Index: scripts/openbabel-python2.i
===================================================================
--- scripts/openbabel-python2.i	(revision 0)
+++ scripts/openbabel-python2.i	(revision 2535)
@@ -0,0 +1,92 @@
+%module obconversion
+
+%{
+// used to set import/export for Cygwin DLLs
+#ifdef WIN32
+#define USING_OBDLL
+#endif
+
+#include <openbabel/base.h>
+
+#include <openbabel/generic.h>
+#include <openbabel/griddata.h>
+#include <openbabel/math/vector3.h>
+#include <openbabel/bitvec.h>
+
+#include <openbabel/mol.h>
+#include <openbabel/obconversion.h>
+#include <openbabel/oberror.h>
+#include <openbabel/plugin.h>
+#include <openbabel/fingerprint.h>
+#include <openbabel/descriptor.h>
+#include <openbabel/format.h>
+#include <openbabel/forcefield.h>
+#include <openbabel/op.h>
+
+%}
+
+// These methods are renamed to valid Python method names, as otherwise
+// they cannot be used from Python
+%rename(inc)   *::operator++;
+%rename(good)  *::operator bool;
+
+%import <openbabel/babelconfig.h>
+
+%import <openbabel/base.h>
+%import <openbabel/generic.h>
+%import <openbabel/griddata.h>
+
+%import <openbabel/math/vector3.h>
+%import <openbabel/bitvec.h>
+
+%import <openbabel/chains.h>
+%import <openbabel/typer.h>
+
+%include <openbabel/plugin.h>
+%include <openbabel/oberror.h>
+%include <openbabel/format.h>
+%include <openbabel/obconversion.h>
+%import <openbabel/residue.h>
+%import <openbabel/internalcoord.h>
+%import <openbabel/atom.h>
+%import <openbabel/bond.h>
+%import <openbabel/mol.h>
+%import <openbabel/ring.h>
+%import <openbabel/parsmart.h>
+
+%include <openbabel/fingerprint.h>
+%include <openbabel/descriptor.h>
+%include <openbabel/forcefield.h>
+
+%include <openbabel/op.h>
+%include <openbabel/bitvec.h>
+
+%ignore *::operator=;
+
+%include "carrays.i"
+%array_class(double, doubleArray)
+%pythoncode %{
+def double_array(mylist):
+    """Create a C array of doubles from a list."""
+    c = doubleArray(len(mylist))
+    for i,v in enumerate(mylist):
+        c[i] = v
+    return c
+%}
+
+# Functions to set the log file to std::cout and std::cerr
+       
+%ignore OBForceField::SetLogFile(std::ostream *pos);
+%extend OpenBabel::OBForceField {
+  void SetLogToStdOut() 
+  {
+    self->SetLogFile(&std::cout);
+  }
+
+  void SetLogToStdErr() 
+  {
+    self->SetLogFile(&std::cerr);
+  }
+};    
+
+
Index: scripts/openbabel-python3.i
===================================================================
--- scripts/openbabel-python3.i	(revision 0)
+++ scripts/openbabel-python3.i	(revision 2535)
@@ -0,0 +1,65 @@
+%module obtemplate
+
+%{
+// used to set import/export for Cygwin DLLs
+#ifdef WIN32
+#define USING_OBDLL
+#endif
+
+#include <openbabel/base.h>
+#include <openbabel/mol.h>
+#include <openbabel/atom.h>
+#include <openbabel/bond.h>
+#include <openbabel/residue.h>
+#include <openbabel/ring.h>
+
+%}
+
+%include "std_list.i"
+%include "std_map.i"
+%include "std_vector.i"
+%include "std_string.i"
+
+namespace std {
+%template (vectorInt)		  vector<int>;
+%template (vectorUnsignedInt)     vector<unsigned int>;
+%template (vvInt)		      vector< vector<int> >;
+%template (vectorDouble) 	vector<double>;
+%template (vectorString)		  vector<std::string>;
+%template (vVector3)		  vector<OpenBabel::vector3>;
+
+%template (vectorMol)		  vector<OpenBabel::OBMol>;
+%template (vectorBond)		vector<OpenBabel::OBBond>;
+%template (vectorResidue)	vector<OpenBabel::OBResidue>;
+%template (vectorRing)		vector<OpenBabel::OBRing>;
+%template (vectorpRing)		vector<OpenBabel::OBRing*>;
+%template (vectorData)    vector<OpenBabel::OBGenericData*>;
+}
+
+// These methods are renamed to valid Python method names, as otherwise
+// they cannot be used from Python
+%rename(inc)   *::operator++;
+%rename(good)  *::operator bool;
+
+%import <openbabel/babelconfig.h>
+
+%import <openbabel/base.h>
+%import <openbabel/residue.h>
+%import <openbabel/atom.h>
+%import <openbabel/bond.h>
+%import <openbabel/mol.h>
+%import <openbabel/ring.h>
+
+%ignore *::operator=;
+
+%include "carrays.i"
+%array_class(double, doubleArray)
+%pythoncode %{
+def double_array(mylist):
+    """Create a C array of doubles from a list."""
+    c = doubleArray(len(mylist))
+    for i,v in enumerate(mylist):
+        c[i] = v
+    return c
+%}
+
Index: scripts/python/setup.py
===================================================================
--- scripts/python/setup.py	(revision 2534)
+++ scripts/python/setup.py	(revision 2535)
@@ -60,13 +60,27 @@
 
 OBinclude,OBlibrary = find_likely_directory()
 
-obExtension = Extension('_openbabel',
-                        ['openbabel_python.cpp'],
-                        include_dirs=OBinclude,
-                        library_dirs=OBlibrary,
-                        libraries=['openbabel']
-                        )
+obCore = Extension('_obcore',
+                   ['obcore.cpp'],
+                   include_dirs=OBinclude,
+                   library_dirs=OBlibrary,
+                   libraries=['openbabel']
+                   )
 
+obConversion = Extension('_obconversion',
+                         ['obconversion.cpp'],
+                         include_dirs=OBinclude,
+                         library_dirs=OBlibrary,
+                         libraries=['openbabel']
+                         )
+
+obTemplate = Extension('_obtemplate',
+                       ['obtemplate.cpp'],
+                       include_dirs=OBinclude,
+                       library_dirs=OBlibrary,
+                       libraries=['openbabel']
+                       )
+
 setup(name='openbabel',
       version='1.3',
       author='Noel O\'Boyle',
@@ -74,7 +88,7 @@
       url='http://openbabel.sourceforge.net/',
       license='http://www.gnu.org/copyleft/gpl.html',
       py_modules=['openbabel','pybel'],
-      ext_modules=[obExtension],
+      ext_modules=[obCore, obConversion, obTemplate],
       description = 'openbabel: Python interface to the Open Babel chemistry library',
       classifiers=[
       'Development Status :: 5 - Production/Stable',
Index: scripts/python/openbabel.py
===================================================================
--- scripts/python/openbabel.py	(revision 0)
+++ scripts/python/openbabel.py	(revision 2535)
@@ -0,0 +1,11 @@
+import sys
+if sys.platform.find("linux") != -1:
+    try:
+        import dl
+    except ImportError:
+        import DLFCN as dl
+    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
+
+import obcore
+import obconversion
+import obtemplate
Index: scripts/Makefile.am
===================================================================
--- scripts/Makefile.am	(revision 2534)
+++ scripts/Makefile.am	(revision 2535)
@@ -20,8 +20,9 @@
 
 if MAINTAINER_MODE
 if BUILD_SWIG
-BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
-	java/openbabel_java.cpp
+BUILT_SOURCES = perl/openbabel_perl.cpp \
+	java/openbabel_java.cpp \
+	python/obcore.cpp python/obconversion.cpp python/obtemplate.cpp
 
 script_includes = $(top_srcdir)/include/openbabel
 script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \
@@ -34,20 +35,18 @@
 	sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" <perl/OpenBabel.pm >perl/OpenBabel.new;
 	mv perl/OpenBabel.new perl/OpenBabel.pm;
 
-python/openbabel_python.cpp: openbabel-python.i $(script_headers)
-	$(SWIG) -python -modern -naturalvar -fastinit \
+python/obconversion.cpp: openbabel-python2.i $(script_headers)
+	$(SWIG) -small -O -python -templatereduce -naturalvar \
 		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
-	echo "import sys" >python/ob.py;
-	echo "if sys.platform.find(\"linux\") != -1:"  >>python/ob.py;
-	echo "    try:" >>python/ob.py;
-	echo "        import dl" >>python/ob.py;
-	echo "    except ImportError:" >>python/ob.py;
-	echo "        import DLFCN as dl" >>python/ob.py;
-	echo "    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >>python/ob.py;
-	echo >>python/ob.py;
-	cat python/openbabel.py >>python/ob.py;
-	mv python/ob.py python/openbabel.py;
 
+python/obtemplate.cpp: openbabel-python3.i $(script_headers)
+	$(SWIG) -small -O -python -templatereduce -naturalvar \
+		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
+
+python/obcore.cpp: openbabel-python.i $(script_headers)
+	$(SWIG) -small -O -python -templatereduce -naturalvar \
+		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
+
 java/openbabel_java.cpp: openbabel-java.i $(script_headers)
 	$(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/include \
   -I$(top_builddir)/include $<;
Index: scripts/openbabel-python.i
===================================================================
--- scripts/openbabel-python.i	(revision 2534)
+++ scripts/openbabel-python.i	(revision 2535)
@@ -1,4 +1,4 @@
-%module openbabel
+%module obcore
 
 %{
 // used to set import/export for Cygwin DLLs
@@ -41,28 +41,6 @@
 
 %}
 
-%include "std_list.i"
-%include "std_map.i"
-%include "std_vector.i"
-%include "std_string.i"
-
-namespace std {
-%template (vectorInt)		  vector<int>;
-%template (vectorUnsignedInt)     vector<unsigned int>;
-%template (vvInt)		      vector< vector<int> >;
-%template (vectorDouble) 	vector<double>;
-%template (vectorString)		  vector<std::string>;
-%template (vVector3)		  vector<OpenBabel::vector3>;
-
-%template (vectorMol)		  vector<OpenBabel::OBMol>;
-%template (vectorBond)		vector<OpenBabel::OBBond>;
-%template (vectorResidue)	vector<OpenBabel::OBResidue>;
-%template (vectorRing)		vector<OpenBabel::OBRing>;
-%template (vectorpRing)		vector<OpenBabel::OBRing*>;
-%template (vectorData)    vector<OpenBabel::OBGenericData*>;
-}
-
-
 %inline %{
 OpenBabel::OBPairData *toPairData(OpenBabel::OBGenericData *data) {
 	return (OpenBabel::OBPairData *) data;
@@ -95,11 +73,11 @@
 //# %import <openbabel/bitvec.h>
 %import <openbabel/typer.h>
 
-%include <openbabel/plugin.h>
+%import <openbabel/plugin.h>
 
-%include <openbabel/oberror.h>
-%include <openbabel/format.h>
-%include <openbabel/obconversion.h>
+%import <openbabel/oberror.h>
+%import <openbabel/format.h>
+%import <openbabel/obconversion.h>
 %include <openbabel/residue.h>
 %include <openbabel/internalcoord.h>
 %include <openbabel/atom.h>
@@ -110,11 +88,11 @@
 %include <openbabel/alias.h>
 %include <openbabel/atomclass.h>
 
-%include <openbabel/fingerprint.h>
-%include <openbabel/descriptor.h>
-%include <openbabel/forcefield.h>
+%import <openbabel/fingerprint.h>
+%import <openbabel/descriptor.h>
+%import <openbabel/forcefield.h>
 
-%include <openbabel/op.h>
+%import <openbabel/op.h>
 
 %include <openbabel/bitvec.h>