rino 0.1.0 → 0.2.0

data/ext/src/inpdef.h

@@ -2,8 +2,8 @@
  * International Union of Pure and Applied Chemistry (IUPAC)
  * International Chemical Identifier (InChI)
  * Version 1
- * Software version 1.00
- * April 13, 2005
+ * Software version 1.01
+ * July 21, 2006
  * Developed at NIST
  */
 
@@ -274,7 +274,8 @@ int DisconnectSalts( ORIG_ATOM_DATA *orig_inp_data, int bDisconnect );
 int DisconnectMetals( ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone );
 int bMayDisconnectMetals( ORIG_ATOM_DATA *orig_inp_data, int bCheckMetalValence, INCHI_MODE *bTautFlagsDone );
 int bHasMetalAtom( ORIG_ATOM_DATA *orig_inp_data );
-int fix_odd_things( int num_atoms, inp_ATOM *at );
+int FixAdjacentRadicals( int num_inp_atoms, inp_ATOM *at ); /* FIX_ADJ_RAD == 1 */
+int fix_odd_things( int num_atoms, inp_ATOM *at, int bFixBug );
 int post_fix_odd_things( int num_atoms, inp_ATOM *at );
 int remove_ion_pairs( int num_atoms, inp_ATOM *at );
 
@@ -288,6 +289,8 @@ void FreeInpAtomData( INP_ATOM_DATA *inp_at_data );
 void FreeCompAtomData( COMP_ATOM_DATA *inp_at_data );
 void FreeInfoAtomData( INF_ATOM_DATA *inf_at_data );
 
+int FixUnkn0DStereoBonds(inp_ATOM *at, int num_at);
+
 inf_ATOM *CreateInfAtom( int num_atoms );
 inp_ATOM *CreateInpAtom( int num_atoms );
 

data/ext/src/libinchi_wrap.c

@@ -0,0 +1,912 @@
+/* ----------------------------------------------------------------------------
+ * This file was automatically generated by SWIG (http://www.swig.org).
+ * Version 1.3.24
+ * 
+ * This file is not intended to be easily readable and contains a number of 
+ * coding conventions designed to improve portability and efficiency. Do not make
+ * changes to this file unless you know what you are doing--modify the SWIG 
+ * interface file instead. 
+ * ----------------------------------------------------------------------------- */
+
+
+#ifndef SWIG_TEMPLATE_DISAMBIGUATOR
+#  if defined(__SUNPRO_CC) 
+#    define SWIG_TEMPLATE_DISAMBIGUATOR template
+#  else
+#    define SWIG_TEMPLATE_DISAMBIGUATOR 
+#  endif
+#endif
+
+/* ruby.swg */
+/* Implementation : RUBY */
+#define SWIGRUBY 1
+
+#include "ruby.h"
+
+/* Flags for pointer conversion */
+#define SWIG_POINTER_EXCEPTION     0x1
+#define SWIG_POINTER_DISOWN        0x2
+
+#define NUM2USHRT(n) (\
+    (0 <= NUM2UINT(n) && NUM2UINT(n) <= USHRT_MAX)\
+    ? (unsigned short) NUM2UINT(n) \
+    : (rb_raise(rb_eArgError, "integer %d out of range of `unsigned short'",\
+               NUM2UINT(n)), (short)0)\
+)
+
+#define NUM2SHRT(n) (\
+    (SHRT_MIN <= NUM2INT(n) && NUM2INT(n) <= SHRT_MAX)\
+    ? (short)NUM2INT(n)\
+    : (rb_raise(rb_eArgError, "integer %d out of range of `short'",\
+               NUM2INT(n)), (short)0)\
+)
+
+/* Ruby 1.7 defines NUM2LL(), LL2NUM() and ULL2NUM() macros */
+#ifndef NUM2LL
+#define NUM2LL(x) NUM2LONG((x))
+#endif
+#ifndef LL2NUM
+#define LL2NUM(x) INT2NUM((long) (x))
+#endif
+#ifndef ULL2NUM
+#define ULL2NUM(x) UINT2NUM((unsigned long) (x))
+#endif
+
+/* Ruby 1.7 doesn't (yet) define NUM2ULL() */
+#ifndef NUM2ULL
+#ifdef HAVE_LONG_LONG
+#define NUM2ULL(x) rb_num2ull((x))
+#else
+#define NUM2ULL(x) NUM2ULONG(x)
+#endif
+#endif
+
+/*
+ * Need to be very careful about how these macros are defined, especially
+ * when compiling C++ code or C code with an ANSI C compiler.
+ *
+ * VALUEFUNC(f) is a macro used to typecast a C function that implements
+ * a Ruby method so that it can be passed as an argument to API functions
+ * like rb_define_method() and rb_define_singleton_method().
+ *
+ * VOIDFUNC(f) is a macro used to typecast a C function that implements
+ * either the "mark" or "free" stuff for a Ruby Data object, so that it
+ * can be passed as an argument to API functions like Data_Wrap_Struct()
+ * and Data_Make_Struct().
+ */
+ 
+#ifdef __cplusplus
+#  ifndef RUBY_METHOD_FUNC /* These definitions should work for Ruby 1.4.6 */
+#    define PROTECTFUNC(f) ((VALUE (*)()) f)
+#    define VALUEFUNC(f) ((VALUE (*)()) f)
+#    define VOIDFUNC(f)  ((void (*)()) f)
+#  else
+#    ifndef ANYARGS /* These definitions should work for Ruby 1.6 */
+#      define PROTECTFUNC(f) ((VALUE (*)()) f)
+#      define VALUEFUNC(f) ((VALUE (*)()) f)
+#      define VOIDFUNC(f)  ((RUBY_DATA_FUNC) f)
+#    else /* These definitions should work for Ruby 1.7+ */
+#      define PROTECTFUNC(f) ((VALUE (*)(VALUE)) f)
+#      define VALUEFUNC(f) ((VALUE (*)(ANYARGS)) f)
+#      define VOIDFUNC(f)  ((RUBY_DATA_FUNC) f)
+#    endif
+#  endif
+#else
+#  define VALUEFUNC(f) (f)
+#  define VOIDFUNC(f) (f)
+#endif
+
+typedef struct {
+  VALUE klass;
+  VALUE mImpl;
+  void  (*mark)(void *);
+  void  (*destroy)(void *);
+} swig_class;
+
+/* Don't use for expressions have side effect */
+#ifndef RB_STRING_VALUE
+#define RB_STRING_VALUE(s) (TYPE(s) == T_STRING ? (s) : (*(volatile VALUE *)&(s) = rb_str_to_str(s)))
+#endif
+#ifndef StringValue
+#define StringValue(s) RB_STRING_VALUE(s)
+#endif
+#ifndef StringValuePtr
+#define StringValuePtr(s) RSTRING(RB_STRING_VALUE(s))->ptr
+#endif
+#ifndef StringValueLen
+#define StringValueLen(s) RSTRING(RB_STRING_VALUE(s))->len
+#endif
+#ifndef SafeStringValue
+#define SafeStringValue(v) do {\
+    StringValue(v);\
+    rb_check_safe_str(v);\
+} while (0)
+#endif
+
+#ifndef HAVE_RB_DEFINE_ALLOC_FUNC
+#define rb_define_alloc_func(klass, func) rb_define_singleton_method((klass), "new", VALUEFUNC((func)), -1)
+#define rb_undef_alloc_func(klass) rb_undef_method(CLASS_OF((klass)), "new")
+#endif
+
+/* Contract support */
+
+#define SWIG_contract_assert(expr, msg) if (!(expr)) { rb_raise(rb_eRuntimeError, (char *) msg ); } else
+
+
+/***********************************************************************
+ * swigrun.swg
+ *
+ *     This file contains generic CAPI SWIG runtime support for pointer
+ *     type checking.
+ *
+ ************************************************************************/
+
+/* This should only be incremented when either the layout of swig_type_info changes,
+   or for whatever reason, the runtime changes incompatibly */
+#define SWIG_RUNTIME_VERSION "1"
+
+/* define SWIG_TYPE_TABLE_NAME as "SWIG_TYPE_TABLE" */
+#ifdef SWIG_TYPE_TABLE
+#define SWIG_QUOTE_STRING(x) #x
+#define SWIG_EXPAND_AND_QUOTE_STRING(x) SWIG_QUOTE_STRING(x)
+#define SWIG_TYPE_TABLE_NAME SWIG_EXPAND_AND_QUOTE_STRING(SWIG_TYPE_TABLE)
+#else
+#define SWIG_TYPE_TABLE_NAME
+#endif
+
+#include <string.h>
+
+#ifndef SWIGINLINE
+#if defined(__cplusplus) || (defined(__GNUC__) && !defined(__STRICT_ANSI__))
+#  define SWIGINLINE inline
+#else
+#  define SWIGINLINE
+#endif
+#endif
+
+/*
+  You can use the SWIGRUNTIME and SWIGRUNTIMEINLINE macros for
+  creating a static or dynamic library from the swig runtime code.
+  In 99.9% of the cases, swig just needs to declare them as 'static'.
+  
+  But only do this if is strictly necessary, ie, if you have problems
+  with your compiler or so.
+*/
+#ifndef SWIGRUNTIME
+#define SWIGRUNTIME static
+#endif
+#ifndef SWIGRUNTIMEINLINE
+#define SWIGRUNTIMEINLINE SWIGRUNTIME SWIGINLINE
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef void *(*swig_converter_func)(void *);
+typedef struct swig_type_info *(*swig_dycast_func)(void **);
+
+typedef struct swig_type_info {
+  const char             *name;
+  swig_converter_func     converter;
+  const char             *str;
+  void                   *clientdata;
+  swig_dycast_func        dcast;
+  struct swig_type_info  *next;
+  struct swig_type_info  *prev;
+} swig_type_info;
+
+/* 
+  Compare two type names skipping the space characters, therefore
+  "char*" == "char *" and "Class<int>" == "Class<int >", etc.
+
+  Return 0 when the two name types are equivalent, as in
+  strncmp, but skipping ' '.
+*/
+SWIGRUNTIME int
+SWIG_TypeNameComp(const char *f1, const char *l1,
+		  const char *f2, const char *l2) {
+  for (;(f1 != l1) && (f2 != l2); ++f1, ++f2) {
+    while ((*f1 == ' ') && (f1 != l1)) ++f1;
+    while ((*f2 == ' ') && (f2 != l2)) ++f2;
+    if (*f1 != *f2) return *f1 - *f2;
+  }
+  return (l1 - f1) - (l2 - f2);
+}
+
+/*
+  Check type equivalence in a name list like <name1>|<name2>|...
+*/
+SWIGRUNTIME int
+SWIG_TypeEquiv(const char *nb, const char *tb) {
+  int equiv = 0;
+  const char* te = tb + strlen(tb);
+  const char* ne = nb;
+  while (!equiv && *ne) {
+    for (nb = ne; *ne; ++ne) {
+      if (*ne == '|') break;
+    }
+    equiv = SWIG_TypeNameComp(nb, ne, tb, te) == 0;
+    if (*ne) ++ne;
+  }
+  return equiv;
+}
+
+/*
+  Register a type mapping with the type-checking
+*/
+SWIGRUNTIME swig_type_info *
+SWIG_TypeRegisterTL(swig_type_info **tl, swig_type_info *ti) {
+  swig_type_info *tc, *head, *ret, *next;
+  /* Check to see if this type has already been registered */
+  tc = *tl;
+  while (tc) {
+    /* check simple type equivalence */
+    int typeequiv = (strcmp(tc->name, ti->name) == 0);   
+    /* check full type equivalence, resolving typedefs */
+    if (!typeequiv) {
+      /* only if tc is not a typedef (no '|' on it) */
+      if (tc->str && ti->str && !strstr(tc->str,"|")) {
+	typeequiv = SWIG_TypeEquiv(ti->str,tc->str);
+      }
+    }
+    if (typeequiv) {
+      /* Already exists in the table.  Just add additional types to the list */
+      if (ti->clientdata) tc->clientdata = ti->clientdata;
+      head = tc;
+      next = tc->next;
+      goto l1;
+    }
+    tc = tc->prev;
+  }
+  head = ti;
+  next = 0;
+
+  /* Place in list */
+  ti->prev = *tl;
+  *tl = ti;
+
+  /* Build linked lists */
+  l1:
+  ret = head;
+  tc = ti + 1;
+  /* Patch up the rest of the links */
+  while (tc->name) {
+    head->next = tc;
+    tc->prev = head;
+    head = tc;
+    tc++;
+  }
+  if (next) next->prev = head;
+  head->next = next;
+
+  return ret;
+}
+
+/*
+  Check the typename
+*/
+SWIGRUNTIME swig_type_info *
+SWIG_TypeCheck(const char *c, swig_type_info *ty) {
+  swig_type_info *s;
+  if (!ty) return 0;        /* Void pointer */
+  s = ty->next;             /* First element always just a name */
+  do {
+    if (strcmp(s->name,c) == 0) {
+      if (s == ty->next) return s;
+      /* Move s to the top of the linked list */
+      s->prev->next = s->next;
+      if (s->next) {
+        s->next->prev = s->prev;
+      }
+      /* Insert s as second element in the list */
+      s->next = ty->next;
+      if (ty->next) ty->next->prev = s;
+      ty->next = s;
+      s->prev = ty;
+      return s;
+    }
+    s = s->next;
+  } while (s && (s != ty->next));
+  return 0;
+}
+
+/*
+  Cast a pointer up an inheritance hierarchy
+*/
+SWIGRUNTIMEINLINE void *
+SWIG_TypeCast(swig_type_info *ty, void *ptr) {
+  return ((!ty) || (!ty->converter)) ? ptr : (*ty->converter)(ptr);
+}
+
+/* 
+   Dynamic pointer casting. Down an inheritance hierarchy
+*/
+SWIGRUNTIME swig_type_info *
+SWIG_TypeDynamicCast(swig_type_info *ty, void **ptr) {
+  swig_type_info *lastty = ty;
+  if (!ty || !ty->dcast) return ty;
+  while (ty && (ty->dcast)) {
+    ty = (*ty->dcast)(ptr);
+    if (ty) lastty = ty;
+  }
+  return lastty;
+}
+
+/*
+  Return the name associated with this type
+*/
+SWIGRUNTIMEINLINE const char *
+SWIG_TypeName(const swig_type_info *ty) {
+  return ty->name;
+}
+
+/*
+  Return the pretty name associated with this type,
+  that is an unmangled type name in a form presentable to the user.
+*/
+SWIGRUNTIME const char *
+SWIG_TypePrettyName(const swig_type_info *type) {
+  /* The "str" field contains the equivalent pretty names of the
+     type, separated by vertical-bar characters.  We choose
+     to print the last name, as it is often (?) the most
+     specific. */
+  if (type->str != NULL) {
+    const char *last_name = type->str;
+    const char *s;
+    for (s = type->str; *s; s++)
+      if (*s == '|') last_name = s+1;
+    return last_name;
+  }
+  else
+    return type->name;
+}
+
+/*
+  Search for a swig_type_info structure
+*/
+SWIGRUNTIME swig_type_info *
+SWIG_TypeQueryTL(swig_type_info *tl, const char *name) {
+  swig_type_info *ty = tl;
+  while (ty) {
+    if (ty->str && (SWIG_TypeEquiv(ty->str,name))) return ty;
+    if (ty->name && (strcmp(name,ty->name) == 0)) return ty;
+    ty = ty->prev;
+  }
+  return 0;
+}
+
+/* 
+   Set the clientdata field for a type
+*/
+SWIGRUNTIME void
+SWIG_TypeClientDataTL(swig_type_info *tl, swig_type_info *ti, void *clientdata) {
+  swig_type_info *tc, *equiv;
+  if (ti->clientdata) return;
+  /* if (ti->clientdata == clientdata) return; */
+  ti->clientdata = clientdata;
+  equiv = ti->next;
+  while (equiv) {
+    if (!equiv->converter) {
+      tc = tl;
+      while (tc) {
+        if ((strcmp(tc->name, equiv->name) == 0))
+          SWIG_TypeClientDataTL(tl,tc,clientdata);
+        tc = tc->prev;
+      }
+    }
+    equiv = equiv->next;
+  }
+}
+
+/* 
+   Pack binary data into a string
+*/
+SWIGRUNTIME char *
+SWIG_PackData(char *c, void *ptr, size_t sz) {
+  static char hex[17] = "0123456789abcdef";
+  unsigned char *u = (unsigned char *) ptr;
+  const unsigned char *eu =  u + sz;
+  register unsigned char uu;
+  for (; u != eu; ++u) {
+    uu = *u;
+    *(c++) = hex[(uu & 0xf0) >> 4];
+    *(c++) = hex[uu & 0xf];
+  }
+  return c;
+}
+
+/* 
+   Unpack binary data from a string
+*/
+SWIGRUNTIME const char *
+SWIG_UnpackData(const char *c, void *ptr, size_t sz) {
+  register unsigned char *u = (unsigned char *) ptr;
+  register const unsigned char *eu =  u + sz;
+  for (; u != eu; ++u) {
+    register int d = *(c++);
+    register unsigned char uu = 0;
+    if ((d >= '0') && (d <= '9'))
+      uu = ((d - '0') << 4);
+    else if ((d >= 'a') && (d <= 'f'))
+      uu = ((d - ('a'-10)) << 4);
+    else 
+      return (char *) 0;
+    d = *(c++);
+    if ((d >= '0') && (d <= '9'))
+      uu |= (d - '0');
+    else if ((d >= 'a') && (d <= 'f'))
+      uu |= (d - ('a'-10));
+    else 
+      return (char *) 0;
+    *u = uu;
+  }
+  return c;
+}
+
+/*
+  This function will propagate the clientdata field of type to any new
+  swig_type_info structures that have been added into the list of
+  equivalent types.  It is like calling SWIG_TypeClientData(type,
+  clientdata) a second time.
+*/
+SWIGRUNTIME void
+SWIG_PropagateClientDataTL(swig_type_info *tl, swig_type_info *type) {
+  swig_type_info *equiv = type->next;
+  swig_type_info *tc;
+  if (!type->clientdata) return;
+  while (equiv) {
+    if (!equiv->converter) {
+      tc = tl;
+      while (tc) {
+        if ((strcmp(tc->name, equiv->name) == 0) && !tc->clientdata)
+          SWIG_TypeClientDataTL(tl,tc, type->clientdata);
+        tc = tc->prev;
+      }
+    }
+    equiv = equiv->next;
+  }
+}
+
+/* 
+   Pack 'void *' into a string buffer.
+*/
+SWIGRUNTIME char *
+SWIG_PackVoidPtr(char *buff, void *ptr, const char *name, size_t bsz) {
+  char *r = buff;
+  if ((2*sizeof(void *) + 2) > bsz) return 0;
+  *(r++) = '_';
+  r = SWIG_PackData(r,&ptr,sizeof(void *));
+  if (strlen(name) + 1 > (bsz - (r - buff))) return 0;
+  strcpy(r,name);
+  return buff;
+}
+
+SWIGRUNTIME const char *
+SWIG_UnpackVoidPtr(const char *c, void **ptr, const char *name) {
+  if (*c != '_') {
+    if (strcmp(c,"NULL") == 0) {
+      *ptr = (void *) 0;
+      return name;
+    } else {
+      return 0;
+    }
+  }
+  return SWIG_UnpackData(++c,ptr,sizeof(void *));
+}
+
+SWIGRUNTIME char *
+SWIG_PackDataName(char *buff, void *ptr, size_t sz, const char *name, size_t bsz) {
+  char *r = buff;
+  size_t lname = (name ? strlen(name) : 0);
+  if ((2*sz + 2 + lname) > bsz) return 0;
+  *(r++) = '_';
+  r = SWIG_PackData(r,ptr,sz);
+  if (lname) {
+    strncpy(r,name,lname+1);
+  } else {
+    *r = 0;
+  }
+  return buff;
+}
+
+SWIGRUNTIME const char *
+SWIG_UnpackDataName(const char *c, void *ptr, size_t sz, const char *name) {
+  if (*c != '_') {
+    if (strcmp(c,"NULL") == 0) {
+      memset(ptr,0,sz);
+      return name;
+    } else {
+      return 0;
+    }
+  }
+  return SWIG_UnpackData(++c,ptr,sz);
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+/***********************************************************************
+ * common.swg
+ *
+ *     This file contains generic SWIG runtime support for pointer
+ *     type checking as well as a few commonly used macros to control
+ *     external linkage.
+ *
+ * Author : David Beazley (beazley@cs.uchicago.edu)
+ *
+ * Copyright (c) 1999-2000, The University of Chicago
+ * 
+ * This file may be freely redistributed without license or fee provided
+ * this copyright message remains intact.
+ ************************************************************************/
+
+
+#if defined(_WIN32) || defined(__WIN32__) || defined(__CYGWIN__)
+#  if !defined(STATIC_LINKED)
+#    define SWIGEXPORT(a) __declspec(dllexport) a
+#  else
+#    define SWIGEXPORT(a) a
+#  endif
+#else
+#  define SWIGEXPORT(a) a
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+/*************************************************************************/
+
+
+/* The static type info list */
+
+static swig_type_info *swig_type_list = 0;
+static swig_type_info **swig_type_list_handle = &swig_type_list;
+  
+
+/* Register a type mapping with the type-checking */
+static swig_type_info *
+SWIG_TypeRegister(swig_type_info *ti) {
+  return SWIG_TypeRegisterTL(swig_type_list_handle, ti);
+}
+
+/* Search for a swig_type_info structure */
+static swig_type_info *
+SWIG_TypeQuery(const char *name) {
+  return SWIG_TypeQueryTL(*swig_type_list_handle, name);
+}
+
+/* Set the clientdata field for a type */
+static void
+SWIG_TypeClientData(swig_type_info *ti, void *clientdata) {
+  SWIG_TypeClientDataTL(*swig_type_list_handle, ti, clientdata);
+}
+
+/* This function will propagate the clientdata field of type to
+* any new swig_type_info structures that have been added into the list
+* of equivalent types.  It is like calling
+* SWIG_TypeClientData(type, clientdata) a second time.
+*/
+static void
+SWIG_PropagateClientData(swig_type_info *type) {
+  SWIG_PropagateClientDataTL(*swig_type_list_handle, type);
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+/* Common SWIG API */
+#define SWIG_ConvertPtr(obj, pp, type, flags) \
+  SWIG_Ruby_ConvertPtr(obj, pp, type, flags)
+#define SWIG_NewPointerObj(p, type, flags) \
+  SWIG_Ruby_NewPointerObj(p, type, flags)
+#define SWIG_MustGetPtr(p, type, argnum, flags) \
+  SWIG_Ruby_MustGetPtr(p, type, argnum, flags)
+
+/* Ruby-specific SWIG API */
+
+#define SWIG_InitRuntime() \
+  SWIG_Ruby_InitRuntime()
+#define SWIG_define_class(ty) \
+  SWIG_Ruby_define_class(ty)
+#define SWIG_NewClassInstance(value, ty) \
+  SWIG_Ruby_NewClassInstance(value, ty)
+#define SWIG_MangleStr(value) \
+  SWIG_Ruby_MangleStr(value)
+#define SWIG_CheckConvert(value, ty) \
+  SWIG_Ruby_CheckConvert(value, ty)
+#define SWIG_NewPackedObj(ptr, sz, ty) \
+  SWIG_Ruby_NewPackedObj(ptr, sz, ty)
+#define SWIG_ConvertPacked(obj, ptr, sz, ty, flags) \
+  SWIG_Ruby_ConvertPacked(obj, ptr, sz, ty, flags)
+
+/* rubydef.swg */
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+static VALUE _mSWIG = Qnil;
+static VALUE _cSWIG_Pointer = Qnil;
+static VALUE swig_runtime_data_type_pointer = Qnil;
+
+/* Initialize Ruby runtime support */
+static void
+SWIG_Ruby_InitRuntime(void)
+{
+    VALUE pointer;
+    
+    if (_mSWIG == Qnil) {
+        _mSWIG = rb_define_module("SWIG");
+    }
+    
+    /* first check if pointer already created */
+    pointer = rb_gv_get("$swig_runtime_data_type_pointer" SWIG_RUNTIME_VERSION SWIG_TYPE_TABLE_NAME);
+    if (pointer != Qnil) {
+      Data_Get_Struct(pointer, swig_type_info *, swig_type_list_handle);
+    } else {
+      /* register a new class */
+      VALUE cl = rb_define_class("swig_runtime_data", rb_cObject);
+      /* create and store the structure pointer to a global variable */
+      swig_runtime_data_type_pointer = Data_Wrap_Struct(cl, 0, 0, swig_type_list_handle);
+      rb_define_readonly_variable("$swig_runtime_data_type_pointer" SWIG_RUNTIME_VERSION SWIG_TYPE_TABLE_NAME, &swig_runtime_data_type_pointer);
+    }
+}
+
+/* Define Ruby class for C type */
+static void
+SWIG_Ruby_define_class(swig_type_info *type)
+{
+    VALUE klass;
+    char *klass_name = (char *) malloc(4 + strlen(type->name) + 1);
+    sprintf(klass_name, "TYPE%s", type->name);
+    if (NIL_P(_cSWIG_Pointer)) {
+	_cSWIG_Pointer = rb_define_class_under(_mSWIG, "Pointer", rb_cObject);
+	rb_undef_method(CLASS_OF(_cSWIG_Pointer), "new");
+    }
+    klass = rb_define_class_under(_mSWIG, klass_name, _cSWIG_Pointer);
+    free((void *) klass_name);
+}
+
+/* Create a new pointer object */
+static VALUE
+SWIG_Ruby_NewPointerObj(void *ptr, swig_type_info *type, int own)
+{
+    char *klass_name;
+    swig_class *sklass;
+    VALUE klass;
+    VALUE obj;
+    
+    if (!ptr)
+	return Qnil;
+    
+    if (type->clientdata) {
+      sklass = (swig_class *) type->clientdata;
+      obj = Data_Wrap_Struct(sklass->klass, VOIDFUNC(sklass->mark), (own ? VOIDFUNC(sklass->destroy) : 0), ptr);
+    } else {
+      klass_name = (char *) malloc(4 + strlen(type->name) + 1);
+      sprintf(klass_name, "TYPE%s", type->name);
+      klass = rb_const_get(_mSWIG, rb_intern(klass_name));
+      free((void *) klass_name);
+      obj = Data_Wrap_Struct(klass, 0, 0, ptr);
+    }
+    rb_iv_set(obj, "__swigtype__", rb_str_new2(type->name));
+    return obj;
+}
+
+/* Create a new class instance (always owned) */
+static VALUE
+SWIG_Ruby_NewClassInstance(VALUE klass, swig_type_info *type)
+{
+    VALUE obj;
+    swig_class *sklass = (swig_class *) type->clientdata;
+    obj = Data_Wrap_Struct(klass, VOIDFUNC(sklass->mark), VOIDFUNC(sklass->destroy), 0);
+    rb_iv_set(obj, "__swigtype__", rb_str_new2(type->name));
+    return obj;
+}
+
+/* Get type mangle from class name */
+static SWIGINLINE char *
+SWIG_Ruby_MangleStr(VALUE obj)
+{
+  VALUE stype = rb_iv_get(obj, "__swigtype__");
+  return StringValuePtr(stype);
+}
+
+/* Convert a pointer value */
+static int
+SWIG_Ruby_ConvertPtr(VALUE obj, void **ptr, swig_type_info *ty, int flags)
+{
+  char *c;
+  swig_type_info *tc;
+
+  /* Grab the pointer */
+  if (NIL_P(obj)) {
+    *ptr = 0;
+    return 0;
+  } else {
+    Data_Get_Struct(obj, void, *ptr);
+  }
+  
+  /* Do type-checking if type info was provided */
+  if (ty) {
+    if (ty->clientdata) {
+        if (rb_obj_is_kind_of(obj, ((swig_class *) (ty->clientdata))->klass)) {
+          if (*ptr == 0)
+            rb_raise(rb_eRuntimeError, "This %s already released", ty->str);
+          return 0;
+        }
+    }
+    if ((c = SWIG_MangleStr(obj)) == NULL) {
+      if (flags & SWIG_POINTER_EXCEPTION)
+        rb_raise(rb_eTypeError, "Expected %s", ty->str);
+      else
+        return -1;
+    }
+    tc = SWIG_TypeCheck(c, ty);
+    if (!tc) {
+      if (flags & SWIG_POINTER_EXCEPTION)
+        rb_raise(rb_eTypeError, "Expected %s", ty->str);
+      else
+        return -1;
+    }
+    *ptr = SWIG_TypeCast(tc, *ptr);
+  }
+  return 0;
+}
+
+/* Convert a pointer value, signal an exception on a type mismatch */
+static SWIGINLINE void *
+SWIG_Ruby_MustGetPtr(VALUE obj, swig_type_info *ty, int argnum, int flags)
+{
+  void *result;
+  SWIG_ConvertPtr(obj, &result, ty, flags | SWIG_POINTER_EXCEPTION);
+  return result;
+}
+
+/* Check convert */
+static SWIGINLINE int
+SWIG_Ruby_CheckConvert(VALUE obj, swig_type_info *ty)
+{
+  char *c = SWIG_MangleStr(obj);
+  if (!c)
+    return 0;
+  return SWIG_TypeCheck(c,ty) != 0;
+}
+
+static VALUE
+SWIG_Ruby_NewPackedObj(void *ptr, int sz, swig_type_info *type) {
+  char result[1024];
+  char *r = result;
+  if ((2*sz + 1 + strlen(type->name)) > 1000) return 0;
+  *(r++) = '_';
+  r = SWIG_PackData(r, ptr, sz);
+  strcpy(r, type->name);
+  return rb_str_new2(result);
+}
+
+/* Convert a packed value value */
+static void
+SWIG_Ruby_ConvertPacked(VALUE obj, void *ptr, int sz, swig_type_info *ty, int flags) {
+  swig_type_info *tc;
+  const char  *c;
+
+  if (TYPE(obj) != T_STRING) goto type_error;
+  c = StringValuePtr(obj);
+  /* Pointer values must start with leading underscore */
+  if (*c != '_') goto type_error;
+  c++;
+  c = SWIG_UnpackData(c, ptr, sz);
+  if (ty) {
+    tc = SWIG_TypeCheck(c, ty);
+    if (!tc) goto type_error;
+  }
+  return;
+
+type_error:
+
+  if (flags) {
+    if (ty) {
+      rb_raise(rb_eTypeError, "Type error. Expected %s", ty->name);
+    } else {
+      rb_raise(rb_eTypeError, "Expected a pointer");
+    }
+  }
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+
+
+/* -------- TYPES TABLE (BEGIN) -------- */
+
+#define  SWIGTYPE_p_unsigned_long swig_types[0] 
+#define  SWIGTYPE_p_p_char swig_types[1] 
+static swig_type_info *swig_types[3];
+
+/* -------- TYPES TABLE (END) -------- */
+
+#define SWIG_init    Init_libinchi
+#define SWIG_name    "Libinchi"
+
+static VALUE mLibinchi;
+static VALUE mRino;
+
+static void SWIG_AsVal(VALUE obj, int *val)
+{
+    *val = (int) NUM2INT(obj);
+}
+
+int run(int,char **);
+static VALUE
+_wrap_run(int argc, VALUE *argv, VALUE self) {
+    int arg1 ;
+    char **arg2 = (char **) 0 ;
+    int result;
+    VALUE vresult = Qnil;
+    
+    if ((argc < 1) || (argc > 1))
+    rb_raise(rb_eArgError, "wrong # of arguments(%d for 1)",argc);
+    {
+        /* Get the length of the array */
+        int size = RARRAY(argv[0])->len; 
+        int i;
+        arg1 = (int) size;
+        arg2 = (char **) malloc((size+1)*sizeof(char *));
+        /* Get the first element in memory */
+        VALUE *ptr = RARRAY(argv[0])->ptr; 
+        for (i=0; i < size; i++, ptr++)
+        /* Convert Ruby Object String to char* */
+        arg2[i]= STR2CSTR(*ptr); 
+        arg2[i]=NULL; /* End of list */
+    }
+    result = (int)run(arg1,arg2);
+    
+    vresult = INT2NUM(result);
+    {
+        free((char *) arg2);
+    }
+    return vresult;
+}
+
+
+
+/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (BEGIN) -------- */
+
+static swig_type_info _swigt__p_unsigned_long[] = {{"_p_unsigned_long", 0, "unsigned long *|VALUE *", 0, 0, 0, 0},{"_p_unsigned_long", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}};
+static swig_type_info _swigt__p_p_char[] = {{"_p_p_char", 0, "char **", 0, 0, 0, 0},{"_p_p_char", 0, 0, 0, 0, 0, 0},{0, 0, 0, 0, 0, 0, 0}};
+
+static swig_type_info *swig_types_initial[] = {
+_swigt__p_unsigned_long, 
+_swigt__p_p_char, 
+0
+};
+
+
+/* -------- TYPE CONVERSION AND EQUIVALENCE RULES (END) -------- */
+
+
+#ifdef __cplusplus
+extern "C"
+#endif
+SWIGEXPORT(void) Init_libinchi(void) {
+    int i;
+    
+    SWIG_InitRuntime();
+    
+    mRino = rb_define_module("Rino");
+    mLibinchi = rb_define_module_under(mRino, "InChI");
+    
+    for (i = 0; swig_types_initial[i]; i++) {
+        swig_types[i] = SWIG_TypeRegister(swig_types_initial[i]);
+        SWIG_define_class(swig_types[i]);
+    }
+    
+    rb_define_module_function(mLibinchi, "run", _wrap_run, -1);
+}
+