* scripts/*: Cleanups and fixes, including for compilation

problems with Perl. (Derives from some macro expansion for THR.)

ChangeLog

@@ -1,3 +1,8 @@
+2006-12-02  Geoffrey Hutchison  <babel@geoffhutchison.net>
+
+	* scripts/*: Cleanups and fixes, including for compilation
+	problems with Perl. (Derives from some macro expansion for THR.)
+
 2006-12-01  Benoit Jacob <jacob@math.jussieu.fr>
 
 	* src/grid.h, src/grid.cpp: In class OBFloatGrid:

scripts/Makefile.am

@@ -17,7 +17,7 @@ dist-hook:
 if MAINTAINER_MODE
 if BUILD_SWIG
 BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
-	ruby/openbabel_ruby.cpp java/openbabel_java.cpp
+	java/openbabel_java.cpp
 
 perl/openbabel_perl.cpp: openbabel-perl.i $(top_srcdir)/src/mol.h  $(top_srcdir)/src/obconversion.h
 	$(SWIG) -perl5 -c++ -naturalvar -o $@ \
@@ -36,10 +36,6 @@ 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;
 
-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 $<;
-	(cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) )
-
 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 $<;
 	(cd java; \
@@ -47,5 +43,13 @@ java/openbabel_java.cpp: openbabel-java.i $(top_srcdir)/src/mol.h  $(top_srcdir)
 		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"); \
 		mv $$file $$tgt; done)
 
+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 $<;
+	(cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) )
+endif # BUILD_RUBY
+
 endif # BUILD_SWIG
 endif # MAINTAINER_MODE

scripts/Makefile.in

@@ -35,6 +35,7 @@ PRE_UNINSTALL = :
 POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
+@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@am__append_1 = ruby/openbabel_ruby.cpp
 subdir = scripts
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -198,9 +199,10 @@ EXTRA_DIST = openbabel-perl.i perl \
 
 # build the scripting language interfaces if --enable-maintainer-mode was set
 # and SWIG is available -- please use the most recent version of SWIG
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
+@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@BUILT_SOURCES = perl/openbabel_perl.cpp \
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	ruby/openbabel_ruby.cpp java/openbabel_java.cpp
+@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)
 all: $(BUILT_SOURCES)
 	$(MAKE) $(AM_MAKEFLAGS) all-am
 
@@ -394,16 +396,16 @@ 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@ruby/openbabel_ruby.cpp: openbabel-ruby.i $(top_srcdir)/src/mol.h  $(top_srcdir)/src/obconversion.h
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<;
-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	(cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) )
-
 @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@	(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 $<;
+@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	(cd ruby; ruby extconf.rb --with-openbabel-include=$(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.
 .NOEXPORT:

scripts/java/OBRandom.java

@@ -7,53 +7,19 @@
  * ----------------------------------------------------------------------------- */
 
 
-public class OBRandom {
+public class SWIGTYPE_p_OpenBabel__OBRandom {
   private long swigCPtr;
-  protected boolean swigCMemOwn;
 
-  protected OBRandom(long cPtr, boolean cMemoryOwn) {
+  protected SWIGTYPE_p_OpenBabel__OBRandom(long cPtr, boolean futureUse) {
-    swigCMemOwn = cMemoryOwn;
     swigCPtr = cPtr;
   }
 
-  protected static long getCPtr(OBRandom obj) {
+  protected SWIGTYPE_p_OpenBabel__OBRandom() {
-    return (obj == null) ? 0 : obj.swigCPtr;
-  }
-
-  protected void finalize() {
-    delete();
-  }
-
-  public synchronized void delete() {
-    if(swigCPtr != 0 && swigCMemOwn) {
-      swigCMemOwn = false;
-      openbabelJNI.delete_OBRandom(swigCPtr);
-    }
     swigCPtr = 0;
   }
 
-  public OBRandom(boolean useSys) {
+  protected static long getCPtr(SWIGTYPE_p_OpenBabel__OBRandom obj) {
-    this(openbabelJNI.new_OBRandom__SWIG_0(useSys), true);
+    return (obj == null) ? 0 : obj.swigCPtr;
   }
-
-  public OBRandom() {
-    this(openbabelJNI.new_OBRandom__SWIG_1(), true);
-  }
-
-  public void Seed(int seed) {
-    openbabelJNI.OBRandom_Seed(swigCPtr, this, seed);
-  }
-
-  public void TimeSeed() {
-    openbabelJNI.OBRandom_TimeSeed(swigCPtr, this);
-  }
-
-  public int NextInt() {
-    return openbabelJNI.OBRandom_NextInt(swigCPtr, this);
-  }
-
-  public double NextFloat() {
-    return openbabelJNI.OBRandom_NextFloat(swigCPtr, this);
-  }
-
 }
+

scripts/java/openbabel.java

@@ -12,18 +12,6 @@ public class openbabel implements openbabelConstants {
     return openbabelJNI.OpenDatafile(SWIGTYPE_p_std__ifstream.getCPtr(fs), filename);
   }
 
-  public static void DoubleMultiply(long arg0, long arg1, DoubleType arg2) {
-    openbabelJNI.DoubleMultiply(arg0, arg1, DoubleType.getCPtr(arg2), arg2);
-  }
-
-  public static void DoubleAdd(DoubleType arg0, long arg1) {
-    openbabelJNI.DoubleAdd(DoubleType.getCPtr(arg0), arg0, arg1);
-  }
-
-  public static long DoubleModulus(DoubleType arg0, long arg1) {
-    return openbabelJNI.DoubleModulus(DoubleType.getCPtr(arg0), arg0, arg1);
-  }
-
   public static double dot(vector3 v1, vector3 v2) {
     return openbabelJNI.dot(vector3.getCPtr(v1), v1, vector3.getCPtr(v2), v2);
   }
@@ -464,14 +452,34 @@ public class openbabel implements openbabelConstants {
     return openbabelJNI.I_get();
   }
 
+  public static long get_1MA() {
+    return openbabelJNI._1MA_get();
+  }
+
+  public static long get_5MC() {
+    return openbabelJNI._5MC_get();
+  }
+
   public static long getOMC() {
     return openbabelJNI.OMC_get();
   }
 
+  public static long get_1MG() {
+    return openbabelJNI._1MG_get();
+  }
+
+  public static long get_2MG() {
+    return openbabelJNI._2MG_get();
+  }
+
   public static long getM2G() {
     return openbabelJNI.M2G_get();
   }
 
+  public static long get_7MG() {
+    return openbabelJNI._7MG_get();
+  }
+
   public static long getOMG() {
     return openbabelJNI.OMG_get();
   }
@@ -484,6 +492,10 @@ public class openbabel implements openbabelConstants {
     return openbabelJNI.H2U_get();
   }
 
+  public static long get_5MU() {
+    return openbabelJNI._5MU_get();
+  }
+
   public static long getPSU() {
     return openbabelJNI.PSU_get();
   }
@@ -626,6 +638,10 @@ public class openbabel implements openbabelConstants {
     return openbabelJNI.tokenize__SWIG_4(SWIGTYPE_p_std__vectorTstd__string_t.getCPtr(arg0), SWIGTYPE_p_std__string.getCPtr(arg1));
   }
 
+  public static void ThrowError(String str) {
+    openbabelJNI.ThrowError__SWIG_0(str);
+  }
+
   public static void ThrowError(SWIGTYPE_p_std__string str) {
     openbabelJNI.ThrowError__SWIG_1(SWIGTYPE_p_std__string.getCPtr(str));
   }

scripts/java/openbabelJNI.java

@@ -189,22 +189,6 @@ class openbabelJNI {
   public final static native void delete_OBSqrtTbl(long jarg1);
   public final static native double OBSqrtTbl_Sqrt(long jarg1, OBSqrtTbl jarg1_, double jarg2);
   public final static native void OBSqrtTbl_Init(long jarg1, OBSqrtTbl jarg1_, double jarg2, double jarg3);
-  public final static native void DoubleType_hi_set(long jarg1, DoubleType jarg1_, long jarg2);
-  public final static native long DoubleType_hi_get(long jarg1, DoubleType jarg1_);
-  public final static native void DoubleType_lo_set(long jarg1, DoubleType jarg1_, long jarg2);
-  public final static native long DoubleType_lo_get(long jarg1, DoubleType jarg1_);
-  public final static native long new_DoubleType();
-  public final static native void delete_DoubleType(long jarg1);
-  public final static native void DoubleMultiply(long jarg1, long jarg2, long jarg3, DoubleType jarg3_);
-  public final static native void DoubleAdd(long jarg1, DoubleType jarg1_, long jarg2);
-  public final static native long DoubleModulus(long jarg1, DoubleType jarg1_, long jarg2);
-  public final static native long new_OBRandom__SWIG_0(boolean jarg1);
-  public final static native long new_OBRandom__SWIG_1();
-  public final static native void OBRandom_Seed(long jarg1, OBRandom jarg1_, int jarg2);
-  public final static native void OBRandom_TimeSeed(long jarg1, OBRandom jarg1_);
-  public final static native int OBRandom_NextInt(long jarg1, OBRandom jarg1_);
-  public final static native double OBRandom_NextFloat(long jarg1, OBRandom jarg1_);
-  public final static native void delete_OBRandom(long jarg1);
   public final static native long new_vector3__SWIG_0(double jarg1, double jarg2, double jarg3);
   public final static native long new_vector3__SWIG_1(double jarg1, double jarg2);
   public final static native long new_vector3__SWIG_2(double jarg1);
@@ -217,7 +201,7 @@ class openbabelJNI {
   public final static native void vector3_SetZ(long jarg1, vector3 jarg1_, double jarg2);
   public final static native void vector3_Get(long jarg1, vector3 jarg1_, long jarg2);
   public final static native long vector3_AsArray(long jarg1, vector3 jarg1_);
-  public final static native void vector3_randomUnitVector__SWIG_0(long jarg1, vector3 jarg1_, long jarg2, OBRandom jarg2_);
+  public final static native void vector3_randomUnitVector__SWIG_0(long jarg1, vector3 jarg1_, long jarg2);
   public final static native void vector3_randomUnitVector__SWIG_1(long jarg1, vector3 jarg1_);
   public final static native long vector3_normalize(long jarg1, vector3 jarg1_);
   public final static native boolean vector3_CanBeNormalized(long jarg1, vector3 jarg1_);
@@ -712,11 +696,17 @@ class openbabelJNI {
   public final static native long U_get();
   public final static native long UPLUS_get();
   public final static native long I_get();
+  public final static native long _1MA_get();
+  public final static native long _5MC_get();
   public final static native long OMC_get();
+  public final static native long _1MG_get();
+  public final static native long _2MG_get();
   public final static native long M2G_get();
+  public final static native long _7MG_get();
   public final static native long OMG_get();
   public final static native long YG_get();
   public final static native long H2U_get();
+  public final static native long _5MU_get();
   public final static native long PSU_get();
   public final static native long UNK_get();
   public final static native long ACE_get();
@@ -1165,6 +1155,7 @@ class openbabelJNI {
   public final static native boolean tokenize__SWIG_2(long jarg1, long jarg2, String jarg3, int jarg4);
   public final static native boolean tokenize__SWIG_3(long jarg1, long jarg2, String jarg3);
   public final static native boolean tokenize__SWIG_4(long jarg1, long jarg2);
+  public final static native void ThrowError__SWIG_0(String jarg1);
   public final static native void ThrowError__SWIG_1(long jarg1);
   public final static native void CartesianToInternal(long jarg1, long jarg2, OBMol jarg2_);
   public final static native void InternalToCartesian(long jarg1, long jarg2, OBMol jarg2_);

scripts/java/openbabel_java.cpp

@@ -3364,223 +3364,6 @@ SWIGEXPORT void JNICALL Java_openbabelJNI_OBSqrtTbl_1Init(JNIEnv *jenv, jclass j
 }
 
 
-SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleType_1hi_1set(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
-  OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
-  unsigned int arg2 ;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::DoubleType **)&jarg1; 
-  arg2 = (unsigned int)jarg2; 
-  if (arg1) (arg1)->hi = arg2;
-  
-}
-
-
-SWIGEXPORT jlong JNICALL Java_openbabelJNI_DoubleType_1hi_1get(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
-  jlong jresult = 0 ;
-  OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
-  unsigned int result;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::DoubleType **)&jarg1; 
-  result = (unsigned int) ((arg1)->hi);
-  jresult = (jlong)result; 
-  return jresult;
-}
-
-
-SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleType_1lo_1set(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
-  OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
-  unsigned int arg2 ;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::DoubleType **)&jarg1; 
-  arg2 = (unsigned int)jarg2; 
-  if (arg1) (arg1)->lo = arg2;
-  
-}
-
-
-SWIGEXPORT jlong JNICALL Java_openbabelJNI_DoubleType_1lo_1get(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
-  jlong jresult = 0 ;
-  OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
-  unsigned int result;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::DoubleType **)&jarg1; 
-  result = (unsigned int) ((arg1)->lo);
-  jresult = (jlong)result; 
-  return jresult;
-}
-
-
-SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1DoubleType(JNIEnv *jenv, jclass jcls) {
-  jlong jresult = 0 ;
-  OpenBabel::DoubleType *result = 0 ;
-  
-  (void)jenv;
-  (void)jcls;
-  result = (OpenBabel::DoubleType *)new OpenBabel::DoubleType();
-  *(OpenBabel::DoubleType **)&jresult = result; 
-  return jresult;
-}
-
-
-SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1DoubleType(JNIEnv *jenv, jclass jcls, jlong jarg1) {
-  OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
-  
-  (void)jenv;
-  (void)jcls;
-  arg1 = *(OpenBabel::DoubleType **)&jarg1; 
-  delete arg1;
-  
-}
-
-
-SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleMultiply(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3, jobject jarg3_) {
-  unsigned int arg1 ;
-  unsigned int arg2 ;
-  OpenBabel::DoubleType *arg3 = (OpenBabel::DoubleType *) 0 ;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg3_;
-  arg1 = (unsigned int)jarg1; 
-  arg2 = (unsigned int)jarg2; 
-  arg3 = *(OpenBabel::DoubleType **)&jarg3; 
-  OpenBabel::DoubleMultiply(arg1,arg2,arg3);
-}
-
-
-SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleAdd(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
-  OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
-  unsigned int arg2 ;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::DoubleType **)&jarg1; 
-  arg2 = (unsigned int)jarg2; 
-  OpenBabel::DoubleAdd(arg1,arg2);
-}
-
-
-SWIGEXPORT jlong JNICALL Java_openbabelJNI_DoubleModulus(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
-  jlong jresult = 0 ;
-  OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
-  unsigned int arg2 ;
-  unsigned int result;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::DoubleType **)&jarg1; 
-  arg2 = (unsigned int)jarg2; 
-  result = (unsigned int)OpenBabel::DoubleModulus(arg1,arg2);
-  jresult = (jlong)result; 
-  return jresult;
-}
-
-
-SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBRandom_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jboolean jarg1) {
-  jlong jresult = 0 ;
-  bool arg1 ;
-  OpenBabel::OBRandom *result = 0 ;
-  
-  (void)jenv;
-  (void)jcls;
-  arg1 = jarg1 ? true : false; 
-  result = (OpenBabel::OBRandom *)new OpenBabel::OBRandom(arg1);
-  *(OpenBabel::OBRandom **)&jresult = result; 
-  return jresult;
-}
-
-
-SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBRandom_1_1SWIG_11(JNIEnv *jenv, jclass jcls) {
-  jlong jresult = 0 ;
-  OpenBabel::OBRandom *result = 0 ;
-  
-  (void)jenv;
-  (void)jcls;
-  result = (OpenBabel::OBRandom *)new OpenBabel::OBRandom();
-  *(OpenBabel::OBRandom **)&jresult = result; 
-  return jresult;
-}
-
-
-SWIGEXPORT void JNICALL Java_openbabelJNI_OBRandom_1Seed(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jint jarg2) {
-  OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
-  int arg2 ;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::OBRandom **)&jarg1; 
-  arg2 = (int)jarg2; 
-  (arg1)->Seed(arg2);
-}
-
-
-SWIGEXPORT void JNICALL Java_openbabelJNI_OBRandom_1TimeSeed(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
-  OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::OBRandom **)&jarg1; 
-  (arg1)->TimeSeed();
-}
-
-
-SWIGEXPORT jint JNICALL Java_openbabelJNI_OBRandom_1NextInt(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
-  jint jresult = 0 ;
-  OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
-  int result;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::OBRandom **)&jarg1; 
-  result = (int)(arg1)->NextInt();
-  jresult = (jint)result; 
-  return jresult;
-}
-
-
-SWIGEXPORT jdouble JNICALL Java_openbabelJNI_OBRandom_1NextFloat(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
-  jdouble jresult = 0 ;
-  OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
-  double result;
-  
-  (void)jenv;
-  (void)jcls;
-  (void)jarg1_;
-  arg1 = *(OpenBabel::OBRandom **)&jarg1; 
-  result = (double)(arg1)->NextFloat();
-  jresult = (jdouble)result; 
-  return jresult;
-}
-
-
-SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1OBRandom(JNIEnv *jenv, jclass jcls, jlong jarg1) {
-  OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
-  
-  (void)jenv;
-  (void)jcls;
-  arg1 = *(OpenBabel::OBRandom **)&jarg1; 
-  delete arg1;
-  
-}
-
-
 SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1vector3_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jdouble jarg1, jdouble jarg2, jdouble jarg3) {
   jlong jresult = 0 ;
   double arg1 ;
@@ -3757,14 +3540,13 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_vector3_1AsArray(JNIEnv *jenv, jclass
 }
 
 
-SWIGEXPORT void JNICALL Java_openbabelJNI_vector3_1randomUnitVector_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) {
+SWIGEXPORT void JNICALL Java_openbabelJNI_vector3_1randomUnitVector_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
   OpenBabel::vector3 *arg1 = (OpenBabel::vector3 *) 0 ;
   OpenBabel::OBRandom *arg2 = (OpenBabel::OBRandom *) 0 ;
   
   (void)jenv;
   (void)jcls;
   (void)jarg1_;
-  (void)jarg2_;
   arg1 = *(OpenBabel::vector3 **)&jarg1; 
   arg2 = *(OpenBabel::OBRandom **)&jarg2; 
   (arg1)->randomUnitVector(arg2);
@@ -11653,6 +11435,30 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_I_1get(JNIEnv *jenv, jclass jcls) {
 }
 
 
+SWIGEXPORT jlong JNICALL Java_openbabelJNI__11MA_1get(JNIEnv *jenv, jclass jcls) {
+  jlong jresult = 0 ;
+  unsigned int result;
+  
+  (void)jenv;
+  (void)jcls;
+  result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_1MA;
+  jresult = (jlong)result; 
+  return jresult;
+}
+
+
+SWIGEXPORT jlong JNICALL Java_openbabelJNI__15MC_1get(JNIEnv *jenv, jclass jcls) {
+  jlong jresult = 0 ;
+  unsigned int result;
+  
+  (void)jenv;
+  (void)jcls;
+  result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_5MC;
+  jresult = (jlong)result; 
+  return jresult;
+}
+
+
 SWIGEXPORT jlong JNICALL Java_openbabelJNI_OMC_1get(JNIEnv *jenv, jclass jcls) {
   jlong jresult = 0 ;
   unsigned int result;
@@ -11665,6 +11471,30 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_OMC_1get(JNIEnv *jenv, jclass jcls) {
 }
 
 
+SWIGEXPORT jlong JNICALL Java_openbabelJNI__11MG_1get(JNIEnv *jenv, jclass jcls) {
+  jlong jresult = 0 ;
+  unsigned int result;
+  
+  (void)jenv;
+  (void)jcls;
+  result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_1MG;
+  jresult = (jlong)result; 
+  return jresult;
+}
+
+
+SWIGEXPORT jlong JNICALL Java_openbabelJNI__12MG_1get(JNIEnv *jenv, jclass jcls) {
+  jlong jresult = 0 ;
+  unsigned int result;
+  
+  (void)jenv;
+  (void)jcls;
+  result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_2MG;
+  jresult = (jlong)result; 
+  return jresult;
+}
+
+
 SWIGEXPORT jlong JNICALL Java_openbabelJNI_M2G_1get(JNIEnv *jenv, jclass jcls) {
   jlong jresult = 0 ;
   unsigned int result;
@@ -11677,6 +11507,18 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_M2G_1get(JNIEnv *jenv, jclass jcls) {
 }
 
 
+SWIGEXPORT jlong JNICALL Java_openbabelJNI__17MG_1get(JNIEnv *jenv, jclass jcls) {
+  jlong jresult = 0 ;
+  unsigned int result;
+  
+  (void)jenv;
+  (void)jcls;
+  result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_7MG;
+  jresult = (jlong)result; 
+  return jresult;
+}
+
+
 SWIGEXPORT jlong JNICALL Java_openbabelJNI_OMG_1get(JNIEnv *jenv, jclass jcls) {
   jlong jresult = 0 ;
   unsigned int result;
@@ -11713,6 +11555,18 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_H2U_1get(JNIEnv *jenv, jclass jcls) {
 }
 
 
+SWIGEXPORT jlong JNICALL Java_openbabelJNI__15MU_1get(JNIEnv *jenv, jclass jcls) {
+  jlong jresult = 0 ;
+  unsigned int result;
+  
+  (void)jenv;
+  (void)jcls;
+  result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_5MU;
+  jresult = (jlong)result; 
+  return jresult;
+}
+
+
 SWIGEXPORT jlong JNICALL Java_openbabelJNI_PSU_1get(JNIEnv *jenv, jclass jcls) {
   jlong jresult = 0 ;
   unsigned int result;
@@ -18414,6 +18268,21 @@ SWIGEXPORT jboolean JNICALL Java_openbabelJNI_tokenize_1_1SWIG_14(JNIEnv *jenv,
 }
 
 
+SWIGEXPORT void JNICALL Java_openbabelJNI_ThrowError_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jstring jarg1) {
+  char *arg1 = (char *) 0 ;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = 0;
+  if (jarg1) {
+    arg1 = (char *)jenv->GetStringUTFChars(jarg1, 0);
+    if (!arg1) return ;
+  }
+  OpenBabel::ThrowError(arg1);
+  if (arg1) jenv->ReleaseStringUTFChars(jarg1, (const char *)arg1);
+}
+
+
 SWIGEXPORT void JNICALL Java_openbabelJNI_ThrowError_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
   std::string *arg1 = 0 ;
   

scripts/java/vector3.java

@@ -81,8 +81,8 @@ public class vector3 {
     return (cPtr == 0) ? null : new SWIGTYPE_p_double(cPtr, false);
   }
 
-  public void randomUnitVector(OBRandom oeRand) {
+  public void randomUnitVector(SWIGTYPE_p_OpenBabel__OBRandom oeRand) {
-    openbabelJNI.vector3_randomUnitVector__SWIG_0(swigCPtr, this, OBRandom.getCPtr(oeRand), oeRand);
+    openbabelJNI.vector3_randomUnitVector__SWIG_0(swigCPtr, this, SWIGTYPE_p_OpenBabel__OBRandom.getCPtr(oeRand));
   }
 
   public void randomUnitVector() {

scripts/openbabel-perl.i

@@ -9,12 +9,18 @@
 
 
 #include "obutil.h"
+#include "rand.h"
 #include "math/vector3.h"
 #include "math/matrix3x3.h"
 #include "generic.h"
 
 #include "base.h"
 #include "mol.h"
+#include "atom.h"
+#include "bond.h"
+#include "residue.h"
+#include "internalcoord.h"
+
 #include "ring.h"
 #include "obconversion.h"
 #include "oberror.h"
@@ -45,6 +51,7 @@ namespace std {
 
 %apply std::string &OUTPUT { std::string &to };
 %include "data.h"
+%include "rand.h"
 %include "obutil.h"
 %include "math/vector3.h"
 %import "math/matrix3x3.h"
@@ -59,6 +66,7 @@ namespace std {
 %include "oberror.h"
 %include "obconversion.h"
 %include "residue.h"
+%include "internalcoord.h"
 %include "atom.h"
 %include "bond.h"
 %include "mol.h"

scripts/openbabel-python.i

@@ -8,12 +8,18 @@
 
 
 #include "obutil.h"
+#include "rand.h"
 #include "math/vector3.h"
 #include "math/matrix3x3.h"
 #include "generic.h"
 
 #include "base.h"
 #include "mol.h"
+#include "atom.h"
+#include "bond.h"
+#include "residue.h"
+#include "internalcoord.h"
+
 #include "ring.h"
 #include "obconversion.h"
 #include "oberror.h"
@@ -44,6 +50,7 @@ namespace std {
 
 %apply std::string &OUTPUT { std::string &to };
 %include "data.h"
+%include "rand.h"
 %include "obutil.h"
 %include "math/vector3.h"
 %import "math/matrix3x3.h"
@@ -58,6 +65,7 @@ namespace std {
 %include "oberror.h"
 %include "obconversion.h"
 %include "residue.h"
+%include "internalcoord.h"
 %include "atom.h"
 %include "bond.h"
 %include "mol.h"

scripts/openbabel-ruby.i

@@ -9,12 +9,18 @@
 #include <math.h>
 
 #include "obutil.h"
+#include "rand.h"
 #include "math/vector3.h"
 #include "math/matrix3x3.h"
 #include "generic.h"
 
 #include "base.h"
 #include "mol.h"
+#include "atom.h"
+#include "bond.h"
+#include "residue.h"
+#include "internalcoord.h"
+
 #include "ring.h"
 #include "obconversion.h"
 #include "oberror.h"
@@ -44,6 +50,7 @@ namespace std {
 
 %apply std::string &OUTPUT { std::string &to };
 %include "data.h"
+%include "rand.h"
 %include "obutil.h"
 %include "math/vector3.h"
 %import "math/matrix3x3.h"
@@ -58,6 +65,7 @@ namespace std {
 %include "oberror.h"
 %include "obconversion.h"
 %include "residue.h"
+%include "internalcoord.h"
 %include "atom.h"
 %include "bond.h"
 %include "mol.h"

scripts/perl/OpenBabel.pm

@@ -741,85 +741,6 @@ sub ACQUIRE {
 }
 
 
-############# Class : Chemistry::OpenBabel::OBStopwatch ##############
-
-package Chemistry::OpenBabel::OBStopwatch;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
-@ISA = qw( Chemistry::OpenBabel );
-%OWNER = ();
-%ITERATORS = ();
-*Start = *Chemistry::OpenBabelc::OBStopwatch_Start;
-*Lap = *Chemistry::OpenBabelc::OBStopwatch_Lap;
-*Elapsed = *Chemistry::OpenBabelc::OBStopwatch_Elapsed;
-sub new {
-    my $pkg = shift;
-    my $self = Chemistry::OpenBabelc::new_OBStopwatch(@_);
-    bless $self, $pkg if defined($self);
-}
-
-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_OBStopwatch($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::OBSqrtTbl ##############
-
-package Chemistry::OpenBabel::OBSqrtTbl;
-use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
-@ISA = qw( Chemistry::OpenBabel );
-%OWNER = ();
-%ITERATORS = ();
-sub new {
-    my $pkg = shift;
-    my $self = Chemistry::OpenBabelc::new_OBSqrtTbl(@_);
-    bless $self, $pkg if defined($self);
-}
-
-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_OBSqrtTbl($self);
-        delete $OWNER{$self};
-    }
-}
-
-*Sqrt = *Chemistry::OpenBabelc::OBSqrtTbl_Sqrt;
-*Init = *Chemistry::OpenBabelc::OBSqrtTbl_Init;
-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::DoubleType ##############
 
 package Chemistry::OpenBabel::DoubleType;
@@ -902,6 +823,85 @@ sub ACQUIRE {
 }
 
 
+############# Class : Chemistry::OpenBabel::OBStopwatch ##############
+
+package Chemistry::OpenBabel::OBStopwatch;
+use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
+@ISA = qw( Chemistry::OpenBabel );
+%OWNER = ();
+%ITERATORS = ();
+*Start = *Chemistry::OpenBabelc::OBStopwatch_Start;
+*Lap = *Chemistry::OpenBabelc::OBStopwatch_Lap;
+*Elapsed = *Chemistry::OpenBabelc::OBStopwatch_Elapsed;
+sub new {
+    my $pkg = shift;
+    my $self = Chemistry::OpenBabelc::new_OBStopwatch(@_);
+    bless $self, $pkg if defined($self);
+}
+
+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_OBStopwatch($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::OBSqrtTbl ##############
+
+package Chemistry::OpenBabel::OBSqrtTbl;
+use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
+@ISA = qw( Chemistry::OpenBabel );
+%OWNER = ();
+%ITERATORS = ();
+sub new {
+    my $pkg = shift;
+    my $self = Chemistry::OpenBabelc::new_OBSqrtTbl(@_);
+    bless $self, $pkg if defined($self);
+}
+
+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_OBSqrtTbl($self);
+        delete $OWNER{$self};
+    }
+}
+
+*Sqrt = *Chemistry::OpenBabelc::OBSqrtTbl_Sqrt;
+*Init = *Chemistry::OpenBabelc::OBSqrtTbl_Init;
+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::vector3 ##############
 
 package Chemistry::OpenBabel::vector3;
@@ -2124,6 +2124,55 @@ sub ACQUIRE {
 }
 
 
+############# Class : Chemistry::OpenBabel::OBInternalCoord ##############
+
+package Chemistry::OpenBabel::OBInternalCoord;
+use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
+@ISA = qw( Chemistry::OpenBabel );
+%OWNER = ();
+%ITERATORS = ();
+*swig__a_get = *Chemistry::OpenBabelc::OBInternalCoord__a_get;
+*swig__a_set = *Chemistry::OpenBabelc::OBInternalCoord__a_set;
+*swig__b_get = *Chemistry::OpenBabelc::OBInternalCoord__b_get;
+*swig__b_set = *Chemistry::OpenBabelc::OBInternalCoord__b_set;
+*swig__c_get = *Chemistry::OpenBabelc::OBInternalCoord__c_get;
+*swig__c_set = *Chemistry::OpenBabelc::OBInternalCoord__c_set;
+*swig__dst_get = *Chemistry::OpenBabelc::OBInternalCoord__dst_get;
+*swig__dst_set = *Chemistry::OpenBabelc::OBInternalCoord__dst_set;
+*swig__ang_get = *Chemistry::OpenBabelc::OBInternalCoord__ang_get;
+*swig__ang_set = *Chemistry::OpenBabelc::OBInternalCoord__ang_set;
+*swig__tor_get = *Chemistry::OpenBabelc::OBInternalCoord__tor_get;
+*swig__tor_set = *Chemistry::OpenBabelc::OBInternalCoord__tor_set;
+sub new {
+    my $pkg = shift;
+    my $self = Chemistry::OpenBabelc::new_OBInternalCoord(@_);
+    bless $self, $pkg if defined($self);
+}
+
+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_OBInternalCoord($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::OBAtom ##############
 
 package Chemistry::OpenBabel::OBAtom;
@@ -4130,7 +4179,6 @@ bless $obErrorLog, Chemistry::OpenBabel::OBMessageHandler;
 *LEU = *Chemistry::OpenBabelc::LEU;
 *SER = *Chemistry::OpenBabelc::SER;
 *VAL = *Chemistry::OpenBabelc::VAL;
-*THR = *Chemistry::OpenBabelc::THR;
 *LYS = *Chemistry::OpenBabelc::LYS;
 *ASP = *Chemistry::OpenBabelc::ASP;
 *ILE = *Chemistry::OpenBabelc::ILE;
@@ -4156,11 +4204,17 @@ bless $obErrorLog, Chemistry::OpenBabel::OBMessageHandler;
 *U = *Chemistry::OpenBabelc::U;
 *UPLUS = *Chemistry::OpenBabelc::UPLUS;
 *I = *Chemistry::OpenBabelc::I;
+*_1MA = *Chemistry::OpenBabelc::_1MA;
+*_5MC = *Chemistry::OpenBabelc::_5MC;
 *OMC = *Chemistry::OpenBabelc::OMC;
+*_1MG = *Chemistry::OpenBabelc::_1MG;
+*_2MG = *Chemistry::OpenBabelc::_2MG;
 *M2G = *Chemistry::OpenBabelc::M2G;
+*_7MG = *Chemistry::OpenBabelc::_7MG;
 *OMG = *Chemistry::OpenBabelc::OMG;
 *YG = *Chemistry::OpenBabelc::YG;
 *H2U = *Chemistry::OpenBabelc::H2U;
+*_5MU = *Chemistry::OpenBabelc::_5MU;
 *PSU = *Chemistry::OpenBabelc::PSU;
 *UNK = *Chemistry::OpenBabelc::UNK;
 *ACE = *Chemistry::OpenBabelc::ACE;

scripts/python/openbabel.py

@@ -566,31 +566,6 @@ OBResidueData_swigregister(OBResidueData)
 
 OpenDatafile = _openbabel.OpenDatafile
 FILE_SEP_CHAR = _openbabel.FILE_SEP_CHAR
-class OBStopwatch(object):
-    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
-    __repr__ = _swig_repr
-    def Start(*args): return _openbabel.OBStopwatch_Start(*args)
-    def Lap(*args): return _openbabel.OBStopwatch_Lap(*args)
-    def Elapsed(*args): return _openbabel.OBStopwatch_Elapsed(*args)
-    def __init__(self, *args): 
-        _openbabel.OBStopwatch_swiginit(self,_openbabel.new_OBStopwatch(*args))
-    __swig_destroy__ = _openbabel.delete_OBStopwatch
-    __del__ = lambda self : None;
-OBStopwatch_swigregister = _openbabel.OBStopwatch_swigregister
-OBStopwatch_swigregister(OBStopwatch)
-
-class OBSqrtTbl(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.OBSqrtTbl_swiginit(self,_openbabel.new_OBSqrtTbl(*args))
-    __swig_destroy__ = _openbabel.delete_OBSqrtTbl
-    __del__ = lambda self : None;
-    def Sqrt(*args): return _openbabel.OBSqrtTbl_Sqrt(*args)
-    def Init(*args): return _openbabel.OBSqrtTbl_Init(*args)
-OBSqrtTbl_swigregister = _openbabel.OBSqrtTbl_swigregister
-OBSqrtTbl_swigregister(OBSqrtTbl)
-
 class DoubleType(object):
     thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
     __repr__ = _swig_repr
@@ -620,6 +595,31 @@ class OBRandom(object):
 OBRandom_swigregister = _openbabel.OBRandom_swigregister
 OBRandom_swigregister(OBRandom)
 
+class OBStopwatch(object):
+    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
+    __repr__ = _swig_repr
+    def Start(*args): return _openbabel.OBStopwatch_Start(*args)
+    def Lap(*args): return _openbabel.OBStopwatch_Lap(*args)
+    def Elapsed(*args): return _openbabel.OBStopwatch_Elapsed(*args)
+    def __init__(self, *args): 
+        _openbabel.OBStopwatch_swiginit(self,_openbabel.new_OBStopwatch(*args))
+    __swig_destroy__ = _openbabel.delete_OBStopwatch
+    __del__ = lambda self : None;
+OBStopwatch_swigregister = _openbabel.OBStopwatch_swigregister
+OBStopwatch_swigregister(OBStopwatch)
+
+class OBSqrtTbl(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.OBSqrtTbl_swiginit(self,_openbabel.new_OBSqrtTbl(*args))
+    __swig_destroy__ = _openbabel.delete_OBSqrtTbl
+    __del__ = lambda self : None;
+    def Sqrt(*args): return _openbabel.OBSqrtTbl_Sqrt(*args)
+    def Init(*args): return _openbabel.OBSqrtTbl_Init(*args)
+OBSqrtTbl_swigregister = _openbabel.OBSqrtTbl_swigregister
+OBSqrtTbl_swigregister(OBSqrtTbl)
+
 class vector3(object):
     thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
     __repr__ = _swig_repr
@@ -1264,6 +1264,113 @@ AA_HIS = _openbabel.AA_HIS
 AA_CYS = _openbabel.AA_CYS
 AA_MET = _openbabel.AA_MET
 AA_TRP = _openbabel.AA_TRP
+class OBInternalCoord(object):
+    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
+    __repr__ = _swig_repr
+    _a = _swig_property(_openbabel.OBInternalCoord__a_get, _openbabel.OBInternalCoord__a_set)
+    _b = _swig_property(_openbabel.OBInternalCoord__b_get, _openbabel.OBInternalCoord__b_set)
+    _c = _swig_property(_openbabel.OBInternalCoord__c_get, _openbabel.OBInternalCoord__c_set)
+    _dst = _swig_property(_openbabel.OBInternalCoord__dst_get, _openbabel.OBInternalCoord__dst_set)
+    _ang = _swig_property(_openbabel.OBInternalCoord__ang_get, _openbabel.OBInternalCoord__ang_set)
+    _tor = _swig_property(_openbabel.OBInternalCoord__tor_get, _openbabel.OBInternalCoord__tor_set)
+    def __init__(self, *args): 
+        _openbabel.OBInternalCoord_swiginit(self,_openbabel.new_OBInternalCoord(*args))
+    __swig_destroy__ = _openbabel.delete_OBInternalCoord
+    __del__ = lambda self : None;
+OBInternalCoord_swigregister = _openbabel.OBInternalCoord_swigregister
+OBInternalCoord_swigregister(OBInternalCoord)
+ACIDIC = cvar.ACIDIC
+ACYCLIC = cvar.ACYCLIC
+ALIPHATIC = cvar.ALIPHATIC
+AROMATIC = cvar.AROMATIC
+BASIC = cvar.BASIC
+BURIED = cvar.BURIED
+CHARGED = cvar.CHARGED
+CYCLIC = cvar.CYCLIC
+HYDROPHOBIC = cvar.HYDROPHOBIC
+LARGE = cvar.LARGE
+MEDIUM = cvar.MEDIUM
+NEGATIVE = cvar.NEGATIVE
+NEUTRAL = cvar.NEUTRAL
+POLAR = cvar.POLAR
+POSITIVE = cvar.POSITIVE
+SMALL = cvar.SMALL
+SURFACE = cvar.SURFACE
+ALPHA_CARBON = cvar.ALPHA_CARBON
+AMINO_BACKBONE = cvar.AMINO_BACKBONE
+BACKBONE = cvar.BACKBONE
+CYSTEINE_SULPHUR = cvar.CYSTEINE_SULPHUR
+LIGAND = cvar.LIGAND
+NUCLEIC_BACKBONE = cvar.NUCLEIC_BACKBONE
+SHAPELY_BACKBONE = cvar.SHAPELY_BACKBONE
+SHAPELY_SPECIAL = cvar.SHAPELY_SPECIAL
+SIDECHAIN = cvar.SIDECHAIN
+SUGAR_PHOSPHATE = cvar.SUGAR_PHOSPHATE
+ALA = cvar.ALA
+GLY = cvar.GLY
+LEU = cvar.LEU
+SER = cvar.SER
+VAL = cvar.VAL
+THR = cvar.THR
+LYS = cvar.LYS
+ASP = cvar.ASP
+ILE = cvar.ILE
+ASN = cvar.ASN
+GLU = cvar.GLU
+PRO = cvar.PRO
+ARG = cvar.ARG
+PHE = cvar.PHE
+GLN = cvar.GLN
+TYR = cvar.TYR
+HIS = cvar.HIS
+CYS = cvar.CYS
+MET = cvar.MET
+TRP = cvar.TRP
+ASX = cvar.ASX
+GLX = cvar.GLX
+PCA = cvar.PCA
+HYP = cvar.HYP
+A = cvar.A
+C = cvar.C
+G = cvar.G
+T = cvar.T
+U = cvar.U
+UPLUS = cvar.UPLUS
+I = cvar.I
+_1MA = cvar._1MA
+_5MC = cvar._5MC
+OMC = cvar.OMC
+_1MG = cvar._1MG
+_2MG = cvar._2MG
+M2G = cvar.M2G
+_7MG = cvar._7MG
+OMG = cvar.OMG
+YG = cvar.YG
+H2U = cvar.H2U
+_5MU = cvar._5MU
+PSU = cvar.PSU
+UNK = cvar.UNK
+ACE = cvar.ACE
+FOR = cvar.FOR
+HOH = cvar.HOH
+DOD = cvar.DOD
+SO4 = cvar.SO4
+PO4 = cvar.PO4
+NAD = cvar.NAD
+COA = cvar.COA
+NAP = cvar.NAP
+NDP = cvar.NDP
+AMINO = cvar.AMINO
+AMINO_NUCLEO = cvar.AMINO_NUCLEO
+COENZYME = cvar.COENZYME
+ION = cvar.ION
+NUCLEO = cvar.NUCLEO
+PROTEIN = cvar.PROTEIN
+PURINE = cvar.PURINE
+PYRIMIDINE = cvar.PYRIMIDINE
+SOLVENT = cvar.SOLVENT
+WATER = cvar.WATER
+
 OB_4RING_ATOM = _openbabel.OB_4RING_ATOM
 OB_3RING_ATOM = _openbabel.OB_3RING_ATOM
 OB_AROMATIC_ATOM = _openbabel.OB_AROMATIC_ATOM
@@ -1411,91 +1518,6 @@ class OBAtom(OBBase):
     def MatchesSMARTS(*args): return _openbabel.OBAtom_MatchesSMARTS(*args)
 OBAtom_swigregister = _openbabel.OBAtom_swigregister
 OBAtom_swigregister(OBAtom)
-ACIDIC = cvar.ACIDIC
-ACYCLIC = cvar.ACYCLIC
-ALIPHATIC = cvar.ALIPHATIC
-AROMATIC = cvar.AROMATIC
-BASIC = cvar.BASIC
-BURIED = cvar.BURIED
-CHARGED = cvar.CHARGED
-CYCLIC = cvar.CYCLIC
-HYDROPHOBIC = cvar.HYDROPHOBIC
-LARGE = cvar.LARGE
-MEDIUM = cvar.MEDIUM
-NEGATIVE = cvar.NEGATIVE
-NEUTRAL = cvar.NEUTRAL
-POLAR = cvar.POLAR
-POSITIVE = cvar.POSITIVE
-SMALL = cvar.SMALL
-SURFACE = cvar.SURFACE
-ALPHA_CARBON = cvar.ALPHA_CARBON
-AMINO_BACKBONE = cvar.AMINO_BACKBONE
-BACKBONE = cvar.BACKBONE
-CYSTEINE_SULPHUR = cvar.CYSTEINE_SULPHUR
-LIGAND = cvar.LIGAND
-NUCLEIC_BACKBONE = cvar.NUCLEIC_BACKBONE
-SHAPELY_BACKBONE = cvar.SHAPELY_BACKBONE
-SHAPELY_SPECIAL = cvar.SHAPELY_SPECIAL
-SIDECHAIN = cvar.SIDECHAIN
-SUGAR_PHOSPHATE = cvar.SUGAR_PHOSPHATE
-ALA = cvar.ALA
-GLY = cvar.GLY
-LEU = cvar.LEU
-SER = cvar.SER
-VAL = cvar.VAL
-THR = cvar.THR
-LYS = cvar.LYS
-ASP = cvar.ASP
-ILE = cvar.ILE
-ASN = cvar.ASN
-GLU = cvar.GLU
-PRO = cvar.PRO
-ARG = cvar.ARG
-PHE = cvar.PHE
-GLN = cvar.GLN
-TYR = cvar.TYR
-HIS = cvar.HIS
-CYS = cvar.CYS
-MET = cvar.MET
-TRP = cvar.TRP
-ASX = cvar.ASX
-GLX = cvar.GLX
-PCA = cvar.PCA
-HYP = cvar.HYP
-A = cvar.A
-C = cvar.C
-G = cvar.G
-T = cvar.T
-U = cvar.U
-UPLUS = cvar.UPLUS
-I = cvar.I
-OMC = cvar.OMC
-M2G = cvar.M2G
-OMG = cvar.OMG
-YG = cvar.YG
-H2U = cvar.H2U
-PSU = cvar.PSU
-UNK = cvar.UNK
-ACE = cvar.ACE
-FOR = cvar.FOR
-HOH = cvar.HOH
-DOD = cvar.DOD
-SO4 = cvar.SO4
-PO4 = cvar.PO4
-NAD = cvar.NAD
-COA = cvar.COA
-NAP = cvar.NAP
-NDP = cvar.NDP
-AMINO = cvar.AMINO
-AMINO_NUCLEO = cvar.AMINO_NUCLEO
-COENZYME = cvar.COENZYME
-ION = cvar.ION
-NUCLEO = cvar.NUCLEO
-PROTEIN = cvar.PROTEIN
-PURINE = cvar.PURINE
-PYRIMIDINE = cvar.PYRIMIDINE
-SOLVENT = cvar.SOLVENT
-WATER = cvar.WATER
 
 OB_AROMATIC_BOND = _openbabel.OB_AROMATIC_BOND
 OB_WEDGE_BOND = _openbabel.OB_WEDGE_BOND
@@ -2814,5 +2836,27 @@ class OBResidueAtomIter(object):
 OBResidueAtomIter_swigregister = _openbabel.OBResidueAtomIter_swigregister
 OBResidueAtomIter_swigregister(OBResidueAtomIter)
 
+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
+    def __init__(self, *args): 
+        _openbabel.doubleArray_swiginit(self,_openbabel.new_doubleArray(*args))
+    __swig_destroy__ = _openbabel.delete_doubleArray
+    __del__ = lambda self : None;
+    def __getitem__(*args): return _openbabel.doubleArray___getitem__(*args)
+    def __setitem__(*args): return _openbabel.doubleArray___setitem__(*args)
+    def cast(*args): return _openbabel.doubleArray_cast(*args)
+    frompointer = staticmethod(_openbabel.doubleArray_frompointer)
+doubleArray_swigregister = _openbabel.doubleArray_swigregister
+doubleArray_swigregister(doubleArray)
+doubleArray_frompointer = _openbabel.doubleArray_frompointer
+
+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
+