114] -#define SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t swig_types[115] -#define SWIGTYPE_p_std__vectorTstd__pairTstd__string_std__string_t_t swig_types[116] -#define SWIGTYPE_p_std__vectorTstd__string_t swig_types[117] -#define SWIGTYPE_p_std__vectorTstd__vectorTOpenBabel__vector3_t_t swig_types[118] -#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t swig_types[119] -#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator swig_types[120] -#define SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t swig_types[121] -#define SWIGTYPE_p_std__vectorTunsigned_int_t swig_types[122] -#define SWIGTYPE_p_std__vectorTunsigned_short_t swig_types[123] -#define SWIGTYPE_p_unsigned_int swig_types[124] -static swig_type_info *swig_types[126]; -static swig_module_info swig_module = {swig_types, 125, 0, 0, 0, 0}; +#define SWIGTYPE_p_OpenBabel__OBMolAngleIter swig_types[35] +#define SWIGTYPE_p_OpenBabel__OBMolAtomBFSIter swig_types[36] +#define SWIGTYPE_p_OpenBabel__OBMolAtomDFSIter swig_types[37] +#define SWIGTYPE_p_OpenBabel__OBMolAtomIter swig_types[38] +#define SWIGTYPE_p_OpenBabel__OBMolBondIter swig_types[39] +#define SWIGTYPE_p_OpenBabel__OBMolPairIter swig_types[40] +#define SWIGTYPE_p_OpenBabel__OBMolRingIter swig_types[41] +#define SWIGTYPE_p_OpenBabel__OBMolTorsionIter swig_types[42] +#define SWIGTYPE_p_OpenBabel__OBPairData swig_types[43] +#define SWIGTYPE_p_OpenBabel__OBPairTemplateTdouble_t swig_types[44] +#define SWIGTYPE_p_OpenBabel__OBPairTemplateTint_t swig_types[45] +#define SWIGTYPE_p_OpenBabel__OBRTree swig_types[46] +#define SWIGTYPE_p_OpenBabel__OBRandom swig_types[47] +#define SWIGTYPE_p_OpenBabel__OBResidue swig_types[48] +#define SWIGTYPE_p_OpenBabel__OBResidueAtomIter swig_types[49] +#define SWIGTYPE_p_OpenBabel__OBResidueData swig_types[50] +#define SWIGTYPE_p_OpenBabel__OBResidueIter swig_types[51] +#define SWIGTYPE_p_OpenBabel__OBRing swig_types[52] +#define SWIGTYPE_p_OpenBabel__OBRingData swig_types[53] +#define SWIGTYPE_p_OpenBabel__OBRingSearch swig_types[54] +#define SWIGTYPE_p_OpenBabel__OBSSMatch swig_types[55] +#define SWIGTYPE_p_OpenBabel__OBSerialNums swig_types[56] +#define SWIGTYPE_p_OpenBabel__OBSetData swig_types[57] +#define SWIGTYPE_p_OpenBabel__OBSmartsPattern swig_types[58] +#define SWIGTYPE_p_OpenBabel__OBSqrtTbl swig_types[59] +#define SWIGTYPE_p_OpenBabel__OBStopwatch swig_types[60] +#define SWIGTYPE_p_OpenBabel__OBSymmetryData swig_types[61] +#define SWIGTYPE_p_OpenBabel__OBTorsion swig_types[62] +#define SWIGTYPE_p_OpenBabel__OBTorsionData swig_types[63] +#define SWIGTYPE_p_OpenBabel__OBTypeTable swig_types[64] +#define SWIGTYPE_p_OpenBabel__OBUnitCell swig_types[65] +#define SWIGTYPE_p_OpenBabel__OBVirtualBond swig_types[66] +#define SWIGTYPE_p_OpenBabel__Pattern swig_types[67] +#define SWIGTYPE_p_OpenBabel__Template swig_types[68] +#define SWIGTYPE_p_OpenBabel__matrix3x3 swig_types[69] +#define SWIGTYPE_p_OpenBabel__obLogBuf swig_types[70] +#define SWIGTYPE_p_OpenBabel__quadTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[71] +#define SWIGTYPE_p_OpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[72] +#define SWIGTYPE_p_OpenBabel__vector3 swig_types[73] +#define SWIGTYPE_p_a_3__double swig_types[74] +#define SWIGTYPE_p_a_4__char swig_types[75] +#define SWIGTYPE_p_char swig_types[76] +#define SWIGTYPE_p_double swig_types[77] +#define SWIGTYPE_p_int swig_types[78] +#define SWIGTYPE_p_p_OpenBabel__OBFingerprint swig_types[79] +#define SWIGTYPE_p_p_OpenBabel__OBFormat swig_types[80] +#define SWIGTYPE_p_p_double swig_types[81] +#define SWIGTYPE_p_p_int swig_types[82] +#define SWIGTYPE_p_std__dequeTint_t swig_types[83] +#define SWIGTYPE_p_std__ifstream swig_types[84] +#define SWIGTYPE_p_std__istream swig_types[85] +#define SWIGTYPE_p_std__mapTchar_const_p_OpenBabel__OBFormat_p_OpenBabel__CharPtrLess_t swig_types[86] +#define SWIGTYPE_p_std__mapTint_OpenBabel__OBAtom_p_t swig_types[87] +#define SWIGTYPE_p_std__mapTstd__string_std__string_t swig_types[88] +#define SWIGTYPE_p_std__multimapTdouble_unsigned_int_t swig_types[89] +#define SWIGTYPE_p_std__ostream swig_types[90] +#define SWIGTYPE_p_std__out_of_range swig_types[91] +#define SWIGTYPE_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[92] +#define SWIGTYPE_p_std__pairTint_int_t swig_types[93] +#define SWIGTYPE_p_std__streampos swig_types[94] +#define SWIGTYPE_p_std__string swig_types[95] +#define SWIGTYPE_p_std__type_info swig_types[96] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t swig_types[97] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator swig_types[98] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t swig_types[99] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator swig_types[100] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_t swig_types[101] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBExternalBond_t swig_types[102] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t swig_types[103] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator swig_types[104] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t swig_types[105] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator swig_types[106] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_t swig_types[107] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator swig_types[108] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_t swig_types[109] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t swig_types[110] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator swig_types[111] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_t swig_types[112] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBTorsion_t swig_types[113] +#define SWIGTYPE_p_std__vectorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_t swig_types[114] +#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_t swig_types[115] +#define SWIGTYPE_p_std__vectorTdouble_p_t swig_types[116] +#define SWIGTYPE_p_std__vectorTdouble_p_t__iterator swig_types[117] +#define SWIGTYPE_p_std__vectorTdouble_t swig_types[118] +#define SWIGTYPE_p_std__vectorTint_t swig_types[119] +#define SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t swig_types[120] +#define SWIGTYPE_p_std__vectorTstd__pairTstd__string_std__string_t_t swig_types[121] +#define SWIGTYPE_p_std__vectorTstd__string_t swig_types[122] +#define SWIGTYPE_p_std__vectorTstd__vectorTOpenBabel__vector3_t_t swig_types[123] +#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t swig_types[124] +#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator swig_types[125] +#define SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t swig_types[126] +#define SWIGTYPE_p_std__vectorTunsigned_int_t swig_types[127] +#define SWIGTYPE_p_std__vectorTunsigned_short_t swig_types[128] +#define SWIGTYPE_p_unsigned_int swig_types[129] +static swig_type_info *swig_types[131]; +static swig_module_info swig_module = {swig_types, 130, 0, 0, 0, 0}; #define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name) #define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name) @@ -1594,27 +1599,27 @@ SWIGEXPORT void SWIG_init (CV *cv, CPerlObj *); #endif -#include "obutil.h" -#include "rand.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "atom.h" -#include "bond.h" -#include "residue.h" -#include "internalcoord.h" +#include +#include +#include +#include +#include +#include -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include #include @@ -18503,6 +18508,144 @@ XS(_wrap_OBRingData_GetData) { } +XS(_wrap_OBRingData_BeginRings) { + { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper::iterator > result; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBRingData_BeginRings(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_BeginRings" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + result = (arg1)->BeginRings(); + ST(argvi) = SWIG_NewPointerObj((new std::vector::iterator(static_cast< const std::vector::iterator& >(result))), SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, SWIG_POINTER_OWN | 0); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBRingData_EndRings) { + { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper::iterator > result; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBRingData_EndRings(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_EndRings" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + result = (arg1)->EndRings(); + ST(argvi) = SWIG_NewPointerObj((new std::vector::iterator(static_cast< const std::vector::iterator& >(result))), SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, SWIG_POINTER_OWN | 0); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBRingData_BeginRing) { + { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBRingData_BeginRing(self,i);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_BeginRing" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBRingData_BeginRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBRingData_BeginRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + arg2 = reinterpret_cast< std::vector::iterator * >(argp2); + result = (OpenBabel::OBRing *)(arg1)->BeginRing(*arg2); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | SWIG_SHADOW); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBRingData_NextRing) { + { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBRingData_NextRing(self,i);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_NextRing" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBRingData_NextRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBRingData_NextRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + arg2 = reinterpret_cast< std::vector::iterator * >(argp2); + result = (OpenBabel::OBRing *)(arg1)->NextRing(*arg2); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | SWIG_SHADOW); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + XS(_wrap_new_OBUnitCell__SWIG_0) { { OpenBabel::OBUnitCell *result = 0 ; @@ -22468,7 +22611,7 @@ XS(_wrap_OBAngleData_Clear) { } -XS(_wrap_OBAngleData_FillAngleArray) { +XS(_wrap_OBAngleData_FillAngleArray__SWIG_0) { { OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; int **arg2 = (int **) 0 ; @@ -22519,6 +22662,136 @@ XS(_wrap_OBAngleData_FillAngleArray) { } +XS(_wrap_OBAngleData_FillAngleArray__SWIG_1) { + { + OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; + std::vector > *arg2 = 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBAngleData_FillAngleArray(self,angles);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBAngleData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBAngleData_FillAngleArray" "', argument " "1"" of type '" "OpenBabel::OBAngleData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBAngleData * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBAngleData_FillAngleArray" "', argument " "2"" of type '" "std::vector > &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBAngleData_FillAngleArray" "', argument " "2"" of type '" "std::vector > &""'"); + } + arg2 = reinterpret_cast< std::vector > * >(argp2); + result = (bool)(arg1)->FillAngleArray(*arg2); + ST(argvi) = SWIG_From_bool SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBAngleData_FillAngleArray) { + dXSARGS; + + { + unsigned long _index = 0; + SWIG_TypeRank _rank = 0; + if (items == 2) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBAngleData, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_1; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(1), &vptr, SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_1; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 1; + if (_rank == _rankm) goto dispatch; + } + } + check_1: + + if (items == 3) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBAngleData, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(1), &vptr, SWIGTYPE_p_p_int, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(2), &vptr, SWIGTYPE_p_unsigned_int, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 2; + if (_rank == _rankm) goto dispatch; + } + } + check_2: + + dispatch: + switch(_index) { + case 1: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBAngleData_FillAngleArray__SWIG_1); return; + case 2: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBAngleData_FillAngleArray__SWIG_0); return; + } + } + + croak("No matching function for overloaded 'OBAngleData_FillAngleArray'"); + XSRETURN(0); +} + + XS(_wrap_OBAngleData_SetData) { { OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; @@ -45428,6 +45701,33 @@ XS(_wrap_OBMol_PerceiveBondOrders) { } +XS(_wrap_OBMol_FindAngles) { + { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMol_FindAngles(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMol_FindAngles" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + (arg1)->FindAngles(); + + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + XS(_wrap_OBMol_FindTorsions) { { OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; @@ -92764,6 +93064,1932 @@ XS(_wrap_OBResidueAtomIter_EndData) { } +XS(_wrap_new_OBMolAngleIter__SWIG_0) { + { + OpenBabel::OBMolAngleIter *result = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_OBMolAngleIter();"); + } + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + XSRETURN(argvi); + fail: + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolAngleIter__SWIG_1) { + { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolAngleIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolAngleIter__SWIG_2) { + { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolAngleIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolAngleIter__SWIG_3) { + { + OpenBabel::OBMolAngleIter *arg1 = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolAngleIter(ai);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter((OpenBabel::OBMolAngleIter const &)*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolAngleIter) { + dXSARGS; + + { + unsigned long _index = 0; + SWIG_TypeRank _rank = 0; + if (items == 0) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 1; + if (_rank == _rankm) goto dispatch; + } + } + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 2; + if (_rank == _rankm) goto dispatch; + } + } + check_2: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_3; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 3; + if (_rank == _rankm) goto dispatch; + } + } + check_3: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_4; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 4; + if (_rank == _rankm) goto dispatch; + } + } + check_4: + + dispatch: + switch(_index) { + case 1: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolAngleIter__SWIG_0); return; + case 2: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolAngleIter__SWIG_1); return; + case 3: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolAngleIter__SWIG_2); return; + case 4: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolAngleIter__SWIG_3); return; + } + } + + croak("No matching function for overloaded 'new_OBMolAngleIter'"); + XSRETURN(0); +} + + +XS(_wrap_OBMolAngleIter___plusplus__) { + { + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + int arg2 ; + OpenBabel::OBMolAngleIter result; + void *argp1 = 0 ; + int res1 = 0 ; + int val2 ; + int ecode2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolAngleIter___plusplus__(self,int);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolAngleIter___plusplus__" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); + if (!SWIG_IsOK(ecode2)) { + SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBMolAngleIter___plusplus__" "', argument " "2"" of type '" "int""'"); + } + arg2 = static_cast< int >(val2); + result = (arg1)->operator ++(arg2); + ST(argvi) = SWIG_NewPointerObj((new OpenBabel::OBMolAngleIter(static_cast< const OpenBabel::OBMolAngleIter& >(result))), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_POINTER_OWN | SWIG_SHADOW); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolAngleIter___ref__) { + { + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + std::vector result; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolAngleIter___ref__(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolAngleIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + result = ((OpenBabel::OBMolAngleIter const *)arg1)->operator *(); + ST(argvi) = SWIG_NewPointerObj((new std::vector(static_cast< const std::vector& >(result))), SWIGTYPE_p_std__vectorTunsigned_int_t, SWIG_POINTER_OWN | 0); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_delete_OBMolAngleIter) { + { + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_OBMolAngleIter(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + delete arg1; + + + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolTorsionIter__SWIG_0) { + { + OpenBabel::OBMolTorsionIter *result = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_OBMolTorsionIter();"); + } + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + XSRETURN(argvi); + fail: + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolTorsionIter__SWIG_1) { + { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolTorsionIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolTorsionIter__SWIG_2) { + { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolTorsionIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolTorsionIter__SWIG_3) { + { + OpenBabel::OBMolTorsionIter *arg1 = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolTorsionIter(ai);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter((OpenBabel::OBMolTorsionIter const &)*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolTorsionIter) { + dXSARGS; + + { + unsigned long _index = 0; + SWIG_TypeRank _rank = 0; + if (items == 0) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 1; + if (_rank == _rankm) goto dispatch; + } + } + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 2; + if (_rank == _rankm) goto dispatch; + } + } + check_2: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_3; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 3; + if (_rank == _rankm) goto dispatch; + } + } + check_3: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_4; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 4; + if (_rank == _rankm) goto dispatch; + } + } + check_4: + + dispatch: + switch(_index) { + case 1: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolTorsionIter__SWIG_0); return; + case 2: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolTorsionIter__SWIG_1); return; + case 3: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolTorsionIter__SWIG_2); return; + case 4: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolTorsionIter__SWIG_3); return; + } + } + + croak("No matching function for overloaded 'new_OBMolTorsionIter'"); + XSRETURN(0); +} + + +XS(_wrap_OBMolTorsionIter___plusplus__) { + { + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + int arg2 ; + OpenBabel::OBMolTorsionIter result; + void *argp1 = 0 ; + int res1 = 0 ; + int val2 ; + int ecode2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolTorsionIter___plusplus__(self,int);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolTorsionIter___plusplus__" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); + if (!SWIG_IsOK(ecode2)) { + SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBMolTorsionIter___plusplus__" "', argument " "2"" of type '" "int""'"); + } + arg2 = static_cast< int >(val2); + result = (arg1)->operator ++(arg2); + ST(argvi) = SWIG_NewPointerObj((new OpenBabel::OBMolTorsionIter(static_cast< const OpenBabel::OBMolTorsionIter& >(result))), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_POINTER_OWN | SWIG_SHADOW); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolTorsionIter___ref__) { + { + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + std::vector result; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolTorsionIter___ref__(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolTorsionIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + result = ((OpenBabel::OBMolTorsionIter const *)arg1)->operator *(); + ST(argvi) = SWIG_NewPointerObj((new std::vector(static_cast< const std::vector& >(result))), SWIGTYPE_p_std__vectorTunsigned_int_t, SWIG_POINTER_OWN | 0); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_delete_OBMolTorsionIter) { + { + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_OBMolTorsionIter(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + delete arg1; + + + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolPairIter__SWIG_0) { + { + OpenBabel::OBMolPairIter *result = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_OBMolPairIter();"); + } + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + XSRETURN(argvi); + fail: + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolPairIter__SWIG_1) { + { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolPairIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolPairIter__SWIG_2) { + { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolPairIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolPairIter__SWIG_3) { + { + OpenBabel::OBMolPairIter *arg1 = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolPairIter(ai);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter((OpenBabel::OBMolPairIter const &)*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolPairIter) { + dXSARGS; + + { + unsigned long _index = 0; + SWIG_TypeRank _rank = 0; + if (items == 0) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 1; + if (_rank == _rankm) goto dispatch; + } + } + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 2; + if (_rank == _rankm) goto dispatch; + } + } + check_2: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_3; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 3; + if (_rank == _rankm) goto dispatch; + } + } + check_3: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolPairIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_4; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 4; + if (_rank == _rankm) goto dispatch; + } + } + check_4: + + dispatch: + switch(_index) { + case 1: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolPairIter__SWIG_0); return; + case 2: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolPairIter__SWIG_1); return; + case 3: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolPairIter__SWIG_2); return; + case 4: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolPairIter__SWIG_3); return; + } + } + + croak("No matching function for overloaded 'new_OBMolPairIter'"); + XSRETURN(0); +} + + +XS(_wrap_OBMolPairIter___plusplus__) { + { + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + int arg2 ; + OpenBabel::OBMolPairIter result; + void *argp1 = 0 ; + int res1 = 0 ; + int val2 ; + int ecode2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolPairIter___plusplus__(self,int);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolPairIter___plusplus__" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); + if (!SWIG_IsOK(ecode2)) { + SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBMolPairIter___plusplus__" "', argument " "2"" of type '" "int""'"); + } + arg2 = static_cast< int >(val2); + result = (arg1)->operator ++(arg2); + ST(argvi) = SWIG_NewPointerObj((new OpenBabel::OBMolPairIter(static_cast< const OpenBabel::OBMolPairIter& >(result))), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_POINTER_OWN | SWIG_SHADOW); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolPairIter___deref__) { + { + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolPairIter___deref__(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolPairIter___deref__" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + result = (std::pair *)((OpenBabel::OBMolPairIter const *)arg1)->operator ->(); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__pairTint_int_t, 0 | 0); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolPairIter___ref__) { + { + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolPairIter___ref__(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolPairIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + { + std::pair &_result_ref = ((OpenBabel::OBMolPairIter const *)arg1)->operator *(); + result = (std::pair *) &_result_ref; + } + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__pairTint_int_t, 0 | 0); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_delete_OBMolPairIter) { + { + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_OBMolPairIter(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + delete arg1; + + + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolRingIter__SWIG_0) { + { + OpenBabel::OBMolRingIter *result = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 0) || (items > 0)) { + SWIG_croak("Usage: new_OBMolRingIter();"); + } + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + XSRETURN(argvi); + fail: + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolRingIter__SWIG_1) { + { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolRingIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolRingIter__SWIG_2) { + { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolRingIter(mol);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolRingIter__SWIG_3) { + { + OpenBabel::OBMolRingIter *arg1 = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: new_OBMolRingIter(ri);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter((OpenBabel::OBMolRingIter const &)*arg1); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_OWNER | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_new_OBMolRingIter) { + dXSARGS; + + { + unsigned long _index = 0; + SWIG_TypeRank _rank = 0; + if (items == 0) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 1; + if (_rank == _rankm) goto dispatch; + } + } + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 2; + if (_rank == _rankm) goto dispatch; + } + } + check_2: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_3; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 3; + if (_rank == _rankm) goto dispatch; + } + } + check_3: + + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_4; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 4; + if (_rank == _rankm) goto dispatch; + } + } + check_4: + + dispatch: + switch(_index) { + case 1: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolRingIter__SWIG_0); return; + case 2: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolRingIter__SWIG_1); return; + case 3: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolRingIter__SWIG_2); return; + case 4: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_new_OBMolRingIter__SWIG_3); return; + } + } + + croak("No matching function for overloaded 'new_OBMolRingIter'"); + XSRETURN(0); +} + + +XS(_wrap_OBMolRingIter___plusplus____SWIG_0) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter___plusplus__(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter___plusplus__" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + OpenBabel::OBMolRingIter &_result_ref = (arg1)->operator ++(); + result = (OpenBabel::OBMolRingIter *) &_result_ref; + } + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter___plusplus____SWIG_1) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int arg2 ; + OpenBabel::OBMolRingIter result; + void *argp1 = 0 ; + int res1 = 0 ; + int val2 ; + int ecode2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolRingIter___plusplus__(self,int);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter___plusplus__" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); + if (!SWIG_IsOK(ecode2)) { + SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBMolRingIter___plusplus__" "', argument " "2"" of type '" "int""'"); + } + arg2 = static_cast< int >(val2); + result = (arg1)->operator ++(arg2); + ST(argvi) = SWIG_NewPointerObj((new OpenBabel::OBMolRingIter(static_cast< const OpenBabel::OBMolRingIter& >(result))), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_POINTER_OWN | SWIG_SHADOW); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter___plusplus__) { + dXSARGS; + + { + unsigned long _index = 0; + SWIG_TypeRank _rank = 0; + if (items == 1) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_1; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 1; + if (_rank == _rankm) goto dispatch; + } + } + check_1: + + if (items == 2) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + { + { + int res = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), NULL); + _v = SWIG_CheckState(res); + } + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 2; + if (_rank == _rankm) goto dispatch; + } + } + check_2: + + dispatch: + switch(_index) { + case 1: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBMolRingIter___plusplus____SWIG_0); return; + case 2: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBMolRingIter___plusplus____SWIG_1); return; + } + } + + croak("No matching function for overloaded 'OBMolRingIter___plusplus__'"); + XSRETURN(0); +} + + +XS(_wrap_OBMolRingIter___deref__) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter___deref__(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter___deref__" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBRing *)((OpenBabel::OBMolRingIter const *)arg1)->operator ->(); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter___ref__) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter___ref__(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + OpenBabel::OBRing &_result_ref = ((OpenBabel::OBMolRingIter const *)arg1)->operator *(); + result = (OpenBabel::OBRing *) &_result_ref; + } + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_delete_OBMolRingIter) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: delete_OBMolRingIter(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + delete arg1; + + + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter__path_set) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector *arg2 = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + std::vector temp2 ; + std::vector *v2 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolRingIter__path_set(self,_path);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__path_set" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + if (SWIG_ConvertPtr(ST(1),(void **) &v2, + SWIGTYPE_p_std__vectorTint_t,1) != -1) { + arg2 = v2; + } else if (SvROK(ST(1))) { + AV *av = (AV *)SvRV(ST(1)); + if (SvTYPE(av) != SVt_PVAV) + SWIG_croak("Type error in argument 2 of OBMolRingIter__path_set. " + "Expected an array of ""int"); + SV **tv; + I32 len = av_len(av) + 1; + for (int i=0; i_path = *arg2; + + + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter__path_get) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter__path_get(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__path_get" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + std::vector const &_result_ref = ((*arg1)->_path); + result = (std::vector *) &_result_ref; + } + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorTint_t, 0 | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter__pathset_set) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *arg2 = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 ; + int res2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolRingIter__pathset_set(self,_pathset);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__pathset_set" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_OpenBabel__OBBitVec, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter__pathset_set" "', argument " "2"" of type '" "OpenBabel::OBBitVec const &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter__pathset_set" "', argument " "2"" of type '" "OpenBabel::OBBitVec const &""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); + if (arg1) (*arg1)->_pathset = *arg2; + + + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter__pathset_get) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter__pathset_get(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__pathset_get" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + OpenBabel::OBBitVec const &_result_ref = ((*arg1)->_pathset); + result = (OpenBabel::OBBitVec *) &_result_ref; + } + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBBitVec, 0 | 0); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_findCenterAndNormal) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::vector3 *arg2 = 0 ; + OpenBabel::vector3 *arg3 = 0 ; + OpenBabel::vector3 *arg4 = 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + void *argp3 = 0 ; + int res3 = 0 ; + void *argp4 = 0 ; + int res4 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 4) || (items > 4)) { + SWIG_croak("Usage: OBMolRingIter_findCenterAndNormal(self,center,norm1,norm2);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "2"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "2"" of type '" "OpenBabel::vector3 &""'"); + } + arg2 = reinterpret_cast< OpenBabel::vector3 * >(argp2); + res3 = SWIG_ConvertPtr(ST(2), &argp3, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res3)) { + SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "3"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp3) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "3"" of type '" "OpenBabel::vector3 &""'"); + } + arg3 = reinterpret_cast< OpenBabel::vector3 * >(argp3); + res4 = SWIG_ConvertPtr(ST(3), &argp4, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res4)) { + SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "4"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp4) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "4"" of type '" "OpenBabel::vector3 &""'"); + } + arg4 = reinterpret_cast< OpenBabel::vector3 * >(argp4); + result = (bool)(*arg1)->findCenterAndNormal(*arg2,*arg3,*arg4); + ST(argvi) = SWIG_From_bool SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ; + + + + + XSRETURN(argvi); + fail: + + + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_Size) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter_Size(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_Size" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (int)(*arg1)->Size(); + ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1(static_cast< int >(result)); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_PathSize) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter_PathSize(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_PathSize" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (int)(*arg1)->PathSize(); + ST(argvi) = SWIG_From_int SWIG_PERL_CALL_ARGS_1(static_cast< int >(result)); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_IsMember__SWIG_0) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBAtom *arg2 = (OpenBabel::OBAtom *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolRingIter_IsMember(self,a);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsMember" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_OpenBabel__OBAtom, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_IsMember" "', argument " "2"" of type '" "OpenBabel::OBAtom *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBAtom * >(argp2); + result = (bool)(*arg1)->IsMember(arg2); + ST(argvi) = SWIG_From_bool SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_IsMember__SWIG_1) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBond *arg2 = (OpenBabel::OBBond *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolRingIter_IsMember(self,b);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsMember" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_OpenBabel__OBBond, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_IsMember" "', argument " "2"" of type '" "OpenBabel::OBBond *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBBond * >(argp2); + result = (bool)(*arg1)->IsMember(arg2); + ST(argvi) = SWIG_From_bool SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_IsMember) { + dXSARGS; + + { + unsigned long _index = 0; + SWIG_TypeRank _rank = 0; + if (items == 2) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_1; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(1), &vptr, SWIGTYPE_p_OpenBabel__OBAtom, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_1; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 1; + if (_rank == _rankm) goto dispatch; + } + } + check_1: + + if (items == 2) { + SWIG_TypeRank _ranki = 0; + SWIG_TypeRank _rankm = 0; + SWIG_TypeRank _pi = 1; + int _v = 0; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(0), &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + { + void *vptr = 0; + int res = SWIG_ConvertPtr(ST(1), &vptr, SWIGTYPE_p_OpenBabel__OBBond, 0); + _v = SWIG_CheckState(res); + } + if (!_v) goto check_2; + _ranki += _v*_pi; + _rankm += _pi; + _pi *= SWIG_MAXCASTRANK; + if (!_index || (_ranki < _rank)) { + _rank = _ranki; _index = 2; + if (_rank == _rankm) goto dispatch; + } + } + check_2: + + dispatch: + switch(_index) { + case 1: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBMolRingIter_IsMember__SWIG_0); return; + case 2: + ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBMolRingIter_IsMember__SWIG_1); return; + } + } + + croak("No matching function for overloaded 'OBMolRingIter_IsMember'"); + XSRETURN(0); +} + + +XS(_wrap_OBMolRingIter_IsAromatic) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter_IsAromatic(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsAromatic" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (bool)(*arg1)->IsAromatic(); + ST(argvi) = SWIG_From_bool SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_IsInRing) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int arg2 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + int val2 ; + int ecode2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolRingIter_IsInRing(self,i);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsInRing" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + ecode2 = SWIG_AsVal_int SWIG_PERL_CALL_ARGS_2(ST(1), &val2); + if (!SWIG_IsOK(ecode2)) { + SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBMolRingIter_IsInRing" "', argument " "2"" of type '" "int""'"); + } + arg2 = static_cast< int >(val2); + result = (bool)(*arg1)->IsInRing(arg2); + ST(argvi) = SWIG_From_bool SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ; + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_SetParent) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *arg2 = (OpenBabel::OBMol *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 2) || (items > 2)) { + SWIG_croak("Usage: OBMolRingIter_SetParent(self,m);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_SetParent" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(ST(1), &argp2,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_SetParent" "', argument " "2"" of type '" "OpenBabel::OBMol *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); + (*arg1)->SetParent(arg2); + + + + XSRETURN(argvi); + fail: + + + SWIG_croak_null(); + } +} + + +XS(_wrap_OBMolRingIter_GetParent) { + { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int argvi = 0; + dXSARGS; + + if ((items < 1) || (items > 1)) { + SWIG_croak("Usage: OBMolRingIter_GetParent(self);"); + } + res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_GetParent" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBMol *)(*arg1)->GetParent(); + ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMol, 0 | SWIG_SHADOW); argvi++ ; + + XSRETURN(argvi); + fail: + + SWIG_croak_null(); + } +} + + /* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */ @@ -92871,10 +95097,14 @@ static swig_type_info _swigt__p_OpenBabel__OBInternalCoord = {"_p_OpenBabel__OBI static swig_type_info _swigt__p_OpenBabel__OBIsotopeTable = {"_p_OpenBabel__OBIsotopeTable", "OpenBabel::OBIsotopeTable *", 0, 0, (void*)"Chemistry::OpenBabel::OBIsotopeTable", 0}; static swig_type_info _swigt__p_OpenBabel__OBMessageHandler = {"_p_OpenBabel__OBMessageHandler", "OpenBabel::OBMessageHandler *", 0, 0, (void*)"Chemistry::OpenBabel::OBMessageHandler", 0}; static swig_type_info _swigt__p_OpenBabel__OBMol = {"_p_OpenBabel__OBMol", "OpenBabel::OBMol *", 0, 0, (void*)"Chemistry::OpenBabel::OBMol", 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolAngleIter = {"_p_OpenBabel__OBMolAngleIter", "OpenBabel::OBMolAngleIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolAngleIter", 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomBFSIter = {"_p_OpenBabel__OBMolAtomBFSIter", "OpenBabel::OBMolAtomBFSIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolAtomBFSIter", 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomDFSIter = {"_p_OpenBabel__OBMolAtomDFSIter", "OpenBabel::OBMolAtomDFSIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolAtomDFSIter", 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomIter = {"_p_OpenBabel__OBMolAtomIter", "OpenBabel::OBMolAtomIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolAtomIter", 0}; static swig_type_info _swigt__p_OpenBabel__OBMolBondIter = {"_p_OpenBabel__OBMolBondIter", "OpenBabel::OBMolBondIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolBondIter", 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolPairIter = {"_p_OpenBabel__OBMolPairIter", "OpenBabel::OBMolPairIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolPairIter", 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolRingIter = {"_p_OpenBabel__OBMolRingIter", "OpenBabel::OBMolRingIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolRingIter", 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolTorsionIter = {"_p_OpenBabel__OBMolTorsionIter", "OpenBabel::OBMolTorsionIter *", 0, 0, (void*)"Chemistry::OpenBabel::OBMolTorsionIter", 0}; static swig_type_info _swigt__p_OpenBabel__OBPairData = {"_p_OpenBabel__OBPairData", "OpenBabel::OBPairData *", 0, 0, (void*)"Chemistry::OpenBabel::OBPairData", 0}; static swig_type_info _swigt__p_OpenBabel__OBPairTemplateTdouble_t = {"_p_OpenBabel__OBPairTemplateTdouble_t", "OpenBabel::OBPairTemplate *|OpenBabel::OBPairFloatingPoint *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBPairTemplateTint_t = {"_p_OpenBabel__OBPairTemplateTint_t", "OpenBabel::OBPairTemplate *|OpenBabel::OBPairInteger *", 0, 0, (void*)0, 0}; @@ -92925,6 +95155,7 @@ static swig_type_info _swigt__p_std__multimapTdouble_unsigned_int_t = {"_p_std__ static swig_type_info _swigt__p_std__ostream = {"_p_std__ostream", "std::ostream *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__out_of_range = {"_p_std__out_of_range", "std::out_of_range *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t = {"_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t", "std::pair *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_std__pairTint_int_t = {"_p_std__pairTint_int_t", "std::pair *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__streampos = {"_p_std__streampos", "std::streampos *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__string = {"_p_std__string", "std::string *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__type_info = {"_p_std__type_info", "std::type_info *", 0, 0, (void*)0, 0}; @@ -92998,10 +95229,14 @@ static swig_type_info *swig_type_initial[] = { &_swigt__p_OpenBabel__OBIsotopeTable, &_swigt__p_OpenBabel__OBMessageHandler, &_swigt__p_OpenBabel__OBMol, + &_swigt__p_OpenBabel__OBMolAngleIter, &_swigt__p_OpenBabel__OBMolAtomBFSIter, &_swigt__p_OpenBabel__OBMolAtomDFSIter, &_swigt__p_OpenBabel__OBMolAtomIter, &_swigt__p_OpenBabel__OBMolBondIter, + &_swigt__p_OpenBabel__OBMolPairIter, + &_swigt__p_OpenBabel__OBMolRingIter, + &_swigt__p_OpenBabel__OBMolTorsionIter, &_swigt__p_OpenBabel__OBPairData, &_swigt__p_OpenBabel__OBPairTemplateTdouble_t, &_swigt__p_OpenBabel__OBPairTemplateTint_t, @@ -93052,6 +95287,7 @@ static swig_type_info *swig_type_initial[] = { &_swigt__p_std__ostream, &_swigt__p_std__out_of_range, &_swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, + &_swigt__p_std__pairTint_int_t, &_swigt__p_std__streampos, &_swigt__p_std__string, &_swigt__p_std__type_info, @@ -93125,10 +95361,14 @@ static swig_cast_info _swigc__p_OpenBabel__OBInternalCoord[] = { {&_swigt__p_Op static swig_cast_info _swigc__p_OpenBabel__OBIsotopeTable[] = { {&_swigt__p_OpenBabel__OBIsotopeTable, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMessageHandler[] = { {&_swigt__p_OpenBabel__OBMessageHandler, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMol[] = { {&_swigt__p_OpenBabel__OBMol, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolAngleIter[] = { {&_swigt__p_OpenBabel__OBMolAngleIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomBFSIter[] = { {&_swigt__p_OpenBabel__OBMolAtomBFSIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomDFSIter[] = { {&_swigt__p_OpenBabel__OBMolAtomDFSIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomIter[] = { {&_swigt__p_OpenBabel__OBMolAtomIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolBondIter[] = { {&_swigt__p_OpenBabel__OBMolBondIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolPairIter[] = { {&_swigt__p_OpenBabel__OBMolPairIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolRingIter[] = { {&_swigt__p_OpenBabel__OBMolRingIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolTorsionIter[] = { {&_swigt__p_OpenBabel__OBMolTorsionIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairData[] = { {&_swigt__p_OpenBabel__OBPairData, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairTemplateTdouble_t[] = { {&_swigt__p_OpenBabel__OBPairTemplateTdouble_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairTemplateTint_t[] = { {&_swigt__p_OpenBabel__OBPairTemplateTint_t, 0, 0, 0},{0, 0, 0, 0}}; @@ -93179,6 +95419,7 @@ static swig_cast_info _swigc__p_std__multimapTdouble_unsigned_int_t[] = { {&_sw static swig_cast_info _swigc__p_std__ostream[] = { {&_swigt__p_std__ostream, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__out_of_range[] = { {&_swigt__p_std__out_of_range, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t[] = { {&_swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_std__pairTint_int_t[] = { {&_swigt__p_std__pairTint_int_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__streampos[] = { {&_swigt__p_std__streampos, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__string[] = { {&_swigt__p_std__string, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__type_info[] = { {&_swigt__p_std__type_info, 0, 0, 0},{0, 0, 0, 0}}; @@ -93252,10 +95493,14 @@ static swig_cast_info *swig_cast_initial[] = { _swigc__p_OpenBabel__OBIsotopeTable, _swigc__p_OpenBabel__OBMessageHandler, _swigc__p_OpenBabel__OBMol, + _swigc__p_OpenBabel__OBMolAngleIter, _swigc__p_OpenBabel__OBMolAtomBFSIter, _swigc__p_OpenBabel__OBMolAtomDFSIter, _swigc__p_OpenBabel__OBMolAtomIter, _swigc__p_OpenBabel__OBMolBondIter, + _swigc__p_OpenBabel__OBMolPairIter, + _swigc__p_OpenBabel__OBMolRingIter, + _swigc__p_OpenBabel__OBMolTorsionIter, _swigc__p_OpenBabel__OBPairData, _swigc__p_OpenBabel__OBPairTemplateTdouble_t, _swigc__p_OpenBabel__OBPairTemplateTint_t, @@ -93306,6 +95551,7 @@ static swig_cast_info *swig_cast_initial[] = { _swigc__p_std__ostream, _swigc__p_std__out_of_range, _swigc__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, + _swigc__p_std__pairTint_int_t, _swigc__p_std__streampos, _swigc__p_std__string, _swigc__p_std__type_info, @@ -93756,6 +96002,10 @@ static swig_command_info swig_commands[] = { {"Chemistry::OpenBabelc::OBRingData_SetData", _wrap_OBRingData_SetData}, {"Chemistry::OpenBabelc::OBRingData_PushBack", _wrap_OBRingData_PushBack}, {"Chemistry::OpenBabelc::OBRingData_GetData", _wrap_OBRingData_GetData}, +{"Chemistry::OpenBabelc::OBRingData_BeginRings", _wrap_OBRingData_BeginRings}, +{"Chemistry::OpenBabelc::OBRingData_EndRings", _wrap_OBRingData_EndRings}, +{"Chemistry::OpenBabelc::OBRingData_BeginRing", _wrap_OBRingData_BeginRing}, +{"Chemistry::OpenBabelc::OBRingData_NextRing", _wrap_OBRingData_NextRing}, {"Chemistry::OpenBabelc::new_OBUnitCell", _wrap_new_OBUnitCell}, {"Chemistry::OpenBabelc::OBUnitCell_Clone", _wrap_OBUnitCell_Clone}, {"Chemistry::OpenBabelc::delete_OBUnitCell", _wrap_delete_OBUnitCell}, @@ -94304,6 +96554,7 @@ static swig_command_info swig_commands[] = { {"Chemistry::OpenBabelc::OBMol_Align", _wrap_OBMol_Align}, {"Chemistry::OpenBabelc::OBMol_ConnectTheDots", _wrap_OBMol_ConnectTheDots}, {"Chemistry::OpenBabelc::OBMol_PerceiveBondOrders", _wrap_OBMol_PerceiveBondOrders}, +{"Chemistry::OpenBabelc::OBMol_FindAngles", _wrap_OBMol_FindAngles}, {"Chemistry::OpenBabelc::OBMol_FindTorsions", _wrap_OBMol_FindTorsions}, {"Chemistry::OpenBabelc::OBMol_GetGTDVector", _wrap_OBMol_GetGTDVector}, {"Chemistry::OpenBabelc::OBMol_GetGIVector", _wrap_OBMol_GetGIVector}, @@ -95358,6 +97609,36 @@ static swig_command_info swig_commands[] = { {"Chemistry::OpenBabelc::OBResidueAtomIter_GetData", _wrap_OBResidueAtomIter_GetData}, {"Chemistry::OpenBabelc::OBResidueAtomIter_BeginData", _wrap_OBResidueAtomIter_BeginData}, {"Chemistry::OpenBabelc::OBResidueAtomIter_EndData", _wrap_OBResidueAtomIter_EndData}, +{"Chemistry::OpenBabelc::new_OBMolAngleIter", _wrap_new_OBMolAngleIter}, +{"Chemistry::OpenBabelc::OBMolAngleIter___plusplus__", _wrap_OBMolAngleIter___plusplus__}, +{"Chemistry::OpenBabelc::OBMolAngleIter___ref__", _wrap_OBMolAngleIter___ref__}, +{"Chemistry::OpenBabelc::delete_OBMolAngleIter", _wrap_delete_OBMolAngleIter}, +{"Chemistry::OpenBabelc::new_OBMolTorsionIter", _wrap_new_OBMolTorsionIter}, +{"Chemistry::OpenBabelc::OBMolTorsionIter___plusplus__", _wrap_OBMolTorsionIter___plusplus__}, +{"Chemistry::OpenBabelc::OBMolTorsionIter___ref__", _wrap_OBMolTorsionIter___ref__}, +{"Chemistry::OpenBabelc::delete_OBMolTorsionIter", _wrap_delete_OBMolTorsionIter}, +{"Chemistry::OpenBabelc::new_OBMolPairIter", _wrap_new_OBMolPairIter}, +{"Chemistry::OpenBabelc::OBMolPairIter___plusplus__", _wrap_OBMolPairIter___plusplus__}, +{"Chemistry::OpenBabelc::OBMolPairIter___deref__", _wrap_OBMolPairIter___deref__}, +{"Chemistry::OpenBabelc::OBMolPairIter___ref__", _wrap_OBMolPairIter___ref__}, +{"Chemistry::OpenBabelc::delete_OBMolPairIter", _wrap_delete_OBMolPairIter}, +{"Chemistry::OpenBabelc::new_OBMolRingIter", _wrap_new_OBMolRingIter}, +{"Chemistry::OpenBabelc::OBMolRingIter___plusplus__", _wrap_OBMolRingIter___plusplus__}, +{"Chemistry::OpenBabelc::OBMolRingIter___deref__", _wrap_OBMolRingIter___deref__}, +{"Chemistry::OpenBabelc::OBMolRingIter___ref__", _wrap_OBMolRingIter___ref__}, +{"Chemistry::OpenBabelc::delete_OBMolRingIter", _wrap_delete_OBMolRingIter}, +{"Chemistry::OpenBabelc::OBMolRingIter__path_set", _wrap_OBMolRingIter__path_set}, +{"Chemistry::OpenBabelc::OBMolRingIter__path_get", _wrap_OBMolRingIter__path_get}, +{"Chemistry::OpenBabelc::OBMolRingIter__pathset_set", _wrap_OBMolRingIter__pathset_set}, +{"Chemistry::OpenBabelc::OBMolRingIter__pathset_get", _wrap_OBMolRingIter__pathset_get}, +{"Chemistry::OpenBabelc::OBMolRingIter_findCenterAndNormal", _wrap_OBMolRingIter_findCenterAndNormal}, +{"Chemistry::OpenBabelc::OBMolRingIter_Size", _wrap_OBMolRingIter_Size}, +{"Chemistry::OpenBabelc::OBMolRingIter_PathSize", _wrap_OBMolRingIter_PathSize}, +{"Chemistry::OpenBabelc::OBMolRingIter_IsMember", _wrap_OBMolRingIter_IsMember}, +{"Chemistry::OpenBabelc::OBMolRingIter_IsAromatic", _wrap_OBMolRingIter_IsAromatic}, +{"Chemistry::OpenBabelc::OBMolRingIter_IsInRing", _wrap_OBMolRingIter_IsInRing}, +{"Chemistry::OpenBabelc::OBMolRingIter_SetParent", _wrap_OBMolRingIter_SetParent}, +{"Chemistry::OpenBabelc::OBMolRingIter_GetParent", _wrap_OBMolRingIter_GetParent}, {0,0} }; /* ----------------------------------------------------------------------------- @@ -96195,6 +98476,10 @@ XS(SWIG_init) { SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBAtomBondIter, (void*) "Chemistry::OpenBabel::OBAtomBondIter"); SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBResidueIter, (void*) "Chemistry::OpenBabel::OBResidueIter"); SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBResidueAtomIter, (void*) "Chemistry::OpenBabel::OBResidueAtomIter"); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolAngleIter, (void*) "Chemistry::OpenBabel::OBMolAngleIter"); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolTorsionIter, (void*) "Chemistry::OpenBabel::OBMolTorsionIter"); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolPairIter, (void*) "Chemistry::OpenBabel::OBMolPairIter"); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolRingIter, (void*) "Chemistry::OpenBabel::OBMolRingIter"); ST(0) = &PL_sv_yes; XSRETURN(1); } diff --git a/scripts/python/openbabel.py b/scripts/python/openbabel.py index acfa2cf4a..c48baea46 100644 --- a/scripts/python/openbabel.py +++ b/scripts/python/openbabel.py @@ -826,6 +826,10 @@ class OBRingData(OBGenericData): def SetData(*args): return _openbabel.OBRingData_SetData(*args) def PushBack(*args): return _openbabel.OBRingData_PushBack(*args) def GetData(*args): return _openbabel.OBRingData_GetData(*args) + def BeginRings(*args): return _openbabel.OBRingData_BeginRings(*args) + def EndRings(*args): return _openbabel.OBRingData_EndRings(*args) + def BeginRing(*args): return _openbabel.OBRingData_BeginRing(*args) + def NextRing(*args): return _openbabel.OBRingData_NextRing(*args) OBRingData_swigregister = _openbabel.OBRingData_swigregister OBRingData_swigregister(OBRingData) @@ -1729,6 +1733,7 @@ class OBMol(OBBase): def Align(*args): return _openbabel.OBMol_Align(*args) def ConnectTheDots(*args): return _openbabel.OBMol_ConnectTheDots(*args) def PerceiveBondOrders(*args): return _openbabel.OBMol_PerceiveBondOrders(*args) + def FindAngles(*args): return _openbabel.OBMol_FindAngles(*args) def FindTorsions(*args): return _openbabel.OBMol_FindTorsions(*args) def GetGTDVector(*args): return _openbabel.OBMol_GetGTDVector(*args) def GetGIVector(*args): return _openbabel.OBMol_GetGIVector(*args) @@ -2918,6 +2923,62 @@ class OBResidueAtomIter(object): OBResidueAtomIter_swigregister = _openbabel.OBResidueAtomIter_swigregister OBResidueAtomIter_swigregister(OBResidueAtomIter) +class OBMolAngleIter(object): + thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag') + __repr__ = _swig_repr + def __init__(self, *args): + _openbabel.OBMolAngleIter_swiginit(self,_openbabel.new_OBMolAngleIter(*args)) + def __ref__(*args): return _openbabel.OBMolAngleIter___ref__(*args) + __swig_destroy__ = _openbabel.delete_OBMolAngleIter + __del__ = lambda self : None; +OBMolAngleIter_swigregister = _openbabel.OBMolAngleIter_swigregister +OBMolAngleIter_swigregister(OBMolAngleIter) + +class OBMolTorsionIter(object): + thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag') + __repr__ = _swig_repr + def __init__(self, *args): + _openbabel.OBMolTorsionIter_swiginit(self,_openbabel.new_OBMolTorsionIter(*args)) + def __ref__(*args): return _openbabel.OBMolTorsionIter___ref__(*args) + __swig_destroy__ = _openbabel.delete_OBMolTorsionIter + __del__ = lambda self : None; +OBMolTorsionIter_swigregister = _openbabel.OBMolTorsionIter_swigregister +OBMolTorsionIter_swigregister(OBMolTorsionIter) + +class OBMolPairIter(object): + thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag') + __repr__ = _swig_repr + def __init__(self, *args): + _openbabel.OBMolPairIter_swiginit(self,_openbabel.new_OBMolPairIter(*args)) + def __deref__(*args): return _openbabel.OBMolPairIter___deref__(*args) + def __ref__(*args): return _openbabel.OBMolPairIter___ref__(*args) + __swig_destroy__ = _openbabel.delete_OBMolPairIter + __del__ = lambda self : None; +OBMolPairIter_swigregister = _openbabel.OBMolPairIter_swigregister +OBMolPairIter_swigregister(OBMolPairIter) + +class OBMolRingIter(object): + thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag') + __repr__ = _swig_repr + def __init__(self, *args): + _openbabel.OBMolRingIter_swiginit(self,_openbabel.new_OBMolRingIter(*args)) + def __deref__(*args): return _openbabel.OBMolRingIter___deref__(*args) + def __ref__(*args): return _openbabel.OBMolRingIter___ref__(*args) + __swig_destroy__ = _openbabel.delete_OBMolRingIter + __del__ = lambda self : None; + _path = _swig_property(_openbabel.OBMolRingIter__path_get, _openbabel.OBMolRingIter__path_set) + _pathset = _swig_property(_openbabel.OBMolRingIter__pathset_get, _openbabel.OBMolRingIter__pathset_set) + def findCenterAndNormal(*args): return _openbabel.OBMolRingIter_findCenterAndNormal(*args) + def Size(*args): return _openbabel.OBMolRingIter_Size(*args) + def PathSize(*args): return _openbabel.OBMolRingIter_PathSize(*args) + def IsMember(*args): return _openbabel.OBMolRingIter_IsMember(*args) + def IsAromatic(*args): return _openbabel.OBMolRingIter_IsAromatic(*args) + def IsInRing(*args): return _openbabel.OBMolRingIter_IsInRing(*args) + def SetParent(*args): return _openbabel.OBMolRingIter_SetParent(*args) + def GetParent(*args): return _openbabel.OBMolRingIter_GetParent(*args) +OBMolRingIter_swigregister = _openbabel.OBMolRingIter_swigregister +OBMolRingIter_swigregister(OBMolRingIter) + class doubleArray(object): thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag') __repr__ = _swig_repr diff --git a/scripts/python/openbabel_python.cpp b/scripts/python/openbabel_python.cpp index b1cf6dca0..b28e3c6df 100644 --- a/scripts/python/openbabel_python.cpp +++ b/scripts/python/openbabel_python.cpp @@ -2500,122 +2500,127 @@ SWIG_Python_MustGetPtr(PyObject *obj, swig_type_info *ty, int argnum, int flags) #define SWIGTYPE_p_OpenBabel__OBIsotopeTable swig_types[32] #define SWIGTYPE_p_OpenBabel__OBMessageHandler swig_types[33] #define SWIGTYPE_p_OpenBabel__OBMol swig_types[34] -#define SWIGTYPE_p_OpenBabel__OBMolAtomBFSIter swig_types[35] -#define SWIGTYPE_p_OpenBabel__OBMolAtomDFSIter swig_types[36] -#define SWIGTYPE_p_OpenBabel__OBMolAtomIter swig_types[37] -#define SWIGTYPE_p_OpenBabel__OBMolBondIter swig_types[38] -#define SWIGTYPE_p_OpenBabel__OBPairData swig_types[39] -#define SWIGTYPE_p_OpenBabel__OBPairTemplateTdouble_t swig_types[40] -#define SWIGTYPE_p_OpenBabel__OBPairTemplateTint_t swig_types[41] -#define SWIGTYPE_p_OpenBabel__OBRTree swig_types[42] -#define SWIGTYPE_p_OpenBabel__OBRandom swig_types[43] -#define SWIGTYPE_p_OpenBabel__OBResidue swig_types[44] -#define SWIGTYPE_p_OpenBabel__OBResidueAtomIter swig_types[45] -#define SWIGTYPE_p_OpenBabel__OBResidueData swig_types[46] -#define SWIGTYPE_p_OpenBabel__OBResidueIter swig_types[47] -#define SWIGTYPE_p_OpenBabel__OBRing swig_types[48] -#define SWIGTYPE_p_OpenBabel__OBRingData swig_types[49] -#define SWIGTYPE_p_OpenBabel__OBRingSearch swig_types[50] -#define SWIGTYPE_p_OpenBabel__OBSSMatch swig_types[51] -#define SWIGTYPE_p_OpenBabel__OBSerialNums swig_types[52] -#define SWIGTYPE_p_OpenBabel__OBSetData swig_types[53] -#define SWIGTYPE_p_OpenBabel__OBSmartsPattern swig_types[54] -#define SWIGTYPE_p_OpenBabel__OBSqrtTbl swig_types[55] -#define SWIGTYPE_p_OpenBabel__OBStopwatch swig_types[56] -#define SWIGTYPE_p_OpenBabel__OBSymmetryData swig_types[57] -#define SWIGTYPE_p_OpenBabel__OBTorsion swig_types[58] -#define SWIGTYPE_p_OpenBabel__OBTorsionData swig_types[59] -#define SWIGTYPE_p_OpenBabel__OBTypeTable swig_types[60] -#define SWIGTYPE_p_OpenBabel__OBUnitCell swig_types[61] -#define SWIGTYPE_p_OpenBabel__OBVirtualBond swig_types[62] -#define SWIGTYPE_p_OpenBabel__Pattern swig_types[63] -#define SWIGTYPE_p_OpenBabel__Template swig_types[64] -#define SWIGTYPE_p_OpenBabel__matrix3x3 swig_types[65] -#define SWIGTYPE_p_OpenBabel__obLogBuf swig_types[66] -#define SWIGTYPE_p_OpenBabel__quadTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[67] -#define SWIGTYPE_p_OpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[68] -#define SWIGTYPE_p_OpenBabel__vector3 swig_types[69] -#define SWIGTYPE_p_a_3__double swig_types[70] -#define SWIGTYPE_p_a_3__doubleArray swig_types[71] -#define SWIGTYPE_p_a_4__char swig_types[72] -#define SWIGTYPE_p_allocator_type swig_types[73] -#define SWIGTYPE_p_char swig_types[74] -#define SWIGTYPE_p_const_reference swig_types[75] -#define SWIGTYPE_p_difference_type swig_types[76] -#define SWIGTYPE_p_double swig_types[77] -#define SWIGTYPE_p_doubleArray swig_types[78] -#define SWIGTYPE_p_int swig_types[79] -#define SWIGTYPE_p_p_OpenBabel__OBFingerprint swig_types[80] -#define SWIGTYPE_p_p_OpenBabel__OBFormat swig_types[81] -#define SWIGTYPE_p_p_PyObject swig_types[82] -#define SWIGTYPE_p_p_double swig_types[83] -#define SWIGTYPE_p_p_doubleArray swig_types[84] -#define SWIGTYPE_p_p_int swig_types[85] -#define SWIGTYPE_p_reference swig_types[86] -#define SWIGTYPE_p_size_type swig_types[87] -#define SWIGTYPE_p_std__dequeTint_t swig_types[88] -#define SWIGTYPE_p_std__ifstream swig_types[89] -#define SWIGTYPE_p_std__invalid_argument swig_types[90] -#define SWIGTYPE_p_std__istream swig_types[91] -#define SWIGTYPE_p_std__mapTchar_const_p_OpenBabel__OBFormat_p_OpenBabel__CharPtrLess_std__allocatorTstd__pairTchar_const_pconst_OpenBabel__OBFormat_p_t_t_t swig_types[92] -#define SWIGTYPE_p_std__mapTint_OpenBabel__OBAtom_p_std__lessTint_t_std__allocatorTstd__pairTint_const_OpenBabel__OBAtom_p_t_t_t swig_types[93] -#define SWIGTYPE_p_std__mapTstd__string_std__string_std__lessTstd__string_t_std__allocatorTstd__pairTstd__string_const_std__string_t_t_t swig_types[94] -#define SWIGTYPE_p_std__multimapTdouble_unsigned_int_t swig_types[95] -#define SWIGTYPE_p_std__ostream swig_types[96] -#define SWIGTYPE_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[97] -#define SWIGTYPE_p_std__streampos swig_types[98] -#define SWIGTYPE_p_std__string swig_types[99] -#define SWIGTYPE_p_std__type_info swig_types[100] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_std__allocatorTOpenBabel__OBAtom_p_t_t swig_types[101] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_std__allocatorTOpenBabel__OBAtom_p_t_t__iterator swig_types[102] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_std__allocatorTOpenBabel__OBBond_p_t_t swig_types[103] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_std__allocatorTOpenBabel__OBBond_p_t_t__iterator swig_types[104] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_std__allocatorTOpenBabel__OBBond_t_t swig_types[105] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_std__allocatorTOpenBabel__OBBond_t_t__allocator_type swig_types[106] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_std__allocatorTOpenBabel__OBBond_t_t__value_type swig_types[107] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBExternalBond_std__allocatorTOpenBabel__OBExternalBond_t_t swig_types[108] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_std__allocatorTOpenBabel__OBGenericData_p_t_t swig_types[109] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_std__allocatorTOpenBabel__OBGenericData_p_t_t__allocator_type swig_types[110] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_std__allocatorTOpenBabel__OBInternalCoord_p_t_t swig_types[111] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_std__allocatorTOpenBabel__OBInternalCoord_p_t_t__iterator swig_types[112] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_std__allocatorTOpenBabel__OBMol_t_t swig_types[113] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_std__allocatorTOpenBabel__OBMol_t_t__allocator_type swig_types[114] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_std__allocatorTOpenBabel__OBMol_t_t__value_type swig_types[115] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_std__allocatorTOpenBabel__OBResidue_p_t_t__iterator swig_types[116] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_std__allocatorTOpenBabel__OBResidue_t_t swig_types[117] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_std__allocatorTOpenBabel__OBResidue_t_t__allocator_type swig_types[118] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_std__allocatorTOpenBabel__OBResidue_t_t__value_type swig_types[119] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t swig_types[120] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t__iterator swig_types[121] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_std__allocatorTOpenBabel__OBRing_t_t swig_types[122] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_std__allocatorTOpenBabel__OBRing_t_t__allocator_type swig_types[123] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_std__allocatorTOpenBabel__OBRing_t_t__value_type swig_types[124] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBTorsion_std__allocatorTOpenBabel__OBTorsion_t_t swig_types[125] -#define SWIGTYPE_p_std__vectorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_std__allocatorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_t_t swig_types[126] -#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t swig_types[127] -#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t__allocator_type swig_types[128] -#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t__value_type swig_types[129] -#define SWIGTYPE_p_std__vectorTdouble_p_std__allocatorTdouble_p_t_t swig_types[130] -#define SWIGTYPE_p_std__vectorTdouble_p_std__allocatorTdouble_p_t_t__iterator swig_types[131] -#define SWIGTYPE_p_std__vectorTdouble_std__allocatorTdouble_t_t swig_types[132] -#define SWIGTYPE_p_std__vectorTdouble_std__allocatorTdouble_t_t__allocator_type swig_types[133] -#define SWIGTYPE_p_std__vectorTint_std__allocatorTint_t_t swig_types[134] -#define SWIGTYPE_p_std__vectorTint_std__allocatorTint_t_t__allocator_type swig_types[135] -#define SWIGTYPE_p_std__vectorTstd__pairTint_int_t_std__allocatorTstd__pairTint_int_t_t_t swig_types[136] -#define SWIGTYPE_p_std__vectorTstd__pairTstd__string_std__string_t_std__allocatorTstd__pairTstd__string_std__string_t_t_t swig_types[137] -#define SWIGTYPE_p_std__vectorTstd__string_std__allocatorTstd__string_t_t swig_types[138] -#define SWIGTYPE_p_std__vectorTstd__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t_std__allocatorTstd__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t_t_t swig_types[139] -#define SWIGTYPE_p_std__vectorTstd__vectorTint_std__allocatorTint_t_t_std__allocatorTstd__vectorTint_std__allocatorTint_t_t_t_t swig_types[140] -#define SWIGTYPE_p_std__vectorTstd__vectorTint_std__allocatorTint_t_t_std__allocatorTstd__vectorTint_std__allocatorTint_t_t_t_t__allocator_type swig_types[141] -#define SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_std__allocatorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_t_t swig_types[142] -#define SWIGTYPE_p_std__vectorTunsigned_int_std__allocatorTunsigned_int_t_t swig_types[143] -#define SWIGTYPE_p_std__vectorTunsigned_short_std__allocatorTunsigned_short_t_t swig_types[144] -#define SWIGTYPE_p_swig__PySwigIterator swig_types[145] -#define SWIGTYPE_p_unsigned_int swig_types[146] -#define SWIGTYPE_p_value_type swig_types[147] -#define SWIGTYPE_std__vectorTOpenBabel__OBGenericData_p_std__allocatorTOpenBabel__OBGenericData_p_t_t__value_type swig_types[148] -static swig_type_info *swig_types[150]; -static swig_module_info swig_module = {swig_types, 149, 0, 0, 0, 0}; +#define SWIGTYPE_p_OpenBabel__OBMolAngleIter swig_types[35] +#define SWIGTYPE_p_OpenBabel__OBMolAtomBFSIter swig_types[36] +#define SWIGTYPE_p_OpenBabel__OBMolAtomDFSIter swig_types[37] +#define SWIGTYPE_p_OpenBabel__OBMolAtomIter swig_types[38] +#define SWIGTYPE_p_OpenBabel__OBMolBondIter swig_types[39] +#define SWIGTYPE_p_OpenBabel__OBMolPairIter swig_types[40] +#define SWIGTYPE_p_OpenBabel__OBMolRingIter swig_types[41] +#define SWIGTYPE_p_OpenBabel__OBMolTorsionIter swig_types[42] +#define SWIGTYPE_p_OpenBabel__OBPairData swig_types[43] +#define SWIGTYPE_p_OpenBabel__OBPairTemplateTdouble_t swig_types[44] +#define SWIGTYPE_p_OpenBabel__OBPairTemplateTint_t swig_types[45] +#define SWIGTYPE_p_OpenBabel__OBRTree swig_types[46] +#define SWIGTYPE_p_OpenBabel__OBRandom swig_types[47] +#define SWIGTYPE_p_OpenBabel__OBResidue swig_types[48] +#define SWIGTYPE_p_OpenBabel__OBResidueAtomIter swig_types[49] +#define SWIGTYPE_p_OpenBabel__OBResidueData swig_types[50] +#define SWIGTYPE_p_OpenBabel__OBResidueIter swig_types[51] +#define SWIGTYPE_p_OpenBabel__OBRing swig_types[52] +#define SWIGTYPE_p_OpenBabel__OBRingData swig_types[53] +#define SWIGTYPE_p_OpenBabel__OBRingSearch swig_types[54] +#define SWIGTYPE_p_OpenBabel__OBSSMatch swig_types[55] +#define SWIGTYPE_p_OpenBabel__OBSerialNums swig_types[56] +#define SWIGTYPE_p_OpenBabel__OBSetData swig_types[57] +#define SWIGTYPE_p_OpenBabel__OBSmartsPattern swig_types[58] +#define SWIGTYPE_p_OpenBabel__OBSqrtTbl swig_types[59] +#define SWIGTYPE_p_OpenBabel__OBStopwatch swig_types[60] +#define SWIGTYPE_p_OpenBabel__OBSymmetryData swig_types[61] +#define SWIGTYPE_p_OpenBabel__OBTorsion swig_types[62] +#define SWIGTYPE_p_OpenBabel__OBTorsionData swig_types[63] +#define SWIGTYPE_p_OpenBabel__OBTypeTable swig_types[64] +#define SWIGTYPE_p_OpenBabel__OBUnitCell swig_types[65] +#define SWIGTYPE_p_OpenBabel__OBVirtualBond swig_types[66] +#define SWIGTYPE_p_OpenBabel__Pattern swig_types[67] +#define SWIGTYPE_p_OpenBabel__Template swig_types[68] +#define SWIGTYPE_p_OpenBabel__matrix3x3 swig_types[69] +#define SWIGTYPE_p_OpenBabel__obLogBuf swig_types[70] +#define SWIGTYPE_p_OpenBabel__quadTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[71] +#define SWIGTYPE_p_OpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[72] +#define SWIGTYPE_p_OpenBabel__vector3 swig_types[73] +#define SWIGTYPE_p_a_3__double swig_types[74] +#define SWIGTYPE_p_a_3__doubleArray swig_types[75] +#define SWIGTYPE_p_a_4__char swig_types[76] +#define SWIGTYPE_p_allocator_type swig_types[77] +#define SWIGTYPE_p_char swig_types[78] +#define SWIGTYPE_p_const_reference swig_types[79] +#define SWIGTYPE_p_difference_type swig_types[80] +#define SWIGTYPE_p_double swig_types[81] +#define SWIGTYPE_p_doubleArray swig_types[82] +#define SWIGTYPE_p_int swig_types[83] +#define SWIGTYPE_p_p_OpenBabel__OBFingerprint swig_types[84] +#define SWIGTYPE_p_p_OpenBabel__OBFormat swig_types[85] +#define SWIGTYPE_p_p_PyObject swig_types[86] +#define SWIGTYPE_p_p_double swig_types[87] +#define SWIGTYPE_p_p_doubleArray swig_types[88] +#define SWIGTYPE_p_p_int swig_types[89] +#define SWIGTYPE_p_reference swig_types[90] +#define SWIGTYPE_p_size_type swig_types[91] +#define SWIGTYPE_p_std__dequeTint_t swig_types[92] +#define SWIGTYPE_p_std__ifstream swig_types[93] +#define SWIGTYPE_p_std__invalid_argument swig_types[94] +#define SWIGTYPE_p_std__istream swig_types[95] +#define SWIGTYPE_p_std__mapTchar_const_p_OpenBabel__OBFormat_p_OpenBabel__CharPtrLess_std__allocatorTstd__pairTchar_const_pconst_OpenBabel__OBFormat_p_t_t_t swig_types[96] +#define SWIGTYPE_p_std__mapTint_OpenBabel__OBAtom_p_std__lessTint_t_std__allocatorTstd__pairTint_const_OpenBabel__OBAtom_p_t_t_t swig_types[97] +#define SWIGTYPE_p_std__mapTstd__string_std__string_std__lessTstd__string_t_std__allocatorTstd__pairTstd__string_const_std__string_t_t_t swig_types[98] +#define SWIGTYPE_p_std__multimapTdouble_unsigned_int_t swig_types[99] +#define SWIGTYPE_p_std__ostream swig_types[100] +#define SWIGTYPE_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[101] +#define SWIGTYPE_p_std__pairTint_int_t swig_types[102] +#define SWIGTYPE_p_std__streampos swig_types[103] +#define SWIGTYPE_p_std__string swig_types[104] +#define SWIGTYPE_p_std__type_info swig_types[105] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_std__allocatorTOpenBabel__OBAtom_p_t_t swig_types[106] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_std__allocatorTOpenBabel__OBAtom_p_t_t__iterator swig_types[107] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_std__allocatorTOpenBabel__OBBond_p_t_t swig_types[108] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_std__allocatorTOpenBabel__OBBond_p_t_t__iterator swig_types[109] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_std__allocatorTOpenBabel__OBBond_t_t swig_types[110] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_std__allocatorTOpenBabel__OBBond_t_t__allocator_type swig_types[111] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_std__allocatorTOpenBabel__OBBond_t_t__value_type swig_types[112] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBExternalBond_std__allocatorTOpenBabel__OBExternalBond_t_t swig_types[113] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_std__allocatorTOpenBabel__OBGenericData_p_t_t swig_types[114] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_std__allocatorTOpenBabel__OBGenericData_p_t_t__allocator_type swig_types[115] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_std__allocatorTOpenBabel__OBInternalCoord_p_t_t swig_types[116] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_std__allocatorTOpenBabel__OBInternalCoord_p_t_t__iterator swig_types[117] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_std__allocatorTOpenBabel__OBMol_t_t swig_types[118] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_std__allocatorTOpenBabel__OBMol_t_t__allocator_type swig_types[119] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_std__allocatorTOpenBabel__OBMol_t_t__value_type swig_types[120] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_std__allocatorTOpenBabel__OBResidue_p_t_t__iterator swig_types[121] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_std__allocatorTOpenBabel__OBResidue_t_t swig_types[122] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_std__allocatorTOpenBabel__OBResidue_t_t__allocator_type swig_types[123] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_std__allocatorTOpenBabel__OBResidue_t_t__value_type swig_types[124] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t swig_types[125] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t__iterator swig_types[126] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_std__allocatorTOpenBabel__OBRing_t_t swig_types[127] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_std__allocatorTOpenBabel__OBRing_t_t__allocator_type swig_types[128] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_std__allocatorTOpenBabel__OBRing_t_t__value_type swig_types[129] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBTorsion_std__allocatorTOpenBabel__OBTorsion_t_t swig_types[130] +#define SWIGTYPE_p_std__vectorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_std__allocatorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_t_t swig_types[131] +#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t swig_types[132] +#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t__allocator_type swig_types[133] +#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t__value_type swig_types[134] +#define SWIGTYPE_p_std__vectorTdouble_p_std__allocatorTdouble_p_t_t swig_types[135] +#define SWIGTYPE_p_std__vectorTdouble_p_std__allocatorTdouble_p_t_t__iterator swig_types[136] +#define SWIGTYPE_p_std__vectorTdouble_std__allocatorTdouble_t_t swig_types[137] +#define SWIGTYPE_p_std__vectorTdouble_std__allocatorTdouble_t_t__allocator_type swig_types[138] +#define SWIGTYPE_p_std__vectorTint_std__allocatorTint_t_t swig_types[139] +#define SWIGTYPE_p_std__vectorTint_std__allocatorTint_t_t__allocator_type swig_types[140] +#define SWIGTYPE_p_std__vectorTstd__pairTint_int_t_std__allocatorTstd__pairTint_int_t_t_t swig_types[141] +#define SWIGTYPE_p_std__vectorTstd__pairTstd__string_std__string_t_std__allocatorTstd__pairTstd__string_std__string_t_t_t swig_types[142] +#define SWIGTYPE_p_std__vectorTstd__string_std__allocatorTstd__string_t_t swig_types[143] +#define SWIGTYPE_p_std__vectorTstd__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t_std__allocatorTstd__vectorTOpenBabel__vector3_std__allocatorTOpenBabel__vector3_t_t_t_t swig_types[144] +#define SWIGTYPE_p_std__vectorTstd__vectorTint_std__allocatorTint_t_t_std__allocatorTstd__vectorTint_std__allocatorTint_t_t_t_t swig_types[145] +#define SWIGTYPE_p_std__vectorTstd__vectorTint_std__allocatorTint_t_t_std__allocatorTstd__vectorTint_std__allocatorTint_t_t_t_t__allocator_type swig_types[146] +#define SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_std__allocatorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_t_t swig_types[147] +#define SWIGTYPE_p_std__vectorTunsigned_int_std__allocatorTunsigned_int_t_t swig_types[148] +#define SWIGTYPE_p_std__vectorTunsigned_short_std__allocatorTunsigned_short_t_t swig_types[149] +#define SWIGTYPE_p_swig__PySwigIterator swig_types[150] +#define SWIGTYPE_p_unsigned_int swig_types[151] +#define SWIGTYPE_p_value_type swig_types[152] +#define SWIGTYPE_std__vectorTOpenBabel__OBGenericData_p_std__allocatorTOpenBabel__OBGenericData_p_t_t__value_type swig_types[153] +static swig_type_info *swig_types[155]; +static swig_module_info swig_module = {swig_types, 154, 0, 0, 0, 0}; #define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name) #define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name) @@ -2717,27 +2722,27 @@ namespace swig { #endif -#include "obutil.h" -#include "rand.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "atom.h" -#include "bond.h" -#include "residue.h" -#include "internalcoord.h" +#include +#include +#include +#include +#include +#include -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include #include @@ -28887,6 +28892,118 @@ fail: } +SWIGINTERN PyObject *_wrap_OBRingData_BeginRings(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper >::iterator > result; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBRingData_BeginRings",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_BeginRings" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + result = (arg1)->BeginRings(); + resultobj = SWIG_NewPointerObj((new std::vector >::iterator(static_cast< const std::vector >::iterator& >(result))), SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t__iterator, SWIG_POINTER_OWN | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBRingData_EndRings(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper >::iterator > result; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBRingData_EndRings",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_EndRings" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + result = (arg1)->EndRings(); + resultobj = SWIG_NewPointerObj((new std::vector >::iterator(static_cast< const std::vector >::iterator& >(result))), SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t__iterator, SWIG_POINTER_OWN | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBRingData_BeginRing(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector >::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBRingData_BeginRing",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_BeginRing" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t__iterator, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBRingData_BeginRing" "', argument " "2"" of type '" "std::vector >::iterator &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBRingData_BeginRing" "', argument " "2"" of type '" "std::vector >::iterator &""'"); + } + arg2 = reinterpret_cast< std::vector >::iterator * >(argp2); + result = (OpenBabel::OBRing *)(arg1)->BeginRing(*arg2); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBRingData_NextRing(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector >::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBRingData_NextRing",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBRingData_NextRing" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_std__allocatorTOpenBabel__OBRing_p_t_t__iterator, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBRingData_NextRing" "', argument " "2"" of type '" "std::vector >::iterator &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBRingData_NextRing" "', argument " "2"" of type '" "std::vector >::iterator &""'"); + } + arg2 = reinterpret_cast< std::vector >::iterator * >(argp2); + result = (OpenBabel::OBRing *)(arg1)->NextRing(*arg2); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + SWIGINTERN PyObject *OBRingData_swigregister(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *obj; if (!PyArg_UnpackTuple(args,(char*)"swigregister", 1, 1,&obj)) return NULL; @@ -31931,7 +32048,7 @@ fail: } -SWIGINTERN PyObject *_wrap_OBAngleData_FillAngleArray(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { +SWIGINTERN PyObject *_wrap_OBAngleData_FillAngleArray__SWIG_0(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0; OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; int **arg2 = (int **) 0 ; @@ -31974,6 +32091,90 @@ fail: } +SWIGINTERN PyObject *_wrap_OBAngleData_FillAngleArray__SWIG_1(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; + std::vector >,std::allocator > > > *arg2 = 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBAngleData_FillAngleArray",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBAngleData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBAngleData_FillAngleArray" "', argument " "1"" of type '" "OpenBabel::OBAngleData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBAngleData * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2, SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_std__allocatorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_t_t, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBAngleData_FillAngleArray" "', argument " "2"" of type '" "std::vector >,std::allocator > > > &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBAngleData_FillAngleArray" "', argument " "2"" of type '" "std::vector >,std::allocator > > > &""'"); + } + arg2 = reinterpret_cast< std::vector >,std::allocator > > > * >(argp2); + result = (bool)(arg1)->FillAngleArray(*arg2); + resultobj = SWIG_From_bool(static_cast< bool >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBAngleData_FillAngleArray(PyObject *self, PyObject *args) { + int argc; + PyObject *argv[4]; + int ii; + + if (!PyTuple_Check(args)) SWIG_fail; + argc = PyObject_Length(args); + for (ii = 0; (ii < argc) && (ii < 3); ii++) { + argv[ii] = PyTuple_GET_ITEM(args,ii); + } + if (argc == 2) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBAngleData, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_std__allocatorTstd__vectorTunsigned_int_std__allocatorTunsigned_int_t_t_t_t, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBAngleData_FillAngleArray__SWIG_1(self, args); + } + } + } + if (argc == 3) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBAngleData, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_p_int, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[2], &vptr, SWIGTYPE_p_unsigned_int, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBAngleData_FillAngleArray__SWIG_0(self, args); + } + } + } + } + +fail: + SWIG_SetErrorMsg(PyExc_NotImplementedError,"Wrong number of arguments for overloaded function 'OBAngleData_FillAngleArray'.\n Possible C/C++ prototypes are:\n FillAngleArray(int **,unsigned int &)\n FillAngleArray(std::vector >,std::allocator > > > &)\n"); + return NULL; +} + + SWIGINTERN PyObject *_wrap_OBAngleData_SetData(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0; OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; @@ -50964,6 +51165,27 @@ fail: } +SWIGINTERN PyObject *_wrap_OBMol_FindAngles(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMol_FindAngles",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMol_FindAngles" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + (arg1)->FindAngles(); + resultobj = SWIG_Py_Void(); + return resultobj; +fail: + return NULL; +} + + SWIGINTERN PyObject *_wrap_OBMol_FindTorsions(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0; OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; @@ -87043,6 +87265,1236 @@ SWIGINTERN PyObject *OBResidueAtomIter_swiginit(PyObject *SWIGUNUSEDPARM(self), return SWIG_Python_InitShadowInstance(args); } +SWIGINTERN PyObject *_wrap_new_OBMolAngleIter__SWIG_0(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolAngleIter *result = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolAngleIter",0,0)) SWIG_fail; + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolAngleIter__SWIG_1(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolAngleIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolAngleIter__SWIG_2(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolAngleIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolAngleIter__SWIG_3(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolAngleIter *arg1 = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolAngleIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0 | 0); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter((OpenBabel::OBMolAngleIter const &)*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolAngleIter(PyObject *self, PyObject *args) { + int argc; + PyObject *argv[2]; + int ii; + + if (!PyTuple_Check(args)) SWIG_fail; + argc = PyObject_Length(args); + for (ii = 0; (ii < argc) && (ii < 1); ii++) { + argv[ii] = PyTuple_GET_ITEM(args,ii); + } + if (argc == 0) { + return _wrap_new_OBMolAngleIter__SWIG_0(self, args); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolAngleIter__SWIG_1(self, args); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolAngleIter__SWIG_2(self, args); + } + } + if (argc == 1) { + int _v; + int res = SWIG_ConvertPtr(argv[0], 0, SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolAngleIter__SWIG_3(self, args); + } + } + +fail: + SWIG_SetErrorMsg(PyExc_NotImplementedError,"Wrong number of arguments for overloaded function 'new_OBMolAngleIter'.\n Possible C/C++ prototypes are:\n OpenBabel::OBMolAngleIter()\n OpenBabel::OBMolAngleIter(OpenBabel::OBMol *)\n OpenBabel::OBMolAngleIter(OpenBabel::OBMol &)\n OpenBabel::OBMolAngleIter(OpenBabel::OBMolAngleIter const &)\n"); + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolAngleIter___ref__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + SwigValueWrapper > > result; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolAngleIter___ref__",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolAngleIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + result = ((OpenBabel::OBMolAngleIter const *)arg1)->operator *(); + resultobj = SWIG_NewPointerObj((new std::vector >(static_cast< const std::vector >& >(result))), SWIGTYPE_p_std__vectorTunsigned_int_std__allocatorTunsigned_int_t_t, SWIG_POINTER_OWN | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_delete_OBMolAngleIter(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"delete_OBMolAngleIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + delete arg1; + + resultobj = SWIG_Py_Void(); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *OBMolAngleIter_swigregister(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *obj; + if (!PyArg_UnpackTuple(args,(char*)"swigregister", 1, 1,&obj)) return NULL; + SWIG_TypeNewClientData(SWIGTYPE_p_OpenBabel__OBMolAngleIter, SWIG_NewClientData(obj)); + return SWIG_Py_Void(); +} + +SWIGINTERN PyObject *OBMolAngleIter_swiginit(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + return SWIG_Python_InitShadowInstance(args); +} + +SWIGINTERN PyObject *_wrap_new_OBMolTorsionIter__SWIG_0(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolTorsionIter *result = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolTorsionIter",0,0)) SWIG_fail; + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolTorsionIter__SWIG_1(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolTorsionIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolTorsionIter__SWIG_2(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolTorsionIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolTorsionIter__SWIG_3(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolTorsionIter *arg1 = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolTorsionIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0 | 0); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter((OpenBabel::OBMolTorsionIter const &)*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolTorsionIter(PyObject *self, PyObject *args) { + int argc; + PyObject *argv[2]; + int ii; + + if (!PyTuple_Check(args)) SWIG_fail; + argc = PyObject_Length(args); + for (ii = 0; (ii < argc) && (ii < 1); ii++) { + argv[ii] = PyTuple_GET_ITEM(args,ii); + } + if (argc == 0) { + return _wrap_new_OBMolTorsionIter__SWIG_0(self, args); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolTorsionIter__SWIG_1(self, args); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolTorsionIter__SWIG_2(self, args); + } + } + if (argc == 1) { + int _v; + int res = SWIG_ConvertPtr(argv[0], 0, SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolTorsionIter__SWIG_3(self, args); + } + } + +fail: + SWIG_SetErrorMsg(PyExc_NotImplementedError,"Wrong number of arguments for overloaded function 'new_OBMolTorsionIter'.\n Possible C/C++ prototypes are:\n OpenBabel::OBMolTorsionIter()\n OpenBabel::OBMolTorsionIter(OpenBabel::OBMol *)\n OpenBabel::OBMolTorsionIter(OpenBabel::OBMol &)\n OpenBabel::OBMolTorsionIter(OpenBabel::OBMolTorsionIter const &)\n"); + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolTorsionIter___ref__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + SwigValueWrapper > > result; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolTorsionIter___ref__",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolTorsionIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + result = ((OpenBabel::OBMolTorsionIter const *)arg1)->operator *(); + resultobj = SWIG_NewPointerObj((new std::vector >(static_cast< const std::vector >& >(result))), SWIGTYPE_p_std__vectorTunsigned_int_std__allocatorTunsigned_int_t_t, SWIG_POINTER_OWN | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_delete_OBMolTorsionIter(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"delete_OBMolTorsionIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + delete arg1; + + resultobj = SWIG_Py_Void(); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *OBMolTorsionIter_swigregister(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *obj; + if (!PyArg_UnpackTuple(args,(char*)"swigregister", 1, 1,&obj)) return NULL; + SWIG_TypeNewClientData(SWIGTYPE_p_OpenBabel__OBMolTorsionIter, SWIG_NewClientData(obj)); + return SWIG_Py_Void(); +} + +SWIGINTERN PyObject *OBMolTorsionIter_swiginit(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + return SWIG_Python_InitShadowInstance(args); +} + +SWIGINTERN PyObject *_wrap_new_OBMolPairIter__SWIG_0(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolPairIter *result = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolPairIter",0,0)) SWIG_fail; + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolPairIter__SWIG_1(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolPairIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolPairIter__SWIG_2(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolPairIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolPairIter__SWIG_3(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolPairIter *arg1 = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolPairIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter((OpenBabel::OBMolPairIter const &)*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolPairIter(PyObject *self, PyObject *args) { + int argc; + PyObject *argv[2]; + int ii; + + if (!PyTuple_Check(args)) SWIG_fail; + argc = PyObject_Length(args); + for (ii = 0; (ii < argc) && (ii < 1); ii++) { + argv[ii] = PyTuple_GET_ITEM(args,ii); + } + if (argc == 0) { + return _wrap_new_OBMolPairIter__SWIG_0(self, args); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolPairIter__SWIG_1(self, args); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolPairIter__SWIG_2(self, args); + } + } + if (argc == 1) { + int _v; + int res = SWIG_ConvertPtr(argv[0], 0, SWIGTYPE_p_OpenBabel__OBMolPairIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolPairIter__SWIG_3(self, args); + } + } + +fail: + SWIG_SetErrorMsg(PyExc_NotImplementedError,"Wrong number of arguments for overloaded function 'new_OBMolPairIter'.\n Possible C/C++ prototypes are:\n OpenBabel::OBMolPairIter()\n OpenBabel::OBMolPairIter(OpenBabel::OBMol *)\n OpenBabel::OBMolPairIter(OpenBabel::OBMol &)\n OpenBabel::OBMolPairIter(OpenBabel::OBMolPairIter const &)\n"); + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolPairIter___deref__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolPairIter___deref__",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolPairIter___deref__" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + result = (std::pair *)((OpenBabel::OBMolPairIter const *)arg1)->operator ->(); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__pairTint_int_t, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolPairIter___ref__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolPairIter___ref__",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolPairIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + { + std::pair &_result_ref = ((OpenBabel::OBMolPairIter const *)arg1)->operator *(); + result = (std::pair *) &_result_ref; + } + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__pairTint_int_t, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_delete_OBMolPairIter(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"delete_OBMolPairIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + delete arg1; + + resultobj = SWIG_Py_Void(); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *OBMolPairIter_swigregister(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *obj; + if (!PyArg_UnpackTuple(args,(char*)"swigregister", 1, 1,&obj)) return NULL; + SWIG_TypeNewClientData(SWIGTYPE_p_OpenBabel__OBMolPairIter, SWIG_NewClientData(obj)); + return SWIG_Py_Void(); +} + +SWIGINTERN PyObject *OBMolPairIter_swiginit(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + return SWIG_Python_InitShadowInstance(args); +} + +SWIGINTERN PyObject *_wrap_new_OBMolRingIter__SWIG_0(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *result = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolRingIter",0,0)) SWIG_fail; + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolRingIter__SWIG_1(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolRingIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolRingIter__SWIG_2(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolRingIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolRingIter__SWIG_3(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"new_OBMolRingIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "new_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter((OpenBabel::OBMolRingIter const &)*arg1); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_POINTER_NEW | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_new_OBMolRingIter(PyObject *self, PyObject *args) { + int argc; + PyObject *argv[2]; + int ii; + + if (!PyTuple_Check(args)) SWIG_fail; + argc = PyObject_Length(args); + for (ii = 0; (ii < argc) && (ii < 1); ii++) { + argv[ii] = PyTuple_GET_ITEM(args,ii); + } + if (argc == 0) { + return _wrap_new_OBMolRingIter__SWIG_0(self, args); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolRingIter__SWIG_1(self, args); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolRingIter__SWIG_2(self, args); + } + } + if (argc == 1) { + int _v; + int res = SWIG_ConvertPtr(argv[0], 0, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolRingIter__SWIG_3(self, args); + } + } + +fail: + SWIG_SetErrorMsg(PyExc_NotImplementedError,"Wrong number of arguments for overloaded function 'new_OBMolRingIter'.\n Possible C/C++ prototypes are:\n OpenBabel::OBMolRingIter()\n OpenBabel::OBMolRingIter(OpenBabel::OBMol *)\n OpenBabel::OBMolRingIter(OpenBabel::OBMol &)\n OpenBabel::OBMolRingIter(OpenBabel::OBMolRingIter const &)\n"); + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter___deref__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter___deref__",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter___deref__" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBRing *)((OpenBabel::OBMolRingIter const *)arg1)->operator ->(); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter___ref__(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter___ref__",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter___ref__" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + OpenBabel::OBRing &_result_ref = ((OpenBabel::OBMolRingIter const *)arg1)->operator *(); + result = (OpenBabel::OBRing *) &_result_ref; + } + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_delete_OBMolRingIter(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"delete_OBMolRingIter",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_POINTER_DISOWN | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "delete_OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + delete arg1; + + resultobj = SWIG_Py_Void(); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter__path_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector > *arg2 = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + int res2 = SWIG_OLDOBJ ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter__path_set",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__path_set" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + std::vector > *ptr = (std::vector > *)0; + res2 = swig::asptr(obj1, &ptr); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter__path_set" "', argument " "2"" of type '" "std::vector > const &""'"); + } + if (!ptr) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter__path_set" "', argument " "2"" of type '" "std::vector > const &""'"); + } + arg2 = ptr; + } + if (arg1) (*arg1)->_path = *arg2; + + resultobj = SWIG_Py_Void(); + if (SWIG_IsNewObj(res2)) delete arg2; + return resultobj; +fail: + if (SWIG_IsNewObj(res2)) delete arg2; + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter__path_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector > *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter__path_get",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__path_get" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + std::vector > const &_result_ref = ((*arg1)->_path); + result = (std::vector > *) &_result_ref; + } + resultobj = swig::from(static_cast< std::vector > >(*result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter__pathset_set(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *arg2 = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter__pathset_set",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__pathset_set" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2, SWIGTYPE_p_OpenBabel__OBBitVec, 0 | 0); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter__pathset_set" "', argument " "2"" of type '" "OpenBabel::OBBitVec const &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter__pathset_set" "', argument " "2"" of type '" "OpenBabel::OBBitVec const &""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); + if (arg1) (*arg1)->_pathset = *arg2; + + resultobj = SWIG_Py_Void(); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter__pathset_get(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter__pathset_get",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter__pathset_get" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + OpenBabel::OBBitVec const &_result_ref = ((*arg1)->_pathset); + result = (OpenBabel::OBBitVec *) &_result_ref; + } + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBBitVec, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_findCenterAndNormal(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::vector3 *arg2 = 0 ; + OpenBabel::vector3 *arg3 = 0 ; + OpenBabel::vector3 *arg4 = 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + void *argp3 = 0 ; + int res3 = 0 ; + void *argp4 = 0 ; + int res4 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + PyObject * obj2 = 0 ; + PyObject * obj3 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_findCenterAndNormal",4,4,&obj0,&obj1,&obj2,&obj3)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "2"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "2"" of type '" "OpenBabel::vector3 &""'"); + } + arg2 = reinterpret_cast< OpenBabel::vector3 * >(argp2); + res3 = SWIG_ConvertPtr(obj2, &argp3, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res3)) { + SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "3"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp3) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "3"" of type '" "OpenBabel::vector3 &""'"); + } + arg3 = reinterpret_cast< OpenBabel::vector3 * >(argp3); + res4 = SWIG_ConvertPtr(obj3, &argp4, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res4)) { + SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "4"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp4) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBMolRingIter_findCenterAndNormal" "', argument " "4"" of type '" "OpenBabel::vector3 &""'"); + } + arg4 = reinterpret_cast< OpenBabel::vector3 * >(argp4); + result = (bool)(*arg1)->findCenterAndNormal(*arg2,*arg3,*arg4); + resultobj = SWIG_From_bool(static_cast< bool >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_Size(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_Size",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_Size" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (int)(*arg1)->Size(); + resultobj = SWIG_From_int(static_cast< int >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_PathSize(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_PathSize",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_PathSize" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (int)(*arg1)->PathSize(); + resultobj = SWIG_From_int(static_cast< int >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_IsMember__SWIG_0(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBAtom *arg2 = (OpenBabel::OBAtom *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_IsMember",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsMember" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2,SWIGTYPE_p_OpenBabel__OBAtom, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_IsMember" "', argument " "2"" of type '" "OpenBabel::OBAtom *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBAtom * >(argp2); + result = (bool)(*arg1)->IsMember(arg2); + resultobj = SWIG_From_bool(static_cast< bool >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_IsMember__SWIG_1(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBond *arg2 = (OpenBabel::OBBond *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_IsMember",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsMember" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2,SWIGTYPE_p_OpenBabel__OBBond, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_IsMember" "', argument " "2"" of type '" "OpenBabel::OBBond *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBBond * >(argp2); + result = (bool)(*arg1)->IsMember(arg2); + resultobj = SWIG_From_bool(static_cast< bool >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_IsMember(PyObject *self, PyObject *args) { + int argc; + PyObject *argv[3]; + int ii; + + if (!PyTuple_Check(args)) SWIG_fail; + argc = PyObject_Length(args); + for (ii = 0; (ii < argc) && (ii < 2); ii++) { + argv[ii] = PyTuple_GET_ITEM(args,ii); + } + if (argc == 2) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_OpenBabel__OBAtom, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBMolRingIter_IsMember__SWIG_0(self, args); + } + } + } + if (argc == 2) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_OpenBabel__OBBond, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBMolRingIter_IsMember__SWIG_1(self, args); + } + } + } + +fail: + SWIG_SetErrorMsg(PyExc_NotImplementedError,"Wrong number of arguments for overloaded function 'OBMolRingIter_IsMember'.\n Possible C/C++ prototypes are:\n IsMember(OpenBabel::OBAtom *)\n IsMember(OpenBabel::OBBond *)\n"); + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_IsAromatic(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_IsAromatic",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsAromatic" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (bool)(*arg1)->IsAromatic(); + resultobj = SWIG_From_bool(static_cast< bool >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_IsInRing(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int arg2 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + int val2 ; + int ecode2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_IsInRing",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_IsInRing" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + ecode2 = SWIG_AsVal_int(obj1, &val2); + if (!SWIG_IsOK(ecode2)) { + SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "OBMolRingIter_IsInRing" "', argument " "2"" of type '" "int""'"); + } + arg2 = static_cast< int >(val2); + result = (bool)(*arg1)->IsInRing(arg2); + resultobj = SWIG_From_bool(static_cast< bool >(result)); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_SetParent(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *arg2 = (OpenBabel::OBMol *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + PyObject * obj0 = 0 ; + PyObject * obj1 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_SetParent",2,2,&obj0,&obj1)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_SetParent" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(obj1, &argp2,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBMolRingIter_SetParent" "', argument " "2"" of type '" "OpenBabel::OBMol *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); + (*arg1)->SetParent(arg2); + resultobj = SWIG_Py_Void(); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *_wrap_OBMolRingIter_GetParent(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *resultobj = 0; + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + PyObject * obj0 = 0 ; + + if(!PyArg_UnpackTuple(args,(char *)"OBMolRingIter_GetParent",1,1,&obj0)) SWIG_fail; + res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBMolRingIter_GetParent" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBMol *)(*arg1)->GetParent(); + resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + return resultobj; +fail: + return NULL; +} + + +SWIGINTERN PyObject *OBMolRingIter_swigregister(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + PyObject *obj; + if (!PyArg_UnpackTuple(args,(char*)"swigregister", 1, 1,&obj)) return NULL; + SWIG_TypeNewClientData(SWIGTYPE_p_OpenBabel__OBMolRingIter, SWIG_NewClientData(obj)); + return SWIG_Py_Void(); +} + +SWIGINTERN PyObject *OBMolRingIter_swiginit(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { + return SWIG_Python_InitShadowInstance(args); +} + SWIGINTERN PyObject *_wrap_new_doubleArray(PyObject *SWIGUNUSEDPARM(self), PyObject *args) { PyObject *resultobj = 0; size_t arg1 ; @@ -87748,6 +89200,10 @@ static PyMethodDef SwigMethods[] = { { (char *)"OBRingData_SetData", _wrap_OBRingData_SetData, METH_VARARGS, NULL}, { (char *)"OBRingData_PushBack", _wrap_OBRingData_PushBack, METH_VARARGS, NULL}, { (char *)"OBRingData_GetData", _wrap_OBRingData_GetData, METH_VARARGS, NULL}, + { (char *)"OBRingData_BeginRings", _wrap_OBRingData_BeginRings, METH_VARARGS, NULL}, + { (char *)"OBRingData_EndRings", _wrap_OBRingData_EndRings, METH_VARARGS, NULL}, + { (char *)"OBRingData_BeginRing", _wrap_OBRingData_BeginRing, METH_VARARGS, NULL}, + { (char *)"OBRingData_NextRing", _wrap_OBRingData_NextRing, METH_VARARGS, NULL}, { (char *)"OBRingData_swigregister", OBRingData_swigregister, METH_VARARGS, NULL}, { (char *)"OBRingData_swiginit", OBRingData_swiginit, METH_VARARGS, NULL}, { (char *)"new_OBUnitCell", _wrap_new_OBUnitCell, METH_VARARGS, NULL}, @@ -88336,6 +89792,7 @@ static PyMethodDef SwigMethods[] = { { (char *)"OBMol_Align", _wrap_OBMol_Align, METH_VARARGS, NULL}, { (char *)"OBMol_ConnectTheDots", _wrap_OBMol_ConnectTheDots, METH_VARARGS, NULL}, { (char *)"OBMol_PerceiveBondOrders", _wrap_OBMol_PerceiveBondOrders, METH_VARARGS, NULL}, + { (char *)"OBMol_FindAngles", _wrap_OBMol_FindAngles, METH_VARARGS, NULL}, { (char *)"OBMol_FindTorsions", _wrap_OBMol_FindTorsions, METH_VARARGS, NULL}, { (char *)"OBMol_GetGTDVector", _wrap_OBMol_GetGTDVector, METH_VARARGS, NULL}, { (char *)"OBMol_GetGIVector", _wrap_OBMol_GetGIVector, METH_VARARGS, NULL}, @@ -89425,6 +90882,40 @@ static PyMethodDef SwigMethods[] = { { (char *)"OBResidueAtomIter_EndData", _wrap_OBResidueAtomIter_EndData, METH_VARARGS, NULL}, { (char *)"OBResidueAtomIter_swigregister", OBResidueAtomIter_swigregister, METH_VARARGS, NULL}, { (char *)"OBResidueAtomIter_swiginit", OBResidueAtomIter_swiginit, METH_VARARGS, NULL}, + { (char *)"new_OBMolAngleIter", _wrap_new_OBMolAngleIter, METH_VARARGS, NULL}, + { (char *)"OBMolAngleIter___ref__", _wrap_OBMolAngleIter___ref__, METH_VARARGS, NULL}, + { (char *)"delete_OBMolAngleIter", _wrap_delete_OBMolAngleIter, METH_VARARGS, NULL}, + { (char *)"OBMolAngleIter_swigregister", OBMolAngleIter_swigregister, METH_VARARGS, NULL}, + { (char *)"OBMolAngleIter_swiginit", OBMolAngleIter_swiginit, METH_VARARGS, NULL}, + { (char *)"new_OBMolTorsionIter", _wrap_new_OBMolTorsionIter, METH_VARARGS, NULL}, + { (char *)"OBMolTorsionIter___ref__", _wrap_OBMolTorsionIter___ref__, METH_VARARGS, NULL}, + { (char *)"delete_OBMolTorsionIter", _wrap_delete_OBMolTorsionIter, METH_VARARGS, NULL}, + { (char *)"OBMolTorsionIter_swigregister", OBMolTorsionIter_swigregister, METH_VARARGS, NULL}, + { (char *)"OBMolTorsionIter_swiginit", OBMolTorsionIter_swiginit, METH_VARARGS, NULL}, + { (char *)"new_OBMolPairIter", _wrap_new_OBMolPairIter, METH_VARARGS, NULL}, + { (char *)"OBMolPairIter___deref__", _wrap_OBMolPairIter___deref__, METH_VARARGS, NULL}, + { (char *)"OBMolPairIter___ref__", _wrap_OBMolPairIter___ref__, METH_VARARGS, NULL}, + { (char *)"delete_OBMolPairIter", _wrap_delete_OBMolPairIter, METH_VARARGS, NULL}, + { (char *)"OBMolPairIter_swigregister", OBMolPairIter_swigregister, METH_VARARGS, NULL}, + { (char *)"OBMolPairIter_swiginit", OBMolPairIter_swiginit, METH_VARARGS, NULL}, + { (char *)"new_OBMolRingIter", _wrap_new_OBMolRingIter, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter___deref__", _wrap_OBMolRingIter___deref__, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter___ref__", _wrap_OBMolRingIter___ref__, METH_VARARGS, NULL}, + { (char *)"delete_OBMolRingIter", _wrap_delete_OBMolRingIter, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter__path_set", _wrap_OBMolRingIter__path_set, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter__path_get", _wrap_OBMolRingIter__path_get, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter__pathset_set", _wrap_OBMolRingIter__pathset_set, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter__pathset_get", _wrap_OBMolRingIter__pathset_get, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_findCenterAndNormal", _wrap_OBMolRingIter_findCenterAndNormal, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_Size", _wrap_OBMolRingIter_Size, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_PathSize", _wrap_OBMolRingIter_PathSize, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_IsMember", _wrap_OBMolRingIter_IsMember, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_IsAromatic", _wrap_OBMolRingIter_IsAromatic, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_IsInRing", _wrap_OBMolRingIter_IsInRing, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_SetParent", _wrap_OBMolRingIter_SetParent, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_GetParent", _wrap_OBMolRingIter_GetParent, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_swigregister", OBMolRingIter_swigregister, METH_VARARGS, NULL}, + { (char *)"OBMolRingIter_swiginit", OBMolRingIter_swiginit, METH_VARARGS, NULL}, { (char *)"new_doubleArray", _wrap_new_doubleArray, METH_VARARGS, NULL}, { (char *)"delete_doubleArray", _wrap_delete_doubleArray, METH_VARARGS, NULL}, { (char *)"doubleArray___getitem__", _wrap_doubleArray___getitem__, METH_VARARGS, NULL}, @@ -89469,15 +90960,15 @@ static void *_p_OpenBabel__OBBondTo_p_OpenBabel__OBBase(void *x) { static void *_p_OpenBabel__OBAtomTo_p_OpenBabel__OBBase(void *x) { return (void *)((OpenBabel::OBBase *) ((OpenBabel::OBAtom *) x)); } -static void *_p_a_3__doubleArrayTo_p_a_3__double(void *x) { - return (void *)((double (*)[3]) ((doubleArray (*)[3]) x)); -} static void *_p_p_doubleArrayTo_p_p_double(void *x) { return (void *)((double **) ((doubleArray **) x)); } static void *_p_doubleArrayTo_p_double(void *x) { return (void *)((double *) ((doubleArray *) x)); } +static void *_p_a_3__doubleArrayTo_p_a_3__double(void *x) { + return (void *)((double (*)[3]) ((doubleArray (*)[3]) x)); +} static void *_p_OpenBabel__OBSymmetryDataTo_p_OpenBabel__OBGenericData(void *x) { return (void *)((OpenBabel::OBGenericData *) ((OpenBabel::OBSymmetryData *) x)); } @@ -89552,10 +91043,14 @@ static swig_type_info _swigt__p_OpenBabel__OBInternalCoord = {"_p_OpenBabel__OBI static swig_type_info _swigt__p_OpenBabel__OBIsotopeTable = {"_p_OpenBabel__OBIsotopeTable", "OpenBabel::OBIsotopeTable *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMessageHandler = {"_p_OpenBabel__OBMessageHandler", "OpenBabel::OBMessageHandler *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMol = {"_p_OpenBabel__OBMol", "OpenBabel::OBMol *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolAngleIter = {"_p_OpenBabel__OBMolAngleIter", "OpenBabel::OBMolAngleIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomBFSIter = {"_p_OpenBabel__OBMolAtomBFSIter", "OpenBabel::OBMolAtomBFSIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomDFSIter = {"_p_OpenBabel__OBMolAtomDFSIter", "OpenBabel::OBMolAtomDFSIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomIter = {"_p_OpenBabel__OBMolAtomIter", "OpenBabel::OBMolAtomIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolBondIter = {"_p_OpenBabel__OBMolBondIter", "OpenBabel::OBMolBondIter *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolPairIter = {"_p_OpenBabel__OBMolPairIter", "OpenBabel::OBMolPairIter *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolRingIter = {"_p_OpenBabel__OBMolRingIter", "OpenBabel::OBMolRingIter *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolTorsionIter = {"_p_OpenBabel__OBMolTorsionIter", "OpenBabel::OBMolTorsionIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBPairData = {"_p_OpenBabel__OBPairData", "OpenBabel::OBPairData *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBPairTemplateTdouble_t = {"_p_OpenBabel__OBPairTemplateTdouble_t", "OpenBabel::OBPairTemplate *|OpenBabel::OBPairFloatingPoint *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBPairTemplateTint_t = {"_p_OpenBabel__OBPairTemplateTint_t", "OpenBabel::OBPairTemplate *|OpenBabel::OBPairInteger *", 0, 0, (void*)0, 0}; @@ -89615,6 +91110,7 @@ static swig_type_info _swigt__p_std__mapTstd__string_std__string_std__lessTstd__ static swig_type_info _swigt__p_std__multimapTdouble_unsigned_int_t = {"_p_std__multimapTdouble_unsigned_int_t", "std::multimap *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__ostream = {"_p_std__ostream", "std::ostream *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t = {"_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t", "std::pair *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_std__pairTint_int_t = {"_p_std__pairTint_int_t", "std::pair *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__streampos = {"_p_std__streampos", "std::streampos *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__string = {"_p_std__string", "std::string *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__type_info = {"_p_std__type_info", "std::type_info *", 0, 0, (void*)0, 0}; @@ -89703,10 +91199,14 @@ static swig_type_info *swig_type_initial[] = { &_swigt__p_OpenBabel__OBIsotopeTable, &_swigt__p_OpenBabel__OBMessageHandler, &_swigt__p_OpenBabel__OBMol, + &_swigt__p_OpenBabel__OBMolAngleIter, &_swigt__p_OpenBabel__OBMolAtomBFSIter, &_swigt__p_OpenBabel__OBMolAtomDFSIter, &_swigt__p_OpenBabel__OBMolAtomIter, &_swigt__p_OpenBabel__OBMolBondIter, + &_swigt__p_OpenBabel__OBMolPairIter, + &_swigt__p_OpenBabel__OBMolRingIter, + &_swigt__p_OpenBabel__OBMolTorsionIter, &_swigt__p_OpenBabel__OBPairData, &_swigt__p_OpenBabel__OBPairTemplateTdouble_t, &_swigt__p_OpenBabel__OBPairTemplateTint_t, @@ -89766,6 +91266,7 @@ static swig_type_info *swig_type_initial[] = { &_swigt__p_std__multimapTdouble_unsigned_int_t, &_swigt__p_std__ostream, &_swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, + &_swigt__p_std__pairTint_int_t, &_swigt__p_std__streampos, &_swigt__p_std__string, &_swigt__p_std__type_info, @@ -89854,10 +91355,14 @@ static swig_cast_info _swigc__p_OpenBabel__OBInternalCoord[] = { {&_swigt__p_Op static swig_cast_info _swigc__p_OpenBabel__OBIsotopeTable[] = { {&_swigt__p_OpenBabel__OBIsotopeTable, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMessageHandler[] = { {&_swigt__p_OpenBabel__OBMessageHandler, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMol[] = { {&_swigt__p_OpenBabel__OBMol, 0, 0, 0}, {&_swigt__p_std__vectorTOpenBabel__OBMol_std__allocatorTOpenBabel__OBMol_t_t__value_type, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolAngleIter[] = { {&_swigt__p_OpenBabel__OBMolAngleIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomBFSIter[] = { {&_swigt__p_OpenBabel__OBMolAtomBFSIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomDFSIter[] = { {&_swigt__p_OpenBabel__OBMolAtomDFSIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomIter[] = { {&_swigt__p_OpenBabel__OBMolAtomIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolBondIter[] = { {&_swigt__p_OpenBabel__OBMolBondIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolPairIter[] = { {&_swigt__p_OpenBabel__OBMolPairIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolRingIter[] = { {&_swigt__p_OpenBabel__OBMolRingIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolTorsionIter[] = { {&_swigt__p_OpenBabel__OBMolTorsionIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairData[] = { {&_swigt__p_OpenBabel__OBPairData, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairTemplateTdouble_t[] = { {&_swigt__p_OpenBabel__OBPairTemplateTdouble_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairTemplateTint_t[] = { {&_swigt__p_OpenBabel__OBPairTemplateTint_t, 0, 0, 0},{0, 0, 0, 0}}; @@ -89917,6 +91422,7 @@ static swig_cast_info _swigc__p_std__mapTstd__string_std__string_std__lessTstd__ static swig_cast_info _swigc__p_std__multimapTdouble_unsigned_int_t[] = { {&_swigt__p_std__multimapTdouble_unsigned_int_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__ostream[] = { {&_swigt__p_std__ostream, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t[] = { {&_swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_std__pairTint_int_t[] = { {&_swigt__p_std__pairTint_int_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__streampos[] = { {&_swigt__p_std__streampos, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__string[] = { {&_swigt__p_std__string, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__type_info[] = { {&_swigt__p_std__type_info, 0, 0, 0},{0, 0, 0, 0}}; @@ -90005,10 +91511,14 @@ static swig_cast_info *swig_cast_initial[] = { _swigc__p_OpenBabel__OBIsotopeTable, _swigc__p_OpenBabel__OBMessageHandler, _swigc__p_OpenBabel__OBMol, + _swigc__p_OpenBabel__OBMolAngleIter, _swigc__p_OpenBabel__OBMolAtomBFSIter, _swigc__p_OpenBabel__OBMolAtomDFSIter, _swigc__p_OpenBabel__OBMolAtomIter, _swigc__p_OpenBabel__OBMolBondIter, + _swigc__p_OpenBabel__OBMolPairIter, + _swigc__p_OpenBabel__OBMolRingIter, + _swigc__p_OpenBabel__OBMolTorsionIter, _swigc__p_OpenBabel__OBPairData, _swigc__p_OpenBabel__OBPairTemplateTdouble_t, _swigc__p_OpenBabel__OBPairTemplateTint_t, @@ -90068,6 +91578,7 @@ static swig_cast_info *swig_cast_initial[] = { _swigc__p_std__multimapTdouble_unsigned_int_t, _swigc__p_std__ostream, _swigc__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, + _swigc__p_std__pairTint_int_t, _swigc__p_std__streampos, _swigc__p_std__string, _swigc__p_std__type_info, diff --git a/scripts/python/setup.py b/scripts/python/setup.py index b244b3c31..d5356e740 100644 --- a/scripts/python/setup.py +++ b/scripts/python/setup.py @@ -30,7 +30,7 @@ def find_likely_directory(): sys.stderr.write("WARNING: Environment variable OPENBABEL_INSTALL is not set\n") sys.stderr.write("INFO: Looking for library and include files in ../../src\n") if os.path.isfile("../../src/atom.o"): - return ["../../src"],["../../src"] + return ["../../include"],["../../src"] for dirname in ["/usr/local","/usr"]: # Look for each of these directories in turn for the directory include/openbabel-2.0 @@ -38,7 +38,7 @@ def find_likely_directory(): # a regular expression to find the latest version of openbabel) if os.path.isdir(dirname+"/include/openbabel-2.0"): sys.stderr.write("INFO: Setting OPENBABEL_INSTALL to %s\n" % dirname) - return ([dirname+"/include/openbabel-2.0",dirname+"/include/openbabel-2.0/openbabel"], + return ([dirname+"/include/openbabel-2.0",dirname+"/include/openbabel-2.0"], [dirname+"/lib"]) sys.stderr.write("ERROR: Cannot find Open Babel library directory\n") diff --git a/scripts/ruby/openbabel_ruby.cpp b/scripts/ruby/openbabel_ruby.cpp index b08d284bf..fb1460baf 100644 --- a/scripts/ruby/openbabel_ruby.cpp +++ b/scripts/ruby/openbabel_ruby.cpp @@ -1576,112 +1576,117 @@ SWIG_Ruby_SetModule(swig_module_info *pointer) #define SWIGTYPE_p_OpenBabel__OBIsotopeTable swig_types[32] #define SWIGTYPE_p_OpenBabel__OBMessageHandler swig_types[33] #define SWIGTYPE_p_OpenBabel__OBMol swig_types[34] -#define SWIGTYPE_p_OpenBabel__OBMolAtomBFSIter swig_types[35] -#define SWIGTYPE_p_OpenBabel__OBMolAtomDFSIter swig_types[36] -#define SWIGTYPE_p_OpenBabel__OBMolAtomIter swig_types[37] -#define SWIGTYPE_p_OpenBabel__OBMolBondIter swig_types[38] -#define SWIGTYPE_p_OpenBabel__OBPairData swig_types[39] -#define SWIGTYPE_p_OpenBabel__OBPairTemplateTdouble_t swig_types[40] -#define SWIGTYPE_p_OpenBabel__OBPairTemplateTint_t swig_types[41] -#define SWIGTYPE_p_OpenBabel__OBRTree swig_types[42] -#define SWIGTYPE_p_OpenBabel__OBRandom swig_types[43] -#define SWIGTYPE_p_OpenBabel__OBResidue swig_types[44] -#define SWIGTYPE_p_OpenBabel__OBResidueAtomIter swig_types[45] -#define SWIGTYPE_p_OpenBabel__OBResidueData swig_types[46] -#define SWIGTYPE_p_OpenBabel__OBResidueIter swig_types[47] -#define SWIGTYPE_p_OpenBabel__OBRing swig_types[48] -#define SWIGTYPE_p_OpenBabel__OBRingData swig_types[49] -#define SWIGTYPE_p_OpenBabel__OBRingSearch swig_types[50] -#define SWIGTYPE_p_OpenBabel__OBSSMatch swig_types[51] -#define SWIGTYPE_p_OpenBabel__OBSerialNums swig_types[52] -#define SWIGTYPE_p_OpenBabel__OBSetData swig_types[53] -#define SWIGTYPE_p_OpenBabel__OBSmartsPattern swig_types[54] -#define SWIGTYPE_p_OpenBabel__OBSqrtTbl swig_types[55] -#define SWIGTYPE_p_OpenBabel__OBStopwatch swig_types[56] -#define SWIGTYPE_p_OpenBabel__OBSymmetryData swig_types[57] -#define SWIGTYPE_p_OpenBabel__OBTorsion swig_types[58] -#define SWIGTYPE_p_OpenBabel__OBTorsionData swig_types[59] -#define SWIGTYPE_p_OpenBabel__OBTypeTable swig_types[60] -#define SWIGTYPE_p_OpenBabel__OBUnitCell swig_types[61] -#define SWIGTYPE_p_OpenBabel__OBVirtualBond swig_types[62] -#define SWIGTYPE_p_OpenBabel__Pattern swig_types[63] -#define SWIGTYPE_p_OpenBabel__Template swig_types[64] -#define SWIGTYPE_p_OpenBabel__matrix3x3 swig_types[65] -#define SWIGTYPE_p_OpenBabel__obLogBuf swig_types[66] -#define SWIGTYPE_p_OpenBabel__quadTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[67] -#define SWIGTYPE_p_OpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[68] -#define SWIGTYPE_p_OpenBabel__vector3 swig_types[69] -#define SWIGTYPE_p_a_3__double swig_types[70] -#define SWIGTYPE_p_a_4__char swig_types[71] -#define SWIGTYPE_p_char swig_types[72] -#define SWIGTYPE_p_double swig_types[73] -#define SWIGTYPE_p_int swig_types[74] -#define SWIGTYPE_p_p_OpenBabel__OBAngleData swig_types[75] -#define SWIGTYPE_p_p_OpenBabel__OBChiralData swig_types[76] -#define SWIGTYPE_p_p_OpenBabel__OBCommentData swig_types[77] -#define SWIGTYPE_p_p_OpenBabel__OBConformerData swig_types[78] -#define SWIGTYPE_p_p_OpenBabel__OBExternalBondData swig_types[79] -#define SWIGTYPE_p_p_OpenBabel__OBFingerprint swig_types[80] -#define SWIGTYPE_p_p_OpenBabel__OBFormat swig_types[81] -#define SWIGTYPE_p_p_OpenBabel__OBGenericData swig_types[82] -#define SWIGTYPE_p_p_OpenBabel__OBPairData swig_types[83] -#define SWIGTYPE_p_p_OpenBabel__OBRingData swig_types[84] -#define SWIGTYPE_p_p_OpenBabel__OBSerialNums swig_types[85] -#define SWIGTYPE_p_p_OpenBabel__OBSetData swig_types[86] -#define SWIGTYPE_p_p_OpenBabel__OBSymmetryData swig_types[87] -#define SWIGTYPE_p_p_OpenBabel__OBTorsionData swig_types[88] -#define SWIGTYPE_p_p_OpenBabel__OBUnitCell swig_types[89] -#define SWIGTYPE_p_p_OpenBabel__OBVirtualBond swig_types[90] -#define SWIGTYPE_p_p_double swig_types[91] -#define SWIGTYPE_p_p_int swig_types[92] -#define SWIGTYPE_p_std__dequeTint_t swig_types[93] -#define SWIGTYPE_p_std__ifstream swig_types[94] -#define SWIGTYPE_p_std__istream swig_types[95] -#define SWIGTYPE_p_std__mapTchar_const_p_OpenBabel__OBFormat_p_OpenBabel__CharPtrLess_t swig_types[96] -#define SWIGTYPE_p_std__mapTint_OpenBabel__OBAtom_p_t swig_types[97] -#define SWIGTYPE_p_std__mapTstd__string_std__string_t swig_types[98] -#define SWIGTYPE_p_std__multimapTdouble_unsigned_int_t swig_types[99] -#define SWIGTYPE_p_std__ostream swig_types[100] -#define SWIGTYPE_p_std__out_of_range swig_types[101] -#define SWIGTYPE_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[102] -#define SWIGTYPE_p_std__streampos swig_types[103] -#define SWIGTYPE_p_std__string swig_types[104] -#define SWIGTYPE_p_std__type_info swig_types[105] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t swig_types[106] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator swig_types[107] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t swig_types[108] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator swig_types[109] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_t swig_types[110] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBExternalBond_t swig_types[111] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t swig_types[112] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator swig_types[113] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t swig_types[114] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator swig_types[115] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_t swig_types[116] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator swig_types[117] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_t swig_types[118] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t swig_types[119] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator swig_types[120] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_t swig_types[121] -#define SWIGTYPE_p_std__vectorTOpenBabel__OBTorsion_t swig_types[122] -#define SWIGTYPE_p_std__vectorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_t swig_types[123] -#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_t swig_types[124] -#define SWIGTYPE_p_std__vectorTdouble_p_t swig_types[125] -#define SWIGTYPE_p_std__vectorTdouble_p_t__iterator swig_types[126] -#define SWIGTYPE_p_std__vectorTdouble_t swig_types[127] -#define SWIGTYPE_p_std__vectorTint_t swig_types[128] -#define SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t swig_types[129] -#define SWIGTYPE_p_std__vectorTstd__pairTstd__string_std__string_t_t swig_types[130] -#define SWIGTYPE_p_std__vectorTstd__string_t swig_types[131] -#define SWIGTYPE_p_std__vectorTstd__vectorTOpenBabel__vector3_t_t swig_types[132] -#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t swig_types[133] -#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator swig_types[134] -#define SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t swig_types[135] -#define SWIGTYPE_p_std__vectorTunsigned_int_t swig_types[136] -#define SWIGTYPE_p_std__vectorTunsigned_short_t swig_types[137] -#define SWIGTYPE_p_unsigned_int swig_types[138] -static swig_type_info *swig_types[140]; -static swig_module_info swig_module = {swig_types, 139, 0, 0, 0, 0}; +#define SWIGTYPE_p_OpenBabel__OBMolAngleIter swig_types[35] +#define SWIGTYPE_p_OpenBabel__OBMolAtomBFSIter swig_types[36] +#define SWIGTYPE_p_OpenBabel__OBMolAtomDFSIter swig_types[37] +#define SWIGTYPE_p_OpenBabel__OBMolAtomIter swig_types[38] +#define SWIGTYPE_p_OpenBabel__OBMolBondIter swig_types[39] +#define SWIGTYPE_p_OpenBabel__OBMolPairIter swig_types[40] +#define SWIGTYPE_p_OpenBabel__OBMolRingIter swig_types[41] +#define SWIGTYPE_p_OpenBabel__OBMolTorsionIter swig_types[42] +#define SWIGTYPE_p_OpenBabel__OBPairData swig_types[43] +#define SWIGTYPE_p_OpenBabel__OBPairTemplateTdouble_t swig_types[44] +#define SWIGTYPE_p_OpenBabel__OBPairTemplateTint_t swig_types[45] +#define SWIGTYPE_p_OpenBabel__OBRTree swig_types[46] +#define SWIGTYPE_p_OpenBabel__OBRandom swig_types[47] +#define SWIGTYPE_p_OpenBabel__OBResidue swig_types[48] +#define SWIGTYPE_p_OpenBabel__OBResidueAtomIter swig_types[49] +#define SWIGTYPE_p_OpenBabel__OBResidueData swig_types[50] +#define SWIGTYPE_p_OpenBabel__OBResidueIter swig_types[51] +#define SWIGTYPE_p_OpenBabel__OBRing swig_types[52] +#define SWIGTYPE_p_OpenBabel__OBRingData swig_types[53] +#define SWIGTYPE_p_OpenBabel__OBRingSearch swig_types[54] +#define SWIGTYPE_p_OpenBabel__OBSSMatch swig_types[55] +#define SWIGTYPE_p_OpenBabel__OBSerialNums swig_types[56] +#define SWIGTYPE_p_OpenBabel__OBSetData swig_types[57] +#define SWIGTYPE_p_OpenBabel__OBSmartsPattern swig_types[58] +#define SWIGTYPE_p_OpenBabel__OBSqrtTbl swig_types[59] +#define SWIGTYPE_p_OpenBabel__OBStopwatch swig_types[60] +#define SWIGTYPE_p_OpenBabel__OBSymmetryData swig_types[61] +#define SWIGTYPE_p_OpenBabel__OBTorsion swig_types[62] +#define SWIGTYPE_p_OpenBabel__OBTorsionData swig_types[63] +#define SWIGTYPE_p_OpenBabel__OBTypeTable swig_types[64] +#define SWIGTYPE_p_OpenBabel__OBUnitCell swig_types[65] +#define SWIGTYPE_p_OpenBabel__OBVirtualBond swig_types[66] +#define SWIGTYPE_p_OpenBabel__Pattern swig_types[67] +#define SWIGTYPE_p_OpenBabel__Template swig_types[68] +#define SWIGTYPE_p_OpenBabel__matrix3x3 swig_types[69] +#define SWIGTYPE_p_OpenBabel__obLogBuf swig_types[70] +#define SWIGTYPE_p_OpenBabel__quadTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[71] +#define SWIGTYPE_p_OpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[72] +#define SWIGTYPE_p_OpenBabel__vector3 swig_types[73] +#define SWIGTYPE_p_a_3__double swig_types[74] +#define SWIGTYPE_p_a_4__char swig_types[75] +#define SWIGTYPE_p_char swig_types[76] +#define SWIGTYPE_p_double swig_types[77] +#define SWIGTYPE_p_int swig_types[78] +#define SWIGTYPE_p_p_OpenBabel__OBAngleData swig_types[79] +#define SWIGTYPE_p_p_OpenBabel__OBChiralData swig_types[80] +#define SWIGTYPE_p_p_OpenBabel__OBCommentData swig_types[81] +#define SWIGTYPE_p_p_OpenBabel__OBConformerData swig_types[82] +#define SWIGTYPE_p_p_OpenBabel__OBExternalBondData swig_types[83] +#define SWIGTYPE_p_p_OpenBabel__OBFingerprint swig_types[84] +#define SWIGTYPE_p_p_OpenBabel__OBFormat swig_types[85] +#define SWIGTYPE_p_p_OpenBabel__OBGenericData swig_types[86] +#define SWIGTYPE_p_p_OpenBabel__OBPairData swig_types[87] +#define SWIGTYPE_p_p_OpenBabel__OBRingData swig_types[88] +#define SWIGTYPE_p_p_OpenBabel__OBSerialNums swig_types[89] +#define SWIGTYPE_p_p_OpenBabel__OBSetData swig_types[90] +#define SWIGTYPE_p_p_OpenBabel__OBSymmetryData swig_types[91] +#define SWIGTYPE_p_p_OpenBabel__OBTorsionData swig_types[92] +#define SWIGTYPE_p_p_OpenBabel__OBUnitCell swig_types[93] +#define SWIGTYPE_p_p_OpenBabel__OBVirtualBond swig_types[94] +#define SWIGTYPE_p_p_double swig_types[95] +#define SWIGTYPE_p_p_int swig_types[96] +#define SWIGTYPE_p_std__dequeTint_t swig_types[97] +#define SWIGTYPE_p_std__ifstream swig_types[98] +#define SWIGTYPE_p_std__istream swig_types[99] +#define SWIGTYPE_p_std__mapTchar_const_p_OpenBabel__OBFormat_p_OpenBabel__CharPtrLess_t swig_types[100] +#define SWIGTYPE_p_std__mapTint_OpenBabel__OBAtom_p_t swig_types[101] +#define SWIGTYPE_p_std__mapTstd__string_std__string_t swig_types[102] +#define SWIGTYPE_p_std__multimapTdouble_unsigned_int_t swig_types[103] +#define SWIGTYPE_p_std__ostream swig_types[104] +#define SWIGTYPE_p_std__out_of_range swig_types[105] +#define SWIGTYPE_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t swig_types[106] +#define SWIGTYPE_p_std__pairTint_int_t swig_types[107] +#define SWIGTYPE_p_std__streampos swig_types[108] +#define SWIGTYPE_p_std__string swig_types[109] +#define SWIGTYPE_p_std__type_info swig_types[110] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t swig_types[111] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator swig_types[112] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t swig_types[113] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator swig_types[114] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBBond_t swig_types[115] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBExternalBond_t swig_types[116] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t swig_types[117] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator swig_types[118] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t swig_types[119] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator swig_types[120] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBMol_t swig_types[121] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator swig_types[122] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_t swig_types[123] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t swig_types[124] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator swig_types[125] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBRing_t swig_types[126] +#define SWIGTYPE_p_std__vectorTOpenBabel__OBTorsion_t swig_types[127] +#define SWIGTYPE_p_std__vectorTOpenBabel__tripleTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_double_t_t swig_types[128] +#define SWIGTYPE_p_std__vectorTOpenBabel__vector3_t swig_types[129] +#define SWIGTYPE_p_std__vectorTdouble_p_t swig_types[130] +#define SWIGTYPE_p_std__vectorTdouble_p_t__iterator swig_types[131] +#define SWIGTYPE_p_std__vectorTdouble_t swig_types[132] +#define SWIGTYPE_p_std__vectorTint_t swig_types[133] +#define SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t swig_types[134] +#define SWIGTYPE_p_std__vectorTstd__pairTstd__string_std__string_t_t swig_types[135] +#define SWIGTYPE_p_std__vectorTstd__string_t swig_types[136] +#define SWIGTYPE_p_std__vectorTstd__vectorTOpenBabel__vector3_t_t swig_types[137] +#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t swig_types[138] +#define SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator swig_types[139] +#define SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t swig_types[140] +#define SWIGTYPE_p_std__vectorTunsigned_int_t swig_types[141] +#define SWIGTYPE_p_std__vectorTunsigned_short_t swig_types[142] +#define SWIGTYPE_p_unsigned_int swig_types[143] +static swig_type_info *swig_types[145]; +static swig_module_info swig_module = {swig_types, 144, 0, 0, 0, 0}; #define SWIG_TypeQuery(name) SWIG_TypeQueryModule(&swig_module, &swig_module, name) #define SWIG_MangledTypeQuery(name) SWIG_MangledTypeQueryModule(&swig_module, &swig_module, name) @@ -1710,27 +1715,27 @@ static VALUE mOpenbabel; #include -#include "obutil.h" -#include "rand.h" -#include "math/vector3.h" -#include "math/matrix3x3.h" -#include "generic.h" +#include +#include +#include +#include +#include -#include "base.h" -#include "mol.h" -#include "atom.h" -#include "bond.h" -#include "residue.h" -#include "internalcoord.h" +#include +#include +#include +#include +#include +#include -#include "ring.h" -#include "obconversion.h" -#include "oberror.h" +#include +#include +#include -#include "fingerprint.h" +#include -#include "data.h" -#include "parsmart.h" +#include +#include #include @@ -14309,6 +14314,124 @@ fail: } +SWIGINTERN VALUE +_wrap_OBRingData_BeginRings(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper::iterator > result; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "BeginRings" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + result = (arg1)->BeginRings(); + vresult = SWIG_NewPointerObj((new std::vector::iterator(static_cast< const std::vector::iterator& >(result))), SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, SWIG_POINTER_OWN | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBRingData_EndRings(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + SwigValueWrapper::iterator > result; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "EndRings" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + result = (arg1)->EndRings(); + vresult = SWIG_NewPointerObj((new std::vector::iterator(static_cast< const std::vector::iterator& >(result))), SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, SWIG_POINTER_OWN | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBRingData_BeginRing(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "BeginRing" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "BeginRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "BeginRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + arg2 = reinterpret_cast< std::vector::iterator * >(argp2); + result = (OpenBabel::OBRing *)(arg1)->BeginRing(*arg2); + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBRingData_NextRing(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBRingData *arg1 = (OpenBabel::OBRingData *) 0 ; + std::vector::iterator *arg2 = 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBRingData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "NextRing" "', argument " "1"" of type '" "OpenBabel::OBRingData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBRingData * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2, SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t__iterator, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "NextRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "NextRing" "', argument " "2"" of type '" "std::vector::iterator &""'"); + } + arg2 = reinterpret_cast< std::vector::iterator * >(argp2); + result = (OpenBabel::OBRing *)(arg1)->NextRing(*arg2); + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + swig_class cOBUnitCell; SWIGINTERN VALUE @@ -17352,7 +17475,7 @@ fail: SWIGINTERN VALUE -_wrap_OBAngleData_FillAngleArray(int argc, VALUE *argv, VALUE self) { +_wrap_OBAngleData_FillAngleArray__SWIG_0(int argc, VALUE *argv, VALUE self) { OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; int **arg2 = (int **) 0 ; unsigned int *arg3 = 0 ; @@ -17394,6 +17517,92 @@ fail: } +SWIGINTERN VALUE +_wrap_OBAngleData_FillAngleArray__SWIG_1(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; + std::vector > *arg2 = 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBAngleData, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "FillAngleArray" "', argument " "1"" of type '" "OpenBabel::OBAngleData *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBAngleData * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2, SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "FillAngleArray" "', argument " "2"" of type '" "std::vector > &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "FillAngleArray" "', argument " "2"" of type '" "std::vector > &""'"); + } + arg2 = reinterpret_cast< std::vector > * >(argp2); + result = (bool)(arg1)->FillAngleArray(*arg2); + vresult = SWIG_From_bool(static_cast< bool >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE _wrap_OBAngleData_FillAngleArray(int nargs, VALUE *args, VALUE self) { + int argc; + VALUE argv[4]; + int ii; + + argc = nargs + 1; + argv[0] = self; + if (argc > 4) SWIG_fail; + for (ii = 1; (ii < argc); ii++) { + argv[ii] = args[ii-1]; + } + if (argc == 2) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBAngleData, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_std__vectorTstd__vectorTunsigned_int_t_t, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBAngleData_FillAngleArray__SWIG_1(nargs, args, self); + } + } + } + if (argc == 3) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBAngleData, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_p_int, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[2], &vptr, SWIGTYPE_p_unsigned_int, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBAngleData_FillAngleArray__SWIG_0(nargs, args, self); + } + } + } + } + +fail: + rb_raise(rb_eArgError, "No matching function for overloaded 'OBAngleData_FillAngleArray'"); + return Qnil; +} + + SWIGINTERN VALUE _wrap_OBAngleData_SetData(int argc, VALUE *argv, VALUE self) { OpenBabel::OBAngleData *arg1 = (OpenBabel::OBAngleData *) 0 ; @@ -36163,6 +36372,27 @@ fail: } +SWIGINTERN VALUE +_wrap_OBMol_FindAngles(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "FindAngles" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + (arg1)->FindAngles(); + return Qnil; +fail: + return Qnil; +} + + SWIGINTERN VALUE _wrap_OBMol_FindTorsions(int argc, VALUE *argv, VALUE self) { OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; @@ -73313,6 +73543,1253 @@ fail: } +swig_class cOBMolAngleIter; + +SWIGINTERN VALUE +_wrap_new_OBMolAngleIter__SWIG_0(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolAngleIter *result = 0 ; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter();DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolAngleIter__SWIG_1(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolAngleIter__SWIG_2(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter(*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +#ifdef HAVE_RB_DEFINE_ALLOC_FUNC +SWIGINTERN VALUE +_wrap_OBMolAngleIter_allocate(VALUE self) { +#else + SWIGINTERN VALUE + _wrap_OBMolAngleIter_allocate(int argc, VALUE *argv, VALUE self) { +#endif + + + VALUE vresult = SWIG_NewClassInstance(self, SWIGTYPE_p_OpenBabel__OBMolAngleIter); +#ifndef HAVE_RB_DEFINE_ALLOC_FUNC + rb_obj_call_init(vresult, argc, argv); +#endif + return vresult; + } + + +SWIGINTERN VALUE +_wrap_new_OBMolAngleIter__SWIG_3(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolAngleIter *arg1 = 0 ; + OpenBabel::OBMolAngleIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolAngleIter" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + result = (OpenBabel::OBMolAngleIter *)new OpenBabel::OBMolAngleIter((OpenBabel::OBMolAngleIter const &)*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE _wrap_new_OBMolAngleIter(int nargs, VALUE *args, VALUE self) { + int argc; + VALUE argv[1]; + int ii; + + argc = nargs; + if (argc > 1) SWIG_fail; + for (ii = 0; (ii < argc); ii++) { + argv[ii] = args[ii]; + } + if (argc == 0) { + return _wrap_new_OBMolAngleIter__SWIG_0(nargs, args, self); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolAngleIter__SWIG_1(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolAngleIter__SWIG_2(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolAngleIter__SWIG_3(nargs, args, self); + } + } + +fail: + rb_raise(rb_eArgError, "No matching function for overloaded 'new_OBMolAngleIter'"); + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolAngleIter___ref__(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolAngleIter *arg1 = (OpenBabel::OBMolAngleIter *) 0 ; + std::vector result; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolAngleIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "operator *" "', argument " "1"" of type '" "OpenBabel::OBMolAngleIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolAngleIter * >(argp1); + result = ((OpenBabel::OBMolAngleIter const *)arg1)->operator *(); + vresult = SWIG_NewPointerObj((new std::vector(static_cast< const std::vector& >(result))), SWIGTYPE_p_std__vectorTunsigned_int_t, SWIG_POINTER_OWN | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN void +free_OpenBabel_OBMolAngleIter(OpenBabel::OBMolAngleIter *arg1) { + delete arg1; +} + +swig_class cOBMolTorsionIter; + +SWIGINTERN VALUE +_wrap_new_OBMolTorsionIter__SWIG_0(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolTorsionIter *result = 0 ; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter();DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolTorsionIter__SWIG_1(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolTorsionIter__SWIG_2(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter(*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +#ifdef HAVE_RB_DEFINE_ALLOC_FUNC +SWIGINTERN VALUE +_wrap_OBMolTorsionIter_allocate(VALUE self) { +#else + SWIGINTERN VALUE + _wrap_OBMolTorsionIter_allocate(int argc, VALUE *argv, VALUE self) { +#endif + + + VALUE vresult = SWIG_NewClassInstance(self, SWIGTYPE_p_OpenBabel__OBMolTorsionIter); +#ifndef HAVE_RB_DEFINE_ALLOC_FUNC + rb_obj_call_init(vresult, argc, argv); +#endif + return vresult; + } + + +SWIGINTERN VALUE +_wrap_new_OBMolTorsionIter__SWIG_3(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolTorsionIter *arg1 = 0 ; + OpenBabel::OBMolTorsionIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolTorsionIter" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + result = (OpenBabel::OBMolTorsionIter *)new OpenBabel::OBMolTorsionIter((OpenBabel::OBMolTorsionIter const &)*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE _wrap_new_OBMolTorsionIter(int nargs, VALUE *args, VALUE self) { + int argc; + VALUE argv[1]; + int ii; + + argc = nargs; + if (argc > 1) SWIG_fail; + for (ii = 0; (ii < argc); ii++) { + argv[ii] = args[ii]; + } + if (argc == 0) { + return _wrap_new_OBMolTorsionIter__SWIG_0(nargs, args, self); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolTorsionIter__SWIG_1(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolTorsionIter__SWIG_2(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolTorsionIter__SWIG_3(nargs, args, self); + } + } + +fail: + rb_raise(rb_eArgError, "No matching function for overloaded 'new_OBMolTorsionIter'"); + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolTorsionIter___ref__(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolTorsionIter *arg1 = (OpenBabel::OBMolTorsionIter *) 0 ; + std::vector result; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolTorsionIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "operator *" "', argument " "1"" of type '" "OpenBabel::OBMolTorsionIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolTorsionIter * >(argp1); + result = ((OpenBabel::OBMolTorsionIter const *)arg1)->operator *(); + vresult = SWIG_NewPointerObj((new std::vector(static_cast< const std::vector& >(result))), SWIGTYPE_p_std__vectorTunsigned_int_t, SWIG_POINTER_OWN | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN void +free_OpenBabel_OBMolTorsionIter(OpenBabel::OBMolTorsionIter *arg1) { + delete arg1; +} + +swig_class cOBMolPairIter; + +SWIGINTERN VALUE +_wrap_new_OBMolPairIter__SWIG_0(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolPairIter *result = 0 ; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter();DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolPairIter__SWIG_1(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolPairIter__SWIG_2(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter(*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +#ifdef HAVE_RB_DEFINE_ALLOC_FUNC +SWIGINTERN VALUE +_wrap_OBMolPairIter_allocate(VALUE self) { +#else + SWIGINTERN VALUE + _wrap_OBMolPairIter_allocate(int argc, VALUE *argv, VALUE self) { +#endif + + + VALUE vresult = SWIG_NewClassInstance(self, SWIGTYPE_p_OpenBabel__OBMolPairIter); +#ifndef HAVE_RB_DEFINE_ALLOC_FUNC + rb_obj_call_init(vresult, argc, argv); +#endif + return vresult; + } + + +SWIGINTERN VALUE +_wrap_new_OBMolPairIter__SWIG_3(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolPairIter *arg1 = 0 ; + OpenBabel::OBMolPairIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolPairIter" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + result = (OpenBabel::OBMolPairIter *)new OpenBabel::OBMolPairIter((OpenBabel::OBMolPairIter const &)*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE _wrap_new_OBMolPairIter(int nargs, VALUE *args, VALUE self) { + int argc; + VALUE argv[1]; + int ii; + + argc = nargs; + if (argc > 1) SWIG_fail; + for (ii = 0; (ii < argc); ii++) { + argv[ii] = args[ii]; + } + if (argc == 0) { + return _wrap_new_OBMolPairIter__SWIG_0(nargs, args, self); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolPairIter__SWIG_1(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolPairIter__SWIG_2(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolPairIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolPairIter__SWIG_3(nargs, args, self); + } + } + +fail: + rb_raise(rb_eArgError, "No matching function for overloaded 'new_OBMolPairIter'"); + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolPairIter___deref__(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "operator ->" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + result = (std::pair *)((OpenBabel::OBMolPairIter const *)arg1)->operator ->(); + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__pairTint_int_t, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolPairIter___ref__(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolPairIter *arg1 = (OpenBabel::OBMolPairIter *) 0 ; + std::pair *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolPairIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "operator *" "', argument " "1"" of type '" "OpenBabel::OBMolPairIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolPairIter * >(argp1); + { + std::pair &_result_ref = ((OpenBabel::OBMolPairIter const *)arg1)->operator *(); + result = (std::pair *) &_result_ref; + } + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__pairTint_int_t, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN void +free_OpenBabel_OBMolPairIter(OpenBabel::OBMolPairIter *arg1) { + delete arg1; +} + +swig_class cOBMolRingIter; + +SWIGINTERN VALUE +_wrap_new_OBMolRingIter__SWIG_0(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *result = 0 ; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter();DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolRingIter__SWIG_1(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = (OpenBabel::OBMol *) 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_new_OBMolRingIter__SWIG_2(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMol *arg1 = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMol, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMol &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMol * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter(*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +#ifdef HAVE_RB_DEFINE_ALLOC_FUNC +SWIGINTERN VALUE +_wrap_OBMolRingIter_allocate(VALUE self) { +#else + SWIGINTERN VALUE + _wrap_OBMolRingIter_allocate(int argc, VALUE *argv, VALUE self) { +#endif + + + VALUE vresult = SWIG_NewClassInstance(self, SWIGTYPE_p_OpenBabel__OBMolRingIter); +#ifndef HAVE_RB_DEFINE_ALLOC_FUNC + rb_obj_call_init(vresult, argc, argv); +#endif + return vresult; + } + + +SWIGINTERN VALUE +_wrap_new_OBMolRingIter__SWIG_3(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = 0 ; + OpenBabel::OBMolRingIter *result = 0 ; + void *argp1 ; + int res1 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(argv[0], &argp1, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OpenBabel::OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const &""'"); + } + if (!argp1) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OpenBabel::OBMolRingIter" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const &""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBMolRingIter *)new OpenBabel::OBMolRingIter((OpenBabel::OBMolRingIter const &)*arg1);DATA_PTR(self) = result; + + return self; +fail: + return Qnil; +} + + +SWIGINTERN VALUE _wrap_new_OBMolRingIter(int nargs, VALUE *args, VALUE self) { + int argc; + VALUE argv[1]; + int ii; + + argc = nargs; + if (argc > 1) SWIG_fail; + for (ii = 0; (ii < argc); ii++) { + argv[ii] = args[ii]; + } + if (argc == 0) { + return _wrap_new_OBMolRingIter__SWIG_0(nargs, args, self); + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolRingIter__SWIG_1(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMol, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolRingIter__SWIG_2(nargs, args, self); + } + } + if (argc == 1) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_new_OBMolRingIter__SWIG_3(nargs, args, self); + } + } + +fail: + rb_raise(rb_eArgError, "No matching function for overloaded 'new_OBMolRingIter'"); + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter___deref__(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "operator ->" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBRing *)((OpenBabel::OBMolRingIter const *)arg1)->operator ->(); + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter___ref__(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBRing *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "operator *" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + OpenBabel::OBRing &_result_ref = ((OpenBabel::OBMolRingIter const *)arg1)->operator *(); + result = (OpenBabel::OBRing *) &_result_ref; + } + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBRing, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN void +free_OpenBabel_OBMolRingIter(OpenBabel::OBMolRingIter *arg1) { + delete arg1; +} + +SWIGINTERN VALUE +_wrap_OBMolRingIter__path_set(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector *arg2 = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + std::vector temp2 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "_path" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + if (rb_obj_is_kind_of(argv[0],rb_cArray)) { + unsigned int size = RARRAY_LEN(argv[0]); + temp2 = std::vector(size); + arg2 = &temp2; + for (unsigned int i=0; i)"); + } + } else { + SWIG_ConvertPtr(argv[0], (void **) &arg2, SWIGTYPE_p_std__vectorTint_t, 1); + } + } + if (arg1) (*arg1)->_path = *arg2; + + return Qnil; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter__path_get(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + std::vector *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "_path" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + std::vector const &_result_ref = ((*arg1)->_path); + result = (std::vector *) &_result_ref; + } + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_std__vectorTint_t, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter__pathset_set(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *arg2 = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 ; + int res2 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "_pathset" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2, SWIGTYPE_p_OpenBabel__OBBitVec, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "_pathset" "', argument " "2"" of type '" "OpenBabel::OBBitVec const &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "_pathset" "', argument " "2"" of type '" "OpenBabel::OBBitVec const &""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); + if (arg1) (*arg1)->_pathset = *arg2; + + return Qnil; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter__pathset_get(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBitVec *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "_pathset" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + { + OpenBabel::OBBitVec const &_result_ref = ((*arg1)->_pathset); + result = (OpenBabel::OBBitVec *) &_result_ref; + } + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBBitVec, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_findCenterAndNormal(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::vector3 *arg2 = 0 ; + OpenBabel::vector3 *arg3 = 0 ; + OpenBabel::vector3 *arg4 = 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + void *argp3 = 0 ; + int res3 = 0 ; + void *argp4 = 0 ; + int res4 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 3) || (argc > 3)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 3)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "findCenterAndNormal" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "findCenterAndNormal" "', argument " "2"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp2) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "findCenterAndNormal" "', argument " "2"" of type '" "OpenBabel::vector3 &""'"); + } + arg2 = reinterpret_cast< OpenBabel::vector3 * >(argp2); + res3 = SWIG_ConvertPtr(argv[1], &argp3, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res3)) { + SWIG_exception_fail(SWIG_ArgError(res3), "in method '" "findCenterAndNormal" "', argument " "3"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp3) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "findCenterAndNormal" "', argument " "3"" of type '" "OpenBabel::vector3 &""'"); + } + arg3 = reinterpret_cast< OpenBabel::vector3 * >(argp3); + res4 = SWIG_ConvertPtr(argv[2], &argp4, SWIGTYPE_p_OpenBabel__vector3, 0 ); + if (!SWIG_IsOK(res4)) { + SWIG_exception_fail(SWIG_ArgError(res4), "in method '" "findCenterAndNormal" "', argument " "4"" of type '" "OpenBabel::vector3 &""'"); + } + if (!argp4) { + SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "findCenterAndNormal" "', argument " "4"" of type '" "OpenBabel::vector3 &""'"); + } + arg4 = reinterpret_cast< OpenBabel::vector3 * >(argp4); + result = (bool)(*arg1)->findCenterAndNormal(*arg2,*arg3,*arg4); + vresult = SWIG_From_bool(static_cast< bool >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_Size(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "Size" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (int)(*arg1)->Size(); + vresult = SWIG_From_int(static_cast< int >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_PathSize(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int result; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "PathSize" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter const *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (int)(*arg1)->PathSize(); + vresult = SWIG_From_int(static_cast< int >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_IsMember__SWIG_0(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBAtom *arg2 = (OpenBabel::OBAtom *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "IsMember" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2,SWIGTYPE_p_OpenBabel__OBAtom, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "IsMember" "', argument " "2"" of type '" "OpenBabel::OBAtom *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBAtom * >(argp2); + result = (bool)(*arg1)->IsMember(arg2); + vresult = SWIG_From_bool(static_cast< bool >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_IsMember__SWIG_1(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBBond *arg2 = (OpenBabel::OBBond *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "IsMember" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2,SWIGTYPE_p_OpenBabel__OBBond, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "IsMember" "', argument " "2"" of type '" "OpenBabel::OBBond *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBBond * >(argp2); + result = (bool)(*arg1)->IsMember(arg2); + vresult = SWIG_From_bool(static_cast< bool >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE _wrap_OBMolRingIter_IsMember(int nargs, VALUE *args, VALUE self) { + int argc; + VALUE argv[3]; + int ii; + + argc = nargs + 1; + argv[0] = self; + if (argc > 3) SWIG_fail; + for (ii = 1; (ii < argc); ii++) { + argv[ii] = args[ii-1]; + } + if (argc == 2) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_OpenBabel__OBAtom, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBMolRingIter_IsMember__SWIG_0(nargs, args, self); + } + } + } + if (argc == 2) { + int _v; + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBMolRingIter, 0); + _v = SWIG_CheckState(res); + if (_v) { + void *vptr = 0; + int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_OpenBabel__OBBond, 0); + _v = SWIG_CheckState(res); + if (_v) { + return _wrap_OBMolRingIter_IsMember__SWIG_1(nargs, args, self); + } + } + } + +fail: + rb_raise(rb_eArgError, "No matching function for overloaded 'OBMolRingIter_IsMember'"); + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_IsAromatic(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "IsAromatic" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (bool)(*arg1)->IsAromatic(); + vresult = SWIG_From_bool(static_cast< bool >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_IsInRing(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + int arg2 ; + bool result; + void *argp1 = 0 ; + int res1 = 0 ; + int val2 ; + int ecode2 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "IsInRing" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + ecode2 = SWIG_AsVal_int(argv[0], &val2); + if (!SWIG_IsOK(ecode2)) { + SWIG_exception_fail(SWIG_ArgError(ecode2), "in method '" "IsInRing" "', argument " "2"" of type '" "int""'"); + } + arg2 = static_cast< int >(val2); + result = (bool)(*arg1)->IsInRing(arg2); + vresult = SWIG_From_bool(static_cast< bool >(result)); + return vresult; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_SetParent(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *arg2 = (OpenBabel::OBMol *) 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + void *argp2 = 0 ; + int res2 = 0 ; + + if ((argc < 1) || (argc > 1)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "SetParent" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + res2 = SWIG_ConvertPtr(argv[0], &argp2,SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + if (!SWIG_IsOK(res2)) { + SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "SetParent" "', argument " "2"" of type '" "OpenBabel::OBMol *""'"); + } + arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); + (*arg1)->SetParent(arg2); + return Qnil; +fail: + return Qnil; +} + + +SWIGINTERN VALUE +_wrap_OBMolRingIter_GetParent(int argc, VALUE *argv, VALUE self) { + OpenBabel::OBMolRingIter *arg1 = (OpenBabel::OBMolRingIter *) 0 ; + OpenBabel::OBMol *result = 0 ; + void *argp1 = 0 ; + int res1 = 0 ; + VALUE vresult = Qnil; + + if ((argc < 0) || (argc > 0)) { + rb_raise(rb_eArgError, "wrong # of arguments(%d for 0)",argc); SWIG_fail; + } + res1 = SWIG_ConvertPtr(self, &argp1,SWIGTYPE_p_OpenBabel__OBMolRingIter, 0 | 0 ); + if (!SWIG_IsOK(res1)) { + SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "GetParent" "', argument " "1"" of type '" "OpenBabel::OBMolRingIter *""'"); + } + arg1 = reinterpret_cast< OpenBabel::OBMolRingIter * >(argp1); + result = (OpenBabel::OBMol *)(*arg1)->GetParent(); + vresult = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBMol, 0 | 0 ); + return vresult; +fail: + return Qnil; +} + + /* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */ @@ -73459,10 +74936,14 @@ static swig_type_info _swigt__p_OpenBabel__OBInternalCoord = {"_p_OpenBabel__OBI static swig_type_info _swigt__p_OpenBabel__OBIsotopeTable = {"_p_OpenBabel__OBIsotopeTable", "OpenBabel::OBIsotopeTable *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMessageHandler = {"_p_OpenBabel__OBMessageHandler", "OpenBabel::OBMessageHandler *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMol = {"_p_OpenBabel__OBMol", "OpenBabel::OBMol *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolAngleIter = {"_p_OpenBabel__OBMolAngleIter", "OpenBabel::OBMolAngleIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomBFSIter = {"_p_OpenBabel__OBMolAtomBFSIter", "OpenBabel::OBMolAtomBFSIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomDFSIter = {"_p_OpenBabel__OBMolAtomDFSIter", "OpenBabel::OBMolAtomDFSIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolAtomIter = {"_p_OpenBabel__OBMolAtomIter", "OpenBabel::OBMolAtomIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBMolBondIter = {"_p_OpenBabel__OBMolBondIter", "OpenBabel::OBMolBondIter *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolPairIter = {"_p_OpenBabel__OBMolPairIter", "OpenBabel::OBMolPairIter *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolRingIter = {"_p_OpenBabel__OBMolRingIter", "OpenBabel::OBMolRingIter *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_OpenBabel__OBMolTorsionIter = {"_p_OpenBabel__OBMolTorsionIter", "OpenBabel::OBMolTorsionIter *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBPairData = {"_p_OpenBabel__OBPairData", "OpenBabel::OBPairData *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBPairTemplateTdouble_t = {"_p_OpenBabel__OBPairTemplateTdouble_t", "OpenBabel::OBPairTemplate *|OpenBabel::OBPairFloatingPoint *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_OpenBabel__OBPairTemplateTint_t = {"_p_OpenBabel__OBPairTemplateTint_t", "OpenBabel::OBPairTemplate *|OpenBabel::OBPairInteger *", 0, 0, (void*)0, 0}; @@ -73527,6 +75008,7 @@ static swig_type_info _swigt__p_std__multimapTdouble_unsigned_int_t = {"_p_std__ static swig_type_info _swigt__p_std__ostream = {"_p_std__ostream", "std::ostream *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__out_of_range = {"_p_std__out_of_range", "std::out_of_range *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t = {"_p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t", "std::pair *", 0, 0, (void*)0, 0}; +static swig_type_info _swigt__p_std__pairTint_int_t = {"_p_std__pairTint_int_t", "std::pair *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__streampos = {"_p_std__streampos", "std::streampos *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__string = {"_p_std__string", "std::string *", 0, 0, (void*)0, 0}; static swig_type_info _swigt__p_std__type_info = {"_p_std__type_info", "std::type_info *", 0, 0, (void*)0, 0}; @@ -73600,10 +75082,14 @@ static swig_type_info *swig_type_initial[] = { &_swigt__p_OpenBabel__OBIsotopeTable, &_swigt__p_OpenBabel__OBMessageHandler, &_swigt__p_OpenBabel__OBMol, + &_swigt__p_OpenBabel__OBMolAngleIter, &_swigt__p_OpenBabel__OBMolAtomBFSIter, &_swigt__p_OpenBabel__OBMolAtomDFSIter, &_swigt__p_OpenBabel__OBMolAtomIter, &_swigt__p_OpenBabel__OBMolBondIter, + &_swigt__p_OpenBabel__OBMolPairIter, + &_swigt__p_OpenBabel__OBMolRingIter, + &_swigt__p_OpenBabel__OBMolTorsionIter, &_swigt__p_OpenBabel__OBPairData, &_swigt__p_OpenBabel__OBPairTemplateTdouble_t, &_swigt__p_OpenBabel__OBPairTemplateTint_t, @@ -73668,6 +75154,7 @@ static swig_type_info *swig_type_initial[] = { &_swigt__p_std__ostream, &_swigt__p_std__out_of_range, &_swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, + &_swigt__p_std__pairTint_int_t, &_swigt__p_std__streampos, &_swigt__p_std__string, &_swigt__p_std__type_info, @@ -73741,10 +75228,14 @@ static swig_cast_info _swigc__p_OpenBabel__OBInternalCoord[] = { {&_swigt__p_Op static swig_cast_info _swigc__p_OpenBabel__OBIsotopeTable[] = { {&_swigt__p_OpenBabel__OBIsotopeTable, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMessageHandler[] = { {&_swigt__p_OpenBabel__OBMessageHandler, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMol[] = { {&_swigt__p_OpenBabel__OBMol, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolAngleIter[] = { {&_swigt__p_OpenBabel__OBMolAngleIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomBFSIter[] = { {&_swigt__p_OpenBabel__OBMolAtomBFSIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomDFSIter[] = { {&_swigt__p_OpenBabel__OBMolAtomDFSIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolAtomIter[] = { {&_swigt__p_OpenBabel__OBMolAtomIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBMolBondIter[] = { {&_swigt__p_OpenBabel__OBMolBondIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolPairIter[] = { {&_swigt__p_OpenBabel__OBMolPairIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolRingIter[] = { {&_swigt__p_OpenBabel__OBMolRingIter, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_OpenBabel__OBMolTorsionIter[] = { {&_swigt__p_OpenBabel__OBMolTorsionIter, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairData[] = { {&_swigt__p_OpenBabel__OBPairData, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairTemplateTdouble_t[] = { {&_swigt__p_OpenBabel__OBPairTemplateTdouble_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_OpenBabel__OBPairTemplateTint_t[] = { {&_swigt__p_OpenBabel__OBPairTemplateTint_t, 0, 0, 0},{0, 0, 0, 0}}; @@ -73809,6 +75300,7 @@ static swig_cast_info _swigc__p_std__multimapTdouble_unsigned_int_t[] = { {&_sw static swig_cast_info _swigc__p_std__ostream[] = { {&_swigt__p_std__ostream, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__out_of_range[] = { {&_swigt__p_std__out_of_range, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t[] = { {&_swigt__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, 0, 0, 0},{0, 0, 0, 0}}; +static swig_cast_info _swigc__p_std__pairTint_int_t[] = { {&_swigt__p_std__pairTint_int_t, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__streampos[] = { {&_swigt__p_std__streampos, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__string[] = { {&_swigt__p_std__string, 0, 0, 0},{0, 0, 0, 0}}; static swig_cast_info _swigc__p_std__type_info[] = { {&_swigt__p_std__type_info, 0, 0, 0},{0, 0, 0, 0}}; @@ -73882,10 +75374,14 @@ static swig_cast_info *swig_cast_initial[] = { _swigc__p_OpenBabel__OBIsotopeTable, _swigc__p_OpenBabel__OBMessageHandler, _swigc__p_OpenBabel__OBMol, + _swigc__p_OpenBabel__OBMolAngleIter, _swigc__p_OpenBabel__OBMolAtomBFSIter, _swigc__p_OpenBabel__OBMolAtomDFSIter, _swigc__p_OpenBabel__OBMolAtomIter, _swigc__p_OpenBabel__OBMolBondIter, + _swigc__p_OpenBabel__OBMolPairIter, + _swigc__p_OpenBabel__OBMolRingIter, + _swigc__p_OpenBabel__OBMolTorsionIter, _swigc__p_OpenBabel__OBPairData, _swigc__p_OpenBabel__OBPairTemplateTdouble_t, _swigc__p_OpenBabel__OBPairTemplateTint_t, @@ -73950,6 +75446,7 @@ static swig_cast_info *swig_cast_initial[] = { _swigc__p_std__ostream, _swigc__p_std__out_of_range, _swigc__p_std__pairTOpenBabel__OBAtom_p_OpenBabel__OBAtom_p_t, + _swigc__p_std__pairTint_int_t, _swigc__p_std__streampos, _swigc__p_std__string, _swigc__p_std__type_info, @@ -74718,6 +76215,10 @@ SWIGEXPORT void Init_openbabel(void) { rb_define_method(cOBRingData.klass, "SetData", VALUEFUNC(_wrap_OBRingData_SetData), -1); rb_define_method(cOBRingData.klass, "PushBack", VALUEFUNC(_wrap_OBRingData_PushBack), -1); rb_define_method(cOBRingData.klass, "GetData", VALUEFUNC(_wrap_OBRingData_GetData), -1); + rb_define_method(cOBRingData.klass, "BeginRings", VALUEFUNC(_wrap_OBRingData_BeginRings), -1); + rb_define_method(cOBRingData.klass, "EndRings", VALUEFUNC(_wrap_OBRingData_EndRings), -1); + rb_define_method(cOBRingData.klass, "BeginRing", VALUEFUNC(_wrap_OBRingData_BeginRing), -1); + rb_define_method(cOBRingData.klass, "NextRing", VALUEFUNC(_wrap_OBRingData_NextRing), -1); cOBRingData.mark = 0; cOBRingData.destroy = (void (*)(void *)) free_OpenBabel_OBRingData; cOBRingData.trackObjects = 0; @@ -75584,6 +77085,7 @@ SWIGEXPORT void Init_openbabel(void) { rb_define_method(cOBMol.klass, "Align", VALUEFUNC(_wrap_OBMol_Align), -1); rb_define_method(cOBMol.klass, "ConnectTheDots", VALUEFUNC(_wrap_OBMol_ConnectTheDots), -1); rb_define_method(cOBMol.klass, "PerceiveBondOrders", VALUEFUNC(_wrap_OBMol_PerceiveBondOrders), -1); + rb_define_method(cOBMol.klass, "FindAngles", VALUEFUNC(_wrap_OBMol_FindAngles), -1); rb_define_method(cOBMol.klass, "FindTorsions", VALUEFUNC(_wrap_OBMol_FindTorsions), -1); rb_define_method(cOBMol.klass, "GetGTDVector", VALUEFUNC(_wrap_OBMol_GetGTDVector), -1); rb_define_method(cOBMol.klass, "GetGIVector", VALUEFUNC(_wrap_OBMol_GetGIVector), -1); @@ -76763,5 +78265,55 @@ SWIGEXPORT void Init_openbabel(void) { cOBResidueAtomIter.mark = 0; cOBResidueAtomIter.destroy = (void (*)(void *)) free_OpenBabel_OBResidueAtomIter; cOBResidueAtomIter.trackObjects = 0; + + cOBMolAngleIter.klass = rb_define_class_under(mOpenbabel, "OBMolAngleIter", rb_cObject); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolAngleIter, (void *) &cOBMolAngleIter); + rb_define_alloc_func(cOBMolAngleIter.klass, _wrap_OBMolAngleIter_allocate); + rb_define_method(cOBMolAngleIter.klass, "initialize", VALUEFUNC(_wrap_new_OBMolAngleIter), -1); + rb_define_method(cOBMolAngleIter.klass, "__ref__", VALUEFUNC(_wrap_OBMolAngleIter___ref__), -1); + cOBMolAngleIter.mark = 0; + cOBMolAngleIter.destroy = (void (*)(void *)) free_OpenBabel_OBMolAngleIter; + cOBMolAngleIter.trackObjects = 0; + + cOBMolTorsionIter.klass = rb_define_class_under(mOpenbabel, "OBMolTorsionIter", rb_cObject); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolTorsionIter, (void *) &cOBMolTorsionIter); + rb_define_alloc_func(cOBMolTorsionIter.klass, _wrap_OBMolTorsionIter_allocate); + rb_define_method(cOBMolTorsionIter.klass, "initialize", VALUEFUNC(_wrap_new_OBMolTorsionIter), -1); + rb_define_method(cOBMolTorsionIter.klass, "__ref__", VALUEFUNC(_wrap_OBMolTorsionIter___ref__), -1); + cOBMolTorsionIter.mark = 0; + cOBMolTorsionIter.destroy = (void (*)(void *)) free_OpenBabel_OBMolTorsionIter; + cOBMolTorsionIter.trackObjects = 0; + + cOBMolPairIter.klass = rb_define_class_under(mOpenbabel, "OBMolPairIter", rb_cObject); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolPairIter, (void *) &cOBMolPairIter); + rb_define_alloc_func(cOBMolPairIter.klass, _wrap_OBMolPairIter_allocate); + rb_define_method(cOBMolPairIter.klass, "initialize", VALUEFUNC(_wrap_new_OBMolPairIter), -1); + rb_define_method(cOBMolPairIter.klass, "__deref__", VALUEFUNC(_wrap_OBMolPairIter___deref__), -1); + rb_define_method(cOBMolPairIter.klass, "__ref__", VALUEFUNC(_wrap_OBMolPairIter___ref__), -1); + cOBMolPairIter.mark = 0; + cOBMolPairIter.destroy = (void (*)(void *)) free_OpenBabel_OBMolPairIter; + cOBMolPairIter.trackObjects = 0; + + cOBMolRingIter.klass = rb_define_class_under(mOpenbabel, "OBMolRingIter", rb_cObject); + SWIG_TypeClientData(SWIGTYPE_p_OpenBabel__OBMolRingIter, (void *) &cOBMolRingIter); + rb_define_alloc_func(cOBMolRingIter.klass, _wrap_OBMolRingIter_allocate); + rb_define_method(cOBMolRingIter.klass, "initialize", VALUEFUNC(_wrap_new_OBMolRingIter), -1); + rb_define_method(cOBMolRingIter.klass, "__deref__", VALUEFUNC(_wrap_OBMolRingIter___deref__), -1); + rb_define_method(cOBMolRingIter.klass, "__ref__", VALUEFUNC(_wrap_OBMolRingIter___ref__), -1); + rb_define_method(cOBMolRingIter.klass, "_path=", VALUEFUNC(_wrap_OBMolRingIter__path_set), -1); + rb_define_method(cOBMolRingIter.klass, "_path", VALUEFUNC(_wrap_OBMolRingIter__path_get), -1); + rb_define_method(cOBMolRingIter.klass, "_pathset=", VALUEFUNC(_wrap_OBMolRingIter__pathset_set), -1); + rb_define_method(cOBMolRingIter.klass, "_pathset", VALUEFUNC(_wrap_OBMolRingIter__pathset_get), -1); + rb_define_method(cOBMolRingIter.klass, "findCenterAndNormal", VALUEFUNC(_wrap_OBMolRingIter_findCenterAndNormal), -1); + rb_define_method(cOBMolRingIter.klass, "Size", VALUEFUNC(_wrap_OBMolRingIter_Size), -1); + rb_define_method(cOBMolRingIter.klass, "PathSize", VALUEFUNC(_wrap_OBMolRingIter_PathSize), -1); + rb_define_method(cOBMolRingIter.klass, "IsMember", VALUEFUNC(_wrap_OBMolRingIter_IsMember), -1); + rb_define_method(cOBMolRingIter.klass, "IsAromatic", VALUEFUNC(_wrap_OBMolRingIter_IsAromatic), -1); + rb_define_method(cOBMolRingIter.klass, "IsInRing", VALUEFUNC(_wrap_OBMolRingIter_IsInRing), -1); + rb_define_method(cOBMolRingIter.klass, "SetParent", VALUEFUNC(_wrap_OBMolRingIter_SetParent), -1); + rb_define_method(cOBMolRingIter.klass, "GetParent", VALUEFUNC(_wrap_OBMolRingIter_GetParent), -1); + cOBMolRingIter.mark = 0; + cOBMolRingIter.destroy = (void (*)(void *)) free_OpenBabel_OBMolRingIter; + cOBMolRingIter.trackObjects = 0; } diff --git a/src/GUI/Makefile.am b/src/GUI/Makefile.am index 977006841..5d40da99e 100644 --- a/src/GUI/Makefile.am +++ b/src/GUI/Makefile.am @@ -1,6 +1,7 @@ EXTRA_DIST = OBGUI.h optswx.h selformats.h stdwx.h -INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data +INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data \ + -I$(top_srcdir)/include AM_CPPFLAGS = @WX_CPPFLAGS@ AM_CXXFLAGS = @WX_CXXFLAGS@ diff --git a/src/GUI/OBGUI.cpp b/src/GUI/OBGUI.cpp index 71b2a7844..e8bd242dc 100644 --- a/src/GUI/OBGUI.cpp +++ b/src/GUI/OBGUI.cpp @@ -15,13 +15,13 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "stdwx.h" +#include +#include #include -#include "obconversion.h" -#include "dlhandler.h" -#include "selformats.h" -#include "OBGUI.h" +#include +#include +#include +#include /* #ifdef _DEBUG diff --git a/src/GUI/optswx.cpp b/src/GUI/optswx.cpp index f93c92f3a..13c457336 100644 --- a/src/GUI/optswx.cpp +++ b/src/GUI/optswx.cpp @@ -15,11 +15,11 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "stdwx.h" +#include +#include #include #include -#include "optswx.h" +#include #ifdef _DEBUG diff --git a/src/GUI/optswx.h b/src/GUI/optswx.h index 28930a734..205490fce 100644 --- a/src/GUI/optswx.h +++ b/src/GUI/optswx.h @@ -19,7 +19,7 @@ GNU General Public License for more details. #define OB_OPTSWX_H #include -#include "obconversion.h" +#include class DynOptionswx { diff --git a/src/GUI/stdwx.cpp b/src/GUI/stdwx.cpp index 0b2f2c5c5..bf00c56c8 100644 --- a/src/GUI/stdwx.cpp +++ b/src/GUI/stdwx.cpp @@ -1,2 +1,2 @@ -#include "stdwx.h" -#include "babelconfig.h" \ No newline at end of file +#include +#include diff --git a/src/Makefile.am b/src/Makefile.am index 853d5ab1e..feaed5f77 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -1,26 +1,13 @@ EXTRA_DIST = \ strncasecmp.c snprintf.c snprintf.h zipstream.h zipstreamimpl.h \ - dlhandler_win32.cpp all.h + dlhandler_win32.cpp SUBDIRS = math formats fingerprints if BUILD_WXGUI SUBDIRS += GUI endif -if BUILD_PCH -BUILT_SOURCES = all.h.gch -PCHFLAGS=-Winvalid-pch -x c++-header $(CXXFLAGS) $(INCLUDES) -all.h.gch: all.h Makefile babelconfig.h mol.h base.h bitvec.h generic.h \ - oberror.h obiter.h obconversion.h atom.h bond.h - rm -f $@ - $(CXX) $(PCHFLAGS) $< -AM_CXXFLAGS= -include $(top_srcdir)/src/all.h - -clean-local: - -rm -f all.h.gch -endif - -INCLUDES = -I$(top_srcdir)/data/ +INCLUDES = -I$(top_srcdir)/data/ -I$(top_srcdir)/include bin_PROGRAMS = babel babel_SOURCES = main.cpp @@ -57,30 +44,3 @@ else !BUILD_SHARED libopenbabel_la_LIBADD = math/libmath.la fingerprints/libfingerprints.la \ formats/libformats.la @LTLIBOBJS@ endif - -libopenbabelincludedir = $(includedir)/openbabel-2.0/openbabel -libopenbabelinclude_HEADERS = \ - atom.h \ - babelconfig.h base.h bond.h bitvec.h \ - bondtyper.h chains.h chiral.h data.h \ - dlhandler.h fingerprint.h forcefield.h \ - generic.h grid.h internalcoord.h kinetics.h \ - newlinebuf.h \ - matrix.h mol.h molchrg.h \ - obconversion.h oberror.h obiter.h \ - obutil.h \ - parsmart.h patty.h phmodel.h rand.h reaction.h \ - residue.h ring.h rotor.h rotamer.h typer.h - -# Use sed to substitute #include "header.h" to #include -install-data-hook: - for header in $(DESTDIR)$(libopenbabelincludedir)/*.h \ - $(DESTDIR)$(libopenbabelincludedir)/math/*.h; do \ - sed -e 's!^#include "\([^"]*\)"!#include !' \ - < $${header} >$${header}.new; \ - mv $${header}.new $${header}; \ - done - -# Remove the configure-generated babelconfig.h -dist-hook: - rm $(distdir)/babelconfig.h diff --git a/src/Makefile.in b/src/Makefile.in index 89016cdec..a728be740 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -15,7 +15,6 @@ @SET_MAKE@ - srcdir = @srcdir@ top_srcdir = @top_srcdir@ VPATH = @srcdir@ @@ -41,9 +40,8 @@ host_triplet = @host@ @BUILD_WXGUI_TRUE@am__append_1 = GUI bin_PROGRAMS = babel$(EXEEXT) subdir = src -DIST_COMMON = $(libopenbabelinclude_HEADERS) $(srcdir)/Makefile.am \ - $(srcdir)/Makefile.in $(srcdir)/config.h.in snprintf.c \ - strncasecmp.c +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \ + $(srcdir)/config.h.in snprintf.c strncasecmp.c ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \ $(top_srcdir)/configure.in @@ -58,8 +56,7 @@ am__vpath_adj = case $$p in \ *) f=$$p;; \ esac; am__strip_dir = `echo $$p | sed -e 's|^.*/||'`; -am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)" \ - "$(DESTDIR)$(libopenbabelincludedir)" +am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)" libLTLIBRARIES_INSTALL = $(INSTALL) LTLIBRARIES = $(lib_LTLIBRARIES) @BUILD_SHARED_FALSE@libopenbabel_la_DEPENDENCIES = math/libmath.la \ @@ -116,8 +113,6 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ install-recursive installcheck-recursive installdirs-recursive \ pdf-recursive ps-recursive uninstall-info-recursive \ uninstall-recursive -libopenbabelincludeHEADERS_INSTALL = $(INSTALL_HEADER) -HEADERS = $(libopenbabelinclude_HEADERS) ETAGS = etags CTAGS = ctags DIST_SUBDIRS = math formats fingerprints GUI @@ -266,13 +261,10 @@ sysconfdir = @sysconfdir@ target_alias = @target_alias@ EXTRA_DIST = \ strncasecmp.c snprintf.c snprintf.h zipstream.h zipstreamimpl.h \ - dlhandler_win32.cpp all.h + dlhandler_win32.cpp SUBDIRS = math formats fingerprints $(am__append_1) -@BUILD_PCH_TRUE@BUILT_SOURCES = all.h.gch -@BUILD_PCH_TRUE@PCHFLAGS = -Winvalid-pch -x c++-header $(CXXFLAGS) $(INCLUDES) -@BUILD_PCH_TRUE@AM_CXXFLAGS = -include $(top_srcdir)/src/all.h -INCLUDES = -I$(top_srcdir)/data/ +INCLUDES = -I$(top_srcdir)/data/ -I$(top_srcdir)/include babel_SOURCES = main.cpp babel_LDADD = libopenbabel.la @LIBDL@ @LIBOBJS@ lib_LTLIBRARIES = libopenbabel.la @@ -298,21 +290,7 @@ libopenbabel_la_LDFLAGS = -version-info 3:0:1 -no-undefined @BUILD_SHARED_TRUE@libopenbabel_la_LIBADD = math/libmath.la fingerprints/libfingerprints.la \ @BUILD_SHARED_TRUE@ @LTLIBOBJS@ @LIBDL@ -libopenbabelincludedir = $(includedir)/openbabel-2.0/openbabel -libopenbabelinclude_HEADERS = \ - atom.h \ - babelconfig.h base.h bond.h bitvec.h \ - bondtyper.h chains.h chiral.h data.h \ - dlhandler.h fingerprint.h forcefield.h \ - generic.h grid.h internalcoord.h kinetics.h \ - newlinebuf.h \ - matrix.h mol.h molchrg.h \ - obconversion.h oberror.h obiter.h \ - obutil.h \ - parsmart.h patty.h phmodel.h rand.h reaction.h \ - residue.h ring.h rotor.h rotamer.h typer.h - -all: $(BUILT_SOURCES) config.h +all: config.h $(MAKE) $(AM_MAKEFLAGS) all-recursive .SUFFIXES: @@ -520,23 +498,6 @@ clean-libtool: distclean-libtool: -rm -f libtool uninstall-info-am: -install-libopenbabelincludeHEADERS: $(libopenbabelinclude_HEADERS) - @$(NORMAL_INSTALL) - test -z "$(libopenbabelincludedir)" || $(mkdir_p) "$(DESTDIR)$(libopenbabelincludedir)" - @list='$(libopenbabelinclude_HEADERS)'; for p in $$list; do \ - if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ - f=$(am__strip_dir) \ - echo " $(libopenbabelincludeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(libopenbabelincludedir)/$$f'"; \ - $(libopenbabelincludeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(libopenbabelincludedir)/$$f"; \ - done - -uninstall-libopenbabelincludeHEADERS: - @$(NORMAL_UNINSTALL) - @list='$(libopenbabelinclude_HEADERS)'; for p in $$list; do \ - f=$(am__strip_dir) \ - echo " rm -f '$(DESTDIR)$(libopenbabelincludedir)/$$f'"; \ - rm -f "$(DESTDIR)$(libopenbabelincludedir)/$$f"; \ - done # This directory's subdirectories are mostly independent; you can cd # into them and run `make' without going through this Makefile. @@ -712,22 +673,17 @@ distdir: $(DISTFILES) || exit 1; \ fi; \ done - $(MAKE) $(AM_MAKEFLAGS) \ - top_distdir="$(top_distdir)" distdir="$(distdir)" \ - dist-hook check-am: all-am -check: $(BUILT_SOURCES) - $(MAKE) $(AM_MAKEFLAGS) check-recursive -all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) $(HEADERS) config.h +check: check-recursive +all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) config.h install-binPROGRAMS: install-libLTLIBRARIES installdirs: installdirs-recursive installdirs-am: - for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(libopenbabelincludedir)"; do \ + for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"; do \ test -z "$$dir" || $(mkdir_p) "$$dir"; \ done -install: $(BUILT_SOURCES) - $(MAKE) $(AM_MAKEFLAGS) install-recursive +install: install-recursive install-exec: install-exec-recursive install-data: install-data-recursive uninstall: uninstall-recursive @@ -751,12 +707,10 @@ distclean-generic: maintainer-clean-generic: @echo "This command is intended for maintainers to use" @echo "it deletes files that may require special tools to rebuild." - -test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES) -@BUILD_PCH_FALSE@clean-local: clean: clean-recursive clean-am: clean-binPROGRAMS clean-generic clean-libLTLIBRARIES \ - clean-libtool clean-local mostlyclean-am + clean-libtool mostlyclean-am distclean: distclean-recursive -rm -rf $(DEPDIR) ./$(DEPDIR) @@ -774,9 +728,7 @@ info: info-recursive info-am: -install-data-am: install-libopenbabelincludeHEADERS - @$(NORMAL_INSTALL) - $(MAKE) $(AM_MAKEFLAGS) install-data-hook +install-data-am: install-exec-am: install-binPROGRAMS install-libLTLIBRARIES @@ -805,49 +757,27 @@ ps: ps-recursive ps-am: uninstall-am: uninstall-binPROGRAMS uninstall-info-am \ - uninstall-libLTLIBRARIES uninstall-libopenbabelincludeHEADERS + uninstall-libLTLIBRARIES uninstall-info: uninstall-info-recursive .PHONY: $(RECURSIVE_TARGETS) CTAGS GTAGS all all-am check check-am \ clean clean-binPROGRAMS clean-generic clean-libLTLIBRARIES \ - clean-libtool clean-local clean-recursive ctags \ - ctags-recursive dist-hook distclean distclean-compile \ - distclean-generic distclean-hdr distclean-libtool \ - distclean-recursive distclean-tags distdir dvi dvi-am html \ - html-am info info-am install install-am install-binPROGRAMS \ - install-data install-data-am install-data-hook install-exec \ + clean-libtool clean-recursive ctags ctags-recursive distclean \ + distclean-compile distclean-generic distclean-hdr \ + distclean-libtool distclean-recursive distclean-tags distdir \ + dvi dvi-am html html-am info info-am install install-am \ + install-binPROGRAMS install-data install-data-am install-exec \ install-exec-am install-info install-info-am \ - install-libLTLIBRARIES install-libopenbabelincludeHEADERS \ - install-man install-strip installcheck installcheck-am \ - installdirs installdirs-am maintainer-clean \ + install-libLTLIBRARIES install-man install-strip installcheck \ + installcheck-am installdirs installdirs-am maintainer-clean \ maintainer-clean-generic maintainer-clean-recursive \ mostlyclean mostlyclean-compile mostlyclean-generic \ mostlyclean-libtool mostlyclean-recursive pdf pdf-am ps ps-am \ tags tags-recursive uninstall uninstall-am \ uninstall-binPROGRAMS uninstall-info-am \ - uninstall-libLTLIBRARIES uninstall-libopenbabelincludeHEADERS + uninstall-libLTLIBRARIES -@BUILD_PCH_TRUE@all.h.gch: all.h Makefile babelconfig.h mol.h base.h bitvec.h generic.h \ -@BUILD_PCH_TRUE@ oberror.h obiter.h obconversion.h atom.h bond.h -@BUILD_PCH_TRUE@ rm -f $@ -@BUILD_PCH_TRUE@ $(CXX) $(PCHFLAGS) $< - -@BUILD_PCH_TRUE@clean-local: -@BUILD_PCH_TRUE@ -rm -f all.h.gch - -# Use sed to substitute #include "header.h" to #include -install-data-hook: - for header in $(DESTDIR)$(libopenbabelincludedir)/*.h \ - $(DESTDIR)$(libopenbabelincludedir)/math/*.h; do \ - sed -e 's!^#include "\([^"]*\)"!#include !' \ - < $${header} >$${header}.new; \ - mv $${header}.new $${header}; \ - done - -# Remove the configure-generated babelconfig.h -dist-hook: - rm $(distdir)/babelconfig.h # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: diff --git a/src/atom.cpp b/src/atom.cpp index c58fd2db0..910f6daf1 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -17,14 +17,14 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "atom.h" -#include "mol.h" -#include "molchrg.h" -#include "phmodel.h" +#include +#include +#include +#include -#include "math/matrix3x3.h" +#include #if !HAVE_STRNCASECMP extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); diff --git a/src/base.cpp b/src/base.cpp index 2556918b6..62f2c4abb 100644 --- a/src/base.cpp +++ b/src/base.cpp @@ -17,8 +17,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "base.h" +#include +#include using namespace std; diff --git a/src/bitvec.cpp b/src/bitvec.cpp index 3dbc65cbb..8e557bd21 100644 --- a/src/bitvec.cpp +++ b/src/bitvec.cpp @@ -16,10 +16,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "bitvec.h" -#include "oberror.h" +#include +#include using namespace std; diff --git a/src/bond.cpp b/src/bond.cpp index f3530f2ad..31eeae5db 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -16,10 +16,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "bond.h" -#include "mol.h" +#include +#include using namespace std; diff --git a/src/bondtyper.cpp b/src/bondtyper.cpp index cdb3ff6d5..004acbf1d 100644 --- a/src/bondtyper.cpp +++ b/src/bondtyper.cpp @@ -15,10 +15,11 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include + +#include +#include -#include "mol.h" -#include "bondtyper.h" #include "bondtyp.h" using namespace std; diff --git a/src/chains.cpp b/src/chains.cpp index 4311a67ab..7e35fb466 100644 --- a/src/chains.cpp +++ b/src/chains.cpp @@ -22,7 +22,7 @@ GNU General Public License for more details. ////////////////////////////////////////////////////////////////////////////// // File Includes ////////////////////////////////////////////////////////////////////////////// -#include "babelconfig.h" +#include #include #include @@ -30,8 +30,8 @@ GNU General Public License for more details. #include #include -#include "mol.h" -#include "chains.h" +#include +#include using namespace std; diff --git a/src/chiral.cpp b/src/chiral.cpp index 879d0e496..01ad650cf 100644 --- a/src/chiral.cpp +++ b/src/chiral.cpp @@ -17,12 +17,12 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "chiral.h" -#include "math/matrix3x3.h" +#include +#include +#include using namespace std; namespace OpenBabel diff --git a/src/data.cpp b/src/data.cpp index 9331874a4..1ecde889e 100644 --- a/src/data.cpp +++ b/src/data.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #pragma warning (disable : 4786) #endif -#include "babelconfig.h" -#include "data.h" -#include "mol.h" +#include +#include +#include // data headers #include "element.h" diff --git a/src/dlhandler_unix.cpp b/src/dlhandler_unix.cpp index 0f316b2e8..bf70e726e 100644 --- a/src/dlhandler_unix.cpp +++ b/src/dlhandler_unix.cpp @@ -17,8 +17,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "dlhandler.h" -#include "babelconfig.h" +#include +#include #include #include diff --git a/src/dlhandler_win32.cpp b/src/dlhandler_win32.cpp index d02fc14cf..2b488ef2c 100644 --- a/src/dlhandler_win32.cpp +++ b/src/dlhandler_win32.cpp @@ -15,7 +15,7 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include #include @@ -24,7 +24,7 @@ GNU General Public License for more details. //#include //#include #include -#include "dlhandler.h" +#include using namespace std; diff --git a/src/fingerprint.cpp b/src/fingerprint.cpp index 50ac99020..23104d467 100644 --- a/src/fingerprint.cpp +++ b/src/fingerprint.cpp @@ -16,15 +16,15 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include #include #include #include -#include "fingerprint.h" -#include "oberror.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/fingerprints/Makefile.am b/src/fingerprints/Makefile.am index 6bd738823..fae202d49 100644 --- a/src/fingerprints/Makefile.am +++ b/src/fingerprints/Makefile.am @@ -1,4 +1,4 @@ noinst_LTLIBRARIES = libfingerprints.la libfingerprints_la_SOURCES = finger2.cpp finger3.cpp -AM_CPPFLAGS = -I$(top_srcdir)/src +AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/include diff --git a/src/fingerprints/Makefile.in b/src/fingerprints/Makefile.in index 6f75e1efc..faad55312 100644 --- a/src/fingerprints/Makefile.in +++ b/src/fingerprints/Makefile.in @@ -210,7 +210,7 @@ sysconfdir = @sysconfdir@ target_alias = @target_alias@ noinst_LTLIBRARIES = libfingerprints.la libfingerprints_la_SOURCES = finger2.cpp finger3.cpp -AM_CPPFLAGS = -I$(top_srcdir)/src +AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/include all: all-am .SUFFIXES: diff --git a/src/fingerprints/finger2.cpp b/src/fingerprints/finger2.cpp index 68b99df13..7e02cfc86 100644 --- a/src/fingerprints/finger2.cpp +++ b/src/fingerprints/finger2.cpp @@ -16,9 +16,9 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "mol.h" -#include "fingerprint.h" +#include +#include +#include #include #include diff --git a/src/fingerprints/finger3.cpp b/src/fingerprints/finger3.cpp index ce110ae49..c8cb1d1d0 100644 --- a/src/fingerprints/finger3.cpp +++ b/src/fingerprints/finger3.cpp @@ -15,14 +15,14 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "mol.h" +#include +#include #include #include #include -#include "fingerprint.h" +#include using namespace std; namespace OpenBabel diff --git a/src/forcefield.cpp b/src/forcefield.cpp index b8b88cf78..abbf798d9 100644 --- a/src/forcefield.cpp +++ b/src/forcefield.cpp @@ -15,14 +15,14 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "forcefield.h" +#include -#include "mol.h" -#include "atom.h" -#include "bond.h" -#include "obiter.h" +#include +#include +#include +#include using namespace std; diff --git a/src/formats/APIInterface.cpp b/src/formats/APIInterface.cpp index 2be3edb78..4fc131c71 100644 --- a/src/formats/APIInterface.cpp +++ b/src/formats/APIInterface.cpp @@ -15,8 +15,8 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obconversion.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/CSRformat.cpp b/src/formats/CSRformat.cpp index e96472587..4ea1cffef 100644 --- a/src/formats/CSRformat.cpp +++ b/src/formats/CSRformat.cpp @@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/Makefile.am b/src/formats/Makefile.am index 4c61a29f9..1ee8fc66a 100644 --- a/src/formats/Makefile.am +++ b/src/formats/Makefile.am @@ -1,7 +1,7 @@ -INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data +INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data -I$(top_srcdir)/include # Make sure to install the inchi_api.h header libopenbabelincludedir = $(includedir)/openbabel-2.0/openbabel -libopenbabelinclude_HEADERS = inchi_api.h obmolecformat.h chemdrawcdx.h +# libopenbabelinclude_HEADERS = inchi_api.h obmolecformat.h chemdrawcdx.h EXTRA_DIST = exampleformat.cpp SUBDIRS = diff --git a/src/formats/Makefile.in b/src/formats/Makefile.in index e58d299a5..8065b4db6 100644 --- a/src/formats/Makefile.in +++ b/src/formats/Makefile.in @@ -14,7 +14,6 @@ @SET_MAKE@ - srcdir = @srcdir@ top_srcdir = @top_srcdir@ VPATH = @srcdir@ @@ -40,8 +39,7 @@ host_triplet = @host@ @BUILD_XML_TRUE@am__append_1 = xml @BUILD_INCHI_TRUE@am__append_2 = inchi subdir = src/formats -DIST_COMMON = $(libopenbabelinclude_HEADERS) $(srcdir)/Makefile.am \ - $(srcdir)/Makefile.in +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \ $(top_srcdir)/configure.in @@ -56,8 +54,7 @@ am__vpath_adj = case $$p in \ *) f=$$p;; \ esac; am__strip_dir = `echo $$p | sed -e 's|^.*/||'`; -am__installdirs = "$(DESTDIR)$(pkglibdir)" \ - "$(DESTDIR)$(libopenbabelincludedir)" +am__installdirs = "$(DESTDIR)$(pkglibdir)" pkglibLTLIBRARIES_INSTALL = $(INSTALL) LTLIBRARIES = $(noinst_LTLIBRARIES) $(pkglib_LTLIBRARIES) APIInterface_la_LIBADD = @@ -155,6 +152,12 @@ am__chemtoolformat_la_SOURCES_DIST = chemtoolformat.cpp @BUILD_SHARED_TRUE@am_chemtoolformat_la_OBJECTS = chemtoolformat.lo chemtoolformat_la_OBJECTS = $(am_chemtoolformat_la_OBJECTS) @BUILD_SHARED_TRUE@am_chemtoolformat_la_rpath = -rpath $(pkglibdir) +cifformat_la_LIBADD = +am__cifformat_la_SOURCES_DIST = cifformat.cpp obmolecformat.cpp +@BUILD_SHARED_TRUE@am_cifformat_la_OBJECTS = cifformat.lo \ +@BUILD_SHARED_TRUE@ obmolecformat.lo +cifformat_la_OBJECTS = $(am_cifformat_la_OBJECTS) +@BUILD_SHARED_TRUE@am_cifformat_la_rpath = -rpath $(pkglibdir) copyformat_la_LIBADD = am__copyformat_la_SOURCES_DIST = copyformat.cpp @BUILD_SHARED_TRUE@am_copyformat_la_OBJECTS = copyformat.lo @@ -263,19 +266,20 @@ am__libformats_la_SOURCES_DIST = APIInterface.cpp obmolecformat.cpp \ balstformat.cpp bgfformat.cpp boxformat.cpp cacaoformat.cpp \ cacheformat.cpp carformat.cpp cccformat.cpp chem3dformat.cpp \ chemdrawct.cpp chemdrawcdx.cpp chemtoolformat.cpp \ - copyformat.cpp crkformat.cpp cssrformat.cpp dmolformat.cpp \ - fastsearchformat.cpp fastaformat.cpp featformat.cpp \ - fhformat.cpp fingerprintformat.cpp freefracformat.cpp \ - gamessformat.cpp gaussformat.cpp ghemicalformat.cpp \ - gromos96format.cpp hinformat.cpp inchiformat.cpp \ - jaguarformat.cpp mdlformat.cpp mmodformat.cpp mol2format.cpp \ - molreport.cpp mopacformat.cpp mpdformat.cpp mpqcformat.cpp \ - nwchemformat.cpp pcmodelformat.cpp pdbformat.cpp \ - povrayformat.cpp qchemformat.cpp reportformat.cpp \ - rxnformat.cpp shelxformat.cpp smilesformat.cpp \ - thermoformat.cpp tinkerformat.cpp titleformat.cpp \ - turbomoleformat.cpp unichemformat.cpp viewmolformat.cpp \ - xedformat.cpp xyzformat.cpp yasaraformat.cpp zindoformat.cpp + cifformat.cpp copyformat.cpp crkformat.cpp cssrformat.cpp \ + dmolformat.cpp fastsearchformat.cpp fastaformat.cpp \ + featformat.cpp fhformat.cpp fingerprintformat.cpp \ + freefracformat.cpp gamessformat.cpp gaussformat.cpp \ + ghemicalformat.cpp gromos96format.cpp hinformat.cpp \ + inchiformat.cpp jaguarformat.cpp mdlformat.cpp mmodformat.cpp \ + mol2format.cpp molreport.cpp mopacformat.cpp mpdformat.cpp \ + mpqcformat.cpp nwchemformat.cpp pcmodelformat.cpp \ + pdbformat.cpp povrayformat.cpp qchemformat.cpp \ + reportformat.cpp rxnformat.cpp shelxformat.cpp \ + smilesformat.cpp thermoformat.cpp tinkerformat.cpp \ + titleformat.cpp turbomoleformat.cpp unichemformat.cpp \ + viewmolformat.cpp xedformat.cpp xyzformat.cpp yasaraformat.cpp \ + zindoformat.cpp @BUILD_SHARED_FALSE@am_libformats_la_OBJECTS = APIInterface.lo \ @BUILD_SHARED_FALSE@ obmolecformat.lo CSRformat.lo PQSformat.lo \ @BUILD_SHARED_FALSE@ alchemyformat.lo amberformat.lo \ @@ -283,9 +287,10 @@ am__libformats_la_SOURCES_DIST = APIInterface.cpp obmolecformat.cpp \ @BUILD_SHARED_FALSE@ cacaoformat.lo cacheformat.lo carformat.lo \ @BUILD_SHARED_FALSE@ cccformat.lo chem3dformat.lo chemdrawct.lo \ @BUILD_SHARED_FALSE@ chemdrawcdx.lo chemtoolformat.lo \ -@BUILD_SHARED_FALSE@ copyformat.lo crkformat.lo cssrformat.lo \ -@BUILD_SHARED_FALSE@ dmolformat.lo fastsearchformat.lo \ -@BUILD_SHARED_FALSE@ fastaformat.lo featformat.lo fhformat.lo \ +@BUILD_SHARED_FALSE@ cifformat.lo copyformat.lo crkformat.lo \ +@BUILD_SHARED_FALSE@ cssrformat.lo dmolformat.lo \ +@BUILD_SHARED_FALSE@ fastsearchformat.lo fastaformat.lo \ +@BUILD_SHARED_FALSE@ featformat.lo fhformat.lo \ @BUILD_SHARED_FALSE@ fingerprintformat.lo freefracformat.lo \ @BUILD_SHARED_FALSE@ gamessformat.lo gaussformat.lo \ @BUILD_SHARED_FALSE@ ghemicalformat.lo gromos96format.lo \ @@ -477,28 +482,29 @@ SOURCES = $(APIInterface_la_SOURCES) $(CSRformat_la_SOURCES) \ $(carformat_la_SOURCES) $(cccformat_la_SOURCES) \ $(chem3dformat_la_SOURCES) $(chemdrawcdxformat_la_SOURCES) \ $(chemdrawctformat_la_SOURCES) $(chemtoolformat_la_SOURCES) \ - $(copyformat_la_SOURCES) $(crkformat_la_SOURCES) \ - $(cssrformat_la_SOURCES) $(dmolformat_la_SOURCES) \ - $(fastaformat_la_SOURCES) $(fastsearchformat_la_SOURCES) \ - $(featformat_la_SOURCES) $(fhformat_la_SOURCES) \ - $(fingerprintformat_la_SOURCES) $(freefracformat_la_SOURCES) \ - $(gamessformat_la_SOURCES) $(gaussformat_la_SOURCES) \ - $(ghemicalformat_la_SOURCES) $(gromos96format_la_SOURCES) \ - $(hinformat_la_SOURCES) $(inchiformat_la_SOURCES) \ - $(jaguarformat_la_SOURCES) $(libformats_la_SOURCES) \ - $(mdlformat_la_SOURCES) $(mmodformat_la_SOURCES) \ - $(mol2format_la_SOURCES) $(molreportformat_la_SOURCES) \ - $(mopacformat_la_SOURCES) $(mpdformat_la_SOURCES) \ - $(mpqcformat_la_SOURCES) $(nwchemformat_la_SOURCES) \ - $(pcmodelformat_la_SOURCES) $(pdbformat_la_SOURCES) \ - $(povrayformat_la_SOURCES) $(qchemformat_la_SOURCES) \ - $(reportformat_la_SOURCES) $(rxnformat_la_SOURCES) \ - $(shelxformat_la_SOURCES) $(smilesformat_la_SOURCES) \ - $(thermoformat_la_SOURCES) $(tinkerformat_la_SOURCES) \ - $(titleformat_la_SOURCES) $(turbomoleformat_la_SOURCES) \ - $(unichemformat_la_SOURCES) $(viewmolformat_la_SOURCES) \ - $(xedformat_la_SOURCES) $(xyzformat_la_SOURCES) \ - $(yasaraformat_la_SOURCES) $(zindoformat_la_SOURCES) + $(cifformat_la_SOURCES) $(copyformat_la_SOURCES) \ + $(crkformat_la_SOURCES) $(cssrformat_la_SOURCES) \ + $(dmolformat_la_SOURCES) $(fastaformat_la_SOURCES) \ + $(fastsearchformat_la_SOURCES) $(featformat_la_SOURCES) \ + $(fhformat_la_SOURCES) $(fingerprintformat_la_SOURCES) \ + $(freefracformat_la_SOURCES) $(gamessformat_la_SOURCES) \ + $(gaussformat_la_SOURCES) $(ghemicalformat_la_SOURCES) \ + $(gromos96format_la_SOURCES) $(hinformat_la_SOURCES) \ + $(inchiformat_la_SOURCES) $(jaguarformat_la_SOURCES) \ + $(libformats_la_SOURCES) $(mdlformat_la_SOURCES) \ + $(mmodformat_la_SOURCES) $(mol2format_la_SOURCES) \ + $(molreportformat_la_SOURCES) $(mopacformat_la_SOURCES) \ + $(mpdformat_la_SOURCES) $(mpqcformat_la_SOURCES) \ + $(nwchemformat_la_SOURCES) $(pcmodelformat_la_SOURCES) \ + $(pdbformat_la_SOURCES) $(povrayformat_la_SOURCES) \ + $(qchemformat_la_SOURCES) $(reportformat_la_SOURCES) \ + $(rxnformat_la_SOURCES) $(shelxformat_la_SOURCES) \ + $(smilesformat_la_SOURCES) $(thermoformat_la_SOURCES) \ + $(tinkerformat_la_SOURCES) $(titleformat_la_SOURCES) \ + $(turbomoleformat_la_SOURCES) $(unichemformat_la_SOURCES) \ + $(viewmolformat_la_SOURCES) $(xedformat_la_SOURCES) \ + $(xyzformat_la_SOURCES) $(yasaraformat_la_SOURCES) \ + $(zindoformat_la_SOURCES) DIST_SOURCES = $(am__APIInterface_la_SOURCES_DIST) \ $(am__CSRformat_la_SOURCES_DIST) \ $(am__PQSformat_la_SOURCES_DIST) \ @@ -515,6 +521,7 @@ DIST_SOURCES = $(am__APIInterface_la_SOURCES_DIST) \ $(am__chemdrawcdxformat_la_SOURCES_DIST) \ $(am__chemdrawctformat_la_SOURCES_DIST) \ $(am__chemtoolformat_la_SOURCES_DIST) \ + $(am__cifformat_la_SOURCES_DIST) \ $(am__copyformat_la_SOURCES_DIST) \ $(am__crkformat_la_SOURCES_DIST) \ $(am__cssrformat_la_SOURCES_DIST) \ @@ -565,8 +572,6 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ install-recursive installcheck-recursive installdirs-recursive \ pdf-recursive ps-recursive uninstall-info-recursive \ uninstall-recursive -libopenbabelincludeHEADERS_INSTALL = $(INSTALL_HEADER) -HEADERS = $(libopenbabelinclude_HEADERS) ETAGS = etags CTAGS = ctags DIST_SUBDIRS = xml inchi @@ -713,10 +718,10 @@ sbindir = @sbindir@ sharedstatedir = @sharedstatedir@ sysconfdir = @sysconfdir@ target_alias = @target_alias@ -INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data +INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data -I$(top_srcdir)/include # Make sure to install the inchi_api.h header libopenbabelincludedir = $(includedir)/openbabel-2.0/openbabel -libopenbabelinclude_HEADERS = inchi_api.h obmolecformat.h chemdrawcdx.h +# libopenbabelinclude_HEADERS = inchi_api.h obmolecformat.h chemdrawcdx.h EXTRA_DIST = exampleformat.cpp SUBDIRS = $(am__append_1) $(am__append_2) @BUILD_PCH_TRUE@BUILT_SOURCES = all.h.gch @@ -734,7 +739,7 @@ SUBDIRS = $(am__append_1) $(am__append_2) @BUILD_SHARED_FALSE@ amberformat.cpp balstformat.cpp bgfformat.cpp boxformat.cpp \ @BUILD_SHARED_FALSE@ cacaoformat.cpp cacheformat.cpp carformat.cpp cccformat.cpp \ @BUILD_SHARED_FALSE@ chem3dformat.cpp chemdrawct.cpp chemdrawcdx.cpp \ -@BUILD_SHARED_FALSE@ chemtoolformat.cpp \ +@BUILD_SHARED_FALSE@ chemtoolformat.cpp cifformat.cpp \ @BUILD_SHARED_FALSE@ copyformat.cpp crkformat.cpp cssrformat.cpp \ @BUILD_SHARED_FALSE@ dmolformat.cpp fastsearchformat.cpp fastaformat.cpp \ @BUILD_SHARED_FALSE@ featformat.cpp fhformat.cpp fingerprintformat.cpp \ @@ -755,7 +760,7 @@ SUBDIRS = $(am__append_1) $(am__append_2) @BUILD_SHARED_TRUE@ amberformat.la balstformat.la bgfformat.la boxformat.la \ @BUILD_SHARED_TRUE@ cacaoformat.la cacheformat.la carformat.la cccformat.la \ @BUILD_SHARED_TRUE@ chem3dformat.la chemdrawctformat.la chemdrawcdxformat.la \ -@BUILD_SHARED_TRUE@ chemtoolformat.la \ +@BUILD_SHARED_TRUE@ chemtoolformat.la cifformat.la \ @BUILD_SHARED_TRUE@ copyformat.la crkformat.la cssrformat.la \ @BUILD_SHARED_TRUE@ dmolformat.la fastsearchformat.la fastaformat.la \ @BUILD_SHARED_TRUE@ featformat.la fhformat.la fingerprintformat.la \ @@ -802,6 +807,8 @@ SUBDIRS = $(am__append_1) $(am__append_2) @BUILD_SHARED_TRUE@chemdrawcdxformat_la_LDFLAGS = -module -avoid-version @BUILD_SHARED_TRUE@chemtoolformat_la_SOURCES = chemtoolformat.cpp @BUILD_SHARED_TRUE@chemtoolformat_la_LDFLAGS = -module -avoid-version +@BUILD_SHARED_TRUE@cifformat_la_SOURCES = cifformat.cpp obmolecformat.cpp +@BUILD_SHARED_TRUE@cifformat_la_LDFLAGS = -module -avoid-version @BUILD_SHARED_TRUE@copyformat_la_SOURCES = copyformat.cpp @BUILD_SHARED_TRUE@copyformat_la_LDFLAGS = -module -avoid-version @BUILD_SHARED_TRUE@crkformat_la_SOURCES = crkformat.cpp obmolecformat.cpp @@ -992,6 +999,8 @@ chemdrawctformat.la: $(chemdrawctformat_la_OBJECTS) $(chemdrawctformat_la_DEPEND $(CXXLINK) $(am_chemdrawctformat_la_rpath) $(chemdrawctformat_la_LDFLAGS) $(chemdrawctformat_la_OBJECTS) $(chemdrawctformat_la_LIBADD) $(LIBS) chemtoolformat.la: $(chemtoolformat_la_OBJECTS) $(chemtoolformat_la_DEPENDENCIES) $(CXXLINK) $(am_chemtoolformat_la_rpath) $(chemtoolformat_la_LDFLAGS) $(chemtoolformat_la_OBJECTS) $(chemtoolformat_la_LIBADD) $(LIBS) +cifformat.la: $(cifformat_la_OBJECTS) $(cifformat_la_DEPENDENCIES) + $(CXXLINK) $(am_cifformat_la_rpath) $(cifformat_la_LDFLAGS) $(cifformat_la_OBJECTS) $(cifformat_la_LIBADD) $(LIBS) copyformat.la: $(copyformat_la_OBJECTS) $(copyformat_la_DEPENDENCIES) $(CXXLINK) $(am_copyformat_la_rpath) $(copyformat_la_LDFLAGS) $(copyformat_la_OBJECTS) $(copyformat_la_LIBADD) $(LIBS) crkformat.la: $(crkformat_la_OBJECTS) $(crkformat_la_DEPENDENCIES) @@ -1103,6 +1112,7 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chemdrawcdx.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chemdrawct.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chemtoolformat.Plo@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cifformat.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/copyformat.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/crkformat.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cssrformat.Plo@am__quote@ @@ -1178,23 +1188,6 @@ clean-libtool: distclean-libtool: -rm -f libtool uninstall-info-am: -install-libopenbabelincludeHEADERS: $(libopenbabelinclude_HEADERS) - @$(NORMAL_INSTALL) - test -z "$(libopenbabelincludedir)" || $(mkdir_p) "$(DESTDIR)$(libopenbabelincludedir)" - @list='$(libopenbabelinclude_HEADERS)'; for p in $$list; do \ - if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ - f=$(am__strip_dir) \ - echo " $(libopenbabelincludeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(libopenbabelincludedir)/$$f'"; \ - $(libopenbabelincludeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(libopenbabelincludedir)/$$f"; \ - done - -uninstall-libopenbabelincludeHEADERS: - @$(NORMAL_UNINSTALL) - @list='$(libopenbabelinclude_HEADERS)'; for p in $$list; do \ - f=$(am__strip_dir) \ - echo " rm -f '$(DESTDIR)$(libopenbabelincludedir)/$$f'"; \ - rm -f "$(DESTDIR)$(libopenbabelincludedir)/$$f"; \ - done # This directory's subdirectories are mostly independent; you can cd # into them and run `make' without going through this Makefile. @@ -1373,10 +1366,10 @@ distdir: $(DISTFILES) check-am: all-am check: $(BUILT_SOURCES) $(MAKE) $(AM_MAKEFLAGS) check-recursive -all-am: Makefile $(LTLIBRARIES) $(HEADERS) +all-am: Makefile $(LTLIBRARIES) installdirs: installdirs-recursive installdirs-am: - for dir in "$(DESTDIR)$(pkglibdir)" "$(DESTDIR)$(libopenbabelincludedir)"; do \ + for dir in "$(DESTDIR)$(pkglibdir)"; do \ test -z "$$dir" || $(mkdir_p) "$$dir"; \ done install: $(BUILT_SOURCES) @@ -1427,7 +1420,7 @@ info: info-recursive info-am: -install-data-am: install-libopenbabelincludeHEADERS +install-data-am: install-exec-am: install-pkglibLTLIBRARIES @@ -1455,8 +1448,7 @@ ps: ps-recursive ps-am: -uninstall-am: uninstall-info-am uninstall-libopenbabelincludeHEADERS \ - uninstall-pkglibLTLIBRARIES +uninstall-am: uninstall-info-am uninstall-pkglibLTLIBRARIES uninstall-info: uninstall-info-recursive @@ -1468,15 +1460,13 @@ uninstall-info: uninstall-info-recursive distclean-recursive distclean-tags distdir dvi dvi-am html \ html-am info info-am install install-am install-data \ install-data-am install-exec install-exec-am install-info \ - install-info-am install-libopenbabelincludeHEADERS install-man \ - install-pkglibLTLIBRARIES install-strip installcheck \ - installcheck-am installdirs installdirs-am maintainer-clean \ - maintainer-clean-generic maintainer-clean-recursive \ - mostlyclean mostlyclean-compile mostlyclean-generic \ - mostlyclean-libtool mostlyclean-recursive pdf pdf-am ps ps-am \ - tags tags-recursive uninstall uninstall-am uninstall-info-am \ - uninstall-libopenbabelincludeHEADERS \ - uninstall-pkglibLTLIBRARIES + install-info-am install-man install-pkglibLTLIBRARIES \ + install-strip installcheck installcheck-am installdirs \ + installdirs-am maintainer-clean maintainer-clean-generic \ + maintainer-clean-recursive mostlyclean mostlyclean-compile \ + mostlyclean-generic mostlyclean-libtool mostlyclean-recursive \ + pdf pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \ + uninstall-info-am uninstall-pkglibLTLIBRARIES @BUILD_PCH_TRUE@all.h.gch: all.h Makefile obmolecformat.h $(srcdir)/../babelconfig.h \ @BUILD_PCH_TRUE@ $(srcdir)/../mol.h $(srcdir)/../obconversion.h $(srcdir)/../base.h \ diff --git a/src/formats/PQSformat.cpp b/src/formats/PQSformat.cpp index db345e3ab..9233a518d 100644 --- a/src/formats/PQSformat.cpp +++ b/src/formats/PQSformat.cpp @@ -12,8 +12,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #include diff --git a/src/formats/alchemyformat.cpp b/src/formats/alchemyformat.cpp index 920c6867a..7b864e72e 100644 --- a/src/formats/alchemyformat.cpp +++ b/src/formats/alchemyformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/amberformat.cpp b/src/formats/amberformat.cpp index b8a21f1ef..ee3f6b630 100644 --- a/src/formats/amberformat.cpp +++ b/src/formats/amberformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/balstformat.cpp b/src/formats/balstformat.cpp index 28e6df29e..5a7bf5fbb 100644 --- a/src/formats/balstformat.cpp +++ b/src/formats/balstformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/bgfformat.cpp b/src/formats/bgfformat.cpp index 7d711d436..88ab2f81f 100644 --- a/src/formats/bgfformat.cpp +++ b/src/formats/bgfformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/boxformat.cpp b/src/formats/boxformat.cpp index 907bfc73c..707c7e492 100644 --- a/src/formats/boxformat.cpp +++ b/src/formats/boxformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/cacaoformat.cpp b/src/formats/cacaoformat.cpp index a03728322..132bae6c4 100644 --- a/src/formats/cacaoformat.cpp +++ b/src/formats/cacaoformat.cpp @@ -12,10 +12,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" -#include "math/matrix3x3.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/cacheformat.cpp b/src/formats/cacheformat.cpp index 1ad02c7c3..dc4ca6380 100644 --- a/src/formats/cacheformat.cpp +++ b/src/formats/cacheformat.cpp @@ -12,8 +12,8 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/carformat.cpp b/src/formats/carformat.cpp index af3e7cd9b..afbdc8982 100644 --- a/src/formats/carformat.cpp +++ b/src/formats/carformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/cccformat.cpp b/src/formats/cccformat.cpp index d90b73582..d04e76801 100644 --- a/src/formats/cccformat.cpp +++ b/src/formats/cccformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/chem3dformat.cpp b/src/formats/chem3dformat.cpp index 93f9bc6e7..2cc4efa05 100644 --- a/src/formats/chem3dformat.cpp +++ b/src/formats/chem3dformat.cpp @@ -12,10 +12,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "math/matrix3x3.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/chemdrawcdx.cpp b/src/formats/chemdrawcdx.cpp index 614469ebd..916285451 100644 --- a/src/formats/chemdrawcdx.cpp +++ b/src/formats/chemdrawcdx.cpp @@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #include "chemdrawcdx.h" #include diff --git a/src/formats/chemdrawct.cpp b/src/formats/chemdrawct.cpp index fc11a445b..7bcfccde9 100644 --- a/src/formats/chemdrawct.cpp +++ b/src/formats/chemdrawct.cpp @@ -12,8 +12,8 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/chemtoolformat.cpp b/src/formats/chemtoolformat.cpp index 05c012624..7c815787a 100644 --- a/src/formats/chemtoolformat.cpp +++ b/src/formats/chemtoolformat.cpp @@ -15,8 +15,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #include using namespace std; diff --git a/src/formats/cifformat.cpp b/src/formats/cifformat.cpp index 86f00b891..4051ba224 100644 --- a/src/formats/cifformat.cpp +++ b/src/formats/cifformat.cpp @@ -16,8 +16,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #include #include diff --git a/src/formats/copyformat.cpp b/src/formats/copyformat.cpp index 7b7721f0b..cd385cffa 100644 --- a/src/formats/copyformat.cpp +++ b/src/formats/copyformat.cpp @@ -10,8 +10,8 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obconversion.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/crkformat.cpp b/src/formats/crkformat.cpp index e1da6b2a8..c776654e8 100644 --- a/src/formats/crkformat.cpp +++ b/src/formats/crkformat.cpp @@ -12,8 +12,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #include diff --git a/src/formats/cssrformat.cpp b/src/formats/cssrformat.cpp index 92edeb915..1e64662e2 100644 --- a/src/formats/cssrformat.cpp +++ b/src/formats/cssrformat.cpp @@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/dmolformat.cpp b/src/formats/dmolformat.cpp index c476b3ba9..12e37bc63 100644 --- a/src/formats/dmolformat.cpp +++ b/src/formats/dmolformat.cpp @@ -11,9 +11,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/exampleformat.cpp b/src/formats/exampleformat.cpp index c0483de86..7d8d8ffef 100644 --- a/src/formats/exampleformat.cpp +++ b/src/formats/exampleformat.cpp @@ -32,8 +32,8 @@ For XML formats extra, support for the parsing is provided, see pubchem.cpp as an example. */ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/fastaformat.cpp b/src/formats/fastaformat.cpp index 9f2b75695..ef86cf6ba 100644 --- a/src/formats/fastaformat.cpp +++ b/src/formats/fastaformat.cpp @@ -11,8 +11,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/fastsearchformat.cpp b/src/formats/fastsearchformat.cpp index 49357b01e..002d9e3ba 100644 --- a/src/formats/fastsearchformat.cpp +++ b/src/formats/fastsearchformat.cpp @@ -11,15 +11,15 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include #include #include -#include "mol.h" -#include "obconversion.h" -#include "fingerprint.h" +#include +#include +#include using namespace std; namespace OpenBabel { diff --git a/src/formats/featformat.cpp b/src/formats/featformat.cpp index 36f9f111a..924797691 100644 --- a/src/formats/featformat.cpp +++ b/src/formats/featformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/fhformat.cpp b/src/formats/fhformat.cpp index 6f144be98..f76cd4a00 100644 --- a/src/formats/fhformat.cpp +++ b/src/formats/fhformat.cpp @@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/fingerprintformat.cpp b/src/formats/fingerprintformat.cpp index 3a8168bbf..44cce0b7e 100644 --- a/src/formats/fingerprintformat.cpp +++ b/src/formats/fingerprintformat.cpp @@ -10,14 +10,14 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include #include #include -#include "obmolecformat.h" -#include "fingerprint.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/freefracformat.cpp b/src/formats/freefracformat.cpp index 9971df6a9..316cc959c 100644 --- a/src/formats/freefracformat.cpp +++ b/src/formats/freefracformat.cpp @@ -11,10 +11,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" -#include "math/matrix3x3.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/gamessformat.cpp b/src/formats/gamessformat.cpp index 2c6a0ef3e..d122b739d 100644 --- a/src/formats/gamessformat.cpp +++ b/src/formats/gamessformat.cpp @@ -13,9 +13,9 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace Gamess diff --git a/src/formats/gaussformat.cpp b/src/formats/gaussformat.cpp index 57a7c858d..c9de421e0 100644 --- a/src/formats/gaussformat.cpp +++ b/src/formats/gaussformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/getinchi.cpp b/src/formats/getinchi.cpp index b22c3d234..0baf0a3d8 100644 --- a/src/formats/getinchi.cpp +++ b/src/formats/getinchi.cpp @@ -14,7 +14,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include #include using namespace std; diff --git a/src/formats/ghemicalformat.cpp b/src/formats/ghemicalformat.cpp index b5add4768..403758f56 100644 --- a/src/formats/ghemicalformat.cpp +++ b/src/formats/ghemicalformat.cpp @@ -12,9 +12,9 @@ GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/gromos96format.cpp b/src/formats/gromos96format.cpp index c53d71830..4a621792b 100644 --- a/src/formats/gromos96format.cpp +++ b/src/formats/gromos96format.cpp @@ -50,8 +50,8 @@ GNU General Public License for more details. *** But now handled by a command line option in new framework. */ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/hinformat.cpp b/src/formats/hinformat.cpp index 1823e99ed..2aa68a8f1 100644 --- a/src/formats/hinformat.cpp +++ b/src/formats/hinformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/inchiformat.cpp b/src/formats/inchiformat.cpp index ce7893908..7d5ad8a1c 100644 --- a/src/formats/inchiformat.cpp +++ b/src/formats/inchiformat.cpp @@ -15,10 +15,11 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" -#include "obmolecformat.h" +#include +#include +#include +#include + #include "inchi_api.h" #include #include diff --git a/src/formats/jaguarformat.cpp b/src/formats/jaguarformat.cpp index b587c14de..ba2bbf151 100644 --- a/src/formats/jaguarformat.cpp +++ b/src/formats/jaguarformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include #include using namespace std; diff --git a/src/formats/mdlformat.cpp b/src/formats/mdlformat.cpp index 0ab27b3ca..7d5c254d5 100644 --- a/src/formats/mdlformat.cpp +++ b/src/formats/mdlformat.cpp @@ -15,7 +15,7 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #ifdef _WIN32 #pragma warning (disable : 4786) @@ -25,8 +25,8 @@ GNU General Public License for more details. #include #include #include -#include "obmolecformat.h" -#include "chiral.h" +#include +#include using namespace std; namespace OpenBabel @@ -890,4 +890,4 @@ public: return td; } -} \ No newline at end of file +} diff --git a/src/formats/mmodformat.cpp b/src/formats/mmodformat.cpp index db601ca62..744f0eb97 100644 --- a/src/formats/mmodformat.cpp +++ b/src/formats/mmodformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/mol2format.cpp b/src/formats/mol2format.cpp index d760a1da0..7fe3cf777 100644 --- a/src/formats/mol2format.cpp +++ b/src/formats/mol2format.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/molreport.cpp b/src/formats/molreport.cpp index 03404f3c9..7b38c3462 100644 --- a/src/formats/molreport.cpp +++ b/src/formats/molreport.cpp @@ -17,8 +17,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/mopacformat.cpp b/src/formats/mopacformat.cpp index 97786f0bf..28f883abb 100644 --- a/src/formats/mopacformat.cpp +++ b/src/formats/mopacformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/mpdformat.cpp b/src/formats/mpdformat.cpp index fcd53810d..425b3bdec 100644 --- a/src/formats/mpdformat.cpp +++ b/src/formats/mpdformat.cpp @@ -17,9 +17,9 @@ GNU General Public License for more details. ***********************************************************************/ // Output format is #Origatomtype;#layer-#frequency-#atomtype;#l-#f-#aty;...Next atomnext molecule -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include #define LAYER_DEPTH 2 // cannot increase past 2 without adding more *nbr atom pointers and loops #define LAYER_SIZE 184 // number of types needed for types system used diff --git a/src/formats/mpqcformat.cpp b/src/formats/mpqcformat.cpp index 16fc34a0c..452f126ca 100644 --- a/src/formats/mpqcformat.cpp +++ b/src/formats/mpqcformat.cpp @@ -11,9 +11,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/nwchemformat.cpp b/src/formats/nwchemformat.cpp index e3a14a1f4..760e0f57f 100644 --- a/src/formats/nwchemformat.cpp +++ b/src/formats/nwchemformat.cpp @@ -11,9 +11,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/obmolecformat.cpp b/src/formats/obmolecformat.cpp index 3a9c93149..5af61bbda 100644 --- a/src/formats/obmolecformat.cpp +++ b/src/formats/obmolecformat.cpp @@ -15,8 +15,8 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #ifdef _DEBUG #undef THIS_FILE diff --git a/src/formats/pcmodelformat.cpp b/src/formats/pcmodelformat.cpp index 91bd68454..ee4e2a04f 100644 --- a/src/formats/pcmodelformat.cpp +++ b/src/formats/pcmodelformat.cpp @@ -13,7 +13,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/pdbformat.cpp b/src/formats/pdbformat.cpp index 141d2d98a..fb19adc78 100644 --- a/src/formats/pdbformat.cpp +++ b/src/formats/pdbformat.cpp @@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #include #include diff --git a/src/formats/povrayformat.cpp b/src/formats/povrayformat.cpp index c5e7aa328..58a79a067 100644 --- a/src/formats/povrayformat.cpp +++ b/src/formats/povrayformat.cpp @@ -12,7 +12,7 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include /* ---- C includes ---- */ #include @@ -20,7 +20,7 @@ GNU General Public License for more details. #include /* ---- OpenBabel include ---- */ -#include "obmolecformat.h" +#include /* ---- C++ includes ---- */ #include diff --git a/src/formats/qchemformat.cpp b/src/formats/qchemformat.cpp index dd409b784..9910225a8 100644 --- a/src/formats/qchemformat.cpp +++ b/src/formats/qchemformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/reportformat.cpp b/src/formats/reportformat.cpp index 443050834..a6e6b2fe0 100644 --- a/src/formats/reportformat.cpp +++ b/src/formats/reportformat.cpp @@ -18,9 +18,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/rxnformat.cpp b/src/formats/rxnformat.cpp index fb108e19d..353983fa7 100644 --- a/src/formats/rxnformat.cpp +++ b/src/formats/rxnformat.cpp @@ -18,11 +18,11 @@ GNU General Public License for more details. #pragma warning (disable : 4251) // #endif -#include "babelconfig.h" +#include -#include "mol.h" -#include "obconversion.h" -#include "reaction.h" +#include +#include +#include namespace OpenBabel { diff --git a/src/formats/shelxformat.cpp b/src/formats/shelxformat.cpp index c9bc1c66a..64568f8cc 100644 --- a/src/formats/shelxformat.cpp +++ b/src/formats/shelxformat.cpp @@ -12,10 +12,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "math/matrix3x3.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/smilesformat.cpp b/src/formats/smilesformat.cpp index de9184e0d..55c0b92d2 100644 --- a/src/formats/smilesformat.cpp +++ b/src/formats/smilesformat.cpp @@ -16,9 +16,9 @@ GNU General Public License for more details. // TODO: Rewrite. Use std::string in place of char * to avoid buffer overflow // use std::string::reserve (or different allocator) to avoid resize slowdown -#include "babelconfig.h" -#include "obmolecformat.h" -#include "chiral.h" +#include +#include +#include using namespace std; diff --git a/src/formats/thermoformat.cpp b/src/formats/thermoformat.cpp index 372f304f9..7a806cdbf 100644 --- a/src/formats/thermoformat.cpp +++ b/src/formats/thermoformat.cpp @@ -13,15 +13,15 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #ifdef WIN32 #pragma warning (disable : 4786) #pragma warning (disable : 4251) // #endif #include #include -#include "obmolecformat.h" -#include "kinetics.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/formats/tinkerformat.cpp b/src/formats/tinkerformat.cpp index ecb161297..fc0838d00 100644 --- a/src/formats/tinkerformat.cpp +++ b/src/formats/tinkerformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/titleformat.cpp b/src/formats/titleformat.cpp index 95f8a8218..a6a2f21c2 100644 --- a/src/formats/titleformat.cpp +++ b/src/formats/titleformat.cpp @@ -15,8 +15,8 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include using namespace std; namespace OpenBabel { diff --git a/src/formats/turbomoleformat.cpp b/src/formats/turbomoleformat.cpp index 0ec1742f2..9b2cf5bba 100644 --- a/src/formats/turbomoleformat.cpp +++ b/src/formats/turbomoleformat.cpp @@ -13,9 +13,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include const double AAU = 0.5291772108; // Ångström per bohr (CODATA 2002) diff --git a/src/formats/unichemformat.cpp b/src/formats/unichemformat.cpp index 418c0372e..15041de82 100644 --- a/src/formats/unichemformat.cpp +++ b/src/formats/unichemformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/viewmolformat.cpp b/src/formats/viewmolformat.cpp index 7a25d288d..bf95098c8 100644 --- a/src/formats/viewmolformat.cpp +++ b/src/formats/viewmolformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/xedformat.cpp b/src/formats/xedformat.cpp index 4923292b8..dc5cc6ebe 100644 --- a/src/formats/xedformat.cpp +++ b/src/formats/xedformat.cpp @@ -12,9 +12,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/formats/xml/Makefile.am b/src/formats/xml/Makefile.am index 8dc0fc295..3b5a2dbed 100644 --- a/src/formats/xml/Makefile.am +++ b/src/formats/xml/Makefile.am @@ -1,6 +1,7 @@ EXTRA_DIST = xml.h -INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data -I$(top_srcdir)/src/formats +INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data \ + -I$(top_srcdir)/src/formats -I$(top_srcdir)/include AM_CPPFLAGS = @XML_CPPFLAGS@ AM_LDFLAGS = @LIBS@ @XML_LIBS@ diff --git a/src/formats/xml/Makefile.in b/src/formats/xml/Makefile.in index 093ecab95..a72ed74cf 100644 --- a/src/formats/xml/Makefile.in +++ b/src/formats/xml/Makefile.in @@ -245,7 +245,9 @@ sharedstatedir = @sharedstatedir@ sysconfdir = @sysconfdir@ target_alias = @target_alias@ EXTRA_DIST = xml.h -INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data -I$(top_srcdir)/src/formats +INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/data \ + -I$(top_srcdir)/src/formats -I$(top_srcdir)/include + AM_CPPFLAGS = @XML_CPPFLAGS@ AM_LDFLAGS = @LIBS@ @XML_LIBS@ @BUILD_SHARED_TRUE@pkglib_LTLIBRARIES = \ diff --git a/src/formats/xml/cdxmlformat.cpp b/src/formats/xml/cdxmlformat.cpp index 94f987198..dc3dc8750 100644 --- a/src/formats/xml/cdxmlformat.cpp +++ b/src/formats/xml/cdxmlformat.cpp @@ -14,7 +14,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include "xml.h" #ifdef WIN32 diff --git a/src/formats/xml/cmlformat.cpp b/src/formats/xml/cmlformat.cpp index 72548c0a9..c970b70f1 100644 --- a/src/formats/xml/cmlformat.cpp +++ b/src/formats/xml/cmlformat.cpp @@ -14,10 +14,11 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include +#include +#include + #include "xml.h" -#include "math/matrix3x3.h" -#include "kinetics.h" #ifdef WIN32 #pragma warning (disable : 4800) diff --git a/src/formats/xml/cmlreactlformat.cpp b/src/formats/xml/cmlreactlformat.cpp index 7f2c60798..8ccb6386b 100644 --- a/src/formats/xml/cmlreactlformat.cpp +++ b/src/formats/xml/cmlreactlformat.cpp @@ -12,7 +12,7 @@ GNU General Public License for more details. ***********************************************************************/ #include "xml.h" -#include "reaction.h" +#include #ifdef WIN32 #pragma warning (disable : 4800) diff --git a/src/formats/xml/pubchem.cpp b/src/formats/xml/pubchem.cpp index 2ee38e45e..706c4bc6e 100644 --- a/src/formats/xml/pubchem.cpp +++ b/src/formats/xml/pubchem.cpp @@ -13,7 +13,7 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include "xml.h" #ifdef WIN32 diff --git a/src/formats/xml/xml.cpp b/src/formats/xml/xml.cpp index 27e0e55db..2cf8be3f3 100644 --- a/src/formats/xml/xml.cpp +++ b/src/formats/xml/xml.cpp @@ -11,7 +11,7 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include "xml.h" diff --git a/src/formats/xml/xml.h b/src/formats/xml/xml.h index ea7d05ea7..56003f252 100644 --- a/src/formats/xml/xml.h +++ b/src/formats/xml/xml.h @@ -13,9 +13,9 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "mol.h" -#include "obconversion.h" -#include "obmolecformat.h" +#include +#include +#include #include #include diff --git a/src/formats/xml/xmlformat.cpp b/src/formats/xml/xmlformat.cpp index fcf58f7f7..990d4b201 100644 --- a/src/formats/xml/xmlformat.cpp +++ b/src/formats/xml/xmlformat.cpp @@ -11,7 +11,7 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include "xml.h" diff --git a/src/formats/xyzformat.cpp b/src/formats/xyzformat.cpp index b47fda4f6..d14eb8b44 100644 --- a/src/formats/xyzformat.cpp +++ b/src/formats/xyzformat.cpp @@ -13,8 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "obmolecformat.h" +#include +#include #include diff --git a/src/formats/yasaraformat.cpp b/src/formats/yasaraformat.cpp index a2615b468..c099da466 100644 --- a/src/formats/yasaraformat.cpp +++ b/src/formats/yasaraformat.cpp @@ -23,7 +23,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************/ -#include "babelconfig.h" +#include /* Adapt on some 64bit machines! */ typedef int int32; @@ -31,7 +31,7 @@ typedef unsigned int uint32; typedef short int16; typedef unsigned short uint16; -#include "obmolecformat.h" +#include #define mem_alloc malloc #define mem_free free diff --git a/src/formats/zindoformat.cpp b/src/formats/zindoformat.cpp index 43175deee..a7b85e6df 100644 --- a/src/formats/zindoformat.cpp +++ b/src/formats/zindoformat.cpp @@ -11,9 +11,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "obmolecformat.h" +#include using namespace std; namespace OpenBabel diff --git a/src/generic.cpp b/src/generic.cpp index 18dde7408..69bb3b3a6 100644 --- a/src/generic.cpp +++ b/src/generic.cpp @@ -16,13 +16,13 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "generic.h" -#include "math/matrix3x3.h" +#include +#include +#include using namespace std; diff --git a/src/grid.cpp b/src/grid.cpp index 7bc57fa4d..43a73146c 100644 --- a/src/grid.cpp +++ b/src/grid.cpp @@ -16,11 +16,11 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "mol.h" -#include "atom.h" -#include "grid.h" +#include +#include +#include using namespace std; diff --git a/src/kekulize.cpp b/src/kekulize.cpp index 552003ac5..440ede7b2 100644 --- a/src/kekulize.cpp +++ b/src/kekulize.cpp @@ -17,9 +17,9 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "mol.h" +#include #include diff --git a/src/main.cpp b/src/main.cpp index 71db9d229..97c2c0555 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -23,7 +23,7 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include #include @@ -39,7 +39,7 @@ GNU General Public License for more details. extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); #endif -#include "obconversion.h" +#include using namespace std; using namespace OpenBabel; diff --git a/src/math/Makefile.am b/src/math/Makefile.am index 4a2fdeca5..c31fa8748 100644 --- a/src/math/Makefile.am +++ b/src/math/Makefile.am @@ -1,8 +1,4 @@ noinst_LTLIBRARIES = libmath.la libmath_la_SOURCES = matrix3x3.cpp vector3.cpp -libmathincludedir = $(includedir)/openbabel-2.0/openbabel/math -libmathinclude_HEADERS = \ - matrix3x3.h vector3.h - -AM_CPPFLAGS = -I$(top_srcdir)/src +AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/include diff --git a/src/math/Makefile.in b/src/math/Makefile.in index 211d3a4dc..d02753736 100644 --- a/src/math/Makefile.in +++ b/src/math/Makefile.in @@ -14,7 +14,6 @@ @SET_MAKE@ - srcdir = @srcdir@ top_srcdir = @top_srcdir@ VPATH = @srcdir@ @@ -38,8 +37,7 @@ POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ subdir = src/math -DIST_COMMON = $(libmathinclude_HEADERS) $(srcdir)/Makefile.am \ - $(srcdir)/Makefile.in +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \ $(top_srcdir)/configure.in @@ -65,15 +63,6 @@ CXXLINK = $(LIBTOOL) --tag=CXX --mode=link $(CXXLD) $(AM_CXXFLAGS) \ $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ SOURCES = $(libmath_la_SOURCES) DIST_SOURCES = $(libmath_la_SOURCES) -am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; -am__vpath_adj = case $$p in \ - $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \ - *) f=$$p;; \ - esac; -am__strip_dir = `echo $$p | sed -e 's|^.*/||'`; -am__installdirs = "$(DESTDIR)$(libmathincludedir)" -libmathincludeHEADERS_INSTALL = $(INSTALL_HEADER) -HEADERS = $(libmathinclude_HEADERS) ETAGS = etags CTAGS = ctags DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) @@ -221,11 +210,7 @@ sysconfdir = @sysconfdir@ target_alias = @target_alias@ noinst_LTLIBRARIES = libmath.la libmath_la_SOURCES = matrix3x3.cpp vector3.cpp -libmathincludedir = $(includedir)/openbabel-2.0/openbabel/math -libmathinclude_HEADERS = \ - matrix3x3.h vector3.h - -AM_CPPFLAGS = -I$(top_srcdir)/src +AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/include all: all-am .SUFFIXES: @@ -310,23 +295,6 @@ clean-libtool: distclean-libtool: -rm -f libtool uninstall-info-am: -install-libmathincludeHEADERS: $(libmathinclude_HEADERS) - @$(NORMAL_INSTALL) - test -z "$(libmathincludedir)" || $(mkdir_p) "$(DESTDIR)$(libmathincludedir)" - @list='$(libmathinclude_HEADERS)'; for p in $$list; do \ - if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ - f=$(am__strip_dir) \ - echo " $(libmathincludeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(libmathincludedir)/$$f'"; \ - $(libmathincludeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(libmathincludedir)/$$f"; \ - done - -uninstall-libmathincludeHEADERS: - @$(NORMAL_UNINSTALL) - @list='$(libmathinclude_HEADERS)'; for p in $$list; do \ - f=$(am__strip_dir) \ - echo " rm -f '$(DESTDIR)$(libmathincludedir)/$$f'"; \ - rm -f "$(DESTDIR)$(libmathincludedir)/$$f"; \ - done ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ @@ -405,11 +373,8 @@ distdir: $(DISTFILES) done check-am: all-am check: check-am -all-am: Makefile $(LTLIBRARIES) $(HEADERS) +all-am: Makefile $(LTLIBRARIES) installdirs: - for dir in "$(DESTDIR)$(libmathincludedir)"; do \ - test -z "$$dir" || $(mkdir_p) "$$dir"; \ - done install: install-am install-exec: install-exec-am install-data: install-data-am @@ -455,7 +420,7 @@ info: info-am info-am: -install-data-am: install-libmathincludeHEADERS +install-data-am: install-exec-am: @@ -483,20 +448,19 @@ ps: ps-am ps-am: -uninstall-am: uninstall-info-am uninstall-libmathincludeHEADERS +uninstall-am: uninstall-info-am .PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \ clean-libtool clean-noinstLTLIBRARIES ctags distclean \ distclean-compile distclean-generic distclean-libtool \ distclean-tags distdir dvi dvi-am html html-am info info-am \ install install-am install-data install-data-am install-exec \ - install-exec-am install-info install-info-am \ - install-libmathincludeHEADERS install-man install-strip \ - installcheck installcheck-am installdirs maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-compile \ - mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \ - tags uninstall uninstall-am uninstall-info-am \ - uninstall-libmathincludeHEADERS + install-exec-am install-info install-info-am install-man \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic mostlyclean-libtool \ + pdf pdf-am ps ps-am tags uninstall uninstall-am \ + uninstall-info-am # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. diff --git a/src/math/matrix3x3.cpp b/src/math/matrix3x3.cpp index 9f07cbc06..b630b4d7a 100644 --- a/src/math/matrix3x3.cpp +++ b/src/math/matrix3x3.cpp @@ -17,10 +17,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "math/matrix3x3.h" -#include "obutil.h" +#include +#include using namespace std; diff --git a/src/math/vector3.cpp b/src/math/vector3.cpp index 543a873c9..4d257b4dd 100644 --- a/src/math/vector3.cpp +++ b/src/math/vector3.cpp @@ -18,12 +18,12 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include -#include "math/vector3.h" -#include "obutil.h" +#include +#include using namespace std; diff --git a/src/matrix.cpp b/src/matrix.cpp index 4f3ab97c0..4e5786c9c 100644 --- a/src/matrix.cpp +++ b/src/matrix.cpp @@ -16,8 +16,8 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "matrix.h" +#include +#include using namespace std; diff --git a/src/mol.cpp b/src/mol.cpp index a4781914a..d0e6f809a 100644 --- a/src/mol.cpp +++ b/src/mol.cpp @@ -17,13 +17,13 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "mol.h" -#include "rotamer.h" -#include "phmodel.h" -#include "bondtyper.h" -#include "math/matrix3x3.h" +#include +#include +#include +#include +#include #include diff --git a/src/molchrg.cpp b/src/molchrg.cpp index 71246fe42..380da0154 100644 --- a/src/molchrg.cpp +++ b/src/molchrg.cpp @@ -16,10 +16,10 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "mol.h" -#include "molchrg.h" +#include +#include using namespace std; namespace OpenBabel diff --git a/src/newlinebuf.cpp b/src/newlinebuf.cpp index 0b8cba90a..effa02ad5 100644 --- a/src/newlinebuf.cpp +++ b/src/newlinebuf.cpp @@ -16,8 +16,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "newlinebuf.h" +#include +#include #include diff --git a/src/obconversion.cpp b/src/obconversion.cpp index 36dc84ad8..cab7d6325 100644 --- a/src/obconversion.cpp +++ b/src/obconversion.cpp @@ -17,7 +17,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ // Definition of OBConversion routines -#include "babelconfig.h" +#include #ifdef _WIN32 #pragma warning (disable : 4786) @@ -36,7 +36,7 @@ GNU General Public License for more details. #include #include #include -#include "obconversion.h" +#include #ifdef HAVE_LIBZ #include "zipstream.h" diff --git a/src/oberror.cpp b/src/oberror.cpp index 18ad2684e..6b1ce41bb 100644 --- a/src/oberror.cpp +++ b/src/oberror.cpp @@ -17,12 +17,12 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include #include -#include "oberror.h" +#include using namespace std; diff --git a/src/obiter.cpp b/src/obiter.cpp index d30adc1fb..841363d4c 100644 --- a/src/obiter.cpp +++ b/src/obiter.cpp @@ -16,12 +16,12 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "obiter.h" +#include +#include using namespace std; diff --git a/src/obutil.cpp b/src/obutil.cpp index 9e55602fe..2dde092cc 100644 --- a/src/obutil.cpp +++ b/src/obutil.cpp @@ -17,10 +17,10 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" -#include "math/matrix3x3.h" -#include "mol.h" -#include "obutil.h" +#include +#include +#include +#include #if HAVE_CONIO_H #include diff --git a/src/parsmart.cpp b/src/parsmart.cpp index 2ffc837f7..ca7a17e57 100644 --- a/src/parsmart.cpp +++ b/src/parsmart.cpp @@ -16,13 +16,13 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #include #include -#include "mol.h" -#include "parsmart.h" +#include +#include using namespace std; diff --git a/src/patty.cpp b/src/patty.cpp index 7221fb4df..2f2b9c78e 100644 --- a/src/patty.cpp +++ b/src/patty.cpp @@ -17,10 +17,10 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "mol.h" -#include "patty.h" +#include +#include // Simple programmable atom typer // WPW - 070199 diff --git a/src/phmodel.cpp b/src/phmodel.cpp index f2d107183..741d1ddba 100644 --- a/src/phmodel.cpp +++ b/src/phmodel.cpp @@ -16,10 +16,11 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include + +#include +#include -#include "mol.h" -#include "phmodel.h" #include "phmodeldata.h" #ifdef WIN32 diff --git a/src/rand.cpp b/src/rand.cpp index 513b29dc9..7c22a4a55 100644 --- a/src/rand.cpp +++ b/src/rand.cpp @@ -22,13 +22,13 @@ GNU General Public License for more details. * Roger Sayle, Metaphorics LLC * Version 1.2, September 1998 */ -#include "babelconfig.h" +#include #include #include #include -#include "rand.h" +#include #if TIME_WITH_SYS_TIME #include diff --git a/src/residue.cpp b/src/residue.cpp index 8e60ac7cf..d0f63e0ee 100644 --- a/src/residue.cpp +++ b/src/residue.cpp @@ -26,13 +26,13 @@ obtained in part or whole from RasMol2 by Roger Sayle. // File Includes /////////////////////////////////////////////////////////////////////////////// -#include "babelconfig.h" +#include -#include "residue.h" -#include "atom.h" -#include "oberror.h" -#include "bitvec.h" -#include "bond.h" +#include +#include +#include +#include +#include using namespace std; diff --git a/src/ring.cpp b/src/ring.cpp index 04b5188d0..4522bd0f1 100644 --- a/src/ring.cpp +++ b/src/ring.cpp @@ -16,9 +16,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "mol.h" +#include #include diff --git a/src/rotamer.cpp b/src/rotamer.cpp index 0991d87cc..cba40bab7 100644 --- a/src/rotamer.cpp +++ b/src/rotamer.cpp @@ -16,9 +16,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "rotamer.h" +#include #define OB_TITLE_SIZE 254 #define OB_BINARY_SETWORD 32 diff --git a/src/rotor.cpp b/src/rotor.cpp index 609ae11d9..68ac19356 100644 --- a/src/rotor.cpp +++ b/src/rotor.cpp @@ -17,10 +17,11 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include + +#include +#include -#include "mol.h" -#include "rotor.h" #include "torlib.h" using namespace std; diff --git a/src/tokenst.cpp b/src/tokenst.cpp index 58284bcec..feca4cf8c 100644 --- a/src/tokenst.cpp +++ b/src/tokenst.cpp @@ -16,7 +16,7 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include #ifdef WIN32 #pragma warning (disable : 4786) diff --git a/src/transform.cpp b/src/transform.cpp index e70d7ce3c..1a15554f2 100644 --- a/src/transform.cpp +++ b/src/transform.cpp @@ -15,9 +15,9 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include -#include "mol.h" +#include using namespace std; namespace OpenBabel diff --git a/src/typer.cpp b/src/typer.cpp index 6df670b0e..e0d8b408e 100644 --- a/src/typer.cpp +++ b/src/typer.cpp @@ -16,10 +16,11 @@ but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ***********************************************************************/ -#include "babelconfig.h" +#include + +#include +#include -#include "mol.h" -#include "typer.h" #include "atomtyp.h" #include "aromatic.h" diff --git a/test/Makefile.am b/test/Makefile.am index 2c8e4e83c..e74f1281e 100644 --- a/test/Makefile.am +++ b/test/Makefile.am @@ -20,7 +20,7 @@ endif LDADD = ../src/libopenbabel.la @LIBDL@ TESTDATADIR = $(top_srcdir)/test/files/ -AM_CPPFLAGS = -I$(top_srcdir)/src -DTESTDATADIR="\"$(TESTDATADIR)\"" +AM_CPPFLAGS = -I$(top_srcdir)/include -DTESTDATADIR="\"$(TESTDATADIR)\"" EXTRA_DIST = files wrapper.sh cml.sh test-set.sh \ aromatic.pl diff --git a/test/Makefile.in b/test/Makefile.in index 67beeae9a..39bd8ce33 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -331,7 +331,7 @@ SUBDIRS = cmltest @PERL_TESTS_TRUE@TESTS = wrapper.sh LDADD = ../src/libopenbabel.la @LIBDL@ TESTDATADIR = $(top_srcdir)/test/files/ -AM_CPPFLAGS = -I$(top_srcdir)/src -DTESTDATADIR="\"$(TESTDATADIR)\"" +AM_CPPFLAGS = -I$(top_srcdir)/include -DTESTDATADIR="\"$(TESTDATADIR)\"" EXTRA_DIST = files wrapper.sh cml.sh test-set.sh \ aromatic.pl diff --git a/test/aromatest.cpp b/test/aromatest.cpp index caf29b3a0..e6ebbc3b7 100644 --- a/test/aromatest.cpp +++ b/test/aromatest.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #if !HAVE_STRNCASECMP extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); diff --git a/test/atom.cpp b/test/atom.cpp index 7285668b3..d93e641bd 100644 --- a/test/atom.cpp +++ b/test/atom.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include #include diff --git a/test/bond.cpp b/test/bond.cpp index 5a201c2e3..92a5459c1 100644 --- a/test/bond.cpp +++ b/test/bond.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include #include diff --git a/test/conversion.cpp b/test/conversion.cpp index 8e0da4ec3..d7efde08c 100644 --- a/test/conversion.cpp +++ b/test/conversion.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include #include diff --git a/test/data.cpp b/test/data.cpp index d0814e5cc..8d7c20c24 100644 --- a/test/data.cpp +++ b/test/data.cpp @@ -21,14 +21,14 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include #include #include -#include "mol.h" -#include "data.h" +#include +#include using namespace std; using namespace OpenBabel; diff --git a/test/formalcharge.cpp b/test/formalcharge.cpp index 49f303fdf..a04c9f9fe 100644 --- a/test/formalcharge.cpp +++ b/test/formalcharge.cpp @@ -21,12 +21,12 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "obconversion.h" +#include +#include namespace OpenBabel { diff --git a/test/format.cpp b/test/format.cpp index 1c28c7f72..caf56aa82 100644 --- a/test/format.cpp +++ b/test/format.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include #include diff --git a/test/formula.cpp b/test/formula.cpp index cb80d07c7..9150df344 100644 --- a/test/formula.cpp +++ b/test/formula.cpp @@ -21,12 +21,12 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "obconversion.h" +#include +#include namespace OpenBabel { diff --git a/test/internalcoord.cpp b/test/internalcoord.cpp index 5ea401fcb..47ec43135 100644 --- a/test/internalcoord.cpp +++ b/test/internalcoord.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include #include diff --git a/test/invalidsmarts.cpp b/test/invalidsmarts.cpp index 674a76c8e..6ed20d80a 100644 --- a/test/invalidsmarts.cpp +++ b/test/invalidsmarts.cpp @@ -21,11 +21,11 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include -#include "mol.h" +#include namespace OpenBabel { diff --git a/test/invalidsmiles.cpp b/test/invalidsmiles.cpp index 3e2131ef4..08660a90f 100644 --- a/test/invalidsmiles.cpp +++ b/test/invalidsmiles.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include diff --git a/test/iterators.cpp b/test/iterators.cpp index f0bf131f7..543223aa5 100644 --- a/test/iterators.cpp +++ b/test/iterators.cpp @@ -22,13 +22,13 @@ #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include -#include "obiter.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include namespace OpenBabel { diff --git a/test/math.cpp b/test/math.cpp index 5d020b0a7..bc4955cf8 100644 --- a/test/math.cpp +++ b/test/math.cpp @@ -23,9 +23,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "math/matrix3x3.h" -#include "obutil.h" +#include +#include +#include #include #include diff --git a/test/mol.cpp b/test/mol.cpp index 77048f6d8..180d15fc9 100644 --- a/test/mol.cpp +++ b/test/mol.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include #include diff --git a/test/residue.cpp b/test/residue.cpp index 48c5e9ebb..ce538bbd8 100644 --- a/test/residue.cpp +++ b/test/residue.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #include #include diff --git a/test/ringtest.cpp b/test/ringtest.cpp index 1df5f10b3..066c97b2e 100644 --- a/test/ringtest.cpp +++ b/test/ringtest.cpp @@ -22,12 +22,12 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "obconversion.h" +#include +#include namespace OpenBabel { diff --git a/test/roundtrip.cpp b/test/roundtrip.cpp index 7adee283b..d0294639e 100644 --- a/test/roundtrip.cpp +++ b/test/roundtrip.cpp @@ -22,10 +22,10 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "data.h" -#include "obconversion.h" +#include +#include +#include +#include #if !HAVE_STRNCASECMP extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); diff --git a/test/smartstest.cpp b/test/smartstest.cpp index 2693a4436..e2eaa7e13 100644 --- a/test/smartstest.cpp +++ b/test/smartstest.cpp @@ -22,12 +22,12 @@ #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "obconversion.h" +#include +#include namespace OpenBabel { diff --git a/test/smilesmatch.cpp b/test/smilesmatch.cpp index c3fb30e16..e0ef445fc 100644 --- a/test/smilesmatch.cpp +++ b/test/smilesmatch.cpp @@ -22,12 +22,12 @@ #define USING_OBDLL #endif -#include "babelconfig.h" +#include #include -#include "mol.h" -#include "obconversion.h" +#include +#include namespace OpenBabel { diff --git a/test/textbuffer.cpp b/test/textbuffer.cpp index 8135cc975..6a0e2abcc 100644 --- a/test/textbuffer.cpp +++ b/test/textbuffer.cpp @@ -21,11 +21,11 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "newlinebuf.h" +#include +#include #ifdef HAVE_LIBZ -#include "zipstream.h" +#include "../src/zipstream.h" #endif #include diff --git a/test/unitcell.cpp b/test/unitcell.cpp index 5b4800073..d048a41cb 100644 --- a/test/unitcell.cpp +++ b/test/unitcell.cpp @@ -19,10 +19,10 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include -#include "mol.h" -#include "math/matrix3x3.h" +#include +#include namespace OpenBabel { diff --git a/tools/Makefile.am b/tools/Makefile.am index de0010402..b92ee99e7 100644 --- a/tools/Makefile.am +++ b/tools/Makefile.am @@ -31,4 +31,4 @@ obxyz_LDADD = ../src/libopenbabel.la @LIBDL@ # obdoc_SOURCES = obdoc.cpp # obdoc_LDADD = ../src/libopenbabel.la @LIBDL@ -AM_CPPFLAGS = -I$(top_srcdir)/src +AM_CPPFLAGS = -I$(top_srcdir)/include diff --git a/tools/Makefile.in b/tools/Makefile.in index 1457334a5..3a2c973e4 100644 --- a/tools/Makefile.in +++ b/tools/Makefile.in @@ -257,7 +257,7 @@ obxyz_LDADD = ../src/libopenbabel.la @LIBDL@ # obdoc_SOURCES = obdoc.cpp # obdoc_LDADD = ../src/libopenbabel.la @LIBDL@ -AM_CPPFLAGS = -I$(top_srcdir)/src +AM_CPPFLAGS = -I$(top_srcdir)/include all: all-am .SUFFIXES: diff --git a/tools/obchiral.cpp b/tools/obchiral.cpp index d04cc0892..466d0239d 100644 --- a/tools/obchiral.cpp +++ b/tools/obchiral.cpp @@ -21,12 +21,12 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include -#include "mol.h" -#include "obconversion.h" +#include +#include #include -#include "chiral.h" +#include using namespace std; using namespace OpenBabel; diff --git a/tools/obdoc.cpp b/tools/obdoc.cpp index c47905255..d61271ec5 100644 --- a/tools/obdoc.cpp +++ b/tools/obdoc.cpp @@ -22,9 +22,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include using namespace std; using namespace OpenBabel; diff --git a/tools/obfit.cpp b/tools/obfit.cpp index 74bde26b2..c147cd858 100644 --- a/tools/obfit.cpp +++ b/tools/obfit.cpp @@ -31,10 +31,10 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "parsmart.h" -#include "obconversion.h" +#include +#include +#include +#include #include diff --git a/tools/obgen.cpp b/tools/obgen.cpp index ef9c37cea..e2c51ad5c 100644 --- a/tools/obgen.cpp +++ b/tools/obgen.cpp @@ -23,10 +23,10 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "base.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include +#include #include using namespace std; diff --git a/tools/obgrep.cpp b/tools/obgrep.cpp index e67bafbe6..1e3b36907 100644 --- a/tools/obgrep.cpp +++ b/tools/obgrep.cpp @@ -22,11 +22,11 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include -#include "mol.h" -#include "obconversion.h" -#include "parsmart.h" +#include +#include +#include #ifdef _WIN32 typedef char TCHAR; diff --git a/tools/obprop.cpp b/tools/obprop.cpp index 15c9ff270..8f43ad5e1 100644 --- a/tools/obprop.cpp +++ b/tools/obprop.cpp @@ -23,10 +23,10 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include -#include "mol.h" -#include "obconversion.h" +#include +#include #include using namespace std; diff --git a/tools/obrotamer.cpp b/tools/obrotamer.cpp index 60ff253fc..9300b4aa2 100644 --- a/tools/obrotamer.cpp +++ b/tools/obrotamer.cpp @@ -21,13 +21,13 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include -#include "rotamer.h" -#include "rotor.h" -#include "obutil.h" +#include +#include +#include #include #include diff --git a/tools/obrotate.cpp b/tools/obrotate.cpp index 5d3092f2f..ad85a4757 100644 --- a/tools/obrotate.cpp +++ b/tools/obrotate.cpp @@ -33,12 +33,12 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "parsmart.h" -#include "rotamer.h" +#include +#include +#include +#include //#include -#include "obconversion.h" +#include using namespace std; using namespace OpenBabel; diff --git a/tools/obseq.cpp b/tools/obseq.cpp index 39ce7555b..7f3b67244 100644 --- a/tools/obseq.cpp +++ b/tools/obseq.cpp @@ -21,9 +21,9 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" -#include "mol.h" -#include "obconversion.h" +#include +#include +#include #if !HAVE_STRNCASECMP extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); diff --git a/tools/obxyz.cpp b/tools/obxyz.cpp index e712fdb2f..a5d87b4b4 100644 --- a/tools/obxyz.cpp +++ b/tools/obxyz.cpp @@ -22,11 +22,11 @@ GNU General Public License for more details. #define USING_OBDLL #endif -#include "babelconfig.h" +#include -#include "mol.h" -#include "math/matrix3x3.h" -#include "obconversion.h" +#include +#include +#include using namespace std; using namespace OpenBabel;