diff --git a/scripts/perl/openbabel_perl.cpp b/scripts/perl/openbabel_perl.cpp
index 129f0111f..ede08615e 100644
--- a/scripts/perl/openbabel_perl.cpp
+++ b/scripts/perl/openbabel_perl.cpp
@@ -20268,35 +20268,37 @@ XS(_wrap_OBBase_HasData__SWIG_0) {
     bool result;
     void *argp1 = 0 ;
     int res1 = 0 ;
-    void *argp2 = 0 ;
-    int res2 = 0 ;
+    int res2 = SWIG_OLDOBJ ;
     int argvi = 0;
     dXSARGS;
     
     if ((items < 2) || (items > 2)) {
-      SWIG_croak("Usage: OBBase_HasData(self,std::string &);");
+      SWIG_croak("Usage: OBBase_HasData(self,std::string const &);");
     }
     res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBBase, 0 |  0 );
     if (!SWIG_IsOK(res1)) {
       SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_HasData" "', argument " "1"" of type '" "OpenBabel::OBBase *""'"); 
     }
     arg1 = reinterpret_cast< OpenBabel::OBBase * >(argp1);
-    res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_std__string,  0 );
-    if (!SWIG_IsOK(res2)) {
-      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string &""'"); 
+    {
+      std::string *ptr = (std::string *)0;
+      res2 = SWIG_AsPtr_std_string SWIG_PERL_CALL_ARGS_2(ST(1), &ptr);
+      if (!SWIG_IsOK(res2)) {
+        SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string const &""'"); 
+      }
+      if (!ptr) {
+        SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string const &""'"); 
+      }
+      arg2 = ptr;
     }
-    if (!argp2) {
-      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string &""'"); 
-    }
-    arg2 = reinterpret_cast< std::string * >(argp2);
-    result = (bool)(arg1)->HasData(*arg2);
+    result = (bool)(arg1)->HasData((std::string const &)*arg2);
     ST(argvi) = SWIG_From_bool  SWIG_PERL_CALL_ARGS_1(static_cast< bool >(result)); argvi++ ;
     
-    
+    if (SWIG_IsNewObj(res2)) delete arg2;
     XSRETURN(argvi);
   fail:
     
-    
+    if (SWIG_IsNewObj(res2)) delete arg2;
     SWIG_croak_null();
   }
 }
@@ -20400,9 +20402,10 @@ XS(_wrap_OBBase_HasData) {
       _rankm += _pi;
       _pi *= SWIG_MAXCASTRANK;
       {
-        void *vptr = 0;
-        int res = SWIG_ConvertPtr(ST(1), &vptr, SWIGTYPE_p_std__string, 0);
-        _v = SWIG_CheckState(res);
+        {
+          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), NULL);
+          _v = SWIG_CheckState(res);
+        }
       }
       if (!_v) goto check_1;
       _ranki += _v*_pi;
@@ -20430,10 +20433,8 @@ XS(_wrap_OBBase_HasData) {
       _rankm += _pi;
       _pi *= SWIG_MAXCASTRANK;
       {
-        {
-          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), NULL);
-          _v = SWIG_CheckState(res);
-        }
+        int res = SWIG_AsPtr_std_string SWIG_PERL_CALL_ARGS_2(ST(1), (std::string**)(0));
+        _v = SWIG_CheckState(res);
       }
       if (!_v) goto check_2;
       _ranki += _v*_pi;
@@ -20478,9 +20479,9 @@ XS(_wrap_OBBase_HasData) {
   dispatch:
     switch(_index) {
     case 1:
-      ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_HasData__SWIG_0); return;
-    case 2:
       ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_HasData__SWIG_2); return;
+    case 2:
+      ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_HasData__SWIG_0); return;
     case 3:
       ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_HasData__SWIG_1); return;
     }
@@ -20769,10 +20770,10 @@ XS(_wrap_OBBase_DataSize) {
     }
     res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBBase, 0 |  0 );
     if (!SWIG_IsOK(res1)) {
-      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_DataSize" "', argument " "1"" of type '" "OpenBabel::OBBase *""'"); 
+      SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_DataSize" "', argument " "1"" of type '" "OpenBabel::OBBase const *""'"); 
     }
     arg1 = reinterpret_cast< OpenBabel::OBBase * >(argp1);
-    result = (unsigned int)(arg1)->DataSize();
+    result = (unsigned int)((OpenBabel::OBBase const *)arg1)->DataSize();
     ST(argvi) = SWIG_From_unsigned_SS_int  SWIG_PERL_CALL_ARGS_1(static_cast< unsigned int >(result)); argvi++ ;
     
     XSRETURN(argvi);
@@ -20828,35 +20829,37 @@ XS(_wrap_OBBase_GetData__SWIG_1) {
     OpenBabel::OBGenericData *result = 0 ;
     void *argp1 = 0 ;
     int res1 = 0 ;
-    void *argp2 = 0 ;
-    int res2 = 0 ;
+    int res2 = SWIG_OLDOBJ ;
     int argvi = 0;
     dXSARGS;
     
     if ((items < 2) || (items > 2)) {
-      SWIG_croak("Usage: OBBase_GetData(self,std::string &);");
+      SWIG_croak("Usage: OBBase_GetData(self,std::string const &);");
     }
     res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBBase, 0 |  0 );
     if (!SWIG_IsOK(res1)) {
       SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_GetData" "', argument " "1"" of type '" "OpenBabel::OBBase *""'"); 
     }
     arg1 = reinterpret_cast< OpenBabel::OBBase * >(argp1);
-    res2 = SWIG_ConvertPtr(ST(1), &argp2, SWIGTYPE_p_std__string,  0 );
-    if (!SWIG_IsOK(res2)) {
-      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string &""'"); 
+    {
+      std::string *ptr = (std::string *)0;
+      res2 = SWIG_AsPtr_std_string SWIG_PERL_CALL_ARGS_2(ST(1), &ptr);
+      if (!SWIG_IsOK(res2)) {
+        SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string const &""'"); 
+      }
+      if (!ptr) {
+        SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string const &""'"); 
+      }
+      arg2 = ptr;
     }
-    if (!argp2) {
-      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string &""'"); 
-    }
-    arg2 = reinterpret_cast< std::string * >(argp2);
-    result = (OpenBabel::OBGenericData *)(arg1)->GetData(*arg2);
+    result = (OpenBabel::OBGenericData *)(arg1)->GetData((std::string const &)*arg2);
     ST(argvi) = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBGenericData, 0 | SWIG_SHADOW); argvi++ ;
     
-    
+    if (SWIG_IsNewObj(res2)) delete arg2;
     XSRETURN(argvi);
   fail:
     
-    
+    if (SWIG_IsNewObj(res2)) delete arg2;
     SWIG_croak_null();
   }
 }
@@ -20974,9 +20977,10 @@ XS(_wrap_OBBase_GetData) {
       _rankm += _pi;
       _pi *= SWIG_MAXCASTRANK;
       {
-        void *vptr = 0;
-        int res = SWIG_ConvertPtr(ST(1), &vptr, SWIGTYPE_p_std__string, 0);
-        _v = SWIG_CheckState(res);
+        {
+          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), NULL);
+          _v = SWIG_CheckState(res);
+        }
       }
       if (!_v) goto check_2;
       _ranki += _v*_pi;
@@ -21004,10 +21008,8 @@ XS(_wrap_OBBase_GetData) {
       _rankm += _pi;
       _pi *= SWIG_MAXCASTRANK;
       {
-        {
-          int res = SWIG_AsVal_unsigned_SS_int SWIG_PERL_CALL_ARGS_2(ST(1), NULL);
-          _v = SWIG_CheckState(res);
-        }
+        int res = SWIG_AsPtr_std_string SWIG_PERL_CALL_ARGS_2(ST(1), (std::string**)(0));
+        _v = SWIG_CheckState(res);
       }
       if (!_v) goto check_3;
       _ranki += _v*_pi;
@@ -21054,9 +21056,9 @@ XS(_wrap_OBBase_GetData) {
     case 1:
       ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_GetData__SWIG_3); return;
     case 2:
-      ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_GetData__SWIG_1); return;
-    case 3:
       ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_GetData__SWIG_0); return;
+    case 3:
+      ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_GetData__SWIG_1); return;
     case 4:
       ++PL_markstack_ptr; SWIG_CALLXS(_wrap_OBBase_GetData__SWIG_2); return;
     }
@@ -28016,7 +28018,7 @@ XS(_wrap_OBResidue_GetBonds__SWIG_0) {
     dXSARGS;
     
     if ((items < 2) || (items > 2)) {
-      SWIG_croak("Usage: OBResidue_GetBonds(self,bool);");
+      SWIG_croak("Usage: OBResidue_GetBonds(self,exterior);");
     }
     res1 = SWIG_ConvertPtr(ST(0), &argp1,SWIGTYPE_p_OpenBabel__OBResidue, 0 |  0 );
     if (!SWIG_IsOK(res1)) {
diff --git a/scripts/python/openbabel_python.cpp b/scripts/python/openbabel_python.cpp
index ae6416567..66faeefa7 100644
--- a/scripts/python/openbabel_python.cpp
+++ b/scripts/python/openbabel_python.cpp
@@ -30922,8 +30922,7 @@ SWIGINTERN PyObject *_wrap_OBBase_HasData__SWIG_0(PyObject *SWIGUNUSEDPARM(self)
   bool result;
   void *argp1 = 0 ;
   int res1 = 0 ;
-  void *argp2 = 0 ;
-  int res2 = 0 ;
+  int res2 = SWIG_OLDOBJ ;
   PyObject * obj0 = 0 ;
   PyObject * obj1 = 0 ;
   
@@ -30933,18 +30932,23 @@ SWIGINTERN PyObject *_wrap_OBBase_HasData__SWIG_0(PyObject *SWIGUNUSEDPARM(self)
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_HasData" "', argument " "1"" of type '" "OpenBabel::OBBase *""'"); 
   }
   arg1 = reinterpret_cast< OpenBabel::OBBase * >(argp1);
-  res2 = SWIG_ConvertPtr(obj1, &argp2, SWIGTYPE_p_std__string,  0 );
-  if (!SWIG_IsOK(res2)) {
-    SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string &""'"); 
+  {
+    std::string *ptr = (std::string *)0;
+    res2 = SWIG_AsPtr_std_string(obj1, &ptr);
+    if (!SWIG_IsOK(res2)) {
+      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string const &""'"); 
+    }
+    if (!ptr) {
+      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string const &""'"); 
+    }
+    arg2 = ptr;
   }
-  if (!argp2) {
-    SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_HasData" "', argument " "2"" of type '" "std::string &""'"); 
-  }
-  arg2 = reinterpret_cast< std::string * >(argp2);
-  result = (bool)(arg1)->HasData(*arg2);
+  result = (bool)(arg1)->HasData((std::string const &)*arg2);
   resultobj = SWIG_From_bool(static_cast< bool >(result));
+  if (SWIG_IsNewObj(res2)) delete arg2;
   return resultobj;
 fail:
+  if (SWIG_IsNewObj(res2)) delete arg2;
   return NULL;
 }
 
@@ -31030,11 +31034,12 @@ SWIGINTERN PyObject *_wrap_OBBase_HasData(PyObject *self, PyObject *args) {
     int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBBase, 0);
     _v = SWIG_CheckState(res);
     if (_v) {
-      void *vptr = 0;
-      int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_std__string, 0);
-      _v = SWIG_CheckState(res);
+      {
+        int res = SWIG_AsVal_unsigned_SS_int(argv[1], NULL);
+        _v = SWIG_CheckState(res);
+      }
       if (_v) {
-        return _wrap_OBBase_HasData__SWIG_0(self, args);
+        return _wrap_OBBase_HasData__SWIG_2(self, args);
       }
     }
   }
@@ -31044,12 +31049,10 @@ SWIGINTERN PyObject *_wrap_OBBase_HasData(PyObject *self, PyObject *args) {
     int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBBase, 0);
     _v = SWIG_CheckState(res);
     if (_v) {
-      {
-        int res = SWIG_AsVal_unsigned_SS_int(argv[1], NULL);
-        _v = SWIG_CheckState(res);
-      }
+      int res = SWIG_AsPtr_std_string(argv[1], (std::string**)(0));
+      _v = SWIG_CheckState(res);
       if (_v) {
-        return _wrap_OBBase_HasData__SWIG_2(self, args);
+        return _wrap_OBBase_HasData__SWIG_0(self, args);
       }
     }
   }
@@ -31267,10 +31270,10 @@ SWIGINTERN PyObject *_wrap_OBBase_DataSize(PyObject *SWIGUNUSEDPARM(self), PyObj
   if(!PyArg_UnpackTuple(args,(char *)"OBBase_DataSize",1,1,&obj0)) SWIG_fail;
   res1 = SWIG_ConvertPtr(obj0, &argp1,SWIGTYPE_p_OpenBabel__OBBase, 0 |  0 );
   if (!SWIG_IsOK(res1)) {
-    SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_DataSize" "', argument " "1"" of type '" "OpenBabel::OBBase *""'"); 
+    SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_DataSize" "', argument " "1"" of type '" "OpenBabel::OBBase const *""'"); 
   }
   arg1 = reinterpret_cast< OpenBabel::OBBase * >(argp1);
-  result = (unsigned int)(arg1)->DataSize();
+  result = (unsigned int)((OpenBabel::OBBase const *)arg1)->DataSize();
   resultobj = SWIG_From_unsigned_SS_int(static_cast< unsigned int >(result));
   return resultobj;
 fail:
@@ -31316,8 +31319,7 @@ SWIGINTERN PyObject *_wrap_OBBase_GetData__SWIG_1(PyObject *SWIGUNUSEDPARM(self)
   OpenBabel::OBGenericData *result = 0 ;
   void *argp1 = 0 ;
   int res1 = 0 ;
-  void *argp2 = 0 ;
-  int res2 = 0 ;
+  int res2 = SWIG_OLDOBJ ;
   PyObject * obj0 = 0 ;
   PyObject * obj1 = 0 ;
   
@@ -31327,18 +31329,23 @@ SWIGINTERN PyObject *_wrap_OBBase_GetData__SWIG_1(PyObject *SWIGUNUSEDPARM(self)
     SWIG_exception_fail(SWIG_ArgError(res1), "in method '" "OBBase_GetData" "', argument " "1"" of type '" "OpenBabel::OBBase *""'"); 
   }
   arg1 = reinterpret_cast< OpenBabel::OBBase * >(argp1);
-  res2 = SWIG_ConvertPtr(obj1, &argp2, SWIGTYPE_p_std__string,  0 );
-  if (!SWIG_IsOK(res2)) {
-    SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string &""'"); 
+  {
+    std::string *ptr = (std::string *)0;
+    res2 = SWIG_AsPtr_std_string(obj1, &ptr);
+    if (!SWIG_IsOK(res2)) {
+      SWIG_exception_fail(SWIG_ArgError(res2), "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string const &""'"); 
+    }
+    if (!ptr) {
+      SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string const &""'"); 
+    }
+    arg2 = ptr;
   }
-  if (!argp2) {
-    SWIG_exception_fail(SWIG_ValueError, "invalid null reference " "in method '" "OBBase_GetData" "', argument " "2"" of type '" "std::string &""'"); 
-  }
-  arg2 = reinterpret_cast< std::string * >(argp2);
-  result = (OpenBabel::OBGenericData *)(arg1)->GetData(*arg2);
+  result = (OpenBabel::OBGenericData *)(arg1)->GetData((std::string const &)*arg2);
   resultobj = SWIG_NewPointerObj(SWIG_as_voidptr(result), SWIGTYPE_p_OpenBabel__OBGenericData, 0 |  0 );
+  if (SWIG_IsNewObj(res2)) delete arg2;
   return resultobj;
 fail:
+  if (SWIG_IsNewObj(res2)) delete arg2;
   return NULL;
 }
 
@@ -31427,11 +31434,12 @@ SWIGINTERN PyObject *_wrap_OBBase_GetData(PyObject *self, PyObject *args) {
     int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBBase, 0);
     _v = SWIG_CheckState(res);
     if (_v) {
-      void *vptr = 0;
-      int res = SWIG_ConvertPtr(argv[1], &vptr, SWIGTYPE_p_std__string, 0);
-      _v = SWIG_CheckState(res);
+      {
+        int res = SWIG_AsVal_unsigned_SS_int(argv[1], NULL);
+        _v = SWIG_CheckState(res);
+      }
       if (_v) {
-        return _wrap_OBBase_GetData__SWIG_1(self, args);
+        return _wrap_OBBase_GetData__SWIG_0(self, args);
       }
     }
   }
@@ -31441,12 +31449,10 @@ SWIGINTERN PyObject *_wrap_OBBase_GetData(PyObject *self, PyObject *args) {
     int res = SWIG_ConvertPtr(argv[0], &vptr, SWIGTYPE_p_OpenBabel__OBBase, 0);
     _v = SWIG_CheckState(res);
     if (_v) {
-      {
-        int res = SWIG_AsVal_unsigned_SS_int(argv[1], NULL);
-        _v = SWIG_CheckState(res);
-      }
+      int res = SWIG_AsPtr_std_string(argv[1], (std::string**)(0));
+      _v = SWIG_CheckState(res);
       if (_v) {
-        return _wrap_OBBase_GetData__SWIG_0(self, args);
+        return _wrap_OBBase_GetData__SWIG_1(self, args);
       }
     }
   }
diff --git a/src/base.cpp b/src/base.cpp
index d4b34e9b9..8de68f56c 100644
--- a/src/base.cpp
+++ b/src/base.cpp
@@ -2,7 +2,7 @@
 base.cpp - Base classes to build a graph
  
 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
-Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
+Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
  
 This file is part of the Open Babel project.
 For more information, see <http://openbabel.sourceforge.net/>
@@ -20,151 +20,142 @@ GNU General Public License for more details.
 #include "babelconfig.h"
 #include "base.h"
 
-#if HAVE_IOSTREAM
 #include <iostream>
-#elif HAVE_IOSTREAM_H
-#include <iostream.h>
-#endif
-
-#if HAVE_FSTREAM
 #include <fstream>
-#elif HAVE_FSTREAM_H
-#include <fstream.h>
-#endif
 
 using namespace std;
 
 //! Global namespace for all Open Babel code
 namespace OpenBabel
 {
-bool OBBase::HasData(string &s)
-{
+  bool OBBase::HasData(const string &s)
+  {
     if (_vdata.empty())
-        return(false);
+      return(false);
 
     vector<OBGenericData*>::iterator i;
 
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if ((*i)->GetAttribute() == s)
-            return(true);
+      if ((*i)->GetAttribute() == s)
+        return(true);
 
     return(false);
-}
+  }
 
-bool OBBase::HasData(const char *s)
-//returns true if the generic attribute/value pair exists
-{
+  bool OBBase::HasData(const char *s)
+    //returns true if the generic attribute/value pair exists
+  {
     if (_vdata.empty())
-        return(false);
+      return(false);
 
     vector<OBGenericData*>::iterator i;
 
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if ((*i)->GetAttribute() == s)
-            return(true);
+      if ((*i)->GetAttribute() == s)
+        return(true);
 
     return(false);
-}
+  }
 
 
-bool OBBase::HasData(unsigned int dt)
-//returns true if the generic attribute/value pair exists
-{
+  bool OBBase::HasData(const unsigned int dt)
+    //returns true if the generic attribute/value pair exists
+  {
     if (_vdata.empty())
-        return(false);
+      return(false);
 
     vector<OBGenericData*>::iterator i;
 
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if ((*i)->GetDataType() == dt)
-            return(true);
+      if ((*i)->GetDataType() == dt)
+        return(true);
 
     return(false);
-}
+  }
 
-//! Returns the value given an attribute name
-OBGenericData *OBBase::GetData(string &s)
-{
+  //! Returns the value given an attribute name
+  OBGenericData *OBBase::GetData(const string &s)
+  {
     vector<OBGenericData*>::iterator i;
 
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if ((*i)->GetAttribute() == s)
-            return(*i);
+      if ((*i)->GetAttribute() == s)
+        return(*i);
 
     return(NULL);
-}
+  }
 
-//! Returns the value given an attribute name
-OBGenericData *OBBase::GetData(const char *s)
-{
+  //! Returns the value given an attribute name
+  OBGenericData *OBBase::GetData(const char *s)
+  {
     vector<OBGenericData*>::iterator i;
 
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if ((*i)->GetAttribute() == s)
-            return(*i);
+      if ((*i)->GetAttribute() == s)
+        return(*i);
 
     return(NULL);
-}
+  }
 
-OBGenericData *OBBase::GetData(unsigned int dt)
-{
+  OBGenericData *OBBase::GetData(const unsigned int dt)
+  {
     vector<OBGenericData*>::iterator i;
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if ((*i)->GetDataType() == dt)
-            return(*i);
+      if ((*i)->GetDataType() == dt)
+        return(*i);
     return(NULL);
-}
+  }
 
-void OBBase::DeleteData(unsigned int dt)
-{
+  void OBBase::DeleteData(unsigned int dt)
+  {
     vector<OBGenericData*> vdata;
     vector<OBGenericData*>::iterator i;
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if ((*i)->GetDataType() == dt)
-            delete *i;
-        else
-            vdata.push_back(*i);
+      if ((*i)->GetDataType() == dt)
+        delete *i;
+      else
+        vdata.push_back(*i);
     _vdata = vdata;
-}
+  }
 
-void OBBase::DeleteData(vector<OBGenericData*> &vg)
-{
+  void OBBase::DeleteData(vector<OBGenericData*> &vg)
+  {
     vector<OBGenericData*> vdata;
     vector<OBGenericData*>::iterator i,j;
 
     bool del;
     for (i = _vdata.begin();i != _vdata.end();i++)
-    {
+      {
         del = false;
         for (j = vg.begin();j != vg.end();j++)
-            if (*i == *j)
+          if (*i == *j)
             {
-                del = true;
-                break;
+              del = true;
+              break;
             }
         if (del)
-            delete *i;
+          delete *i;
         else
-            vdata.push_back(*i);
-    }
+          vdata.push_back(*i);
+      }
     _vdata = vdata;
-}
+  }
 
-void OBBase::DeleteData(OBGenericData *gd)
-{
+  void OBBase::DeleteData(OBGenericData *gd)
+  {
     vector<OBGenericData*>::iterator i;
     for (i = _vdata.begin();i != _vdata.end();i++)
-        if (*i == gd)
+      if (*i == gd)
         {
-            delete *i;
-            _vdata.erase(i);
+          delete *i;
+          _vdata.erase(i);
         }
 
-}
+  }
 
-/*
-bool OBGraphBase::Match(OBGraphBase &g,bool singleMatch)
-{
+  /*
+    bool OBGraphBase::Match(OBGraphBase &g,bool singleMatch)
+    {
     SetFinishedMatch(false);
     SetSingleMatch(singleMatch);
     ClearMatches();
@@ -176,235 +167,235 @@ bool OBGraphBase::Match(OBGraphBase &g,bool singleMatch)
     vector<OBNodeBase*>::iterator i;
 
     for (node = g.Begin(i);node;node = g.Next(i))
-        if (!node->Visit && seed->Eval(node))
-        {
-            node->Visit = true;
-            seed->SetMatch(node);
-            Match(g,BgnMatch(),BgnMatch()->second.begin());
-            seed->SetMatch((OBNodeBase*)NULL);
-            node->Visit = false;
-            if (SingleMatch() && FinishedMatch())
-                break;
-        }
+    if (!node->Visit && seed->Eval(node))
+    {
+    node->Visit = true;
+    seed->SetMatch(node);
+    Match(g,BgnMatch(),BgnMatch()->second.begin());
+    seed->SetMatch((OBNodeBase*)NULL);
+    node->Visit = false;
+    if (SingleMatch() && FinishedMatch())
+    break;
+    }
 
     g.SetVisitLock(false);
 
     return(FinishedMatch());
-}
+    }
 
-bool OBGraphBase::Match(OBGraphBase &g,
-                        vector<pair<OBNodeBase*,vector<OBEdgeBase*> > >::iterator i,
-                        vector<OBEdgeBase*>::iterator j)
-{
+    bool OBGraphBase::Match(OBGraphBase &g,
+    vector<pair<OBNodeBase*,vector<OBEdgeBase*> > >::iterator i,
+    vector<OBEdgeBase*>::iterator j)
+    {
     //bail if only one match has been requested
     if (SingleMatch() && FinishedMatch())
-        return(true);
+    return(true);
 
     //full match completed
     if (i == EndMatch() || (j == i->second.end() && (i+1) == EndMatch()))
     {
-        SetFinishedMatch(true);
-        OBNodeBase *node;
-        vector<OBNodeBase*> vn;
-        vector<OBNodeBase*>::iterator i;
-        for (node = Begin(i);node;node = Next(i))
-            vn.push_back(node->GetMatch());
-        PushBack(vn);
+    SetFinishedMatch(true);
+    OBNodeBase *node;
+    vector<OBNodeBase*> vn;
+    vector<OBNodeBase*>::iterator i;
+    for (node = Begin(i);node;node = Next(i))
+    vn.push_back(node->GetMatch());
+    PushBack(vn);
 
-        return(true);
+    return(true);
     }
 
     //handle next seed of disconnected pattern
     if (j == i->second.end())
     {
-        i++;
-        OBNodeBase *node;
-        OBNodeBase *seed = i->first;
-        vector<OBNodeBase*>::iterator k;
-        for (node = g.Begin(k);node;node = g.Next(k))
-            if (!node->Visit && seed->Eval(node))
-            {
-                node->Visit = true;
-                seed->SetMatch(node);
-                Match(g,i,i->second.begin());
-                seed->SetMatch((OBNodeBase*)NULL);
-                node->Visit = false;
-                if (SingleMatch() && FinishedMatch())
-                    break;
-            }
-        return(true);
+    i++;
+    OBNodeBase *node;
+    OBNodeBase *seed = i->first;
+    vector<OBNodeBase*>::iterator k;
+    for (node = g.Begin(k);node;node = g.Next(k))
+    if (!node->Visit && seed->Eval(node))
+    {
+    node->Visit = true;
+    seed->SetMatch(node);
+    Match(g,i,i->second.begin());
+    seed->SetMatch((OBNodeBase*)NULL);
+    node->Visit = false;
+    if (SingleMatch() && FinishedMatch())
+    break;
+    }
+    return(true);
     }
 
     OBEdgeBase *edge = *j++;
     if (edge->IsClosure()) //check to see if matched atoms are bonded
     {
-        if (edge->GetBgn()->GetMatch()->IsConnected(edge->GetEnd()->GetMatch()))
-            Match(g,i,j);
+    if (edge->GetBgn()->GetMatch()->IsConnected(edge->GetEnd()->GetMatch()))
+    Match(g,i,j);
     }
     else //bond hasn't been covered yet
     {
-        OBNodeBase *nbr;
-        OBNodeBase *curr = edge->GetBgn();
-        OBNodeBase *next = edge->GetEnd();
-        OBNodeBase *match = curr->GetMatch();
-        vector<OBEdgeBase*>::iterator k;
+    OBNodeBase *nbr;
+    OBNodeBase *curr = edge->GetBgn();
+    OBNodeBase *next = edge->GetEnd();
+    OBNodeBase *match = curr->GetMatch();
+    vector<OBEdgeBase*>::iterator k;
 
-        for (nbr = match->BeginNbr(k);nbr;nbr = match->NextNbr(k))
-            if (!nbr->Visit && next->Eval(nbr) && edge->Eval(*k))
-            {
-                nbr->Visit = true;
-                next->SetMatch(nbr);
-                Match(g,i,j);
-                next->SetMatch(NULL);
-                nbr->Visit = false;
-            }
+    for (nbr = match->BeginNbr(k);nbr;nbr = match->NextNbr(k))
+    if (!nbr->Visit && next->Eval(nbr) && edge->Eval(*k))
+    {
+    nbr->Visit = true;
+    next->SetMatch(nbr);
+    Match(g,i,j);
+    next->SetMatch(NULL);
+    nbr->Visit = false;
+    }
     }
 
     return(false);
-}
-*/
-OBNodeBase *OBGraphBase::Begin(vector<OBNodeBase*>::iterator &i)
-{
+    }
+  */
+  OBNodeBase *OBGraphBase::Begin(vector<OBNodeBase*>::iterator &i)
+  {
     i = _vatom.begin();
     return((i != _vatom.end()) ? *i : NULL);
-}
+  }
 
-OBNodeBase *OBGraphBase::Next(vector<OBNodeBase*>::iterator &i)
-{
+  OBNodeBase *OBGraphBase::Next(vector<OBNodeBase*>::iterator &i)
+  {
     i++;
     return((i != _vatom.end()) ? *i : NULL);
-}
+  }
 
-OBEdgeBase *OBGraphBase::Begin(vector<OBEdgeBase*>::iterator &i)
-{
+  OBEdgeBase *OBGraphBase::Begin(vector<OBEdgeBase*>::iterator &i)
+  {
     i = _vbond.begin();
     return((i != _vbond.end()) ? *i : NULL);
-}
+  }
 
-OBEdgeBase *OBGraphBase::Next(vector<OBEdgeBase*>::iterator &i)
-{
+  OBEdgeBase *OBGraphBase::Next(vector<OBEdgeBase*>::iterator &i)
+  {
     i++;
     return((i != _vbond.end()) ? *i : NULL);
-}
+  }
 
-OBNodeBase *OBNodeBase::BeginNbr(vector<OBEdgeBase*>::iterator &i)
-{
+  OBNodeBase *OBNodeBase::BeginNbr(vector<OBEdgeBase*>::iterator &i)
+  {
     i = _vbond.begin();
 
     if (i == _vbond.end())
-        return(NULL);
+      return(NULL);
     return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());
-}
+  }
 
-OBNodeBase *OBNodeBase::NextNbr(vector<OBEdgeBase*>::iterator &i)
-{
+  OBNodeBase *OBNodeBase::NextNbr(vector<OBEdgeBase*>::iterator &i)
+  {
     i++;
     if (i == _vbond.end())
-        return(NULL);
+      return(NULL);
     return((this == (*i)->GetBgn()) ? (*i)->GetEnd() : (*i)->GetBgn());
-}
+  }
 
-void OBNodeBase::SetParent(OBGraphBase *p)
-{
+  void OBNodeBase::SetParent(OBGraphBase *p)
+  {
     _parent = p;
-}
+  }
 
-void OBEdgeBase::SetParent(OBGraphBase *p)
-{
+  void OBEdgeBase::SetParent(OBGraphBase *p)
+  {
     _parent = p;
-}
+  }
 
-bool OBNodeBase::IsConnected(OBNodeBase *nb)
-{
+  bool OBNodeBase::IsConnected(OBNodeBase *nb)
+  {
     vector<OBEdgeBase*>::iterator i;
     for (i = _vbond.begin();i != _vbond.end();i++)
-        if (nb == (*i)->GetBgn() || nb == (*i)->GetEnd())
-            return(true);
+      if (nb == (*i)->GetBgn() || nb == (*i)->GetEnd())
+        return(true);
 
     return(false);
-}
+  }
 
-void OBGraphBase::ResetVisitFlags()
-{
+  void OBGraphBase::ResetVisitFlags()
+  {
     OBNodeBase *nb;
     vector<OBNodeBase*>::iterator i;
     for (nb = Begin(i);nb;nb = Next(i))
-        nb->Visit = false;
+      nb->Visit = false;
 
     OBEdgeBase *eb;
     vector<OBEdgeBase*>::iterator j;
     for (eb = Begin(j);eb;eb = Next(j))
-        eb->Visit = false;
-}
+      eb->Visit = false;
+  }
 
-bool OBGraphBase::SetVisitLock(bool v)
-{
+  bool OBGraphBase::SetVisitLock(bool v)
+  {
     if (v && _vlock)
-        return(false);
+      return(false);
     _vlock = v;
     return(true);
-}
+  }
 
-/*! \mainpage
+  /*! \mainpage
 
   \section intro Introduction and History
  
-It is fair to say that Open Babel is a direct result of the original Babel.
-Application development is facilitated
-by building software on top of libraries rich in functionality. Babel
-was the first experience for Matt Stahl in designing a molecule
-library. In addition to developing Babel, Pat Walters and Matt
-developed `OBabel' at Vertex Pharmaceuticals, a first
-attempt at developing an object oriented molecule library.
-Matt later designed a new molecule class library, OELib -- designed
-to be flexible, extensible, portable, and efficient.
+  It is fair to say that Open Babel is a direct result of the original Babel.
+  Application development is facilitated
+  by building software on top of libraries rich in functionality. Babel
+  was the first experience for Matt Stahl in designing a molecule
+  library. In addition to developing Babel, Pat Walters and Matt
+  developed `OBabel' at Vertex Pharmaceuticals, a first
+  attempt at developing an object oriented molecule library.
+  Matt later designed a new molecule class library, OELib -- designed
+  to be flexible, extensible, portable, and efficient.
  
-OELib was released under the GNU General Public License (GPL) by Matt Stahl
-and Open Eye Scientific Software, Inc. to take advantage of many of
-the "great minds writing chemical software." Open Babel took up where
-OELib and Babel left off, starting from the existing GPL version of
-OELib, and has continued to evolve and improve into a separate
-high-quality chemistry class library and tool. Open Babel is now a
-separate project and library and has changed considerably from the OELib days.
+  OELib was released under the GNU General Public License (GPL) by Matt Stahl
+  and Open Eye Scientific Software, Inc. to take advantage of many of
+  the "great minds writing chemical software." Open Babel took up where
+  OELib and Babel left off, starting from the existing GPL version of
+  OELib, and has continued to evolve and improve into a separate
+  high-quality chemistry class library and tool. Open Babel is now a
+  separate project and library and has changed considerably from the OELib days.
  
-Thanks to all who have helped with Babel, OBabel, OELib and Open Babel.
-The list is long and growing.
+  Thanks to all who have helped with Babel, OBabel, OELib and Open Babel.
+  The list is long and growing.
  
   \section pointers Key Modules
  
-The heart of Open Babel lies in the \link OpenBabel::OBMol OBMol\endlink, 
-\link OpenBabel::OBAtom OBAtom\endlink, and 
-\link OpenBabel::OBBond OBBond\endlink classes,
-which handle operations on atoms, bonds and molecules. Newcomers should 
-start with looking at the \link OpenBabel::OBMol OBMol\endlink class, 
-designed to store the basic information
-in a molecule and to perceive information about a molecule.
+  The heart of Open Babel lies in the \link OpenBabel::OBMol OBMol\endlink, 
+  \link OpenBabel::OBAtom OBAtom\endlink, and 
+  \link OpenBabel::OBBond OBBond\endlink classes,
+  which handle operations on atoms, bonds and molecules. Newcomers should 
+  start with looking at the \link OpenBabel::OBMol OBMol\endlink class, 
+  designed to store the basic information
+  in a molecule and to perceive information about a molecule.
 
-One of the key philosophies in the code is that transformations and
-automatic perception of properties are performed in a <a href="http://en.wikipedia.org/wiki/Lazy_evaluation">"lazy"</a>
-manner. That is, until you call for partial atomic charges, no
-charges are calculated. This ensures faster transformations of
-chemical data -- properties that are not needed for your code will
-typically not be calculated. When such data is needed, appropriate
-routines are called, and a "flag" is set (e.g., via OBMol::SetFlag
-or OBAtom::SetFlag etc.) so that the code is only run once.
+  One of the key philosophies in the code is that transformations and
+  automatic perception of properties are performed in a <a href="http://en.wikipedia.org/wiki/Lazy_evaluation">"lazy"</a>
+  manner. That is, until you call for partial atomic charges, no
+  charges are calculated. This ensures faster transformations of
+  chemical data -- properties that are not needed for your code will
+  typically not be calculated. When such data is needed, appropriate
+  routines are called, and a "flag" is set (e.g., via OBMol::SetFlag
+  or OBAtom::SetFlag etc.) so that the code is only run once.
 
-Arbitrary custom data and text descriptors can be stored in any atom,
-bond, molecule, or residue using the \link OpenBabel::OBGenericData
-OBGenericData\endlink or \link OpenBabel::OBPairData
-OBPairData\endlink classes.
+  Arbitrary custom data and text descriptors can be stored in any atom,
+  bond, molecule, or residue using the \link OpenBabel::OBGenericData
+  OBGenericData\endlink or \link OpenBabel::OBPairData
+  OBPairData\endlink classes.
 
-Conversion between various chemical file formats is accomplished through
-the \link OpenBabel::OBConversion OBConversion\endlink and \link 
-OpenBabel::OBFormat OBFormat\endlink classes, often through use of the \link 
-OpenBabel::OBMoleculeFormat OBMoleculeFormat\endlink subclass which is designed
-for easy read/write access to one or more \link OpenBabel::OBMol OBMol\endlink
-objects. The philosophy of the file format codes is to parse as much
-chemical information from a given file as possible (no data left
-behind) and ideally any perception or transformations will occur when
-writing to some other format later.
+  Conversion between various chemical file formats is accomplished through
+  the \link OpenBabel::OBConversion OBConversion\endlink and \link 
+  OpenBabel::OBFormat OBFormat\endlink classes, often through use of the \link 
+  OpenBabel::OBMoleculeFormat OBMoleculeFormat\endlink subclass which is designed
+  for easy read/write access to one or more \link OpenBabel::OBMol OBMol\endlink
+  objects. The philosophy of the file format codes is to parse as much
+  chemical information from a given file as possible (no data left
+  behind) and ideally any perception or transformations will occur when
+  writing to some other format later.
 
-*/
+  */
 
 } // namespace OpenBabel
 
diff --git a/src/base.h b/src/base.h
index 3428290f6..82c88bfac 100644
--- a/src/base.h
+++ b/src/base.h
@@ -25,110 +25,108 @@ GNU General Public License for more details.
 #include <vector>
 #include <map>
 
-#if HAVE_IOSTREAM
 #include <iostream>
-#elif HAVE_IOSTREAM_H
-#include <iostream.h>
-#endif
+
 #include "generic.h"
 
 namespace OpenBabel
 {
 
-class OBBase;
-class OBNodeBase;
-class OBEdgeBase;
-class OBGraphBase;
+  class OBBase;
+  class OBNodeBase;
+  class OBEdgeBase;
+  class OBGraphBase;
 
-/** \brief Base Class
+  /** \brief Base Class
  
- The various classes (Atom, Bond, Molecule) inherit from base classes--
- OBBase is just a placeholder class
-*/
-class OBAPI OBBase
-{
-public:
-	virtual ~OBBase()
-	{
-		if (!_vdata.empty())
-		{
-			std::vector<OBGenericData*>::iterator m;
-			for (m = _vdata.begin();m != _vdata.end();m++)
-					delete *m;
-			_vdata.clear();
-		}
-}
-	; //NF
-	virtual OBBase* DoTransformations(const std::map<std::string,std::string>*pOptions)
-	{
-			return this;
-	} 
-	//Base type does nothing
-	static const char* ClassDescription()
-	{
-			return "";
-	} 
+  The various classes (Atom, Bond, Molecule) inherit from base classes--
+  OBBase is just a placeholder class
+  */
+  class OBAPI OBBase
+    {
+    public:
+      virtual ~OBBase()
+        {
+          if (!_vdata.empty())
+            {
+              std::vector<OBGenericData*>::iterator m;
+              for (m = _vdata.begin();m != _vdata.end();m++)
+                delete *m;
+              _vdata.clear();
+            }
+        }
 
-	//! \name Generic data handling methods (via OBGenericData)
-	//@{
-	//! \returns whether the generic attribute/value pair exists
-	bool                              HasData(std::string &);
-	//! \returns whether the generic attribute/value pair exists
-	bool                              HasData(const char *);
-	//! \returns whether the generic attribute/value pair exists, for a given
-  //!  OBGenericDataType
-	bool                              HasData(unsigned int type);
-  //! Delete any data matching the given OBGenericDataType
-	void                              DeleteData(unsigned int type);
-  //! delete the given generic data from this object
-	void                              DeleteData(OBGenericData*);
-  //! delete all of the given generic data from this object
-	void                              DeleteData(std::vector<OBGenericData*>&);
-	//! \adds a data object; does nothing if d==NULL
-	void                              SetData(OBGenericData *d)
-	{
-			if(d)
-				_vdata.push_back(d);
-	}
-	//! \return the number of OBGenericData items attached to this molecule.
-	unsigned int                      DataSize(){ return(_vdata.size()); }
-  //! \return the first matching data for a given type from OBGenericDataType
-  //!    or NULL if nothing matches
-	OBGenericData                    *GetData(unsigned int type);
-  //! \return any data matching the given attribute name 
-  //!     or NULL if nothing matches
-	OBGenericData                    *GetData(std::string&);
-  //! \return any data matching the given attribute name 
-  //!     or NULL if nothing matches
-	OBGenericData                    *GetData(const char *);
-  //! \return all data, suitable for iterating
-	std::vector<OBGenericData*>      &GetData() { return(_vdata); }
-	std::vector<OBGenericData*>::iterator  BeginData()
-	{
-			return(_vdata.begin());
-	}
-	std::vector<OBGenericData*>::iterator  EndData()
-	{
-			return(_vdata.end());
-	}
-	//@}
-protected:
-	std::vector<OBGenericData*> _vdata; //!< Custom data
+      virtual OBBase* DoTransformations(const std::map<std::string,std::string>*pOptions)
+        {
+          return this;
+        } 
+      //Base type does nothing
+      static const char* ClassDescription()
+        {
+          return "";
+        } 
+
+      //! \name Generic data handling methods (via OBGenericData)
+      //@{
+      //! \returns whether the generic attribute/value pair exists
+      bool                              HasData(const std::string &);
+      //! \returns whether the generic attribute/value pair exists
+      bool                              HasData(const char *);
+      //! \returns whether the generic attribute/value pair exists, for a given
+      //!  OBGenericDataType
+      bool                              HasData(const unsigned int type);
+      //! Delete any data matching the given OBGenericDataType
+      void                              DeleteData(unsigned int type);
+      //! delete the given generic data from this object
+      void                              DeleteData(OBGenericData*);
+      //! delete all of the given generic data from this object
+      void                              DeleteData(std::vector<OBGenericData*>&);
+      //! \adds a data object; does nothing if d==NULL
+      void                              SetData(OBGenericData *d)
+        {
+          if(d)
+            _vdata.push_back(d);
+        }
+      //! \return the number of OBGenericData items attached to this molecule.
+      unsigned int                      DataSize() const 
+        { return(_vdata.size()); }
+      //! \return the first matching data for a given type from OBGenericDataType
+      //!    or NULL if nothing matches
+      OBGenericData                    *GetData(const unsigned int type);
+      //! \return any data matching the given attribute name 
+      //!     or NULL if nothing matches
+      OBGenericData                    *GetData(const std::string&);
+      //! \return any data matching the given attribute name 
+      //!     or NULL if nothing matches
+      OBGenericData                    *GetData(const char *);
+      //! \return all data, suitable for iterating
+      std::vector<OBGenericData*>      &GetData() { return(_vdata); }
+      std::vector<OBGenericData*>::iterator  BeginData()
+        {
+          return(_vdata.begin());
+        }
+      std::vector<OBGenericData*>::iterator  EndData()
+        {
+          return(_vdata.end());
+        }
+      //@}
+    protected:
+      std::vector<OBGenericData*> _vdata; //!< Custom data
 
 
-};
+    };
 
-/** \brief Node Base Class
+  /** \brief Node Base Class
  
-The base class for nodes (e.g. atoms) in a graph-theoretical representation.
- */
-class OBAPI OBNodeBase : public OBBase
-{
-protected:
-    //! What is my unique node index? 	GetIdx(), SetIdx(int idx).
-    unsigned short int  _idx;
-    //! To which graph do I belong?	GetParent(), SetParent(OBGraphBase*).
-    OBGraphBase        *_parent;
+  The base class for nodes (e.g. atoms) in a graph-theoretical representation.
+  */
+  class OBAPI OBNodeBase : public OBBase
+    {
+    protected:
+      //! What is my unique node index? 	GetIdx(), SetIdx(int idx).
+      unsigned short int  _idx;
+      //! To which graph do I belong?	GetParent(), SetParent(OBGraphBase*).
+      OBGraphBase        *_parent;
     /** \brief What edges or bonds do I have? \sa AddEdge(), GetValence(),
         This node is assumed to be one of the edge endpoints.
     */