Fix patch to actually apply:
omit the scripts/Makefile.in hunks, we run autoreconf anyway, omit the scripts/perl/Makefile.PL hunk which is unrelated and unnecessary.
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@ -228,109 +228,6 @@ Index: scripts/python/openbabel.py
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+import obcore
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+import obconversion
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+import obtemplate
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Index: scripts/Makefile.in
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===================================================================
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--- scripts/Makefile.in (revision 2534)
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+++ scripts/Makefile.in (revision 2535)
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@@ -34,8 +34,12 @@
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subdir = scripts
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DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
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ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
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-am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
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- $(top_srcdir)/configure.in
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+am__aclocal_m4_deps = $(top_srcdir)/autoconf/libtool.m4 \
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+ $(top_srcdir)/autoconf/ltoptions.m4 \
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+ $(top_srcdir)/autoconf/ltsugar.m4 \
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+ $(top_srcdir)/autoconf/ltversion.m4 \
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+ $(top_srcdir)/autoconf/lt~obsolete.m4 \
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+ $(top_srcdir)/acinclude.m4 $(top_srcdir)/configure.in
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am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
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$(ACLOCAL_M4)
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mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
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@@ -89,6 +93,7 @@
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LIBOBJS = @LIBOBJS@
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LIBS = @LIBS@
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LIBTOOL = @LIBTOOL@
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+LIPO = @LIPO@
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LN_S = @LN_S@
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LTLIBOBJS = @LTLIBOBJS@
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MAINT = @MAINT@
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@@ -98,6 +103,8 @@
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NMEDIT = @NMEDIT@
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OBJDUMP = @OBJDUMP@
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OBJEXT = @OBJEXT@
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+OTOOL = @OTOOL@
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+OTOOL64 = @OTOOL64@
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PACKAGE = @PACKAGE@
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PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
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PACKAGE_NAME = @PACKAGE_NAME@
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@@ -173,6 +180,7 @@
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srcdir = @srcdir@
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sysconfdir = @sysconfdir@
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target_alias = @target_alias@
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+top_build_prefix = @top_build_prefix@
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top_builddir = @top_builddir@
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top_srcdir = @top_srcdir@
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EXTRA_DIST = openbabel-perl.i perl \
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@@ -185,9 +193,11 @@
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# build the scripting language interfaces if --enable-maintainer-mode was set
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# and SWIG is available -- please use the most recent version of SWIG
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@BUILT_SOURCES = perl/openbabel_perl.cpp \
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ python/openbabel_python.cpp \
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ java/openbabel_java.cpp \
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ csharp/openbabel_csharp.cpp \
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ python/obcore.cpp \
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ python/obconversion.cpp \
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ python/obtemplate.cpp \
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(am__append_1)
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_includes = $(top_srcdir)/include/openbabel
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \
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@@ -386,20 +396,18 @@
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" <perl/OpenBabel.pm >perl/OpenBabel.new;
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ mv perl/OpenBabel.new perl/OpenBabel.pm;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/openbabel_python.cpp: openbabel-python.i $(script_headers)
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obconversion.cpp: openbabel-python2.i $(script_headers)
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -small -O -python -templatereduce -naturalvar \
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo "import sys" >python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo "if sys.platform.find(\"linux\") != -1:" >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo " try:" >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo " import dl" >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo " except ImportError:" >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo " import DLFCN as dl" >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo " sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ echo >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ cat python/openbabel.py >>python/ob.py;
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-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ mv python/ob.py python/openbabel.py;
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obtemplate.cpp: openbabel-python3.i $(script_headers)
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -small -O -python -templatereduce -naturalvar \
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
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+
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obcore.cpp: openbabel-python.i $(script_headers)
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -small -O -python -templatereduce -naturalvar \
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+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
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+
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@java/openbabel_java.cpp: openbabel-java.i $(script_headers)
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -small -O -java -naturalvar -templatereduce -c++ -o $@ \
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@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
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Index: scripts/perl/Makefile.PL
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===================================================================
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--- scripts/perl/Makefile.PL (revision 2534)
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+++ scripts/perl/Makefile.PL (revision 2535)
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@@ -9,9 +9,9 @@
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# check if we're compiling in the source directory
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$ldfrom = "\$(OBJECT) -L$srcdir/.libs -lopenbabel -lz"
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+ if (-r "$srcdir/.libs/libopenbabel.dylib") and (-s _) and (-B _);
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+$ldfrom = "\$(OBJECT) -L$srcdir/.libs -lopenbabel -lz"
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if (-r "$srcdir/.libs/libopenbabel.so") and (-s _) and (-B _);
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-$ldfrom = "\$(OBJECT) -L$srcdir/.libs -lopenbabel -lz"
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- if (-r "$srcdir/.libs/libopenbabel.dylib") and (-s _) and (-B _);
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$ldfrom = "\$(OBJECT) $srcdir/.libs/libopenbabel.a -lz"
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if (-r "$srcdir/.libs/libopenbabel.a") and (-s _) and (-B _);
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Index: scripts/Makefile.am
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===================================================================
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--- scripts/Makefile.am (revision 2534)
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